docs: release 0.18.0 (#2413)

* Bump version: 0.17.0 → 0.18.0-rc.0

* Bump version: 0.18.0-rc.0 → 0.18.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.17.0
+current_version = 0.18.0
 commit = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<prerel>rc)\.(?P<prerelversion>\d+))?
 serialize = 

.github/workflows/compatibility_tests.yml

@@ -9,6 +9,7 @@ on:
 
 env:
   JEST_ENV: prod
+  CXG_AUTH_TYPE: none
 
 jobs:
   docker-build:

.github/workflows/deploy.yml

@@ -1,13 +0,0 @@
-name: Deploy via single cell infra repo
-
-on:
-  push:
-    branches: main
-
-jobs:
-  deploy:
-    runs-on: ubuntu-latest
-    steps:
-      - name: repository dispatch
-        run: |
-          curl -XPOST -u czi-sci-single-cell-eng:${{secrets.SCI_GITHUB_TOKEN}} -H "Accept: application/vnd.github.everest-preview+json"  -H "Content-Type: application/json" https://api.github.com/repos/chanzuckerberg/single-cell-infra/dispatches --data '{"event_type": "cellxgene-hook"}'

backend/common/compute/estimate_distribution.py

@@ -1,3 +1,4 @@
+from typing import Tuple
 import numba
 import concurrent.futures
 import numpy as np
@@ -6,7 +7,7 @@ from backend.common.constants import XApproximateDistribution
 
 
 @numba.njit(error_model="numpy", nogil=True)
-def min_max(arr: np.ndarray):
+def min_max_fast(arr: np.ndarray) -> Tuple[float, float]:
     """Return (min, max) values for the ndarray."""
 
     # initialize to first finite value in array.  Normally,
@@ -47,6 +48,24 @@ def min_max(arr: np.ndarray):
     return min_val, max_val
 
 
+def min_max_numpy(arr: np.ndarray) -> Tuple[float, float]:
+    return arr.min(), arr.max()
+
+
+def numba_has_support_for_scalar_type(arr: np.ndarray) -> bool:
+    """Numba does not support half-floats, 128 bit floats, ints > 64 bit or non-scalars."""
+    if arr.dtype == np.float32 or arr.dtype == np.float64:
+        return True
+
+    if np.issubdtype(arr.dtype, np.integer) and arr.dtype <= np.int64:
+        return True
+
+    if arr.dtype == np.bool_:
+        return True
+
+    return False
+
+
 def estimate_approximate_distribution(X) -> XApproximateDistribution:
     """
     Estimate the distribution (normal, count) of the X matrix.
@@ -72,6 +91,8 @@ def estimate_approximate_distribution(X) -> XApproximateDistribution:
     else:
         raise TypeError(f"Unsupported matrix format: {str(type(X))}")
 
+    min_max = min_max_fast if numba_has_support_for_scalar_type(Xdata) else min_max_numpy
+
     CHUNKSIZE = 1 << 24
     if Xdata.size > CHUNKSIZE:
         min_val = max_val = Xdata[0]

backend/common/utils/utils.py

@@ -65,7 +65,13 @@ def path_join(base, *urls):
     return btpl._replace(path=path).geturl()
 
 
-class Float32JSONEncoder(json.JSONEncoder):
+class StrictJSONEncoder(json.JSONEncoder):
+    """
+    Custom JSON encoder set-up performing two tasks:
+    1. Strict JSON conformance with non-finite floats (NaN, +/-Inf) via allow_nan=False
+    2. Convert various Numpy types into python types so the encoder will correctly encode.
+    """
+
     def __init__(self, *args, **kwargs):
         """
         NaN/Infinities are illegal in standard JSON.  Python extends JSON with
@@ -78,9 +84,11 @@ class Float32JSONEncoder(json.JSONEncoder):
         super().__init__(*args, **kwargs)
 
     def default(self, obj):
-        if isinstance(obj, np.float32):
+        """This helps us convert types not supported by the native JSON encoder into
+        standard python types, eg, np.int64."""
+        if isinstance(obj, np.floating):
             return float(obj)
-        elif isinstance(obj, np.integer):
+        if isinstance(obj, np.integer):
             return int(obj)
         return json.JSONEncoder.default(self, obj)
 
@@ -89,8 +97,8 @@ def custom_format_warning(msg, *args, **kwargs):
     return f"[cellxgene] Warning: {msg} \n"
 
 
-def jsonify_numpy(data):
+def jsonify_strict(data):
-    return json.dumps(data, cls=Float32JSONEncoder, allow_nan=False)
+    return json.dumps(data, cls=StrictJSONEncoder, allow_nan=False)
 
 
 def import_plugins(plugin_module):

backend/czi_hosted/app/app.py

@@ -24,7 +24,7 @@ import backend.czi_hosted.common.rest as common_rest
 from backend.common.utils.data_locator import DataLocator
 from backend.common.errors import DatasetAccessError, RequestException
 from backend.czi_hosted.common.health import health_check
-from backend.common.utils.utils import path_join, Float32JSONEncoder
+from backend.common.utils.utils import path_join, StrictJSONEncoder
 from backend.czi_hosted.data_common.matrix_loader import MatrixDataLoader
 
 webbp = Blueprint("webapp", "backend.czi_hosted.common.web", template_folder="templates")
@@ -396,7 +396,7 @@ class Server:
         self.app = Flask(__name__, static_folder=None)
         handle_api_base_url(self.app, app_config)
         self._before_adding_routes(self.app, app_config)
-        self.app.json_encoder = Float32JSONEncoder
+        self.app.json_encoder = StrictJSONEncoder
         server_config = app_config.server_config
         if server_config.app__server_timing_headers:
             ServerTiming(self.app, force_debug=True)

backend/czi_hosted/data_common/data_adaptor.py

@@ -15,7 +15,7 @@ from backend.common.errors import (
     UnsupportedSummaryMethod,
     DatasetAccessError,
 )
-from backend.common.utils.utils import jsonify_numpy
+from backend.common.utils.utils import jsonify_strict
 from backend.common.fbs.matrix import encode_matrix_fbs
 
 
@@ -336,7 +336,7 @@ class DataAdaptor(metaclass=ABCMeta):
         )
 
         try:
-            return jsonify_numpy(result)
+            return jsonify_strict(result)
         except ValueError:
             raise JSONEncodingValueError("Error encoding differential expression to JSON")
 

backend/czi_hosted/default_config.py

@@ -108,7 +108,7 @@ server:
     #   false or null:  this returns a 404 code
     #   true:  loads a test index page, which links to the datasets that are available in the dataroot
     #   string/URL:  redirect to this URL:  flask.redirect(config.multi_dataset__index)
-    index: true
+    index: false
 
     # A list of allowed matrix types.  If an empty list, then all matrix types are allowed
     allowed_matrix_types: []

backend/server/__init__.py

@@ -2,7 +2,7 @@ import logging
 import sys
 from backend.common.utils.utils import import_plugins
 
-__version__ = "0.17.0"
+__version__ = "0.18.0"
 display_version = "cellxgene v" + __version__
 
 try:

backend/server/app/app.py

@@ -17,7 +17,7 @@ from flask_restful import Api, Resource
 import backend.server.common.rest as common_rest
 from backend.common.errors import DatasetAccessError, RequestException
 from backend.server.common.health import health_check
-from backend.common.utils.utils import Float32JSONEncoder
+from backend.common.utils.utils import StrictJSONEncoder
 
 webbp = Blueprint("webapp", "backend.server.common.web", template_folder="templates")
 
@@ -257,7 +257,7 @@ class Server:
     def __init__(self, app_config):
         self.app = Flask(__name__, static_folder=None)
         self._before_adding_routes(self.app, app_config)
-        self.app.json_encoder = Float32JSONEncoder
+        self.app.json_encoder = StrictJSONEncoder
         server_config = app_config.server_config
 
         # enable session data

backend/server/data_anndata/anndata_adaptor.py

@@ -232,7 +232,7 @@ class AnndataAdaptor(DataAdaptor):
                 "Anndata data matrix is sparse, but not a CSC (columnar) matrix.  "
                 "Performance may be improved by using CSC."
             )
-        if self.data.X.dtype != "float32":
+        if self.data.X.dtype > np.dtype(np.float32):
             warnings.warn(
                 f"Anndata data matrix is in {self.data.X.dtype} format not float32. " f"Precision may be truncated."
             )

backend/server/data_common/data_adaptor.py

@@ -8,7 +8,7 @@ from server_timing import Timing as ServerTiming
 from backend.server.common.config.app_config import AppConfig
 from backend.common.constants import Axis, XApproximateDistribution
 from backend.common.errors import FilterError, JSONEncodingValueError, ExceedsLimitError, UnsupportedSummaryMethod
-from backend.common.utils.utils import jsonify_numpy
+from backend.common.utils.utils import jsonify_strict
 from backend.common.fbs.matrix import encode_matrix_fbs
 from backend.common.genesets import validate_gene_sets
 
@@ -331,7 +331,7 @@ class DataAdaptor(metaclass=ABCMeta):
         )
 
         try:
-            return jsonify_numpy(result)
+            return jsonify_strict(result)
         except ValueError:
             raise JSONEncodingValueError("Error encoding differential expression to JSON")
 

backend/test/test_common/unit/utils/test_jsonify_strict.py

@@ -0,0 +1,58 @@
+import unittest
+import numpy as np
+
+from backend.common.utils.utils import (
+    jsonify_strict,
+)
+
+
+class TestJsonifyStrict(unittest.TestCase):
+    def test_jsonify_numpy_general_cases(self):
+        self.assertEqual(jsonify_strict({}), "{}")
+        self.assertEqual(jsonify_strict({"a": [], "b": "hello", "c": True}), '{"a": [], "b": "hello", "c": true}')
+
+    def test_jsonify_numpy_float_edges(self):
+        with self.assertRaises(ValueError):
+            jsonify_strict({"nan": [np.nan]})
+
+        with self.assertRaises(ValueError):
+            jsonify_strict({"pinf": [np.PINF]})
+
+        with self.assertRaises(ValueError):
+            jsonify_strict({"ninf": [np.NINF]})
+
+    def test_jsonify_numpy_ndarray(self):
+        values = {
+            "integer": [
+                np.int8(0),
+                np.int16(1),
+                np.int32(2),
+                np.int64(3),
+                np.uint8(4),
+                np.uint16(5),
+                np.uint32(6),
+                np.uint64(7),
+            ],
+            "floating": [
+                np.float16(100.0),
+                np.float32(101.0),
+                np.float64(102.0),
+            ],
+        }
+        # these just confirm our test assumptions
+        self.assertTrue(isinstance(values["floating"][0], np.float16))
+        self.assertTrue(isinstance(values["floating"][1], np.float32))
+        self.assertTrue(isinstance(values["floating"][2], np.float64))
+        self.assertTrue(isinstance(values["integer"][0], np.int8))
+        self.assertTrue(isinstance(values["integer"][1], np.int16))
+        self.assertTrue(isinstance(values["integer"][2], np.int32))
+        self.assertTrue(isinstance(values["integer"][3], np.int64))
+        self.assertTrue(isinstance(values["integer"][4], np.uint8))
+        self.assertTrue(isinstance(values["integer"][5], np.uint16))
+        self.assertTrue(isinstance(values["integer"][6], np.uint32))
+        self.assertTrue(isinstance(values["integer"][7], np.uint64))
+        # the actual test!
+        self.assertEqual(
+            jsonify_strict(values),
+            '{"floating": [100.0, 101.0, 102.0], "integer": [0, 1, 2, 3, 4, 5, 6, 7]}',
+        )

backend/test/test_czi_hosted/unit/common/config/test_base_config.py

@@ -38,7 +38,7 @@ class BaseConfigTest(ConfigTests):
         self.assertIsNotNone(mapping["dataset__presentation__max_categories"])
         self.assertIsNotNone(mapping["server__multi_dataset__allowed_matrix_types"])
 
-    def xtest_changes_from_default_returns_list_of_nondefault_config_values(self):
+    def test_changes_from_default_returns_list_of_nondefault_config_values(self):
         config = self.get_config(verbose="true", lfc_cutoff=0.05)
         server_changes = config.server_config.changes_from_default()
         dataset_changes = config.default_dataset_config.changes_from_default()

client/Makefile

@@ -5,7 +5,9 @@ GENE_SETS := $(if $(GENE_SETS),$(GENE_SETS),../backend/test/fixtures/pbmc3k-gene
 ANNOTATIONS_FILENAME := $(shell basename $(ANNOTATIONS))
 GENE_SETS_FILENAME := $(shell basename $(GENE_SETS))
 
-CXG_CONFIG := $(if $(CXG_CONFIG), $(CXG_CONFIG), ./__tests__/e2e/test_config.yaml)
+CXG_CONFIG := $(if $(CXG_CONFIG),$(CXG_CONFIG),./__tests__/e2e/test_config.yaml)
+
+CXG_AUTH_TYPE := $(if $(CXG_AUTH_TYPE),$(CXG_AUTH_TYPE),"test")
 
 
 # Packaging
@@ -38,7 +40,7 @@ smoke-test:
 	start_server_and_test \
 		'CXG_OPTIONS="--config-file $(CXG_CONFIG)" $(MAKE) start-server' \
 		$(CXG_SERVER_PORT) \
-		'CXG_URL_BASE="http://localhost:$(CXG_SERVER_PORT)" CXG_AUTH_TYPE="test" npm run e2e -- --verbose false'
+		'CXG_URL_BASE="http://localhost:$(CXG_SERVER_PORT)" CXG_AUTH_TYPE=$(CXG_AUTH_TYPE) npm run e2e -- --verbose false'
 
 # start an instance of cellxgene and run the end-to-end annotations tests
 .PHONY: smoke-test-annotations

client/__tests__/e2e/__snapshots__/e2e.test.js.snap

@@ -0,0 +1,5 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`did launch page launched 1`] = `"<span style=\\"max-width: 155px; display: flex; overflow: hidden; justify-content: flex-start; width: 100%; padding: 0px;\\"><span style=\\"overflow: hidden; text-overflow: ellipsis; white-space: nowrap; flex-shrink: 1; min-width: 5px;\\">pbm</span><span style=\\"position: relative; overflow: hidden; white-space: nowrap;\\"><span style=\\"color: transparent;\\">c3k</span><span style=\\"position: absolute; right: 0px; color: inherit;\\">c3k</span></span></span>"`;
+
+exports[`metadata loads categories and values from dataset appear 1`] = `"<div style=\\"display: flex; justify-content: space-between; align-items: baseline;\\"><div style=\\"display: flex; justify-content: flex-start; align-items: flex-start;\\"><label class=\\"bp3-control bp3-checkbox\\" for=\\"category-select-louvain\\"><input id=\\"category-select-louvain\\" data-testclass=\\"category-select\\" data-testid=\\"louvain:category-select\\" type=\\"checkbox\\" checked=\\"\\"><span class=\\"bp3-control-indicator\\"></span></label><span role=\\"menuitem\\" tabindex=\\"0\\" data-testclass=\\"category-expand\\" data-testid=\\"louvain:category-expand\\" style=\\"cursor: pointer;\\"><span aria-haspopup=\\"true\\" class=\\"bp3-popover2-target\\"><span data-testid=\\"louvain:category-label\\" tabindex=\\"-1\\" aria-label=\\"louvain\\" class=\\"\\" style=\\"max-width: 265px;\\"><span style=\\"max-width: 265px; display: flex; overflow: hidden; justify-content: flex-start; width: 100%; padding: 0px;\\"><span style=\\"overflow: hidden; text-overflow: ellipsis; white-space: nowrap; flex-shrink: 1; min-width: 5px;\\">lou</span><span style=\\"position: relative; overflow: hidden; white-space: nowrap;\\"><span style=\\"color: transparent;\\">vain</span><span style=\\"position: absolute; right: 0px; color: inherit;\\">vain</span></span></span></span></span><svg stroke=\\"currentColor\\" fill=\\"currentColor\\" stroke-width=\\"0\\" viewBox=\\"0 0 320 512\\" data-testclass=\\"category-expand-is-not-expanded\\" height=\\"1em\\" width=\\"1em\\" xmlns=\\"http://www.w3.org/2000/svg\\" style=\\"font-size: 10px; margin-left: 5px;\\"><path d=\\"M285.476 272.971L91.132 467.314c-9.373 9.373-24.569 9.373-33.941 0l-22.667-22.667c-9.357-9.357-9.375-24.522-.04-33.901L188.505 256 34.484 101.255c-9.335-9.379-9.317-24.544.04-33.901l22.667-22.667c9.373-9.373 24.569-9.373 33.941 0L285.475 239.03c9.373 9.372 9.373 24.568.001 33.941z\\"></path></svg></span></div><div><span class=\\"bp3-popover-wrapper\\"><span aria-haspopup=\\"true\\" class=\\"bp3-popover-target\\"><a role=\\"button\\" data-testclass=\\"colorby\\" data-testid=\\"colorby-louvain\\" class=\\"bp3-button\\" tabindex=\\"0\\"><span icon=\\"tint\\" class=\\"bp3-icon bp3-icon-tint\\"><svg data-icon=\\"tint\\" width=\\"16\\" height=\\"16\\" viewBox=\\"0 0 16 16\\"><desc>tint</desc><path d=\\"M7.88 1s-4.9 6.28-4.9 8.9c.01 2.82 2.34 5.1 4.99 5.1 2.65-.01 5.03-2.3 5.03-5.13C12.99 7.17 7.88 1 7.88 1z\\" fill-rule=\\"evenodd\\"></path></svg></span></a></span></span></div></div><div style=\\"margin-left: 26px;\\"></div>"`;

client/__tests__/e2e/__snapshots__/e2e.test.ts.snap

@@ -1,5 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`did launch page launched 1`] = `"<span style=\\"max-width: 155px; display: flex; overflow: hidden; justify-content: flex-start; width: 100%; padding: 0px;\\"><span style=\\"overflow: hidden; text-overflow: ellipsis; white-space: nowrap; flex-shrink: 1; min-width: 5px;\\">pbm</span><span style=\\"position: relative; overflow: hidden; white-space: nowrap;\\"><span style=\\"color: transparent;\\">c3k</span><span style=\\"position: absolute; right: 0px; color: inherit;\\">c3k</span></span></span>"`;
-
-exports[`metadata loads categories and values from dataset appear 1`] = `"<div style=\\"display: flex; justify-content: space-between; align-items: baseline;\\"><div style=\\"display: flex; justify-content: flex-start; align-items: flex-start;\\"><label class=\\"bp3-control bp3-checkbox\\" for=\\"category-select-louvain\\"><input id=\\"category-select-louvain\\" data-testclass=\\"category-select\\" data-testid=\\"louvain:category-select\\" type=\\"checkbox\\" checked=\\"\\"><span class=\\"bp3-control-indicator\\"></span></label><span role=\\"menuitem\\" tabindex=\\"0\\" data-testclass=\\"category-expand\\" data-testid=\\"louvain:category-expand\\" style=\\"cursor: pointer;\\"><span class=\\"bp3-popover2-target\\"><span data-testid=\\"louvain:category-label\\" tabindex=\\"-1\\" aria-label=\\"louvain\\" class=\\"\\" style=\\"max-width: 265px;\\"><span style=\\"max-width: 265px; display: flex; overflow: hidden; justify-content: flex-start; width: 100%; padding: 0px;\\"><span style=\\"overflow: hidden; text-overflow: ellipsis; white-space: nowrap; flex-shrink: 1; min-width: 5px;\\">lou</span><span style=\\"position: relative; overflow: hidden; white-space: nowrap;\\"><span style=\\"color: transparent;\\">vain</span><span style=\\"position: absolute; right: 0px; color: inherit;\\">vain</span></span></span></span></span><svg stroke=\\"currentColor\\" fill=\\"currentColor\\" stroke-width=\\"0\\" viewBox=\\"0 0 320 512\\" data-testclass=\\"category-expand-is-not-expanded\\" height=\\"1em\\" width=\\"1em\\" xmlns=\\"http://www.w3.org/2000/svg\\" style=\\"font-size: 10px; margin-left: 5px;\\"><path d=\\"M285.476 272.971L91.132 467.314c-9.373 9.373-24.569 9.373-33.941 0l-22.667-22.667c-9.357-9.357-9.375-24.522-.04-33.901L188.505 256 34.484 101.255c-9.335-9.379-9.317-24.544.04-33.901l22.667-22.667c9.373-9.373 24.569-9.373 33.941 0L285.475 239.03c9.373 9.372 9.373 24.568.001 33.941z\\"></path></svg></span></div><div><span class=\\"bp3-popover-wrapper\\"><span aria-haspopup=\\"true\\" class=\\"bp3-popover-target\\"><a role=\\"button\\" data-testclass=\\"colorby\\" data-testid=\\"colorby-louvain\\" class=\\"bp3-button\\" tabindex=\\"0\\"><span icon=\\"tint\\" class=\\"bp3-icon bp3-icon-tint\\"><svg data-icon=\\"tint\\" width=\\"16\\" height=\\"16\\" viewBox=\\"0 0 16 16\\"><desc>tint</desc><path d=\\"M7.88 1s-4.9 6.28-4.9 8.9c.01 2.82 2.34 5.1 4.99 5.1 2.65-.01 5.03-2.3 5.03-5.13C12.99 7.17 7.88 1 7.88 1z\\" fill-rule=\\"evenodd\\"></path></svg></span></a></span></span></div></div><div style=\\"margin-left: 26px;\\"></div>"`;

client/__tests__/e2e/cellxgeneActions.js

@@ -0,0 +1,506 @@
+/* eslint-disable no-await-in-loop -- await in loop is needed to emulate sequential user actions  */
+import { strict as assert } from "assert";
+import {
+  clearInputAndTypeInto,
+  clickOn,
+  getAllByClass,
+  getOneElementInnerText,
+  typeInto,
+  waitByID,
+  waitByClass,
+  waitForAllByIds,
+  clickOnUntil,
+  getTestClass,
+  getTestId,
+  isElementPresent,
+  goToPage,
+} from "./puppeteerUtils";
+
+import { appUrlBase, TEST_EMAIL, TEST_PASSWORD } from "./config";
+
+export async function drag(testId, start, end, lasso = false) {
+  const layout = await waitByID(testId);
+  const elBox = await layout.boxModel();
+  const x1 = elBox.content[0].x + start.x;
+  const x2 = elBox.content[0].x + end.x;
+  const y1 = elBox.content[0].y + start.y;
+  const y2 = elBox.content[0].y + end.y;
+  await page.mouse.move(x1, y1);
+  await page.mouse.down();
+  if (lasso) {
+    await page.mouse.move(x2, y1);
+    await page.mouse.move(x2, y2);
+    await page.mouse.move(x1, y2);
+    await page.mouse.move(x1, y1);
+  } else {
+    await page.mouse.move(x2, y2);
+  }
+  await page.mouse.up();
+}
+
+export async function clickOnCoordinate(testId, coord) {
+  const layout = await expect(page).toMatchElement(getTestId(testId));
+  const elBox = await layout.boxModel();
+
+  if (!elBox) {
+    throw Error("Layout's boxModel is not available!");
+  }
+
+  const x = elBox.content[0].x + coord.x;
+  const y = elBox.content[0].y + coord.y;
+  await page.mouse.click(x, y);
+}
+
+export async function getAllHistograms(testclass, testIds) {
+  const histTestIds = testIds.map((tid) => `histogram-${tid}`);
+
+  // these load asynchronously, so we need to wait for each histogram individually,
+  // and they may be quite slow in some cases.
+  await waitForAllByIds(histTestIds, { timeout: 4 * 60 * 1000 });
+
+  const allHistograms = await getAllByClass(testclass);
+
+  const testIDs = await Promise.all(
+    allHistograms.map((hist) => page.evaluate((elem) => elem.dataset.testid, hist))
+  );
+
+  return testIDs.map((id) => id.replace(/^histogram-/, ""));
+}
+
+export async function getAllCategoriesAndCounts(category) {
+  // these load asynchronously, so we have to wait for the specific category.
+  await waitByID(`category-${category}`);
+
+  return page.$$eval(
+    `[data-testid="category-${category}"] [data-testclass='categorical-row']`,
+    (rows) =>
+      Object.fromEntries(
+        rows.map((row) => {
+          const cat = row
+            .querySelector("[data-testclass='categorical-value']")
+            .getAttribute("aria-label");
+
+          const count = row.querySelector(
+            "[data-testclass='categorical-value-count']"
+          ).innerText;
+
+          return [cat, count];
+        })
+      )
+  );
+}
+
+export async function getCellSetCount(num) {
+  await clickOn(`cellset-button-${num}`);
+  return getOneElementInnerText(`[data-testid='cellset-count-${num}']`);
+}
+
+export async function resetCategory(category) {
+  const checkboxId = `${category}:category-select`;
+  await waitByID(checkboxId);
+  const checkedPseudoclass = await page.$eval(
+    `[data-testid='${checkboxId}']`,
+    (el) => el.matches(":checked")
+  );
+  if (!checkedPseudoclass) await clickOn(checkboxId);
+
+  const categoryRow = await waitByID(`${category}:category-expand`);
+
+  const isExpanded = await categoryRow.$(
+    "[data-testclass='category-expand-is-expanded']"
+  );
+
+  if (isExpanded) await clickOn(`${category}:category-expand`);
+}
+
+export async function calcCoordinate(testId, xAsPercent, yAsPercent) {
+  const el = await waitByID(testId);
+  const size = await el.boxModel();
+  return {
+    x: Math.floor(size.width * xAsPercent),
+    y: Math.floor(size.height * yAsPercent),
+  };
+}
+
+export async function calcDragCoordinates(testId, coordinateAsPercent) {
+  return {
+    start: await calcCoordinate(
+      testId,
+      coordinateAsPercent.x1,
+      coordinateAsPercent.y1
+    ),
+    end: await calcCoordinate(
+      testId,
+      coordinateAsPercent.x2,
+      coordinateAsPercent.y2
+    ),
+  };
+}
+
+export async function selectCategory(category, values, reset = true) {
+  if (reset) await resetCategory(category);
+
+  await clickOn(`${category}:category-expand`);
+  await clickOn(`${category}:category-select`);
+
+  for (const value of values) {
+    await clickOn(`categorical-value-select-${category}-${value}`);
+  }
+}
+
+export async function expandCategory(category) {
+  const expand = await waitByID(`${category}:category-expand`);
+  const notExpanded = await expand.$(
+    "[data-testclass='category-expand-is-not-expanded']"
+  );
+  if (notExpanded) await clickOn(`${category}:category-expand`);
+}
+
+export async function clip(min = 0, max = 100) {
+  await clickOn("visualization-settings");
+  await clearInputAndTypeInto("clip-min-input", min);
+  await clearInputAndTypeInto("clip-max-input", max);
+  await clickOn("clip-commit");
+}
+
+export async function createCategory(categoryName) {
+  await clickOnUntil("open-annotation-dialog", async () => {
+    await expect(page).toMatchElement(getTestId("new-category-name"));
+  });
+
+  await typeInto("new-category-name", categoryName);
+  await clickOn("submit-category");
+}
+
+/* 
+
+  GENESET 
+
+*/
+
+export async function colorByGeneset(genesetName) {
+  await clickOn(`${genesetName}:colorby-entire-geneset`);
+}
+
+export async function colorByGene(gene) {
+  await clickOn(`colorby-${gene}`);
+}
+
+export async function assertColorLegendLabel(label) {
+  const handle = await waitByID("continuous_legend_color_by_label");
+
+  const result = await handle.evaluate((node) => node.getAttribute("aria-label"));
+
+  return expect(result).toBe(label);
+}
+
+export async function expandGeneset(genesetName) {
+  const expand = await waitByID(`${genesetName}:geneset-expand`);
+  const notExpanded = await expand.$(
+    "[data-testclass='geneset-expand-is-not-expanded']"
+  );
+  if (notExpanded) await clickOn(`${genesetName}:geneset-expand`);
+}
+
+export async function createGeneset(genesetName) {
+  await clickOnUntil("open-create-geneset-dialog", async () => {
+    await expect(page).toMatchElement(getTestId("create-geneset-input"));
+  });
+
+  await typeInto("create-geneset-input", genesetName);
+  await clickOn("submit-geneset");
+  await waitByClass("autosave-complete");
+}
+
+export async function editGenesetName(genesetName, editText) {
+  const editButton = `${genesetName}:edit-genesetName-mode`;
+  const submitButton = `${genesetName}:submit-geneset`;
+  await clickOnUntil(`${genesetName}:see-actions`, async () => {
+    await expect(page).toMatchElement(getTestId(editButton));
+  });
+  await clickOn(editButton);
+  await typeInto("rename-geneset-modal", editText);
+  await clickOn(submitButton);
+}
+
+export async function deleteGeneset(genesetName) {
+  const targetId = `${genesetName}:delete-geneset`;
+
+  await clickOnUntil(`${genesetName}:see-actions`, async () => {
+    await expect(page).toMatchElement(getTestId(targetId));
+  });
+
+  await clickOn(targetId);
+
+  await assertGenesetDoesNotExist(genesetName);
+  await waitByClass("autosave-complete");
+}
+
+export async function assertGenesetDoesNotExist(genesetName) {
+  const result = await isElementPresent(
+    getTestId(`${genesetName}:geneset-name`)
+  );
+  await expect(result).toBe(false);
+}
+
+export async function assertGenesetExists(genesetName) {
+  const handle = await waitByID(`${genesetName}:geneset-name`);
+
+  const result = await handle.evaluate((node) => node.getAttribute("aria-label"));
+
+  return expect(result).toBe(genesetName);
+}
+
+/* 
+
+  GENE
+
+*/
+
+export async function addGeneToSet(genesetName, geneToAddToSet) {
+  const submitButton = `${genesetName}:submit-gene`;
+
+  await clickOn(`${genesetName}:add-new-gene-to-geneset`);
+  await typeInto("add-genes", geneToAddToSet);
+  await clickOn(submitButton);
+}
+
+export async function removeGene(geneSymbol) {
+  const targetId = `delete-from-geneset:${geneSymbol}`;
+
+  await clickOn(targetId);
+
+  await waitByClass("autosave-complete");
+}
+
+export async function assertGeneExistsInGeneset(geneSymbol) {
+  const handle = await waitByID(`${geneSymbol}:gene-label`);
+
+  const result = await handle.evaluate((node) => node.getAttribute("aria-label"));
+
+  return expect(result).toBe(geneSymbol);
+}
+
+export async function assertGeneDoesNotExist(geneSymbol) {
+  const result = await isElementPresent(getTestId(`${geneSymbol}:gene-label`));
+
+  await expect(result).toBe(false);
+}
+
+export async function expandGene(geneSymbol) {
+  await clickOn(`maximize-${geneSymbol}`);
+}
+
+/* 
+
+  CATEGORY 
+
+*/
+
+export async function duplicateCategory(categoryName) {
+  await clickOn("open-annotation-dialog");
+
+  await typeInto("new-category-name", categoryName);
+
+  const dropdownOptionClass = "duplicate-category-dropdown-option";
+
+  await clickOnUntil("duplicate-category-dropdown", async () => {
+    await expect(page).toMatchElement(getTestClass(dropdownOptionClass));
+  });
+
+  const option = await expect(page).toMatchElement(
+    getTestClass(dropdownOptionClass)
+  );
+
+  await option.click();
+
+  await clickOnUntil("submit-category", async () => {
+    await expect(page).toMatchElement(
+      getTestId(`${categoryName}:category-expand`)
+    );
+  });
+
+  await waitByClass("autosave-complete");
+}
+
+export async function renameCategory(oldCategoryName, newCategoryName) {
+  await clickOn(`${oldCategoryName}:see-actions`);
+  await clickOn(`${oldCategoryName}:edit-category-mode`);
+  await clearInputAndTypeInto(
+    `${oldCategoryName}:edit-category-name-text`,
+    newCategoryName
+  );
+  await clickOn(`${oldCategoryName}:submit-category-edit`);
+}
+
+export async function deleteCategory(categoryName) {
+  const targetId = `${categoryName}:delete-category`;
+
+  await clickOnUntil(`${categoryName}:see-actions`, async () => {
+    await expect(page).toMatchElement(getTestId(targetId));
+  });
+
+  await clickOn(targetId);
+
+  await assertCategoryDoesNotExist();
+}
+
+export async function createLabel(categoryName, labelName) {
+  /**
+   * (thuang): This explicit wait is needed, since currently showing
+   * the modal again quickly after the previous action dismissing the
+   * modal will persist the input value from the previous action.
+   *
+   * To reproduce:
+   * 1. Click on the plus sign to show the modal to add a new label to the category
+   * 2. Type `123` in the input box
+   * 3. Hover over your mouse over the plus sign and double click to quickly dismiss and
+   * invoke the modal again
+   * 4. You will see `123` is persisted in the input box
+   * 5. Expected behavior is to get an empty input box
+   */
+  await page.waitForTimeout(500);
+
+  await clickOn(`${categoryName}:see-actions`);
+
+  await clickOn(`${categoryName}:add-new-label-to-category`);
+
+  await typeInto(`${categoryName}:new-label-name`, labelName);
+
+  await clickOn(`${categoryName}:submit-label`);
+}
+
+export async function deleteLabel(categoryName, labelName) {
+  await expandCategory(categoryName);
+  await clickOn(`${categoryName}:${labelName}:see-actions`);
+  await clickOn(`${categoryName}:${labelName}:delete-label`);
+}
+
+export async function renameLabel(categoryName, oldLabelName, newLabelName) {
+  await expandCategory(categoryName);
+  await clickOn(`${categoryName}:${oldLabelName}:see-actions`);
+  await clickOn(`${categoryName}:${oldLabelName}:edit-label`);
+  await clearInputAndTypeInto(
+    `${categoryName}:${oldLabelName}:edit-label-name`,
+    newLabelName
+  );
+  await clickOn(`${categoryName}:${oldLabelName}:submit-label-edit`);
+}
+
+export async function addGeneToSearch(geneName) {
+  await typeInto("gene-search", geneName);
+  await page.keyboard.press("Enter");
+  await page.waitForSelector(`[data-testid='histogram-${geneName}']`);
+}
+
+export async function subset(coordinatesAsPercent) {
+  // In order to deselect the selection after the subset, make sure we have some clear part
+  // of the scatterplot we can click on
+  assert(coordinatesAsPercent.x2 < 0.99 || coordinatesAsPercent.y2 < 0.99);
+  const lassoSelection = await calcDragCoordinates(
+    "layout-graph",
+    coordinatesAsPercent
+  );
+  await drag("layout-graph", lassoSelection.start, lassoSelection.end, true);
+  await clickOn("subset-button");
+  const clearCoordinate = await calcCoordinate("layout-graph", 0.5, 0.99);
+  await clickOnCoordinate("layout-graph", clearCoordinate);
+}
+
+export async function setSellSet(cellSet, cellSetNum) {
+  const selections = cellSet.filter((sel) => sel.kind === "categorical");
+
+  for (const selection of selections) {
+    await selectCategory(selection.metadata, selection.values, true);
+  }
+
+  await getCellSetCount(cellSetNum);
+}
+
+export async function runDiffExp(cellSet1, cellSet2) {
+  await setSellSet(cellSet1, 1);
+  await setSellSet(cellSet2, 2);
+  await clickOn("diffexp-button");
+}
+
+export async function bulkAddGenes(geneNames) {
+  await clickOn("section-bulk-add");
+  await typeInto("input-bulk-add", geneNames.join(","));
+  await page.keyboard.press("Enter");
+}
+
+export async function assertCategoryDoesNotExist(categoryName) {
+  const result = await isElementPresent(
+    getTestId(`${categoryName}:category-label`)
+  );
+
+  await expect(result).toBe(false);
+}
+
+export async function login() {
+  await goToPage(appUrlBase);
+
+  await clickOn("log-in");
+
+  // (thuang): Auth0 form is unstable and unsafe for input until verified
+  await waitUntilFormFieldStable('[name="email"]');
+
+  await expect(page).toFillForm("form", {
+    email: TEST_EMAIL,
+    password: TEST_PASSWORD,
+  });
+
+  await Promise.all([
+    page.waitForNavigation({ waitUntil: "networkidle0" }),
+    expect(page).toClick('[name="submit"]'),
+  ]);
+
+  expect(page.url()).toContain(appUrlBase);
+}
+
+export async function logout() {
+  await clickOnUntil("user-info", async () => {
+    await waitByID("log-out");
+    await Promise.all([
+      page.waitForNavigation({ waitUntil: "networkidle0" }),
+      clickOn("log-out"),
+    ]);
+  });
+
+  await waitByID("log-in");
+}
+
+async function waitUntilFormFieldStable(selector) {
+  const MAX_RETRY = 10;
+  const WAIT_FOR_MS = 200;
+
+  const EXPECTED_VALUE = "aaa";
+
+  let retry = 0;
+
+  while (retry < MAX_RETRY) {
+    try {
+      await expect(page).toFill(selector, EXPECTED_VALUE);
+
+      const fieldHandle = await expect(page).toMatchElement(selector);
+
+      const fieldValue = await page.evaluate(
+        (input) => input.value,
+        fieldHandle
+      );
+
+      expect(fieldValue).toBe(EXPECTED_VALUE);
+
+      break;
+    } catch (error) {
+      retry += 1;
+
+      await page.waitForTimeout(WAIT_FOR_MS);
+    }
+  }
+
+  if (retry === MAX_RETRY) {
+    throw Error("clickOnUntil() assertion failed!");
+  }
+}
+/* eslint-enable no-await-in-loop -- await in loop is needed to emulate sequential user actions */

client/__tests__/e2e/cellxgeneActions.ts

@@ -1,596 +0,0 @@
-/* eslint-disable no-await-in-loop -- await in loop is needed to emulate sequential user actions  */
-import { strict as assert } from "assert";
-import {
-  clearInputAndTypeInto,
-  clickOn,
-  getAllByClass,
-  getOneElementInnerText,
-  typeInto,
-  waitByID,
-  waitByClass,
-  waitForAllByIds,
-  clickOnUntil,
-  getTestClass,
-  getTestId,
-  isElementPresent,
-  goToPage,
-} from "./puppeteerUtils";
-
-import { appUrlBase, TEST_EMAIL, TEST_PASSWORD } from "./config";
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function drag(testId: any, start: any, end: any, lasso = false) {
-  const layout = await waitByID(testId);
-  // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-  const elBox = await layout.boxModel();
-  // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-  const x1 = elBox.content[0].x + start.x;
-  // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-  const x2 = elBox.content[0].x + end.x;
-  // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-  const y1 = elBox.content[0].y + start.y;
-  // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-  const y2 = elBox.content[0].y + end.y;
-  await page.mouse.move(x1, y1);
-  await page.mouse.down();
-  if (lasso) {
-    await page.mouse.move(x2, y1);
-    await page.mouse.move(x2, y2);
-    await page.mouse.move(x1, y2);
-    await page.mouse.move(x1, y1);
-  } else {
-    await page.mouse.move(x2, y2);
-  }
-  await page.mouse.up();
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function clickOnCoordinate(testId: any, coord: any) {
-  const layout = await expect(page).toMatchElement(getTestId(testId));
-  const elBox = await layout.boxModel();
-
-  if (!elBox) {
-    throw Error("Layout's boxModel is not available!");
-  }
-
-  const x = elBox.content[0].x + coord.x;
-  const y = elBox.content[0].y + coord.y;
-  await page.mouse.click(x, y);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function getAllHistograms(testclass: any, testIds: any) {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  const histTestIds = testIds.map((tid: any) => `histogram-${tid}`);
-
-  // these load asynchronously, so we need to wait for each histogram individually,
-  // and they may be quite slow in some cases.
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 2.
-  await waitForAllByIds(histTestIds, { timeout: 4 * 60 * 1000 });
-
-  const allHistograms = await getAllByClass(testclass);
-
-  const testIDs = await Promise.all(
-    allHistograms.map((hist) =>
-      page.evaluate((elem) => elem.dataset.testid, hist)
-    )
-  );
-
-  return testIDs.map((id) => id.replace(/^histogram-/, ""));
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function getAllCategoriesAndCounts(category: any) {
-  // these load asynchronously, so we have to wait for the specific category.
-  await waitByID(`category-${category}`);
-
-  return page.$$eval(
-    `[data-testid="category-${category}"] [data-testclass='categorical-row']`,
-    (rows) =>
-      Object.fromEntries(
-        rows.map((row) => {
-          // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-          const cat = row
-            .querySelector("[data-testclass='categorical-value']")
-            .getAttribute("aria-label");
-
-          const count = (row.querySelector(
-            "[data-testclass='categorical-value-count']"
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          ) as any).innerText;
-
-          return [cat, count];
-        })
-      )
-  );
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function getCellSetCount(num: any) {
-  await clickOn(`cellset-button-${num}`);
-  return getOneElementInnerText(`[data-testid='cellset-count-${num}']`);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function resetCategory(category: any) {
-  const checkboxId = `${category}:category-select`;
-  await waitByID(checkboxId);
-  const checkedPseudoclass = await page.$eval(
-    `[data-testid='${checkboxId}']`,
-    (el) => el.matches(":checked")
-  );
-  if (!checkedPseudoclass) await clickOn(checkboxId);
-
-  const categoryRow = await waitByID(`${category}:category-expand`);
-
-  // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-  const isExpanded = await categoryRow.$(
-    "[data-testclass='category-expand-is-expanded']"
-  );
-
-  if (isExpanded) await clickOn(`${category}:category-expand`);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export async function calcCoordinate(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  testId: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  xAsPercent: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  yAsPercent: any
-) {
-  const el = await waitByID(testId);
-  // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-  const size = await el.boxModel();
-  return {
-    // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-    x: Math.floor(size.width * xAsPercent),
-    // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-    y: Math.floor(size.height * yAsPercent),
-  };
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export async function calcDragCoordinates(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  testId: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  coordinateAsPercent: any
-) {
-  return {
-    start: await calcCoordinate(
-      testId,
-      coordinateAsPercent.x1,
-      coordinateAsPercent.y1
-    ),
-    end: await calcCoordinate(
-      testId,
-      coordinateAsPercent.x2,
-      coordinateAsPercent.y2
-    ),
-  };
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function selectCategory(category: any, values: any, reset = true) {
-  if (reset) await resetCategory(category);
-
-  await clickOn(`${category}:category-expand`);
-  await clickOn(`${category}:category-select`);
-
-  for (const value of values) {
-    await clickOn(`categorical-value-select-${category}-${value}`);
-  }
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function expandCategory(category: any) {
-  const expand = await waitByID(`${category}:category-expand`);
-  // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-  const notExpanded = await expand.$(
-    "[data-testclass='category-expand-is-not-expanded']"
-  );
-  if (notExpanded) await clickOn(`${category}:category-expand`);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export async function clip(min = 0, max = 100) {
-  await clickOn("visualization-settings");
-  await clearInputAndTypeInto("clip-min-input", min);
-  await clearInputAndTypeInto("clip-max-input", max);
-  await clickOn("clip-commit");
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function createCategory(categoryName: any) {
-  await clickOnUntil("open-annotation-dialog", async () => {
-    await expect(page).toMatchElement(getTestId("new-category-name"));
-  });
-
-  await typeInto("new-category-name", categoryName);
-  await clickOn("submit-category");
-}
-
-/**
- * GENESET
- */
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function colorByGeneset(genesetName: any) {
-  await clickOn(`${genesetName}:colorby-entire-geneset`);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function colorByGene(gene: any) {
-  await clickOn(`colorby-${gene}`);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function assertColorLegendLabel(label: any) {
-  const handle = await waitByID("continuous_legend_color_by_label");
-
-  // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-  const result = await handle.evaluate((node) =>
-    node.getAttribute("aria-label")
-  );
-
-  return expect(result).toBe(label);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function expandGeneset(genesetName: any) {
-  const expand = await waitByID(`${genesetName}:geneset-expand`);
-  // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-  const notExpanded = await expand.$(
-    "[data-testclass='geneset-expand-is-not-expanded']"
-  );
-  if (notExpanded) await clickOn(`${genesetName}:geneset-expand`);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function createGeneset(genesetName: any) {
-  await clickOnUntil("open-create-geneset-dialog", async () => {
-    await expect(page).toMatchElement(getTestId("create-geneset-input"));
-  });
-
-  await typeInto("create-geneset-input", genesetName);
-  await clickOn("submit-geneset");
-  await waitByClass("autosave-complete");
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function editGenesetName(genesetName: any, editText: any) {
-  const editButton = `${genesetName}:edit-genesetName-mode`;
-  const submitButton = `${genesetName}:submit-geneset`;
-  await clickOnUntil(`${genesetName}:see-actions`, async () => {
-    await expect(page).toMatchElement(getTestId(editButton));
-  });
-  await clickOn(editButton);
-  await typeInto("rename-geneset-modal", editText);
-  await clickOn(submitButton);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function deleteGeneset(genesetName: any) {
-  const targetId = `${genesetName}:delete-geneset`;
-
-  await clickOnUntil(`${genesetName}:see-actions`, async () => {
-    await expect(page).toMatchElement(getTestId(targetId));
-  });
-
-  await clickOn(targetId);
-
-  await assertGenesetDoesNotExist(genesetName);
-  await waitByClass("autosave-complete");
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function assertGenesetDoesNotExist(genesetName: any) {
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
-  const result = await isElementPresent(
-    getTestId(`${genesetName}:geneset-name`)
-  );
-  await expect(result).toBe(false);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function assertGenesetExists(genesetName: any) {
-  const handle = await waitByID(`${genesetName}:geneset-name`);
-
-  // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-  const result = await handle.evaluate((node) =>
-    node.getAttribute("aria-label")
-  );
-
-  return expect(result).toBe(genesetName);
-}
-
-/**
- * GENE
- */
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function addGeneToSet(genesetName: any, geneToAddToSet: any) {
-  const submitButton = `${genesetName}:submit-gene`;
-
-  await clickOn(`${genesetName}:add-new-gene-to-geneset`);
-  await typeInto("add-genes", geneToAddToSet);
-  await clickOn(submitButton);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function removeGene(geneSymbol: any) {
-  const targetId = `delete-from-geneset:${geneSymbol}`;
-
-  await clickOn(targetId);
-
-  await waitByClass("autosave-complete");
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function assertGeneExistsInGeneset(geneSymbol: any) {
-  const handle = await waitByID(`${geneSymbol}:gene-label`);
-
-  // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-  const result = await handle.evaluate((node) =>
-    node.getAttribute("aria-label")
-  );
-
-  return expect(result).toBe(geneSymbol);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function assertGeneDoesNotExist(geneSymbol: any) {
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
-  const result = await isElementPresent(getTestId(`${geneSymbol}:gene-label`));
-
-  await expect(result).toBe(false);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function expandGene(geneSymbol: any) {
-  await clickOn(`maximize-${geneSymbol}`);
-}
-
-/**
- * CATEGORY
- */
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function duplicateCategory(categoryName: any) {
-  await clickOn("open-annotation-dialog");
-
-  await typeInto("new-category-name", categoryName);
-
-  const dropdownOptionClass = "duplicate-category-dropdown-option";
-
-  await clickOnUntil("duplicate-category-dropdown", async () => {
-    await expect(page).toMatchElement(getTestClass(dropdownOptionClass));
-  });
-
-  const option = await expect(page).toMatchElement(
-    getTestClass(dropdownOptionClass)
-  );
-
-  await option.click();
-
-  await clickOnUntil("submit-category", async () => {
-    await expect(page).toMatchElement(
-      getTestId(`${categoryName}:category-expand`)
-    );
-  });
-
-  await waitByClass("autosave-complete");
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export async function renameCategory(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  oldCategoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  newCategoryName: any
-) {
-  await clickOn(`${oldCategoryName}:see-actions`);
-  await clickOn(`${oldCategoryName}:edit-category-mode`);
-  await clearInputAndTypeInto(
-    `${oldCategoryName}:edit-category-name-text`,
-    newCategoryName
-  );
-  await clickOn(`${oldCategoryName}:submit-category-edit`);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function deleteCategory(categoryName: any) {
-  const targetId = `${categoryName}:delete-category`;
-
-  await clickOnUntil(`${categoryName}:see-actions`, async () => {
-    await expect(page).toMatchElement(getTestId(targetId));
-  });
-
-  await clickOn(targetId);
-
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
-  await assertCategoryDoesNotExist();
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function createLabel(categoryName: any, labelName: any) {
-  /**
-   * (thuang): This explicit wait is needed, since currently showing
-   * the modal again quickly after the previous action dismissing the
-   * modal will persist the input value from the previous action.
-   *
-   * To reproduce:
-   * 1. Click on the plus sign to show the modal to add a new label to the category
-   * 2. Type `123` in the input box
-   * 3. Hover over your mouse over the plus sign and double click to quickly dismiss and
-   * invoke the modal again
-   * 4. You will see `123` is persisted in the input box
-   * 5. Expected behavior is to get an empty input box
-   */
-  await page.waitForTimeout(500);
-
-  await clickOn(`${categoryName}:see-actions`);
-
-  await clickOn(`${categoryName}:add-new-label-to-category`);
-
-  await typeInto(`${categoryName}:new-label-name`, labelName);
-
-  await clickOn(`${categoryName}:submit-label`);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function deleteLabel(categoryName: any, labelName: any) {
-  await expandCategory(categoryName);
-  await clickOn(`${categoryName}:${labelName}:see-actions`);
-  await clickOn(`${categoryName}:${labelName}:delete-label`);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export async function renameLabel(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  categoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  oldLabelName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  newLabelName: any
-) {
-  await expandCategory(categoryName);
-  await clickOn(`${categoryName}:${oldLabelName}:see-actions`);
-  await clickOn(`${categoryName}:${oldLabelName}:edit-label`);
-  await clearInputAndTypeInto(
-    `${categoryName}:${oldLabelName}:edit-label-name`,
-    newLabelName
-  );
-  await clickOn(`${categoryName}:${oldLabelName}:submit-label-edit`);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function addGeneToSearch(geneName: any) {
-  await typeInto("gene-search", geneName);
-  await page.keyboard.press("Enter");
-  await page.waitForSelector(`[data-testid='histogram-${geneName}']`);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function subset(coordinatesAsPercent: any) {
-  // In order to deselect the selection after the subset, make sure we have some clear part
-  // of the scatterplot we can click on
-  assert(coordinatesAsPercent.x2 < 0.99 || coordinatesAsPercent.y2 < 0.99);
-  const lassoSelection = await calcDragCoordinates(
-    "layout-graph",
-    coordinatesAsPercent
-  );
-  await drag("layout-graph", lassoSelection.start, lassoSelection.end, true);
-  await clickOn("subset-button");
-  const clearCoordinate = await calcCoordinate("layout-graph", 0.5, 0.99);
-  await clickOnCoordinate("layout-graph", clearCoordinate);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function setSellSet(cellSet: any, cellSetNum: any) {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  const selections = cellSet.filter((sel: any) => sel.kind === "categorical");
-
-  for (const selection of selections) {
-    await selectCategory(selection.metadata, selection.values, true);
-  }
-
-  await getCellSetCount(cellSetNum);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function runDiffExp(cellSet1: any, cellSet2: any) {
-  await setSellSet(cellSet1, 1);
-  await setSellSet(cellSet2, 2);
-  await clickOn("diffexp-button");
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function bulkAddGenes(geneNames: any) {
-  await clickOn("section-bulk-add");
-  await typeInto("input-bulk-add", geneNames.join(","));
-  await page.keyboard.press("Enter");
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function assertCategoryDoesNotExist(categoryName: any) {
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
-  const result = await isElementPresent(
-    getTestId(`${categoryName}:category-label`)
-  );
-
-  await expect(result).toBe(false);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export async function login() {
-  await goToPage(appUrlBase);
-
-  await clickOn("log-in");
-
-  // (thuang): Auth0 form is unstable and unsafe for input until verified
-  await waitUntilFormFieldStable('[name="email"]');
-
-  await expect(page).toFillForm("form", {
-    email: TEST_EMAIL,
-    password: TEST_PASSWORD,
-  });
-
-  await Promise.all([
-    page.waitForNavigation({ waitUntil: "networkidle0" }),
-    expect(page).toClick('[name="submit"]'),
-  ]);
-
-  expect(page.url()).toContain(appUrlBase);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export async function logout() {
-  await clickOnUntil("user-info", async () => {
-    await waitByID("log-out");
-    await Promise.all([
-      page.waitForNavigation({ waitUntil: "networkidle0" }),
-      clickOn("log-out"),
-    ]);
-  });
-
-  await waitByID("log-in");
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-async function waitUntilFormFieldStable(selector: any) {
-  const MAX_RETRY = 10;
-  const WAIT_FOR_MS = 200;
-
-  const EXPECTED_VALUE = "aaa";
-
-  let retry = 0;
-
-  while (retry < MAX_RETRY) {
-    try {
-      await expect(page).toFill(selector, EXPECTED_VALUE);
-
-      const fieldHandle = await expect(page).toMatchElement(selector);
-
-      const fieldValue = await page.evaluate(
-        (input) => input.value,
-        fieldHandle
-      );
-
-      expect(fieldValue).toBe(EXPECTED_VALUE);
-
-      break;
-    } catch (error) {
-      retry += 1;
-
-      await page.waitForTimeout(WAIT_FOR_MS);
-    }
-  }
-
-  if (retry === MAX_RETRY) {
-    throw Error("clickOnUntil() assertion failed!");
-  }
-}
-/* eslint-enable no-await-in-loop -- await in loop is needed to emulate sequential user actions */

client/__tests__/e2e/e2e.test.js

@@ -58,12 +58,10 @@ describe("metadata loads", () => {
       const categories = await getAllCategoriesAndCounts(label);
 
       expect(Object.keys(categories)).toMatchObject(
-        // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
         Object.keys(data.categorical[label])
       );
 
       expect(Object.values(categories)).toMatchObject(
-        // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
         Object.values(data.categorical[label])
       );
     }
@@ -161,12 +159,10 @@ describe("subset", () => {
       const categories = await getAllCategoriesAndCounts(label);
 
       expect(Object.keys(categories)).toMatchObject(
-        // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
         Object.keys(data.subset.categorical[label])
       );
 
       expect(Object.values(categories)).toMatchObject(
-        // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
         Object.values(data.subset.categorical[label])
       );
     }
@@ -199,7 +195,6 @@ describe("clipping", () => {
   test("clip continuous", async () => {
     await goToPage(appUrlBase);
 
-    // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string' is not assignable to par... Remove this comment to see the full error message
     await clip(data.clip.min, data.clip.max);
     const histBrushableAreaId = `histogram-${data.clip.metadata}-plot-brushable-area`;
     const coords = await calcDragCoordinates(
@@ -259,7 +254,6 @@ describe("centroid labels", () => {
       const generatedLabels = await getAllByClass("centroid-label");
       // Number of labels generated should be equal to size of the object
       expect(generatedLabels).toHaveLength(
-        // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
         Object.keys(data.categorical[label]).length
       );
     }
@@ -281,7 +275,6 @@ describe("graph overlay", () => {
       data.pan["coordinates-as-percent"]
     );
 
-    // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
     const categoryValue = Object.keys(data.categorical[category])[0];
     const initialCoordinates = await getElementCoordinates(
       `${categoryValue}-centroid-label`

client/__tests__/e2e/e2eAnnotations.test.js

@@ -82,8 +82,7 @@ const genesetDescriptionID =
 const genesetDescriptionString = "fourth_gene_set: fourth description";
 const genesetToCheckForDescription = "fourth_gene_set";
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+async function setup(config) {
-async function setup(config: any) {
   await goToPage(appUrlBase);
 
   if (config.categoricalAnno) {
@@ -157,8 +156,7 @@ describe.each([
     await expect(page).toClick(getTestClass("pop-1-geneset-expand"));
 
     await page.waitForFunction(
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      (selector) => !document.querySelector(selector),
-      (selector: any) => !document.querySelector(selector),
       {},
       getTestClass("gene-loading-spinner")
     );
@@ -173,8 +171,7 @@ describe.each([
     await expect(page).toClick(getTestClass("pop-2-geneset-expand"));
 
     await page.waitForFunction(
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      (selector) => !document.querySelector(selector),
-      (selector: any) => !document.querySelector(selector),
       {},
       getTestClass("gene-loading-spinner")
     );
@@ -405,13 +402,8 @@ describe.each([
     expect(actualLabelName).toBe(expectedLabelName);
     expect(actualLabelCount).toBe(expectedLabelCount);
 
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    async function getInnerText(element, className) {
-    async function getInnerText(element: any, className: any) {
+      return element.$eval(getTestClass(className), (node) => node?.innerText);
-      return element.$eval(
-        getTestClass(className),
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-        (node: any) => node?.innerText
-      );
     }
   });
 
@@ -436,9 +428,7 @@ describe.each([
       `categorical-value-count-${perTestCategoryName}-${perTestLabelName}`
     );
 
-    // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
     expect(await result.evaluate((node) => node.innerText)).toBe(
-      // @ts-expect-error ts-migrate(2538) FIXME: Type 'boolean' cannot be used as an index type.
       data.categoryLabel.newCount.bySubsetConfig[config.withSubset]
     );
   });
@@ -498,7 +488,6 @@ describe.each([
     await createLabel(perTestCategoryName, labelName);
     await assertLabelExists(perTestCategoryName, labelName);
     await clickOn("undo");
-    // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
     await assertLabelDoesNotExist(perTestCategoryName);
     await clickOn("redo");
     await assertLabelExists(perTestCategoryName, labelName);
@@ -508,12 +497,10 @@ describe.each([
     await setup(config);
 
     await deleteLabel(perTestCategoryName, perTestLabelName);
-    // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
     await assertLabelDoesNotExist(perTestCategoryName);
     await clickOn("undo");
     await assertLabelExists(perTestCategoryName, perTestLabelName);
     await clickOn("redo");
-    // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
     await assertLabelDoesNotExist(perTestCategoryName);
   });
 
@@ -544,9 +531,7 @@ describe.each([
     const labels = await getAllByClass("categorical-row");
 
     const result = await Promise.all(
-      labels.map((label) =>
+      labels.map((label) => page.evaluate((element) => element.outerHTML, label))
-        page.evaluate((element) => element.outerHTML, label)
-      )
     );
 
     expect(result).toMatchSnapshot();
@@ -574,11 +559,9 @@ describe.each([
     expect(result).toMatchSnapshot();
   });
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  async function assertCategoryExists(categoryName) {
-  async function assertCategoryExists(categoryName: any) {
     const handle = await waitByID(`${categoryName}:category-label`);
 
-    // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
     const result = await handle.evaluate((node) =>
       node.getAttribute("aria-label")
     );
@@ -586,8 +569,7 @@ describe.each([
     return expect(result).toBe(categoryName);
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  async function assertLabelExists(categoryName, labelName) {
-  async function assertLabelExists(categoryName: any, labelName: any) {
     await expect(page).toMatchElement(
       getTestId(`${categoryName}:category-expand`)
     );
@@ -599,13 +581,11 @@ describe.each([
     );
 
     expect(
-      // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
       await previous.evaluate((node) => node.getAttribute("aria-label"))
     ).toBe(labelName);
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  async function assertLabelDoesNotExist(categoryName, labelName) {
-  async function assertLabelDoesNotExist(categoryName: any, labelName: any) {
     await expandCategory(categoryName);
     const result = await page.$(
       `[data-testid='categorical-value-${categoryName}-${labelName}']`

client/__tests__/e2e/e2eJestConfig.json

@@ -1,10 +1,10 @@
 {
   "testRunner": "jest-circus/runner",
   "preset": "jest-puppeteer",
-  "testMatch": ["**/__tests__/**/?(*.)(spec|test).ts?(x)"],
+  "testMatch": ["**/__tests__/**/?(*.)(spec|test).js?(x)"],
-  "setupFiles": ["../setupMissingGlobals.ts"],
+  "setupFiles": ["../setupMissingGlobals.js"],
-  "setupFilesAfterEnv": ["expect-puppeteer", "./puppeteer.setup.ts"],
+  "setupFilesAfterEnv": ["expect-puppeteer", "./puppeteer.setup.js"],
-  "globalSetup": "../globalSetup.ts",
+  "globalSetup": "../globalSetup.js",
   "globalTeardown": "jest-environment-puppeteer/teardown",
   "testEnvironment": "./screenshot_env.js"
 }

client/__tests__/e2e/puppeteer.setup.js

@@ -23,7 +23,6 @@ beforeEach(async () => {
   const userAgent = await browser.userAgent();
   await page.setUserAgent(`${userAgent}bot`);
 
-  // @ts-expect-error ts-migrate(2341) FIXME: Property '_client' is private and only accessible ... Remove this comment to see the full error message
   await page._client.send("Animation.setPlaybackRate", { playbackRate: 12 });
 
   page.on("pageerror", (err) => {
@@ -50,8 +49,7 @@ beforeEach(async () => {
         }
         const errorMsgText = await Promise.all(
           // TODO can we do this without internal properties?
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          msg.args().map((arg) => arg._remoteObject.description)
-          msg.args().map((arg: any) => arg._remoteObject.description)
         );
         throw new Error(`Console error: ${errorMsgText}`);
       }

client/__tests__/e2e/puppeteerUtils.js

@@ -0,0 +1,131 @@
+/* eslint-disable no-await-in-loop -- await in loop is needed to emulate sequential user actions */
+export function getTestId(id) {
+  return `[data-testid='${id}']`;
+}
+
+export function getTestClass(className) {
+  return `[data-testclass='${className}']`;
+}
+
+export async function waitByID(testId, props = {}) {
+  return page.waitForSelector(getTestId(testId), props);
+}
+
+export async function waitByClass(testClass, props = {}) {
+  return page.waitForSelector(`[data-testclass='${testClass}']`, props);
+}
+
+export async function waitForAllByIds(testIds) {
+  await Promise.all(
+    testIds.map((testId) => page.waitForSelector(getTestId(testId)))
+  );
+}
+
+export async function getAllByClass(testClass) {
+  return page.$$(`[data-testclass=${testClass}]`);
+}
+
+export async function typeInto(testId, text) {
+  // blueprint's  typeahead is treating typing weird, clicking & waiting first solves this
+  // only works for text without special characters
+  await waitByID(testId);
+  const selector = getTestId(testId);
+  // type ahead can be annoying if you don't pause before you type
+  await page.click(selector);
+  await page.waitForTimeout(200);
+  await page.type(selector, text);
+}
+
+export async function clearInputAndTypeInto(testId, text) {
+  await waitByID(testId);
+  const selector = getTestId(testId);
+  // only works for text without special characters
+  // type ahead can be annoying if you don't pause before you type
+  await page.click(selector);
+  await page.waitForTimeout(200);
+  // select all
+  await page.click(selector, { clickCount: 3 });
+  await page.keyboard.press("Backspace");
+  await page.type(selector, text);
+}
+
+export async function clickOn(testId, options = {}) {
+  await expect(page).toClick(getTestId(testId), options);
+}
+
+/**
+ * (thuang): There are times when Puppeteer clicks on a button and the page doesn't respond.
+ * So I added clickOnUntil() to retry clicking until a given condition is met.
+ */
+export async function clickOnUntil(testId, assert) {
+  const MAX_RETRY = 10;
+  const WAIT_FOR_MS = 200;
+
+  let retry = 0;
+
+  while (retry < MAX_RETRY) {
+    try {
+      await clickOn(testId);
+      await assert();
+
+      break;
+    } catch (error) {
+      retry += 1;
+
+      await page.waitForTimeout(WAIT_FOR_MS);
+    }
+  }
+
+  if (retry === MAX_RETRY) {
+    throw Error("clickOnUntil() assertion failed!");
+  }
+}
+
+export async function getOneElementInnerHTML(selector, options = {}) {
+  await page.waitForSelector(selector, options);
+
+  return page.$eval(selector, (el) => el.innerHTML);
+}
+
+export async function getOneElementInnerText(selector) {
+  expect(page).toMatchElement(selector);
+
+  return page.$eval(selector, (el) => el.innerText);
+}
+
+export async function getElementCoordinates(testId) {
+  return page.$eval(getTestId(testId), (elem) => {
+    const { left, top } = elem.getBoundingClientRect();
+    return [left, top];
+  });
+}
+
+async function clickTermsOfService() {
+  if (!(await isElementPresent(getTestId("tos-cookies-accept")))) return;
+
+  await clickOn("tos-cookies-accept");
+}
+
+async function nameNewAnnotation() {
+  if (await isElementPresent(getTestId("annotation-dialog"))) {
+    await typeInto("new-annotation-name", "ignoreE2E");
+    await clickOn("submit-annotation");
+
+    // wait for the page to load
+    await waitByClass("autosave-complete");
+  }
+}
+
+export async function goToPage(url) {
+  await page.goto(url, {
+    waitUntil: "networkidle0",
+  });
+
+  await nameNewAnnotation();
+  await clickTermsOfService();
+}
+
+export async function isElementPresent(selector, options) {
+  return Boolean(await page.$(selector, options));
+}
+/* eslint-enable no-await-in-loop -- await in loop is needed to emulate sequential user actions */

client/__tests__/e2e/puppeteerUtils.ts

@@ -1,151 +0,0 @@
-/* eslint-disable no-await-in-loop -- await in loop is needed to emulate sequential user actions */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export function getTestId(id: any) {
-  return `[data-testid='${id}']`;
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export function getTestClass(className: any) {
-  return `[data-testclass='${className}']`;
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function waitByID(testId: any, props = {}) {
-  return page.waitForSelector(getTestId(testId), props);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function waitByClass(testClass: any, props = {}) {
-  return page.waitForSelector(`[data-testclass='${testClass}']`, props);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function waitForAllByIds(testIds: any) {
-  await Promise.all(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    testIds.map((testId: any) => page.waitForSelector(getTestId(testId)))
-  );
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function getAllByClass(testClass: any) {
-  return page.$$(`[data-testclass=${testClass}]`);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function typeInto(testId: any, text: any) {
-  // blueprint's  typeahead is treating typing weird, clicking & waiting first solves this
-  // only works for text without special characters
-  await waitByID(testId);
-  const selector = getTestId(testId);
-  // type ahead can be annoying if you don't pause before you type
-  await page.click(selector);
-  await page.waitForTimeout(200);
-  await page.type(selector, text);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function clearInputAndTypeInto(testId: any, text: any) {
-  await waitByID(testId);
-  const selector = getTestId(testId);
-  // only works for text without special characters
-  // type ahead can be annoying if you don't pause before you type
-  await page.click(selector);
-  await page.waitForTimeout(200);
-  // select all
-  await page.click(selector, { clickCount: 3 });
-  await page.keyboard.press("Backspace");
-  await page.type(selector, text);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function clickOn(testId: any, options = {}) {
-  await expect(page).toClick(getTestId(testId), options);
-}
-
-/**
- * (thuang): There are times when Puppeteer clicks on a button and the page doesn't respond.
- * So I added clickOnUntil() to retry clicking until a given condition is met.
- */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function clickOnUntil(testId: any, assert: any) {
-  const MAX_RETRY = 10;
-  const WAIT_FOR_MS = 200;
-
-  let retry = 0;
-
-  while (retry < MAX_RETRY) {
-    try {
-      await clickOn(testId);
-      await assert();
-
-      break;
-    } catch (error) {
-      retry += 1;
-
-      await page.waitForTimeout(WAIT_FOR_MS);
-    }
-  }
-
-  if (retry === MAX_RETRY) {
-    throw Error("clickOnUntil() assertion failed!");
-  }
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function getOneElementInnerHTML(selector: any, options = {}) {
-  await page.waitForSelector(selector, options);
-
-  return page.$eval(selector, (el) => el.innerHTML);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function getOneElementInnerText(selector: any) {
-  expect(page).toMatchElement(selector);
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  return page.$eval(selector, (el) => (el as any).innerText);
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function getElementCoordinates(testId: any) {
-  return page.$eval(getTestId(testId), (elem) => {
-    const { left, top } = elem.getBoundingClientRect();
-    return [left, top];
-  });
-}
-
-async function clickTermsOfService() {
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
-  if (!(await isElementPresent(getTestId("tos-cookies-accept")))) return;
-
-  await clickOn("tos-cookies-accept");
-}
-
-async function nameNewAnnotation() {
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
-  if (await isElementPresent(getTestId("annotation-dialog"))) {
-    await typeInto("new-annotation-name", "ignoreE2E");
-    await clickOn("submit-annotation");
-
-    // wait for the page to load
-    await waitByClass("autosave-complete");
-  }
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function goToPage(url: any) {
-  await page.goto(url, {
-    waitUntil: "networkidle0",
-  });
-
-  await nameNewAnnotation();
-  await clickTermsOfService();
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-export async function isElementPresent(selector: any, options: any) {
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 2.
-  return Boolean(await page.$(selector, options));
-}
-/* eslint-enable no-await-in-loop -- await in loop is needed to emulate sequential user actions */

client/__tests__/e2e/screenshot_env.js

@@ -1,11 +1,7 @@
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const PuppeteerEnvironment = require("jest-environment-puppeteer");
 require("jest-circus");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const ENV_DEFAULT = require("../../../environment.default.json");
 
-// @ts-expect-error ts-migrate(2451) FIXME: Cannot redeclare block-scoped variable 'takeScreen... Remove this comment to see the full error message
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const takeScreenshot = require("./takeScreenshot");
 
 class ScreenshotEnvironment extends PuppeteerEnvironment {

client/__tests__/globalSetup.js

@@ -1,12 +1,8 @@
-// eslint-disable-next-line @typescript-eslint/ban-ts-comment --- FIXME: disabled temporarily on migrate to TS.
-// @ts-ignore FIXME: 'globalSetup.ts' cannot be compiled under '--isola... Remove this comment to see the full error message
 const {
   SecretsManagerClient,
   GetSecretValueCommand,
-  // eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 } = require("@aws-sdk/client-secrets-manager");
 
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const { setup } = require("jest-environment-puppeteer");
 
 const client = new SecretsManagerClient({ region: "us-west-2" });

client/__tests__/reducers/cascade.test.js

@@ -20,16 +20,7 @@ describe("cascade", () => {
     const reducer = cascadeReducers([
       [
         "foo",
-        (
+        (currentState, action, nextSharedState, prevSharedState) => {
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          currentState: any,
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          action: any,
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          nextSharedState: any,
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          prevSharedState: any
-        ) => {
           expect(currentState).toBeUndefined();
           expect(action).toEqual(topLevelAction);
           expect(nextSharedState).toStrictEqual({});
@@ -39,16 +30,7 @@ describe("cascade", () => {
       ],
       [
         "bar",
-        (
+        (currentState, action, nextSharedState, prevSharedState) => {
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          currentState: any,
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          action: any,
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          nextSharedState: any,
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          prevSharedState: any
-        ) => {
           expect(currentState).toBeUndefined();
           expect(action).toEqual(topLevelAction);
           expect(nextSharedState).toStrictEqual({ foo: 0 });

client/__tests__/reducers/genesets.test.js

@@ -501,7 +501,6 @@ describe("geneset: set tid", () => {
   test("not a number error", () => {
     expect(() => {
       genesetsReducer(
-        // @ts-expect-error ts-migrate(2322) FIXME: Type 'number' is not assignable to type 'undefined... Remove this comment to see the full error message
         { lastTid: 1 },
         {
           type: "geneset: set tid",
@@ -514,7 +513,6 @@ describe("geneset: set tid", () => {
   test("decrement error", () => {
     expect(() => {
       genesetsReducer(
-        // @ts-expect-error ts-migrate(2322) FIXME: Type 'number' is not assignable to type 'undefined... Remove this comment to see the full error message
         { lastTid: 1 },
         {
           type: "geneset: set tid",

client/__tests__/reducers/undoable.test.js

@@ -2,7 +2,6 @@ import undoable from "../../src/reducers/undoable";
 
 describe("create", () => {
   test("no keys", () => {
-    // @ts-expect-error ts-migrate(2554) FIXME: Expected 2-3 arguments, but got 1.
     expect(() => undoable(() => {})).toThrow();
     expect(() => undoable(() => {}, null)).toThrow();
     expect(() => undoable(() => {}, [])).toThrow();
@@ -24,8 +23,7 @@ describe("create", () => {
 describe("undo", () => {
   test("expected state modifications", () => {
     const initialState = { a: 0, b: 1000 };
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    const reducer = (state) => ({ a: state.a + 1, b: state.b + 1 });
-    const reducer = (state: any) => ({ a: state.a + 1, b: state.b + 1 });
     const undoableReducer = undoable(reducer, ["a"]);
 
     const s1 = undoableReducer(initialState, { type: "test" });
@@ -43,10 +41,8 @@ describe("undo", () => {
 
 describe("redo", () => {
   const initialState = { a: 0, b: 1000 };
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  const reducer = (state) => ({ a: state.a + 1, b: state.b + 1 });
-  const reducer = (state: any) => ({ a: state.a + 1, b: state.b + 1 });
+  let UR;
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  let UR: any;
 
   beforeEach(() => {
     UR = undoable(reducer, ["a"]);

client/__tests__/setupMissingGlobals.js

@@ -5,6 +5,5 @@ the jest test environment).
 
 import { TextDecoder, TextEncoder } from "util";
 
-// @ts-expect-error ts-migrate(2322) FIXME: Type 'typeof TextDecoder' is not assignable to typ... Remove this comment to see the full error message
 global.TextDecoder = TextDecoder;
 global.TextEncoder = TextEncoder;

client/__tests__/util/actionHelpers.test.js

@@ -11,18 +11,14 @@ describe("rangeEncodeIndices", () => {
 
   test("sorted flag", () => {
     expect(rangeEncodeIndices([1, 9, 432], 10, true)).toMatchObject([
-      1,
+      1, 9, 432,
-      9,
-      432,
     ]);
     expect(rangeEncodeIndices([1, 9, 432], 10, false)).toMatchObject([
-      1,
+      1, 9, 432,
-      9,
-      432,
     ]);
-    expect(
+    expect(rangeEncodeIndices([0, 1, 2, 3, 9, 10, 432], 2, true)).toMatchObject(
-      rangeEncodeIndices([0, 1, 2, 3, 9, 10, 432], 2, true)
+      [[0, 3], [9, 10], 432]
-    ).toMatchObject([[0, 3], [9, 10], 432]);
+    );
     expect(
       rangeEncodeIndices([0, 1, 2, 3, 9, 10, 432], 2, false)
     ).toMatchObject([[0, 3], [9, 10], 432]);

client/__tests__/util/annoMatrix/annoMatrix.test.js

@@ -14,13 +14,10 @@ import { Dataframe } from "../../../src/util/dataframe";
 enableFetchMocks();
 
 describe("AnnoMatrix", () => {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  let annoMatrix;
-  let annoMatrix: any;
 
   beforeEach(async () => {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    fetch.resetMocks(); // reset all fetch mocking state
-    (fetch as any).resetMocks(); // reset all fetch mocking state
-    // reset all fetch mocking state
     annoMatrix = new AnnoMatrixLoader(
       serverMocks.baseDataURL,
       serverMocks.schema.schema
@@ -39,8 +36,7 @@ describe("AnnoMatrix", () => {
     });
 
     test("simple single column fetch", async () => {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.once(serverMocks.annotationsObs(["name_0"]));
-      (fetch as any).once(serverMocks.annotationsObs(["name_0"]));
 
       const df = await annoMatrix.fetch("obs", "name_0");
       expect(df).toBeInstanceOf(Dataframe);
@@ -49,8 +45,7 @@ describe("AnnoMatrix", () => {
     });
 
     test("simple multi column fetch", async () => {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch
-      (fetch as any)
         .once(serverMocks.annotationsObs(["name_0"]))
         .once(serverMocks.annotationsObs(["n_genes"]));
 
@@ -60,13 +55,9 @@ describe("AnnoMatrix", () => {
     });
 
     describe("fetch from field", () => {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      const getLastTwo = async (field) => {
-      const getLastTwo = async (field: any) => {
         const columnNames = annoMatrix.getMatrixColumns(field).slice(-2);
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+        fetch.mockResponses(...columnNames.map(() => serverMocks.responder));
-        (fetch as any).mockResponses(
-          ...columnNames.map(() => serverMocks.responder)
-        );
         await expect(
           annoMatrix.fetch(field, columnNames)
         ).resolves.toBeInstanceOf(Dataframe);
@@ -79,22 +70,19 @@ describe("AnnoMatrix", () => {
 
     test("fetch - test all query forms", async () => {
       // single string is a column name
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.once(serverMocks.annotationsObs(["n_genes"]));
-      (fetch as any).once(serverMocks.annotationsObs(["n_genes"]));
       await expect(annoMatrix.fetch("obs", "n_genes")).resolves.toBeInstanceOf(
         Dataframe
       );
 
       // array of column names, expecting n_genes to be cached.
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.once(serverMocks.annotationsObs(["percent_mito"]));
-      (fetch as any).once(serverMocks.annotationsObs(["percent_mito"]));
       await expect(
         annoMatrix.fetch("obs", ["n_genes", "percent_mito"])
       ).resolves.toBeInstanceOf(Dataframe);
 
       // more complex value filter query, enumerated
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.once(serverMocks.responder);
-      (fetch as any).once(serverMocks.responder);
       await expect(
         annoMatrix.fetch("X", {
           where: {
@@ -107,8 +95,7 @@ describe("AnnoMatrix", () => {
 
       // more complex value filter query, range
       const varIndex = annoMatrix.schema.annotations.var.index;
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch
-      (fetch as any)
         .once(
           serverMocks.withExpected("/data/var", [[`var:${varIndex}`, "SUMO3"]])
         )
@@ -184,8 +171,7 @@ describe("AnnoMatrix", () => {
       expect(am1.nObs).toEqual(am2.nObs);
       expect(am1.nVar).toEqual(am2.nVar);
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch
-      (fetch as any)
         .once(serverMocks.annotationsObs(["n_genes"]))
         .once(serverMocks.annotationsObs(["n_genes"]));
       const ng1 = await am1.fetch("obs", "n_genes");
@@ -199,11 +185,9 @@ describe("AnnoMatrix", () => {
   });
 
   describe("add/drop column", () => {
-    // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'base' implicitly has an 'any' type.
     async function addDrop(base) {
       expect(base.getMatrixColumns("obs")).not.toContain("foo");
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.mockRejectOnce(new Error("unknown column name"));
-      (fetch as any).mockRejectOnce(new Error("unknown column name"));
       await expect(base.fetch("obs", "foo")).rejects.toThrow(
         "unknown column name"
       );
@@ -228,8 +212,7 @@ describe("AnnoMatrix", () => {
       const am2 = am1.dropObsColumn("foo");
       expect(base.getMatrixColumns("obs")).not.toContain("foo");
       expect(am2.getMatrixColumns("obs")).not.toContain("foo");
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.mockRejectOnce(new Error("unknown column name"));
-      (fetch as any).mockRejectOnce(new Error("unknown column name"));
       await expect(am2.fetch("obs", "foo")).rejects.toThrow(
         "unknown column name"
       );
@@ -252,16 +235,14 @@ describe("AnnoMatrix", () => {
       const am4 = clip(am3, 0, 1);
       await addDrop(am4);
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.mockResponse(serverMocks.responder);
-      (fetch as any).mockResponse(serverMocks.responder);
 
       await am1.fetch("obs", am1.getMatrixColumns("obs"));
       await am2.fetch("obs", am2.getMatrixColumns("obs"));
       await am3.fetch("obs", am3.getMatrixColumns("obs"));
       await am4.fetch("obs", am4.getMatrixColumns("obs"));
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.resetMocks();
-      (fetch as any).resetMocks();
 
       await addDrop(am1);
       await addDrop(am2);
@@ -271,7 +252,6 @@ describe("AnnoMatrix", () => {
   });
 
   describe("setObsColumnValues", () => {
-    // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'base' implicitly has an 'any' type.
     async function addSetDrop(base) {
       /* add column */
       let am = base.addObsColumn(
@@ -307,8 +287,7 @@ describe("AnnoMatrix", () => {
       );
 
       /* drop column */
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.mockRejectOnce(new Error("unknown column name"));
-      (fetch as any).mockRejectOnce(new Error("unknown column name"));
       am = am1.dropObsColumn("test");
       await expect(am.fetch("obs", "test")).rejects.toThrow(
         "unknown column name"
@@ -329,8 +308,7 @@ describe("AnnoMatrix", () => {
       const am3 = isubset(annoMatrix, [10, 1, 0, 30, 2]);
       await addSetDrop(am3);
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.mockResponse(serverMocks.responder);
-      (fetch as any).mockResponse(serverMocks.responder);
 
       await am1.fetch("obs", am1.getMatrixColumns("obs"));
       await am2.fetch("obs", am2.getMatrixColumns("obs"));

client/__tests__/util/annoMatrix/crossfilter.test.js

@@ -17,15 +17,11 @@ import { rangeFill } from "../../../src/util/range";
 enableFetchMocks();
 
 describe("AnnoMatrixCrossfilter", () => {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  let annoMatrix;
-  let annoMatrix: any;
+  let crossfilter;
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  let crossfilter: any;
 
   beforeEach(async () => {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    fetch.resetMocks(); // reset all fetch mocking state
-    (fetch as any).resetMocks(); // reset all fetch mocking state
-    // reset all fetch mocking state
     annoMatrix = new AnnoMatrixLoader(
       serverMocks.baseDataURL,
       serverMocks.schema.schema
@@ -71,10 +67,7 @@ describe("AnnoMatrixCrossfilter", () => {
         crossfilter.obsCrossfilter.hasDimension("obs/louvain")
       ).toBeFalsy();
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.once(serverMocks.dataframeResponse(["louvain"], [obsLouvain]));
-      (fetch as any).once(
-        serverMocks.dataframeResponse(["louvain"], [obsLouvain])
-      );
       let newCrossfilter = await crossfilter.select("obs", "louvain", {
         mode: "none",
       });
@@ -83,8 +76,7 @@ describe("AnnoMatrixCrossfilter", () => {
       expect(
         newCrossfilter.obsCrossfilter.hasDimension("obs/louvain")
       ).toBeTruthy();
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      expect(fetch.mock.calls).toHaveLength(1);
-      expect((fetch as any).mock.calls).toHaveLength(1);
 
       newCrossfilter = await crossfilter.select("obs", "louvain", {
         mode: "all",
@@ -95,10 +87,7 @@ describe("AnnoMatrixCrossfilter", () => {
     test("simple column select", async () => {
       let xfltr;
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.once(serverMocks.dataframeResponse(["louvain"], [obsLouvain]));
-      (fetch as any).once(
-        serverMocks.dataframeResponse(["louvain"], [obsLouvain])
-      );
       xfltr = await crossfilter.select("obs", "louvain", {
         mode: "exact",
         values: ["NK cells", "B cells"],
@@ -116,7 +105,6 @@ describe("AnnoMatrixCrossfilter", () => {
       expect(xfltr.allSelectedLabels()).toEqual(
         Int32Array.from(
           obsLouvain.reduce((acc, val, idx) => {
-            // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'number' is not assignable to par... Remove this comment to see the full error message
             if (val === "NK cells" || val === "B cells") acc.push(idx);
             return acc;
           }, [])
@@ -136,13 +124,10 @@ describe("AnnoMatrixCrossfilter", () => {
       const values = df.col("louvain").asArray();
       const selected = xfltr.allSelectedMask();
       values.every(
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+        (val, idx) => !["NK cells", "B cells"].includes(val) !== !selected[idx]
-        (val: any, idx: any) =>
-          !["NK cells", "B cells"].includes(val) !== !selected[idx]
       );
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.once(
-      (fetch as any).once(
         serverMocks.dataframeResponse(["n_genes"], [new Int32Array(obsNGenes)])
       );
       xfltr = await xfltr.select("obs", "n_genes", {
@@ -161,7 +146,6 @@ describe("AnnoMatrixCrossfilter", () => {
               val < 500 &&
               (louvain === "NK cells" || louvain === "B cells")
             )
-              // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'number' is not assignable to par... Remove this comment to see the full error message
               acc.push(idx);
             return acc;
           }, [])
@@ -176,8 +160,7 @@ describe("AnnoMatrixCrossfilter", () => {
       const varIndex = annoMatrix.schema.annotations.var.index;
 
       const { nObs } = annoMatrix.schema.dataframe;
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.once(
-      (fetch as any).once(
         serverMocks.dataframeResponse(
           ["TEST"],
           [rangeFill(new Float32Array(nObs), 0, 0.1)]
@@ -213,19 +196,14 @@ describe("AnnoMatrixCrossfilter", () => {
       });
       const values = df.icol(0).asArray();
       const selected = xfltr.allSelectedMask();
-      values.every(
+      values.every((val, idx) => !(val >= 0 && val <= 50) !== !selected[idx]);
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      expect(selected.reduce((acc, val) => (val ? acc + 1 : acc), 0)).toEqual(
-        (val: any, idx: any) => !(val >= 0 && val <= 50) !== !selected[idx]
+        xfltr.countSelected()
       );
-      expect(
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-        selected.reduce((acc: any, val: any) => (val ? acc + 1 : acc), 0)
-      ).toEqual(xfltr.countSelected());
     });
 
     test("spatial column select", async () => {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.once(
-      (fetch as any).once(
         serverMocks.dataframeResponse(
           ["umap_0", "umap_1"],
           [Float32Array.from(embUmap[0]), Float32Array.from(embUmap[1])]
@@ -244,7 +222,6 @@ describe("AnnoMatrixCrossfilter", () => {
     test("select on subset", async () => {
       const mask = new Uint8Array(annoMatrix.nObs).fill(0);
       for (let i = 0; i < mask.length; i += 2) {
-        // @ts-expect-error ts-migrate(2322) FIXME: Type 'boolean' is not assignable to type 'number'.
         mask[i] = true;
       }
       const annoMatrixSubset = isubsetMask(annoMatrix, mask);
@@ -253,10 +230,7 @@ describe("AnnoMatrixCrossfilter", () => {
       let xfltr = new AnnoMatrixObsCrossfilter(annoMatrixSubset);
       expect(xfltr.countSelected()).toEqual(annoMatrixSubset.nObs);
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.once(serverMocks.dataframeResponse(["louvain"], [obsLouvain]));
-      (fetch as any).once(
-        serverMocks.dataframeResponse(["louvain"], [obsLouvain])
-      );
       xfltr = await xfltr.select("obs", "louvain", {
         mode: "exact",
         values: ["NK cells", "B cells"],
@@ -269,9 +243,7 @@ describe("AnnoMatrixCrossfilter", () => {
       const values = df.col("louvain").asArray();
       const selected = xfltr.allSelectedMask();
       values.every(
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+        (val, idx) => !["NK cells", "B cells"].includes(val) !== !selected[idx]
-        (val: any, idx: any) =>
-          !["NK cells", "B cells"].includes(val) !== !selected[idx]
       );
     });
 
@@ -284,8 +256,7 @@ describe("AnnoMatrixCrossfilter", () => {
         "unable to obsSelect upon the var dimension"
       );
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.mockRejectOnce(new Error("unknown column name"));
-      (fetch as any).mockRejectOnce(new Error("unknown column name"));
       await expect(crossfilter.select("obs", "foo")).rejects.toThrow(
         "unknown column name"
       );
@@ -296,29 +267,24 @@ describe("AnnoMatrixCrossfilter", () => {
     /*
     test the matrix mutators via crossfilter proxy
     */
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    async function helperAddTestCol(cf, colName, colSchema = null) {
-    async function helperAddTestCol(cf: any, colName: any, colSchema = null) {
       expect(
         cf.annoMatrix.getMatrixColumns("obs").includes(colName)
       ).toBeFalsy();
 
       if (colSchema === null) {
-        // @ts-expect-error ts-migrate(2322) FIXME: Type '{ name: any; type: string; categories: strin... Remove this comment to see the full error message
         colSchema = {
           name: colName,
           type: "categorical",
           categories: ["toasty"],
         };
       }
-      // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
       colSchema.name = colName;
-      // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
       const initValue = colSchema.categories[0];
       const xfltr = cf.addObsColumn(colSchema, Array, initValue);
       expect(
         xfltr.annoMatrix.schema.annotations.obs.columns.filter(
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          (v) => v.name === colName
-          (v: any) => v.name === colName
         )
       ).toHaveLength(1);
       const df = await xfltr.annoMatrix.fetch("obs", colName);
@@ -348,8 +314,7 @@ describe("AnnoMatrixCrossfilter", () => {
       });
       expect(
         xfltr.annoMatrix.schema.annotations.obs.columns.filter(
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          (v) => v.name === "foo"
-          (v: any) => v.name === "foo"
         )
       ).toHaveLength(1);
 
@@ -358,8 +323,8 @@ describe("AnnoMatrixCrossfilter", () => {
       expect(
         df
           .col("foo")
-          .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          .asArray()
-          .every((v: any) => v === "A")
+          .every((v) => v === "A")
       ).toBeTruthy();
 
       // check that we catch dups
@@ -396,13 +361,11 @@ describe("AnnoMatrixCrossfilter", () => {
       xfltr = xfltr.dropObsColumn("foo");
       expect(
         xfltr.annoMatrix.schema.annotations.obs.columns.filter(
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          (v) => v.name === "foo"
-          (v: any) => v.name === "foo"
         )
       ).toHaveLength(0);
       expect(xfltr.annoMatrix.schema.annotations.obsByName.foo).toBeUndefined();
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.mockRejectOnce(new Error("unknown column name"));
-      (fetch as any).mockRejectOnce(new Error("unknown column name"));
       await expect(xfltr.annoMatrix.fetch("obs", "foo")).rejects.toThrow(
         "unknown column name"
       );
@@ -415,8 +378,7 @@ describe("AnnoMatrixCrossfilter", () => {
       });
       xfltr = xfltr.dropObsColumn("bar");
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.mockRejectOnce(new Error("unknown column name"));
-      (fetch as any).mockRejectOnce(new Error("unknown column name"));
       await expect(xfltr.select("obs", "bar", { mode: "all" })).rejects.toThrow(
         "unknown column name"
       );
@@ -442,8 +404,7 @@ describe("AnnoMatrixCrossfilter", () => {
         type: "categorical",
       });
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.mockRejectOnce(new Error("unknown column name"));
-      (fetch as any).mockRejectOnce(new Error("unknown column name"));
       await expect(xfltr.annoMatrix.fetch("obs", "foo")).rejects.toThrow(
         "unknown column name"
       );
@@ -458,8 +419,7 @@ describe("AnnoMatrixCrossfilter", () => {
       });
       xfltr = xfltr.renameObsColumn("bar", "xyz");
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.mockRejectOnce(new Error("unknown column name"));
-      (fetch as any).mockRejectOnce(new Error("unknown column name"));
       await expect(xfltr.select("obs", "bar", { mode: "all" })).rejects.toThrow(
         "unknown column name"
       );
@@ -469,8 +429,7 @@ describe("AnnoMatrixCrossfilter", () => {
     });
 
     test("addObsAnnoCategory", async () => {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      let xfltr;
-      let xfltr: any;
 
       // catch unknown or readonly columns
       expect(() => crossfilter.addObsAnnoCategory("louvain", "mumble")).toThrow(
@@ -481,7 +440,6 @@ describe("AnnoMatrixCrossfilter", () => {
       ).toThrow("Unknown or readonly obs column");
 
       // add a column and then add category to it
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message
       xfltr = await helperAddTestCol(crossfilter, "foo", {
         name: "foo",
         type: "categorical",
@@ -500,7 +458,6 @@ describe("AnnoMatrixCrossfilter", () => {
       );
 
       // now same, but ensure we have built an index before doing the operation
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message
       xfltr = await helperAddTestCol(crossfilter, "bar", {
         name: "bar",
         type: "categorical",
@@ -529,7 +486,6 @@ describe("AnnoMatrixCrossfilter", () => {
         crossfilter.removeObsAnnoCategory("undefined-name", "mumble")
       ).rejects.toThrow("Unknown or readonly obs column");
 
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message
       xfltr = await helperAddTestCol(crossfilter, "foo", {
         name: "foo",
         type: "categorical",
@@ -539,8 +495,8 @@ describe("AnnoMatrixCrossfilter", () => {
       expect(
         (await xfltr.annoMatrix.fetch("obs", "foo"))
           .col("foo")
-          .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          .asArray()
-          .every((v: any) => v === "unassigned")
+          .every((v) => v === "unassigned")
       ).toBeTruthy();
       expect(xfltr.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
         name: "foo",
@@ -558,8 +514,8 @@ describe("AnnoMatrixCrossfilter", () => {
       expect(
         (await xfltr1.annoMatrix.fetch("obs", "foo"))
           .col("foo")
-          .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          .asArray()
-          .every((v: any) => v === "unassigned")
+          .every((v) => v === "unassigned")
       ).toBeTruthy();
       expect(xfltr1.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
         name: "foo",
@@ -581,8 +537,8 @@ describe("AnnoMatrixCrossfilter", () => {
       expect(
         (await xfltr2.annoMatrix.fetch("obs", "foo"))
           .col("foo")
-          .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          .asArray()
-          .every((v: any) => v === "red")
+          .every((v) => v === "red")
       ).toBeTruthy();
       expect(xfltr2.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
         name: "foo",
@@ -600,7 +556,6 @@ describe("AnnoMatrixCrossfilter", () => {
         crossfilter.setObsColumnValues("undefined-name", [0], "mumble")
       ).rejects.toThrow("Unknown or readonly obs column");
 
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message
       let xfltr = await helperAddTestCol(crossfilter, "foo", {
         name: "foo",
         type: "categorical",
@@ -617,8 +572,8 @@ describe("AnnoMatrixCrossfilter", () => {
       expect(
         (await xfltr.annoMatrix.fetch("obs", "foo"))
           .col("foo")
-          .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          .asArray()
-          .every((v: any) => v === "unassigned")
+          .every((v) => v === "unassigned")
       ).toBeTruthy();
       const xfltr1 = await xfltr.setObsColumnValues("foo", [0, 10], "purple");
       expect(
@@ -626,8 +581,7 @@ describe("AnnoMatrixCrossfilter", () => {
           .col("foo")
           .asArray()
           .every(
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+            (v, i) =>
-            (v: any, i: any) =>
               v === "unassigned" || (v === "purple" && (i === 0 || i === 10))
           )
       ).toBeTruthy();
@@ -661,7 +615,6 @@ describe("AnnoMatrixCrossfilter", () => {
         crossfilter.resetObsColumnValues("undefined-name", "red", "blue")
       ).rejects.toThrow("Unknown or readonly obs column");
 
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message
       let xfltr = await helperAddTestCol(crossfilter, "foo", {
         name: "foo",
         type: "categorical",
@@ -685,22 +638,22 @@ describe("AnnoMatrixCrossfilter", () => {
       expect(
         (await xfltr1.annoMatrix.fetch("obs", "foo"))
           .col("foo")
-          .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          .asArray()
-          .filter((v: any) => v === "purple")
+          .filter((v) => v === "purple")
       ).toHaveLength(2);
 
       xfltr1 = await xfltr1.resetObsColumnValues("foo", "purple", "magenta");
       expect(
         (await xfltr1.annoMatrix.fetch("obs", "foo"))
           .col("foo")
-          .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          .asArray()
-          .filter((v: any) => v === "magenta")
+          .filter((v) => v === "magenta")
       ).toHaveLength(2);
       expect(
         (await xfltr1.annoMatrix.fetch("obs", "foo"))
           .col("foo")
-          .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          .asArray()
-          .filter((v: any) => v === "purple")
+          .filter((v) => v === "purple")
       ).toHaveLength(0);
       expect(xfltr1.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
         name: "foo",
@@ -720,16 +673,12 @@ describe("AnnoMatrixCrossfilter", () => {
   describe("edge cases", () => {
     test("transition from empty annoMatrix", async () => {
       // select before fetch needs to work
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      fetch.once(serverMocks.dataframeResponse(["louvain"], [obsLouvain]));
-      (fetch as any).once(
-        serverMocks.dataframeResponse(["louvain"], [obsLouvain])
-      );
       const xfltr = await crossfilter.select("obs", "louvain", {
         mode: "exact",
         values: "B cells",
       });
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      expect(fetch.mock.calls).toHaveLength(1);
-      expect((fetch as any).mock.calls).toHaveLength(1);
       expect(xfltr.obsCrossfilter.hasDimension("obs/louvain")).toBeTruthy();
       expect(xfltr.obsCrossfilter.all()).toBe(xfltr.annoMatrix._cache.obs);
       expect(xfltr.countSelected()).toEqual(

client/__tests__/util/annoMatrix/serverMocks/index.js

@@ -1,7 +1,6 @@
 export const baseDataURL = "https://a.fake.url/api/v0.2";
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+window.CELLXGENE = {
-(window as any).CELLXGENE = {
   API: {
     prefix: baseDataURL,
     version: "v0.2/",

client/__tests__/util/annoMatrix/serverMocks/routes.js

@@ -0,0 +1,211 @@
+import { schema } from "./schema";
+import { Dataframe, KeyIndex } from "../../../../src/util/dataframe";
+import { encodeMatrixFBS } from "../../../../src/util/stateManager/matrix";
+
+const indexedSchema = {
+  obsByName: Object.fromEntries(
+    schema.schema.annotations.obs.columns.map((v) => [v.name, v]) ?? []
+  ),
+  varByName: Object.fromEntries(
+    schema.schema.annotations.var.columns.map((v) => [v.name, v]) ?? []
+  ),
+  embByName: Object.fromEntries(
+    schema.schema.layout.obs.map((v) => [v.name, v]) ?? []
+  ),
+};
+
+function makeMockColumn(s, length) {
+  const { type } = s;
+  switch (type) {
+    case "int32":
+      return new Int32Array(length).fill(Math.floor(99 * Math.random()));
+
+    case "string":
+      return new Array(length).fill("test");
+
+    case "float32":
+      return new Float32Array(length).fill(99 * Math.random());
+
+    case "boolean":
+      return new Array(length).fill(false);
+
+    case "categorical":
+      return new Array(length).fill(s.categories[0]);
+
+    default:
+      throw new Error("unkonwn type");
+  }
+}
+
+function getEncodedDataframe(colNames, length, colSchemas) {
+  const colIndex = new KeyIndex(colNames);
+  const columns = colSchemas.map((s) => makeMockColumn(s, length));
+  const df = new Dataframe([length, colNames.length], columns, null, colIndex);
+  const body = encodeMatrixFBS(df);
+  return body;
+}
+
+export function dataframeResponse(colNames, columns) {
+  const colIndex = new KeyIndex(colNames);
+  const df = new Dataframe(
+    [columns[0].length, colNames.length],
+    columns,
+    null,
+    colIndex
+  );
+  const body = encodeMatrixFBS(df);
+  const headers = new Headers({
+    "Content-Type": "application/octet-stream",
+  });
+  return () => Promise.resolve({ body, init: { status: 200, headers } });
+}
+
+function annotationObsResponse(request) {
+  const url = new URL(request.url);
+  const params = Array.from(url.searchParams.entries());
+  const names = params
+    .filter(([k]) => k === "annotation-name")
+    .map(([, v]) => v);
+  if (!names.every((n) => indexedSchema.obsByName[n])) {
+    return Promise.reject(new Error("bad obs annotation name in URL"));
+  }
+  const colSchemas = names.map((n) => indexedSchema.obsByName[n]);
+  const body = getEncodedDataframe(
+    names,
+    schema.schema.dataframe.nObs,
+    colSchemas
+  );
+
+  const headers = new Headers({
+    "Content-Type": "application/octet-stream",
+  });
+  return Promise.resolve({
+    body,
+    init: { status: 200, headers },
+  });
+}
+
+function annotationVarResponse(request) {
+  const url = new URL(request.url);
+  const params = Array.from(url.searchParams.entries());
+  const names = params
+    .filter(([k]) => k === "annotation-name")
+    .map(([, v]) => v);
+  if (!names.every((n) => indexedSchema.varByName[n])) {
+    return Promise.reject(new Error("bad var annotation name in URL"));
+  }
+  const colSchemas = names.map((n) => indexedSchema.varByName[n]);
+  const body = getEncodedDataframe(
+    names,
+    schema.schema.dataframe.nVar,
+    colSchemas
+  );
+
+  const headers = new Headers({
+    "Content-Type": "application/octet-stream",
+  });
+  return Promise.resolve({
+    body,
+    init: { status: 200, headers },
+  });
+}
+
+function layoutObsResponse(request) {
+  const url = new URL(request.url);
+  const params = Array.from(url.searchParams.entries());
+  const names = params.filter(([k]) => k === "layout-name").map(([, v]) => v);
+  if (!names.every((n) => indexedSchema.embByName[n])) {
+    return Promise.reject(new Error("bad layout name in URL"));
+  }
+  const dims = names.map((n) => indexedSchema.embByName[n].dims).flat();
+  const colSchemas = names
+    .map((n) => [indexedSchema.embByName[n], indexedSchema.embByName[n]])
+    .flat();
+  const body = getEncodedDataframe(
+    dims,
+    schema.schema.dataframe.nObs,
+    colSchemas
+  );
+
+  const headers = new Headers({
+    "Content-Type": "application/octet-stream",
+  });
+  return Promise.resolve({
+    body,
+    init: { status: 200, headers },
+  });
+}
+
+function dataVarResponse(request) {
+  const url = new URL(request.url);
+  const params = Array.from(url.searchParams.entries());
+
+  const colNames = params.map((v) => `${v[0]}/${v[1]}`);
+  const colSchemas = colNames.map(() => schema.schema.dataframe);
+  const body = getEncodedDataframe(
+    colNames,
+    schema.schema.dataframe.nObs,
+    colSchemas
+  );
+
+  const headers = new Headers({
+    "Content-Type": "application/octet-stream",
+  });
+  return Promise.resolve({
+    body,
+    init: { status: 200, headers },
+  });
+}
+
+export function responder(request) {
+  const url = new URL(request.url);
+  const { pathname } = url;
+  if (pathname.endsWith("/annotations/obs")) {
+    return annotationObsResponse(request);
+  }
+  if (pathname.endsWith("/annotations/var")) {
+    return annotationVarResponse(request);
+  }
+  if (pathname.endsWith("/layout/obs")) {
+    return layoutObsResponse(request);
+  }
+  if (pathname.endsWith("/data/var")) {
+    return dataVarResponse(request);
+  }
+  return Promise.reject(new Error("bad URL"));
+}
+
+export function withExpected(expectedURL, expectedParams) {
+  /*
+  Do some additional error checking
+  */
+  return (request) => {
+    // if URL is bogus, reject the promise
+    const url = new URL(request.url);
+    if (!url.pathname.endsWith(expectedURL)) {
+      return Promise.reject(new Error("Unexpected URL!"));
+    }
+    const params = Array.from(url.searchParams.entries()).sort(
+      (a, b) => a[0] < b[0]
+    );
+    expectedParams = expectedParams.slice().sort((a, b) => a[0] < b[0]);
+
+    if (
+      params.length !== expectedParams.length ||
+      !params.every(
+        (p, i) => p[0] === expectedParams[i][0] && p[1] === expectedParams[i][1]
+      )
+    ) {
+      return Promise.reject(new Error("unexpected name requested in URL"));
+    }
+
+    return responder(request);
+  };
+}
+
+export function annotationsObs(names) {
+  return withExpected(
+    "/annotations/obs",
+    names.map((name) => ["annotation-name", name])
+  );
+}

client/__tests__/util/annoMatrix/serverMocks/routes.ts

@@ -1,251 +0,0 @@
-import { schema } from "./schema";
-import { Dataframe, KeyIndex } from "../../../../src/util/dataframe";
-import { encodeMatrixFBS } from "../../../../src/util/stateManager/matrix";
-
-const indexedSchema = {
-  obsByName: Object.fromEntries(
-    schema.schema.annotations.obs.columns.map((v) => [v.name, v]) ?? []
-  ),
-  varByName: Object.fromEntries(
-    schema.schema.annotations.var.columns.map((v) => [v.name, v]) ?? []
-  ),
-  embByName: Object.fromEntries(
-    schema.schema.layout.obs.map((v) => [v.name, v]) ?? []
-  ),
-};
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function makeMockColumn(s: any, length: any) {
-  const { type } = s;
-  switch (type) {
-    case "int32":
-      return new Int32Array(length).fill(Math.floor(99 * Math.random()));
-
-    case "string":
-      return new Array(length).fill("test");
-
-    case "float32":
-      return new Float32Array(length).fill(99 * Math.random());
-
-    case "boolean":
-      return new Array(length).fill(false);
-
-    case "categorical":
-      return new Array(length).fill(s.categories[0]);
-
-    default:
-      throw new Error("unkonwn type");
-  }
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function getEncodedDataframe(colNames: any, length: any, colSchemas: any) {
-  const colIndex = new KeyIndex(colNames);
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  const columns = colSchemas.map((s: any) => makeMockColumn(s, length));
-  // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
-  const df = new Dataframe([length, colNames.length], columns, null, colIndex);
-  const body = encodeMatrixFBS(df);
-  return body;
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export function dataframeResponse(colNames: any, columns: any) {
-  const colIndex = new KeyIndex(colNames);
-  const df = new Dataframe(
-    [columns[0].length, colNames.length],
-    columns,
-    null,
-    // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
-    colIndex
-  );
-  const body = encodeMatrixFBS(df);
-  const headers = new Headers({
-    "Content-Type": "application/octet-stream",
-  });
-  return () => Promise.resolve({ body, init: { status: 200, headers } });
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function annotationObsResponse(request: any) {
-  const url = new URL(request.url);
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  const params = Array.from((url.searchParams as any).entries());
-  const names = params
-    // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
-    .filter(([k]) => k === "annotation-name")
-    // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '([, v]: [any, any]) => any' is n... Remove this comment to see the full error message
-    .map(([, v]) => v);
-  // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
-  if (!names.every((n) => indexedSchema.obsByName[n])) {
-    return Promise.reject(new Error("bad obs annotation name in URL"));
-  }
-  // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
-  const colSchemas = names.map((n) => indexedSchema.obsByName[n]);
-  const body = getEncodedDataframe(
-    names,
-    schema.schema.dataframe.nObs,
-    colSchemas
-  );
-
-  const headers = new Headers({
-    "Content-Type": "application/octet-stream",
-  });
-  return Promise.resolve({
-    body,
-    init: { status: 200, headers },
-  });
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function annotationVarResponse(request: any) {
-  const url = new URL(request.url);
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  const params = Array.from((url.searchParams as any).entries());
-  const names = params
-    // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
-    .filter(([k]) => k === "annotation-name")
-    // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '([, v]: [any, any]) => any' is n... Remove this comment to see the full error message
-    .map(([, v]) => v);
-  // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
-  if (!names.every((n) => indexedSchema.varByName[n])) {
-    return Promise.reject(new Error("bad var annotation name in URL"));
-  }
-  // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
-  const colSchemas = names.map((n) => indexedSchema.varByName[n]);
-  const body = getEncodedDataframe(
-    names,
-    schema.schema.dataframe.nVar,
-    colSchemas
-  );
-
-  const headers = new Headers({
-    "Content-Type": "application/octet-stream",
-  });
-  return Promise.resolve({
-    body,
-    init: { status: 200, headers },
-  });
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function layoutObsResponse(request: any) {
-  const url = new URL(request.url);
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  const params = Array.from((url.searchParams as any).entries());
-  // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
-  const names = params.filter(([k]) => k === "layout-name").map(([, v]) => v);
-  // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
-  if (!names.every((n) => indexedSchema.embByName[n])) {
-    return Promise.reject(new Error("bad layout name in URL"));
-  }
-  // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
-  const dims = names.map((n) => indexedSchema.embByName[n].dims).flat();
-  const colSchemas = names
-    // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
-    .map((n) => [indexedSchema.embByName[n], indexedSchema.embByName[n]])
-    .flat();
-  const body = getEncodedDataframe(
-    dims,
-    schema.schema.dataframe.nObs,
-    colSchemas
-  );
-
-  const headers = new Headers({
-    "Content-Type": "application/octet-stream",
-  });
-  return Promise.resolve({
-    body,
-    init: { status: 200, headers },
-  });
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function dataVarResponse(request: any) {
-  const url = new URL(request.url);
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  const params = Array.from((url.searchParams as any).entries());
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  const colNames = params.map((v) => `${(v as any)[0]}/${(v as any)[1]}`);
-  const colSchemas = colNames.map(() => schema.schema.dataframe);
-  const body = getEncodedDataframe(
-    colNames,
-    schema.schema.dataframe.nObs,
-    colSchemas
-  );
-
-  const headers = new Headers({
-    "Content-Type": "application/octet-stream",
-  });
-  return Promise.resolve({
-    body,
-    init: { status: 200, headers },
-  });
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export function responder(request: any) {
-  const url = new URL(request.url);
-  const { pathname } = url;
-  if (pathname.endsWith("/annotations/obs")) {
-    return annotationObsResponse(request);
-  }
-  if (pathname.endsWith("/annotations/var")) {
-    return annotationVarResponse(request);
-  }
-  if (pathname.endsWith("/layout/obs")) {
-    return layoutObsResponse(request);
-  }
-  if (pathname.endsWith("/data/var")) {
-    return dataVarResponse(request);
-  }
-  return Promise.reject(new Error("bad URL"));
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export function withExpected(expectedURL: any, expectedParams: any) {
-  /*
-  Do some additional error checking
-  */
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  return (request: any) => {
-    // if URL is bogus, reject the promise
-    const url = new URL(request.url);
-    if (!url.pathname.endsWith(expectedURL)) {
-      return Promise.reject(new Error("Unexpected URL!"));
-    }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const params = Array.from((url.searchParams as any).entries()).sort(
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '(a: unknown, b: unknown) => bool... Remove this comment to see the full error message
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (a, b) => (a as any)[0] < (b as any)[0]
-    );
-    expectedParams = expectedParams
-      .slice() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      .sort((a: any, b: any) => a[0] < b[0]);
-
-    if (
-      params.length !== expectedParams.length ||
-      !params.every(
-        (p, i) =>
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          (p as any)[0] === expectedParams[i][0] && // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          (p as any)[1] === expectedParams[i][1]
-      )
-    ) {
-      return Promise.reject(new Error("unexpected name requested in URL"));
-    }
-
-    return responder(request);
-  };
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export function annotationsObs(names: any) {
-  return withExpected(
-    "/annotations/obs",
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    names.map((name: any) => ["annotation-name", name])
-  );
-}

client/__tests__/util/annoMatrix/serverMocks/schema.js

@@ -1,6 +1,4 @@
-import { RawSchema } from "../../../../src/common/types/entities";
+export const schema = {
-
-export const schema: { schema: RawSchema } = {
   schema: {
     annotations: {
       obs: {

client/__tests__/util/annoMatrix/whereCache.test.js

@@ -218,18 +218,10 @@ describe("whereCache", () => {
         },
       })
     );
-    // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
+    expect(wc.where.field.queryField.has("queryColumn")).toEqual(true);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    expect(wc.where.field.queryField.get("queryColumn")).toBeInstanceOf(Map);
-    expect((wc.where as any).field.queryField.has("queryColumn")).toEqual(true);
     expect(
-      // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
+      wc.where.field.queryField.get("queryColumn").has("queryValue")
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (wc.where as any).field.queryField.get("queryColumn")
-    ).toBeInstanceOf(Map);
-    expect(
-      // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (wc.where as any).field.queryField.get("queryColumn").has("queryValue")
     ).toEqual(true);
     expect(_whereCacheGet(wc, schema, "field", query)).toEqual([0, 1, 2]);
   });

client/__tests__/util/centroid.test.js

@@ -8,12 +8,9 @@ import { indexEntireSchema } from "../../src/util/stateManager/schemaHelpers";
 import { normalizeWritableCategoricalSchema } from "../../src/annoMatrix/normalize";
 
 describe("centroid", () => {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  let schema;
-  let schema: any;
+  let obsAnnotations;
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  let obsLayout;
-  let obsAnnotations: any;
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  let obsLayout: any;
 
   beforeAll(() => {
     schema = indexEntireSchema(cloneDeep(REST.schema.schema));
@@ -47,8 +44,7 @@ describe("centroid", () => {
       quantile([0.5], obsLayout.col("umap_1").asArray())[0],
     ];
 
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    centroidResult.forEach((coordinate) => {
-    centroidResult.forEach((coordinate: any) => {
       expect(coordinate).toEqual(expectedResult);
     });
   });
@@ -72,8 +68,7 @@ describe("centroid", () => {
       quantile([0.5], obsLayout.col("umap_1").asArray())[0],
     ];
 
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    centroidResult.forEach((coordinate) => {
-    centroidResult.forEach((coordinate: any) => {
       expect(coordinate).toEqual(expectedResult);
     });
   });

client/__tests__/util/dataframe/dataframe.test.js

@@ -29,7 +29,6 @@ describe("dataframe constructor", () => {
     const df = new Dataframe.Dataframe(
       [3, 2],
       [new Int32Array([0, 1, 2]), new Int32Array([3, 4, 5])],
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
       new Dataframe.DenseInt32Index([2, 1, 0]),
       new Dataframe.KeyIndex(["A", "B"])
     );
@@ -56,7 +55,6 @@ describe("simple data access", () => {
       new Float64Array([0.0, Number.NaN, Number.POSITIVE_INFINITY, 3.14159]),
       ["red", "blue", "green", "nan"],
     ],
-    // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
     new Dataframe.DenseInt32Index([3, 2, 1, 0]),
     new Dataframe.KeyIndex(["numbers", "colors"])
   );
@@ -141,12 +139,10 @@ describe("dataframe subsetting", () => {
         ["red", "green", "blue"],
       ],
       null, // identity index
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
       new Dataframe.KeyIndex(["int32", "string", "float32", "colors"])
     );
 
     test("all rows, one column", () => {
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
       const dfA = sourceDf.subset(null, ["colors"]);
       expect(dfA).toBeDefined();
       expect(dfA.dims).toEqual([3, 1]);
@@ -162,7 +158,6 @@ describe("dataframe subsetting", () => {
     });
 
     test("all rows, two columns", () => {
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
       const dfB = sourceDf.subset(null, ["float32", "colors"]);
       expect(dfB).toBeDefined();
       expect(dfB.dims).toEqual([3, 2]);
@@ -232,7 +227,6 @@ describe("dataframe subsetting", () => {
     });
 
     test("two rows, two colums", () => {
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
       const dfF = sourceDf.subset([0, 2], ["int32", "float32"]);
       expect(dfF).toBeDefined();
       expect(dfF.dims).toEqual([2, 2]);
@@ -242,7 +236,6 @@ describe("dataframe subsetting", () => {
       expect(dfF.colIndex.labels()).toEqual(["int32", "float32"]);
 
       // reverse the row and column order
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
       const dfFr = sourceDf.subset([2, 0], ["float32", "int32"]);
       expect(dfFr).toBeDefined();
       expect(dfFr.dims).toEqual([2, 2]);
@@ -255,7 +248,6 @@ describe("dataframe subsetting", () => {
     test("withRowIndex", () => {
       const df = sourceDf.subset(
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
         ["int32", "float32"],
         new Dataframe.DenseInt32Index([3, 2, 1])
       );
@@ -266,15 +258,12 @@ describe("dataframe subsetting", () => {
 
     test("withRowIndex error checks", () => {
       expect(() =>
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
         sourceDf.subset(null, ["red"], new Dataframe.IdentityInt32Index(1))
       ).toThrow(RangeError);
       expect(() =>
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
         sourceDf.subset(null, ["red"], new Dataframe.DenseInt32Index([0, 1]))
       ).toThrow(RangeError);
       expect(() =>
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
         sourceDf.subset(null, ["red"], new Dataframe.KeyIndex([0, 1, 2, 3]))
       ).toThrow(RangeError);
     });
@@ -289,14 +278,12 @@ describe("dataframe subsetting", () => {
         new Float32Array([4.4, 5.5, 6.6]),
         ["red", "green", "blue"],
       ],
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
       new Dataframe.DenseInt32Index([2, 4, 6]),
       new Dataframe.KeyIndex(["int32", "string", "float32", "colors"])
     );
 
     const dfA = sourceDf.isubsetMask(
       new Uint8Array([0, 1, 1]),
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'Uint8Array' is not assignable to... Remove this comment to see the full error message
       new Uint8Array([1, 0, 0, 1])
     );
     expect(dfA.dims).toEqual([2, 2]);
@@ -316,7 +303,6 @@ describe("dataframe subsetting", () => {
         ["red", "green", "blue"],
       ],
       null, // identity index
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
       new Dataframe.KeyIndex(["int32", "string", "float32", "colors"])
     );
 
@@ -330,7 +316,6 @@ describe("dataframe subsetting", () => {
     });
 
     test("all rows, two cols", () => {
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'number[]' is not assignable to p... Remove this comment to see the full error message
       const dfA = sourceDf.isubset(null, [1, 2]);
       expect(dfA.dims).toEqual([3, 2]);
       expect(dfA.icol(0).asArray()).toEqual(["A", "B", "C"]);
@@ -376,7 +361,6 @@ describe("dataframe factories", () => {
     const dfA = new Dataframe.Dataframe(
       [3, 2],
       [new Int32Array([0, 1, 2]), new Int32Array([3, 4, 5])],
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
       new Dataframe.DenseInt32Index([2, 1, 0]),
       new Dataframe.KeyIndex(["A", "B"])
     );
@@ -401,7 +385,6 @@ describe("dataframe factories", () => {
           [true, false],
         ],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
         new Dataframe.KeyIndex(["colors", "bools"])
       );
       const dfA = df.withCol("numbers", [1, 0]);
@@ -425,7 +408,6 @@ describe("dataframe factories", () => {
           [true, false],
         ],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
         new Dataframe.DenseInt32Index([74, 75])
       );
       const dfA = df.withCol(72, [1, 0]);
@@ -451,7 +433,6 @@ describe("dataframe factories", () => {
           [true, false],
         ],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
         new Dataframe.DenseInt32Index([74, 75])
       );
       const dfA = df.withCol(999, [1, 0]);
@@ -560,7 +541,6 @@ describe("dataframe factories", () => {
           [1, 0],
         ],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
         new Dataframe.KeyIndex(["colors", "bools", "numbers"])
       );
 
@@ -569,14 +549,11 @@ describe("dataframe factories", () => {
         [3, 1],
         [["red", "blue", "green"]],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
         new Dataframe.KeyIndex(["colorsA"])
       );
-      // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
       expect(() => dfA.withColsFrom(dfB)).toThrow(RangeError);
 
       /* duplicate labels should throw an error */
-      // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
       expect(() => dfA.withColsFrom(dfA)).toThrow(Error);
     });
 
@@ -587,18 +564,15 @@ describe("dataframe factories", () => {
         [2, 1],
         [["red", "blue"]],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
         new Dataframe.KeyIndex(["colors"])
       );
       const dfB = new Dataframe.Dataframe(
         [2, 1],
         [[true, false]],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
         new Dataframe.KeyIndex(["bools"])
       );
 
-      // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
       const dfLikeA = dfEmpty.withColsFrom(dfA);
       expect(dfLikeA).toBeDefined();
       expect(dfLikeA.dims).toEqual(dfA.dims);
@@ -607,7 +581,6 @@ describe("dataframe factories", () => {
       expect(dfLikeA.rowIndex.labels()).toEqual(dfA.rowIndex.labels());
       expect(dfLikeA.icol(0).asArray()).toEqual(dfA.icol(0).asArray());
 
-      // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
       const dfAlsoLikeA = dfA.withColsFrom(dfEmpty);
       expect(dfAlsoLikeA).toBeDefined();
       expect(dfAlsoLikeA.dims).toEqual(dfA.dims);
@@ -616,7 +589,6 @@ describe("dataframe factories", () => {
       expect(dfAlsoLikeA.rowIndex.labels()).toEqual(dfA.rowIndex.labels());
       expect(dfAlsoLikeA.icol(0).asArray()).toEqual(dfA.icol(0).asArray());
 
-      // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
       const dfC = dfA.withColsFrom(dfB);
       expect(dfC).toBeDefined();
       expect(dfC.dims).toEqual([2, 2]);
@@ -633,7 +605,6 @@ describe("dataframe factories", () => {
         [2, 1],
         [["red", "blue"]],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
         new Dataframe.KeyIndex(["colors"])
       );
       const dfB = new Dataframe.Dataframe(
@@ -644,7 +615,6 @@ describe("dataframe factories", () => {
           [1, 0],
         ],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
         new Dataframe.KeyIndex(["colors", "bools", "numbers"])
       );
 
@@ -677,7 +647,6 @@ describe("dataframe factories", () => {
         [2, 1],
         [["red", "blue"]],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
         new Dataframe.KeyIndex(["colors"])
       );
       const dfB = new Dataframe.Dataframe(
@@ -688,7 +657,6 @@ describe("dataframe factories", () => {
           [1, 0],
         ],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
         new Dataframe.KeyIndex(["colors", "bools", "numbers"])
       );
 
@@ -712,7 +680,6 @@ describe("dataframe factories", () => {
           [1, 0],
         ],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
         new Dataframe.KeyIndex(["colors", "bools", "numbers"])
       );
       const dfA = df.dropCol("colors");
@@ -784,7 +751,6 @@ describe("dataframe factories", () => {
           [1, 0],
         ],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
         new Dataframe.DenseInt32Index([102, 101, 100])
       );
       const dfA = df.dropCol(101);
@@ -811,8 +777,7 @@ describe("dataframe factories", () => {
           new Float64Array(3).fill(1.1),
         ]
       );
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      const dfB = dfA.mapColumns((col, idx) => {
-      const dfB = dfA.mapColumns((col: any, idx: any) => {
         expect(dfA.icol(idx).asArray()).toBe(col);
         return col;
       });
@@ -855,7 +820,6 @@ describe("dataframe factories", () => {
           [1, 0],
         ],
         null,
-        // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
         new Dataframe.KeyIndex(["A", "B"])
       );
       const dfB = dfA.renameCol("B", "C");
@@ -868,8 +832,7 @@ describe("dataframe factories", () => {
 });
 
 describe("dataframe col", () => {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  let df = null;
-  let df: any = null;
   beforeEach(() => {
     df = new Dataframe.Dataframe(
       [2, 2],
@@ -878,7 +841,6 @@ describe("dataframe col", () => {
         [1, 0],
       ],
       null,
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
       new Dataframe.KeyIndex(["A", "B"])
     );
   });
@@ -1231,7 +1193,6 @@ describe("label indexing", () => {
     test("create", () => {
       expect(Dataframe.isLabelIndex(idx)).toBeTruthy();
       expect(() => new Dataframe.KeyIndex(["dup", "dup"])).toThrow(Error);
-      // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
       expect(new Dataframe.KeyIndex().size()).toEqual(0);
     });
 
@@ -1404,7 +1365,6 @@ describe("corner cases", () => {
         [1, 0],
       ],
       null,
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
       new Dataframe.KeyIndex(["A", "B"])
     );
 

client/__tests__/util/dataframe/histogram.test.js

@@ -6,7 +6,6 @@ describe("Dataframe column histogram", () => {
       [3, 3],
       [["n1", "n2", "n3"], ["c1", "c2", "c3"], new Int32Array([0, 1, 2])],
       null,
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
       new Dataframe.KeyIndex(["name", "cat", "value"])
     );
 
@@ -27,7 +26,6 @@ describe("Dataframe column histogram", () => {
       [3, 3],
       [["n1", "n2", "n3"], ["c1", "c2", "c3"], new Int32Array([0, 1, 2])],
       null,
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
       new Dataframe.KeyIndex(["name", "cat", "value"])
     );
 
@@ -50,7 +48,6 @@ describe("Dataframe column histogram", () => {
       [3, 3],
       [["n1", "n2", "n3"], ["c1", "c2", "c3"], new Int32Array([0, 1, 2])],
       null,
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
       new Dataframe.KeyIndex(["name", "cat", "value"])
     );
 
@@ -71,7 +68,6 @@ describe("Dataframe column histogram", () => {
       [3, 3],
       [["n1", "n2", "n3"], ["c1", "c2", "c3"], new Int32Array([0, 1, 2])],
       null,
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
       new Dataframe.KeyIndex(["name", "cat", "value"])
     );
 
@@ -92,16 +88,7 @@ describe("Dataframe column histogram", () => {
     expect(df.col(1).histogram(5, [0, 100])).toEqual([5, 1, 0, 0, 2]);
     expect(df.col(0).histogram(2, [0, 10])).toEqual([2, 2]);
     expect(df.col(0).histogram(10, [0, 100])).toEqual([
-      3,
+      3, 2, 1, 0, 0, 0, 0, 0, 0, 2,
-      2,
-      1,
-      0,
-      0,
-      0,
-      0,
-      0,
-      0,
-      2,
     ]);
   });
 });

client/__tests__/util/dataframe/summarize.test.js

@@ -1,7 +1,6 @@
 import * as Dataframe from "../../../src/util/dataframe";
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function float32Conversion(f) {
-function float32Conversion(f: any) {
   return new Float32Array([f])[0];
 }
 
@@ -31,7 +30,6 @@ describe("Dataframe column summary", () => {
         [1],
       ],
       null,
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
       new Dataframe.KeyIndex([
         "name",
         "nameString",
@@ -108,7 +106,6 @@ describe("Dataframe column summary", () => {
         [1, false, "0"],
       ],
       null,
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
       new Dataframe.KeyIndex([
         "name",
         "nameString",
@@ -177,7 +174,6 @@ describe("Dataframe column summary", () => {
       expect.objectContaining({
         categorical: true,
         categories: expect.arrayContaining([1, false, "0"]),
-        // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
         categoryCounts: new Map([
           [1, 1],
           [false, 1],
@@ -205,7 +201,6 @@ describe("Dataframe column summary", () => {
         [1, false, "0", "0"],
       ],
       null,
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
       new Dataframe.KeyIndex([
         "name",
         "nameString",
@@ -274,7 +269,6 @@ describe("Dataframe column summary", () => {
       expect.objectContaining({
         categorical: true,
         categories: expect.arrayContaining([1, false, "0"]),
-        // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
         categoryCounts: new Map([
           [1, 1],
           [false, 1],

client/__tests__/util/promiseLimit.test.js

@@ -1,8 +1,7 @@
 import PromiseLimit from "../../src/util/promiseLimit";
 import { range } from "../../src/util/range";
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+const delay = (t) => new Promise((resolve) => setTimeout(resolve, t));
-const delay = (t: any) => new Promise((resolve) => setTimeout(resolve, t));
 
 describe("PromiseLimit", () => {
   test("simple evaluation, concurrency 1", async () => {
@@ -52,9 +51,7 @@ describe("PromiseLimit", () => {
       running -= 1;
     };
 
-    // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 1.
+    await Promise.all(range(10).map((i) => plimit.add(() => callback(i))));
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    await Promise.all(range(10).map((i: any) => plimit.add(() => callback(i))));
 
     expect(maxRunning).toEqual(2);
   });

client/__tests__/util/quantile.test.js

@@ -19,11 +19,7 @@ describe("quantile", () => {
   test("multi q", () => {
     const arr = new Float32Array([9, 3, 5, 6, 0]);
     expect(quantile([0, 0.25, 0.5, 0.75, 1.0], arr)).toMatchObject([
-      0,
+      0, 3, 5, 6, 9,
-      3,
-      5,
-      6,
-      9,
     ]);
   });
 });

client/__tests__/util/range.test.js

@@ -6,20 +6,14 @@ describe("range", () => {
   });
 
   test("range(stop)", () => {
-    // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 1.
     expect(range(3)).toMatchObject([0, 1, 2]);
-    // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 1.
     expect(range(0)).toMatchObject([]);
-    // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 1.
     expect(range(1)).toMatchObject([0]);
   });
 
   test("range(start,stop)", () => {
-    // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 2.
     expect(range(0, 0)).toMatchObject([]);
-    // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 2.
     expect(range(0, 2)).toMatchObject([0, 1]);
-    // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 2.
     expect(range(4, 8)).toMatchObject([4, 5, 6, 7]);
   });
 

client/__tests__/util/stateManager/colorHelpers.test.js

@@ -81,7 +81,6 @@ describe("categorical color helpers", () => {
         ),
     ],
     null,
-    // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
     new Dataframe.KeyIndex(["continuousColumn", "categoricalColumn"])
   );
 
@@ -96,7 +95,6 @@ describe("categorical color helpers", () => {
     const data = obsDataframe.col("categoricalColumn").asArray();
     const cats = schema.annotations.obsByName.categoricalColumn.categories;
     for (let i = 0; i < schema.dataframe.nObs; i += 1) {
-      // @ts-expect-error ts-migrate(2722) FIXME: Cannot invoke an object which is possibly 'undefin... Remove this comment to see the full error message
       expect(makeScale(ct.rgb[i])).toEqual(ct.scale(cats.indexOf(data[i])));
     }
   });
@@ -114,7 +112,6 @@ describe("categorical color helpers", () => {
     const data = obsDataframe.col("categoricalColumn").asArray();
     const cats = schemaClone.annotations.obsByName.categoricalColumn.categories;
     for (let i = 0; i < schemaClone.dataframe.nObs; i += 1) {
-      // @ts-expect-error ts-migrate(2722) FIXME: Cannot invoke an object which is possibly 'undefin... Remove this comment to see the full error message
       expect(makeScale(ct.rgb[i])).toEqual(ct.scale(cats.indexOf(data[i])));
     }
   });
@@ -125,8 +122,7 @@ describe("categorical color helpers", () => {
       Array.from(schema.annotations.obsByName.categoricalColumn.categories)
     );
     const userDefinedColorTable = {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      categoricalColumn: shuffleCats.reduce((acc, label) => {
-      categoricalColumn: shuffleCats.reduce((acc: any, label: any) => {
         acc[label] = randRGBColor();
         return acc;
       }, {}),
@@ -140,14 +136,12 @@ describe("categorical color helpers", () => {
       "categoricalColumn",
       obsDataframe,
       schema,
-      // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{}' is not assignable to paramet... Remove this comment to see the full error message
       userColors
     );
     expect(ct).toBeDefined();
     const data = obsDataframe.col("categoricalColumn").asArray();
     for (let i = 0; i < schema.dataframe.nObs; i += 1) {
       expect(makeScale(ct.rgb[i])).toEqual(
-        // @ts-expect-error ts-migrate(2722) FIXME: Cannot invoke an object which is possibly 'undefin... Remove this comment to see the full error message
         ct.scale(cats.indexOf(data[i])).toString()
       );
     }
@@ -160,38 +154,31 @@ TODO:
 2. user defined colors
 */
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function indexSchema(schema) {
-function indexSchema(schema: any) {
   schema.annotations.obsByName = Object.fromEntries(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    schema.annotations?.obs?.columns?.map((v) => [v.name, v]) ?? []
-    schema.annotations?.obs?.columns?.map((v: any) => [v.name, v]) ?? []
   );
   schema.annotations.varByName = Object.fromEntries(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    schema.annotations?.var?.columns?.map((v) => [v.name, v]) ?? []
-    schema.annotations?.var?.columns?.map((v: any) => [v.name, v]) ?? []
   );
   schema.layout.obsByName = Object.fromEntries(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    schema.layout?.obs?.map((v) => [v.name, v]) ?? []
-    schema.layout?.obs?.map((v: any) => [v.name, v]) ?? []
   );
   schema.layout.varByName = Object.fromEntries(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    schema.layout?.var?.map((v) => [v.name, v]) ?? []
-    schema.layout?.var?.map((v: any) => [v.name, v]) ?? []
   );
 
   return schema;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function makeScale(rgb) {
-function makeScale(rgb: any) {
   // make a scale string from a rgb float triple
   return `rgb(${(rgb[0] * 255) >>> 0}, ${(rgb[1] * 255) >>> 0}, ${
     (rgb[2] * 256) >>> 0
   })`;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function shuffle(array) {
-function shuffle(array: any) {
   for (let i = array.length - 1; i > 0; i -= 1) {
     const j = (Math.random() * (i + 1)) >>> 0;
     [array[i], array[j]] = [array[j], array[i]];

client/__tests__/util/stateManager/fbs.test.js

@@ -24,7 +24,6 @@ describe("encode/decode", () => {
     expect(dfA.columns).toEqual(columns);
 
     const colIndex = new KeyIndex(["a", "b", "c", "d"]);
-    // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
     const dfWithColIdx = new Dataframe([3, 4], columns, null, colIndex);
     const dfB = decodeMatrixFBS(encodeMatrixFBS(dfWithColIdx));
     expect([dfB.nRows, dfB.nCols]).toEqual(dfWithColIdx.dims);

client/__tests__/util/stateManager/sampleResponses.js

@@ -5,7 +5,6 @@ import zip from "lodash.zip";
 import _ from "lodash";
 import { flatbuffers } from "flatbuffers";
 import { NetEncoding } from "../../../src/util/stateManager/matrix_generated";
-import { RawSchema } from "../../../src/common/types/entities";
 
 /*
 test data mocking REST 0.2 API responses.  Used in several tests.
@@ -30,7 +29,7 @@ const aConfigResponse = {
   },
 };
 
-const aSchemaResponse: { schema: RawSchema } = {
+const aSchemaResponse = {
   schema: {
     dataframe: {
       nObs,
@@ -41,30 +40,28 @@ const aSchemaResponse: { schema: RawSchema } = {
       obs: {
         index: "name",
         columns: [
-          { name: "name", type: "string", writable: false },
+          { name: "name", type: "string" },
-          { name: "field1", type: "int32", writable: false },
+          { name: "field1", type: "int32" },
-          { name: "field2", type: "float32", writable: false },
+          { name: "field2", type: "float32" },
-          { name: "field3", type: "boolean", writable: false },
+          { name: "field3", type: "boolean" },
           {
             name: "field4",
             type: "categorical",
             categories: field4Categories,
-            writable: false,
           },
         ],
       },
       var: {
         index: "name",
         columns: [
-          { name: "name", type: "string", writable: false },
+          { name: "name", type: "string" },
-          { name: "fieldA", type: "int32", writable: false },
+          { name: "fieldA", type: "int32" },
-          { name: "fieldB", type: "float32", writable: false },
+          { name: "fieldB", type: "float32" },
-          { name: "fieldC", type: "boolean", writable: false },
+          { name: "fieldC", type: "boolean" },
           {
             name: "fieldD",
             type: "categorical",
             categories: fieldDCategories,
-            writable: false,
           },
         ],
       },
@@ -78,7 +75,6 @@ const aSchemaResponse: { schema: RawSchema } = {
 
 const anAnnotationsObsJSONResponse = {
   names: ["name", "field1", "field2", "field3", "field4"],
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
   data: _()
     .range(nObs)
     .map((idx) => [
@@ -95,7 +91,6 @@ const anAnnotationsObsJSONResponse = {
 
 const anAnnotationsVarJSONResponse = {
   names: ["fieldA", "fieldB", "fieldC", "fieldD", "name"],
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
   data: _()
     .range(nVar)
     .map((idx) => [
@@ -110,11 +105,8 @@ const anAnnotationsVarJSONResponse = {
     .value(),
 };
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function encodeTypedArray(builder, uType, uData) {
-function encodeTypedArray(builder: any, uType: any, uData: any) {
-  // @ts-expect-error --- FIXME: Element implicitly has an 'any' type.
   const uTypeName = NetEncoding.TypedArray[uType];
-  // @ts-expect-error --- FIXME: Element implicitly has an 'any' type.
   const ArrayType = NetEncoding[uTypeName];
   const dv = ArrayType.createDataVector(builder, uData);
   builder.startObject(1);
@@ -122,8 +114,7 @@ function encodeTypedArray(builder: any, uType: any, uData: any) {
   return builder.endObject();
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function encodeMatrix(columns, colIndex = undefined) {
-function encodeMatrix(columns: any, colIndex = undefined) {
   /*
   IMPORTANT: this is not a general purpose encoder.  in particular,
   it doesn't correctly handle all column index types, nor does it
@@ -132,7 +123,6 @@ function encodeMatrix(columns: any, colIndex = undefined) {
   encodeMatrixFBS in matrix.py is more general.  This is used only
   as a testing santity check (alt implementation).
   */
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1.
   const utf8Encoder = new TextEncoder("utf-8");
   const builder = new flatbuffers.Builder(1024);
   const cols = map(columns, (carr) => {
@@ -182,13 +172,11 @@ function encodeMatrix(columns: any, colIndex = undefined) {
 
 const anAnnotationsObsFBSResponse = (() => {
   const columns = zip(...anAnnotationsObsJSONResponse.data).slice(1);
-  // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
   return encodeMatrix(columns, anAnnotationsObsJSONResponse.names);
 })();
 
 const anAnnotationsVarFBSResponse = (() => {
   const columns = zip(...anAnnotationsVarJSONResponse.data).slice(1);
-  // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
   return encodeMatrix(columns, anAnnotationsVarJSONResponse.names);
 })();
 
@@ -197,13 +185,11 @@ const aLayoutFBSResponse = (() => {
     new Float32Array(nObs).fill(Math.random()),
     new Float32Array(nObs).fill(Math.random()),
   ];
-  // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
   return encodeMatrix(coords, ["umap_0", "umap_1"]);
 })();
 
 const aDataObsResponse = {
   var: [2, 4, 29],
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
   obs: _()
     .range(nObs)
     .map((idx) => [idx, Math.random(), Math.random(), Math.random()])

client/__tests__/util/typedCrossfilter/crossfilter.test.js

@@ -126,8 +126,7 @@ const someData = [
   },
 ];
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+let payments = null;
-let payments: any = null;
 beforeEach(() => {
   payments = new Crossfilter(someData);
 });
@@ -139,13 +138,7 @@ describe("ImmutableTypedCrossfilter", () => {
     expect(payments.all()).toEqual(someData);
 
     const p = payments
-      .addDimension(
+      .addDimension("quantity", "scalar", (i, d) => d[i].quantity, Int32Array)
-        "quantity",
-        "scalar",
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-        (i: any, d: any) => d[i].quantity,
-        Int32Array
-      )
       .select("quantity", { mode: "all" });
     expect(p).toBeDefined();
     expect(p.all()).toEqual(someData);
@@ -165,8 +158,7 @@ describe("ImmutableTypedCrossfilter", () => {
     const p2 = payments.addDimension(
       "quantity",
       "scalar",
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      (i, data) => data[i].quantity,
-      (i: any, data: any) => data[i].quantity,
       Int32Array
     );
 
@@ -183,22 +175,10 @@ describe("ImmutableTypedCrossfilter", () => {
 
   test("select all and none", () => {
     let p = payments
-      .addDimension(
+      .addDimension("quantity", "scalar", (i, d) => d[i].quantity, Int32Array)
-        "quantity",
+      .addDimension("tip", "scalar", (i, d) => d[i].tip, Float32Array)
-        "scalar",
+      .addDimension("total", "scalar", (i, d) => d[i].total, Float32Array)
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      .addDimension("type", "enum", (i, d) => d[i].type);
-        (i: any, d: any) => d[i].quantity,
-        Int32Array
-      ) // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      .addDimension("tip", "scalar", (i: any, d: any) => d[i].tip, Float32Array)
-      .addDimension(
-        "total",
-        "scalar",
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-        (i: any, d: any) => d[i].total,
-        Float32Array
-      ) // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      .addDimension("type", "enum", (i: any, d: any) => d[i].type);
     expect(p).toBeDefined();
 
     /* expect all records to be selected - default init state */
@@ -250,24 +230,11 @@ describe("ImmutableTypedCrossfilter", () => {
   });
 
   describe("scalar dimension", () => {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    let p;
-    let p: any;
     beforeEach(() => {
       p = payments
-        .addDimension(
+        .addDimension("quantity", "scalar", (i, d) => d[i].quantity, Int32Array)
-          "quantity",
+        .addDimension("tip", "scalar", (i, d) => d[i].tip, Float32Array)
-          "scalar",
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          (i: any, d: any) => d[i].quantity,
-          Int32Array
-        )
-        .addDimension(
-          "tip",
-          "scalar",
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          (i: any, d: any) => d[i].tip,
-          Float32Array
-        )
         .select("tip", { mode: "all" });
     });
 
@@ -310,11 +277,9 @@ describe("ImmutableTypedCrossfilter", () => {
   });
 
   describe("enum dimension", () => {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    let p;
-    let p: any;
     beforeEach(() => {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      p = payments.addDimension("type", "enum", (i, d) => d[i].type);
-      p = payments.addDimension("type", "enum", (i: any, d: any) => d[i].type);
     });
 
     test("all", () => {
@@ -352,8 +317,7 @@ describe("ImmutableTypedCrossfilter", () => {
   });
 
   describe("spatial dimension", () => {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    let p;
-    let p: any;
     beforeEach(() => {
       const X = someData.map((r) => r.coords[0]);
       const Y = someData.map((r) => r.coords[1]);
@@ -442,22 +406,14 @@ describe("ImmutableTypedCrossfilter", () => {
   });
 
   describe("non-finite scalars", () => {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    let p;
-    let p: any;
     beforeEach(() => {
       p = payments
-        .addDimension(
+        .addDimension("quantity", "scalar", (i, d) => d[i].quantity, Int32Array)
-          "quantity",
-          "scalar",
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-          (i: any, d: any) => d[i].quantity,
-          Int32Array
-        )
         .addDimension(
           "nonFinite",
           "scalar",
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          (i, d) => d[i].nonFinite,
-          (i: any, d: any) => d[i].nonFinite,
           Float32Array
         )
         .select("quantity", { mode: "all" });

client/__tests__/util/typedCrossfilter/positiveInterval.test.js

@@ -151,9 +151,9 @@ describe("intersection", () => {
       [1, 2],
       [6, 9],
     ]);
-    expect(
+    expect(PositiveIntervals.intersection([[0, 2638]], [[1363, 2638]])).toEqual(
-      PositiveIntervals.intersection([[0, 2638]], [[1363, 2638]])
+      [[1363, 2638]]
-    ).toEqual([[1363, 2638]]);
+    );
     expect(PositiveIntervals.intersection([[1, 2]], [[1, 2]])).toEqual([
       [1, 2],
     ]);

client/__tests__/util/typedCrossfilter/sort.test.js

@@ -15,8 +15,7 @@ paths for:
 const pInf = Number.POSITIVE_INFINITY;
 const nInf = Number.NEGATIVE_INFINITY;
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function fillRange(arr, start = 0) {
-function fillRange(arr: any, start = 0) {
   const larr = arr;
   for (let i = 0, len = larr.length; i < len; i += 1) {
     larr[i] = i + start;
@@ -24,8 +23,7 @@ function fillRange(arr: any, start = 0) {
   return larr;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function fillRand(arr) {
-function fillRand(arr: any) {
   for (let i = 0, len = arr.length; i < len; i += 1) {
     arr[i] = Math.random();
   }
@@ -50,22 +48,16 @@ describe("sortArray", () => {
   describe("finite numbers", () => {
     [Array, Float32Array, Uint32Array, Int32Array, Float64Array].map((Type) =>
       test(Type.name, () => {
-        // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
         expect(sortArray(Type.from([6, 5, 4, 3, 2, 1, 0]))).toMatchObject(
-          // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
           Type.from([0, 1, 2, 3, 4, 5, 6])
         );
 
-        // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
         expect(sortArray(Type.from([6, 5, 4, 3, 2, 1]))).toMatchObject(
-          // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
           Type.from([1, 2, 3, 4, 5, 6])
         );
 
         const source = fillRand(new Type(1000));
-        // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
         expect(sortArray(Type.from(source))).toMatchObject(
-          // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
           Type.from(source).sort()
         );
       })
@@ -138,27 +130,22 @@ describe("sortIndex", () => {
   describe("finite numbers", () => {
     [Array, Float32Array, Uint32Array, Int32Array, Float64Array].map((Type) =>
       test(Type.name, () => {
-        // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
         const source1 = Type.from([6, 5, 4, 3, 2, 1, 0]);
         const index1 = fillRange(new Uint32Array(source1.length));
         expect(sortIndex(index1, source1)).toMatchObject(
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          index1.sort((a, b) => source1[a] - source1[b])
-          index1.sort((a: any, b: any) => source1[a] - source1[b])
         );
 
-        // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
         const source2 = Type.from([6, 5, 4, 3, 2, 1]);
         const index2 = fillRange(new Uint32Array(source2.length));
         expect(sortIndex(index2, source2)).toMatchObject(
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          index2.sort((a, b) => source1[a] - source1[b])
-          index2.sort((a: any, b: any) => source1[a] - source1[b])
         );
 
         const source3 = fillRand(new Type(1000));
         const index3 = fillRange(new Uint32Array(source3.length));
         expect(sortIndex(index3, source3)).toMatchObject(
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+          index3.sort((a, b) => source1[a] - source1[b])
-          index3.sort((a: any, b: any) => source1[a] - source1[b])
         );
       })
     );

client/configuration/babel/babel.dev.js

@@ -11,13 +11,13 @@ module.exports = {
       },
     ],
     "@babel/preset-react",
-    "@babel/preset-typescript",
   ],
   plugins: [
     "@babel/plugin-proposal-function-bind",
     ["@babel/plugin-proposal-decorators", { legacy: true }],
     ["@babel/plugin-proposal-class-properties", { loose: true }],
     ["@babel/plugin-proposal-private-methods", { loose: true }],
+    ["@babel/plugin-proposal-private-property-in-object", { loose: true }],
     "@babel/plugin-proposal-export-namespace-from",
     "@babel/plugin-proposal-optional-chaining",
     "@babel/plugin-proposal-nullish-coalescing-operator",

client/configuration/babel/babel.prod.js

@@ -10,13 +10,13 @@ module.exports = {
       },
     ],
     "@babel/preset-react",
-    "@babel/preset-typescript",
   ],
   plugins: [
     "@babel/plugin-proposal-function-bind",
     ["@babel/plugin-proposal-decorators", { legacy: true }],
     ["@babel/plugin-proposal-class-properties", { loose: true }],
     ["@babel/plugin-proposal-private-methods", { loose: true }],
+    ["@babel/plugin-proposal-private-property-in-object", { loose: true }],
     "@babel/plugin-proposal-export-namespace-from",
     "@babel/plugin-transform-react-constant-elements",
     "@babel/plugin-transform-runtime",

client/configuration/eslint/eslint.js

@@ -1,10 +1,8 @@
-/* eslint-disable @blueprintjs/classes-constants -- we don't import blueprint here  */
 module.exports = {
   root: true,
-  parser: "@typescript-eslint/parser",
+
   extends: [
-    "airbnb-typescript",
+    "airbnb",
-    "plugin:@typescript-eslint/recommended",
     "plugin:eslint-comments/recommended",
     "plugin:@blueprintjs/recommended",
     "plugin:compat/recommended",
@@ -30,6 +28,7 @@ module.exports = {
     context: true,
     beforeEach: true,
   },
+  parser: "@babel/eslint-parser",
   parserOptions: {
     ecmaVersion: 2017,
     sourceType: "module",
@@ -37,50 +36,21 @@ module.exports = {
       jsx: true,
       generators: true,
     },
-    // (thuang): Pairing with `tsconfigRootDir`, which points to the directory
+    babelOptions: {
-    // of eslint.js
+      configFile: "./configuration/babel/babel.prod.js",
-    project: "../../tsconfig.json",
+    },
-    tsconfigRootDir: __dirname,
   },
   rules: {
     "react/jsx-no-target-blank": "off",
     "eslint-comments/require-description": ["error"],
     "no-magic-numbers": "off",
-    "@typescript-eslint/no-magic-numbers": "off",
     "no-nested-ternary": "off",
     "func-style": "off",
     "arrow-parens": "off",
     "no-use-before-define": "off",
-    "@typescript-eslint/no-use-before-define": "off",
     "react/jsx-filename-extension": "off",
     "comma-dangle": "off",
-    "@typescript-eslint/comma-dangle": "off",
     "no-underscore-dangle": "off",
-    // Override airbnb config to allow leading underscore
-    // https://github.com/iamturns/eslint-config-airbnb-typescript/blob/master/lib/shared.js#L35
-    "@typescript-eslint/naming-convention": [
-      "error",
-      {
-        selector: "class",
-        format: ["PascalCase"],
-        leadingUnderscore: "allow",
-      },
-      {
-        selector: "function",
-        format: ["camelCase", "PascalCase"],
-        leadingUnderscore: "allowSingleOrDouble",
-      },
-      {
-        selector: "typeLike",
-        format: ["PascalCase"],
-      },
-      {
-        selector: "variable",
-        format: ["camelCase", "PascalCase", "UPPER_CASE"],
-        leadingUnderscore: "allowSingleOrDouble",
-        trailingUnderscore: "allowDouble",
-      },
-    ],
     "implicit-arrow-linebreak": "off",
     "no-console": "off",
     "spaced-comment": ["error", "always", { exceptions: ["*"] }],
@@ -88,7 +58,6 @@ module.exports = {
     "object-curly-newline": ["error", { consistent: true }],
     "react/prop-types": [0],
     "space-before-function-paren": "off",
-    "@typescript-eslint/space-before-function-paren": "off",
     "function-paren-newline": "off",
     "prefer-destructuring": ["error", { object: true, array: false }],
     "import/prefer-default-export": "off",
@@ -107,9 +76,9 @@ module.exports = {
   },
   overrides: [
     {
-      files: ["**/*.test.ts"],
+      files: ["**/*.test.js"],
       env: {
-        jest: true, // now **/*.test.ts files' env has both es6 *and* jest
+        jest: true, // now **/*.test.js files' env has both es6 *and* jest
       },
       // Can't extend in overrides: https://github.com/eslint/eslint/issues/8813
       // "extends": ["plugin:jest/recommended"]
@@ -124,4 +93,3 @@ module.exports = {
     },
   ],
 };
-/* eslint-enable @blueprintjs/classes-constants -- we don't import blueprint here  */

client/configuration/lint-staged/lint-staged.config.js

@@ -1,4 +1,4 @@
 module.exports = {
-  "*.{js,ts,jsx,tsx}": "eslint --fix",
+  "*.js": "eslint --fix",
   "**/*": "prettier --write --ignore-unknown",
 };

client/configuration/webpack/cspHashPlugin.js

@@ -1,10 +1,6 @@
 /* eslint-disable import/no-extraneous-dependencies -- this file is a devDependency*/
-/* eslint-disable @blueprintjs/classes-constants -- we don't import blueprint here  */
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const cheerio = require("cheerio");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const crypto = require("crypto");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const HtmlWebpackPlugin = require("html-webpack-plugin");
 
 const digest = (str) => {
@@ -54,5 +50,4 @@ class CspHashPlugin {
 }
 
 module.exports = CspHashPlugin;
-/* eslint-enable @blueprintjs/classes-constants -- we don't import blueprint here  */
 /* eslint-enable import/no-extraneous-dependencies -- enable*/

client/configuration/webpack/obsoleteHTMLTemplate.html

@@ -22,7 +22,7 @@
 >
   <img
     src="https://cellxgene.cziscience.com/s3/cellxgene/static/images/cellxgene-logo.png"
-    style="width: 320px"
+    style="width: 320px;"
   />
   <div
     style="
@@ -37,34 +37,36 @@
       max-width: 550px;
     "
   >
-    <div style="margin-bottom: 0; font-weight: bolder; font-size: 1.2em">
+    <div style="margin-bottom: 0; font-weight: bolder; font-size: 1.2em;">
       Unsupported Browser
     </div>
-    <div style="margin-top: 0">
+    <div style="margin-top: 0;">
       cellxgene is currently supported on the following browsers
     </div>
-    <div style="display: flex; justify-content: space-around; margin-top: 16px">
+    <div
+      style="display: flex; justify-content: space-around; margin-top: 16px;"
+    >
       <a
         href="https://www.google.com/chrome/?hl=en%22"
         aria-label="Download Google Chrome"
       >
         <img
           src="https://cellxgene.cziscience.com/s3/cellxgene/static/images/chrome.png"
-          style="width: 80px; height: 80px"
+          style="width: 80px; height: 80px;"
         />
         <div>Chrome &gt; 60</div>
       </a>
       <a href="https://www.mozilla.com/firefox/" aria-label="Download Firefox">
         <img
           src="https://cellxgene.cziscience.com/s3/cellxgene/static/images/firefox.png"
-          style="width: 80px; height: 80px"
+          style="width: 80px; height: 80px;"
         />
         <div>Firefox ≥ 60</div>
       </a>
       <a href="//www.microsoft.com/edge" aria-label="Download Edge">
         <img
           src="https://cellxgene.cziscience.com/s3/cellxgene/static/images/edge.png"
-          style="width: 80px; height: 80px"
+          style="width: 80px; height: 80px;"
         />
         <div>Edge ≥ 79</div>
       </a>

client/configuration/webpack/webpack.config.dev.js

@@ -1,23 +1,13 @@
-/* eslint-disable @blueprintjs/classes-constants -- we don't import blueprint here  */
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const path = require("path");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const webpack = require("webpack");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const HtmlWebpackPlugin = require("html-webpack-plugin");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const FaviconsWebpackPlugin = require("favicons-webpack-plugin");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const ScriptExtHtmlWebpackPlugin = require("script-ext-html-webpack-plugin");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const MiniCssExtractPlugin = require("mini-css-extract-plugin");
 
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const { merge } = require("webpack-merge");
 
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const sharedConfig = require("./webpack.config.shared");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const babelOptions = require("../babel/babel.dev");
 
 const fonts = path.resolve("src/fonts");
@@ -25,7 +15,7 @@ const nodeModules = path.resolve("node_modules");
 
 const devConfig = {
   mode: "development",
-  devtool: "source-map",
+  devtool: "eval",
   output: {
     pathinfo: true,
     filename: "static/js/bundle.js",
@@ -33,7 +23,7 @@ const devConfig = {
   module: {
     rules: [
       {
-        test: /\.(ts|js)x?$/,
+        test: /\.jsx?$/,
         loader: "babel-loader",
         options: babelOptions,
       },
@@ -93,4 +83,3 @@ const devConfig = {
 };
 
 module.exports = merge(sharedConfig, devConfig);
-/* eslint-enable @blueprintjs/classes-constants -- we don't import blueprint here  */

client/configuration/webpack/webpack.config.prod.js

@@ -1,31 +1,18 @@
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const path = require("path");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const webpack = require("webpack");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const HtmlWebpackPlugin = require("html-webpack-plugin");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const { CleanWebpackPlugin } = require("clean-webpack-plugin");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const TerserJSPlugin = require("terser-webpack-plugin");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const CleanCss = require("clean-css");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const OptimizeCSSAssetsPlugin = require("optimize-css-assets-webpack-plugin");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const FaviconsWebpackPlugin = require("favicons-webpack-plugin");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const MiniCssExtractPlugin = require("mini-css-extract-plugin");
 
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const { merge } = require("webpack-merge");
 
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const babelOptions = require("../babel/babel.prod");
 
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const CspHashPlugin = require("./cspHashPlugin");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const sharedConfig = require("./webpack.config.shared");
 
 const fonts = path.resolve("src/fonts");
@@ -51,7 +38,7 @@ const prodConfig = {
   module: {
     rules: [
       {
-        test: /\.(ts|js)x?$/,
+        test: /\.jsx?$/,
         loader: "babel-loader",
         options: babelOptions,
       },

client/configuration/webpack/webpack.config.shared.js

@@ -1,13 +1,8 @@
-/* eslint-disable @blueprintjs/classes-constants -- we don't import blueprint here  */
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const path = require("path");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const fs = require("fs");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const MiniCssExtractPlugin = require("mini-css-extract-plugin");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
 const ObsoleteWebpackPlugin = require("obsolete-webpack-plugin");
-// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS.
+// eslint-disable-next-line @blueprintjs/classes-constants -- incorrect match
 const ScriptExtHtmlWebpackPlugin = require("script-ext-html-webpack-plugin");
 
 const src = path.resolve("src");
@@ -34,9 +29,6 @@ module.exports = {
     path: path.resolve("build"),
     publicPath,
   },
-  resolve: {
-    extensions: [".ts", ".tsx", "..."],
-  },
   module: {
     rules: [
       {
@@ -80,4 +72,3 @@ module.exports = {
     }),
   ],
 };
-/* eslint-enable @blueprintjs/classes-constants -- we don't import blueprint here  */

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "cellxgene",
-  "version": "0.17.0",
+  "version": "0.18.0",
   "license": "MIT",
   "description": "cellxgene is a web application for the interactive exploration of single cell sequence data.",
   "repository": "https://github.com/chanzuckerberg/cellxgene",
@@ -8,14 +8,13 @@
     "build": "npm run clean && webpack --config",
     "clean": "rimraf build",
     "dev": "npm run build -- configuration/webpack/webpack.config.dev.js",
-    "e2e": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.ts",
+    "e2e": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.js",
-    "e2e-annotations": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2eAnnotations.test.ts",
+    "e2e-annotations": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2eAnnotations.test.js",
-    "e2e-prod": "CXG_URL_BASE='https://cellxgene.cziscience.com/d/pbmc3k.cxg/' jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.ts",
+    "e2e-prod": "CXG_URL_BASE='https://cellxgene.cziscience.com/d/pbmc3k.cxg/' jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.js",
     "fmt": "eslint --fix src __tests__",
-    "lint": "eslint src __tests__ & npm run type-check",
+    "lint": "eslint --fix src __tests__",
     "prod": "npm run build -- configuration/webpack/webpack.config.prod.js",
-    "test": "jest --testPathIgnorePatterns e2e",
+    "test": "jest --testPathIgnorePatterns e2e"
-    "type-check": "tsc --noEmit"
   },
   "engineStrict": true,
   "engines": {
@@ -40,12 +39,13 @@
   ],
   "dependencies": {
     "@aws-sdk/client-secrets-manager": "^3.13.0",
+    "@babel/eslint-parser": "^7.15.0",
     "@blueprintjs/core": "^3.44.0",
     "@blueprintjs/icons": "^3.19.0",
-    "@blueprintjs/popover2": "^0.6.0",
+    "@blueprintjs/popover2": "^0.11.2",
     "@blueprintjs/select": "^3.16.0",
     "abort-controller": "^3.0.0",
-    "core-js": "^3.6.5",
+    "core-js": "^3.16.3",
     "d3": "^4.10.0",
     "d3-scale-chromatic": "^1.5.0",
     "flatbuffers": "^1.11.0",
@@ -89,39 +89,10 @@
     "@babel/plugin-transform-runtime": "^7.13.15",
     "@babel/preset-env": "^7.13.15",
     "@babel/preset-react": "^7.13.13",
-    "@babel/preset-typescript": "^7.14.5",
     "@babel/register": "^7.13.16",
     "@babel/runtime": "^7.13.16",
     "@blueprintjs/eslint-plugin": "^0.3.0",
     "@sentry/webpack-plugin": "^1.15.0",
-    "@types/d3": "^7.0.0",
-    "@types/d3-scale-chromatic": "^3.0.0",
-    "@types/expect-puppeteer": "^4.4.6",
-    "@types/flatbuffers": "^1.10.0",
-    "@types/is-number": "^7.0.1",
-    "@types/jest": "^26.0.24",
-    "@types/jest-environment-puppeteer": "^4.4.1",
-    "@types/lodash.clonedeep": "^4.5.6",
-    "@types/lodash.difference": "^4.5.6",
-    "@types/lodash.every": "^4.6.6",
-    "@types/lodash.filter": "^4.6.6",
-    "@types/lodash.foreach": "^4.5.6",
-    "@types/lodash.isnumber": "^3.0.6",
-    "@types/lodash.map": "^4.6.13",
-    "@types/lodash.pull": "^4.1.6",
-    "@types/lodash.sortby": "^4.7.6",
-    "@types/lodash.uniq": "^4.5.6",
-    "@types/lodash.zip": "^4.2.6",
-    "@types/pako": "^1.0.2",
-    "@types/puppeteer": "^5.4.4",
-    "@types/react": "^17.0.14",
-    "@types/react-dom": "^17.0.9",
-    "@types/react-helmet": "^6.1.2",
-    "@types/react-redux": "^7.1.18",
-    "@types/sha1": "^1.1.3",
-    "@typescript-eslint/eslint-plugin": "^4.28.4",
-    "@typescript-eslint/parser": "^4.28.4",
-    "babel-eslint": "^10.1.0",
     "babel-jest": "^26.1.0",
     "babel-loader": "^8.1.0",
     "babel-preset-modern-browsers": "^15.0.2",
@@ -132,13 +103,12 @@
     "codecov": "^3.7.1",
     "css-loader": "^5.2.4",
     "eslint": "^7.24.0",
-    "eslint-config-airbnb-typescript": "^12.3.1",
+    "eslint-config-airbnb": "^18.2.0",
     "eslint-config-prettier": "^8.2.0",
-    "eslint-loader": "^4.0.2",
     "eslint-plugin-compat": "^3.8.0",
     "eslint-plugin-eslint-comments": "^3.2.0",
     "eslint-plugin-filenames": "^1.3.2",
-    "eslint-plugin-import": "^2.22.0",
+    "eslint-plugin-import": "^2.24.2",
     "eslint-plugin-jest": "^24.3.5",
     "eslint-plugin-jsx-a11y": "^6.3.1",
     "eslint-plugin-react": "^7.23.2",
@@ -150,8 +120,8 @@
     "file-loader": "^6.0.0",
     "html-webpack-plugin": "^5.3.1",
     "husky": "^4.2.5",
-    "jest": "^26.1.0",
+    "jest": "^27.0.6",
-    "jest-circus": "^26.1.0",
+    "jest-circus": "^27.0.6",
     "jest-environment-puppeteer": "^5.0.1",
     "jest-fetch-mock": "^3.0.3",
     "jest-puppeteer": "^5.0.1",
@@ -172,7 +142,6 @@
     "script-ext-html-webpack-plugin": "^2.1.4",
     "serve-favicon": "^2.5.0",
     "terser-webpack-plugin": "^5.1.1",
-    "typescript": "^4.3.5",
     "webpack": "^5.34.0",
     "webpack-cli": "^4.6.0",
     "webpack-dev-middleware": "^4.1.0",
@@ -180,10 +149,10 @@
   },
   "jest": {
     "testMatch": [
-      "**/__tests__/**/?(*.)(spec|test).ts?(x)"
+      "**/__tests__/**/?(*.)(spec|test).js?(x)"
     ],
     "setupFiles": [
-      "./__tests__/setupMissingGlobals.ts"
+      "./__tests__/setupMissingGlobals.js"
     ],
     "coverageDirectory": "./coverage/",
     "collectCoverage": true
@@ -193,8 +162,7 @@
       "test": {
         "presets": [
           "@babel/preset-env",
-          "@babel/preset-react",
+          "@babel/preset-react"
-          "@babel/preset-typescript"
         ],
         "plugins": [
           "@babel/plugin-proposal-function-bind",
@@ -216,6 +184,12 @@
               "loose": true
             }
           ],
+          [
+            "@babel/plugin-proposal-private-property-in-object",
+            {
+              "loose": true
+            }
+          ],
           "@babel/plugin-proposal-export-namespace-from",
           "@babel/plugin-transform-react-constant-elements",
           "@babel/plugin-transform-runtime",

client/src/actions/annotation.js

@@ -0,0 +1,455 @@
+/*
+Action creators for user annotation
+*/
+import difference from "lodash.difference";
+import pako from "pako";
+import * as globals from "../globals";
+import { MatrixFBS, AnnotationsHelpers } from "../util/stateManager";
+
+const { isUserAnnotation } = AnnotationsHelpers;
+
+export const annotationCreateCategoryAction =
+  (newCategoryName, categoryToDuplicate) => async (dispatch, getState) => {
+    /*
+  Add a new user-created category to the obs annotations.
+
+  Arguments:
+    newCategoryName - string name for the category.
+    categoryToDuplicate - obs category to use for initial values, or null.
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    const { schema } = prevAnnoMatrix;
+
+    /* name must be a string,  non-zero length */
+    if (typeof newCategoryName !== "string" || newCategoryName.length === 0)
+      throw new Error("user annotations require string name");
+
+    /* ensure the name isn't already in use! */
+    if (schema.annotations.obsByName[newCategoryName])
+      throw new Error("name collision on annotation category create");
+
+    let initialValue;
+    let newSchema;
+    let ctor;
+    if (categoryToDuplicate) {
+      /* if we are duplicating a category, retrieve it */
+      const catDupSchema = schema.annotations.obsByName[categoryToDuplicate];
+      const catDupType = catDupSchema?.type;
+      if (catDupType !== "string" && catDupType !== "categorical")
+        throw new Error(
+          "categoryToDuplicate does not exist or has invalid type"
+        );
+
+      const catToDupDf = await prevAnnoMatrix
+        .base()
+        .fetch("obs", categoryToDuplicate);
+      const col = catToDupDf.col(categoryToDuplicate);
+      initialValue = col.asArray();
+      const { categories } = col.summarizeCategorical();
+      // all user-created annotations must have the unassigned category
+      if (!categories.includes(globals.unassignedCategoryLabel)) {
+        categories.push(globals.unassignedCategoryLabel);
+      }
+      ctor = initialValue.constructor;
+      newSchema = {
+        ...catDupSchema,
+        name: newCategoryName,
+        categories,
+        writable: true,
+      };
+    } else {
+      /* else assign to the standard default value */
+      initialValue = globals.unassignedCategoryLabel;
+      ctor = Array;
+      newSchema = {
+        name: newCategoryName,
+        type: "categorical",
+        categories: [globals.unassignedCategoryLabel],
+        writable: true,
+      };
+    }
+
+    const obsCrossfilter = prevObsCrossfilter.addObsColumn(
+      newSchema,
+      ctor,
+      initialValue
+    );
+
+    dispatch({
+      type: "annotation: create category",
+      data: newCategoryName,
+      categoryToDuplicate,
+      annoMatrix: obsCrossfilter.annoMatrix,
+      obsCrossfilter,
+    });
+  };
+
+export const annotationRenameCategoryAction =
+  (oldCategoryName, newCategoryName) => (dispatch, getState) => {
+    /*
+  Rename a user-created annotation category
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    if (!isUserAnnotation(prevAnnoMatrix, oldCategoryName))
+      throw new Error("not a user annotation");
+
+    /* name must be a string,  non-zero length */
+    if (typeof newCategoryName !== "string" || newCategoryName.length === 0)
+      throw new Error("user annotations require string name");
+
+    if (oldCategoryName === newCategoryName) return;
+
+    const obsCrossfilter = prevObsCrossfilter.renameObsColumn(
+      oldCategoryName,
+      newCategoryName
+    );
+
+    dispatch({
+      type: "annotation: category edited",
+      annoMatrix: obsCrossfilter.annoMatrix,
+      obsCrossfilter,
+      metadataField: oldCategoryName,
+      newCategoryText: newCategoryName,
+      data: newCategoryName,
+    });
+  };
+
+export const annotationDeleteCategoryAction =
+  (categoryName) => (dispatch, getState) => {
+    /*
+  Delete a user-created category
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    if (!isUserAnnotation(prevAnnoMatrix, categoryName))
+      throw new Error("not a user annotation");
+
+    const obsCrossfilter = prevObsCrossfilter.dropObsColumn(categoryName);
+    dispatch({
+      type: "annotation: delete category",
+      annoMatrix: obsCrossfilter.annoMatrix,
+      obsCrossfilter,
+      metadataField: categoryName,
+    });
+  };
+
+export const annotationCreateLabelInCategory =
+  (categoryName, labelName, assignSelected) => async (dispatch, getState) => {
+    /*
+  Add a new label to a user-defined category.  If assignSelected is true, assign
+  the label to all currently selected cells.
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    if (!isUserAnnotation(prevAnnoMatrix, categoryName))
+      throw new Error("not a user annotation");
+
+    let obsCrossfilter = prevObsCrossfilter.addObsAnnoCategory(
+      categoryName,
+      labelName
+    );
+    if (assignSelected) {
+      obsCrossfilter = await obsCrossfilter.setObsColumnValues(
+        categoryName,
+        prevObsCrossfilter.allSelectedLabels(),
+        labelName
+      );
+    }
+
+    dispatch({
+      type: "annotation: add new label to category",
+      annoMatrix: obsCrossfilter.annoMatrix,
+      obsCrossfilter,
+      metadataField: categoryName,
+      newLabelText: labelName,
+      assignSelectedCells: assignSelected,
+    });
+  };
+
+export const annotationDeleteLabelFromCategory =
+  (categoryName, labelName) => async (dispatch, getState) => {
+    /*
+  delete a label from a user-defined category
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    if (!isUserAnnotation(prevAnnoMatrix, categoryName))
+      throw new Error("not a user annotation");
+
+    const obsCrossfilter = await prevObsCrossfilter.removeObsAnnoCategory(
+      categoryName,
+      labelName,
+      globals.unassignedCategoryLabel
+    );
+
+    dispatch({
+      type: "annotation: delete label",
+      metadataField: categoryName,
+      label: labelName,
+      annoMatrix: obsCrossfilter.annoMatrix,
+      obsCrossfilter,
+    });
+  };
+
+export const annotationRenameLabelInCategory =
+  (categoryName, oldLabelName, newLabelName) => async (dispatch, getState) => {
+    /*
+  label name change
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    if (!isUserAnnotation(prevAnnoMatrix, categoryName))
+      throw new Error("not a user annotation");
+
+    let obsCrossfilter = await prevObsCrossfilter.resetObsColumnValues(
+      categoryName,
+      oldLabelName,
+      newLabelName
+    );
+    obsCrossfilter = await obsCrossfilter.removeObsAnnoCategory(
+      categoryName,
+      oldLabelName,
+      globals.unassignedCategoryLabel
+    );
+
+    dispatch({
+      type: "annotation: label edited",
+      editedLabel: newLabelName,
+      metadataField: categoryName,
+      label: oldLabelName,
+      annoMatrix: obsCrossfilter.annoMatrix,
+      obsCrossfilter,
+    });
+  };
+
+export const annotationLabelCurrentSelection =
+  (categoryName, labelName) => async (dispatch, getState) => {
+    /*
+  set the label on all currently selected
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
+      getState();
+    if (!prevAnnoMatrix || !prevObsCrossfilter) return;
+    if (!isUserAnnotation(prevAnnoMatrix, categoryName))
+      throw new Error("not a user annotation");
+
+    const obsCrossfilter = await prevObsCrossfilter.setObsColumnValues(
+      categoryName,
+      prevObsCrossfilter.allSelectedLabels(),
+      labelName
+    );
+
+    dispatch({
+      type: "annotation: label current cell selection",
+      metadataField: categoryName,
+      label: labelName,
+      obsCrossfilter,
+      annoMatrix: obsCrossfilter.annoMatrix,
+    });
+  };
+
+function writableAnnotations(annoMatrix) {
+  return annoMatrix.schema.annotations.obs.columns
+    .filter((s) => s.writable)
+    .map((s) => s.name);
+}
+
+export const needToSaveObsAnnotations = (annoMatrix, lastSavedAnnoMatrix) => {
+  /*
+  Return true if there are LIKELY user-defined annotation modifications between the two
+  annoMatrices.  Technically not an action creator, but intimately intertwined
+  with the save process.
+
+  Two conditions will trigger a need to save:
+    * the collection of user-defined columns have changed
+    * the contents of the user-defined columns have change
+  */
+
+  annoMatrix = annoMatrix.base();
+
+  // if the annoMatrix hasn't changed, we are guaranteed no changes to the matrix schema or contents.
+  if (annoMatrix === lastSavedAnnoMatrix) return false;
+
+  // if the schema has changed, we need to save
+  const currentWritable = writableAnnotations(annoMatrix);
+  if (difference(currentWritable, writableAnnotations(lastSavedAnnoMatrix))) {
+    return true;
+  }
+
+  // no schema changes; check for change in contents
+  return currentWritable.some(
+    (col) => annoMatrix.col(col) !== lastSavedAnnoMatrix.col(col)
+  );
+};
+
+export const saveObsAnnotationsAction = () => async (dispatch, getState) => {
+  /*
+  Save the user-created obs annotations IF any have changed.
+  */
+  const state = getState();
+  const { annotations, autosave } = state;
+  const { dataCollectionNameIsReadOnly, dataCollectionName } = annotations;
+  const { lastSavedAnnoMatrix, saveInProgress } = autosave;
+
+  const annoMatrix = state.annoMatrix.base();
+
+  if (saveInProgress || annoMatrix === lastSavedAnnoMatrix) return;
+  if (!needToSaveObsAnnotations(annoMatrix, lastSavedAnnoMatrix)) {
+    dispatch({
+      type: "writable obs annotations - save complete",
+      lastSavedAnnoMatrix: annoMatrix,
+    });
+    return;
+  }
+
+  /*
+  Else, we really do need to save
+  */
+
+  dispatch({
+    type: "writable obs annotations - save started",
+  });
+
+  const df = await annoMatrix.fetch("obs", writableAnnotations(annoMatrix));
+  const matrix = MatrixFBS.encodeMatrixFBS(df);
+  const compressedMatrix = pako.deflate(matrix);
+  try {
+    const queryString =
+      !dataCollectionNameIsReadOnly && !!dataCollectionName
+        ? `?annotation-collection-name=${encodeURIComponent(
+            dataCollectionName
+          )}`
+        : "";
+    const res = await fetch(
+      `${globals.API.prefix}${globals.API.version}annotations/obs${queryString}`,
+      {
+        method: "PUT",
+        body: compressedMatrix,
+        headers: new Headers({
+          "Content-Type": "application/octet-stream",
+        }),
+        credentials: "include",
+      }
+    );
+    if (res.ok) {
+      dispatch({
+        type: "writable obs annotations - save complete",
+        lastSavedAnnoMatrix: annoMatrix,
+      });
+    } else {
+      dispatch({
+        type: "writable obs annotations - save error",
+        message: `HTTP error ${res.status} - ${res.statusText}`,
+        res,
+      });
+    }
+  } catch (error) {
+    dispatch({
+      type: "writable obs annotations - save error",
+      message: error.toString(),
+      error,
+    });
+  }
+};
+
+export const saveGenesetsAction = () => async (dispatch, getState) => {
+  const state = getState();
+
+  // bail if gene sets not available, or in readonly mode.
+  const { config } = state;
+  const { lastTid, genesets } = state.genesets;
+
+  const genesetsAreAvailable =
+    config?.parameters?.annotations_genesets ?? false;
+  const genesetsReadonly =
+    config?.parameters?.annotations_genesets_readonly ?? true;
+  if (!genesetsAreAvailable || genesetsReadonly) {
+    // our non-save was completed!
+    return dispatch({
+      type: "autosave: genesets complete",
+      lastSavedGenesets: genesets,
+    });
+  }
+
+  dispatch({
+    type: "autosave: genesets started",
+  });
+
+  /* Create the JSON OTA data structure */
+  const tid = (lastTid ?? 0) + 1;
+  const genesetsOTA = [];
+  for (const [name, gs] of genesets) {
+    const genes = [];
+    for (const g of gs.genes.values()) {
+      genes.push({
+        gene_symbol: g.geneSymbol,
+        gene_description: g.geneDescription,
+      });
+    }
+    genesetsOTA.push({
+      geneset_name: name,
+      geneset_description: gs.genesetDescription,
+      genes,
+    });
+  }
+  const ota = {
+    tid,
+    genesets: genesetsOTA,
+  };
+
+  /* Save to server */
+  try {
+    const { dataCollectionNameIsReadOnly, dataCollectionName } =
+      state.annotations;
+    const queryString =
+      !dataCollectionNameIsReadOnly && !!dataCollectionName
+        ? `?annotation-collection-name=${encodeURIComponent(
+            dataCollectionName
+          )}`
+        : "";
+
+    const res = await fetch(
+      `${globals.API.prefix}${globals.API.version}genesets${queryString}`,
+      {
+        method: "PUT",
+        headers: new Headers({
+          Accept: "application/json",
+          "Content-Type": "application/json",
+        }),
+        body: JSON.stringify(ota),
+        credentials: "include",
+      }
+    );
+    if (!res.ok) {
+      return dispatch({
+        type: "autosave: genesets error",
+        message: `HTTP error ${res.status} - ${res.statusText}`,
+        res,
+      });
+    }
+    return Promise.all([
+      dispatch({
+        type: "autosave: genesets complete",
+        lastSavedGenesets: genesets,
+      }),
+      dispatch({
+        type: "geneset: set tid",
+        tid,
+      }),
+    ]);
+  } catch (error) {
+    return dispatch({
+      type: "autosave: genesets error",
+      message: error.toString(),
+      error,
+    });
+  }
+};

client/src/actions/annotation.ts

@@ -1,530 +0,0 @@
-/*
-Action creators for user annotation
-*/
-import difference from "lodash.difference";
-import pako from "pako";
-import * as globals from "../globals";
-import { MatrixFBS, AnnotationsHelpers } from "../util/stateManager";
-
-const { isUserAnnotation } = AnnotationsHelpers;
-
-export const annotationCreateCategoryAction = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  newCategoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  categoryToDuplicate: any
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  /*
-  Add a new user-created category to the obs annotations.
-
-  Arguments:
-    newCategoryName - string name for the category.
-    categoryToDuplicate - obs category to use for initial values, or null.
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  const { schema } = prevAnnoMatrix;
-
-  /* name must be a string,  non-zero length */
-  if (typeof newCategoryName !== "string" || newCategoryName.length === 0)
-    throw new Error("user annotations require string name");
-
-  /* ensure the name isn't already in use! */
-  if (schema.annotations.obsByName[newCategoryName])
-    throw new Error("name collision on annotation category create");
-
-  let initialValue;
-  let newSchema;
-  let ctor;
-  if (categoryToDuplicate) {
-    /* if we are duplicating a category, retrieve it */
-    const catDupSchema = schema.annotations.obsByName[categoryToDuplicate];
-    const catDupType = catDupSchema?.type;
-    if (catDupType !== "string" && catDupType !== "categorical")
-      throw new Error("categoryToDuplicate does not exist or has invalid type");
-
-    const catToDupDf = await prevAnnoMatrix
-      .base()
-      .fetch("obs", categoryToDuplicate);
-    const col = catToDupDf.col(categoryToDuplicate);
-    initialValue = col.asArray();
-    const { categories } = col.summarizeCategorical();
-    // all user-created annotations must have the unassigned category
-    if (!categories.includes(globals.unassignedCategoryLabel)) {
-      categories.push(globals.unassignedCategoryLabel);
-    }
-    ctor = initialValue.constructor;
-    newSchema = {
-      ...catDupSchema,
-      name: newCategoryName,
-      categories,
-      writable: true,
-    };
-  } else {
-    /* else assign to the standard default value */
-    initialValue = globals.unassignedCategoryLabel;
-    ctor = Array;
-    newSchema = {
-      name: newCategoryName,
-      type: "categorical",
-      categories: [globals.unassignedCategoryLabel],
-      writable: true,
-    };
-  }
-
-  const obsCrossfilter = prevObsCrossfilter.addObsColumn(
-    newSchema,
-    ctor,
-    initialValue
-  );
-
-  dispatch({
-    type: "annotation: create category",
-    data: newCategoryName,
-    categoryToDuplicate,
-    annoMatrix: obsCrossfilter.annoMatrix,
-    obsCrossfilter,
-  });
-};
-
-export const annotationRenameCategoryAction = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  oldCategoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  newCategoryName: any
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => (dispatch: any, getState: any) => {
-  /*
-  Rename a user-created annotation category
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  if (!isUserAnnotation(prevAnnoMatrix, oldCategoryName))
-    throw new Error("not a user annotation");
-
-  /* name must be a string,  non-zero length */
-  if (typeof newCategoryName !== "string" || newCategoryName.length === 0)
-    throw new Error("user annotations require string name");
-
-  if (oldCategoryName === newCategoryName) return;
-
-  const obsCrossfilter = prevObsCrossfilter.renameObsColumn(
-    oldCategoryName,
-    newCategoryName
-  );
-
-  dispatch({
-    type: "annotation: category edited",
-    annoMatrix: obsCrossfilter.annoMatrix,
-    obsCrossfilter,
-    metadataField: oldCategoryName,
-    newCategoryText: newCategoryName,
-    data: newCategoryName,
-  });
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const annotationDeleteCategoryAction = (categoryName: any) => (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  /*
-  Delete a user-created category
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  if (!isUserAnnotation(prevAnnoMatrix, categoryName))
-    throw new Error("not a user annotation");
-
-  const obsCrossfilter = prevObsCrossfilter.dropObsColumn(categoryName);
-  dispatch({
-    type: "annotation: delete category",
-    annoMatrix: obsCrossfilter.annoMatrix,
-    obsCrossfilter,
-    metadataField: categoryName,
-  });
-};
-
-export const annotationCreateLabelInCategory = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  categoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  labelName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  assignSelected: any // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  /*
-  Add a new label to a user-defined category.  If assignSelected is true, assign
-  the label to all currently selected cells.
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  if (!isUserAnnotation(prevAnnoMatrix, categoryName))
-    throw new Error("not a user annotation");
-
-  let obsCrossfilter = prevObsCrossfilter.addObsAnnoCategory(
-    categoryName,
-    labelName
-  );
-  if (assignSelected) {
-    obsCrossfilter = await obsCrossfilter.setObsColumnValues(
-      categoryName,
-      prevObsCrossfilter.allSelectedLabels(),
-      labelName
-    );
-  }
-
-  dispatch({
-    type: "annotation: add new label to category",
-    annoMatrix: obsCrossfilter.annoMatrix,
-    obsCrossfilter,
-    metadataField: categoryName,
-    newLabelText: labelName,
-    assignSelectedCells: assignSelected,
-  });
-};
-
-export const annotationDeleteLabelFromCategory = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  categoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  labelName: any // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  /*
-  delete a label from a user-defined category
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  if (!isUserAnnotation(prevAnnoMatrix, categoryName))
-    throw new Error("not a user annotation");
-
-  const obsCrossfilter = await prevObsCrossfilter.removeObsAnnoCategory(
-    categoryName,
-    labelName,
-    globals.unassignedCategoryLabel
-  );
-
-  dispatch({
-    type: "annotation: delete label",
-    metadataField: categoryName,
-    label: labelName,
-    annoMatrix: obsCrossfilter.annoMatrix,
-    obsCrossfilter,
-  });
-};
-
-export const annotationRenameLabelInCategory = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  categoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  oldLabelName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  newLabelName: any
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  /*
-  label name change
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  if (!isUserAnnotation(prevAnnoMatrix, categoryName))
-    throw new Error("not a user annotation");
-
-  let obsCrossfilter = await prevObsCrossfilter.resetObsColumnValues(
-    categoryName,
-    oldLabelName,
-    newLabelName
-  );
-  obsCrossfilter = await obsCrossfilter.removeObsAnnoCategory(
-    categoryName,
-    oldLabelName,
-    globals.unassignedCategoryLabel
-  );
-
-  dispatch({
-    type: "annotation: label edited",
-    editedLabel: newLabelName,
-    metadataField: categoryName,
-    label: oldLabelName,
-    annoMatrix: obsCrossfilter.annoMatrix,
-    obsCrossfilter,
-  });
-};
-
-export const annotationLabelCurrentSelection = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  categoryName: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  labelName: any
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  /*
-  set the label on all currently selected
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
-  if (!prevAnnoMatrix || !prevObsCrossfilter) return;
-  if (!isUserAnnotation(prevAnnoMatrix, categoryName))
-    throw new Error("not a user annotation");
-
-  const obsCrossfilter = await prevObsCrossfilter.setObsColumnValues(
-    categoryName,
-    prevObsCrossfilter.allSelectedLabels(),
-    labelName
-  );
-
-  dispatch({
-    type: "annotation: label current cell selection",
-    metadataField: categoryName,
-    label: labelName,
-    obsCrossfilter,
-    annoMatrix: obsCrossfilter.annoMatrix,
-  });
-};
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function writableAnnotations(annoMatrix: any) {
-  return (
-    annoMatrix.schema.annotations.obs.columns
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      .filter((s: any) => s.writable)
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      .map((s: any) => s.name)
-  );
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export const needToSaveObsAnnotations = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  annoMatrix: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  lastSavedAnnoMatrix: any
-) => {
-  /*
-  Return true if there are LIKELY user-defined annotation modifications between the two
-  annoMatrices.  Technically not an action creator, but intimately intertwined
-  with the save process.
-
-  Two conditions will trigger a need to save:
-    * the collection of user-defined columns have changed
-    * the contents of the user-defined columns have change
-  */
-
-  annoMatrix = annoMatrix.base();
-
-  // if the annoMatrix hasn't changed, we are guaranteed no changes to the matrix schema or contents.
-  if (annoMatrix === lastSavedAnnoMatrix) return false;
-
-  // if the schema has changed, we need to save
-  const currentWritable = writableAnnotations(annoMatrix);
-  if (difference(currentWritable, writableAnnotations(lastSavedAnnoMatrix))) {
-    return true;
-  }
-
-  // no schema changes; check for change in contents
-  return currentWritable.some(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (col: any) => annoMatrix.col(col) !== lastSavedAnnoMatrix.col(col)
-  );
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export const saveObsAnnotationsAction = () => async (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  /*
-  Save the user-created obs annotations IF any have changed.
-  */
-  const state = getState();
-  const { annotations, autosave } = state;
-  const { dataCollectionNameIsReadOnly, dataCollectionName } = annotations;
-  const { lastSavedAnnoMatrix, saveInProgress } = autosave;
-
-  const annoMatrix = state.annoMatrix.base();
-
-  if (saveInProgress || annoMatrix === lastSavedAnnoMatrix) return;
-  if (!needToSaveObsAnnotations(annoMatrix, lastSavedAnnoMatrix)) {
-    dispatch({
-      type: "writable obs annotations - save complete",
-      lastSavedAnnoMatrix: annoMatrix,
-    });
-    return;
-  }
-
-  /*
-  Else, we really do need to save
-  */
-
-  dispatch({
-    type: "writable obs annotations - save started",
-  });
-
-  const df = await annoMatrix.fetch("obs", writableAnnotations(annoMatrix));
-  const matrix = MatrixFBS.encodeMatrixFBS(df);
-  const compressedMatrix = pako.deflate(matrix);
-  try {
-    const queryString =
-      !dataCollectionNameIsReadOnly && !!dataCollectionName
-        ? `?annotation-collection-name=${encodeURIComponent(
-            dataCollectionName
-          )}`
-        : "";
-    const res = await fetch(
-      `${globals.API.prefix}${globals.API.version}annotations/obs${queryString}`,
-      {
-        method: "PUT",
-        body: compressedMatrix,
-        headers: new Headers({
-          "Content-Type": "application/octet-stream",
-        }),
-        credentials: "include",
-      }
-    );
-    if (res.ok) {
-      dispatch({
-        type: "writable obs annotations - save complete",
-        lastSavedAnnoMatrix: annoMatrix,
-      });
-    } else {
-      dispatch({
-        type: "writable obs annotations - save error",
-        message: `HTTP error ${res.status} - ${res.statusText}`,
-        res,
-      });
-    }
-  } catch (error) {
-    dispatch({
-      type: "writable obs annotations - save error",
-      message: error.toString(),
-      error,
-    });
-  }
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export const saveGenesetsAction = () => async (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  const state = getState();
-
-  // bail if gene sets not available, or in readonly mode.
-  const { config } = state;
-  const { lastTid, genesets } = state.genesets;
-
-  const genesetsAreAvailable =
-    config?.parameters?.annotations_genesets ?? false;
-  const genesetsReadonly =
-    config?.parameters?.annotations_genesets_readonly ?? true;
-  if (!genesetsAreAvailable || genesetsReadonly) {
-    // our non-save was completed!
-    return dispatch({
-      type: "autosave: genesets complete",
-      lastSavedGenesets: genesets,
-    });
-  }
-
-  dispatch({
-    type: "autosave: genesets started",
-  });
-
-  /* Create the JSON OTA data structure */
-  const tid = (lastTid ?? 0) + 1;
-  const genesetsOTA = [];
-  for (const [name, gs] of genesets) {
-    const genes = [];
-    for (const g of gs.genes.values()) {
-      genes.push({
-        gene_symbol: g.geneSymbol,
-        gene_description: g.geneDescription,
-      });
-    }
-    genesetsOTA.push({
-      geneset_name: name,
-      geneset_description: gs.genesetDescription,
-      genes,
-    });
-  }
-  const ota = {
-    tid,
-    genesets: genesetsOTA,
-  };
-
-  /* Save to server */
-  try {
-    const {
-      dataCollectionNameIsReadOnly,
-      dataCollectionName,
-    } = state.annotations;
-    const queryString =
-      !dataCollectionNameIsReadOnly && !!dataCollectionName
-        ? `?annotation-collection-name=${encodeURIComponent(
-            dataCollectionName
-          )}`
-        : "";
-
-    const res = await fetch(
-      `${globals.API.prefix}${globals.API.version}genesets${queryString}`,
-      {
-        method: "PUT",
-        headers: new Headers({
-          Accept: "application/json",
-          "Content-Type": "application/json",
-        }),
-        body: JSON.stringify(ota),
-        credentials: "include",
-      }
-    );
-    if (!res.ok) {
-      return dispatch({
-        type: "autosave: genesets error",
-        message: `HTTP error ${res.status} - ${res.statusText}`,
-        res,
-      });
-    }
-    return await Promise.all([
-      dispatch({
-        type: "autosave: genesets complete",
-        lastSavedGenesets: genesets,
-      }),
-      dispatch({
-        type: "geneset: set tid",
-        tid,
-      }),
-    ]);
-  } catch (error) {
-    return dispatch({
-      type: "autosave: genesets error",
-      message: error.toString(),
-      error,
-    });
-  }
-};

client/src/actions/embedding.js

@@ -0,0 +1,47 @@
+/*
+action creators related to embeddings choice
+*/
+
+import { AnnoMatrixObsCrossfilter } from "../annoMatrix";
+import { _setEmbeddingSubset } from "../util/stateManager/viewStackHelpers";
+
+export async function _switchEmbedding(
+  prevAnnoMatrix,
+  prevCrossfilter,
+  newEmbeddingName
+) {
+  /*
+  DRY helper used by embedding action creators
+  */
+  const base = prevAnnoMatrix.base();
+  const embeddingDf = await base.fetch("emb", newEmbeddingName);
+  const annoMatrix = _setEmbeddingSubset(prevAnnoMatrix, embeddingDf);
+  const obsCrossfilter = await new AnnoMatrixObsCrossfilter(
+    annoMatrix,
+    prevCrossfilter.obsCrossfilter
+  ).select("emb", newEmbeddingName, {
+    mode: "all",
+  });
+  return [annoMatrix, obsCrossfilter];
+}
+
+export const layoutChoiceAction =
+  (newLayoutChoice) => async (dispatch, getState) => {
+    /*
+  On layout choice, make sure we have selected all on the previous layout, AND the new
+  layout.
+  */
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevCrossfilter } =
+      getState();
+    const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
+      prevAnnoMatrix,
+      prevCrossfilter,
+      newLayoutChoice
+    );
+    dispatch({
+      type: "set layout choice",
+      layoutChoice: newLayoutChoice,
+      obsCrossfilter,
+      annoMatrix,
+    });
+  };

client/src/actions/embedding.ts

@@ -1,58 +0,0 @@
-/*
-action creators related to embeddings choice
-*/
-
-import { AnnoMatrixObsCrossfilter } from "../annoMatrix";
-import { _setEmbeddingSubset } from "../util/stateManager/viewStackHelpers";
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export async function _switchEmbedding(
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  prevAnnoMatrix: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  prevCrossfilter: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  newEmbeddingName: any
-) {
-  /*
-  DRY helper used by embedding action creators
-  */
-  const base = prevAnnoMatrix.base();
-  const embeddingDf = await base.fetch("emb", newEmbeddingName);
-  const annoMatrix = _setEmbeddingSubset(prevAnnoMatrix, embeddingDf);
-  const obsCrossfilter = await new AnnoMatrixObsCrossfilter(
-    annoMatrix,
-    prevCrossfilter.obsCrossfilter
-  ).select("emb", newEmbeddingName, {
-    mode: "all",
-  });
-  return [annoMatrix, obsCrossfilter];
-}
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const layoutChoiceAction = (newLayoutChoice: any) => async (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  /*
-  On layout choice, make sure we have selected all on the previous layout, AND the new
-  layout.
-  */
-  const {
-    annoMatrix: prevAnnoMatrix,
-    obsCrossfilter: prevCrossfilter,
-  } = getState();
-  const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
-    prevAnnoMatrix,
-    prevCrossfilter,
-    newLayoutChoice
-  );
-  dispatch({
-    type: "set layout choice",
-    layoutChoice: newLayoutChoice,
-    obsCrossfilter,
-    annoMatrix,
-  });
-};

client/src/actions/geneset.js

@@ -0,0 +1,149 @@
+import { postUserErrorToast } from "../components/framework/toasters";
+/*
+Action creators for gene sets
+
+Primarily used to keep the crossfilter and underlying data in sync with the UI.
+
+The behavior manifest in these action creators:
+
+    Delete a gene set, will
+      * drop index & clear selection state on the gene set summary
+      * drop index & clear selection state of each gene in the geneset
+
+    Delete a gene from a gene set, will:
+      * drop index & clear selection state on the gene set summary
+      * drop index & clear selection state on the gene
+
+    Add a gene to a gene set, will:
+      * drop index & clear selection state on the gene set summary
+      * will NOT touch the selection state for the gene
+
+Note that crossfilter indices are lazy created, as needed.
+*/
+
+export const genesetDelete = (genesetName) => (dispatch, getState) => {
+  const state = getState();
+  const { genesets } = state;
+  const gs = genesets?.genesets?.get(genesetName) ?? {};
+  const geneSymbols = Array.from(gs.genes.keys());
+  const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
+  if (genesetName === state.colors.colorAccessor) {
+    dispatch({
+      type: "reset colorscale",
+    });
+  }
+  dispatch({
+    type: "geneset: delete",
+    genesetName,
+    obsCrossfilter,
+    annoMatrix: obsCrossfilter.annoMatrix,
+  });
+};
+
+export const genesetAddGenes =
+  (genesetName, genes) => async (dispatch, getState) => {
+    const state = getState();
+    const { obsCrossfilter: prevObsCrossfilter, annoMatrix } = state;
+    const { schema } = annoMatrix;
+    const varIndex = schema.annotations.var.index;
+    const df = await annoMatrix.fetch("var", varIndex);
+    const geneNames = df.col(varIndex).asArray();
+    genes = genes.reduce((acc, gene) => {
+      if (geneNames.indexOf(gene.geneSymbol) === -1) {
+        postUserErrorToast(
+          `${gene.geneSymbol} doesn't appear to be a valid gene name.`
+        );
+      } else acc.push(gene);
+      return acc;
+    }, []);
+
+    const obsCrossfilter = dropGenesetSummaryDimension(
+      prevObsCrossfilter,
+      state,
+      genesetName
+    );
+    dispatch({
+      type: "continuous metadata histogram cancel",
+      continuousNamespace: { isGeneSetSummary: true },
+      selection: genesetName,
+    });
+    return dispatch({
+      type: "geneset: add genes",
+      genesetName,
+      genes,
+      obsCrossfilter,
+      annoMatrix: obsCrossfilter.annoMatrix,
+    });
+  };
+
+export const genesetDeleteGenes =
+  (genesetName, geneSymbols) => (dispatch, getState) => {
+    const state = getState();
+    const obsCrossfilter = dropGeneset(
+      dispatch,
+      state,
+      genesetName,
+      geneSymbols
+    );
+    return dispatch({
+      type: "geneset: delete genes",
+      genesetName,
+      geneSymbols,
+      obsCrossfilter,
+      annoMatrix: obsCrossfilter.annoMatrix,
+    });
+  };
+
+/*
+Private
+*/
+
+function dropGenesetSummaryDimension(obsCrossfilter, state, genesetName) {
+  const { annoMatrix, genesets } = state;
+  const varIndex = annoMatrix.schema.annotations?.var?.index;
+  const gs = genesets?.genesets?.get(genesetName) ?? {};
+  const genes = Array.from(gs.genes.keys());
+  const query = {
+    summarize: {
+      method: "mean",
+      field: "var",
+      column: varIndex,
+      values: genes,
+    },
+  };
+  return obsCrossfilter.dropDimension("X", query);
+}
+
+function dropGeneDimension(obsCrossfilter, state, gene) {
+  const { annoMatrix } = state;
+  const varIndex = annoMatrix.schema.annotations?.var?.index;
+  const query = {
+    where: {
+      field: "var",
+      column: varIndex,
+      value: gene,
+    },
+  };
+  return obsCrossfilter.dropDimension("X", query);
+}
+
+function dropGeneset(dispatch, state, genesetName, geneSymbols) {
+  const { obsCrossfilter: prevObsCrossfilter } = state;
+  const obsCrossfilter = geneSymbols.reduce(
+    (crossfilter, gene) => dropGeneDimension(crossfilter, state, gene),
+    dropGenesetSummaryDimension(prevObsCrossfilter, state, genesetName)
+  );
+  dispatch({
+    type: "continuous metadata histogram cancel",
+    continuousNamespace: { isGeneSetSummary: true },
+    selection: genesetName,
+  });
+  geneSymbols.forEach((g) =>
+    dispatch({
+      type: "continuous metadata histogram cancel",
+      continuousNamespace: { isUserDefined: true },
+      selection: g,
+    })
+  );
+  return obsCrossfilter;
+}

client/src/actions/geneset.ts

@@ -1,181 +0,0 @@
-import { postUserErrorToast } from "../components/framework/toasters";
-/*
-Action creators for gene sets
-
-Primarily used to keep the crossfilter and underlying data in sync with the UI.
-
-The behavior manifest in these action creators:
-
-    Delete a gene set, will
-      * drop index & clear selection state on the gene set summary
-      * drop index & clear selection state of each gene in the geneset
-
-    Delete a gene from a gene set, will:
-      * drop index & clear selection state on the gene set summary
-      * drop index & clear selection state on the gene
-
-    Add a gene to a gene set, will:
-      * drop index & clear selection state on the gene set summary
-      * will NOT touch the selection state for the gene
-
-Note that crossfilter indices are lazy created, as needed.
-*/
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const genesetDelete = (genesetName: any) => (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  const state = getState();
-  const { genesets } = state;
-  const gs = genesets?.genesets?.get(genesetName) ?? {};
-  const geneSymbols = Array.from(gs.genes.keys());
-  const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
-  if (genesetName === state.colors.colorAccessor) {
-    dispatch({
-      type: "reset colorscale",
-    });
-  }
-  dispatch({
-    type: "geneset: delete",
-    genesetName,
-    obsCrossfilter,
-    annoMatrix: obsCrossfilter.annoMatrix,
-  });
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const genesetAddGenes = (genesetName: any, genes: any) => async (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  const state = getState();
-  const { obsCrossfilter: prevObsCrossfilter, annoMatrix } = state;
-  const { schema } = annoMatrix;
-  const varIndex = schema.annotations.var.index;
-  const df = await annoMatrix.fetch("var", varIndex);
-  const geneNames = df.col(varIndex).asArray();
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  genes = genes.reduce((acc: any, gene: any) => {
-    if (geneNames.indexOf(gene.geneSymbol) === -1) {
-      postUserErrorToast(
-        `${gene.geneSymbol} doesn't appear to be a valid gene name.`
-      );
-    } else acc.push(gene);
-    return acc;
-  }, []);
-
-  const obsCrossfilter = dropGenesetSummaryDimension(
-    prevObsCrossfilter,
-    state,
-    genesetName
-  );
-  dispatch({
-    type: "continuous metadata histogram cancel",
-    continuousNamespace: { isGeneSetSummary: true },
-    selection: genesetName,
-  });
-  return dispatch({
-    type: "geneset: add genes",
-    genesetName,
-    genes,
-    obsCrossfilter,
-    annoMatrix: obsCrossfilter.annoMatrix,
-  });
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const genesetDeleteGenes = (genesetName: any, geneSymbols: any) => (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  const state = getState();
-  const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
-  return dispatch({
-    type: "geneset: delete genes",
-    genesetName,
-    geneSymbols,
-    obsCrossfilter,
-    annoMatrix: obsCrossfilter.annoMatrix,
-  });
-};
-
-/*
-Private
-*/
-
-function dropGenesetSummaryDimension(
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  obsCrossfilter: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  state: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  genesetName: any
-) {
-  const { annoMatrix, genesets } = state;
-  const varIndex = annoMatrix.schema.annotations?.var?.index;
-  const gs = genesets?.genesets?.get(genesetName) ?? {};
-  const genes = Array.from(gs.genes.keys());
-  const query = {
-    summarize: {
-      method: "mean",
-      field: "var",
-      column: varIndex,
-      values: genes,
-    },
-  };
-  return obsCrossfilter.dropDimension("X", query);
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function dropGeneDimension(obsCrossfilter: any, state: any, gene: any) {
-  const { annoMatrix } = state;
-  const varIndex = annoMatrix.schema.annotations?.var?.index;
-  const query = {
-    where: {
-      field: "var",
-      column: varIndex,
-      value: gene,
-    },
-  };
-  return obsCrossfilter.dropDimension("X", query);
-}
-
-function dropGeneset(
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  state: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  genesetName: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  geneSymbols: any
-) {
-  const { obsCrossfilter: prevObsCrossfilter } = state;
-  const obsCrossfilter = geneSymbols.reduce(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (crossfilter: any, gene: any) =>
-      dropGeneDimension(crossfilter, state, gene),
-    dropGenesetSummaryDimension(prevObsCrossfilter, state, genesetName)
-  );
-  dispatch({
-    type: "continuous metadata histogram cancel",
-    continuousNamespace: { isGeneSetSummary: true },
-    selection: genesetName,
-  });
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  geneSymbols.forEach((g: any) =>
-    dispatch({
-      type: "continuous metadata histogram cancel",
-      continuousNamespace: { isUserDefined: true },
-      selection: g,
-    })
-  );
-  return obsCrossfilter;
-}

client/src/actions/index.js

@@ -1,12 +1,5 @@
 import * as globals from "../globals";
 import { AnnoMatrixLoader, AnnoMatrixObsCrossfilter } from "../annoMatrix";
-import { postExplainNewTab } from "../components/framework/toasters";
-import {
-  KEYS,
-  storageGet,
-  storageSet,
-  WORK_IN_PROGRESS_WARN_STATE,
-} from "../components/util/localStorage";
 import {
   catchErrorsWrap,
   doJsonRequest,
@@ -17,15 +10,9 @@ import * as selnActions from "./selection";
 import * as annoActions from "./annotation";
 import * as viewActions from "./viewStack";
 import * as embActions from "./embedding";
-import {
-  createDatasetUrl,
-  createExplorerUrl,
-  createAPIPrefix,
-} from "../util/stateManager/collectionsHelpers";
 import * as genesetActions from "./geneset";
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function setGlobalConfig(config) {
-function setGlobalConfig(config: any) {
   /**
    * Set any global run-time config not _exclusively_ managed by the config reducer.
    * This should only set fields defined in globals.globalConfig.
@@ -38,8 +25,7 @@ function setGlobalConfig(config: any) {
 /*
 return promise fetching user-configured colors
 */
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+async function userColorsFetchAndLoad(dispatch) {
-async function userColorsFetchAndLoad(dispatch: any) {
   return fetchJson("colors").then((response) =>
     dispatch({
       type: "universe: user color load success",
@@ -52,8 +38,7 @@ async function schemaFetch() {
   return fetchJson("schema");
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+async function configFetch(dispatch) {
-async function configFetch(dispatch: any) {
   return fetchJson("config").then((response) => {
     const config = { ...globals.configDefaults, ...response.config };
 
@@ -67,24 +52,7 @@ async function configFetch(dispatch: any) {
   });
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+async function userInfoFetch(dispatch) {
-async function collectionFetchAndLoad(dispatch: any) {
-  /*
-  Fetch dataset meta for the current visualization then fetch the corresponding collection.
-   */
-  const datasetMeta = await datasetMetaFetch();
-  const { collection_id: collectionId, dataset_id: selectedDatasetId } =
-    datasetMeta;
-  const collection = await collectionFetch(collectionId);
-  dispatch({
-    type: "collection load complete",
-    collection,
-    selectedDatasetId,
-  });
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-async function userInfoFetch(dispatch: any) {
   return fetchJson("userinfo").then((response) => {
     const { userinfo: userInfo } = response || {};
     dispatch({
@@ -95,8 +63,7 @@ async function userInfoFetch(dispatch: any) {
   });
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+async function genesetsFetch(dispatch, config) {
-async function genesetsFetch(dispatch: any, config: any) {
   /* request genesets ONLY if the backend supports the feature */
   const defaultResponse = {
     genesets: [],
@@ -117,52 +84,28 @@ async function genesetsFetch(dispatch: any, config: any) {
   }
 }
 
-async function datasetMetaFetch() {
+function prefetchEmbeddings(annoMatrix) {
-  /*
-   Fetch dataset meta for the current dataset.
-   TODO(cc) revisit swap of explorer URL origin for environments without a corresponding Portal instance (eg local, canary)
-   */
-  const explorerUrl = createExplorerUrl();
-  const explorerUrlParam = encodeURIComponent(explorerUrl);
-  return fetchPortalJson(`datasets/meta?url=${explorerUrlParam}`);
-}
-
-async function collectionFetch(collectionId: string) {
-  /*
-   Fetch collection with the given ID.
-   */
-  return fetchPortalJson(`collections/${collectionId}`);
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function prefetchEmbeddings(annoMatrix: any) {
   /*
   prefetch requests for all embeddings
   */
   const { schema } = annoMatrix;
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  const available = schema.layout.obs.map((v) => v.name);
-  const available = schema.layout.obs.map((v: any) => v.name);
+  available.forEach((embName) => annoMatrix.prefetch("emb", embName));
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  available.forEach((embName: any) => annoMatrix.prefetch("emb", embName));
 }
 
 /*
 Application bootstrap
 */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
 const doInitialDataLoad = () =>
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  catchErrorsWrap(async (dispatch) => {
-  catchErrorsWrap(async (dispatch: any) => {
     dispatch({ type: "initial data load start" });
 
     try {
       const [config, schema] = await Promise.all([
         configFetch(dispatch),
-        // @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1.
         schemaFetch(dispatch),
         userColorsFetchAndLoad(dispatch),
         userInfoFetch(dispatch),
-        collectionFetchAndLoad(dispatch),
       ]);
 
       genesetsFetch(dispatch, config);
@@ -183,8 +126,7 @@ const doInitialDataLoad = () =>
       const layoutSchema = schema?.schema?.layout?.obs ?? [];
       if (
         defaultEmbedding &&
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+        layoutSchema.some((s) => s.name === defaultEmbedding)
-        layoutSchema.some((s: any) => s.name === defaultEmbedding)
       ) {
         dispatch(embActions.layoutChoiceAction(defaultEmbedding));
       }
@@ -193,25 +135,21 @@ const doInitialDataLoad = () =>
     }
   }, true);
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+function requestSingleGeneExpressionCountsForColoringPOST(gene) {
-function requestSingleGeneExpressionCountsForColoringPOST(gene: any) {
   return {
     type: "color by expression",
     gene,
   };
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+const requestUserDefinedGene = (gene) => ({
-const requestUserDefinedGene = (gene: any) => ({
   type: "request user defined gene success",
-
   data: {
     genes: [gene],
   },
 });
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+const dispatchDiffExpErrors = (dispatch, response) => {
-const dispatchDiffExpErrors = (dispatch: any, response: any) => {
   switch (response.status) {
     case 403:
       dispatchNetworkErrorMessageToUser(
@@ -235,15 +173,8 @@ const dispatchDiffExpErrors = (dispatch: any, response: any) => {
 };
 
 const requestDifferentialExpression =
-  (
+  (set1, set2, num_genes = 50) =>
-    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  async (dispatch, getState) => {
-    set1: any,
-    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-    set2: any,
-    num_genes = 50
-    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  ) =>
-  async (dispatch: any, getState: any) => {
     dispatch({ type: "request differential expression started" });
     try {
       /*
@@ -291,9 +222,7 @@ const requestDifferentialExpression =
       const varIndex = await annoMatrix.fetch("var", varIndexName);
       const diffexpLists = { negative: [], positive: [] };
       for (const polarity of Object.keys(diffexpLists)) {
-        // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
+        diffexpLists[polarity] = response[polarity].map((v) => [
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-        diffexpLists[polarity] = response[polarity].map((v: any) => [
           varIndex.at(v[0], varIndexName),
           ...v.slice(1),
         ]);
@@ -312,86 +241,17 @@ const requestDifferentialExpression =
     }
   };
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+function fetchJson(pathAndQuery) {
-export const checkExplainNewTab = () => (dispatch: any) => {
-  /*
-  Opens toast "work in progress" warning.
-   */
-  if (
-    storageGet(KEYS.WORK_IN_PROGRESS_WARN) === WORK_IN_PROGRESS_WARN_STATE.ON
-  ) {
-    dispatch({ type: "work in progress warning displayed" });
-    postExplainNewTab(
-      "To maintain your in-progress work on the previous dataset, we opened this dataset in a new tab."
-    );
-    storageSet(KEYS.WORK_IN_PROGRESS_WARN, WORK_IN_PROGRESS_WARN_STATE.OFF);
-  }
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const openDataset = (dataset: any) => (dispatch: any) => {
-  /*
-  Update in a new tab the browser location to dataset's deployment URL, kick off data load.
-  */
-
-  const deploymentUrl = dataset.dataset_deployments?.[0].url ?? "";
-  const datasetUrl = createDatasetUrl(deploymentUrl);
-
-  dispatch({ type: "dataset opened" });
-  storageSet(KEYS.WORK_IN_PROGRESS_WARN, WORK_IN_PROGRESS_WARN_STATE.ON);
-  window.open(datasetUrl, "_blank");
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const switchDataset = (dataset: any) => (dispatch: any) => {
-  /*
-  Update browser location to dataset's deployment URL, kick off data load. 
-  TODO(cc) revisit:
-    - origin (and data root) switch for environments without corresponding Portal instance (eg local, canary)
-    - globals update: move to server-side, split from initial doc returned from server?
-   */
-  dispatch({ type: "dataset switch" });
-
-  const deploymentUrl = dataset.dataset_deployments?.[0].url ?? "";
-  const datasetUrl = createDatasetUrl(deploymentUrl);
-  dispatch(updateLocation(datasetUrl));
-
-  globals.API.prefix = createAPIPrefix(globals.API.prefix, datasetUrl);
-  dispatch(doInitialDataLoad());
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-const updateLocation = (url: string) => (dispatch: any) => {
-  /*
-  Add entry to the session's history stack.
-   */
-  dispatch({ type: "location update" });
-  window.history.pushState(null, "", url);
-};
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function fetchJson(pathAndQuery: any) {
   return doJsonRequest(
     `${globals.API.prefix}${globals.API.version}${pathAndQuery}`
   );
 }
 
-function fetchPortalJson(url: string) {
-  /* 
-  Fetch JSON from Portal API.
-  TODO(cc) revisit - required for dataset meta and collection requests from Portal 
-   */
-  return doJsonRequest(`${globals.API.portalPrefix}${url}`);
-}
-
 export default {
   doInitialDataLoad,
   requestDifferentialExpression,
   requestSingleGeneExpressionCountsForColoringPOST,
   requestUserDefinedGene,
-  checkExplainNewTab,
-  openDataset,
-  switchDataset,
   selectContinuousMetadataAction: selnActions.selectContinuousMetadataAction,
   selectCategoricalMetadataAction: selnActions.selectCategoricalMetadataAction,
   selectCategoricalAllMetadataAction:

client/src/actions/selection.js

@@ -0,0 +1,192 @@
+/*
+Action creators for selection 
+*/
+export const selectContinuousMetadataAction =
+  (type, query, range, oldProps = {}) =>
+  async (dispatch, getState) => {
+    const { obsCrossfilter: prevObsCrossfilter } = getState();
+
+    const selection = range
+      ? {
+          mode: "range",
+          lo: range[0],
+          hi: range[1],
+          inclusive: true, // [lo, hi] incluisve selection
+        }
+      : { mode: "all" };
+
+    const obsCrossfilter = await prevObsCrossfilter.select(...query, selection);
+
+    dispatch({
+      type,
+      obsCrossfilter,
+      range,
+      ...oldProps,
+    });
+  };
+
+export const selectCategoricalMetadataAction =
+  (
+    type, // action type
+    metadataField, // annotation category name
+    labels,
+    label, // the label being selected/deselected
+    isSelected, // bool
+    oldProps = {}
+  ) =>
+  async (dispatch, getState) => {
+    const { obsCrossfilter: prevObsCrossfilter, categoricalSelection } =
+      getState();
+
+    const labelSelectionState = new Map(categoricalSelection[metadataField]);
+    labels.forEach(
+      (l) => labelSelectionState.has(l) || labelSelectionState.set(l, true)
+    );
+    labelSelectionState.set(label, isSelected);
+
+    const values = Array.from(labelSelectionState.keys()).filter((k) =>
+      labelSelectionState.get(k)
+    );
+    const selection = {
+      mode: "exact",
+      values,
+    };
+    const obsCrossfilter = await prevObsCrossfilter.select(
+      "obs",
+      metadataField,
+      selection
+    );
+
+    dispatch({
+      type,
+      obsCrossfilter,
+      metadataField,
+      labelSelectionState,
+      ...oldProps,
+    });
+  };
+
+export const selectCategoricalAllMetadataAction =
+  (
+    type, // action type
+    metadataField, // annotation category name
+    labels,
+    isSelected, // bool, select all or none
+    oldProps = {}
+  ) =>
+  async (dispatch, getState) => {
+    const { obsCrossfilter: prevObsCrossfilter, categoricalSelection } =
+      getState();
+
+    const labelSelectionState = new Map(categoricalSelection[metadataField]);
+    labels.forEach((label) => labelSelectionState.set(label, isSelected));
+
+    const selection = { mode: isSelected ? "all" : "none" };
+    const obsCrossfilter = await prevObsCrossfilter.select(
+      "obs",
+      metadataField,
+      selection
+    );
+
+    dispatch({
+      type,
+      obsCrossfilter,
+      metadataField,
+      labelSelectionState,
+      ...oldProps,
+    });
+  };
+
+/**
+ ** Graph selection-related actions
+ **/
+
+export const graphBrushStartAction = () =>
+  /* no change to crossfilter until a change fires */
+  ({ type: "graph brush start" });
+
+const _graphBrushWithinRectAction =
+  (type, embName, brushCoords) => async (dispatch, getState) => {
+    const { obsCrossfilter: prevObsCrossfilter } = getState();
+
+    const selection = { mode: "within-rect", ...brushCoords };
+    const obsCrossfilter = await prevObsCrossfilter.select(
+      "emb",
+      embName,
+      selection
+    );
+
+    dispatch({
+      type,
+      obsCrossfilter,
+      brushCoords,
+    });
+  };
+
+const _graphAllAction = (type, embName) => async (dispatch, getState) => {
+  const { obsCrossfilter: prevObsCrossfilter } = getState();
+
+  const obsCrossfilter = await prevObsCrossfilter.select("emb", embName, {
+    mode: "all",
+  });
+
+  dispatch({
+    type,
+    obsCrossfilter,
+  });
+};
+
+export const graphBrushChangeAction = (embName, brushCoords) =>
+  _graphBrushWithinRectAction("graph brush change", embName, brushCoords);
+
+export const graphBrushEndAction = (embName, brushCoords) =>
+  _graphBrushWithinRectAction("graph brush end", embName, brushCoords);
+
+export const graphBrushCancelAction = (embName) =>
+  _graphAllAction("graph brush cancel", embName);
+export const graphBrushDeselectAction = (embName) =>
+  _graphAllAction("graph brush deselect", embName);
+
+export const graphLassoStartAction = () =>
+  /* no change to crossfilter until a change fires */
+  ({ type: "graph lasso start" });
+
+export const graphLassoCancelAction = (embName) =>
+  _graphAllAction("graph lasso cancel", embName);
+
+export const graphLassoDeselectAction = (embName) =>
+  _graphAllAction("graph lasso cancel", embName);
+
+export const graphLassoEndAction =
+  (embName, polygon) => async (dispatch, getState) => {
+    const { obsCrossfilter: prevObsCrossfilter } = getState();
+
+    const selection = {
+      mode: "within-polygon",
+      polygon,
+    };
+    const obsCrossfilter = await prevObsCrossfilter.select(
+      "emb",
+      embName,
+      selection
+    );
+
+    dispatch({
+      type: "graph lasso end",
+      obsCrossfilter,
+      polygon,
+    });
+  };
+
+/*
+Differential expression set selection
+*/
+export const setCellSetFromSelection = (cellSetId) => (dispatch, getState) => {
+  const { obsCrossfilter } = getState();
+  const selected = obsCrossfilter.allSelectedLabels();
+
+  dispatch({
+    type: `store current cell selection as differential set ${cellSetId}`,
+    data: selected.length > 0 ? selected : null,
+  });
+};

client/src/actions/selection.ts

@@ -1,248 +0,0 @@
-/*
-Action creators for selection 
-*/
-export const selectContinuousMetadataAction = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  type: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  query: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  range: any,
-  oldProps = {} // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  const { obsCrossfilter: prevObsCrossfilter } = getState();
-
-  const selection = range
-    ? {
-        mode: "range",
-        lo: range[0],
-        hi: range[1],
-        inclusive: true, // [lo, hi] incluisve selection
-      }
-    : { mode: "all" };
-
-  const obsCrossfilter = await prevObsCrossfilter.select(...query, selection);
-
-  dispatch({
-    type,
-    obsCrossfilter,
-    range,
-    ...oldProps,
-  });
-};
-
-export const selectCategoricalMetadataAction = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  type: any, // action type
-  // annotation category name
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  metadataField: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  labels: any,
-  // the label being selected/deselected
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  label: any,
-  // bool
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  isSelected: any,
-  oldProps = {}
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  const {
-    obsCrossfilter: prevObsCrossfilter,
-    categoricalSelection,
-  } = getState();
-
-  const labelSelectionState = new Map(categoricalSelection[metadataField]);
-  labels.forEach(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (l: any) => labelSelectionState.has(l) || labelSelectionState.set(l, true)
-  );
-  labelSelectionState.set(label, isSelected);
-
-  const values = Array.from(labelSelectionState.keys()).filter((k) =>
-    labelSelectionState.get(k)
-  );
-  const selection = {
-    mode: "exact",
-    values,
-  };
-  const obsCrossfilter = await prevObsCrossfilter.select(
-    "obs",
-    metadataField,
-    selection
-  );
-
-  dispatch({
-    type,
-    obsCrossfilter,
-    metadataField,
-    labelSelectionState,
-    ...oldProps,
-  });
-};
-
-export const selectCategoricalAllMetadataAction = (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  type: any, // action type
-  // annotation category name
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  metadataField: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  labels: any,
-  // bool, select all or none
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  isSelected: any,
-  oldProps = {}
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  const {
-    obsCrossfilter: prevObsCrossfilter,
-    categoricalSelection,
-  } = getState();
-
-  const labelSelectionState = new Map(categoricalSelection[metadataField]);
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  labels.forEach((label: any) => labelSelectionState.set(label, isSelected));
-
-  const selection = { mode: isSelected ? "all" : "none" };
-  const obsCrossfilter = await prevObsCrossfilter.select(
-    "obs",
-    metadataField,
-    selection
-  );
-
-  dispatch({
-    type,
-    obsCrossfilter,
-    metadataField,
-    labelSelectionState,
-    ...oldProps,
-  });
-};
-
-/**
- ** Graph selection-related actions
- **/
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export const graphBrushStartAction = () =>
-  /* no change to crossfilter until a change fires */
-  ({ type: "graph brush start" });
-
-const _graphBrushWithinRectAction = (
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  type: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  embName: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  brushCoords: any
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-) => async (dispatch: any, getState: any) => {
-  const { obsCrossfilter: prevObsCrossfilter } = getState();
-
-  const selection = { mode: "within-rect", ...brushCoords };
-  const obsCrossfilter = await prevObsCrossfilter.select(
-    "emb",
-    embName,
-    selection
-  );
-
-  dispatch({
-    type,
-    obsCrossfilter,
-    brushCoords,
-  });
-};
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-const _graphAllAction = (type: any, embName: any) => async (
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  const { obsCrossfilter: prevObsCrossfilter } = getState();
-
-  const obsCrossfilter = await prevObsCrossfilter.select("emb", embName, {
-    mode: "all",
-  });
-
-  dispatch({
-    type,
-    obsCrossfilter,
-  });
-};
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphBrushChangeAction = (embName: any, brushCoords: any) =>
-  _graphBrushWithinRectAction("graph brush change", embName, brushCoords);
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphBrushEndAction = (embName: any, brushCoords: any) =>
-  _graphBrushWithinRectAction("graph brush end", embName, brushCoords);
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphBrushCancelAction = (embName: any) =>
-  _graphAllAction("graph brush cancel", embName);
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphBrushDeselectAction = (embName: any) =>
-  _graphAllAction("graph brush deselect", embName);
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-export const graphLassoStartAction = () =>
-  /* no change to crossfilter until a change fires */
-  ({ type: "graph lasso start" });
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphLassoCancelAction = (embName: any) =>
-  _graphAllAction("graph lasso cancel", embName);
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphLassoDeselectAction = (embName: any) =>
-  _graphAllAction("graph lasso cancel", embName);
-
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const graphLassoEndAction = (embName: any, polygon: any) => async (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  const { obsCrossfilter: prevObsCrossfilter } = getState();
-
-  const selection = {
-    mode: "within-polygon",
-    polygon,
-  };
-  const obsCrossfilter = await prevObsCrossfilter.select(
-    "emb",
-    embName,
-    selection
-  );
-
-  dispatch({
-    type: "graph lasso end",
-    obsCrossfilter,
-    polygon,
-  });
-};
-
-/*
-Differential expression set selection
-*/
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export const setCellSetFromSelection = (cellSetId: any) => (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  const { obsCrossfilter } = getState();
-  const selected = obsCrossfilter.allSelectedLabels();
-
-  dispatch({
-    type: `store current cell selection as differential set ${cellSetId}`,
-    data: selected.length > 0 ? selected : null,
-  });
-};

client/src/actions/viewStack.js

@@ -18,13 +18,7 @@ import {
   _userResetSubsetAnnoMatrix,
 } from "../util/stateManager/viewStackHelpers";
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export const clipAction = (min, max) => (dispatch, getState) => {
-export const clipAction = (min: any, max: any) => (
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
   /*
   apply a clip to the current annoMatrix.  By convention, the clip
   view is ALWAYS the top view.
@@ -40,8 +34,7 @@ export const clipAction = (min: any, max: any) => (
   });
 };
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export const subsetAction = () => (dispatch, getState) => {
-export const subsetAction = () => (dispatch: any, getState: any) => {
   /*
   Subset the annoMatrix to the current crossfilter selection by pushing a 
   subset view.
@@ -49,10 +42,8 @@ export const subsetAction = () => (dispatch: any, getState: any) => {
   By convention, a clip view is ALWAYS the top view, so if present, pop
   off and re-apply
   */
-  const {
+  const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevObsCrossfilter } =
-    annoMatrix: prevAnnoMatrix,
+    getState();
-    obsCrossfilter: prevObsCrossfilter,
-  } = getState();
   const annoMatrix = _userSubsetAnnoMatrix(
     prevAnnoMatrix,
     prevObsCrossfilter.allSelectedMask()
@@ -65,8 +56,7 @@ export const subsetAction = () => (dispatch: any, getState: any) => {
   });
 };
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export const resetSubsetAction = () => (dispatch, getState) => {
-export const resetSubsetAction = () => (dispatch: any, getState: any) => {
   /*
   Reset the annoMatrix to all data.  Because we may have multiple views
   stacked, we pop them all.  By convention, any clip transformation will

client/src/annoMatrix/annoMatrix.js

@@ -17,39 +17,6 @@ import { _queryValidate, _queryCacheKey } from "./query";
 const _dataframeCache = dataframeMemo(128);
 
 export default class AnnoMatrix {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  public isView: any;
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  public nObs: any;
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  public nVar: any;
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  public rowIndex: any;
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  public schema: any;
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  public userFlags: any;
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  public viewOf: any;
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  protected _cache: any;
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  private _pendingLoad: any;
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  private _whereCache: any;
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  private _gcInfo: any;
-
   /*
   Abstract base class for all AnnoMatrix objects.  This class provides a proxy
   to the annotated matrix data authoritatively served by the server/back-end.
@@ -80,7 +47,6 @@ export default class AnnoMatrix {
       subset(annoMatrix, rowLabels) -> annoMatrix
   etc.
   */
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   static fields() {
     /*
     return the fields present in the AnnoMatrix instance.
@@ -88,8 +54,7 @@ export default class AnnoMatrix {
     return ["obs", "var", "emb", "X"];
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  constructor(schema, nObs, nVar, rowIndex = null) {
-  constructor(schema: any, nObs: any, nVar: any, rowIndex = null) {
     /*
     Private constructor - this is an abstract base class.  Do not use.
     */
@@ -118,13 +83,13 @@ export default class AnnoMatrix {
     this.userFlags = {};
 
     /*
-    Private instance variables.
+		Private instance variables.
 
-    These are caches - lazily loaded. The only guarantee is that if they
+		These are caches - lazily loaded. The only guarantee is that if they
-    are loaded, they will conform to the schema & dimensionality constraints.
+		are loaded, they will conform to the schema & dimensionality constraints.
 
-    Do NOT use directly - instead, use the fetch() and preload() API.
+		Do NOT use directly - instead, use the fetch() and preload() API.
-    */
+		*/
     this._cache = {
       obs: Dataframe.empty(this.rowIndex),
       var: Dataframe.empty(this.rowIndex),
@@ -144,8 +109,6 @@ export default class AnnoMatrix {
   /**
    ** Schema helper/accessors
    **/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   getMatrixColumns(field) {
     /*
     Return array of column names in the field.  ONLY supported on the
@@ -158,7 +121,7 @@ export default class AnnoMatrix {
     return _schemaColumns(this.schema, field);
   }
 
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/explicit-module-boundary-types -- need to be able to call this on instances
+  // eslint-disable-next-line class-methods-use-this -- need to be able to call this on instances
   getMatrixFields() {
     /*
     Return array of fields in this annoMatrix.  Currently hard-wired to
@@ -169,8 +132,6 @@ export default class AnnoMatrix {
     return AnnoMatrix.fields();
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   getColumnSchema(field, col) {
     /*
     Return the schema for the field & column ,eg,
@@ -183,8 +144,6 @@ export default class AnnoMatrix {
     return _getColumnSchema(this.schema, field, col);
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   getColumnDimensions(field, col) {
     /*
     Return the dimensions on this field / column.  For most fields, which are 1D,
@@ -203,12 +162,10 @@ export default class AnnoMatrix {
   /**
    ** General utility methods
    **/
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   base() {
     /*
     return the base of view, or `this` if not a view.
     */
-    // eslint-disable-next-line @typescript-eslint/no-this-alias --- FIXME: disabled temporarily on migrate to TS.
     let annoMatrix = this;
     while (annoMatrix.isView) annoMatrix = annoMatrix.viewOf;
     return annoMatrix;
@@ -217,8 +174,6 @@ export default class AnnoMatrix {
   /**
    ** Load / read interfaces
    **/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   fetch(field, q) {
     /*
 		Return the given query on a single matrix field as a single dataframe.
@@ -276,8 +231,6 @@ export default class AnnoMatrix {
     return this._fetch(field, q);
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   prefetch(field, q) {
     /*
 		Start a data fetch & cache fill.  Identical to fetch() except it does
@@ -308,8 +261,7 @@ export default class AnnoMatrix {
    ** The actual implementation is in the sub-classes, which MUST override these.
    **/
 
-  // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
+  // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
   addObsAnnoCategory(col, category) {
     /*
     Add a new category value (aka "label") to a writable obs column, and return the new AnnoMatrix.
@@ -326,8 +278,7 @@ export default class AnnoMatrix {
     _subclassResponsibility();
   }
 
-  // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
+  // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
   async removeObsAnnoCategory(col, category, unassignedCategory) {
     /*
     Remove a category value from an obs column, reassign any obs having that value
@@ -348,8 +299,7 @@ export default class AnnoMatrix {
     _subclassResponsibility();
   }
 
-  // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
+  // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
   dropObsColumn(col) {
     /*
     Drop an entire writable column, eg a user-created obs annotation.  Typical use
@@ -365,8 +315,7 @@ export default class AnnoMatrix {
     _subclassResponsibility();
   }
 
-  // @ts-expect-error ts-migrate(6133) FIXME: 'colSchema' is declared but its value is never rea... Remove this comment to see the full error message
+  // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
   addObsColumn(colSchema, Ctor, value) {
     /*
     Add a new writable OBS annotation column, with the caller-specified schema, initial value
@@ -395,8 +344,7 @@ export default class AnnoMatrix {
     _subclassResponsibility();
   }
 
-  // @ts-expect-error ts-migrate(6133) FIXME: 'oldCol' is declared but its value is never read.
+  // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
   renameObsColumn(oldCol, newCol) {
     /*
     Rename the obs column 'oldCol' to have name 'newCol' and returns new AnnoMatrix.
@@ -411,8 +359,7 @@ export default class AnnoMatrix {
     _subclassResponsibility();
   }
 
-  // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
+  // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
   async setObsColumnValues(col, obsLabels, value) {
     /*
     Set all obs with label in array 'obsLabels' to have 'value'.  Typical use would be
@@ -430,8 +377,7 @@ export default class AnnoMatrix {
     _subclassResponsibility();
   }
 
-  // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
+  // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
   async resetObsColumnValues(col, oldValue, newValue) {
     /*
     Set by value - all elements in the column with value 'oldValue' are set to 'newValue'.
@@ -448,8 +394,7 @@ export default class AnnoMatrix {
     _subclassResponsibility();
   }
 
-  // @ts-expect-error ts-migrate(6133) FIXME: 'colSchema' is declared but its value is never rea... Remove this comment to see the full error message
+  // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
   addEmbedding(colSchema) {
     /*
     Add a new obs embedding to the AnnoMatrix, with provided schema.
@@ -462,38 +407,28 @@ export default class AnnoMatrix {
     _subclassResponsibility();
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   getCacheKeys(field, query) {
     /*
-Return cache keys for columns associated with this query.  May return
+    Return cache keys for columns associated with this query.  May return
-[unknown] if no keys are known (ie, nothing is or was cached).
+    [unknown] if no keys are known (ie, nothing is or was cached).
-*/
+    */
     return _whereCacheGet(this._whereCache, this.schema, field, query);
   }
 
   /**
    ** Private interfaces below.
    **/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   _resolveCachedQueries(field, queries) {
-    return (
+    return queries
-      queries
+      .map((query) =>
-        // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'query' implicitly has an 'any' type.
+        _whereCacheGet(this._whereCache, this.schema, field, query).filter(
-        .map((query) =>
+          (cacheKey) =>
-          _whereCacheGet(this._whereCache, this.schema, field, query).filter(
+            cacheKey !== undefined && this._cache[field].hasCol(cacheKey)
-            // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'cacheKey' implicitly has an 'any' type.
-            (cacheKey) =>
-              cacheKey !== undefined && this._cache[field].hasCol(cacheKey)
-          )
         )
-        .flat()
+      )
-    );
+      .flat();
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   async _fetch(field, q) {
     if (!AnnoMatrix.fields().includes(field)) return undefined;
     const queries = Array.isArray(q) ? q : [q];
@@ -506,7 +441,6 @@ Return cache keys for columns associated with this query.  May return
     /* find any query not already cached */
     const uncachedQueries = queries.filter((query) =>
       _whereCacheGet(this._whereCache, this.schema, field, query).some(
-        // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'cacheKey' implicitly has an 'any' type.
         (cacheKey) =>
           cacheKey === undefined || !this._cache[field].hasCol(cacheKey)
       )
@@ -516,10 +450,8 @@ Return cache keys for columns associated with this query.  May return
     if (uncachedQueries.length > 0) {
       await Promise.all(
         uncachedQueries.map((query) =>
-          // @ts-expect-error ts-migrate(7006) FIXME: Parameter '_field' implicitly has an 'any' type.
           this._getPendingLoad(field, query, async (_field, _query) => {
             /* fetch, then index.  _doLoad is subclass interface */
-            // @ts-expect-error ts-migrate(2488) FIXME: Type 'void' must have a '[Symbol.iterator]()' meth... Remove this comment to see the full error message
             const [whereCacheUpdate, df] = await this._doLoad(_field, _query);
             this._cache[_field] = this._cache[_field].withColsFrom(df);
             this._whereCache = _whereCacheMerge(
@@ -540,8 +472,6 @@ Return cache keys for columns associated with this query.  May return
     return response;
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   async _getPendingLoad(field, query, fetchFn) {
     /*
     Given a query on a field, ensure that we only have a single outstanding
@@ -563,7 +493,7 @@ Return cache keys for columns associated with this query.  May return
     return this._pendingLoad[field][key];
   }
 
-  // eslint-disable-next-line class-methods-use-this, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements
+  // eslint-disable-next-line class-methods-use-this -- make sure subclass implements
   async _doLoad() {
     _subclassResponsibility();
   }
@@ -597,22 +527,19 @@ Return cache keys for columns associated with this query.  May return
   To be effective, the GC callback needs to be invoked from the undo/redo code,
   as much of the cache is pinned by that data structure.
   */
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   _gcField(field, isHot, pinnedColumns) {
-    const maxColumns = isHot ? 256 : 10;
+    const maxColumns = isHot ? 256 : 10; // maybe to aggressive?
+
     const cache = this._cache[field];
     if (cache.colIndex.size() < maxColumns) return; // trivial rejection
 
     const candidates = cache.colIndex
       .labels()
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
       .filter((col) => !pinnedColumns.includes(col));
 
     const excessCount = candidates.length + pinnedColumns.length - maxColumns;
     if (excessCount > 0) {
       const { _gcInfo } = this;
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'a' implicitly has an 'any' type.
       candidates.sort((a, b) => {
         let atime = _gcInfo.get(_columnCacheKey(field, a));
         if (atime === undefined) atime = 0;
@@ -631,17 +558,13 @@ Return cache keys for columns associated with this query.  May return
       //   )}]`
       // );
       this._cache[field] = toDrop.reduce(
-        // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'df' implicitly has an 'any' type.
         (df, col) => df.dropCol(col),
         this._cache[field]
       );
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
       toDrop.forEach((col) => _gcInfo.delete(_columnCacheKey(field, col)));
     }
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   _gcFetchCleanup(field, pinnedColumns) {
     /*
     Called during data load/fetch.  By definition, this is 'hot', so we
@@ -656,8 +579,6 @@ Return cache keys for columns associated with this query.  May return
     }
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'hints' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   _gc(hints) {
     /*
     Called from middleware, or elsewhere.  isHot is true if we are in the active store, 
@@ -670,8 +591,6 @@ Return cache keys for columns associated with this query.  May return
     );
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   _gcUpdateStats(field, dataframe) {
     /*
     called each time a query is performed, allowing the gc to update any bookkeeping
@@ -681,7 +600,6 @@ Return cache keys for columns associated with this query.  May return
     const cols = dataframe.colIndex.labels();
     const { _gcInfo } = this;
     const now = Date.now();
-    // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'c' implicitly has an 'any' type.
     cols.forEach((c) => {
       _gcInfo.set(_columnCacheKey(field, c), now);
     });
@@ -699,8 +617,6 @@ Return cache keys for columns associated with this query.  May return
 
   Do not override _clone();
   **/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'clone' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   _cloneDeeper(clone) {
     clone._cache = _shallowClone(this._cache);
     clone._gcInfo = new Map();
@@ -713,7 +629,6 @@ Return cache keys for columns associated with this query.  May return
     return clone;
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   _clone() {
     const clone = _shallowClone(this);
     this._cloneDeeper(clone);
@@ -725,7 +640,6 @@ Return cache keys for columns associated with this query.  May return
 /*
 private utility functions below
 */
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
 function _columnCacheKey(field, column) {
   return `${field}/${column}`;
 }

client/src/annoMatrix/clone.js

@@ -0,0 +1,6 @@
+/*
+Shallow clone an object, correctly handling prototype
+*/
+export default function _shallowClone(orig) {
+  return Object.assign(Object.create(Object.getPrototypeOf(orig)), orig);
+}

client/src/annoMatrix/clone.ts

@@ -1,7 +0,0 @@
-/*
-Shallow clone an object, correctly handling prototype
-*/
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export default function _shallowClone(orig: any) {
-  return Object.assign(Object.create(Object.getPrototypeOf(orig)), orig);
-}

client/src/annoMatrix/crossfilter.js

@@ -0,0 +1,284 @@
+/*
+Row crossfilter proxy for an AnnoMatrix.  This wraps Crossfilter,
+providing a number of services, and ensuring that the crossfilter and
+AnnoMatrix stay in sync:
+	- on-demand index creation as data is loaded
+	- transparently mapping between queries and crossfilter index names.
+  - for mutation of the matrix by user annotations, maintain synchronization
+    between Crossfilter and AnnoMatrix.
+*/
+import Crossfilter from "../util/typedCrossfilter";
+import { _getColumnSchema } from "./schema";
+
+function _dimensionNameFromDf(field, df) {
+  const colNames = df.colIndex.labels();
+  return _dimensionName(field, colNames);
+}
+
+function _dimensionName(field, colNames) {
+  if (!Array.isArray(colNames)) return `${field}/${colNames}`;
+  return `${field}/${colNames.join(":")}`;
+}
+
+export default class AnnoMatrixObsCrossfilter {
+  constructor(annoMatrix, _obsCrossfilter = null) {
+    this.annoMatrix = annoMatrix;
+    this.obsCrossfilter =
+      _obsCrossfilter || new Crossfilter(annoMatrix._cache.obs);
+    this.obsCrossfilter = this.obsCrossfilter.setData(annoMatrix._cache.obs);
+  }
+
+  size() {
+    return this.obsCrossfilter.size();
+  }
+
+  /**
+  Managing the associated annoMatrix.  These wrappers are necessary to 
+  make coordinated changes to BOTH the crossfilter and annoMatrix, and
+  ensure that all state stays synchronized.
+
+  See API documentation in annoMatrix.js.
+  **/
+  addObsColumn(colSchema, Ctor, value) {
+    const annoMatrix = this.annoMatrix.addObsColumn(colSchema, Ctor, value);
+    const obsCrossfilter = this.obsCrossfilter.setData(annoMatrix._cache.obs);
+    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
+  }
+
+  dropObsColumn(col) {
+    const annoMatrix = this.annoMatrix.dropObsColumn(col);
+    let { obsCrossfilter } = this;
+    const dimName = _dimensionName("obs", col);
+    if (obsCrossfilter.hasDimension(dimName)) {
+      obsCrossfilter = obsCrossfilter.delDimension(dimName);
+    }
+    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
+  }
+
+  renameObsColumn(oldCol, newCol) {
+    const annoMatrix = this.annoMatrix.renameObsColumn(oldCol, newCol);
+    const oldDimName = _dimensionName("obs", oldCol);
+    const newDimName = _dimensionName("obs", newCol);
+    let { obsCrossfilter } = this;
+    if (obsCrossfilter.hasDimension(oldDimName)) {
+      obsCrossfilter = obsCrossfilter.renameDimension(oldDimName, newDimName);
+    }
+    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
+  }
+
+  addObsAnnoCategory(col, category) {
+    const annoMatrix = this.annoMatrix.addObsAnnoCategory(col, category);
+    const dimName = _dimensionName("obs", col);
+    let { obsCrossfilter } = this;
+    if (obsCrossfilter.hasDimension(dimName)) {
+      obsCrossfilter = obsCrossfilter.delDimension(dimName);
+    }
+    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
+  }
+
+  async removeObsAnnoCategory(col, category, unassignedCategory) {
+    const annoMatrix = await this.annoMatrix.removeObsAnnoCategory(
+      col,
+      category,
+      unassignedCategory
+    );
+    const dimName = _dimensionName("obs", col);
+    let { obsCrossfilter } = this;
+    if (obsCrossfilter.hasDimension(dimName)) {
+      obsCrossfilter = obsCrossfilter.delDimension(dimName);
+    }
+    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
+  }
+
+  async setObsColumnValues(col, rowLabels, value) {
+    const annoMatrix = await this.annoMatrix.setObsColumnValues(
+      col,
+      rowLabels,
+      value
+    );
+    const dimName = _dimensionName("obs", col);
+    let { obsCrossfilter } = this;
+    if (obsCrossfilter.hasDimension(dimName)) {
+      obsCrossfilter = obsCrossfilter.delDimension(dimName);
+    }
+    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
+  }
+
+  async resetObsColumnValues(col, oldValue, newValue) {
+    const annoMatrix = await this.annoMatrix.resetObsColumnValues(
+      col,
+      oldValue,
+      newValue
+    );
+    const dimName = _dimensionName("obs", col);
+    let { obsCrossfilter } = this;
+    if (obsCrossfilter.hasDimension(dimName)) {
+      obsCrossfilter = obsCrossfilter.delDimension(dimName);
+    }
+    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
+  }
+
+  addEmbedding(colSchema) {
+    const annoMatrix = this.annoMatrix.addEmbedding(colSchema);
+    return new AnnoMatrixObsCrossfilter(annoMatrix, this.obsCrossfilter);
+  }
+
+  /**
+   * Drop the crossfilter dimension. Do not change the annoMatrix. Useful when we
+   * want to stop trackin the selection state, but aren't sure we want to blow the
+   * annomatrix cache.
+   */
+  dropDimension(field, query) {
+    const { annoMatrix } = this;
+    let { obsCrossfilter } = this;
+    const keys = annoMatrix
+      .getCacheKeys(field, query)
+      .filter((k) => k !== undefined);
+    const dimName = _dimensionName(field, keys);
+    if (obsCrossfilter.hasDimension(dimName)) {
+      obsCrossfilter = obsCrossfilter.delDimension(dimName);
+    }
+    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
+  }
+
+  /**
+  Selection state - API is identical to ImmutableTypedCrossfilter, as these
+  are just wrappers to lazy create indices.
+  **/
+
+  async select(field, query, spec) {
+    const { annoMatrix } = this;
+    let { obsCrossfilter } = this;
+
+    if (!annoMatrix?._cache?.[field]) {
+      throw new Error("Unknown field name");
+    }
+    if (field === "var") {
+      throw new Error("unable to obsSelect upon the var dimension");
+    }
+
+    // grab the data, so we can grab the index.
+    const df = await annoMatrix.fetch(field, query);
+
+    const dimName = _dimensionNameFromDf(field, df);
+    if (!obsCrossfilter.hasDimension(dimName)) {
+      // lazy index generation - add dimension when first used
+      obsCrossfilter = this._addObsCrossfilterDimension(
+        annoMatrix,
+        obsCrossfilter,
+        field,
+        df
+      );
+    }
+
+    // select
+    obsCrossfilter = obsCrossfilter.select(dimName, spec);
+    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
+  }
+
+  selectAll() {
+    /*
+		Select all on any dimension in this field.
+		*/
+    const { annoMatrix } = this;
+    const currentDims = this.obsCrossfilter.dimensionNames();
+    const obsCrossfilter = currentDims.reduce((xfltr, dim) => xfltr.select(dim, { mode: "all" }), this.obsCrossfilter);
+    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
+  }
+
+  countSelected() {
+    /* if no data yet indexed in the crossfilter, just say everything is selected */
+    if (this.obsCrossfilter.size() === 0) return this.annoMatrix.nObs;
+    return this.obsCrossfilter.countSelected();
+  }
+
+  allSelectedMask() {
+    /* if no data yet indexed in the crossfilter, just say everything is selected */
+    if (
+      this.obsCrossfilter.size() === 0 ||
+      this.obsCrossfilter.dimensionNames().length === 0
+    ) {
+      /* fake the mask */
+      return new Uint8Array(this.annoMatrix.nObs).fill(1);
+    }
+    return this.obsCrossfilter.allSelectedMask();
+  }
+
+  allSelectedLabels() {
+    /* if no data yet indexed in the crossfilter, just say everything is selected */
+    if (
+      this.obsCrossfilter.size() === 0 ||
+      this.obsCrossfilter.dimensionNames().length === 0
+    ) {
+      return this.annoMatrix.rowIndex.labels();
+    }
+
+    const mask = this.obsCrossfilter.allSelectedMask();
+    const index = this.annoMatrix.rowIndex.isubsetMask(mask);
+    return index.labels();
+  }
+
+  fillByIsSelected(array, selectedValue, deselectedValue) {
+    /* if no data yet indexed in the crossfilter, just say everything is selected */
+    if (
+      this.obsCrossfilter.size() === 0 ||
+      this.obsCrossfilter.dimensionNames().length === 0
+    ) {
+      return array.fill(selectedValue);
+    }
+    return this.obsCrossfilter.fillByIsSelected(
+      array,
+      selectedValue,
+      deselectedValue
+    );
+  }
+
+  /**
+   ** Private below
+   **/
+
+  _addObsCrossfilterDimension(annoMatrix, obsCrossfilter, field, df) {
+    if (field === "var") return obsCrossfilter;
+    const dimName = _dimensionNameFromDf(field, df);
+    const dimParams = this._getObsDimensionParams(field, df);
+    obsCrossfilter = obsCrossfilter.setData(annoMatrix._cache.obs);
+    obsCrossfilter = obsCrossfilter.addDimension(dimName, ...dimParams);
+    return obsCrossfilter;
+  }
+
+  _getColumnBaseType(field, col) {
+    /* Look up the primitive type for this field/col */
+    const colSchema = _getColumnSchema(this.annoMatrix.schema, field, col);
+    return colSchema.type;
+  }
+
+  _getObsDimensionParams(field, df) {
+    /* return the crossfilter dimensiontype type and params for this field/dataframe */
+
+    if (field === "emb") {
+      /* assumed to be 2D */
+      return ["spatial", df.icol(0).asArray(), df.icol(1).asArray()];
+    }
+
+    /* assumed to be 1D */
+    const col = df.icol(0);
+    const colName = df.colIndex.getLabel(0);
+    const type = this._getColumnBaseType(field, colName);
+    if (type === "string" || type === "categorical" || type === "boolean") {
+      return ["enum", col.asArray()];
+    }
+    if (type === "int32") {
+      return ["scalar", col.asArray(), Int32Array];
+    }
+    if (type === "float32") {
+      return ["scalar", col.asArray(), Float32Array];
+    }
+    // Currently not supporting boolean and categorical types.
+    console.error(
+      `Warning - unknown metadata schema (${type}) for field ${field} ${colName}.`
+    );
+    // skip it - we don't know what to do with this type
+
+    return undefined;
+  }
+}

client/src/annoMatrix/crossfilter.ts

@@ -1,389 +0,0 @@
-/*
-Row crossfilter proxy for an AnnoMatrix.  This wraps Crossfilter,
-providing a number of services, and ensuring that the crossfilter and
-AnnoMatrix stay in sync:
-	- on-demand index creation as data is loaded
-	- transparently mapping between queries and crossfilter index names.
-  - for mutation of the matrix by user annotations, maintain synchronization
-    between Crossfilter and AnnoMatrix.
-*/
-import Crossfilter from "../util/typedCrossfilter";
-import { _getColumnSchema } from "./schema";
-
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-function _dimensionNameFromDf(field, df) {
-  const colNames = df.colIndex.labels();
-  return _dimensionName(field, colNames);
-}
-
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-function _dimensionName(field, colNames) {
-  if (!Array.isArray(colNames)) return `${field}/${colNames}`;
-  return `${field}/${colNames.join(":")}`;
-}
-
-export default class AnnoMatrixObsCrossfilter {
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  constructor(annoMatrix, _obsCrossfilter = null) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (this as any).annoMatrix = annoMatrix;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (this as any).obsCrossfilter =
-      _obsCrossfilter || new Crossfilter(annoMatrix._cache.obs);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (this as any).obsCrossfilter = (this as any).obsCrossfilter.setData(
-      annoMatrix._cache.obs
-    );
-  }
-
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  size() {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    return (this as any).obsCrossfilter.size();
-  }
-
-  /**
-  Managing the associated annoMatrix.  These wrappers are necessary to
-  make coordinated changes to BOTH the crossfilter and annoMatrix, and
-  ensure that all state stays synchronized.
-
-  See API documentation in annoMatrix.js.
-  **/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  addObsColumn(colSchema, Ctor, value) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const annoMatrix = (this as any).annoMatrix.addObsColumn(
-      colSchema,
-      Ctor,
-      value
-    );
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const obsCrossfilter = (this as any).obsCrossfilter.setData(
-      annoMatrix._cache.obs
-    );
-    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
-  }
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  dropObsColumn(col) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const annoMatrix = (this as any).annoMatrix.dropObsColumn(col);
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
-    let { obsCrossfilter } = this;
-    const dimName = _dimensionName("obs", col);
-    if (obsCrossfilter.hasDimension(dimName)) {
-      obsCrossfilter = obsCrossfilter.delDimension(dimName);
-    }
-    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
-  }
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'oldCol' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  renameObsColumn(oldCol, newCol) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const annoMatrix = (this as any).annoMatrix.renameObsColumn(oldCol, newCol);
-    const oldDimName = _dimensionName("obs", oldCol);
-    const newDimName = _dimensionName("obs", newCol);
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
-    let { obsCrossfilter } = this;
-    if (obsCrossfilter.hasDimension(oldDimName)) {
-      obsCrossfilter = obsCrossfilter.renameDimension(oldDimName, newDimName);
-    }
-    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
-  }
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  addObsAnnoCategory(col, category) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const annoMatrix = (this as any).annoMatrix.addObsAnnoCategory(
-      col,
-      category
-    );
-    const dimName = _dimensionName("obs", col);
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
-    let { obsCrossfilter } = this;
-    if (obsCrossfilter.hasDimension(dimName)) {
-      obsCrossfilter = obsCrossfilter.delDimension(dimName);
-    }
-    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
-  }
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  async removeObsAnnoCategory(col, category, unassignedCategory) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const annoMatrix = await (this as any).annoMatrix.removeObsAnnoCategory(
-      col,
-      category,
-      unassignedCategory
-    );
-    const dimName = _dimensionName("obs", col);
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
-    let { obsCrossfilter } = this;
-    if (obsCrossfilter.hasDimension(dimName)) {
-      obsCrossfilter = obsCrossfilter.delDimension(dimName);
-    }
-    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
-  }
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  async setObsColumnValues(col, rowLabels, value) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const annoMatrix = await (this as any).annoMatrix.setObsColumnValues(
-      col,
-      rowLabels,
-      value
-    );
-    const dimName = _dimensionName("obs", col);
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
-    let { obsCrossfilter } = this;
-    if (obsCrossfilter.hasDimension(dimName)) {
-      obsCrossfilter = obsCrossfilter.delDimension(dimName);
-    }
-    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
-  }
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  async resetObsColumnValues(col, oldValue, newValue) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const annoMatrix = await (this as any).annoMatrix.resetObsColumnValues(
-      col,
-      oldValue,
-      newValue
-    );
-    const dimName = _dimensionName("obs", col);
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
-    let { obsCrossfilter } = this;
-    if (obsCrossfilter.hasDimension(dimName)) {
-      obsCrossfilter = obsCrossfilter.delDimension(dimName);
-    }
-    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
-  }
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  addEmbedding(colSchema) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const annoMatrix = (this as any).annoMatrix.addEmbedding(colSchema);
-    return new AnnoMatrixObsCrossfilter(
-      annoMatrix,
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).obsCrossfilter
-    );
-  }
-
-  /**
-   * Drop the crossfilter dimension. Do not change the annoMatrix. Useful when we
-   * want to stop trackin the selection state, but aren't sure we want to blow the
-   * annomatrix cache.
-   */
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  dropDimension(field, query) {
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Anno... Remove this comment to see the full error message
-    const { annoMatrix } = this;
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
-    let { obsCrossfilter } = this;
-    const keys = annoMatrix
-      .getCacheKeys(field, query)
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'k' implicitly has an 'any' type.
-      .filter((k) => k !== undefined);
-    const dimName = _dimensionName(field, keys);
-    if (obsCrossfilter.hasDimension(dimName)) {
-      obsCrossfilter = obsCrossfilter.delDimension(dimName);
-    }
-    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
-  }
-
-  /**
-  Selection state - API is identical to ImmutableTypedCrossfilter, as these
-  are just wrappers to lazy create indices.
-  **/
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  async select(field, query, spec) {
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Anno... Remove this comment to see the full error message
-    const { annoMatrix } = this;
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
-    let { obsCrossfilter } = this;
-
-    if (!annoMatrix?._cache?.[field]) {
-      throw new Error("Unknown field name");
-    }
-    if (field === "var") {
-      throw new Error("unable to obsSelect upon the var dimension");
-    }
-
-    // grab the data, so we can grab the index.
-    const df = await annoMatrix.fetch(field, query);
-
-    const dimName = _dimensionNameFromDf(field, df);
-    if (!obsCrossfilter.hasDimension(dimName)) {
-      // lazy index generation - add dimension when first used
-      obsCrossfilter = this._addObsCrossfilterDimension(
-        annoMatrix,
-        obsCrossfilter,
-        field,
-        df
-      );
-    }
-
-    // select
-    obsCrossfilter = obsCrossfilter.select(dimName, spec);
-    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
-  }
-
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  selectAll() {
-    /*
-		Select all on any dimension in this field.
-		*/
-    // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Anno... Remove this comment to see the full error message
-    const { annoMatrix } = this;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const currentDims = (this as any).obsCrossfilter.dimensionNames();
-    const obsCrossfilter = currentDims.reduce(
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'xfltr' implicitly has an 'any' type.
-      (xfltr, dim) => xfltr.select(dim, { mode: "all" }),
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).obsCrossfilter
-    ); // eslint-disable-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
-  }
-
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  countSelected() {
-    /* if no data yet indexed in the crossfilter, just say everything is selected */
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    if ((this as any).obsCrossfilter.size() === 0)
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      return (this as any).annoMatrix.nObs;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    return (this as any).obsCrossfilter.countSelected();
-  }
-
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  allSelectedMask() {
-    /* if no data yet indexed in the crossfilter, just say everything is selected */
-    if (
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).obsCrossfilter.size() === 0 ||
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).obsCrossfilter.dimensionNames().length === 0
-    ) {
-      /* fake the mask */
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      return new Uint8Array((this as any).annoMatrix.nObs).fill(1);
-    }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    return (this as any).obsCrossfilter.allSelectedMask();
-  }
-
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  allSelectedLabels() {
-    /* if no data yet indexed in the crossfilter, just say everything is selected */
-    if (
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).obsCrossfilter.size() === 0 ||
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).obsCrossfilter.dimensionNames().length === 0
-    ) {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      return (this as any).annoMatrix.rowIndex.labels();
-    }
-
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const mask = (this as any).obsCrossfilter.allSelectedMask();
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    const index = (this as any).annoMatrix.rowIndex.isubsetMask(mask);
-    return index.labels();
-  }
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'array' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  fillByIsSelected(array, selectedValue, deselectedValue) {
-    /* if no data yet indexed in the crossfilter, just say everything is selected */
-    if (
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).obsCrossfilter.size() === 0 ||
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).obsCrossfilter.dimensionNames().length === 0
-    ) {
-      return array.fill(selectedValue);
-    }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    return (this as any).obsCrossfilter.fillByIsSelected(
-      array,
-      selectedValue,
-      deselectedValue
-    );
-  }
-
-  /**
-   ** Private below
-   **/
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  _addObsCrossfilterDimension(annoMatrix, obsCrossfilter, field, df) {
-    if (field === "var") return obsCrossfilter;
-    const dimName = _dimensionNameFromDf(field, df);
-    const dimParams = this._getObsDimensionParams(field, df);
-    obsCrossfilter = obsCrossfilter.setData(annoMatrix._cache.obs);
-    // @ts-expect-error ts-migrate(2488) FIXME: Type 'any[] | undefined' must have a '[Symbol.iter... Remove this comment to see the full error message
-    obsCrossfilter = obsCrossfilter.addDimension(dimName, ...dimParams);
-    return obsCrossfilter;
-  }
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  _getColumnBaseType(field, col) {
-    /* Look up the primitive type for this field/col */
-    const colSchema = _getColumnSchema(
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      (this as any).annoMatrix.schema,
-      field,
-      col
-    );
-    return colSchema.type;
-  }
-
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
-  _getObsDimensionParams(field, df) {
-    /* return the crossfilter dimensiontype type and params for this field/dataframe */
-
-    if (field === "emb") {
-      /* assumed to be 2D */
-      return ["spatial", df.icol(0).asArray(), df.icol(1).asArray()];
-    }
-
-    /* assumed to be 1D */
-    const col = df.icol(0);
-    const colName = df.colIndex.getLabel(0);
-    const type = this._getColumnBaseType(field, colName);
-    if (type === "string" || type === "categorical" || type === "boolean") {
-      return ["enum", col.asArray()];
-    }
-    if (type === "int32") {
-      return ["scalar", col.asArray(), Int32Array];
-    }
-    if (type === "float32") {
-      return ["scalar", col.asArray(), Float32Array];
-    }
-    // Currently not supporting boolean and categorical types.
-    console.error(
-      `Warning - unknown metadata schema (${type}) for field ${field} ${colName}.`
-    );
-    // skip it - we don't know what to do with this type
-
-    return undefined;
-  }
-}

client/src/annoMatrix/fetchHelpers.js

@@ -0,0 +1,25 @@
+export { doBinaryRequest, doFetch } from "../util/actionHelpers";
+
+/* double URI encode - needed for query-param filters */
+export function _dubEncURIComp(s) {
+  return encodeURIComponent(encodeURIComponent(s));
+}
+
+/* currently unused, consider deleting */
+export function _fetchResult(promise) {
+  let _status = "pending";
+  const res = promise.then(
+    (r) => {
+      _status = "success";
+      return r;
+    },
+    (e) => {
+      _status = "error";
+      throw e;
+    }
+  );
+
+  res.status = () => _status;
+
+  return res;
+}

client/src/annoMatrix/fetchHelpers.ts

@@ -1,29 +0,0 @@
-export { doBinaryRequest, doFetch } from "../util/actionHelpers";
-
-/* double URI encode - needed for query-param filters */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export function _dubEncURIComp(s: any) {
-  return encodeURIComponent(encodeURIComponent(s));
-}
-
-/* currently unused, consider deleting */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-export function _fetchResult(promise: any) {
-  let _status = "pending";
-  const res = promise.then(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (r: any) => {
-      _status = "success";
-      return r;
-    },
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (e: any) => {
-      _status = "error";
-      throw e;
-    }
-  );
-
-  res.status = () => _status;
-
-  return res;
-}

client/src/annoMatrix/loader.js

@@ -27,9 +27,6 @@ import {
 const promiseThrottle = new PromiseLimit(5);
 
 export default class AnnoMatrixLoader extends AnnoMatrix {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-  baseURL: any;
-
   /*
   AnnoMatrix implementation which proxies to HTTP server using the CXG REST API.
   Used as the base (non-view) instance.
@@ -40,8 +37,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     new AnnoMatrixLoader(serverBaseURL, schema) -> instance
 
   */
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  constructor(baseURL, schema) {
-  constructor(baseURL: any, schema: any) {
     const { nObs, nVar } = schema.dataframe;
     super(schema, nObs, nVar);
 
@@ -56,8 +52,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
   /**
    ** Public.  API described in base class.
    **/
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  addObsAnnoCategory(col, category) {
-  addObsAnnoCategory(col: any, category: any) {
     /*
     Add a new category (aka label) to the schema for an obs column.
     */
@@ -69,15 +64,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+  async removeObsAnnoCategory(col, category, unassignedCategory) {
-  async removeObsAnnoCategory(
-    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-    col: any,
-    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-    category: any,
-    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-    unassignedCategory: any
-  ) {
     /*
     Remove a single "category" (aka "label") from the data & schema of an obs column.
     */
@@ -97,8 +84,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  dropObsColumn(col) {
-  dropObsColumn(col: any) {
     /*
 		drop column from field
 		*/
@@ -106,14 +92,11 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     _writableCheck(colSchema); // throws on error
 
     const newAnnoMatrix = this._clone();
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
-    newAnnoMatrix._cache.obs = (this as any)._cache.obs.dropCol(col);
     newAnnoMatrix.schema = removeObsAnnoColumn(this.schema, col);
     return newAnnoMatrix;
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   addObsColumn(colSchema, Ctor, value) {
     /*
 		add a column to field, initializing with value.  Value may 
@@ -126,8 +109,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     const colName = colSchema.name;
     if (
       _getColumnSchema(this.schema, "obs", colName) ||
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      this._cache.obs.hasCol(colName)
-      (this as any)._cache.obs.hasCol(colName)
     ) {
       throw new Error("column already exists");
     }
@@ -143,8 +125,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     } else {
       data = new Ctor(this.nObs).fill(value);
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    newAnnoMatrix._cache.obs = this._cache.obs.withCol(colName, data);
-    newAnnoMatrix._cache.obs = (this as any)._cache.obs.withCol(colName, data);
     normalizeWritableCategoricalSchema(
       colSchema,
       newAnnoMatrix._cache.obs.col(colName)
@@ -153,18 +134,15 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'oldCol' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   renameObsColumn(oldCol, newCol) {
     /*
     Rename the obs oldColName to newColName.  oldCol must be writable.
     */
     const oldColSchema = _getColumnSchema(this.schema, "obs", oldCol);
-    _writableCheck(oldColSchema);
+    _writableCheck(oldColSchema); // throws on error
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+
-    const value = (this as any)._cache.obs.hasCol(oldCol)
+    const value = this._cache.obs.hasCol(oldCol)
-      ? // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      ? this._cache.obs.col(oldCol).asArray()
-        (this as any)._cache.obs.col(oldCol).asArray()
       : undefined;
     return this.dropObsColumn(oldCol).addObsColumn(
       {
@@ -176,8 +154,6 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     );
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   async setObsColumnValues(col, rowLabels, value) {
     /*
 		Set all rows identified by rowLabels to value.
@@ -187,13 +163,11 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
 
     // ensure that we have the data in cache before we manipulate it
     await this.fetch("obs", col);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    if (!this._cache.obs.hasCol(col))
-    if (!(this as any)._cache.obs.hasCol(col))
       throw new Error("Internal error - user annotation data missing");
 
     const rowIndices = this.rowIndex.getOffsets(rowLabels);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    const data = this._cache.obs.col(col).asArray().slice();
-    const data = (this as any)._cache.obs.col(col).asArray().slice();
     for (let i = 0, len = rowIndices.length; i < len; i += 1) {
       const idx = rowIndices[i];
       if (idx === undefined) throw new Error("Unknown row label");
@@ -201,11 +175,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     }
 
     const newAnnoMatrix = this._clone();
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    newAnnoMatrix._cache.obs = this._cache.obs.replaceColData(col, data);
-    newAnnoMatrix._cache.obs = (this as any)._cache.obs.replaceColData(
-      col,
-      data
-    );
     const { categories } = colSchema;
     if (!categories?.includes(value)) {
       newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, value);
@@ -213,8 +183,6 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   async resetObsColumnValues(col, oldValue, newValue) {
     /*
     Set all rows with value 'oldValue' to 'newValue'.
@@ -228,22 +196,16 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
 
     // ensure that we have the data in cache before we manipulate it
     await this.fetch("obs", col);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    if (!this._cache.obs.hasCol(col))
-    if (!(this as any)._cache.obs.hasCol(col))
       throw new Error("Internal error - user annotation data missing");
 
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    const data = this._cache.obs.col(col).asArray().slice();
-    const data = (this as any)._cache.obs.col(col).asArray().slice();
     for (let i = 0, l = data.length; i < l; i += 1) {
       if (data[i] === oldValue) data[i] = newValue;
     }
 
     const newAnnoMatrix = this._clone();
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    newAnnoMatrix._cache.obs = this._cache.obs.replaceColData(col, data);
-    newAnnoMatrix._cache.obs = (this as any)._cache.obs.replaceColData(
-      col,
-      data
-    );
     const { categories } = colSchema;
     if (!categories?.includes(newValue)) {
       newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, newValue);
@@ -251,8 +213,6 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   addEmbedding(colSchema) {
     /*
     add new layout to the obs embeddings
@@ -270,8 +230,6 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
   /**
    ** Private below
    **/
-  // @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixLoader' is n... Remove this comment to see the full error message
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   async _doLoad(field, query) {
     /*
     _doLoad - evaluates the query against the field. Returns:
@@ -310,7 +268,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
       result.colIndex.labels()
     );
 
-    result = normalizeResponse(field, this.schema, result);
+    result = normalizeResponse(field, query, this.schema, result);
 
     return [whereCacheUpdate, result];
   }
@@ -320,14 +278,12 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
 Utility functions below
 */
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
 function _writableCheck(colSchema) {
   if (!colSchema?.writable) {
     throw new Error("Unknown or readonly obs column");
   }
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
 function _writableCategoryTypeCheck(colSchema) {
   _writableCheck(colSchema);
   if (colSchema.type !== "categorical") {
@@ -335,7 +291,6 @@ function _writableCategoryTypeCheck(colSchema) {
   }
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type.
 function _embLoader(baseURL, _field, query) {
   _expectSimpleQuery(query);
 
@@ -345,7 +300,6 @@ function _embLoader(baseURL, _field, query) {
   return () => doBinaryRequest(url);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type.
 function _obsOrVarLoader(baseURL, field, query) {
   _expectSimpleQuery(query);
 
@@ -355,7 +309,6 @@ function _obsOrVarLoader(baseURL, field, query) {
   return () => doBinaryRequest(url);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type.
 function _XLoader(baseURL, field, query) {
   _expectComplexQuery(query);
 

client/src/annoMatrix/middleware.js

@@ -11,8 +11,7 @@ Undoable metareducer and the AnnoMatrix private API.  It would be helpful
 to make the Undoable interface better factored.
 */
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+const annoMatrixGC = (store) => (next) => (action) => {
-const annoMatrixGC = (store: any) => (next: any) => (action: any) => {
   if (_itIsTimeForGC()) {
     _doGC(store);
   }
@@ -35,8 +34,7 @@ function _itIsTimeForGC() {
   return false;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function _doGC(store) {
-function _doGC(store: any) {
   const state = store.getState();
 
   // these should probably be a function imported from undoable.js, etc, as
@@ -45,10 +43,8 @@ function _doGC(store: any) {
   const undoableFuture = state["@@undoable/future"];
   const undoableStack = undoablePast
     .concat(undoableFuture)
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    .flatMap((snapshot) =>
-    .flatMap((snapshot: any) =>
+      snapshot.filter((v) => v[0] === "annoMatrix").map((v) => v[1])
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      snapshot.filter((v: any) => v[0] === "annoMatrix").map((v: any) => v[1])
     );
   const currentAnnoMatrix = state.annoMatrix;
 
@@ -57,18 +53,14 @@ function _doGC(store: any) {
   as our current gc algo is more aggressive with those not hot.
   */
   const allAnnoMatrices = new Map(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    undoableStack.map((m) => [m, { isHot: false }])
-    undoableStack.map((m: any) => [m, { isHot: false }])
   );
   let am = currentAnnoMatrix;
   while (am) {
     allAnnoMatrices.set(am, { isHot: true });
     am = am.viewOf;
   }
-  allAnnoMatrices.forEach((hints, annoMatrix) =>
+  allAnnoMatrices.forEach((hints, annoMatrix) => annoMatrix._gc(hints));
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (annoMatrix as any)._gc(hints)
-  );
 }
 
 export default annoMatrixGC;

client/src/annoMatrix/normalize.js

@@ -5,14 +5,8 @@ import {
   overflowCategoryLabel,
   globalConfig,
 } from "../globals";
-import { Dataframe } from "../util/dataframe";
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function normalizeResponse(field, query, schema, response) {
-export function normalizeResponse(
-  field: string,
-  schema: any, // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  response: Dataframe
-): Dataframe {
   /**
    * There are a number of assumptions in the front-end about data typing and data
    * characteristics. This routine will normalize a server response dataframe
@@ -65,8 +59,7 @@ export function normalizeResponse(
   return response;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+function castColumnToBoolean(df, label) {
-function castColumnToBoolean(df: Dataframe, label: any): Dataframe {
   const colData = df.col(label).asArray();
   const newColData = new Array(colData.length);
   for (let i = 0; i < colData.length; i += 1) newColData[i] = !!colData[i];
@@ -74,8 +67,7 @@ function castColumnToBoolean(df: Dataframe, label: any): Dataframe {
   return df;
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function normalizeWritableCategoricalSchema(colSchema, col) {
-export function normalizeWritableCategoricalSchema(colSchema: any, col: any) {
   /*
   Ensure all enum writable / categorical schema have a categories array, that
   the categories array contains all unique values in the data array, AND that
@@ -91,15 +83,9 @@ export function normalizeWritableCategoricalSchema(colSchema: any, col: any) {
   return colSchema;
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function normalizeCategorical(df, colLabel, colSchema) {
-export function normalizeCategorical(
-  df: Dataframe,
-  colLabel: any, // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  colSchema: any // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-) {
   /*
   If writable, ensure schema matches data and we have an unassigned label
-
   If not writable, ensure schema matches data and that we consolidate labels in excess
   of "top N" into an overflow labels.
   */

client/src/annoMatrix/query.js

@@ -10,8 +10,7 @@ import { _dubEncURIComp } from "./fetchHelpers";
  * @param {object | string} query - the query
  * @returns {object | string} - the normalized query
  */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _queryValidate(query) {
-export function _queryValidate(query: any) {
   if (typeof query !== "object") return query;
 
   if (query.where && query.summarize)
@@ -41,13 +40,11 @@ export function _queryValidate(query: any) {
   throw new Error("query must specify one of where or summarize");
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _expectSimpleQuery(query) {
-export function _expectSimpleQuery(query: any) {
   if (typeof query === "object") throw new Error("expected simple query");
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _expectComplexQuery(query) {
-export function _expectComplexQuery(query: any) {
   if (typeof query !== "object") throw new Error("expected complex query");
 }
 
@@ -58,8 +55,7 @@ export function _expectComplexQuery(query: any) {
  * @param {string|object} query
  * @returns the key
  */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _queryCacheKey(field, query) {
-export function _queryCacheKey(field: any, query: any) {
   if (typeof query === "object") {
     // complex query
     if (query.where) {
@@ -88,25 +84,22 @@ export function _queryCacheKey(field: any, query: any) {
   return `${field}/${query}`;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function _urlEncodeWhereQuery(q) {
-function _urlEncodeWhereQuery(q: any) {
   const { field: queryField, column: queryColumn, value: queryValue } = q;
   return `${_dubEncURIComp(queryField)}:${_dubEncURIComp(
     queryColumn
   )}=${_dubEncURIComp(queryValue)}`;
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+function _urlEncodeSummarizeQuery(q) {
-function _urlEncodeSummarizeQuery(q: any) {
   const { method, field, column, values } = q;
-  const filter = values // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  const filter = values
-    .map((value: any) => _urlEncodeWhereQuery({ field, column, value }))
+    .map((value) => _urlEncodeWhereQuery({ field, column, value }))
     .join("&");
   return `method=${method}&${filter}`;
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _urlEncodeComplexQuery(q) {
-export function _urlEncodeComplexQuery(q: any) {
   if (typeof q === "object") {
     if (q.where) {
       return _urlEncodeWhereQuery(q.where);
@@ -118,8 +111,7 @@ export function _urlEncodeComplexQuery(q: any) {
   throw new Error("Unrecognized complex query type");
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _urlEncodeLabelQuery(colKey, q) {
-export function _urlEncodeLabelQuery(colKey: any, q: any) {
   if (!colKey) throw new Error("Unsupported query by name");
   if (typeof q !== "string") throw new Error("Query must be a simple label.");
   return `${colKey}=${encodeURIComponent(q)}`;
@@ -128,8 +120,7 @@ export function _urlEncodeLabelQuery(colKey: any, q: any) {
 /**
  * Generate the column key the server will send us for this query.
  */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _hashStringValues(arrayOfString) {
-export function _hashStringValues(arrayOfString: any) {
   const hash = sha1(arrayOfString.join(""));
   return hash;
 }

client/src/annoMatrix/schema.js

@@ -1,8 +1,7 @@
 /*
 Private helper functions related to schema
 */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _getColumnSchema(schema, field, col) {
-export function _getColumnSchema(schema: any, field: any, col: any) {
   /* look up the column definition */
   switch (field) {
     case "obs":
@@ -24,14 +23,12 @@ export function _getColumnSchema(schema: any, field: any, col: any) {
   }
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function _isIndex(schema, field, col) {
-export function _isIndex(schema: any, field: any, col: any): boolean {
   const index = schema.annotations?.[field].index;
   return index && index === col;
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+export function _getColumnDimensionNames(schema, field, col) {
-export function _getColumnDimensionNames(schema: any, field: any, col: any) {
   /*
 		field/col may be an alias for multiple columns. Currently used to map ND 
 		values to 1D dataframe columns for embeddings/layout. Signified by the presence
@@ -44,8 +41,6 @@ export function _getColumnDimensionNames(schema: any, field: any, col: any) {
   return colSchema.dims || [col];
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
 export function _schemaColumns(schema, field) {
   switch (field) {
     case "obs":
@@ -59,21 +54,13 @@ export function _schemaColumns(schema, field) {
   }
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
 export function _getWritableColumns(schema, field) {
   if (field !== "obs") return [];
-  return (
+  return schema.annotations.obs.columns
-    schema.annotations.obs.columns
+    .filter((v) => v.writable)
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'v' implicitly has an 'any' type.
+    .map((v) => v.name);
-      .filter((v) => v.writable)
-      // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'v' implicitly has an 'any' type.
-      .map((v) => v.name)
-  );
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
 export function _isContinuousType(schema) {
   const { type } = schema;
   return !(type === "string" || type === "boolean" || type === "categorical");

client/src/annoMatrix/viewCreators.js

@@ -5,8 +5,7 @@ instances of AnnoMatrix, implementing common UI functions.
 
 import { AnnoMatrixRowSubsetView, AnnoMatrixClipView } from "./views";
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export function isubsetMask(annoMatrix, obsMask) {
-export function isubsetMask(annoMatrix: any, obsMask: any) {
   /*
 		Subset annomatrix to contain the rows which have truish value in the mask.
     Maks length must equal annoMatrix.nObs (row count).
@@ -14,8 +13,6 @@ export function isubsetMask(annoMatrix: any, obsMask: any) {
   return isubset(annoMatrix, _maskToList(obsMask));
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
 export function isubset(annoMatrix, obsOffsets) {
   /*
 		Subset annomatrix to contain the positions contained in the obsOffsets array
@@ -28,8 +25,6 @@ export function isubset(annoMatrix, obsOffsets) {
   return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
 export function subset(annoMatrix, obsLabels) {
   /*
 		subset based on labels
@@ -38,8 +33,6 @@ export function subset(annoMatrix, obsLabels) {
   return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
 export function subsetByIndex(annoMatrix, obsIndex) {
   /*
   subset based upon the new obs index.
@@ -47,8 +40,6 @@ export function subsetByIndex(annoMatrix, obsIndex) {
   return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex);
 }
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
 export function clip(annoMatrix, qmin, qmax) {
   /*
 		Create a view that clips all continuous data to the [min, max] range.
@@ -62,7 +53,6 @@ export function clip(annoMatrix, qmin, qmax) {
 Private utility functions below
 */
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'mask' implicitly has an 'any' type.
 function _maskToList(mask) {
   /* convert masks to lists - method wastes space, but is fast */
   if (!mask) {

client/src/annoMatrix/views.js

@@ -9,31 +9,21 @@ import { _whereCacheCreate } from "./whereCache";
 import { _isContinuousType, _getColumnSchema } from "./schema";
 
 class AnnoMatrixView extends AnnoMatrix {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  constructor(viewOf, rowIndex = null) {
-  constructor(viewOf: any, rowIndex = null) {
-    // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
     const nObs = rowIndex ? rowIndex.size() : viewOf.nObs;
     super(viewOf.schema, nObs, viewOf.nVar, rowIndex || viewOf.rowIndex);
     this.viewOf = viewOf;
     this.isView = true;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  addObsAnnoCategory(col, category) {
-  addObsAnnoCategory(col: any, category: any) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = this.viewOf.addObsAnnoCategory(col, category);
     newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
     return newAnnoMatrix;
   }
 
-  async removeObsAnnoCategory(
+  async removeObsAnnoCategory(col, category, unassignedCategory) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    col: any,
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    category: any,
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    unassignedCategory: any
-  ) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = await this.viewOf.removeObsAnnoCategory(
       col,
@@ -44,8 +34,7 @@ class AnnoMatrixView extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  dropObsColumn(col) {
-  dropObsColumn(col: any) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = this.viewOf.dropObsColumn(col);
     newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
@@ -53,24 +42,21 @@ class AnnoMatrixView extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  addObsColumn(colSchema, Ctor, value) {
-  addObsColumn(colSchema: any, Ctor: any, value: any) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = this.viewOf.addObsColumn(colSchema, Ctor, value);
     newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  renameObsColumn(oldCol, newCol) {
-  renameObsColumn(oldCol: any, newCol: any) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = this.viewOf.renameObsColumn(oldCol, newCol);
     newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  async setObsColumnValues(col, rowLabels, value) {
-  async setObsColumnValues(col: any, rowLabels: any, value: any) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = await this.viewOf.setObsColumnValues(
       col,
@@ -82,8 +68,7 @@ class AnnoMatrixView extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  async resetObsColumnValues(col, oldValue, newValue) {
-  async resetObsColumnValues(col: any, oldValue: any, newValue: any) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = await this.viewOf.resetObsColumnValues(
       col,
@@ -95,8 +80,7 @@ class AnnoMatrixView extends AnnoMatrix {
     return newAnnoMatrix;
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  addEmbedding(colSchema) {
-  addEmbedding(colSchema: any) {
     const newAnnoMatrix = this._clone();
     newAnnoMatrix.viewOf = this.viewOf.addEmbedding(colSchema);
     newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
@@ -108,22 +92,17 @@ class AnnoMatrixMapView extends AnnoMatrixView {
   /*
 	A view which knows how to transform its data.
 	*/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'viewOf' implicitly has an 'any' type.
   constructor(viewOf, mapFn) {
     super(viewOf);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    this.mapFn = mapFn;
-    (this as any).mapFn = mapFn;
   }
 
-  // @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixMapView' is ... Remove this comment to see the full error message
   async _doLoad(field, query) {
     const df = await this.viewOf._fetch(field, query);
-    // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colData' implicitly has an 'any' type.
     const dfMapped = df.mapColumns((colData, colIdx) => {
       const colLabel = df.colIndex.getLabel(colIdx);
       const colSchema = _getColumnSchema(this.schema, field, colLabel);
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+      return this.mapFn(field, colLabel, colSchema, colData, df);
-      return (this as any).mapFn(field, colLabel, colSchema, colData, df);
     });
     const whereCacheUpdate = _whereCacheCreate(
       field,
@@ -138,17 +117,12 @@ export class AnnoMatrixClipView extends AnnoMatrixMapView {
   /*
 	A view which is a clipped transformation of its parent
 	*/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'viewOf' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   constructor(viewOf, qmin, qmax) {
-    // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
     super(viewOf, (field, colLabel, colSchema, colData, df) =>
       _clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax)
     );
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+    this.isClipped = true;
-    (this as any).isClipped = true;
+    this.clipRange = [qmin, qmax];
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-    (this as any).clipRange = [qmin, qmax];
     Object.seal(this);
   }
 }
@@ -157,15 +131,11 @@ export class AnnoMatrixRowSubsetView extends AnnoMatrixView {
   /*
 	A view which is a subset of total rows.
 	*/
-  // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'viewOf' implicitly has an 'any' type.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   constructor(viewOf, rowIndex) {
     super(viewOf, rowIndex);
     Object.seal(this);
   }
 
-  // @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixRowSubsetVie... Remove this comment to see the full error message
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   async _doLoad(field, query) {
     const df = await this.viewOf._fetch(field, query);
 
@@ -188,7 +158,6 @@ export class AnnoMatrixRowSubsetView extends AnnoMatrixView {
 Utility functions below
 */
 
-// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
 function _clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax) {
   /* only clip obs and var scalar columns */
   if (field !== "obs" && field !== "X") return colData;