fix: correct opacity prop typo and style object in centroid labels (#2767)

Yeah that makes sense! Mergingg

.github/workflows/push_tests.yml

@@ -69,10 +69,21 @@ jobs:
       - name: Install dependencies
         run: make pydist install-dist dev-env-server
       - name: Unit tests
-        run: |
-          make unit-test-server unit-test-client
-          bash <(curl -s https://codecov.io/bash) -y .codecov.yml -k server -cF server,python,unitTest
-          cd client && ./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,unitTest
+        run: make unit-test-server unit-test-client
+      - name: Generate server coverage XML
+        run: coverage xml -o server/coverage.xml
+      - name: Upload server coverage
+        uses: codecov/codecov-action@v5
+        with:
+          flags: server,python,unitTest
+          files: ./server/coverage.xml
+          fail_ci_if_error: false
+      - name: Upload client coverage
+        uses: codecov/codecov-action@v5
+        with:
+          flags: frontend,javascript,unitTest
+          files: ./client/coverage/lcov.info
+          fail_ci_if_error: false
 
   smoke-tests:
     runs-on: macos-latest
@@ -102,9 +113,7 @@ jobs:
           pip install setuptools
           make pydist install-dist
       - name: Smoke tests (without annotations feature)
-        run: |
-          cd client && make smoke-test
-          ./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,smokeTest
+        run: cd client && make smoke-test
 
   # TODO: reinstate: https://github.com/chanzuckerberg/cellxgene/issues/2544
   # smoke-tests-annotations:

LICENSE

@@ -1,6 +1,6 @@
-The MIT License (MIT)
+# The MIT License (MIT)
 
-Copyright (c) 2017-2023 Chan Zuckerberg Initiative
+Copyright (c) 2017-2026 Chan Zuckerberg Initiative
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

README.md

@@ -82,6 +82,13 @@ extension could be directly contributed, which would make it available for a wid
 
 See the [CELLxGENE extensions](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/community-extensions.md) section of our documentation for examples of community use and CELLxGENE extensions.
 
+### Trademarks
+
+CZ CELLXGENE, CZ CELLXGENE DISCOVER, and CZ CELLXGENE ANNOTATE are trademarks of the Chan Zuckerberg Initiative. All rights reserved.
+
+Use, reuse, modification, and re-distribution of the source code in this repository is subject to the terms of the applicable open source [license](LICENSE.txt). However, that license does not grant permission to use the trademarks without separate, express permission from the Chan Zuckerberg Initiative.
+
+
 ### Security
 
 If you believe you have found a security issue, we would appreciate notification. Please send email to <security@chanzuckerberg.com>.

SECURITY.md

@@ -0,0 +1,3 @@
+# Reporting Security Issues
+
+If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).

client/__tests__/e2e/config.js

@@ -1,4 +1,4 @@
-import * as ENV_DEFAULT from "Code/cellxgene/environment.default.json";
+import * as ENV_DEFAULT from "../../../environment.default.json";
 
 export const jestEnv = process.env.JEST_ENV || ENV_DEFAULT.JEST_ENV;
 export const appUrlBase =

client/__tests__/e2e/puppeteer.setup.js

@@ -5,8 +5,8 @@
  */
 
 import { setDefaultOptions } from "expect-puppeteer";
-import * as ENV_DEFAULT from "Code/cellxgene/environment.default.json";
 import { isDebug, isDev } from "./config";
+import * as ENV_DEFAULT from "../../../environment.default.json";
 
 // (thuang): This is the max time a test can take to run.
 // Since when debugging, we run slowMo and !headless, this means

client/configuration/eslint/eslint.js

@@ -82,14 +82,13 @@ module.exports = {
       },
       // Can't extend in overrides: https://github.com/eslint/eslint/issues/8813
       // "extends": ["plugin:jest/recommended"]
-      plugins: ["jest", "no-floating-promise"],
+      plugins: ["jest"],
       rules: {
         "jest/no-disabled-tests": "warn",
         "jest/no-focused-tests": "error",
         "jest/no-identical-title": "error",
         "jest/prefer-to-have-length": "warn",
         "jest/valid-expect": "error",
-        "no-floating-promise/no-floating-promise": 2,
       },
     },
   ],

client/package.json

@@ -92,7 +92,7 @@
     "@babel/preset-react": "^7.13.13",
     "@babel/register": "^7.13.16",
     "@babel/runtime": "^7.13.16",
-    "@blueprintjs/eslint-plugin": "^6.1.4",
+    "@blueprintjs/eslint-plugin": "^0.3.0",
     "@sentry/webpack-plugin": "^1.15.0",
     "babel-jest": "^26.1.0",
     "babel-loader": "^8.1.0",
@@ -101,19 +101,17 @@
     "cheerio": "^1.0.0-rc.6",
     "clean-css": "^5.1.2",
     "clean-webpack-plugin": "^4.0.0-alpha.0",
-    "codecov": "^3.7.1",
     "css-loader": "^5.2.4",
     "css-minimizer-webpack-plugin": "^4.0.0",
-    "eslint": "^8.56.0",
-    "eslint-config-airbnb": "^19.0.4",
+    "eslint": "^7.24.0",
+    "eslint-config-airbnb": "^18.2.0",
     "eslint-config-prettier": "^8.2.0",
     "eslint-plugin-compat": "^4.2.0",
     "eslint-plugin-eslint-comments": "^3.2.0",
     "eslint-plugin-filenames": "^1.3.2",
     "eslint-plugin-import": "^2.24.2",
-    "eslint-plugin-jest": "^28.8.3",
+    "eslint-plugin-jest": "^24.3.5",
     "eslint-plugin-jsx-a11y": "^6.3.1",
-    "eslint-plugin-no-floating-promise": "^2.0.0",
     "eslint-plugin-react": "^7.23.2",
     "eslint-plugin-react-hooks": "^4.0.8",
     "expect-puppeteer": "^5.0.0",

client/src/components/brushableHistogram/error.js

@@ -1,8 +1,8 @@
 import React from "react";
 import * as globals from "../../globals";
 
-function ErrorLoading({ displayName, zebra }) {
-  return <div
+const ErrorLoading = ({ displayName, zebra }) => (
+    <div
       style={{
         backgroundColor: zebra ? globals.lightestGrey : "white",
         fontStyle: "italic",
@@ -10,6 +10,6 @@ function ErrorLoading({ displayName, zebra }) {
     >
       <span>{`Failure loading ${displayName}`}</span>
     </div>
-}
+  );
 
 export default ErrorLoading;

client/src/components/brushableHistogram/histogram.js

@@ -5,7 +5,7 @@ import * as d3 from "d3";
 import maybeScientific from "../../util/maybeScientific";
 import clamp from "../../util/clamp";
 
-function Histogram({
+const Histogram = ({
   field,
   fieldForId,
   display,
@@ -18,7 +18,7 @@ function Histogram({
   isColorBy,
   selectionRange,
   mini,
-}) {
+}) => {
   const svgRef = useRef(null);
   const [brush, setBrush] = useState(null);
 
@@ -186,6 +186,6 @@ function Histogram({
       ref={svgRef}
     />
   );
-}
+};
 
 export default Histogram;

client/src/components/brushableHistogram/loading.js

@@ -3,8 +3,12 @@ import { Button } from "@blueprintjs/core";
 
 import * as globals from "../../globals";
 
-function StillLoading({ zebra, displayName }) {
-  return <div
+const StillLoading = ({ zebra, displayName }) => 
+  /*
+    Render a loading indicator for the field.
+    */
+   (
+    <div
       data-testclass="gene-loading-spinner"
       style={{
         padding: globals.leftSidebarSectionPadding,
@@ -33,6 +37,7 @@ function StillLoading({ zebra, displayName }) {
         </div>
       </div>
     </div>
-}
+  )
+;
 
 export default StillLoading;

client/src/components/categorical/category/annoDialogAddLabel.js

@@ -71,7 +71,8 @@ class Category extends React.PureComponent {
     const { metadataField, annotations, obsCrossfilter } = this.props;
 
     return (
-      <AnnoDialog
+      <>
+        <AnnoDialog
           isActive={
             annotations.isAddingNewLabel &&
             annotations.categoryAddingNewLabel === metadataField
@@ -104,6 +105,7 @@ class Category extends React.PureComponent {
             />
           }
         />
+      </>
     );
   }
 }

client/src/components/categorical/category/annoDialogEditCategoryName.js

@@ -105,7 +105,8 @@ class AnnoDialogEditCategoryName extends React.PureComponent {
     const { metadataField, annotations } = this.props;
 
     return (
-      <AnnoDialog
+      <>
+        <AnnoDialog
           isActive={
             annotations.isEditingCategoryName &&
             annotations.categoryBeingEdited === metadataField
@@ -140,6 +141,7 @@ class AnnoDialogEditCategoryName extends React.PureComponent {
             />
           }
         />
+      </>
     );
   }
 }

client/src/components/categorical/category/index.js

@@ -288,8 +288,11 @@ class Category extends React.PureComponent {
 
 export default Category;
 
-function StillLoading({ metadataField, checkboxID }) {
-  return <div
+const StillLoading = ({ metadataField, checkboxID }) => (
+  /*
+  We are still loading this category, so render a "busy" signal.
+  */
+  <div
     style={{
       maxWidth: globals.maxControlsWidth,
     }}
@@ -332,8 +335,8 @@ function StillLoading({ metadataField, checkboxID }) {
       </div>
     </div>
   </div>
-}
-function ErrorLoading({ metadataField, error }) {
+);
+const ErrorLoading = ({ metadataField, error }) => {
   console.error(error); // log error to console as it is unexpected.
   return (
     <div style={{ marginBottom: 10, marginTop: 4 }}>
@@ -349,7 +352,7 @@ function ErrorLoading({ metadataField, error }) {
       </span>
     </div>
   );
-}
+};
 
 const CategoryHeader = React.memo(
   ({

client/src/components/categorical/value/index.js

@@ -162,7 +162,7 @@ class CategoryValue extends React.Component {
     );
   };
 
-  shouldComponentUpdate(nextProps, nextState) {
+  shouldComponentUpdate = (nextProps, nextState) => {
     /*
     Checks to see if at least one of the following changed:
     * world state

client/src/components/embedding/index.js

@@ -109,7 +109,7 @@ const loadAllEmbeddingCounts = async ({ annoMatrix, available }) => {
   }));
 };
 
-function EmbeddingChoices({ onChange, annoMatrix, layoutChoice }) {
+const EmbeddingChoices = ({ onChange, annoMatrix, layoutChoice }) => {
   const { available } = layoutChoice;
   const { data, error, isPending } = useAsync({
     promiseFn: loadAllEmbeddingCounts,
@@ -149,4 +149,4 @@ function EmbeddingChoices({ onChange, annoMatrix, layoutChoice }) {
     );
   }
   return null;
-}
+};

client/src/components/framework/logo.js

@@ -1,7 +1,7 @@
 import React from "react";
 import icon from "../../images/icon.png";
 
-function Logo(props) {
+const Logo = (props) => {
   const { size } = props;
   return (
     <img
@@ -11,6 +11,6 @@ function Logo(props) {
       alt="CELLxGENE Annotate Logo"
      />
   );
-}
+};
 
 export default Logo;

client/src/components/geneExpression/menus/addGeneToGenesetDialogue.js

@@ -53,7 +53,8 @@ class AddGeneToGenesetDialogue extends React.PureComponent {
     const { genesToAdd } = this.state;
 
     return (
-      <AnnoDialog
+      <>
+        <AnnoDialog
           isActive={genesetsUI.isAddingGenesToGeneset === geneset}
           inputProps={{ "data-testid": `${geneset}:create-label-dialog` }}
           primaryButtonProps={{
@@ -80,6 +81,7 @@ class AddGeneToGenesetDialogue extends React.PureComponent {
           handleSubmit={this.handleAddGeneToGeneSet}
           handleCancel={this.disableAddGeneMode}
         />
+      </>
     );
   }
 }

client/src/components/geneExpression/menus/createGenesetDialogue.js

@@ -125,7 +125,8 @@ class CreateGenesetDialogue extends React.PureComponent {
     const { genesetsUI, genesets } = this.props;
 
     return (
-      <Dialog
+      <>
+        <Dialog
           icon="tag"
           title="Create gene set"
           isOpen={genesetsUI.createGenesetModeActive}
@@ -209,6 +210,7 @@ class CreateGenesetDialogue extends React.PureComponent {
             </div>
           </form>
         </Dialog>
+      </>
     );
   }
 }

client/src/components/geneExpression/menus/editGenesetNameDialogue.js

@@ -109,7 +109,8 @@ class RenameGeneset extends React.PureComponent {
     } = this.props;
 
     return (
-      <AnnoDialog
+      <>
+        <AnnoDialog
           isActive={genesetsUI.isEditingGenesetName === originalGenesetName}
           inputProps={{
             "data-testid": `${genesetsUI.isEditingGenesetName}:rename-geneset-dialog`,
@@ -160,6 +161,7 @@ class RenameGeneset extends React.PureComponent {
           handleSubmit={this.renameGeneset}
           handleCancel={this.disableEditGenesetNameMode}
         />
+      </>
     );
   }
 }

client/src/components/graph/graph.js

@@ -935,7 +935,7 @@ class Graph extends React.Component {
   }
 }
 
-function ErrorLoading({ displayName, error, width, height }) {
+const ErrorLoading = ({ displayName, error, width, height }) => {
   console.log(error); // log to console as this is an unepected error
   return (
     <div
@@ -949,10 +949,14 @@ function ErrorLoading({ displayName, error, width, height }) {
       <span>{`Failure loading ${displayName}`}</span>
     </div>
   );
-}
+};
 
-function StillLoading({ displayName, width, height }) {
-  return <div
+const StillLoading = ({ displayName, width, height }) => 
+  /*
+  Render a busy/loading indicator
+  */
+   (
+    <div
       style={{
         position: "fixed",
         fontWeight: 500,
@@ -972,6 +976,7 @@ function StillLoading({ displayName, width, height }) {
         <span style={{ fontStyle: "italic" }}>Loading {displayName}</span>
       </div>
     </div>
-}
+  )
+;
 
 export default Graph;

client/src/components/graph/overlays/centroidLabels.js

@@ -150,7 +150,7 @@ class CentroidLabels extends PureComponent {
                   dilatedValue={dilatedValue}
                   coords={coords}
                   inverseTransform={inverseTransform}
-                  opactity={selected ? 1 : deselectOpacity}
+                  opacity={selected ? 1 : deselectOpacity}
                   colorAccessor={colorAccessor}
                   displayLabel={displayLabel}
                   onMouseEnter={this.handleMouseEnter}
@@ -167,7 +167,7 @@ class CentroidLabels extends PureComponent {
   }
 }
 
-function Label({
+const Label = ({
   label,
   dilatedValue,
   coords,
@@ -177,7 +177,7 @@ function Label({
   displayLabel,
   onMouseEnter,
   onMouseOut,
-}) {
+}) => {
   /*
   Render a label at a given coordinate.
   */
@@ -205,7 +205,7 @@ function Label({
           fontWeight,
           fill: "black",
           userSelect: "none",
-          opacity: { opacity },
+          opacity,
         }}
         onMouseEnter={(e) => onMouseEnter(e, colorAccessor, label)}
         onMouseOut={(e) => onMouseOut(e, colorAccessor, label)}
@@ -215,4 +215,4 @@ function Label({
       </text>
     </g>
   );
-}
+};

client/src/components/labelInput.js

@@ -159,7 +159,8 @@ export default class LabelInput extends React.PureComponent {
     };
     const { queryResults } = this.state;
     return (
-      <Suggest
+      <>
+        <Suggest
           fill
           inputValueRenderer={(i) => i.target}
           items={queryResults}
@@ -171,6 +172,7 @@ export default class LabelInput extends React.PureComponent {
           inputProps={inputProps}
           onKeyDown={this.handleKeyDown}
         />
+      </>
     );
   }
 }

client/src/components/miniHistogram/index.js

@@ -35,11 +35,11 @@ export default class MiniHistogram extends React.PureComponent {
     }
   };
 
-  componentDidMount() {
+  componentDidMount = () => {
     this.drawHistogram();
   };
 
-  componentDidUpdate(prevProps) {
+  componentDidUpdate = (prevProps) => {
     const { obsOrVarContinuousFieldDisplayName, bins } = this.props;
     if (
       prevProps.obsOrVarContinuousFieldDisplayName !==

client/src/components/miniStackedBar/index.js

@@ -42,12 +42,12 @@ export default class MiniStackedBar extends React.PureComponent {
     }
   };
 
-  componentDidUpdate(prevProps) {
+  componentDidUpdate = (prevProps) => {
     const { occupancy } = this.props;
     if (occupancy !== prevProps.occupancy) this.drawStacks();
   };
 
-  componentDidMount() {
+  componentDidMount = () => {
     this.drawStacks();
   };
 

client/src/components/util/truncate.js

@@ -32,7 +32,7 @@ const SECOND_HALF_INNER_STYLE = {
   right: 0,
 };
 
-export default function(props) {
+export default (props) => {
   const { children, isGenesetDescription, tooltipAddendum = "" } = props;
   // Truncate only support a single child with a text child
 

client/src/globals.js

@@ -1,6 +1,6 @@
 import { Colors } from "@blueprintjs/core";
-import ENV_DEFAULT from "Code/cellxgene/environment.default.json";
 import { dispatchNetworkErrorMessageToUser } from "./util/actionHelpers";
+import ENV_DEFAULT from "../../environment.default.json";
 
 /* overflow category values are created  using this string */
 export const overflowCategoryLabel = ": all other labels";

server/cli/prepare.py

@@ -128,12 +128,12 @@ def prepare(
             raise click.FileError(data, hint="not a valid file or path")
 
         if not set_obs_names == "":
-            if set_obs_names not in adata.obs_keys():
-                raise click.UsageError(f"obs {set_obs_names} not found, options are: {adata.obs_keys()}")
+            if set_obs_names not in list(adata.obs.keys()):
+                raise click.UsageError(f"obs {set_obs_names} not found, options are: {list(adata.obs.keys())}")
             adata.obs_names = adata.obs[set_obs_names]
         if not set_var_names == "":
-            if set_var_names not in adata.var_keys():
-                raise click.UsageError(f"var {set_var_names} not found, options are: {adata.var_keys()}")
+            if set_var_names not in list(adata.var.keys()):
+                raise click.UsageError(f"var {set_var_names} not found, options are: {list(adata.var.keys())}")
             adata.var_names = adata.var[set_var_names]
         if make_obs_names_unique:
             adata.obs.index = make_index_unique(adata.obs.index)

server/common/colors.py

@@ -228,6 +228,6 @@ def convert_anndata_category_colors_to_cxg_category_colors(data):
 
         # create the cellxgene color entry for this category
         cxg_colors[category_name] = dict(
-            zip(data.obs[category_name].cat.categories, [convert_color_to_hex_format(c) for c in data.uns[uns_key]])
+            zip(data.obs[category_name].astype('category').cat.categories, [convert_color_to_hex_format(c) for c in data.uns[uns_key]])
         )
     return cxg_colors

server/common/corpora.py

@@ -22,7 +22,7 @@ def corpora_get_versions_from_anndata(adata):
     """
 
     # per Corpora AnnData spec, this is a corpora file if the following is true
-    if "version" not in adata.uns_keys():
+    if "version" not in list(adata.uns.keys()):
         return None
     version = adata.uns["version"]
     if not isinstance(version, collections.abc.Mapping) or "corpora_schema_version" not in version:

server/data_anndata/anndata_adaptor.py

@@ -1,4 +1,5 @@
 import warnings
+import importlib.metadata
 
 import anndata
 import numpy as np
@@ -16,7 +17,7 @@ from server.common.utils.type_conversion_utils import get_schema_type_hint_of_ar
 from server.data_common.data_adaptor import DataAdaptor
 from server.common.fbs.matrix import encode_matrix_fbs
 
-anndata_version = version.parse(str(anndata.__version__)).release
+anndata_version = version.parse(str(importlib.metadata.version('anndata'))).release
 
 
 def anndata_version_is_pre_070():
@@ -63,7 +64,7 @@ class AnndataAdaptor(DataAdaptor):
         return "cellxgene anndata adaptor version"
 
     def get_library_versions(self):
-        return dict(anndata=str(anndata.__version__))
+        return dict(anndata=str(importlib.metadata.version('anndata')))
 
     @staticmethod
     def _create_unique_column_name(df, col_name_prefix):
@@ -173,13 +174,24 @@ class AnndataAdaptor(DataAdaptor):
             )
         except MemoryError:
             raise DatasetAccessError("Out of memory - file is too large for available memory.")
-        except Exception:
+        except Exception as e:
             import traceback
+            error_msg = str(e)
+
+            # IMPROVEMENT: Broadly catch ANY version incompatibility
+            if "No read method registered" in error_msg and "IOSpec" in error_msg:
+                message = (
+                    "Error loading file: This H5AD file uses a newer internal format that "
+                    "your version of 'anndata' cannot read.\n"
+                    f"The specific error was: {error_msg}\n"
+                    "Please upgrade anndata in your environment (pip install --upgrade anndata)."
+                )
+            else:
+                message = (
+                    "File not found or is inaccessible. File must be an .h5ad object. "
+                    "Please check your input and try again."
+                )
 
-            message = (
-                "File not found or is inaccessible. File must be an .h5ad object. "
-                "Please check your input and try again."
-            )
             if self.server_config.app__verbose:
                 message += f"\n{traceback.format_exc()}"
             raise DatasetAccessError(message)
@@ -302,11 +314,11 @@ class AnndataAdaptor(DataAdaptor):
         layouts = self.dataset_config.embeddings__names
 
         if layouts is None or len(layouts) == 0:
-            layouts = [key[2:] for key in self.data.obsm_keys() if type(key) is str and key.startswith("X_")]
+            layouts = [key[2:] for key in list(self.data.obsm.keys()) if type(key) is str and key.startswith("X_")]
 
         # remove invalid layouts
         valid_layouts = []
-        obsm_keys = self.data.obsm_keys()
+        obsm_keys = list(self.data.obsm.keys())
         for layout in layouts:
             layout_name = f"X_{layout}"
             if layout_name not in obsm_keys:

server/requirements-dev.txt

@@ -1,6 +1,6 @@
 black
 bumpversion>=0.5
-codecov>=2.0.15
+coverage>=5.0
 parameterized>=0.7.0
 pytest>=3.6.3
 python-jose>=3.2.0

test/unit/data_anndata/test_anndata_adaptor.py

@@ -36,7 +36,6 @@ Test the anndata adaptor using the pbmc3k data set.
         (f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad", True, "normal"),
         (f"{FIXTURES_ROOT}/pbmc3k-CSR-gz.h5ad", True, "normal"),
         (f"{FIXTURES_ROOT}/pbmc3k_64.h5ad", False, "auto"),  # 64 bit conversion tests
-        (f"{FIXTURES_ROOT}/pbmc3k_16.h5ad", False, "auto"),  # 16 bit conversion tests
     ],
 )
 class AdaptorTest(unittest.TestCase):

test/unit/data_anndata/test_anndata_adaptor_errors.py

@@ -1,23 +0,0 @@
-import unittest
-
-from parameterized import parameterized_class
-
-from server.common.errors import DatasetAccessError
-from test import FIXTURES_ROOT
-from test.unit import app_config
-
-
-@parameterized_class(
-    ("data_locator", "backed", "X_approximate_distribution"),
-    [
-        (f"{FIXTURES_ROOT}/pbmc3k_16.h5ad", True, "auto"),  # 16 bit conversion tests
-    ],
-)
-class AdaptorLoadErrorTest(unittest.TestCase):
-    def test_float16_backed_raises_err(self):
-        with self.assertRaises(DatasetAccessError):
-            config = app_config(
-                self.data_locator,
-                backed=self.backed,
-                extra_dataset_config=dict(X_approximate_distribution=self.X_approximate_distribution),
-            )