#79 added cellxgene-data directory so it actually works

.github/workflows/pr-checks.yaml

@@ -6,7 +6,7 @@ on: [push, pull_request]
 
 jobs:
   black:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     steps:
       - uses: actions/checkout@v2
         name: Checkout repository
@@ -25,7 +25,7 @@ jobs:
           black . --check
   # This job is copied over from `deploy.yaml`
   run-tests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     steps:
       - uses: actions/checkout@v2
 

Changelog.md

@@ -1,7 +1,3 @@
-# 0.3.11
-
-* #81 added support for gene sets
-
 # 0.3.10
 
 * #65 Added GATEWAY_EXPIRE_SECONDS to set how long cellxgene servers can remain idle before being terminated.

README.md

@@ -75,7 +75,7 @@ Optional environment variables:
 * `GATEWAY_PORT` - local port that the gateway should bind to, defaults to 5005
 * `GATEWAY_EXPIRE_SECONDS` - time in seconds that a cellxgene process will remain idle before being terminated. Defaults to 3600 (one hour)
 * `GATEWAY_EXTRA_SCRIPTS` - JSON array of script paths, will be embedded into each page and forwarded with `--scripts` to cellxgene server
-* `GATEWAY_ENABLE_ANNOTATIONS` - Set to `true` or to `1` to enable cellxgene annotations and gene sets.
+* `GATEWAY_ENABLE_ANNOTATIONS` - Set to `true` or to `1` to enable cellxgene annotations. 
 * `GATEWAY_ENABLE_BACKED_MODE` - Set to `true` or to `1` to load AnnData in file-backed mode. This saves memory and speeds up launch time but may reduce overall performance.
 * `GATEWAY_LOG_LEVEL` - default is `INFO`. set to `DEBUG` to increase logging and to `WARNING` to decrease logging.
 * `S3_ENABLE_LISTINGS_CACHE` - Set to `true` or to `1` to cache listings of S3 folders for performance. If the cache becomes stale, set `filecrawl.html?refresh=true` query parameter to refresh the cache.

cellxgene_gateway/cache_entry.py

@@ -58,6 +58,7 @@ class CacheEntry:
 
     @classmethod
     def for_key(cls, key, port):
+
         return cls(
             None,
             key,

cellxgene_gateway/gateway.py

@@ -80,6 +80,7 @@ cache = BackendCache()
 
 @app.errorhandler(CellxgeneException)
 def handle_invalid_usage(error):
+
     message = f"{error.http_status} Error : {error.message}"
 
     return (
@@ -94,6 +95,7 @@ def handle_invalid_usage(error):
 
 @app.errorhandler(ProcessException)
 def handle_invalid_process(error):
+
     message = []
 
     message.append(error.message)

cellxgene_gateway/items/file/fileitem_source.py

@@ -35,11 +35,6 @@ class FileItemSource(ItemSource):
     def name(self):
         return self._name or f"Files:{self.base_path}"
 
-    def is_gene_set(self, path: str) -> bool:
-        return ("_gene_sets" in path or "-gene-sets" in path) and path.endswith(
-            self.annotation_file_suffix
-        )
-
     def is_h5ad_file(self, path: str) -> bool:
         return path.endswith(self.h5ad_suffix) and os.path.isfile(path)
 
@@ -185,7 +180,6 @@ class FileItemSource(ItemSource):
                 self.make_fileitem_from_path(annotation, annotations_subpath, True)
                 for annotation in sorted(os.listdir(annotations_fullpath))
                 if annotation.endswith(self.annotation_file_suffix)
-                and not self.is_gene_set(annotation)
                 and os.path.isfile(os.path.join(annotations_fullpath, annotation))
             ]
         else:

cellxgene_gateway/subprocess_backend.py

@@ -14,11 +14,7 @@ from flask_api import status
 
 from cellxgene_gateway.cache_entry import CacheEntryStatus
 from cellxgene_gateway.dir_util import make_annotations
-from cellxgene_gateway.env import (
-    cellxgene_args,
-    enable_annotations,
-    enable_backed_mode,
-)
+from cellxgene_gateway.env import cellxgene_args, enable_annotations, enable_backed_mode
 from cellxgene_gateway.process_exception import ProcessException
 
 logger = logging.getLogger(__name__)
@@ -34,11 +30,8 @@ class SubprocessBackend:
                 extra_args = f" --annotations-dir {make_annotations(file_path)}"
             else:
                 extra_args = f" --annotations-file {annotation_file_path}"
-                gene_sets_file_path = annotation_file_path[:-4] + "_gene_sets.csv"
-                extra_args += f" --gene-sets-file {gene_sets_file_path}"
         else:
             extra_args = " --disable-annotations"
-            extra_args += " --disable-gene-sets-save"
         if enable_backed_mode:
             extra_args += " --backed"
         if not cellxgene_args is None:

examples/customized_docker_image/Dockerfile

@@ -0,0 +1,14 @@
+FROM python:3.9
+
+RUN pip install cellxgene-gateway 'MarkupSafe<2.1'
+
+COPY customize_ui.sh customize_ui.sh
+RUN CELLXGENE_GATEWAY_DIR=/usr/local/lib/python3.9/site-packages/cellxgene_gateway . ./customize_ui.sh
+
+ENV CELLXGENE_DATA=/cellxgene-data
+ENV CELLXGENE_LOCATION=/usr/local/bin/cellxgene
+EXPOSE 5005
+
+RUN mkdir /cellxgene-data
+
+CMD ["cellxgene-gateway"]

examples/customized_docker_image/README.md

@@ -0,0 +1,14 @@
+# Purpose
+
+This is a simple example of how to make a small script to customize the UI of cellxgene-gateway. The script that does the customization is `customize_ui.sh`, it simply makes the main header green using CSS but you could do anything you want there (including adding more script tags, etc).
+
+# Usage
+
+```
+docker build -t cellxgene_custom .
+CELLXGENE_DATA=`pwd`/../../../cellxgene_data
+docker run -p 5005:5005 --mount src=$CELLXGENE_DATA,target=/cellxgene-data,type=bind cellxgene_custom
+```
+
+If you now open http://localhost:5005 you should see a green cellxgene gateway header.
+

examples/customized_docker_image/customize_ui.sh

@@ -0,0 +1,3 @@
+# make the header bright green
+find "${CELLXGENE_GATEWAY_DIR}/templates" -name index.html -exec sed -i -e 's/<head>/<head>\
+> <style> header h3 {color: #0F0;} <\/style>/g' {} \;

tests/test_subprocess_backend.py

@@ -1,6 +1,7 @@
 import unittest
 from unittest.mock import MagicMock, patch
 
+from cellxgene_gateway.backend_cache import BackendCache
 from cellxgene_gateway.cache_entry import CacheEntry
 from cellxgene_gateway.cache_key import CacheKey
 from cellxgene_gateway.items.file.fileitem import FileItem
@@ -32,46 +33,10 @@ class TestSubprocessBackend(unittest.TestCase):
             backend.launch(cellxgene_loc, scripts, entry)
         popen.assert_called_once_with(
             [
-                "yes | /some/cellxgene launch /tmp/czi/pbmc3k.h5ad --port 8000 --host 127.0.0.1 --disable-annotations --disable-gene-sets-save --scripts http://example.com/script.js --scripts http://example.com/script2.js"
+                "yes | /some/cellxgene launch /tmp/czi/pbmc3k.h5ad --port 8000 --host 127.0.0.1 --disable-annotations --scripts http://example.com/script.js --scripts http://example.com/script2.js"
             ],
             shell=True,
             stderr=-1,
             stdout=-1,
         )
         self.assertEqual("An unexpected error", context.exception.stderr)
-
-    @patch("subprocess.Popen")
-    def test_launch_GIVEN_annotations_enabled_THEN_set_flags(self, popen):
-        subprocess = MagicMock()
-        subprocess.stdout.readline().decode.return_value = (
-            "[cellxgene] Type CTRL-C at any time to exit.\n"
-        )
-        subprocess.stderr.read().decode.return_value = ""
-        popen.return_value = subprocess
-
-        key = CacheKey(
-            FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
-            FileItemSource("/tmp", "local"),
-            FileItem(
-                "/czi/pbmc3k_annotations/", name="foo.csv", type=ItemType.annotation
-            ),
-        )
-        entry = CacheEntry.for_key(key, 8000)
-        import cellxgene_gateway.subprocess_backend
-
-        cellxgene_gateway.subprocess_backend.enable_annotations = True
-        try:
-            backend = cellxgene_gateway.subprocess_backend.SubprocessBackend()
-            cellxgene_loc = "/some/cellxgene"
-
-            backend.launch(cellxgene_loc, [], entry)
-        finally:
-            cellxgene_gateway.subprocess_backend.enable_annotations = False
-        popen.assert_called_once_with(
-            [
-                "yes | /some/cellxgene launch /tmp/czi/pbmc3k.h5ad --port 8000 --host 127.0.0.1 --annotations-file /tmp/czi/pbmc3k_annotations/foo.csv --gene-sets-file /tmp/czi/pbmc3k_annotations/foo_gene_sets.csv"
-            ],
-            shell=True,
-            stderr=-1,
-            stdout=-1,
-        )