#81 Combined GATEWAY_ENABLE_ANNOTATIONS and GATEWAY_ENABLE_GENE_SETS flags

Changelog.md

@@ -1,6 +1,6 @@
 # 0.3.11
 
-* #81 added support for gene sets via GATEWAY_ENABLE_GENE_SETS
+* #81 added support for gene sets
 
 # 0.3.10
 

README.md

@@ -75,8 +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. 
+* `GATEWAY_ENABLE_ANNOTATIONS` - Set to `true` or to `1` to enable cellxgene annotations and gene sets.
-* `GATEWAY_ENABLE_GENE_SETS` - Set to `true` or to `1` to enable cellxgene gene sets. Also enables `GATEWAY_ENABLE_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

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

cellxgene_gateway/env.py

@@ -26,16 +26,10 @@ extra_scripts = os.environ.get("GATEWAY_EXTRA_SCRIPTS")
 expire_seconds = int(
     os.environ.get("GATEWAY_EXPIRE_SECONDS", os.environ.get("GATEWAY_TTL", "3600"))
 )
-enable_gene_sets = os.environ.get("GATEWAY_ENABLE_GENE_SETS", "").lower() in [
-    "true",
-    "1",
-]
 enable_annotations = os.environ.get("GATEWAY_ENABLE_ANNOTATIONS", "").lower() in [
     "true",
     "1",
 ]
-# Enable annotations if gene sets are enabled:
-enable_annotations = enable_annotations or enable_gene_sets
 enable_backed_mode = os.environ.get("GATEWAY_ENABLE_BACKED_MODE", "").lower() in [
     "true",
     "1",
@@ -60,7 +54,6 @@ optional_env_vars = {
     "GATEWAY_EXTRA_SCRIPTS": extra_scripts,
     "GATEWAY_EXPIRE_SECONDS": expire_seconds,
     "GATEWAY_ENABLE_ANNOTATIONS": enable_annotations,
-    "GATEWAY_ENABLE_GENE_SETS": enable_gene_sets,
     "GATEWAY_ENABLE_BACKED_MODE": enable_backed_mode,
     "GATEWAY_LOG_LEVEL": log_level,
     "CELLXGENE_ARGS": cellxgene_args,

cellxgene_gateway/gateway.py

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

@@ -35,8 +35,11 @@ class FileItemSource(ItemSource):
     def name(self):
         return self._name or f"Files:{self.base_path}"
 
-    def is_gene_set(self, path:str) -> bool:
+    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)
+        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)
 

cellxgene_gateway/subprocess_backend.py

@@ -18,7 +18,6 @@ from cellxgene_gateway.env import (
     cellxgene_args,
     enable_annotations,
     enable_backed_mode,
-    enable_gene_sets,
 )
 from cellxgene_gateway.process_exception import ProcessException
 
@@ -35,17 +34,10 @@ class SubprocessBackend:
                 extra_args = f" --annotations-dir {make_annotations(file_path)}"
             else:
                 extra_args = f" --annotations-file {annotation_file_path}"
-        else:
-            extra_args = " --disable-annotations"
-        if enable_gene_sets and not annotation_file_path is None:
-            if annotation_file_path == "":
-                raise Exception(
-                    "GATEWAY_ENABLE_GENE_SETS is true but --annotation_file_path not set"
-                )
-            else:
                 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"