#81 Add support for gene sets

This adds the flag `GATEWAY_ENABLE_GENE_SETS` to enable support for gene
sets.  To simplify implementation, activating this flag also activates
`GATEWAY_ENABLE_ANNOTATIONS`.  The gene sets are saved in a file that
has the same name as the annotations `csv` but with `_gene_sets`
appended to the file name (before the extension).  This file is hidden
in filecrawler, and the gene sets are loaded when the associated
annotations file is loaded.

If the annotations file is missing, then an Exception is raised.

I have updated one unit test to make it expect
`--disable-gene-sets-save` in the default case (i.e. if
`GATEWAY_ENABLE_ANNOTATIONS = 0`).  All units tests pass.

I have updated the README to document `GATEWAY_ENABLE_GENE_SETS`.

cellxgene_gateway/subprocess_backend.py

@@ -14,7 +14,12 @@ 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,
+    enable_gene_sets,
+)
 from cellxgene_gateway.process_exception import ProcessException
 
 logger = logging.getLogger(__name__)
@@ -32,6 +37,16 @@ class SubprocessBackend:
                 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-gene-sets-save"
         if enable_backed_mode:
             extra_args += " --backed"
         if not cellxgene_args is None: