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#81 Combined GATEWAY_ENABLE_ANNOTATIONS and GATEWAY_ENABLE_GENE_SETS flags

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Alok Saldanha
2023-07-06 08:53:19 -06:00
parent 5a650334df
commit 2754bc1ef1
7 changed files with 8 additions and 24 deletions
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cellxgene_gateway/subprocess_backend.py
+1 -9
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@@ -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"