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Save gene sets without cell annotations

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This fixes a bug whereby new gene_sets csv files created without
accompanying cell-level annotations could not be detected by the
filecrawler.
This commit is contained in:
george-hall-ucl
2023-08-08 15:49:57 +01:00
parent 9d10932b06
commit 56bd079024
1 changed files with 17 additions and 5 deletions
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cellxgene_gateway/items/file/fileitem_source.py
+17 -5
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@@ -24,21 +24,21 @@ class FileItemSource(ItemSource):
h5ad_suffix=dir_util.h5ad_suffix,
annotation_dir_suffix=dir_util.annotations_suffix,
annotation_file_suffix=".csv",
gene_set_file_suffix="_gene_sets.csv",
):
self._name = name
self.base_path = base_path
self.h5ad_suffix = h5ad_suffix
self.annotation_dir_suffix = annotation_dir_suffix
self.annotation_file_suffix = annotation_file_suffix
self.gene_set_file_suffix = gene_set_file_suffix
@property
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
)
return path.endswith(self.gene_set_file_suffix)
def is_h5ad_file(self, path: str) -> bool:
return path.endswith(self.h5ad_suffix) and os.path.isfile(path)
@@ -186,12 +186,24 @@ class FileItemSource(ItemSource):
annotations_subpath = self.get_annotations_subpath(item)
annotations_fullpath = self.full_path(annotations_subpath)
if os.path.isdir(annotations_fullpath):
return [
sorted_files = sorted(os.listdir(annotations_fullpath))
annotation_files = [
self.make_fileitem_from_path(annotation, annotations_subpath, True)
for annotation in sorted(os.listdir(annotations_fullpath))
for annotation in sorted_files
if annotation.endswith(self.annotation_file_suffix)
and not self.is_gene_set(annotation)
and os.path.isfile(os.path.join(annotations_fullpath, annotation))
]
# Catch gene sets without accompanying [annotations].csv
gene_sets_files = [
self.make_fileitem_from_path(annotation[:-len(self.gene_set_file_suffix)] + ".csv", annotations_subpath, True)
for annotation in sorted_files
if self.is_gene_set(annotation)
and annotation[:-len(self.gene_set_file_suffix)] not in [a.name for a in annotation_files]
and os.path.isfile(os.path.join(annotations_fullpath, annotation))
]
return sorted(annotation_files + gene_sets_files, key = lambda x: x.name)
else:
return None