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#14 added custom method to create data dirs

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This commit is contained in:
Alok Saldanha
2020-01-01 01:24:18 -05:00
parent 736541c4ec
commit 201f876341
5 changed files with 48 additions and 11 deletions
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cellxgene_gateway/path_util.py
+7 -5
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@@ -28,12 +28,13 @@ def get_key(path):
if trimmed.endswith('.h5ad') and data_file_exists(trimmed):
# 1) somedir/dataset.h5ad: a dataset
return CacheKey(trimmed, trimmed, None)
elif trimmed.endswith('.csv') and data_file_exists(trimmed):
elif trimmed.endswith('.csv'):
# 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotaitons file.
# 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotations file.
annotations_dir = os.path.split(trimmed)[0]
dataset = make_h5ad(annotations_dir)
if data_file_exists(dataset):
data_dir_ensure(annotations_dir)
return CacheKey(trimmed, dataset, trimmed)
elif trimmed.endswith('_annotations') and data_dir_exists(trimmed):
# 3) somedir/dataset_annotations: an annotation directory. The corresponding h5ad must exist, but the directory may not.
@@ -74,6 +75,10 @@ def data_dir_exists(dataset):
file_path = os.path.join(env.cellxgene_data, dataset)
validate_is_dir(file_path)
return True
def data_dir_ensure(dataset):
file_path = os.path.join(env.cellxgene_data, dataset)
if not os.path.exists(file_path):
os.makedirs(file_path)
def get_file_path(key):
dataset = key.dataset
@@ -82,12 +87,9 @@ def get_file_path(key):
return file_path
def get_annotation_file_path(key):
print(f"getting annotaiton_file_path for {key.annotation_file}")
if key.annotation_file is None:
return None
if key.annotation_file == '':
return ''
file_path = os.path.join(env.cellxgene_data, key.annotation_file)
print(f"getting annotaiton_file_path for {key}, file_path {file_path}")
validate_is_file(file_path)
return file_path