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#45 implemented test__scan_directory__properly_recurses_suburls

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This commit is contained in:
Alok Saldanha
2021-04-21 08:21:46 -04:00
parent 687dc31b7a
commit a3e3b6cea8
3 changed files with 165 additions and 9 deletions
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cellxgene_gateway/items/s3/s3item_source.py
+7 -9
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@@ -41,6 +41,9 @@ class S3ItemSource(ItemSource):
def url(self, key):
return "s3://" + self.bucket + "/" + key
def remove_bucket(self, filepath):
return filepath[len(self.bucket) :].lstrip("/")
@property
def name(self):
return self._name or f"Items:{self.url('')}"
@@ -71,7 +74,7 @@ class S3ItemSource(ItemSource):
raise Exception(f"S3 url '{url}' does not exist.")
s3key_map = dict(
(filepath[len(self.bucket) :].lstrip("/"), "s3://" + filepath)
(self.remove_bucket(filepath), "s3://" + filepath)
for filepath in sorted(self.s3.ls(url))
)
@@ -93,12 +96,7 @@ class S3ItemSource(ItemSource):
if self.s3.isdir(item_url) and not is_annotation_dir(filepath)
]
items = [
self.make_s3item_from_key(
key[key.rindex("/") + 1 :] if "/" in key else key, key
)
for key in h5ad_keys
]
items = [self.make_s3item_from_key(basename(key), key) for key in h5ad_keys]
branches = None
if len(subdir_keys) > 0:
branches = [self.scan_directory(key) for key in subdir_keys]
@@ -163,11 +161,11 @@ class S3ItemSource(ItemSource):
if self.s3.isdir(annotations_fullpath):
return [
self.make_s3item_from_key(
annotation, join(annotations_subpath, annotation), True
basename(annotation), self.remove_bucket(annotation), True
)
for annotation in sorted(self.s3.ls(annotations_fullpath))
if annotation.endswith(self.annotation_file_suffix)
and self.s3.isfile(join(annotations_fullpath, annotation))
and self.s3.isfile("s3://" + annotation)
]
else:
return None