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fix: s3 user annotations (#2541)

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do _not_ attempt to create the user annotations directory if an s3 location is specified
This commit is contained in:
Andrew Tolopko
2022-07-28 20:00:15 +00:00
committed by GitHub
parent 69a6d52240
commit 4df50a7677
1 changed files with 10 additions and 5 deletions
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server/common/config/dataset_config.py
+10 -5
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@@ -4,6 +4,7 @@ from os.path import splitext, isdir
from server.common.annotations.local_file_csv import AnnotationsLocalFile from server.common.annotations.local_file_csv import AnnotationsLocalFile
from server.common.config.base_config import BaseConfig from server.common.config.base_config import BaseConfig
from server.common.errors import ConfigurationError, AnnotationsError from server.common.errors import ConfigurationError, AnnotationsError
from server.common.utils.data_locator import DataLocator
from server.data_common.matrix_loader import MatrixDataLoader from server.data_common.matrix_loader import MatrixDataLoader
@@ -127,11 +128,15 @@ class DatasetConfig(BaseConfig):
if lf_ext and lf_ext != ".csv": if lf_ext and lf_ext != ".csv":
raise ConfigurationError(f"genesets file type must be .csv: {genesets_filename}") raise ConfigurationError(f"genesets file type must be .csv: {genesets_filename}")
if dirname is not None and not isdir(dirname): if dirname is not None:
try: if not DataLocator(dirname).islocal():
os.mkdir(dirname) # remote object stores only support objects but not directories, do nothing
except OSError: pass
raise ConfigurationError("Unable to create directory specified by --user-generated-data-dir") elif not isdir(dirname):
try:
os.mkdir(dirname)
except OSError:
raise ConfigurationError("Unable to create directory specified by --user-generated-data-dir")
anno_config = { anno_config = {
"user-annotations": self.user_annotations__enable, "user-annotations": self.user_annotations__enable,