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fix: iRODS functionality - issue #1510 #1611

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merged 5 commits into from May 16, 2022
Merged

fix: iRODS functionality - issue #1510 #1611

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a21c837
fix: iRODS functionality - issue #1510
ScottMastro Apr 27, 2022
045015c
fix: iRODS functionality - issue #1510
ScottMastro May 2, 2022
7b830ba
fmt with black
ScottMastro May 2, 2022
3abd643
Merge branch 'snakemake:main' into main
ScottMastro May 9, 2022
110233e
iRODS correctly handles subdirectories
ScottMastro May 9, 2022
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17 changes: 14 additions & 3 deletions snakemake/remote/iRODS.py
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Expand Up @@ -24,7 +24,11 @@
from irods.session import iRODSSession
from irods.meta import iRODSMeta
from irods.models import DataObject
from irods.exception import CollectionDoesNotExist, DataObjectDoesNotExist
from irods.exception import (
CollectionDoesNotExist,
DataObjectDoesNotExist,
CAT_NO_ACCESS_PERMISSION,
)
import irods.keywords as kw
except ImportError as e:
raise WorkflowError(
Expand Down Expand Up @@ -90,6 +94,10 @@ def available_protocols(self):
"""List of valid protocols for this remote provider."""
return ["irods://"]

def glob_wildcards(self, pattern, *args, **kwargs):
remote_pattern = os.path.join(os.sep, self._irods_session.zone, pattern)
return super().glob_wildcards(remote_pattern, *args, **kwargs)


class RemoteObject(AbstractRemoteRetryObject):
"""This is a class to interact with an iRODS server."""
Expand Down Expand Up @@ -200,13 +208,16 @@ def _upload(self):

# create folder structure on remote
folders = os.path.dirname(self.remote_path).split(os.sep)[1:]
collpath = os.sep
# add zone name to path
collpath = os.sep + folders.pop(0) + os.sep + folders.pop(0)

for folder in folders:
collpath = os.path.join(collpath, folder)

try:
self._irods_session.collections.get(collpath)
# ignore subdirectories where user does not have access
except (CAT_NO_ACCESS_PERMISSION):
pass
except:
self._irods_session.collections.create(collpath)

Expand Down