Commit 8b5f13b2 authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

fix test, reformat

parent 33321730

lib/galaxy/datatypes/data.py

+0 −1
Original line number Diff line number Diff line
@@ -584,7 +584,6 @@ class Data(metaclass=DataMeta): 


        dataset.sync_cache(trans=trans)





        downloading = to_ext is not None

        file_size = _get_file_size(dataset)

lib/galaxy/files/sources/sshoidc.py

+3 −3
Original line number Diff line number Diff line
@@ -4,14 +4,14 @@ except ImportError: 
    SSHFS = None

import logging

import re



import jwt

from paramiko.transport import Transport

from typing import (

    Optional,

    Union,

)



import jwt

from paramiko.transport import Transport



from . import (

    FilesSourceOptions,

    FilesSourceProperties,

lib/galaxy/model/__init__.py

+2 −1
Original line number Diff line number Diff line
@@ -4932,6 +4932,7 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable): 
    def sync_cache(self, **kwargs):

        self.dataset.sync_cache(**kwargs)





class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable):

    """

    Resource class that creates a relation between a dataset and a user history.

lib/galaxy/objectstore/irods.py

+0 −1
Original line number Diff line number Diff line
@@ -723,7 +723,6 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin): 
        return self._get_cache_path(rel_path)



    def _sync_cache(self, obj, **kwargs):



        ipt_timer = ExecutionTimer()

        base_dir = kwargs.get("base_dir", None)

        dir_only = kwargs.get("dir_only", False)

lib/galaxy/objectstore/rucio.py

+11 −13
Original line number Diff line number Diff line
@@ -41,6 +41,7 @@ from ..objectstore import ConcreteObjectStore 


log = logging.getLogger(__name__)





class DeleteClient(UploadClient):

    def delete(self, items, forced_schemes=None, ignore_availability=False):

        for item in items:
@@ -59,30 +60,29 @@ class DeleteClient(UploadClient): 
                    force_scheme = rse_scheme["scheme"]

            if not self.rses.get(rse):

                rse_settings = self.rses.setdefault(rse, rsemgr.get_rse_info(rse, vo=self.client.vo))

                if not ignore_availability and rse_settings['availability_delete'] != 1:

                    logger(logging.DEBUG, '%s is not available for deletion. No actions have been taken' % rse)

                if not ignore_availability and rse_settings["availability_delete"] != 1:

                    logger(logging.DEBUG, "%s is not available for deletion. No actions have been taken" % rse)

                    continue



            # protocol handling and deletion

            rse_settings = self.rses[rse]

            protocols = rsemgr.get_protocols_ordered(rse_settings=rse_settings, operation='delete',

                                                     scheme=force_scheme)

            protocols = rsemgr.get_protocols_ordered(rse_settings=rse_settings, operation="delete", scheme=force_scheme)

            protocols.reverse()

            success = False

            while not success and len(protocols):

                protocol = protocols.pop()

                cur_scheme = protocol['scheme']

                cur_scheme = protocol["scheme"]

                try:

                    protocol_delete = self._create_protocol(rse_settings, 'delete', force_scheme=cur_scheme)

                    protocol_delete = self._create_protocol(rse_settings, "delete", force_scheme=cur_scheme)

                    protocol_delete.delete(pfn)

                    success = True

                except Exception as error:

                    logger(logging.WARNING, 'Delete attempt failed')

                    logger(logging.INFO, 'Exception: %s' % str(error), exc_info=True)

            logger(logging.DEBUG, 'Successfully deleted dataset %s' % pfn)

                    logger(logging.WARNING, "Delete attempt failed")

                    logger(logging.INFO, "Exception: %s" % str(error), exc_info=True)

            logger(logging.DEBUG, "Successfully deleted dataset %s" % pfn)



class InPlaceIngestClient(UploadClient):



class InPlaceIngestClient(UploadClient):

    def ingest(self, items, summary_file_path=None, traces_copy_out=None, ignore_availability=False, activity=None):

        """

        :param items: List of dictionaries. Each dictionary describing a file to upload. Keys:
@@ -404,9 +404,7 @@ class RucioBroker: 
    def delete(self, key, auth_token):

        key = os.path.basename(key)

        try:

            items = [

                {"did": {"scope": self.scope, "name": key}}

            ]

            items = [{"did": {"scope": self.scope, "name": key}}]

            self.get_rucio_delete_client(auth_token=auth_token).delete(items, self.download_schemes, True)

        except Exception as e:

            log.exception("Cannot delete file:" + str(e))