Unverified Commit 6c354e22 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #13182 from kxk302/release_21.09 

[21.09] Backport of iRODS Object Store path name fix in #13080
parents 043371e0 2b70e34a

lib/galaxy/objectstore/irods.py

+1 −1
Original line number Diff line number Diff line
@@ -429,7 +429,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin): 
                log.debug("Pushing cache file '%s' of size %s bytes to collection '%s'", source_file, os.path.getsize(source_file), rel_path)



                # Add the source file to the irods collection

                self.session.data_objects.put(source_file, f"{collection_path}/", **options)

                self.session.data_objects.put(source_file, data_object_path, **options)



                end_time = datetime.now()

                log.debug("Pushed cache file '%s' to collection '%s' (%s bytes transfered in %s sec)",

test/integration/objectstore/test_objectstore_datatype_upload.py

+1 −1
Original line number Diff line number Diff line
@@ -183,7 +183,7 @@ def test_upload_datatype_dos_disk_and_disk(distributed_instance, test_data, temp 


@pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))

def test_upload_datatype_irods(irods_instance, test_data, temp_file):

    upload_datatype_helper(irods_instance, test_data, temp_file)

    upload_datatype_helper(irods_instance, test_data, temp_file, True)





@pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))

test/integration/test_datatype_upload.py

+10 −1
Original line number Diff line number Diff line 
import collections

import os

import shutil



import pytest
@@ -59,7 +60,7 @@ def test_upload_datatype_auto(instance, test_data, temp_file): 
    upload_datatype_helper(instance, test_data, temp_file)





def upload_datatype_helper(instance, test_data, temp_file):

def upload_datatype_helper(instance, test_data, temp_file, delete_cache_dir=False):

    is_compressed = False

    for is_method in (is_bz2, is_gzip, is_zip):

        is_compressed = is_method(test_data.path)
@@ -93,6 +94,14 @@ def upload_datatype_helper(instance, test_data, temp_file): 
    datatype = registry.datatypes_by_extension[file_ext]

    datatype_compressed = getattr(datatype, "compressed", False)

    if not is_compressed or datatype_compressed:

        if delete_cache_dir:

            # Delete cache directory and then re-create it. This way we confirm

            # that dataset is fetched from the object store, not from the cache

            temp_dir = instance.get_object_store_kwargs()['temp_directory']

            cache_dir = temp_dir + '/object_store_cache'

            shutil.rmtree(cache_dir)

            os.mkdir(cache_dir)



        # download file and verify it hasn't been manipulated

        temp_file.write(instance.dataset_populator.get_history_dataset_content(history_id=instance.history_id,

                                                                               dataset=dataset,