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Merge pull request #13182 from kxk302/release_21.09

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[21.09] Backport of iRODS Object Store path name fix in #13080
This commit is contained in:
Marius van den Beek
2022-01-18 18:57:46 +01:00
committed by GitHub
parent 043371e0e5 2b70e34a61
commit 6c354e2203
3 changed files with 12 additions and 3 deletions
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lib/galaxy/objectstore/irods.py
+1 -1
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@@ -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
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@@ -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
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@@ -1,5 +1,6 @@
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,