opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Add test for metadata generation

Browse Source
This commit is contained in:
davelopez
2022-11-17 11:10:36 +01:00
parent a1df2d5f4e
commit 0c2f9d98de
2 changed files with 18 additions and 3 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/model/store/__init__.py
+5 -2
View File
@@ -632,8 +632,11 @@ class ModelImportStore(metaclass=abc.ABCMeta):
)
else:
# Try to set metadata directly. TODO: check efficiency of this?
if dataset_instance.has_metadata_files:
dataset_instance.datatype.set_meta(dataset_instance)
try:
if dataset_instance.has_metadata_files:
dataset_instance.datatype.set_meta(dataset_instance)
except Exception:
dataset_instance.dataset.state = dataset_instance.dataset.states.FAILED_METADATA
if model_class == "HistoryDatasetAssociation":
if object_key in dataset_attrs:
test/integration/test_history_import_export.py
+13 -1
View File
@@ -60,6 +60,10 @@ class TestImportExportHistoryViaTasksIntegration(
def test_import_model_store_from_file_source_async_with_format(self):
history_name = f"for_export_format_async_{uuid4()}"
history_id = self.dataset_populator.setup_history_for_export_testing(history_name)
# Add bam dataset to test metadata generation on import
self.dataset_populator.new_dataset(
history_id, content=open(self.test_data_resolver.get_filename("1.bam"), "rb"), file_type="bam", wait=True
)
model_store_format = "rocrate.zip"
target_uri = f"gxfiles://posix_test/history.{model_store_format}"
@@ -72,14 +76,22 @@ class TestImportExportHistoryViaTasksIntegration(
imported_history_id = imported_history["id"]
assert imported_history_id != history_id
assert imported_history["name"] == history_name
self.dataset_populator.wait_for_history(imported_history_id)
history_contents = self.dataset_populator.get_history_contents(imported_history_id)
assert len(history_contents) == 2
assert len(history_contents) == 3
# Only deleted datasets should appear as "discarded"
for dataset in history_contents:
if dataset["deleted"] is True:
assert dataset["state"] == "discarded"
else:
assert dataset["state"] == "ok"
# Check metadata generation
if dataset["extension"] == "bam":
imported_bam_details = self.dataset_populator.get_history_dataset_details(
imported_history_id, dataset_id=dataset["id"]
)
bai_metadata = imported_bam_details["meta_files"][0]
assert bai_metadata["file_type"] == "bam_index"
class TestImportExportHistoryContentsViaTasksIntegration(IntegrationTestCase, UsesCeleryTasks):