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Explicitly create extra_files_path when discovering outputs with extra files

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mvdbeek
2019-05-17 14:04:23 +02:00
parent b777e1b5d8
commit 3d2c243b4d
3 changed files with 6 additions and 1 deletions
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lib/galaxy/model/__init__.py
+4
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@@ -2184,6 +2184,10 @@ class Dataset(StorableObject, RepresentById):
else:
return os.path.abspath(self.external_extra_files_path)
def create_extra_files_path(self):
if not self.extra_files_path_exists():
self.object_store.create(self, dir_only=True, extra_dir=self._extra_files_rel_path)
def set_extra_files_path(self, extra_files_path):
if not extra_files_path:
self.external_extra_files_path = None
lib/galaxy/tools/parameters/output_collect.py
+1
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@@ -316,6 +316,7 @@ def collect_primary_datasets(job_context, output, input_ext):
extra_files_path = new_primary_datasets_attributes.get('extra_files', None)
if extra_files_path:
extra_files_path_joined = os.path.join(job_working_directory, extra_files_path)
primary_data.dataset.create_extra_files_path()
for root, dirs, files in os.walk(extra_files_path_joined):
extra_dir = os.path.join(primary_data.extra_files_path, root.replace(extra_files_path_joined, '', 1).lstrip(os.path.sep))
extra_dir = os.path.normpath(extra_dir)
test/unit/test_model_store.py
+1 -1
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@@ -283,7 +283,7 @@ def test_import_export_composite_datasets():
h = model.History(name="Test History", user=u)
d1 = _create_datasets(sa_session, h, 1, extension="html")[0]
app.object_store.create(d1.dataset, dir_only=True, extra_dir=d1.dataset._extra_files_rel_path)
d1.dataset.create_extra_files_path()
sa_session.add_all((h, d1))
sa_session.flush()