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Simplify history import to fix extra files and ObjectStore interactions. #7193

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merged 1 commit into from Jan 14, 2019
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Simplify history import to fix extra files and ObjectStore interactions. #7193

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46 changes: 16 additions & 30 deletions lib/galaxy/tools/imp_exp/__init__.py
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Expand Up @@ -101,16 +101,6 @@ def get_tag_str(tag, value):
provenance_attrs = load(open(provenance_file_name))
datasets_attrs += provenance_attrs

# Get counts of how often each dataset file is used; a file can
# be linked to multiple dataset objects (HDAs).
datasets_usage_counts = {}
for dataset_attrs in datasets_attrs:
temp_dataset_file_name = \
os.path.realpath(os.path.join(archive_dir, dataset_attrs['file_name']))
if (temp_dataset_file_name not in datasets_usage_counts):
datasets_usage_counts[temp_dataset_file_name] = 0
datasets_usage_counts[temp_dataset_file_name] += 1

# Create datasets.
for dataset_attrs in datasets_attrs:
metadata = dataset_attrs['metadata']
Expand Down Expand Up @@ -150,26 +140,22 @@ def get_tag_str(tag, value):
os.path.realpath(os.path.abspath(os.path.join(archive_dir, dataset_attrs['file_name'])))
if not file_in_dir(temp_dataset_file_name, os.path.join(archive_dir, "datasets")):
raise MalformedContents("Invalid dataset path: %s" % temp_dataset_file_name)
if datasets_usage_counts[temp_dataset_file_name] == 1:
self.app.object_store.update_from_file(hda.dataset, file_name=temp_dataset_file_name, create=True)

# Import additional files if present. Histories exported previously might not have this attribute set.
dataset_extra_files_path = dataset_attrs.get('extra_files_path', None)
if dataset_extra_files_path:
try:
file_list = os.listdir(os.path.join(archive_dir, dataset_extra_files_path))
except OSError:
file_list = []

if file_list:
for extra_file in file_list:
self.app.object_store.update_from_file(
hda.dataset, extra_dir='dataset_%s_files' % hda.dataset.id,
alt_name=extra_file, file_name=os.path.join(archive_dir, dataset_extra_files_path, extra_file),
create=True)
else:
datasets_usage_counts[temp_dataset_file_name] -= 1
shutil.copyfile(temp_dataset_file_name, hda.file_name)
self.app.object_store.update_from_file(hda.dataset, file_name=temp_dataset_file_name, create=True)
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# Import additional files if present. Histories exported previously might not have this attribute set.
dataset_extra_files_path = dataset_attrs.get('extra_files_path', None)
if dataset_extra_files_path:
try:
file_list = os.listdir(os.path.join(archive_dir, dataset_extra_files_path))
except OSError:
file_list = []

if file_list:
for extra_file in file_list:
self.app.object_store.update_from_file(
hda.dataset, extra_dir='dataset_%s_files' % hda.dataset.id,
alt_name=extra_file, file_name=os.path.join(archive_dir, dataset_extra_files_path, extra_file),
create=True)
hda.dataset.set_total_size() # update the filesize record in the database

# Set tags, annotations.
Expand Down