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Better I/O when exporting histories.

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This commit is contained in:
John Chilton
2019-03-24 13:53:19 -04:00
parent d7d9da9750
commit 0011463ce5
1 changed files with 10 additions and 13 deletions
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lib/galaxy/tools/imp_exp/__init__.py
+10 -13
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@@ -4,7 +4,7 @@ import logging
import os
import shutil
import tempfile
from json import dumps, load
from json import dump, dumps, load
from sqlalchemy.orm import eagerload_all
from sqlalchemy.sql import expression
@@ -359,9 +359,9 @@ class JobExportHistoryArchiveWrapper:
"tags": history.make_tag_string_list()
}
history_attrs_filename = os.path.join(temp_output_dir, ATTRS_FILENAME_HISTORY)
history_attrs_out = open(history_attrs_filename, 'w')
history_attrs_out.write(dumps(history_attrs))
history_attrs_out.close()
with open(history_attrs_filename, 'w') as history_attrs_out:
dump(history_attrs, history_attrs_out)
jeha.history_attrs_filename = history_attrs_filename
# Write datasets' attributes to file.
@@ -379,13 +379,11 @@ class JobExportHistoryArchiveWrapper:
included_datasets.append(dataset)
datasets_attrs_filename = os.path.join(temp_output_dir, ATTRS_FILENAME_DATASETS)
datasets_attrs_out = open(datasets_attrs_filename, 'w')
datasets_attrs_out.write(dumps(datasets_attrs, cls=HistoryDatasetAssociationEncoder))
datasets_attrs_out.close()
with open(datasets_attrs_filename, 'w') as datasets_attrs_out:
dump(datasets_attrs, datasets_attrs_out, cls=HistoryDatasetAssociationEncoder)
provenance_attrs_out = open(datasets_attrs_filename + ".provenance", 'w')
provenance_attrs_out.write(dumps(provenance_attrs, cls=HistoryDatasetAssociationEncoder))
provenance_attrs_out.close()
with open(datasets_attrs_filename + ".provenance", 'w') as provenance_attrs_out:
dump(provenance_attrs, provenance_attrs_out, cls=HistoryDatasetAssociationEncoder)
#
# Write jobs attributes file.
@@ -456,9 +454,8 @@ class JobExportHistoryArchiveWrapper:
jobs_attrs.append(job_attrs)
jobs_attrs_filename = os.path.join(temp_output_dir, ATTRS_FILENAME_JOBS)
jobs_attrs_out = open(jobs_attrs_filename, 'w')
jobs_attrs_out.write(dumps(jobs_attrs, cls=HistoryDatasetAssociationEncoder))
jobs_attrs_out.close()
with open(jobs_attrs_filename, 'w') as jobs_attrs_out:
dump(jobs_attrs, jobs_attrs_out, cls=HistoryDatasetAssociationEncoder)
#
# Create and return command line for running tool.