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Re-work upload clarification from #5206. #5264

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merged 1 commit into from Jan 4, 2018
Merged

Re-work upload clarification from #5206. #5264

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2 changes: 1 addition & 1 deletion lib/galaxy/tools/actions/upload_common.py
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Expand Up @@ -448,7 +448,7 @@ def _chown(path):
auto_decompress=getattr(uploaded_dataset, "auto_decompress", True),
purge_source=purge_source,
space_to_tab=uploaded_dataset.space_to_tab,
run_as_real_user=trans.app.config.external_chown_script is None,
run_as_real_user=trans.app.config.external_chown_script is not None,
check_content=trans.app.config.check_upload_content,
path=uploaded_dataset.path)
# TODO: This will have to change when we start bundling inputs.
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8 changes: 5 additions & 3 deletions tools/data_source/upload.py
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Expand Up @@ -96,10 +96,12 @@ def add_file(dataset, registry, json_file, output_path):
# if running as the real user so the file can be cleaned up by Galaxy.
purge_source = dataset.get('purge_source', True) and not run_as_real_user

# in_place is True only if we are running as a real user and not importing external paths (i.e.
# in_place is True unless we are running as a real user or importing external paths (i.e.
# this is a real upload and not a path paste or ftp import).
# In this case we try to reuse the uploaded file that has been chowned to this user already.
in_place = run_as_real_user and dataset.type not in ('server_dir', 'path_paste', 'ftp_import')
# in_place should always be False if running as real user because the uploaded file will
# be owned by Galaxy and not the user and it should be False for external paths so Galaxy doesn't
# modify files not controlled by Galaxy.
in_place = not run_as_real_user and dataset.type not in ('server_dir', 'path_paste', 'ftp_import')

# Base on the check_upload_content Galaxy config option and on by default, this enables some
# security related checks on the uploaded content, but can prevent uploads from working in some cases.
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