Mercurial > repos > chrisw > data_manager_monorail_index_fetcher
changeset 9:79f33bace3da draft
Uploaded
| author | chrisw |
|---|---|
| date | Wed, 13 Nov 2019 20:56:31 +0000 |
| parents | b7ad296c8837 |
| children | 7d7328ce424b |
| files | data_manager_monorail_index/data_manager/data_manager.py data_manager_monorail_index/data_manager_conf.xml |
| diffstat | 2 files changed, 11 insertions(+), 18 deletions(-) [+] |
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--- a/data_manager_monorail_index/data_manager/data_manager.py Wed Nov 13 20:22:23 2019 +0000 +++ b/data_manager_monorail_index/data_manager/data_manager.py Wed Nov 13 20:56:31 2019 +0000 @@ -20,16 +20,16 @@ workdir = os.path.join(os.getcwd(), 'monorail_index') data_manager_entry = {} ref = args.url.split('/')[-1] - data_manager_entry['dbkey'] = ref + data_manager_entry['dbkey'] = 'mrail.'+ref data_manager_entry['value'] = ref.lower() jsonin = open(args.output).read() params = json.loads(jsonin) target_directory = params['output_data'][0]['extra_files_path'] #data_manager_entry['path'] = params['output_data'][0]['extra_files_path'] - data_manager_entry['path'] = ref - data_manager_entry['exons_path'] = data_manager_entry['path'] + os.sep + 'gtf' + os.sep + 'exons.bed' - data_manager_json = dict(data_tables=dict(monorail_index=data_manager_entry)) - file(args.output, 'w').write(json.dumps(data_manager_json)) + data_manager_entry['path'] = target_directory + #data_manager_entry['exons_path'] = data_manager_entry['path'] + os.sep + 'gtf' + os.sep + 'exons.bed' + data_manager_json = dict(data_tables={'monorail_index': [data_manager_entry]}) + file(args.output, 'wb').write(json.dumps(data_manager_json)) if __name__ == '__main__': main(args)
--- a/data_manager_monorail_index/data_manager_conf.xml Wed Nov 13 20:22:23 2019 +0000 +++ b/data_manager_monorail_index/data_manager_conf.xml Wed Nov 13 20:56:31 2019 +0000 @@ -3,21 +3,14 @@ <data_manager tool_file="data_manager/monorail_index_fetcher.xml" id="monorail_index_fetcher" version="1.0.0"> <data_table name="monorail_index"> <output> - <column name="value"/> - <column name="dbkey"/> + <column name="value" /> + <column name="dbkey" /> <column name="path" output_ref="out_file"> - <move relativize_symlinks="True" type="directory"> - <!-- <source>${path}</source> - out_file.extra_files_path is used as base by default - if no source, eg for type=directory, then refers to base - --> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">monorail_index/${dbkey}</target> + <move relative_symlinks="True" type="directory"> + <!-- no need to set source, gets taken from out_dir.extra_files_path --> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/monorail_index/${dbkey}</value_translation> - <value_translation type="function">abspath</value_translation> - </column> - <column name="exons_path"> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/monorail_index/${dbkey}/gtf/exons.bed</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/{$dbkey}/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>