Mercurial > repos > chrisw > data_manager_monorail_index_fetcher
changeset 6:0d90ce4ea724 draft
Uploaded
| author | chrisw |
|---|---|
| date | Wed, 13 Nov 2019 19:57:57 +0000 |
| parents | 0299ada36cce |
| children | 0aabefdd8b9f |
| files | data_manager_monorail_index/.data_manager_conf.xml.swp data_manager_monorail_index/data_manager/.data_manager.py.swp data_manager_monorail_index/data_manager/.monorail_index_fetcher.xml.swp data_manager_monorail_index/data_manager/data_manager.py data_manager_monorail_index/data_manager/monorail_index_fetcher.xml data_manager_monorail_index/data_manager_conf.xml |
| diffstat | 6 files changed, 10 insertions(+), 17 deletions(-) [+] |
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--- a/data_manager_monorail_index/data_manager/data_manager.py Tue Nov 12 01:18:47 2019 -0500 +++ b/data_manager_monorail_index/data_manager/data_manager.py Wed Nov 13 19:57:57 2019 +0000 @@ -20,18 +20,16 @@ workdir = os.path.join(os.getcwd(), 'monorail_index') data_manager_entry = {} ref = args.url.split('/')[-1] - if args.name is None: - args.name = ref - data_manager_entry['value'] = args.name.lower() - data_manager_entry['name'] = args.name + data_manager_entry['dbkey'] = ref + data_manager_entry['value'] = ref.lower() jsonin = open(args.output).read() - sys.stdout.write(jsonin) 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['exons_path'] = data_manager_entry['path'] + os.sep + ref + os.sep + 'gtf' + os.sep + 'exons.bed' + #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, 'a').write(json.dumps(data_manager_json)) + file(args.output, 'w').write(json.dumps(data_manager_json)) if __name__ == '__main__': main(args)
--- a/data_manager_monorail_index/data_manager/monorail_index_fetcher.xml Tue Nov 12 01:18:47 2019 -0500 +++ b/data_manager_monorail_index/data_manager/monorail_index_fetcher.xml Wed Nov 13 19:57:57 2019 +0000 @@ -14,12 +14,8 @@ #if $monorail_index_url: --url "${monorail_index_url}" #end if - #if $index_name: - --name "${index_name}" - #end if ]]></command> <inputs> - <param help="Enter a unique identifier, or leave blank to use the reference ID at end of base URL below" label="Name for this Monorail index set" name="index_name" type="text" optional="True" /> <param label="Enter base URL for Monorail index directories (e.g. http://snaptron.cs.jhu.edu/data/monorail/ath10)" name="monorail_index_url" type="text" /> </inputs> <outputs>
--- a/data_manager_monorail_index/data_manager_conf.xml Tue Nov 12 01:18:47 2019 -0500 +++ b/data_manager_monorail_index/data_manager_conf.xml Wed Nov 13 19:57:57 2019 +0000 @@ -6,20 +6,19 @@ <output> <column name="value"/> <column name="dbkey"/> - <column name="name"/> <column name="path" output_ref="out_file"> <move relativize_symlinks="True" type="directory"> <!-- <source>${path}</source> out_file.extra_files_path is used as base by default - if no source, eg for type=directory, then refers to base + if no source, eg for type=directory, then refers to base --> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">monorail_index/${name}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">monorail_index/${dbkey}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/monorail_index/${name}</value_translation> + <value_translation>${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/${name}/gtf/exons.bed</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/monorail_index/${dbkey}/gtf/exons.bed</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>