Mercurial > repos > chrisw > data_manager_monorail_index_fetcher
changeset 3:1032e2599a5e draft
Uploaded
| author | chrisw |
|---|---|
| date | Tue, 12 Nov 2019 00:24:25 -0500 |
| parents | 5615f4cee039 |
| children | cdf5caf02a4f |
| files | data_manager_monorail_index/data_manager/data_manager.py data_manager_monorail_index/data_manager_conf.xml |
| diffstat | 2 files changed, 9 insertions(+), 2 deletions(-) [+] |
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--- a/data_manager_monorail_index/data_manager/data_manager.py Mon Nov 11 23:38:27 2019 -0500 +++ b/data_manager_monorail_index/data_manager/data_manager.py Tue Nov 12 00:24:25 2019 -0500 @@ -19,11 +19,17 @@ def main(args): workdir = os.path.join(os.getcwd(), 'monorail_index') data_manager_entry = {} + ref = args.url.split('/')[-1] if args.name is None: - args.name = args.url.split('/')[-1] + args.name = ref data_manager_entry['value'] = args.name.lower() data_manager_entry['name'] = args.name - data_manager_entry['path'] = args.output + jsonin = open(args.output).read() + sys.stderr.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_json = dict(data_tables=dict(monorail_index=data_manager_entry)) file(args.output, 'w').write(json.dumps(data_manager_json))
--- a/data_manager_monorail_index/data_manager_conf.xml Mon Nov 11 23:38:27 2019 -0500 +++ b/data_manager_monorail_index/data_manager_conf.xml Tue Nov 12 00:24:25 2019 -0500 @@ -8,6 +8,7 @@ <column name="dbkey" /> <column name="name" /> <column name="path"/> + <column name="exons_path"/> </output> </data_table> </data_manager>