| Previous changeset 36:f38beb0743d5 (2016-06-23) Next changeset 38:d27c122c2424 (2016-06-24) |
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Commit message:
planemo upload |
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modified:
data_manager_gene_annotation/data_manager/data_manager.py data_manager_gene_annotation/data_manager_conf.xml data_manager_gene_annotation/test-data/gene_annotation_out.json |
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| diff -r f38beb0743d5 -r 7af38f95bc8d data_manager_gene_annotation/data_manager/data_manager.py --- a/data_manager_gene_annotation/data_manager/data_manager.py Thu Jun 23 17:18:20 2016 -0400 +++ b/data_manager_gene_annotation/data_manager/data_manager.py Thu Jun 23 17:56:47 2016 -0400 |
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| @@ -7,28 +7,14 @@ import requests from requests.exceptions import ContentDecodingError -parser = argparse.ArgumentParser(description='Create data manager json.') -parser.add_argument('--out', - dest='output', - action='store', - help='JSON filename', - ) -parser.add_argument('--name', - dest='name', - action='store', - default=uuid.uuid4(), - help='Data table entry unique ID' - ) -parser.add_argument('--url', - dest='url', - action='store', - help='Download URL' - ) - -args = parser.parse_args() - def url_download(url): + """Attempt to download gene annotation file from a given url + :param url: NodeSet UUID. + :type url: str. + :returns: name of downloaded gene annotation file + :raises: ContentDecodingError, IOError + """ response = requests.get(url=url, stream=True) # Generate file_name @@ -38,7 +24,8 @@ with open(file_name, 'w+') as f: try: # Good to note here that requests' iter_content() will - # automatically handle decoding "gzip" and "deflate" formats + # automatically handle decoding "gzip" and "deflate" encoding + # formats for buf in response.iter_content(block_size): f.write(buf) except (ContentDecodingError, IOError) as e: @@ -46,14 +33,22 @@ % e) os.remove(file_name) - with open("/Users/scott/Desktop/cool.txt", "w+") as f: - f.write(os.path.join(os.getcwd(), file_name)) - f.write("\n") - return file_name -def main(args): +def main(): + + # Generate and parse command line args + parser = argparse.ArgumentParser(description='Create data manager JSON.') + parser.add_argument('--out', dest='output', action='store', + help='JSON filename') + parser.add_argument('--name', dest='name', action='store', + default=uuid.uuid4(), help='Data table entry unique ID' + ) + parser.add_argument('--url', dest='url', action='store', + help='Url to download gtf file from') + + args = parser.parse_args() work_dir = os.getcwd() @@ -76,4 +71,4 @@ f.write(json.dumps(data_manager_entry)) if __name__ == '__main__': - main(args) + main() |
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| diff -r f38beb0743d5 -r 7af38f95bc8d data_manager_gene_annotation/data_manager_conf.xml --- a/data_manager_gene_annotation/data_manager_conf.xml Thu Jun 23 17:18:20 2016 -0400 +++ b/data_manager_gene_annotation/data_manager_conf.xml Thu Jun 23 17:56:47 2016 -0400 |
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| @@ -8,11 +8,11 @@ <column name="dbkey" /> <column name="name" /> <column name="path" output_ref="out_file"> - <move type="file" relativize_symlinks="False"> + <move type="file"> <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/gene_annotations/${name}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">gene_annotations/${name}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/gene_annotations/${name}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gene_annotations/${name}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> |
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| diff -r f38beb0743d5 -r 7af38f95bc8d data_manager_gene_annotation/test-data/gene_annotation_out.json --- a/data_manager_gene_annotation/test-data/gene_annotation_out.json Thu Jun 23 17:18:20 2016 -0400 +++ b/data_manager_gene_annotation/test-data/gene_annotation_out.json Thu Jun 23 17:56:47 2016 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"gene_annotation": {"path": "/Users/scott/PyCharmProjects/Galaxy/galaxy/database/job_working_directory/003/3702/chr1-hg19_genes.gtf", "dbkey": "cool_name", "value": "2016-06-23 17:19:39.412249", "name": "chr1-hg19_genes.gtf"}}} \ No newline at end of file |