| Previous changeset 21:096657afd137 (2016-06-23) Next changeset 23:cb42506ae8ce (2016-06-23) |
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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/gene_annotation_fetcher.xml data_manager_gene_annotation/data_manager_conf.xml |
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added:
data_manager_gene_annotation/test-data/gene_annotation_out.json |
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removed:
data_manager_gene_annotation/data_manager/gene_annotation/gene_annotation.json |
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| diff -r 096657afd137 -r b47ce1c4373e data_manager_gene_annotation/data_manager/data_manager.py --- a/data_manager_gene_annotation/data_manager/data_manager.py Thu Jun 23 14:25:15 2016 -0400 +++ b/data_manager_gene_annotation/data_manager/data_manager.py Thu Jun 23 15:11:30 2016 -0400 |
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| @@ -12,7 +12,6 @@ dest='output', action='store', help='JSON filename', - default="gene_annotation.json" ) parser.add_argument('--name', dest='name', @@ -30,10 +29,12 @@ def url_download(url, name): + # Good to note here that requests will automatically handle + # content_encoding types: "gzip" and "deflate" response = requests.get(url=url, stream=True) - # Create path that we will write the file to - file_path = 'download_{}.dat'.format(name) + # Generate file_name + file_path = 'gene_annotation_{}'.format(name) block_size = 10 * 1024 * 1024 # 10MB chunked download with open(file_path, 'w+') as f: @@ -53,11 +54,11 @@ # Attempt to download gene annotation file from given url gene_annotation_file_path = url_download(args.url, args.name) - # Update Data Manager Json and write out + # Update Data Manager JSON and write to file data_manager_entry = { 'data_tables': { 'gene_annotation': { - 'date': str(datetime.datetime.now()), + 'value': str(datetime.datetime.now()), 'dbkey': str(args.name), 'name': str(args.name), 'path': gene_annotation_file_path, |
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| diff -r 096657afd137 -r b47ce1c4373e data_manager_gene_annotation/data_manager/gene_annotation/gene_annotation.json --- a/data_manager_gene_annotation/data_manager/gene_annotation/gene_annotation.json Thu Jun 23 14:25:15 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -{"data_tables": {"gene_annotation": {"date": "2016-06-22 15:48:23.783455", "path": "download_a340d4c9-041a-4583-b970-20f949c53872.dat", "name": "a340d4c9-041a-4583-b970-20f949c53872", "dbkey": "a340d4c9-041a-4583-b970-20f949c53872"}}} \ No newline at end of file |
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| diff -r 096657afd137 -r b47ce1c4373e data_manager_gene_annotation/data_manager/gene_annotation_fetcher.xml --- a/data_manager_gene_annotation/data_manager/gene_annotation_fetcher.xml Thu Jun 23 14:25:15 2016 -0400 +++ b/data_manager_gene_annotation/data_manager/gene_annotation_fetcher.xml Thu Jun 23 15:11:30 2016 -0400 |
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| @@ -16,11 +16,17 @@ ]]> </command> <inputs> - <param - help="Enter a unique identifier, or leave blank for an auto-generated uuid" label="Name for this database" name="database_name" type="text" optional="True" /> + <param help="Enter a unique identifier, or leave blank for an auto-generated uuid" label="Name for this database" name="database_name" type="text" optional="True" /> <param label="Enter URL for gene annotation files" name="gene_annotation_url" type="text" optional="False"/> </inputs> <outputs> <data format="data_manager_json" name="out_file" /> </outputs> + <tests> + <test> + <param name="database_name" value="cool_name"/> + <param name="gene_annotation_url" value="http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf"/> + <output name="out_file" file="chr1-hg19_genes.gtf.data_manager_json"/> + </test> + </tests> </tool> |
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| diff -r 096657afd137 -r b47ce1c4373e data_manager_gene_annotation/data_manager_conf.xml --- a/data_manager_gene_annotation/data_manager_conf.xml Thu Jun 23 14:25:15 2016 -0400 +++ b/data_manager_gene_annotation/data_manager_conf.xml Thu Jun 23 15:11:30 2016 -0400 |
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| @@ -4,12 +4,13 @@ <data_manager tool_file="data_manager/gene_annotation_fetcher.xml" id="gene_annotation_fetcher" version="1.0.0"> <data_table name="gene_annotation"> <output> - <column name="date" /> + <column name="value" /> <column name="dbkey" /> <column name="name" /> <column name="path" output_ref="out_file"> <move type="file"> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/gene_annotations/${path}</target> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/gene_annotations/${path}</target> </move> <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/gene_annotations/${path}</value_translation> <value_translation type="function">abspath</value_translation> |