Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation
changeset 24:a70b4c3bdd8b draft
planemo upload
| author | scottx611x |
|---|---|
| date | Thu, 23 Jun 2016 15:28:06 -0400 |
| parents | cb42506ae8ce |
| children | 689075526eb3 |
| files | data_manager_gene_annotation/data_manager/data_manager.py |
| diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/data_manager_gene_annotation/data_manager/data_manager.py Thu Jun 23 15:23:35 2016 -0400 +++ b/data_manager_gene_annotation/data_manager/data_manager.py Thu Jun 23 15:28:06 2016 -0400 @@ -29,8 +29,6 @@ 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) # Generate file_name @@ -39,6 +37,8 @@ block_size = 10 * 1024 * 1024 # 10MB chunked download with open(file_name, 'w+') as f: try: + # Good to note here that requests' iter_content() will + # automatically handle decoding "gzip" and "deflate" formats for buf in response.iter_content(block_size): f.write(buf) except (ContentDecodingError, IOError) as e: @@ -46,13 +46,13 @@ % e) os.remove(file_name) - return file_name + return os.path.join(os.getcwd(), file_name) def main(args): # Attempt to download gene annotation file from given url - gene_annotation_file_name = url_download( + gene_annotation_file_path = url_download( "http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf", args.name) # Update Data Manager JSON and write to file @@ -61,8 +61,8 @@ 'gene_annotation': { 'value': str(datetime.datetime.now()), 'dbkey': str(args.name), - 'name': gene_annotation_file_name.split(".")[0], - 'path': gene_annotation_file_name, + 'name': gene_annotation_file_path.split(".")[0], + 'path': gene_annotation_file_path, } } }