Mercurial > repos > mvdbeek > data_manager_fetch_genome_dbkeys_all_fasta_compressed
changeset 5:86a9ce3761d8 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit c6314fce6475715c091db463f26703440d71349c-dirty
| author | mvdbeek |
|---|---|
| date | Thu, 25 Aug 2016 06:10:18 -0400 |
| parents | 0007b48a5bb9 |
| children | 8364a73bd363 |
| files | data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py |
| diffstat | 1 files changed, 10 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py Thu Aug 25 05:51:13 2016 -0400 +++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py Thu Aug 25 06:10:18 2016 -0400 @@ -14,7 +14,7 @@ try: # For Python 3.0 and later from urllib.request import urlopen - from io import BytesIO as StringIO + from io import StringIO from io import UnsupportedOperation except ImportError: # Fall back to Python 2's urllib2 @@ -37,6 +37,13 @@ sys.exit(1) +def read_urllib(response): + charset = response.headers.get_content_charset() + if not charset: + charset = 'utf-8' + response.read().decode(charset)) + + def get_dbkey_dbname_id_name( params, dbkey_description=None ): dbkey = params['param_dict']['dbkey_source']['dbkey'] #TODO: ensure sequence_id is unique and does not already appear in location file @@ -204,7 +211,7 @@ def _download_file(start, fh): tmp = tempfile.NamedTemporaryFile() tmp.write(start) - tmp.write(fh.read()) + tmp.write(read_urllib(fh)) tmp.flush() tmp.seek(0) return tmp @@ -430,7 +437,7 @@ filename = args[0] - params = loads( open( filename ).read() ) + params = loads( open( filename ).read().decode('utf-8')) target_directory = params[ 'output_data' ][0]['extra_files_path'] os.mkdir( target_directory ) data_manager_dict = {}