# HG changeset patch
# User sanbi-uwc
# Date 1457178475 18000
# Node ID c276a826fc4b2963a0abb6da8ae2b94eef6652ac
# Parent 38d9721a5251d3d4cea6f9fbfff5708541761884
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 1e4e16c747ca6ef261d3307f47a09ff1d49756a1
diff -r 38d9721a5251 -r c276a826fc4b data_manager/novocraft_index_builder.py
--- a/data_manager/novocraft_index_builder.py Fri Mar 04 09:24:47 2016 -0500
+++ b/data_manager/novocraft_index_builder.py Sat Mar 05 06:47:55 2016 -0500
@@ -14,6 +14,8 @@
from json import loads, dumps
+DEFAULT_DATA_TABLE_NAME = "novocraft_indexes"
+
def get_dbkey_id_name(params, dbkey_description=None):
dbkey = params['param_dict']['dbkey']
# TODO: ensure sequence_id is unique and does not already appear in location file
@@ -28,8 +30,7 @@
sequence_name = dbkey
return dbkey, sequence_id, sequence_name
-
-def _make_novocraft_index(fasta_filename, target_directory):
+def _make_novocraft_index(data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME):
if os.path.exists(target_directory) and not os.path.isdir(target_directory):
print("Output directory path already exists but is not a directory: {}".format(target_directory),
file=sys.stderr)
@@ -51,22 +52,28 @@
check_call(cmdline)
except CalledProcessError:
print("Error building RNA STAR index", file=sys.stderr)
- return (target_directory)
+
+ data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=target_directory )
+ _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
+ data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+ data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
+ data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
+ return data_manager_dict
-def download_from_url(params, target_directory):
+def download_from_url( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
# TODO: we should automatically do decompression here
urls = filter(bool, map(lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split('\n')))
fasta_reader = [urllib2.urlopen(url) for url in urls]
- _make_novocraft_index(fasta_reader, target_directory)
+ _make_novocraft_index(data_manager_dict, fasta_reader, target_directory, dbkey, sequence_id, sequence_name, data_table_name)
-
-def download_from_history( params, target_directory):
+def download_from_history( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
# TODO: allow multiple FASTA input files
input_filename = params['param_dict']['reference_source']['input_fasta']
- _make_novocraft_index(input_filename, target_directory)
+ _make_novocraft_index(data_manager_dict, input_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name)
REFERENCE_SOURCE_TO_DOWNLOAD = dict(url=download_from_url, history=download_from_history)
@@ -82,18 +89,17 @@
params = loads(open(filename).read())
target_directory = params['output_data'][0]['extra_files_path']
os.makedirs(target_directory)
+ data_manager_dict = {}
dbkey, sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description)
+
if dbkey in [None, '', '?']:
raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
# Fetch the FASTA
REFERENCE_SOURCE_TO_DOWNLOAD[params['param_dict']['reference_source']['reference_source_selector']]\
- (params, target_directory)
+ (data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=args.data_table_name or DEFAULT_DATA_TABLE_NAME)
- data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=target_directory)
-
- output_datatable_dict = dict(data_tables={args.data_table_name: [data_table_entry]})
- open(filename, 'wb').write(dumps(output_datatable_dict))
+ open(filename, 'wb').write(dumps( data_manager_dict ))
if __name__ == "__main__": main()
diff -r 38d9721a5251 -r c276a826fc4b data_manager/novocraft_index_builder.xml
--- a/data_manager/novocraft_index_builder.xml Fri Mar 04 09:24:47 2016 -0500
+++ b/data_manager/novocraft_index_builder.xml Sat Mar 05 06:47:55 2016 -0500
@@ -6,7 +6,7 @@
- novocraft_index_builder.py "${out_file}" --dbkey_description ${ dbkey.get_display_text() } --data_table_name "novocraft_index"
+ novocraft_index_builder.py "${out_file}" --dbkey_description ${ dbkey.get_display_text() } --data_table_name "novocraft_indexes"
diff -r 38d9721a5251 -r c276a826fc4b data_manager_conf.xml
--- a/data_manager_conf.xml Fri Mar 04 09:24:47 2016 -0500
+++ b/data_manager_conf.xml Sat Mar 05 06:47:55 2016 -0500
@@ -1,14 +1,13 @@
-
+