--- a/data_manager/kallisto_index_builder.py	Sat Aug 05 04:02:01 2017 -0400
+++ b/data_manager/kallisto_index_builder.py	Sun Nov 22 12:50:23 2020 +0000
@@ -3,15 +3,15 @@
 from __future__ import print_function
 
 import argparse
+import json
 import os
 import subprocess
 import sys
-from json import dumps, loads
 
 DEFAULT_DATA_TABLE_NAME = "kallisto_indexes"
 
 
-def get_id_name( params, dbkey, fasta_description=None):
+def get_id_name(params, dbkey, fasta_description=None):
     # TODO: ensure sequence_id is unique and does not already appear in location file
     sequence_id = params['param_dict']['sequence_id']
     if not sequence_id:
@@ -25,57 +25,59 @@
     return sequence_id, sequence_name
 
 
-def build_kallisto_index( data_manager_dict, options, params, sequence_id, sequence_name ):
+def build_kallisto_index(data_manager_dict, options, params, sequence_id, sequence_name):
     data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME
-    target_directory = params[ 'output_data' ][0]['extra_files_path']
-    if not os.path.exists( target_directory ):
-        os.mkdir( target_directory )
-    fasta_base_name = os.path.split( options.fasta_filename )[-1]
-    sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
-    os.symlink( options.fasta_filename, sym_linked_fasta_filename )
-    args = [ 'kallisto', 'index' ]
-    args.extend( [ sym_linked_fasta_filename, '-i', sequence_id ] )
-    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
+    target_directory = params['output_data'][0]['extra_files_path']
+    if not os.path.exists(target_directory):
+        os.mkdir(target_directory)
+    fasta_base_name = os.path.split(options.fasta_filename)[-1]
+    sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
+    os.symlink(options.fasta_filename, sym_linked_fasta_filename)
+    args = ['kallisto', 'index']
+    args.extend([sym_linked_fasta_filename, '-i', sequence_id])
+    proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
     return_code = proc.wait()
     if return_code:
         print("Error building index.", file=sys.stderr)
-        sys.exit( return_code )
-    data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id )
-    _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+        sys.exit(return_code)
+    data_table_entry = dict(value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id)
+    _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 )
+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 main():
     # Parse Command Line
     parser = argparse.ArgumentParser()
-    parser.add_argument( '--output', dest='output', action='store', type=str, default=None )
-    parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None )
-    parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None )
-    parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None )
-    parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='kallisto_indexes' )
+    parser.add_argument('--output', dest='output', action='store', type=str, default=None)
+    parser.add_argument('--fasta_filename', dest='fasta_filename', action='store', type=str, default=None)
+    parser.add_argument('--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None)
+    parser.add_argument('--fasta_description', dest='fasta_description', action='store', type=str, default=None)
+    parser.add_argument('--data_table_name', dest='data_table_name', action='store', type=str, default='kallisto_indexes')
     options = parser.parse_args()
 
     filename = options.output
 
-    params = loads( open( filename ).read() )
+    with open(filename) as fh:
+        params = json.load(fh)
     data_manager_dict = {}
 
-    if options.fasta_dbkey in [ None, '', '?' ]:
-        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) )
+    if options.fasta_dbkey in [None, '', '?']:
+        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (options.fasta_dbkey))
 
-    sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description )
+    sequence_id, sequence_name = get_id_name(params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description)
 
     # build the index
-    build_kallisto_index( data_manager_dict, options, params, sequence_id, sequence_name )
+    build_kallisto_index(data_manager_dict, options, params, sequence_id, sequence_name)
 
     # save info to json file
-    open( filename, 'w' ).write( dumps( data_manager_dict ) )
+    with open(filename, 'w') as fh:
+        json.dump(data_manager_dict, fh, sort_keys=True)
 
 
 if __name__ == "__main__":