# HG changeset patch
# User rhpvorderman
# Date 1504882571 14400
# Node ID 7bdc452bec9b710cd7cde48b699c835f48740ea3
# Parent afd01fcbea26cc45cb9b3b00a986cdfc184ef315
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit f7e0688eca04c26ceef980c78eb79fc3edbf92db
diff -r afd01fcbea26 -r 7bdc452bec9b data_manager/data_manager_select_index_by_path.xml
--- a/data_manager/data_manager_select_index_by_path.xml Fri Sep 08 08:57:33 2017 -0400
+++ b/data_manager/data_manager_select_index_by_path.xml Fri Sep 08 10:56:11 2017 -0400
@@ -15,7 +15,7 @@
-
+
@@ -26,7 +26,7 @@
-
+
diff -r afd01fcbea26 -r 7bdc452bec9b data_manager/path_name_value_key_manager.py
--- a/data_manager/path_name_value_key_manager.py Fri Sep 08 08:57:33 2017 -0400
+++ b/data_manager/path_name_value_key_manager.py Fri Sep 08 10:56:11 2017 -0400
@@ -1,8 +1,8 @@
#!/usr/bin/env python
import json
-import optparse
-import os.path
+import argparse
+import os
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', {} )
@@ -22,6 +22,15 @@
raise Exception( '{0} is not a valid {1}. It may not contain a tab because these are used as seperators by galaxy .'.format( value, name ) )
return value
+def prefix_exists(directory, prefix):
+ '''checks if files exist with prefix in a directory. Returns Boolean'''
+ matched_files = []
+ directory_files = os.listdir(directory)
+ for directory_file in directory_files:
+ if directory_file.startswith(prefix):
+ matched_files.append(directory_file)
+ # Empty list should return False
+ return bool(matched_files)
def main():
@@ -31,18 +40,28 @@
#print '{0} is not a valid {1}. It may not contain a tab.'.format( value, name )
#Parse Command Line
- parser = optparse.OptionParser()
- parser.add_option( '--value', action='store', type="string", default=None, help='value' )
- parser.add_option( '--dbkey', action='store', type="string", default=None, help='dbkey' )
- parser.add_option( '--name', action='store', type="string", default=None, help='name' )
- parser.add_option( '--path', action='store', type="string", default=None, help='path' )
- parser.add_option( '--data_table_name', action='store', type="string", default=None, help='path' )
- parser.add_option( '--json_output_file', action='store', type="string", default=None, help='path' )
- (options, args) = parser.parse_args()
-
+ parser = argparse.ArgumentParser()
+ parser.add_argument( '--value', action='store', type=str, default=None, help='value' )
+ parser.add_argument( '--dbkey', action='store', type=str, default=None, help='dbkey' )
+ parser.add_argument( '--name', action='store', type=str, default=None, help='name' )
+ parser.add_argument( '--path', action='store', type=str, default=None, help='path' )
+ parser.add_argument( '--data_table_name', action='store', type=str, default=None, help='path' )
+ parser.add_argument( '--json_output_file', action='store', type=str, default=None, help='path' )
+ parser.add_argument( '--no_prefix', action='store_true', help='Does not check the prefix but checks the path. Useful for indexes that reference a single file.')
+ options = parser.parse_args()
+
path = check_param("path", options.path)
- if not os.path.exists(path):
- raise Exception( 'Unable to find path {0}.'.format( path ) )
+
+ # Check if file or prefix exists
+ if not options.no_prefix:
+ dirname = os.path.dirname(path)
+ prefix = os.path.basename(path)
+ if not prefix_exists(dirname,prefix):
+ raise Exception( 'Unable to find files with prefix "{0}" in {1}.'.format( prefix, dirname ) )
+ else:
+ if not os.path.exists(path):
+ raise Exception( 'Unable to find path {0}.'.format( path ) )
+
basename = os.path.basename(path)
filename = os.path.splitext(basename)[0]
name = check_param("name", options.name, default=filename)
@@ -66,5 +85,5 @@
output_file.write( json.dumps( data_manager_dict ) )
output_file.write( "\n" )
-if __name__ == "__main__":
+if __name__ == "__main__":
main()
diff -r afd01fcbea26 -r 7bdc452bec9b test.json
--- a/test.json Fri Sep 08 08:57:33 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"data_tables": {"all_fasta": [{"path": "/home/christian/Dropbox/Gene_data/ercc_and_TPA_mouse_rRNA.fa", "dbkey": "ercc_and_TPA_mouse_rRNA", "name": "ercc_and_TPA_mouse_rRNA", "value": "ercc_and_TPA_mouse_rRNA"}]}}