Mercurial > repos > rhpvorderman > data_manager_select_index_by_path

comparison data_manager/path_name_value_key_manager.py @ 0:5f8d9309058b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
author rhpvorderman
date Mon, 25 Sep 2017 03:35:26 -0400
parents
children 8495c49cd056
comparison
equal deleted inserted replaced
-1:000000000000 0:5f8d9309058b
1 #!/usr/bin/env python
2
3 import json
4 import argparse
5 import os
6 import yaml
7
8 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
9 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
10 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
11 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
12 return data_manager_dict
13
14
15 def check_param(name, value, default=None, check_tab=True):
16 if value in [ None, '', '?' ]:
17 if default:
18 print "Using {0} for {1} as no value provided".format( default, name )
19 value = default
20 else:
21 raise Exception( '{0} is not a valid {1}. You must specify a valid {1}.'.format( value, name ) )
22 if check_tab and "\t" in value:
23 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 ) )
24 return value
25
26 def prefix_exists(directory, prefix):
27 '''checks if files exist with prefix in a directory. Returns Boolean'''
28 matched_files = []
29 directory_files = os.listdir(directory)
30 for directory_file in directory_files:
31 if directory_file.startswith(prefix):
32 matched_files.append(directory_file)
33 # Empty list should return False
34 return bool(matched_files)
35
36 def prefix_plus_extension_exists(directory, prefix, extension):
37 '''checks if files exist with prefix in a directory. Returns Boolean'''
38 matched_files = []
39 directory_files = os.listdir(directory)
40 for directory_file in directory_files:
41 if directory_file.startswith(prefix) and directory_file.endswith(extension):
42 matched_files.append(directory_file)
43 # Empty list should return False
44 return bool(matched_files)
45
46 def main():
47
48 #value = "test_value"
49 #name = "test_name"
50 #print '{0} other {1} more{0}'.format(value, name )
51 #print '{0} is not a valid {1}. It may not contain a tab.'.format( value, name )
52
53 #Parse Command Line
54 parser = argparse.ArgumentParser()
55 parser.add_argument( '--value', action='store', type=str, default=None, help='value' )
56 parser.add_argument( '--dbkey', action='store', type=str, default=None, help='dbkey' )
57 parser.add_argument( '--name', action='store', type=str, default=None, help='name' )
58 parser.add_argument( '--path', action='store', type=str, default=None, help='path' )
59 parser.add_argument( '--data_table_name', action='store', type=str, default=None, help='path' )
60 parser.add_argument( '--json_output_file', action='store', type=str, default=None, help='path' )
61 options = parser.parse_args()
62
63 path = check_param("path", options.path)
64 basename = os.path.basename(path)
65 filename = os.path.splitext(basename)[0]
66 name = check_param("name", options.name, default=filename)
67 value = check_param("value", options.value, default=name)
68 dbkey = check_param("dbkey", options.dbkey, default=value)
69 data_table_name = check_param("data_table_name", options.data_table_name)
70 json_output_file = check_param("json_output_file", options.json_output_file, check_tab=False)
71
72 # Check if file or prefix exists
73 indexes = yaml.load(file(os.path.join(os.path.dirname(__file__), 'indexes.yml')))
74 index_dict = indexes.get(data_table_name,{})
75 index_name = index_dict.get('name','index')
76 index_extensions = index_dict.get('extensions', [''])
77 no_prefix = index_dict.get('no_prefix', False)
78 if not no_prefix:
79 dirname = os.path.dirname(path)
80 prefix = basename
81 for extension in index_extensions:
82 if not prefix_plus_extension_exists(dirname,prefix,extension):
83 raise Exception( 'Unable to find files with prefix "{0}" and extension "{1}" in {2}. Is this a valid {3}?'.format( prefix, extension, dirname, index_name ) )
84 else:
85 if not os.path.exists(path):
86 raise Exception( 'Unable to find path {0}.'.format( path ) )
87
88 if os.path.exists(json_output_file):
89 params = json.loads( open( json_output_file ).read() )
90 print "params", params
91 else:
92 params = {}
93
94 data_manager_dict = {}
95 data_table_entry = dict( value=value, dbkey=dbkey, name=name, path=path )
96 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
97
98 #save info to json file
99 with open( json_output_file, 'wb' ) as output_file:
100 output_file.write( json.dumps( data_manager_dict ) )
101 output_file.write( "\n" )
102
103 if __name__ == "__main__":
104 main()