Mercurial > repos > crs4 > dorina
comparison data_source.py @ 1:7e66353ca9d0 draft default tip
Deleted selected files
author | crs4 |
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date | Mon, 10 Oct 2016 06:15:50 -0400 |
parents | c3a93255587e |
children |
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0:c3a93255587e | 1:7e66353ca9d0 |
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1 #!/usr/bin/env python | |
2 # Retrieves data from external data source applications and stores in a dataset file. | |
3 # Data source application parameters are temporarily stored in the dataset file. | |
4 import socket, urllib, sys, os | |
5 from galaxy import eggs #eggs needs to be imported so that galaxy.util can find docutils egg... | |
6 from json import loads, dumps | |
7 from galaxy.util import get_charset_from_http_headers | |
8 import galaxy.model # need to import model before sniff to resolve a circular import dependency | |
9 from galaxy.datatypes import sniff | |
10 from galaxy.datatypes.registry import Registry | |
11 from galaxy.jobs import TOOL_PROVIDED_JOB_METADATA_FILE | |
12 | |
13 assert sys.version_info[:2] >= ( 2, 4 ) | |
14 | |
15 def stop_err( msg ): | |
16 sys.stderr.write( msg ) | |
17 sys.exit() | |
18 | |
19 GALAXY_PARAM_PREFIX = 'GALAXY' | |
20 GALAXY_ROOT_DIR = os.path.realpath( os.path.join( os.path.split( os.path.realpath( __file__ ) )[0], '..', '..' ) ) | |
21 GALAXY_DATATYPES_CONF_FILE = os.path.join( GALAXY_ROOT_DIR, 'datatypes_conf.xml' ) | |
22 | |
23 def load_input_parameters( filename, erase_file = True ): | |
24 datasource_params = {} | |
25 try: | |
26 json_params = loads( open( filename, 'r' ).read() ) | |
27 datasource_params = json_params.get( 'param_dict' ) | |
28 except: | |
29 json_params = None | |
30 for line in open( filename, 'r' ): | |
31 try: | |
32 line = line.strip() | |
33 fields = line.split( '\t' ) | |
34 datasource_params[ fields[0] ] = fields[1] | |
35 except: | |
36 continue | |
37 if erase_file: | |
38 open( filename, 'w' ).close() #open file for writing, then close, removes params from file | |
39 return json_params, datasource_params | |
40 | |
41 def __main__(): | |
42 filename = sys.argv[1] | |
43 try: | |
44 max_file_size = int( sys.argv[2] ) | |
45 except: | |
46 max_file_size = 0 | |
47 | |
48 job_params, params = load_input_parameters( filename ) | |
49 | |
50 if job_params is None: #using an older tabular file | |
51 enhanced_handling = False | |
52 job_params = dict( param_dict = params ) | |
53 job_params[ 'output_data' ] = [ dict( out_data_name = 'output', | |
54 ext = 'data', | |
55 file_name = filename, | |
56 extra_files_path = None ) ] | |
57 job_params[ 'job_config' ] = dict( GALAXY_ROOT_DIR=GALAXY_ROOT_DIR, GALAXY_DATATYPES_CONF_FILE=GALAXY_DATATYPES_CONF_FILE, TOOL_PROVIDED_JOB_METADATA_FILE = TOOL_PROVIDED_JOB_METADATA_FILE ) | |
58 else: | |
59 enhanced_handling = True | |
60 json_file = open( job_params[ 'job_config' ][ 'TOOL_PROVIDED_JOB_METADATA_FILE' ], 'w' ) #specially named file for output junk to pass onto set metadata | |
61 | |
62 datatypes_registry = Registry() | |
63 datatypes_registry.load_datatypes( root_dir = job_params[ 'job_config' ][ 'GALAXY_ROOT_DIR' ], config = job_params[ 'job_config' ][ 'GALAXY_DATATYPES_CONF_FILE' ] ) | |
64 | |
65 URL = params.get( 'URL', None ) #using exactly URL indicates that only one dataset is being downloaded | |
66 URL_method = params.get( 'URL_method', None ) | |
67 | |
68 # The Python support for fetching resources from the web is layered. urllib uses the httplib | |
69 # library, which in turn uses the socket library. As of Python 2.3 you can specify how long | |
70 # a socket should wait for a response before timing out. By default the socket module has no | |
71 # timeout and can hang. Currently, the socket timeout is not exposed at the httplib or urllib2 | |
72 # levels. However, you can set the default timeout ( in seconds ) globally for all sockets by | |
73 # doing the following. | |
74 socket.setdefaulttimeout( 600 ) | |
75 | |
76 for data_dict in job_params[ 'output_data' ]: | |
77 cur_filename = data_dict.get( 'file_name', filename ) | |
78 cur_URL = params.get( '%s|%s|URL' % ( GALAXY_PARAM_PREFIX, data_dict[ 'out_data_name' ] ), URL ) | |
79 if not cur_URL: | |
80 open( cur_filename, 'w' ).write( "" ) | |
81 stop_err( 'The remote data source application has not sent back a URL parameter in the request.' ) | |
82 | |
83 # The following calls to urllib.urlopen() will use the above default timeout | |
84 try: | |
85 if not URL_method or URL_method == 'get': | |
86 page = urllib.urlopen( cur_URL ) | |
87 elif URL_method == 'post': | |
88 page = urllib.urlopen( cur_URL, urllib.urlencode( params ) ) | |
89 except Exception, e: | |
90 stop_err( 'The remote data source application may be off line, please try again later. Error: %s' % str( e ) ) | |
91 if max_file_size: | |
92 file_size = int( page.info().get( 'Content-Length', 0 ) ) | |
93 if file_size > max_file_size: | |
94 stop_err( 'The size of the data (%d bytes) you have requested exceeds the maximum allowed (%d bytes) on this server.' % ( file_size, max_file_size ) ) | |
95 #do sniff stream for multi_byte | |
96 try: | |
97 cur_filename, is_multi_byte = sniff.stream_to_open_named_file( page, os.open( cur_filename, os.O_WRONLY | os.O_CREAT ), cur_filename, source_encoding=get_charset_from_http_headers( page.headers ) ) | |
98 except Exception, e: | |
99 stop_err( 'Unable to fetch %s:\n%s' % ( cur_URL, e ) ) | |
100 | |
101 #here import checks that upload tool performs | |
102 if enhanced_handling: | |
103 try: | |
104 ext = sniff.handle_uploaded_dataset_file( filename, datatypes_registry, ext = data_dict[ 'ext' ], is_multi_byte = is_multi_byte ) | |
105 except Exception, e: | |
106 stop_err( str( e ) ) | |
107 info = dict( type = 'dataset', | |
108 dataset_id = data_dict[ 'dataset_id' ], | |
109 ext = ext) | |
110 | |
111 json_file.write( "%s\n" % dumps( info ) ) | |
112 | |
113 if __name__ == "__main__": __main__() |