|
0
|
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
|
|
|
5 import urllib
|
|
|
6 import sys
|
|
|
7 import os
|
|
|
8 import optparse
|
|
|
9 import xml.etree.ElementTree as ElementTree
|
|
|
10 from galaxy import eggs #eggs needs to be imported so that galaxy.util can find docutils egg...
|
|
|
11 from galaxy.util.json import from_json_string, to_json_string
|
|
|
12 from galaxy.util import get_charset_from_http_headers
|
|
|
13 import galaxy.model # need to import model before sniff to resolve a circular import dependency
|
|
|
14 from galaxy.datatypes import sniff
|
|
|
15 from galaxy.datatypes.registry import Registry
|
|
|
16 from galaxy.jobs import TOOL_PROVIDED_JOB_METADATA_FILE
|
|
|
17
|
|
|
18 assert sys.version_info[:2] >= ( 2, 4 )
|
|
|
19
|
|
|
20 def stop_err( msg ):
|
|
|
21 sys.stderr.write( msg )
|
|
|
22 sys.exit()
|
|
|
23
|
|
|
24 GALAXY_PARAM_PREFIX = 'GALAXY'
|
|
|
25 GALAXY_ROOT_DIR = os.path.realpath( os.path.join( os.path.split( os.path.realpath( __file__ ) )[0], '..', '..' ) )
|
|
|
26 GALAXY_DATATYPES_CONF_FILE = os.path.join( GALAXY_ROOT_DIR, 'datatypes_conf.xml' )
|
|
|
27
|
|
|
28 def load_input_parameters( filename, erase_file = True ):
|
|
|
29 datasource_params = {}
|
|
|
30 try:
|
|
|
31 json_params = from_json_string( open( filename, 'r' ).read() )
|
|
|
32 datasource_params = json_params.get( 'param_dict' )
|
|
|
33 except:
|
|
|
34 json_params = None
|
|
|
35 for line in open( filename, 'r' ):
|
|
|
36 try:
|
|
|
37 line = line.strip()
|
|
|
38 fields = line.split( '\t' )
|
|
|
39 datasource_params[ fields[0] ] = fields[1]
|
|
|
40 except:
|
|
|
41 continue
|
|
|
42 if erase_file:
|
|
|
43 open( filename, 'w' ).close() #open file for writing, then close, removes params from file
|
|
|
44 return json_params, datasource_params
|
|
|
45
|
|
|
46 def deconstruct_multi_filename( multi_filename ):
|
|
|
47 keys = ['primary', 'id', 'name', 'visible', 'file_type', 'dbkey']
|
|
|
48 return ( dict( zip( keys, multi_filename.split('_') ) ) )
|
|
|
49
|
|
|
50 def construct_multi_filename( id, name, file_type, dbkey=None):
|
|
|
51 """ Implementation of *Number of Output datasets cannot be determined until tool run* from documentation_.
|
|
|
52 .. _documentation: http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
|
|
|
53 """
|
|
|
54 if dbkey:
|
|
|
55 filename = "%s_%s_%s_%s_%s_%s" % ( 'primary', id, name, 'visible', file_type, dbkey )
|
|
|
56 else:
|
|
|
57 filename = "%s_%s_%s_%s_%s" % ( 'primary', id, name, 'visible', file_type )
|
|
|
58
|
|
|
59 return filename
|
|
|
60
|
|
|
61 def xml_save_to_newfile_directory( xmlfile, directory, id, enhanced_handling=False, datatypes_registry=None ):
|
|
|
62 """ Open xmlfile, parse all URLs to fetch. Fetch each file, saving to ``directory``.
|
|
|
63 Save first file for last and return for ``page``.
|
|
|
64
|
|
|
65 Schema
|
|
|
66
|
|
|
67 ::
|
|
|
68
|
|
|
69 <?xml version="1.0"?>
|
|
|
70 <!DOCTYPE downloads [
|
|
|
71 <!ELEMENT downloads (download)>
|
|
|
72 <!ELEMENT download (resource,url,meta)>
|
|
|
73 <!ELEMENT resource (#PCDATA)>
|
|
|
74 <!ELEMENT url (#PCDATA)>
|
|
|
75 <!ELEMENT id (#PCDATA)>
|
|
|
76 <!ELEMENT meta (id,format,type,summary,feature,genome,technique,instrument,assay,sample,description,PMID)>
|
|
|
77 <!ELEMENT id (#PCDATA)>
|
|
|
78 <!ELEMENT format (#PCDATA)>
|
|
|
79 <!ELEMENT type (#PCDATA)>
|
|
|
80 <!ELEMENT summary (#PCDATA)>
|
|
|
81 <!ELEMENT feature (#PCDATA)>
|
|
|
82 <!ELEMENT genome (#PCDATA)>
|
|
|
83 <!ELEMENT technique (#PCDATA)>
|
|
|
84 <!ELEMENT instrument (#PCDATA)>
|
|
|
85 <!ELEMENT assay (#PCDATA)>
|
|
|
86 <!ELEMENT sample (#PCDATA)>
|
|
|
87 <!ELEMENT description (#PCDATA)>
|
|
|
88 <!ELEMENT PMID (#PCDATA)>
|
|
|
89 ]>
|
|
|
90 """
|
|
|
91 root = ElementTree.fromstring(xmlfile.read())
|
|
|
92 if root.tag != 'downloads':
|
|
|
93 stop_err( 'The remote data source application has not sent back a URL parameter in the request.' )
|
|
|
94 # traverse xml schema to find URLs, names, and dbkeys
|
|
|
95 files_to_fetch = []
|
|
|
96 complete = False
|
|
|
97
|
|
|
98 for child in root:
|
|
|
99 if (child.tag == 'download') and (complete == True):
|
|
|
100 files_to_fetch.append( ( construct_multi_filename( id, name, file_type, dbkey ), URL ) )
|
|
|
101
|
|
|
102 for sub in child:
|
|
|
103 if sub.tag == 'url':
|
|
|
104 URL = sub.text
|
|
|
105 elif sub.tag == 'meta':
|
|
|
106
|
|
|
107 for meta in sub:
|
|
|
108 if meta.tag == 'id':
|
|
|
109 name = meta.text
|
|
|
110 elif meta.tag == 'genome':
|
|
|
111 dbkey = meta.text
|
|
|
112 elif meta.tag == 'format':
|
|
|
113 file_type = meta.text
|
|
|
114 # hit the end of our schema
|
|
|
115 files_to_fetch.append( ( construct_multi_filename( id, name, file_type, dbkey ), URL ) )
|
|
|
116
|
|
|
117 if len(files_to_fetch) > 1:
|
|
|
118 for filename, URL in files_to_fetch[1:]:
|
|
|
119 try:
|
|
|
120 cur_filename = os.path.join( directory, filename )
|
|
|
121 page = urllib.urlopen( URL )
|
|
|
122 multi_dict = deconstruct_multi_filename( filename )
|
|
|
123 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 ) )
|
|
|
124 if enhanced_handling:
|
|
|
125 ext = sniff.handle_uploaded_dataset_file( cur_filename, datatypes_registry, ext = multi_dict['file_type'], is_multi_byte = is_multi_byte )
|
|
|
126 except Exception, e:
|
|
|
127 stop_err( 'Unable to fetch %s:\n%s' % ( URL, e ) )
|
|
|
128
|
|
|
129 # pass page back to main
|
|
|
130 return ( files_to_fetch[0][0], urllib.urlopen( files_to_fetch[0][1] ) )
|
|
|
131
|
|
|
132 def __main__():
|
|
|
133 # Parse the command line options
|
|
|
134 usage = "Usage: ncbi_connector.py filename max_size [options]"
|
|
|
135 parser = optparse.OptionParser(usage = usage)
|
|
|
136 parser.add_option("-x", "--xml",
|
|
|
137 action="store_true", dest="xmlfile", help="filename defines external resources as xml")
|
|
|
138 parser.add_option("-i", "--id", type="string",
|
|
|
139 action="store", dest="id", help="output id")
|
|
|
140 parser.add_option("-p", "--path", type="string",
|
|
|
141 action="store", dest="newfilepath", help="new file path")
|
|
|
142
|
|
|
143 (options, args) = parser.parse_args()
|
|
|
144
|
|
|
145 filename = args[0]
|
|
|
146 try:
|
|
|
147 max_file_size = int( args[1] )
|
|
|
148 except:
|
|
|
149 max_file_size = 0
|
|
|
150
|
|
|
151 job_params, params = load_input_parameters( filename )
|
|
|
152 if job_params is None: #using an older tabular file
|
|
|
153 enhanced_handling = False
|
|
|
154 job_params = dict( param_dict = params )
|
|
|
155 job_params[ 'output_data' ] = [ dict( out_data_name = 'output',
|
|
|
156 ext = 'data',
|
|
|
157 file_name = filename,
|
|
|
158 extra_files_path = None ) ]
|
|
|
159 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 )
|
|
|
160 else:
|
|
|
161 enhanced_handling = True
|
|
|
162 json_file = open( job_params[ 'job_config' ][ 'TOOL_PROVIDED_JOB_METADATA_FILE' ], 'w' ) #specially named file for output junk to pass onto set metadata
|
|
|
163
|
|
|
164 datatypes_registry = Registry()
|
|
|
165 datatypes_registry.load_datatypes( root_dir = job_params[ 'job_config' ][ 'GALAXY_ROOT_DIR' ], config = job_params[ 'job_config' ][ 'GALAXY_DATATYPES_CONF_FILE' ] )
|
|
|
166
|
|
|
167 URL = params.get( 'URL', None ) #using exactly URL indicates that only one dataset is being downloaded
|
|
|
168 URL_method = params.get( 'URL_method', None )
|
|
|
169
|
|
|
170 # The Python support for fetching resources from the web is layered. urllib uses the httplib
|
|
|
171 # library, which in turn uses the socket library. As of Python 2.3 you can specify how long
|
|
|
172 # a socket should wait for a response before timing out. By default the socket module has no
|
|
|
173 # timeout and can hang. Currently, the socket timeout is not exposed at the httplib or urllib2
|
|
|
174 # levels. However, you can set the default timeout ( in seconds ) globally for all sockets by
|
|
|
175 # doing the following.
|
|
|
176 socket.setdefaulttimeout( 600 )
|
|
|
177
|
|
|
178 for data_dict in job_params[ 'output_data' ]:
|
|
|
179 cur_filename = data_dict.get( 'file_name', filename )
|
|
|
180 cur_URL = params.get( '%s|%s|URL' % ( GALAXY_PARAM_PREFIX, data_dict[ 'out_data_name' ] ), URL )
|
|
|
181 if not cur_URL:
|
|
|
182 open( cur_filename, 'w' ).write( "" )
|
|
|
183 stop_err( 'The remote data source application has not sent back a URL parameter in the request.' )
|
|
|
184
|
|
|
185 # The following calls to urllib.urlopen() will use the above default timeout
|
|
|
186 try:
|
|
|
187 if not URL_method or URL_method == 'get':
|
|
|
188 page = urllib.urlopen( cur_URL )
|
|
|
189 elif URL_method == 'post':
|
|
|
190 page = urllib.urlopen( cur_URL, urllib.urlencode( params ) )
|
|
|
191 except Exception, e:
|
|
|
192 stop_err( 'The remote data source application may be off line, please try again later. Error: %s' % str( e ) )
|
|
|
193 if max_file_size:
|
|
|
194 file_size = int( page.info().get( 'Content-Length', 0 ) )
|
|
|
195 if file_size > max_file_size:
|
|
|
196 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 ) )
|
|
|
197 # If xmlfile is provided, fetch files 2 through n and save to new_file_path, replace page with file 1
|
|
|
198 if options.xmlfile:
|
|
|
199 multi_filename, page = xml_save_to_newfile_directory( page, options.newfilepath, options.id, enhanced_handling, datatypes_registry )
|
|
|
200 multi_dict = deconstruct_multi_filename( multi_filename )
|
|
|
201
|
|
|
202 #do sniff stream for multi_byte
|
|
|
203 try:
|
|
|
204 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 ) )
|
|
|
205 except Exception, e:
|
|
|
206 stop_err( 'Unable to fetch %s:\n%s' % ( cur_URL, e ) )
|
|
|
207
|
|
|
208 #here import checks that upload tool performs
|
|
|
209 if enhanced_handling:
|
|
|
210 try:
|
|
|
211 ext = sniff.handle_uploaded_dataset_file( filename, datatypes_registry, ext = data_dict[ 'ext' ], is_multi_byte = is_multi_byte )
|
|
|
212 except Exception, e:
|
|
|
213 stop_err( str( e ) )
|
|
|
214 info = dict( type = 'dataset',
|
|
|
215 dataset_id = data_dict[ 'dataset_id' ],
|
|
|
216 ext = ext)
|
|
|
217
|
|
|
218 json_file.write( "%s\n" % to_json_string( info ) )
|
|
|
219
|
|
|
220 if __name__ == "__main__": __main__()
|
