Mercurial > repos > matt-shirley > ncbi_epi_browse

comparison ncbi_connector.py @ 9:58917de44665 draft

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author matt-shirley
date Mon, 30 Sep 2013 12:46:06 -0400
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8:3e7669c9ecbc 9:58917de44665
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__()