--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ncbi_connector.py	Mon Sep 30 12:46:06 2013 -0400
@@ -0,0 +1,220 @@
+#!/usr/bin/env python
+# Retrieves data from external data source applications and stores in a dataset file.
+# Data source application parameters are temporarily stored in the dataset file.
+import socket
+import urllib
+import sys
+import os
+import optparse
+import xml.etree.ElementTree as ElementTree
+from galaxy import eggs #eggs needs to be imported so that galaxy.util can find docutils egg...
+from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util import get_charset_from_http_headers
+import galaxy.model # need to import model before sniff to resolve a circular import dependency
+from galaxy.datatypes import sniff
+from galaxy.datatypes.registry import Registry
+from galaxy.jobs import TOOL_PROVIDED_JOB_METADATA_FILE
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+GALAXY_PARAM_PREFIX = 'GALAXY'
+GALAXY_ROOT_DIR = os.path.realpath( os.path.join( os.path.split( os.path.realpath( __file__ ) )[0], '..', '..' ) )
+GALAXY_DATATYPES_CONF_FILE = os.path.join( GALAXY_ROOT_DIR, 'datatypes_conf.xml' )
+
+def load_input_parameters( filename, erase_file = True ):
+    datasource_params = {}
+    try:
+        json_params = from_json_string( open( filename, 'r' ).read() )
+        datasource_params = json_params.get( 'param_dict' )
+    except:
+        json_params = None
+        for line in open( filename, 'r' ):
+            try:
+                line = line.strip()
+                fields = line.split( '\t' )
+                datasource_params[ fields[0] ] = fields[1]
+            except:
+                continue
+    if erase_file:
+        open( filename, 'w' ).close() #open file for writing, then close, removes params from file
+    return json_params, datasource_params
+
+def deconstruct_multi_filename( multi_filename ):
+    keys = ['primary', 'id', 'name', 'visible', 'file_type', 'dbkey']
+    return ( dict( zip( keys, multi_filename.split('_') ) ) )
+    
+def construct_multi_filename( id, name, file_type, dbkey=None):
+    """ Implementation of *Number of Output datasets cannot be determined until tool run* from documentation_.
+    .. _documentation: http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
+    """
+    if dbkey:
+        filename = "%s_%s_%s_%s_%s_%s" % ( 'primary', id, name, 'visible', file_type, dbkey )
+    else:
+        filename = "%s_%s_%s_%s_%s" % ( 'primary', id, name, 'visible', file_type )
+        
+    return filename
+    
+def xml_save_to_newfile_directory( xmlfile, directory, id, enhanced_handling=False, datatypes_registry=None ):
+    """ Open xmlfile, parse all URLs to fetch. Fetch each file, saving to ``directory``. 
+    Save first file for last and return for ``page``. 
+    
+    Schema
+    
+    ::
+    
+        <?xml version="1.0"?>
+        <!DOCTYPE downloads [
+        <!ELEMENT downloads (download)>
+        <!ELEMENT download (resource,url,meta)>
+        <!ELEMENT resource (#PCDATA)>
+        <!ELEMENT url (#PCDATA)>
+        <!ELEMENT id (#PCDATA)>
+        <!ELEMENT meta (id,format,type,summary,feature,genome,technique,instrument,assay,sample,description,PMID)>
+        <!ELEMENT id (#PCDATA)>
+        <!ELEMENT format (#PCDATA)>
+        <!ELEMENT type (#PCDATA)>
+        <!ELEMENT summary (#PCDATA)>
+        <!ELEMENT feature (#PCDATA)>
+        <!ELEMENT genome (#PCDATA)>
+        <!ELEMENT technique (#PCDATA)>
+        <!ELEMENT instrument (#PCDATA)>
+        <!ELEMENT assay (#PCDATA)>
+        <!ELEMENT sample (#PCDATA)>
+        <!ELEMENT description (#PCDATA)>
+        <!ELEMENT PMID (#PCDATA)>
+        ]>
+    """
+    root = ElementTree.fromstring(xmlfile.read())
+    if root.tag != 'downloads':
+        stop_err( 'The remote data source application has not sent back a URL parameter in the request.' )
+    # traverse xml schema to find URLs, names, and dbkeys
+    files_to_fetch = []
+    complete = False
+    
+    for child in root:
+      if (child.tag == 'download') and (complete == True):
+        files_to_fetch.append( ( construct_multi_filename( id, name, file_type, dbkey ), URL ) )
+        
+      for sub in child:
+        if sub.tag == 'url':
+          URL = sub.text
+        elif sub.tag == 'meta':
+        
+          for meta in sub:
+            if meta.tag == 'id':
+              name = meta.text
+            elif meta.tag == 'genome':
+              dbkey = meta.text
+            elif meta.tag == 'format':
+              file_type = meta.text
+          # hit the end of our schema    
+          files_to_fetch.append( ( construct_multi_filename( id, name, file_type, dbkey ), URL ) )
+    
+    if len(files_to_fetch) > 1:
+        for filename, URL in files_to_fetch[1:]:
+            try:
+                cur_filename = os.path.join( directory, filename )
+                page = urllib.urlopen( URL )
+                multi_dict = deconstruct_multi_filename( filename )
+                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 ) )
+                if enhanced_handling:
+                    ext = sniff.handle_uploaded_dataset_file( cur_filename, datatypes_registry, ext = multi_dict['file_type'], is_multi_byte = is_multi_byte )
+            except Exception, e:
+                stop_err( 'Unable to fetch %s:\n%s' % ( URL, e ) )
+    
+    # pass page back to main
+    return ( files_to_fetch[0][0], urllib.urlopen( files_to_fetch[0][1] ) )
+
+def __main__():
+    # Parse the command line options
+    usage = "Usage: ncbi_connector.py filename max_size [options]"
+    parser = optparse.OptionParser(usage = usage)
+    parser.add_option("-x", "--xml",
+                    action="store_true", dest="xmlfile", help="filename defines external resources as xml")
+    parser.add_option("-i", "--id", type="string",
+                    action="store", dest="id", help="output id")
+    parser.add_option("-p", "--path", type="string",
+                    action="store", dest="newfilepath", help="new file path")
+                    
+    (options, args) = parser.parse_args()
+  
+    filename = args[0]
+    try:
+        max_file_size = int( args[1] )
+    except:
+        max_file_size = 0
+    
+    job_params, params = load_input_parameters( filename )
+    if job_params is None: #using an older tabular file
+        enhanced_handling = False
+        job_params = dict( param_dict = params )
+        job_params[ 'output_data' ] =  [ dict( out_data_name = 'output',
+                                               ext = 'data',
+                                               file_name = filename,
+                                               extra_files_path = None ) ]
+        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 )
+    else:
+        enhanced_handling = True
+        json_file = open( job_params[ 'job_config' ][ 'TOOL_PROVIDED_JOB_METADATA_FILE' ], 'w' ) #specially named file for output junk to pass onto set metadata
+    
+    datatypes_registry = Registry()
+    datatypes_registry.load_datatypes( root_dir = job_params[ 'job_config' ][ 'GALAXY_ROOT_DIR' ], config = job_params[ 'job_config' ][ 'GALAXY_DATATYPES_CONF_FILE' ] )
+    
+    URL = params.get( 'URL', None ) #using exactly URL indicates that only one dataset is being downloaded
+    URL_method = params.get( 'URL_method', None )
+    
+    # The Python support for fetching resources from the web is layered. urllib uses the httplib
+    # library, which in turn uses the socket library.  As of Python 2.3 you can specify how long
+    # a socket should wait for a response before timing out. By default the socket module has no
+    # timeout and can hang. Currently, the socket timeout is not exposed at the httplib or urllib2
+    # levels. However, you can set the default timeout ( in seconds ) globally for all sockets by
+    # doing the following.
+    socket.setdefaulttimeout( 600 )
+    
+    for data_dict in job_params[ 'output_data' ]:
+        cur_filename =  data_dict.get( 'file_name', filename )
+        cur_URL =  params.get( '%s|%s|URL' % ( GALAXY_PARAM_PREFIX, data_dict[ 'out_data_name' ] ), URL )
+        if not cur_URL:
+            open( cur_filename, 'w' ).write( "" )
+            stop_err( 'The remote data source application has not sent back a URL parameter in the request.' )
+        
+        # The following calls to urllib.urlopen() will use the above default timeout
+        try:
+            if not URL_method or URL_method == 'get':
+                page = urllib.urlopen( cur_URL )
+            elif URL_method == 'post':
+                page = urllib.urlopen( cur_URL, urllib.urlencode( params ) )
+        except Exception, e:
+            stop_err( 'The remote data source application may be off line, please try again later. Error: %s' % str( e ) )
+        if max_file_size:
+            file_size = int( page.info().get( 'Content-Length', 0 ) )
+            if file_size > max_file_size:
+                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 ) )
+        # If xmlfile is provided, fetch files 2 through n and save to new_file_path, replace page with file 1
+        if options.xmlfile:
+            multi_filename, page = xml_save_to_newfile_directory( page, options.newfilepath, options.id, enhanced_handling, datatypes_registry )
+            multi_dict = deconstruct_multi_filename( multi_filename )
+            
+        #do sniff stream for multi_byte
+        try:
+            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 ) )
+        except Exception, e:
+            stop_err( 'Unable to fetch %s:\n%s' % ( cur_URL, e ) )
+        
+        #here import checks that upload tool performs
+        if enhanced_handling:
+            try:
+                ext = sniff.handle_uploaded_dataset_file( filename, datatypes_registry, ext = data_dict[ 'ext' ], is_multi_byte = is_multi_byte )
+            except Exception, e:
+                stop_err( str( e ) )
+            info = dict( type = 'dataset',
+                         dataset_id = data_dict[ 'dataset_id' ],
+                         ext = ext)
+            
+            json_file.write( "%s\n" % to_json_string( info ) )
+    
+if __name__ == "__main__": __main__()