comparison ncbi_connector.py @ 9:58917de44665 draft

Uploaded

9:58917de44665

#!/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__()