Add SOAP method getdbSNPDescriptions.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@346 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

extras/soap-tools/getdbsnpdescription.py

+#!/usr/bin/env python
+
+from mutalyzer.util import monkey_patch_suds; monkey_patch_suds()
+
+import sys
+from suds.client import Client
+
+URL = 'http://localhost/mutalyzer/services/?wsdl'
+
+if len(sys.argv) < 2:
+    print 'Please provide a dbSNP rs number'
+    sys.exit(1)
+
+c = Client(URL, cache=None)
+o = c.service
+
+# Example: rs9919552
+print 'Getting HGVS descriptions for ' + sys.argv[1] + ' ...'
+
+r = o.getdbSNPDescriptions(sys.argv[1])
+
+if r:
+    for description in r.string:
+        print description

mutalyzer/webservice.py

@@ -913,6 +913,38 @@ class MutalyzerService(DefinitionBase):
 
         return map(cache_entry_to_soap, cache)
     #getCache
+
+    @soap(Mandatory.String, _returns = Array(Mandatory.String))
+    def getdbSNPDescriptions(self, rs_id):
+        """
+        Lookup HGVS descriptions for a dbSNP rs identifier.
+
+        @arg rs_id: The dbSNP rs identifier, e.g. 'rs9919552'.
+        @type rs_id: string
+
+        @return: List of HGVS descriptions.
+        @rtype: list(string)
+        """
+        output = Output(__file__, self._config.Output)
+
+        output.addMessage(__file__, -1, 'INFO',
+                          'Received request getdbSNPDescription(%s)' % rs_id)
+
+        retriever = Retriever.Retriever(self._config.Retriever, output, None)
+        descriptions = retriever.snpConvert(rs_id)
+
+        output.addMessage(__file__, -1, 'INFO',
+                          'Finished processing getdbSNPDescription(%s)' % rs_id)
+
+        # Todo: use SOAP Fault object here (see Trac issue #41).
+        messages = output.getMessages()
+        if messages:
+            error = 'The request could not be completed\n' \
+                    + '\n'.join(map(lambda m: str(m), output.getMessages()))
+            raise Exception(error)
+
+        return descriptions
+    #getdbSNPDescriptions
 #MutalyzerService
 
 

tests/test_webservice.py

@@ -12,13 +12,25 @@ from mutalyzer.config import Config
 from mutalyzer.output import Output
 from mutalyzer.sync import CacheSync
 from mutalyzer import Db
-import logging; logging.raiseExceptions = 0
+import logging
 import urllib2
 from suds.client import Client
 from suds import WebFault
 from nose.tools import *
 
 
+# Suds logs an awful lot of things with level=DEBUG, including entire WSDL
+# files and SOAP responses. On any error, this is all dumped to the console,
+# which is very unconvenient. The following suppresses most of this.
+logging.raiseExceptions = 0
+logging.basicConfig(level=logging.INFO)
+for logger in ('suds.metrics', 'suds.wsdl', 'suds.xsd.schema',
+               'suds.xsd.sxbasic', 'suds.xsd.sxbase', 'suds.xsd.query',
+               'suds.transport.http', 'suds.xsd.deplist', 'suds.mx.core',
+               'suds.mx.literal', 'suds.resolver'):
+    logging.getLogger(logger).setLevel(logging.ERROR)
+
+
 WSDL_URL = 'http://localhost/mutalyzer/services/?wsdl'
 
 
@@ -179,3 +191,14 @@ class TestWebservice():
 
         r = self.client.service.getCache(created_since)
         assert_equal(len(r.CacheEntry), len(cache))
+
+    def test_getdbsnpdescriptions(self):
+        """
+        Running getdbSNPDescriptions method should give us the expected HGVS
+        descriptions for the given dbSNP id.
+        """
+        r = self.client.service.getdbSNPDescriptions('rs9919552')
+        assert 'NC_000011.9:g.111959625C>T' in r.string
+        assert 'NG_012337.1:g.7055C>T' in r.string
+        assert 'NM_003002.2:c.204C>T' in r.string
+        assert 'NP_002993.1:p.Ser68=' in r.string

tests/test_website.py

@@ -202,11 +202,12 @@ class TestWSGI():
         form = r.forms[0]
         form['rsId'] = 'rs9919552'
         r = form.submit()
-        #r.mustcontain('0 Errors',
-        #              '0 Warnings',
-        #              'NG_012337.1:g.7055C>T',
-        #              'NM_003002.2:c.204C>T',
-        #              'NT_033899.8:g.15522041C>T')
+        r.mustcontain('0 Errors',
+                      '0 Warnings',
+                      'NC_000011.9:g.111959625C>T',
+                      'NG_012337.1:g.7055C>T',
+                      'NM_003002.2:c.204C>T',
+                      'NP_002993.1:p.Ser68=')
 
     def test_snp_converter_invalid(self):
         """