Merge pull request #1299 from david4096/1294_fix

Fix VA search bug
ga4gh · Jul 26, 2016 · 1b549f2 · 1b549f2
2 parents 7fae9f6 + 56191a5
commit 1b549f2
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Showing 3 changed files with 11 additions and 11 deletions.
diff --git a/ga4gh/backend.py b/ga4gh/backend.py
@@ -290,15 +290,17 @@ def _matchAnyEffects(self, effect):
 
     def _removeNonMatchingTranscriptEffects(self, ann):
         newTxE = []
+        oldTxE = ann.transcript_effects
         if len(self._effects) == 0:
             return ann
-        for txe in ann.transcript_effects:
+        for txe in oldTxE:
             add = False
             for effect in txe.effects:
                 if self._matchAnyEffects(effect):
                     add = True
             if add:
                 newTxE.append(txe)
+        ann.ClearField('transcript_effects')
         ann.transcript_effects.extend(newTxE)
         return ann
 

diff --git a/ga4gh/datamodel/variants.py b/ga4gh/datamodel/variants.py
@@ -968,11 +968,10 @@ def generateVariantAnnotation(self, variant):
         ann.created = datetime.datetime.now().isoformat() + "Z"
         # make a transcript effect for each alternate base element
         # multiplied by a random integer (1,5)
-        for i in range(randomNumberGenerator.randint(1, 5)):
-            for base in variant.alternate_bases:
-                ann.transcript_effects.add().CopyFrom(
-                    self.generateTranscriptEffect(
-                        variant, ann, base, randomNumberGenerator))
+        for base in variant.alternate_bases:
+            ann.transcript_effects.add().CopyFrom(
+                self.generateTranscriptEffect(
+                    variant, ann, base, randomNumberGenerator))
         ann.id = self.getVariantAnnotationId(variant, ann)
         return ann
 
@@ -986,10 +985,6 @@ def _addTranscriptEffectLocations(self, effect, ann, variant):
         effect.cdna_location.start = variant.start
         return effect
 
-    def _addTranscriptEffectId(self, effect):
-        effect.id = str(self.getTranscriptEffectId(effect))
-        return effect
-
     def _getRandomOntologyTerm(self, randomNumberGenerator):
         # TODO more mock options from simulated seqOnt?
         ontologyTuples = [
@@ -1032,7 +1027,7 @@ def generateTranscriptEffect(
             effect, randomNumberGenerator)
         effect = self._addTranscriptEffectOntologyTerm(
             effect, randomNumberGenerator)
-        effect = self._addTranscriptEffectId(effect)
+        effect.id = self.getTranscriptEffectId(effect)
         effect = self._addAnalysisResult(effect, ann, randomNumberGenerator)
         return effect
 

diff --git a/tests/unit/test_simulated_stack.py b/tests/unit/test_simulated_stack.py
@@ -722,6 +722,9 @@ def testVariantAnnotationsSearch(self):
                            "There should be some results for a good effect ID")
         for ann in responseData.variant_annotations:
             effectPresent = False
+            txIds = map(lambda t: t.id, ann.transcript_effects)
+            self.assertEqual(len(txIds), len(set(txIds)),
+                             "Transcript effects should be unique")
             for effect in ann.transcript_effects:
                 for featureType in effect.effects:
                     if featureType.id in map(