Protobuf 3.2.0

.travis.yml

@@ -6,7 +6,7 @@ sudo: false
 cache:
   directories:
     - $HOME/.cache/pip
-    - /tmp/proto3.1.0
+    - /tmp/proto3.2.0
 
 install:
   - pip install pip --upgrade
@@ -24,8 +24,8 @@ before_script:
   - python scripts/build_test_data.py 
 
 before_install:
-    - bash tools/travis-install-protoc.sh 3.1.0
-    - export PATH=/tmp/proto3.1.0/bin:$PATH
+    - bash tools/travis-install-protoc.sh 3.2.0
+    - export PATH=/tmp/proto3.2.0/bin:$PATH
 
 # run_tests.py runs everything under the script: tag so only put commands
 # under it that we want to run (and want to be able to run) as local tests

constraints.txt

@@ -22,5 +22,5 @@
 # the pinned packages in requirements.txt are used instead.
 #
 #git+git://github.com/ga4gh/ga4gh-common.git@master#egg=ga4gh_common
-#git+git://github.com/ga4gh/schemas.git@master#egg=ga4gh_schemas
-#git+git://github.com/ga4gh/ga4gh-client.git@master#egg=ga4gh_client
+git+git://github.com/ljdursi/ga4gh-schemas.git@protobuf_3.2.0#egg=ga4gh_schemas
+git+git://github.com/ljdursi/ga4gh-client.git@protobuf_3.2.0#egg=ga4gh_client

ga4gh/server/backend.py

@@ -205,7 +205,7 @@ def _readGroupSetsGenerator(self, request, numObjects, getByIndexMethod):
             if request.name and request.name != obj.getLocalId():
                 include = False
             if request.biosample_id and include:
-                rgsp.ClearField("read_groups")
+                rgsp.ClearField(b"read_groups")
                 for readGroup in obj.getReadGroups():
                     if request.biosample_id == readGroup.getBiosampleId():
                         rgsp.read_groups.extend(

ga4gh/server/datamodel/reads.py

@@ -145,7 +145,7 @@ def convertReadAlignment(self, read, readGroupSet, readGroupId):
         ret.aligned_quality.extend(read.query_qualities)
         ret.aligned_sequence = read.query_sequence
         if SamFlags.isFlagSet(read.flag, SamFlags.READ_UNMAPPED):
-            ret.ClearField("alignment")
+            ret.ClearField(b"alignment")
         else:
             ret.alignment.CopyFrom(protocol.LinearAlignment())
             ret.alignment.mapping_quality = read.mapping_quality

ga4gh/server/paging.py

@@ -297,7 +297,7 @@ def _removeNonMatchingTranscriptEffects(self, ann):
                     add = True
             if add:
                 newTxE.append(txe)
-        ann.ClearField('transcript_effects')
+        ann.ClearField(b'transcript_effects')
         ann.transcript_effects.extend(newTxE)
         return ann
 

requirements.txt

@@ -13,8 +13,8 @@
 # the constraints file will point at the current master branch 
 # of the respective module.
 ga4gh-common==0.0.7
-ga4gh-schemas==0.6.0a10.post1
-ga4gh-client==0.6.0a10
+ga4gh-schemas
+ga4gh-client
 
 Werkzeug==0.11.5
 MarkupSafe==0.23
@@ -46,7 +46,7 @@ peewee==2.8.5
 # prefix due to a setuptools bug.
 Flask-Cors==2.0.1
 Flask==0.10.1
-protobuf==3.1.0.post1
+protobuf==3.2.0
 humanize==0.5.1
 pysam==0.9.0
 requests==2.7.0

tests/datadriven/__init__.py

@@ -11,6 +11,7 @@
 import fnmatch
 import os
 import inspect
+import array
 
 import google.protobuf.json_format as json_format
 
@@ -68,9 +69,18 @@ def assertEqual(self, a, b):
         Tests if a an b are equal. If not, output an error and raise
         an assertion error.
         """
+        def compare_as_float_32s(a_dbl, b_dbl):
+            a_flt = array.array(b"f", [a_dbl])[0]
+            b_flt = array.array(b"f", [b_dbl])[0]
+            return a_flt == b_flt
+
         if a == b:
             return
 
+        if isinstance(a, float) and isinstance(b, float):
+            if compare_as_float_32s(a, b):
+                return
+
         # Protocol Buffers has default string as "", not None
         if a in TestCase.consideredNone and b in TestCase.consideredNone:
             return

tests/unit/test_simulated_stack.py

@@ -11,6 +11,7 @@
 import logging
 import random
 import json
+import array
 import ga4gh.server.datamodel.reads as reads
 import ga4gh.server.datamodel.references as references
 import ga4gh.server.datamodel.variants as variants
@@ -52,6 +53,12 @@ def setUpClass(cls):
     def tearDownClass(cls):
         cls.app = None
 
+    @classmethod
+    def as_float32(cls, x):
+        x_dbl = float(x)
+        x_flt = array.array(b"f", [x_dbl])[0]
+        return x_flt
+
     def setUp(self):
         self.backend = frontend.app.backend
         self.dataRepo = self.backend.getDataRepository()
@@ -217,7 +224,8 @@ def verifyReferencesEqual(self, gaReference, reference):
             gaReference.source_accessions, reference.getSourceAccessions())
         self.assertEqual(gaReference.is_derived, reference.getIsDerived())
         self.assertEqual(
-            gaReference.source_divergence, reference.getSourceDivergence())
+            TestSimulatedStack.as_float32(gaReference.source_divergence),
+            TestSimulatedStack.as_float32(reference.getSourceDivergence()))
 
     def verifySearchMethod(
             self, request, path, responseClass, objects, objectVerifier):