From ef15ba195794b7d19f94fef3f33dd8599177efa3 Mon Sep 17 00:00:00 2001
From: David Steinberg <david@resium.com>
Date: Mon, 9 Jan 2017 19:34:59 -0800
Subject: [PATCH] Clean up imports Add tests that show basic attributes
 examples

---
 .../ga4gh/genotype_phenotype_service.proto    |  1 -
 .../proto/ga4gh/sequence_annotations.proto    |  1 -
 tests/test_imports.py                         | 84 ++++++++++++++++++-
 3 files changed, 82 insertions(+), 4 deletions(-)

diff --git a/src/main/proto/ga4gh/genotype_phenotype_service.proto b/src/main/proto/ga4gh/genotype_phenotype_service.proto
index 56c3ce4d..8a8cf537 100644
--- a/src/main/proto/ga4gh/genotype_phenotype_service.proto
+++ b/src/main/proto/ga4gh/genotype_phenotype_service.proto
@@ -3,7 +3,6 @@ syntax = "proto3";
 package ga4gh;
 
 import "ga4gh/common.proto";
-import "ga4gh/metadata.proto";
 import "ga4gh/genotype_phenotype.proto";
 import "google/api/annotations.proto";
 
diff --git a/src/main/proto/ga4gh/sequence_annotations.proto b/src/main/proto/ga4gh/sequence_annotations.proto
index 8d688486..cea5024e 100644
--- a/src/main/proto/ga4gh/sequence_annotations.proto
+++ b/src/main/proto/ga4gh/sequence_annotations.proto
@@ -3,7 +3,6 @@ syntax = "proto3";
 package ga4gh;
 
 import "ga4gh/common.proto";
-import "ga4gh/metadata.proto";
 
 
 // This protocol defines annotations on GA4GH genomic sequences It includes two
diff --git a/tests/test_imports.py b/tests/test_imports.py
index 52a52efa..e65664d6 100644
--- a/tests/test_imports.py
+++ b/tests/test_imports.py
@@ -9,16 +9,17 @@
 
 # similar to dev_glue.py
 import ga4gh
+
 ga4gh.__path__.insert(0, 'python/ga4gh')
 
 import ga4gh.schemas._protocol_version as version  # NOQA
 import ga4gh.schemas.google.api.http_pb2 as http_pb2  # NOQA
 import ga4gh.schemas.ga4gh.common_pb2 as common_pb2  # NOQA
+import ga4gh.schemas.ga4gh.metadata_pb2 as metadata  # NOQA
 import ga4gh.schemas.pb as pb  # NOQA
 
 
 class TestPb(unittest.TestCase):
-
     def testString(self):
         self.assertEqual(pb.DEFAULT_STRING, pb.string(None))
         self.assertEqual('A', pb.string('A'))
@@ -29,7 +30,6 @@ def testInt(self):
 
 
 class TestSchemas(unittest.TestCase):
-
     def testVersion(self):
         version.version.split('.')
         self.assertIsNotNone(version.version)
@@ -37,5 +37,85 @@ def testVersion(self):
     def testGa4ghCommon(self):
         self.assertIsNotNone(common_pb2.DESCRIPTOR)
 
+    def testDatasetAttributes(self):
+        """
+        Demonstrates the usage of the Attribute's field on a dataset message.
+        This field is available on many other messages as well.
+        """
+        key = "numbers_and_strings"
+        string_value = "hello"
+        int32_value = 5
+        double_value = 3.14159
+        attributes = {key: [string_value, int32_value, double_value]}
+        dataset = metadata.Dataset()
+        myattribute = dataset.attributes.attr[key].values
+
+        myattribute.add().string_value = string_value
+        myattribute.add().int32_value = int32_value
+        myattribute.add().double_value = double_value
+
+        self.assertEqual(
+            dataset.attributes.attr[key].values[0].string_value,
+            attributes[key][0])
+
+        self.assertEqual(
+            dataset.attributes.attr[key].values[1].int32_value,
+            attributes[key][1])
+
+        self.assertEqual(
+            dataset.attributes.attr[key].values[2].double_value,
+            attributes[key][2])
+
+    def testNestedAttributes(self):
+        """
+        Demonstrates how nested attributes can be used to interchange
+        arbitrary unstructured, typed data.
+        """
+        dataset = metadata.Dataset()
+        key1 = "key1"
+        key2 = "key2"
+        string_value = "hello"
+        int32_value = 32
+        attributes = {key1: [{key2: [string_value]}, int32_value]}
+        myAttribute = dataset.attributes.attr[key1].values
+        nestedAttribute = myAttribute.add().attributes.attr[key2].values
+        nestedAttribute.add().string_value = string_value
+        myAttribute.add().int32_value = int32_value
+
+        self.assertEqual(
+            dataset.attributes.attr[key1].values[0].
+                attributes.attr[key2].values[0].string_value,
+            attributes[key1][0][key2][0])
+
+        self.assertEqual(dataset.attributes.attr[key1].
+                         values[1].int32_value, attributes[key1][1])
+
+    def testTypedAttributes(self):
+        """
+        Demonstrates how to use other types defined in common to create an
+        attribute message.
+        """
+        dataset = metadata.Dataset()
+        ontologyTerm = common_pb2.OntologyTerm()
+        ontologyTerm.id = "test"
+        ontologyKey = "my_ontology_term"
+
+        dataset.attributes.attr[ontologyKey] \
+            .values.add().ontology_term.MergeFrom(ontologyTerm)
+
+        self.assertEqual(
+            dataset.attributes.attr[ontologyKey].values[0].ontology_term.id,
+            ontologyTerm.id)
+
+        experiment = common_pb2.Experiment()
+        experiment.id = "test"
+        key = "my_experiment"
+
+        dataset.attributes.attr[key] \
+            .values.add().experiment.MergeFrom(experiment)
+        self.assertEqual(
+            dataset.attributes.attr[key].values[0].experiment.id, experiment.id)
+
+
     def testGoogle(self):
         self.assertIsNotNone(http_pb2.DESCRIPTOR)