Rename process_type and protocol_type (#68)

HumanCellAtlas · May 2, 2019 · e366e9e · e366e9e
1 parent 6c2f166
commit e366e9e
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Showing 2 changed files with 34 additions and 6 deletions.
diff --git a/src/humancellatlas/data/metadata/api.py b/src/humancellatlas/data/metadata/api.py
@@ -643,14 +643,20 @@ def from_json(cls, json: JSON) -> Iterable['Link']:
             # vx
             process_id = UUID4(json['process'])
             for source_id in json['inputs']:
-                yield cls(source_id=UUID4(source_id), source_type=json['input_type'],
-                          destination_id=process_id, destination_type='process')
+                yield cls(source_id=UUID4(source_id),
+                          source_type=json['input_type'],
+                          destination_id=process_id,
+                          destination_type='process')
             for destination_id in json['outputs']:
-                yield cls(source_id=process_id, source_type='process',
-                          destination_id=UUID4(destination_id), destination_type=json['output_type'])
+                yield cls(source_id=process_id,
+                          source_type='process',
+                          destination_id=UUID4(destination_id),
+                          destination_type=json['output_type'])
             for protocol in json['protocols']:
-                yield cls(source_id=process_id, source_type='process',
-                          destination_id=UUID4(protocol['protocol_id']), destination_type=protocol['protocol_type'])
+                yield cls(source_id=process_id,
+                          source_type='process',
+                          destination_id=UUID4(protocol['protocol_id']),
+                          destination_type=lookup(protocol, 'type', 'protocol_type'))
 
 
 @dataclass(init=False)

diff --git a/test/test.py b/test/test.py
@@ -565,6 +565,7 @@ def assert_bundle():
             self._rename_keys(contributor, name='contact_name')
 
         assert_bundle()
+
     def test_file_format(self):
         uuid = '6b498499-c5b4-452f-9ff9-2318dbb86000'
         version = '2019-01-03T163633.780215Z'
@@ -588,6 +589,27 @@ def assert_bundle():
 
         assert_bundle()
 
+    def test_link_destination_type(self):
+        uuid = '6b498499-c5b4-452f-9ff9-2318dbb86000'
+        version = '2019-01-03T163633.780215Z'
+        replica = 'aws'
+        deployment = 'prod'
+        manifest, metadata_files = self._load_bundle(uuid, version, replica, deployment)
+
+        def assert_bundle():
+            bundle = Bundle(uuid, version, manifest, metadata_files)
+            destination_types = {link.destination_type for link in bundle.links}
+            expected_types = {'library_preparation_protocol', 'sequencing_protocol', 'dissociation_protocol',
+                              'differentiation_protocol', 'ipsc_induction_protocol', 'biomaterial', 'process', 'file'}
+            self.assertEqual(destination_types, expected_types)
+
+        assert_bundle()
+
+        for link in metadata_files['links.json']['links']:
+            for protocol in link['protocols']:
+                self._rename_keys(protocol, type='protocol_type')
+
+        assert_bundle()
 
 # noinspection PyUnusedLocal
 def load_tests(loader, tests, ignore):