Absorb renaming of AnVIL fields (#4617)

DataBiosphere · Nov 22, 2022 · 487fb5b · 487fb5b
1 parent 274baae
commit 487fb5b
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Showing 6 changed files with 48 additions and 48 deletions.
diff --git a/src/azul/plugins/metadata/anvil/__init__.py b/src/azul/plugins/metadata/anvil/__init__.py
@@ -160,7 +160,7 @@ def _field_mapping(self) -> MetadataPlugin._FieldMapping:
                     # These field names are hard-coded in the implementation of
                     # the repository service/controller.
                     **{
-                        'byte_size': 'size',
+                        'file_size': 'size',
                         # Not in schema
                         'version': 'fileVersion',
                         'uuid': 'fileId',

diff --git a/src/azul/plugins/metadata/anvil/indexer/transform.py b/src/azul/plugins/metadata/anvil/indexer/transform.py
@@ -241,7 +241,7 @@ def _file_types(cls) -> FieldTypes:
             'file_id': null_str,
             'data_modality': [null_str],
             'file_format': null_str,
-            'byte_size': null_int,
+            'file_size': null_int,
             'reference_assembly': [null_str],
             # Not in schema
             'version': null_str,
@@ -343,7 +343,7 @@ def _file(self, manifest_entry: JSON) -> MutableJSON:
         metadata = self.bundle.metadata_files[manifest_entry['name']]
         return self._entity(manifest_entry,
                             self._file_types(),
-                            size=metadata['byte_size'])
+                            size=metadata['file_size'])
 
     def _only_dataset(self) -> MutableJSON:
         return self._dataset(self._entries_by_entity_id[one(self._entities_by_type['dataset'])])

diff --git a/src/azul/plugins/repository/tdr_anvil/__init__.py b/src/azul/plugins/repository/tdr_anvil/__init__.py
@@ -512,7 +512,7 @@ def convert_column(value):
             'file_id',
             'data_modality',
             'file_format',
-            'byte_size',
+            'file_size',
             'reference_assembly',
             'file_ref',
         },

diff --git a/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.metadata.json b/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.metadata.json
diff --git a/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.result.tdr.json b/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.result.tdr.json
diff --git a/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.results.json b/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.results.json