diff --git a/src/azul/plugins/metadata/anvil/__init__.py b/src/azul/plugins/metadata/anvil/__init__.py index a1487bdabe..5892eccacb 100644 --- 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 index 0049ed8654..4ad660a15c 100644 --- 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 index cb78210bc3..800a850f52 100644 --- 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 index f5a4f8fd9a..3afe50c884 100644 --- a/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.metadata.json +++ b/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.metadata.json @@ -42,7 +42,7 @@ ] }, "file_23d57a3c-dc24-596a-8142-1215fc2ffa74": { - "byte_size": 64526928, + "file_size": 64526928, "data_modality": [], "datarepo_row_id": "f422c79e-33e1-4f0c-b39b-e698a1b564d0", "file_format": ".gvcf.gz", @@ -54,7 +54,7 @@ ] }, "file_8822d3c7-0498-50a3-b717-a6acef5a8588": { - "byte_size": 7455178165, + "file_size": 7455178165, "data_modality": [], "datarepo_row_id": "1035f90f-e1ce-4102-9528-7a9227d361cc", "file_format": ".bam", 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 index 036d40e710..25e5954eac 100644 --- a/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.result.tdr.json +++ b/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.result.tdr.json @@ -109,7 +109,7 @@ ] }, "file_23d57a3c-dc24-596a-8142-1215fc2ffa74": { - "byte_size": 64526928, + "file_size": 64526928, "data_modality": [], "datarepo_row_id": "f422c79e-33e1-4f0c-b39b-e698a1b564d0", "file_format": ".gvcf.gz", @@ -121,7 +121,7 @@ ] }, "file_8822d3c7-0498-50a3-b717-a6acef5a8588": { - "byte_size": 7455178165, + "file_size": 7455178165, "data_modality": [], "datarepo_row_id": "1035f90f-e1ce-4102-9528-7a9227d361cc", "file_format": ".bam", diff --git a/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.results.json b/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.results.json index 8f1606e2c0..982bb815c1 100644 --- a/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.results.json +++ b/test/indexer/data/3fdc952d-7eec-a8d9-be70-876aa4377a53.results.json @@ -133,10 +133,10 @@ "file_id": [ "8822d3c7-0498-50a3-b717-a6acef5a8588" ], - "byte_size": [ + "file_size": [ 7455178165 ], - "byte_size_": [ + "file_size_": [ 7455178165 ], "size": [ @@ -184,10 +184,10 @@ "file_id": [ "23d57a3c-dc24-596a-8142-1215fc2ffa74" ], - "byte_size": [ + "file_size": [ 64526928 ], - "byte_size_": [ + "file_size_": [ 64526928 ], "size": [ @@ -331,8 +331,8 @@ ], "file_format": ".bam", "file_id": "8822d3c7-0498-50a3-b717-a6acef5a8588", - "byte_size": 7455178165, - "byte_size_": 7455178165, + "file_size": 7455178165, + "file_size_": 7455178165, "size": 7455178165, "size_": 7455178165, "name": "file_8822d3c7-0498-50a3-b717-a6acef5a8588", @@ -355,8 +355,8 @@ ], "file_format": ".gvcf.gz", "file_id": "23d57a3c-dc24-596a-8142-1215fc2ffa74", - "byte_size": 64526928, - "byte_size_": 64526928, + "file_size": 64526928, + "file_size_": 64526928, "size": 64526928, "size_": 64526928, "name": "file_23d57a3c-dc24-596a-8142-1215fc2ffa74", @@ -484,8 +484,8 @@ ], "file_format": ".bam", "file_id": "8822d3c7-0498-50a3-b717-a6acef5a8588", - "byte_size": 7455178165, - "byte_size_": 7455178165, + "file_size": 7455178165, + "file_size_": 7455178165, "size": 7455178165, "size_": 7455178165, "name": "file_8822d3c7-0498-50a3-b717-a6acef5a8588", @@ -608,8 +608,8 @@ ], "file_format": ".bam", "file_id": "8822d3c7-0498-50a3-b717-a6acef5a8588", - "byte_size": 7455178165, - "byte_size_": 7455178165, + "file_size": 7455178165, + "file_size_": 7455178165, "size": 7455178165, "size_": 7455178165, "name": "file_8822d3c7-0498-50a3-b717-a6acef5a8588", @@ -772,10 +772,10 @@ "file_id": [ "8822d3c7-0498-50a3-b717-a6acef5a8588" ], - "byte_size": [ + "file_size": [ 7455178165 ], - "byte_size_": [ + "file_size_": [ 7455178165 ], "size": [ @@ -823,10 +823,10 @@ "file_id": [ "23d57a3c-dc24-596a-8142-1215fc2ffa74" ], - "byte_size": [ + "file_size": [ 64526928 ], - "byte_size_": [ + "file_size_": [ 64526928 ], "size": [ @@ -970,8 +970,8 @@ ], "file_format": ".bam", "file_id": "8822d3c7-0498-50a3-b717-a6acef5a8588", - "byte_size": 7455178165, - "byte_size_": 7455178165, + "file_size": 7455178165, + "file_size_": 7455178165, "size": 7455178165, "size_": 7455178165, "name": "file_8822d3c7-0498-50a3-b717-a6acef5a8588", @@ -994,8 +994,8 @@ ], "file_format": ".gvcf.gz", "file_id": "23d57a3c-dc24-596a-8142-1215fc2ffa74", - "byte_size": 64526928, - "byte_size_": 64526928, + "file_size": 64526928, + "file_size_": 64526928, "size": 64526928, "size_": 64526928, "name": "file_23d57a3c-dc24-596a-8142-1215fc2ffa74", @@ -1143,10 +1143,10 @@ "file_id": [ "8822d3c7-0498-50a3-b717-a6acef5a8588" ], - "byte_size": [ + "file_size": [ 7455178165 ], - "byte_size_": [ + "file_size_": [ 7455178165 ], "size": [ @@ -1276,8 +1276,8 @@ ], "file_format": ".bam", "file_id": "8822d3c7-0498-50a3-b717-a6acef5a8588", - "byte_size": 7455178165, - "byte_size_": 7455178165, + "file_size": 7455178165, + "file_size_": 7455178165, "size": 7455178165, "size_": 7455178165, "name": "file_8822d3c7-0498-50a3-b717-a6acef5a8588", @@ -1425,10 +1425,10 @@ "file_id": [ "23d57a3c-dc24-596a-8142-1215fc2ffa74" ], - "byte_size": [ + "file_size": [ 64526928 ], - "byte_size_": [ + "file_size_": [ 64526928 ], "size": [ @@ -1558,8 +1558,8 @@ ], "file_format": ".gvcf.gz", "file_id": "23d57a3c-dc24-596a-8142-1215fc2ffa74", - "byte_size": 64526928, - "byte_size_": 64526928, + "file_size": 64526928, + "file_size_": 64526928, "size": 64526928, "size_": 64526928, "name": "file_23d57a3c-dc24-596a-8142-1215fc2ffa74", @@ -1714,10 +1714,10 @@ "file_id": [ "8822d3c7-0498-50a3-b717-a6acef5a8588" ], - "byte_size": [ + "file_size": [ 7455178165 ], - "byte_size_": [ + "file_size_": [ 7455178165 ], "size": [ @@ -1765,10 +1765,10 @@ "file_id": [ "23d57a3c-dc24-596a-8142-1215fc2ffa74" ], - "byte_size": [ + "file_size": [ 64526928 ], - "byte_size_": [ + "file_size_": [ 64526928 ], "size": [ @@ -1912,8 +1912,8 @@ ], "file_format": ".bam", "file_id": "8822d3c7-0498-50a3-b717-a6acef5a8588", - "byte_size": 7455178165, - "byte_size_": 7455178165, + "file_size": 7455178165, + "file_size_": 7455178165, "size": 7455178165, "size_": 7455178165, "name": "file_8822d3c7-0498-50a3-b717-a6acef5a8588", @@ -1936,8 +1936,8 @@ ], "file_format": ".gvcf.gz", "file_id": "23d57a3c-dc24-596a-8142-1215fc2ffa74", - "byte_size": 64526928, - "byte_size_": 64526928, + "file_size": 64526928, + "file_size_": 64526928, "size": 64526928, "size_": 64526928, "name": "file_23d57a3c-dc24-596a-8142-1215fc2ffa74", @@ -2065,8 +2065,8 @@ ], "file_format": ".gvcf.gz", "file_id": "23d57a3c-dc24-596a-8142-1215fc2ffa74", - "byte_size": 64526928, - "byte_size_": 64526928, + "file_size": 64526928, + "file_size_": 64526928, "size": 64526928, "size_": 64526928, "name": "file_23d57a3c-dc24-596a-8142-1215fc2ffa74", @@ -2189,8 +2189,8 @@ ], "file_format": ".gvcf.gz", "file_id": "23d57a3c-dc24-596a-8142-1215fc2ffa74", - "byte_size": 64526928, - "byte_size_": 64526928, + "file_size": 64526928, + "file_size_": 64526928, "size": 64526928, "size_": 64526928, "name": "file_23d57a3c-dc24-596a-8142-1215fc2ffa74",