Fix: File fields size and name are inconsistently named in AnVIL (#4642…

…, PR #4833)
DataBiosphere · Dec 17, 2022 · d6c531a · d6c531a
2 parents 0aa860a + 50aa0e9
commit d6c531a
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Showing 2 changed files with 3 additions and 7 deletions.
diff --git a/src/azul/plugins/metadata/anvil/__init__.py b/src/azul/plugins/metadata/anvil/__init__.py
@@ -155,8 +155,10 @@ def _field_mapping(self) -> MetadataPlugin._FieldMapping:
                             'file_id',
                             'data_modality',
                             'file_format',
+                            'file_size',
                             'file_md5sum',
                             'reference_assembly',
+                            'file_name',
                             # Not in schema
                             'crc32',
                             'sha256',
@@ -166,8 +168,6 @@ def _field_mapping(self) -> MetadataPlugin._FieldMapping:
                     # These field names are hard-coded in the implementation of
                     # the repository service/controller.
                     **{
-                        'file_size': 'size',
-                        'file_name': 'name',
                         # Not in schema
                         'version': 'fileVersion',
                         'uuid': 'fileId',

diff --git a/test/integration_test.py b/test/integration_test.py
@@ -564,7 +564,7 @@ def _get_one_file(self, catalog: CatalogName) -> JSON:
         if config.is_hca_enabled(catalog):
             file_size_facet = 'fileSize'
         elif config.is_anvil_enabled(catalog):
-            file_size_facet = 'size'
+            file_size_facet = 'files.file_size'
         else:
             assert False, catalog
         for filters in [self._fastq_filter(catalog), {}]:
@@ -785,10 +785,6 @@ def _check_curl_manifest(self, _catalog: CatalogName, response: bytes):
 
     def _test_repository_files(self, catalog: str):
         with self.subTest('repository_files', catalog=catalog):
-            # FIXME: File downloads are broken on AnVIL deployments
-            #        https://github.com/DataBiosphere/azul/issues/4507
-            if config.is_anvil_enabled(catalog):
-                self.skipTest('File downloads are broken on AnVIL deployments')
             file = self._get_one_file(catalog)
             file_uuid, file_version = file['uuid'], file['version']
             endpoint_url = config.service_endpoint