[r] Replace snapshot and remove workaround (#5229, PR #5313)

DataBiosphere · Jun 21, 2023 · f1330a3 · f1330a3
2 parents 37bcbc2 + efdec9f
commit f1330a3
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Showing 2 changed files with 10 additions and 9 deletions.
diff --git a/deployments/anvilprod/environment.py b/deployments/anvilprod/environment.py
@@ -56,7 +56,7 @@ def mkdict(previous_catalog: dict[str, str],
 
 
 anvil_sources = mkdict({}, 3, mkdelta([
-    mksrc('datarepo-dev-43738c90', 'ANVIL_1000G_2019_Dev_20230302_ANV5_202303032342', 22814),
+    mksrc('datarepo-dev-e53e74aa', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),
     mksrc('datarepo-dev-42c70e6a', 'ANVIL_CCDG_Sample_1_20230228_ANV5_202302281520', 28),
     mksrc('datarepo-dev-97ad270b', 'ANVIL_CMG_Sample_1_20230225_ANV5_202302281509', 25)
 ]))

diff --git a/test/integration_test.py b/test/integration_test.py
@@ -22,6 +22,7 @@
     TextIOWrapper,
 )
 from itertools import (
+    chain,
     starmap,
 )
 import json
@@ -71,9 +72,11 @@
     service_account,
 )
 from more_itertools import (
+    always_iterable,
     first,
     grouper,
     one,
+    only,
 )
 from openapi_spec_validator import (
     validate_spec,
@@ -985,16 +988,14 @@ def _get_indexed_bundles(self,
                     version=bundle['bundleVersion']
                 )
                 if config.is_anvil_enabled(catalog):
-                    # Biosamples are used as bundle entities for primary bundles
-                    # and are never present in supplementary bundles.
-                    # We cannot use the `files.is_supplementary` field to
-                    # determine whether a bundle is supplementary or not due to
-                    # false positives in the current snapshots
-                    # (https://github.com/DataBiosphere/azul/issues/5229)
+                    is_supplementary = only(set(chain.from_iterable(
+                        always_iterable(file['is_supplementary'])
+                        for file in hit['files']
+                    )), default=False)
                     bundle_fqid['entity_type'] = (
-                        BundleEntityType.primary.value
-                        if hit['biosamples'] else
                         BundleEntityType.supplementary.value
+                        if is_supplementary else
+                        BundleEntityType.primary.value
                     )
                 bundle_fqid = self.repository_plugin(catalog).resolve_bundle(bundle_fqid)
                 indexed_fqids.add(bundle_fqid)