From e028a049d138d48e396c9c52166de178276f27bc Mon Sep 17 00:00:00 2001 From: Noa Aviel Dove Date: Sat, 27 May 2023 15:15:59 -0700 Subject: [PATCH] fixup! Push down HCA specifics to a Bundle subclass (#4940) --- scripts/can_bundle.py | 2 +- src/azul/indexer/__init__.py | 3 ++- src/azul/plugins/metadata/anvil/__init__.py | 8 ++++++-- src/azul/plugins/{anvil.py => metadata/anvil/bundle.py} | 3 +++ src/azul/plugins/metadata/anvil/indexer/transform.py | 2 +- src/azul/plugins/metadata/hca/__init__.py | 8 ++++++-- src/azul/plugins/{hca.py => metadata/hca/bundle.py} | 4 ++++ src/azul/plugins/metadata/hca/indexer/transform.py | 2 +- src/azul/plugins/repository/canned/__init__.py | 4 ++-- src/azul/plugins/repository/dss/__init__.py | 4 ++-- src/azul/plugins/repository/tdr_anvil/__init__.py | 6 +++++- src/azul/plugins/repository/tdr_hca/__init__.py | 6 +++++- ... => 00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json} | 0 ... => 02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json} | 0 ... => 04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json} | 0 ... => 0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json} | 0 ... => 17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json} | 0 ... => 1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json} | 0 ...d8348-d6e9-406a-aa6a-7ee886e52bf9.tables.tdr.hca.json} | 0 ... => 1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json} | 0 ... => 1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json} | 0 ... => 1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json} | 0 ... => 1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json} | 0 ... => 2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json} | 0 ... => 2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json} | 0 ... => 3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json} | 0 ... => 3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json} | 0 ... => 3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json} | 0 ... => 411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json} | 0 ... => 412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json} | 0 ...6adc5-b3c5-5aab-ab86-51d8ce44dfbe.tables.tdr.hca.json} | 0 ... => 4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json} | 0 ... => 4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json} | 0 ... => 4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json} | 0 ... => 4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json} | 0 ... => 56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json} | 0 ... => 587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json} | 0 ...b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json} | 0 ... => 7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json} | 0 ... => 7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json} | 0 ... => 80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json} | 0 ... => 8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json} | 0 ... => 8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json} | 0 ... => 8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json} | 0 ... => 8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json} | 0 ... => 94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json} | 0 ... => 97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json} | 0 ... => 9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json} | 0 ...b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json} | 0 ...b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json} | 0 ... => b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json} | 0 ... => b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json} | 0 ... => b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json} | 0 ... => c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json} | 0 ... => cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json} | 0 ... => d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json} | 0 ... => d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json} | 0 ... => d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json} | 0 ... => dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json} | 0 ... => e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json} | 0 ... => e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json} | 0 ... => f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json} | 0 ... => f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json} | 0 ... => fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json} | 0 ... => fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json} | 0 ... => ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json} | 0 test/integration_test.py | 2 +- 67 files changed, 39 insertions(+), 15 deletions(-) rename src/azul/plugins/{anvil.py => metadata/anvil/bundle.py} (98%) rename src/azul/plugins/{hca.py => metadata/hca/bundle.py} (92%) rename test/indexer/data/{00f48893-5e9d-52cd-b32d-af88edccabfa.dss.json => 00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json} (100%) rename test/indexer/data/{02e69c25-71e2-48ca-a87b-e256938c6a98.dss.json => 02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json} (100%) rename test/indexer/data/{04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.json => 04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json} (100%) rename test/indexer/data/{0722b70c-6778-423d-8fe9-869e2a515d35.dss.json => 0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json} (100%) rename test/indexer/data/{17a3d288-01a0-464a-9599-7375fda3353d.dss.json => 17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json} (100%) rename test/indexer/data/{1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.json => 1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json} (100%) rename test/indexer/data/{1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tables.tdr.json => 1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tables.tdr.hca.json} (100%) rename test/indexer/data/{1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.json => 1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json} (100%) rename test/indexer/data/{1ed68210-eaba-531d-ba9e-db80164d65ef.dss.json => 1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json} (100%) rename test/indexer/data/{1f6afb64-fa14-5c6f-a474-a742540108a3.dss.json => 1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json} (100%) rename test/indexer/data/{1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.json => 1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json} (100%) rename test/indexer/data/{2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.json => 2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json} (100%) rename test/indexer/data/{2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.json => 2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json} (100%) rename test/indexer/data/{3ac62c33-93e1-56b4-b857-59497f5d942d.dss.json => 3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json} (100%) rename test/indexer/data/{3db604da-940e-49b1-9bcc-25699a55b295.dss.json => 3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json} (100%) rename test/indexer/data/{3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.json => 3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json} (100%) rename test/indexer/data/{411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.json => 411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json} (100%) rename test/indexer/data/{412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.json => 412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json} (100%) rename test/indexer/data/{4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tables.tdr.json => 4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tables.tdr.hca.json} (100%) rename test/indexer/data/{4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.json => 4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json} (100%) rename test/indexer/data/{4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.json => 4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json} (100%) rename test/indexer/data/{4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.json => 4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json} (100%) rename test/indexer/data/{4da04038-adab-59a9-b6c4-3a61242cc972.dss.json => 4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json} (100%) rename test/indexer/data/{56a338fe-7554-4b5d-96a2-7df127a7640b.dss.json => 56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json} (100%) rename test/indexer/data/{587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.json => 587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json} (100%) rename test/indexer/data/{79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.json => 79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json} (100%) rename test/indexer/data/{7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.json => 7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json} (100%) rename test/indexer/data/{7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.json => 7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json} (100%) rename test/indexer/data/{80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.json => 80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json} (100%) rename test/indexer/data/{8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.json => 8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json} (100%) rename test/indexer/data/{8543d32f-4c01-48d5-a79f-1c5439659da3.dss.json => 8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json} (100%) rename test/indexer/data/{8c1773c3-1885-545f-9381-0dab1edf6074.dss.json => 8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json} (100%) rename test/indexer/data/{8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.json => 8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json} (100%) rename test/indexer/data/{94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.json => 94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json} (100%) rename test/indexer/data/{97f0cc83-f0ac-417a-8a29-221c77debde8.dss.json => 97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json} (100%) rename test/indexer/data/{9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.json => 9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json} (100%) rename test/indexer/data/{aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.json => aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json} (100%) rename test/indexer/data/{aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.json => aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json} (100%) rename test/indexer/data/{b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.json => b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json} (100%) rename test/indexer/data/{b2216048-7eaa-45f4-8077-5a3fb4204953.dss.json => b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json} (100%) rename test/indexer/data/{b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.json => b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json} (100%) rename test/indexer/data/{c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.json => c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json} (100%) rename test/indexer/data/{cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.json => cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json} (100%) rename test/indexer/data/{d0e17014-9a58-4763-9e66-59894efbdaa8.dss.json => d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json} (100%) rename test/indexer/data/{d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.json => d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json} (100%) rename test/indexer/data/{d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.json => d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json} (100%) rename test/indexer/data/{dcccb551-4766-4210-966c-f9ee25d19190.dss.json => dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json} (100%) rename test/indexer/data/{e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.json => e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json} (100%) rename test/indexer/data/{e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.json => e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json} (100%) rename test/indexer/data/{f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.json => f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json} (100%) rename test/indexer/data/{f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.json => f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json} (100%) rename test/indexer/data/{fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.json => fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json} (100%) rename test/indexer/data/{fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.json => fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json} (100%) rename test/indexer/data/{ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.json => ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json} (100%) diff --git a/scripts/can_bundle.py b/scripts/can_bundle.py index 7288ff83f..e0f3a3e0e 100644 --- a/scripts/can_bundle.py +++ b/scripts/can_bundle.py @@ -38,7 +38,7 @@ from azul.plugins import ( RepositoryPlugin, ) -from azul.plugins.anvil import ( +from azul.plugins.metadata.anvil.bundle import ( AnvilBundle, ) from azul.types import ( diff --git a/src/azul/indexer/__init__.py b/src/azul/indexer/__init__.py index 2d397ff98..87ad71938 100644 --- a/src/azul/indexer/__init__.py +++ b/src/azul/indexer/__init__.py @@ -431,11 +431,12 @@ def _reject_joiner(self, value: AnyJSON): msg = f'{config.manifest_column_joiner!r} is disallowed in metadata' raise RequirementError(msg, self.fqid) + @abstractmethod def reject_joiner(self): """ Raise a requirement error if the given string is found in the bundle """ - self._reject_joiner(self.to_json()) + raise NotImplementedError @classmethod @abstractmethod diff --git a/src/azul/plugins/metadata/anvil/__init__.py b/src/azul/plugins/metadata/anvil/__init__.py index 73a6b575d..e58bc2393 100644 --- a/src/azul/plugins/metadata/anvil/__init__.py +++ b/src/azul/plugins/metadata/anvil/__init__.py @@ -12,7 +12,7 @@ MetadataPlugin, Sorting, ) -from azul.plugins.anvil import ( +from azul.plugins.metadata.anvil.bundle import ( AnvilBundle, ) from azul.plugins.metadata.anvil.indexer.transform import ( @@ -67,7 +67,11 @@ def transformer_types(self) -> Iterable[Type[BaseTransformer]]: FileTransformer, ) - def transformers(self, bundle: AnvilBundle, *, delete: bool) -> Iterable[BaseTransformer]: + def transformers(self, + bundle: AnvilBundle, + *, + delete: bool + ) -> Iterable[BaseTransformer]: return [ transformer_cls(bundle=bundle, deleted=delete) for transformer_cls in self.transformer_types() diff --git a/src/azul/plugins/anvil.py b/src/azul/plugins/metadata/anvil/bundle.py similarity index 98% rename from src/azul/plugins/anvil.py rename to src/azul/plugins/metadata/anvil/bundle.py index 38114dd8c..4c718ce7e 100644 --- a/src/azul/plugins/anvil.py +++ b/src/azul/plugins/metadata/anvil/bundle.py @@ -83,6 +83,9 @@ class AnvilBundle(Bundle[BUNDLE_FQID], ABC): entities: dict[EntityReference, MutableJSON] = attr.ib(factory=dict) links: set[Link[EntityReference]] = attr.ib(factory=set) + def reject_joiner(self): + pass + def to_json(self) -> MutableJSON: return { 'entities': { diff --git a/src/azul/plugins/metadata/anvil/indexer/transform.py b/src/azul/plugins/metadata/anvil/indexer/transform.py index 447e03dbc..f8cdc53e7 100644 --- a/src/azul/plugins/metadata/anvil/indexer/transform.py +++ b/src/azul/plugins/metadata/anvil/indexer/transform.py @@ -53,7 +53,7 @@ from azul.indexer.transform import ( Transformer, ) -from azul.plugins.anvil import ( +from azul.plugins.metadata.anvil.bundle import ( AnvilBundle, Link, ) diff --git a/src/azul/plugins/metadata/hca/__init__.py b/src/azul/plugins/metadata/hca/__init__.py index e952e41f3..b3e937f5f 100644 --- a/src/azul/plugins/metadata/hca/__init__.py +++ b/src/azul/plugins/metadata/hca/__init__.py @@ -17,7 +17,7 @@ MetadataPlugin, Sorting, ) -from azul.plugins.hca import ( +from azul.plugins.metadata.hca.bundle import ( HCABundle, ) from azul.plugins.metadata.hca.indexer.aggregate import ( @@ -64,7 +64,11 @@ def transformer_types(self) -> Iterable[Type[BaseTransformer]]: BundleTransformer ) - def transformers(self, bundle: HCABundle, *, delete: bool) -> Iterable[BaseTransformer]: + def transformers(self, + bundle: HCABundle, + *, + delete: bool + ) -> Iterable[BaseTransformer]: api_bundle = api.Bundle(uuid=bundle.uuid, version=bundle.version, manifest=bundle.manifest, diff --git a/src/azul/plugins/hca.py b/src/azul/plugins/metadata/hca/bundle.py similarity index 92% rename from src/azul/plugins/hca.py rename to src/azul/plugins/metadata/hca/bundle.py index 365bba6f5..6f46c5fc8 100644 --- a/src/azul/plugins/hca.py +++ b/src/azul/plugins/metadata/hca/bundle.py @@ -38,6 +38,10 @@ class HCABundle(Bundle[BUNDLE_FQID], ABC): """ metadata_files: MutableJSON + def reject_joiner(self): + self._reject_joiner(self.manifest) + self._reject_joiner(self.metadata_files) + def to_json(self) -> MutableJSON: return { 'manifest': self.manifest, diff --git a/src/azul/plugins/metadata/hca/indexer/transform.py b/src/azul/plugins/metadata/hca/indexer/transform.py index 029595d73..5c572a7a7 100644 --- a/src/azul/plugins/metadata/hca/indexer/transform.py +++ b/src/azul/plugins/metadata/hca/indexer/transform.py @@ -86,7 +86,7 @@ from azul.openapi import ( schema, ) -from azul.plugins.hca import ( +from azul.plugins.metadata.hca.bundle import ( HCABundle, ) from azul.plugins.metadata.hca.indexer.aggregate import ( diff --git a/src/azul/plugins/repository/canned/__init__.py b/src/azul/plugins/repository/canned/__init__.py index 44d837b8c..101b5cc17 100644 --- a/src/azul/plugins/repository/canned/__init__.py +++ b/src/azul/plugins/repository/canned/__init__.py @@ -47,7 +47,7 @@ RepositoryFileDownload, RepositoryPlugin, ) -from azul.plugins.hca import ( +from azul.plugins.metadata.hca.bundle import ( HCABundle, ) from azul.time import ( @@ -81,7 +81,7 @@ class CannedBundle(HCABundle[CannedBundleFQID]): @classmethod def canning_qualifier(cls) -> str: - return 'gh' + return 'gh.hca' def drs_path(self, manifest_entry: JSON) -> Optional[str]: return 'dss' diff --git a/src/azul/plugins/repository/dss/__init__.py b/src/azul/plugins/repository/dss/__init__.py index e5582bf77..d49bacee9 100644 --- a/src/azul/plugins/repository/dss/__init__.py +++ b/src/azul/plugins/repository/dss/__init__.py @@ -47,7 +47,7 @@ RepositoryFileDownload, RepositoryPlugin, ) -from azul.plugins.hca import ( +from azul.plugins.metadata.hca.bundle import ( HCABundle, ) from azul.time import ( @@ -86,7 +86,7 @@ class DSSBundle(HCABundle[DSSBundleFQID]): @classmethod def canning_qualifier(cls) -> str: - return 'dss' + return 'dss.hca' def drs_path(self, manifest_entry: JSON) -> str: file_uuid = manifest_entry['uuid'] diff --git a/src/azul/plugins/repository/tdr_anvil/__init__.py b/src/azul/plugins/repository/tdr_anvil/__init__.py index 6f1d5fb4b..ea51f85c2 100644 --- a/src/azul/plugins/repository/tdr_anvil/__init__.py +++ b/src/azul/plugins/repository/tdr_anvil/__init__.py @@ -37,7 +37,7 @@ EntityReference, EntityType, ) -from azul.plugins.anvil import ( +from azul.plugins.metadata.anvil.bundle import ( AnvilBundle, Key, KeyReference, @@ -115,6 +115,10 @@ class TDRAnvilBundle(AnvilBundle[AnvilBundleFQID], TDRBundle): def extension(cls) -> str: return 'tdr.anvil' + @classmethod + def canning_qualifier(cls) -> str: + return super().canning_qualifier() + '.anvil' + def add_entity(self, entity: EntityReference, version: str, diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py index 06ba473d8..aeb5a7111 100644 --- a/src/azul/plugins/repository/tdr_hca/__init__.py +++ b/src/azul/plugins/repository/tdr_hca/__init__.py @@ -50,7 +50,7 @@ EntityReference, EntityType, ) -from azul.plugins.hca import ( +from azul.plugins.metadata.hca.bundle import ( HCABundle, ) from azul.plugins.repository.tdr import ( @@ -177,6 +177,10 @@ def extract_field(field: attr.Attribute) -> tuple[str, Any]: class TDRHCABundle(HCABundle[TDRBundleFQID], TDRBundle): + @classmethod + def canning_qualifier(cls) -> str: + return super().canning_qualifier() + '.hca' + def add_entity(self, *, entity_key: str, diff --git a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.json b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json similarity index 100% rename from test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.json rename to test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json diff --git a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.json b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json similarity index 100% rename from test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.json rename to test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json diff --git 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a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.json b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json similarity index 100% rename from test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.json rename to test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json diff --git a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.json b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json similarity index 100% rename from test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.json rename to test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json diff --git a/test/integration_test.py b/test/integration_test.py index 11b42c098..f1553ebd2 100644 --- a/test/integration_test.py +++ b/test/integration_test.py @@ -130,7 +130,7 @@ MetadataPlugin, RepositoryPlugin, ) -from azul.plugins.anvil import ( +from azul.plugins.metadata.anvil.bundle import ( Link, ) from azul.plugins.repository.tdr import (