Fix: No replicas for donors in HCA (#6582) #6584
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #6584 +/- ##
===========================================
- Coverage 85.38% 85.36% -0.02%
===========================================
Files 155 155
Lines 20788 20765 -23
===========================================
- Hits 17749 17726 -23
Misses 3039 3039 ☔ View full report in Codecov by Sentry. |
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achave11-ucsc
requested changes
Sep 27, 2024
| super().__init__(entity.address + | ||
| ' cannot ' + ('reference ' if forward else 'be referenced by ') + | ||
| other_entity.address) | ||
| super().__init__(f'{entity.ref} cannot {"reference" if forward else "be referenced by"} ' |
src/azul/indexer/transform.py
Outdated
| @@ -87,7 +85,7 @@ def estimate(self, partition: BundlePartition) -> int: | |||
| """ | |||
|
|
|||
| @abstractmethod | |||
| def transform(self, partition: BundlePartition) -> Iterable[Transform]: | |||
| def transform(self, partition: BundlePartition) -> Iterable[Contribution | Replica]: | |||
| for entity in self._list_entities() | ||
| if self._contains(partition, entity) | ||
| ) | ||
| def transform(self, partition: BundlePartition) -> Iterable[Contribution | Replica]: |
| @@ -1418,7 +1406,7 @@ def _entities_in(self, partition: BundlePartition) -> Iterator[ENTITY]: | |||
| def estimate(self, partition: BundlePartition) -> int: | |||
| return ilen(self._entities_in(partition)) | |||
|
|
|||
| def transform(self, partition: BundlePartition) -> Iterable[Transform]: | |||
| def transform(self, partition: BundlePartition) -> Iterable[Contribution | Replica]: | |||
| @@ -619,7 +597,7 @@ class DonorTransformer(BaseTransformer): | |||
| def entity_type(cls) -> str: | |||
| return 'donors' | |||
|
|
|||
| def _transform(self, entity: EntityReference) -> Transform: | |||
| def _transform(self, entity: EntityReference) -> Iterable[Contribution | Replica]: | |||
| @@ -1431,7 +1419,7 @@ def entity_type(cls) -> str: | |||
| def _entities(self) -> Iterable[api.File]: | |||
| return self.api_bundle.not_stitched(self.api_bundle.files) | |||
|
|
|||
| def _transform(self, files: Iterable[api.File]) -> Iterable[Contribution]: | |||
| def _transform(self, files: Iterable[api.File]) -> Iterable[Contribution | Replica]: | |||
| @@ -1649,11 +1643,11 @@ def _dated_entities(self) -> Iterable[DatedEntity]: | |||
| def estimate(self, partition: BundlePartition) -> int: | |||
| return int(partition.contains(self._singleton_id)) | |||
|
|
|||
| def transform(self, partition: BundlePartition) -> Iterable[Transform]: | |||
| def transform(self, partition: BundlePartition) -> Iterable[Contribution | Replica]: | |||
Comment on lines
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| # The other hubs will be added when the indexer consolidates duplicate replicas. | ||
| [file_id]) | ||
| yield self._replica(one(self.api_bundle.projects.values()).ref, | ||
| # Projects are linked to every file in their snapshot, making an explicit list | ||
| # of hub IDs for the project both redundant and impractically large. Therefore, | ||
| # we leave the hub IDs field empty for projects and rely on the tenet that every | ||
| # file is an implicit hub of its parent project. |
There was a problem hiding this comment.
L, https://github.com/DataBiosphere/azul/blob/develop/CONTRIBUTING.rst#12line-length
diff --git a/src/azul/plugins/metadata/hca/indexer/transform.py b/src/azul/plugins/metadata/hca/indexer/transform.py
index d263e7c2..f1942292 100644
--- a/src/azul/plugins/metadata/hca/indexer/transform.py
+++ b/src/azul/plugins/metadata/hca/indexer/transform.py
@@ -1469,13 +1469,19 @@ class FileTransformer(PartitionedTransformer[api.File]):
yield self._contribution(contents, file_id)
if config.enable_replicas:
yield self._replica(self.api_bundle.ref,
- # The other hubs will be added when the indexer consolidates duplicate replicas.
+ # The other hubs will be added when the
+ # indexer consolidates duplicate
+ # replicas.
[file_id])
yield self._replica(one(self.api_bundle.projects.values()).ref,
- # Projects are linked to every file in their snapshot, making an explicit list
- # of hub IDs for the project both redundant and impractically large. Therefore,
- # we leave the hub IDs field empty for projects and rely on the tenet that every
- # file is an implicit hub of its parent project.
+ # Projects are linked to every file in
+ # their snapshot, making an explicit
+ # list of hub IDs for the project both
+ # redundant and impractically large.
+ # Therefore, we leave the hub IDs field
+ # empty for projects and rely on the
+ # tenet that every file is an implicit
+ # hub of its parent project.
[])
for linked_entity in visitor.entities:
yield self._replica(linked_entity, [file_id])
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| # The other hubs will be added when the indexer consolidates duplicate replicas. | ||
| yield self._replica(entity, [entity.entity_id]) | ||
| for linked_entity in linked: | ||
| # Datasets are linked to every file in their snapshot, making an explicit list | ||
| # of hub IDs for the dataset both redundant and impractically large. Therefore, | ||
| # we leave the hub IDs field empty for datasets and rely on the tenet that every | ||
| # file is an implicit hub of its parent dataset. |
There was a problem hiding this comment.
L
diff --git a/src/azul/plugins/metadata/anvil/indexer/transform.py b/src/azul/plugins/metadata/anvil/indexer/transform.py
index 06464c9a..5e004beb 100644
--- a/src/azul/plugins/metadata/anvil/indexer/transform.py
+++ b/src/azul/plugins/metadata/anvil/indexer/transform.py
@@ -610,12 +610,14 @@ class FileTransformer(BaseTransformer):
)
yield self._contribution(contents, entity.entity_id)
if config.enable_replicas:
- # The other hubs will be added when the indexer consolidates duplicate replicas.
+ # The other hubs will be added when the indexer consolidates
+ # duplicate replicas.
yield self._replica(entity, [entity.entity_id])
for linked_entity in linked:
- # Datasets are linked to every file in their snapshot, making an explicit list
- # of hub IDs for the dataset both redundant and impractically large. Therefore,
- # we leave the hub IDs field empty for datasets and rely on the tenet that every
- # file is an implicit hub of its parent dataset.
+ # Datasets are linked to every file in their snapshot, making an
+ # explicit list of hub IDs for the dataset both redundant and
+ # impractically large. Therefore, we leave the hub IDs field
+ # empty for datasets and rely on the tenet that every file is an
+ # implicit hub of its parent dataset.
yield self._replica(linked_entity,
hub_ids=[] if linked_entity.entity_type == 'dataset' else [entity.entity_id])
|
|
||
| ENTITY = TypeVar('ENTITY', bound=api.Entity) | ||
|
|
||
|
|
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| class PartitionedTransformer(BaseTransformer, Generic[ENTITY]): | ||
|
|
||
| @abstractmethod | ||
| def _transform(self, entities: Iterable[ENTITY]) -> Iterable[Transform]: | ||
| def _transform(self, entities: Iterable[ENTITY]) -> Iterable[Contribution | Replica]: |
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hannes-ucsc
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Oct 4, 2024
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Connected issues: #6582
Checklist
Author
developissues/<GitHub handle of author>/<issue#>-<slug>1 when the issue title describes a problem, the corresponding PR
title is
Fix:followed by the issue titleAuthor (partiality)
ptag to titles of partial commitspartialor completely resolves all connected issuespartiallabelAuthor (chains)
baseor this PR is not chained to another PRchainedor is not chained to another PRAuthor (reindex, API changes)
rtag to commit title or the changes introduced by this PR will not require reindexing of any deploymentreindex:devor the changes introduced by it will not require reindexing ofdevreindex:anvildevor the changes introduced by it will not require reindexing ofanvildevreindex:anvilprodor the changes introduced by it will not require reindexing ofanvilprodreindex:prodor the changes introduced by it will not require reindexing ofprodreindex:partialand its description documents the specific reindexing procedure fordev,anvildev,anvilprodandprodor requires a full reindex or carries none of the labelsreindex:dev,reindex:anvildev,reindex:anvilprodandreindex:prodAPIor this PR does not modify a REST APIa(A) tag to commit title for backwards (in)compatible changes or this PR does not modify a REST APIapp.pyor this PR does not modify a REST APIAuthor (upgrading deployments)
make docker_images.jsonand committed the resulting changes or this PR does not modifyazul_docker_images, or any other variables referenced in the definition of that variableutag to commit title or this PR does not require upgrading deploymentsupgradeor does not require upgrading deploymentsdeploy:sharedor does not modifydocker_images.json, and does not require deploying thesharedcomponent for any other reasondeploy:gitlabor does not require deploying thegitlabcomponentdeploy:runneror does not require deploying therunnerimageAuthor (hotfixes)
Ftag to main commit title or this PR does not include permanent fix for a temporary hotfixanvilprodandprod) have temporary hotfixes for any of the issues connected to this PRAuthor (before every review)
develop, squashed old fixupsmake requirements_updateor this PR does not modifyrequirements*.txt,common.mk,MakefileandDockerfileRtag to commit title or this PR does not modifyrequirements*.txtreqsor does not modifyrequirements*.txtmake integration_testpasses in personal deployment or this PR does not modify functionality that could affect the IT outcomePeer reviewer (after approval)
System administrator (after approval)
demoorno demono demono sandboxN reviewslabel is accurateOperator (before pushing merge the commit)
reindex:…labels andrcommit title tagno demodevelop_select dev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unusedor this PR is not labeleddeploy:shared_select dev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab applyor this PR is not labeleddeploy:gitlab_select anvildev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unusedor this PR is not labeleddeploy:shared_select anvildev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab applyor this PR is not labeleddeploy:gitlabdeploy:gitlabdeploy:gitlabSystem administrator
dev.gitlabare complete or this PR is not labeleddeploy:gitlabanvildev.gitlabare complete or this PR is not labeleddeploy:gitlabOperator (before pushing merge the commit)
_select dev.gitlab && make -C terraform/gitlab/runneror this PR is not labeleddeploy:runner_select anvildev.gitlab && make -C terraform/gitlab/runneror this PR is not labeleddeploy:runnersandboxlabel or PR is labeledno sandboxdevor PR is labeledno sandboxanvildevor PR is labeledno sandboxsandboxdeployment or PR is labeledno sandboxanvilboxdeployment or PR is labeledno sandboxsandboxdeployment or PR is labeledno sandboxanvilboxdeployment or PR is labeledno sandboxsandboxor this PR does not remove catalogs or otherwise causes unreferenced indices indevanvilboxor this PR does not remove catalogs or otherwise causes unreferenced indices inanvildevsandboxor this PR is not labeledreindex:devanvilboxor this PR is not labeledreindex:anvildevsandboxor this PR is not labeledreindex:devanvilboxor this PR is not labeledreindex:anvildevpif the PR is also labeledpartialOperator (chain shortening)
developor this PR is not labeledbasechainedlabel from the blocked PR or this PR is not labeledbasebasebaselabel from this PR or this PR is not labeledbaseOperator (after pushing the merge commit)
devanvildevdevdevanvildevanvildev_select dev.shared && make -C terraform/shared applyor this PR is not labeleddeploy:shared_select anvildev.shared && make -C terraform/shared applyor this PR is not labeleddeploy:shareddevanvildevOperator (reindex)
devor this PR is neither labeledreindex:partialnorreindex:devanvildevor this PR is neither labeledreindex:partialnorreindex:anvildevdevor this PR is neither labeledreindex:partialnorreindex:devanvildevor this PR is neither labeledreindex:partialnorreindex:anvildevdevor this PR is neither labeledreindex:partialnorreindex:devanvildevor this PR is neither labeledreindex:partialnorreindex:anvildevdevor this PR does not require reindexingdevanvildevor this PR does not require reindexinganvildevdevor this PR does not require reindexingdevanvildevor this PR does not require reindexinganvildevdevor this PR does not require reindexingdevanvildevor this PR does not require reindexinganvildevOperator
deploy:shared,deploy:gitlab,deploy:runner,API,reindex:partial,reindex:anvilprodandreindex:prodlabels to the next promotion PRs or this PR carries none of these labelsdeploy:shared,deploy:gitlab,deploy:runner,API,reindex:partial,reindex:anvilprodandreindex:prodlabels, from the description of this PR to that of the next promotion PRs or this PR carries none of these labelsShorthand for review comments
Lline is too longWline wrapping is wrongQbad quotesFother formatting problem