Processing versioning tasks #182
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…pairing and other work done in the last week, before losing power and wifi.
…l other tasks for now, will be working on that next. Updated test fixture's annotation-configuration to match current Rosalution annotation configuration. Paired with Angelina on some of this stuff.
…with dependencies
… unit tests when processing annotation unit tasks; agreed upon a base set of datasets to use in configuration; and updated the neccesary code patching
…test methods to have more then one test case peer unit test
…ution' type version for rosalution's manifest. Paired with Angelina on Wednesday to create a couple of helper functions for testing. Thursday - Rabab worked on combining & testing all 3 versioning types in one test.
* Updated backend to include annotation retrieval for dependencies and ui * Updated unit tests and integration to pass
…g if transcripts exists is still broken, the case where transcript_id and no transcripts are listed in the variant is the case that needs to be fixed
…gating why transcripts are showing as not existing when they do
…atted; paired with Rabab
SeriousHorncat
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Sep 19, 2024
fatimarabab
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Sep 23, 2024
* Pushing up pulled in code changes from the annotation-task refactor, pairing and other work done in the last week, before losing power and wifi. * Was able to process versioning tasks for annotation units. Skipped all other tasks for now, will be working on that next. Updated test fixture's annotation-configuration to match current Rosalution annotation configuration. Paired with Angelina on some of this stuff. * testing process tasks for datasets without dependencies and datasets with dependencies * Tests pass for CPAM0002, need to rework CPAM0046 * Paired with Rabab to refactor how we manage skipping a dependency for unit tests when processing annotation unit tasks; agreed upon a base set of datasets to use in configuration; and updated the neccesary code patching * Missed a file. * got it working; heck ya * tests passing, linting & formatting passing * wip for genomic units;linting; and formatting * finished cleaning up genomic unit unit tests and added parameterized test methods to have more then one test case peer unit test * wip * wip to get annotation by analysis name' * backend wip for getting annotations by analysis * rabab & angelina pair for getting version result * formatted backend files * Able to retrieve version for 'rest' versioning type. Hardcoded 'rosalution' type version for rosalution's manifest. Paired with Angelina on Wednesday to create a couple of helper functions for testing. Thursday - Rabab worked on combining & testing all 3 versioning types in one test. * Fixed some of the linting errors * Retrieve and show annotations (#180) * Updated backend to include annotation retrieval for dependencies and ui * Updated unit tests and integration to pass * finished added the version calcs and fixed version retrieval, checking if transcripts exists is still broken, the case where transcript_id and no transcripts are listed in the variant is the case that needs to be fixed * fixed creatining multiple genomic units when uploading twice, investigating why transcripts are showing as not existing when they do * wrapped up cleaning the tests; removed extra logging; linted and formatted; paired with Rabab --------- Co-authored-by: SeriousHorncat <ange.unoantonison@gmail.com>
fatimarabab
added a commit
that referenced
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Sep 30, 2024
* Refactored annotation_task to use annotation_units. Updated tests and linted. Should be passing. * Refactored annotation_task to use annotation units in AnnotationTaskInterface * Wrapped up refactor. All tests should be passing. * Added some comments, refactored annotation-task further to get genomic unit and dataset directly from annotation-unit * Refactored annotation-task further. Added get_genomic_unit_type() and get_dependencies() in AnnotationUnit. Clarified some function names and docstrings. Tests and linting passing locally. * Processing versioning tasks (#182) * Pushing up pulled in code changes from the annotation-task refactor, pairing and other work done in the last week, before losing power and wifi. * Was able to process versioning tasks for annotation units. Skipped all other tasks for now, will be working on that next. Updated test fixture's annotation-configuration to match current Rosalution annotation configuration. Paired with Angelina on some of this stuff. * testing process tasks for datasets without dependencies and datasets with dependencies * Tests pass for CPAM0002, need to rework CPAM0046 * Paired with Rabab to refactor how we manage skipping a dependency for unit tests when processing annotation unit tasks; agreed upon a base set of datasets to use in configuration; and updated the neccesary code patching * Missed a file. * got it working; heck ya * tests passing, linting & formatting passing * wip for genomic units;linting; and formatting * finished cleaning up genomic unit unit tests and added parameterized test methods to have more then one test case peer unit test * wip * wip to get annotation by analysis name' * backend wip for getting annotations by analysis * rabab & angelina pair for getting version result * formatted backend files * Able to retrieve version for 'rest' versioning type. Hardcoded 'rosalution' type version for rosalution's manifest. Paired with Angelina on Wednesday to create a couple of helper functions for testing. Thursday - Rabab worked on combining & testing all 3 versioning types in one test. * Fixed some of the linting errors * Retrieve and show annotations (#180) * Updated backend to include annotation retrieval for dependencies and ui * Updated unit tests and integration to pass * finished added the version calcs and fixed version retrieval, checking if transcripts exists is still broken, the case where transcript_id and no transcripts are listed in the variant is the case that needs to be fixed * fixed creatining multiple genomic units when uploading twice, investigating why transcripts are showing as not existing when they do * wrapped up cleaning the tests; removed extra logging; linted and formatted; paired with Rabab --------- Co-authored-by: SeriousHorncat <ange.unoantonison@gmail.com> * wrapping up first draft of migration script;and and tidying up (#183) * wrapping up first draft of migration script;and tidying up feature * added a port for local mongodb developer so vscode can connect to mongodb in the container; fixed documentation in script for the example run command * updated the script to handle the rename and removed overwrite input * Adding back in the test case Rabab created that i accidently removed via a force-push; updated initial seed fixtures to use calculated annotation versions; cleaned up the documentation for the create annotation manifest script for migration * Added back the feature to append annotations to an existing dataset within genomic units * caught a mistake with the initial seed fixtures; changes were incomplete; this should fix that * missed fixing some unit tests affected by a change, ended up refactoring the tests to test more clearly --------- Co-authored-by: SeriousHorncat <ange.unoantonison@gmail.com>
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Pull Request Details
Wrike Ticket - Get latest version of the dataset within the annotation unit
Changes made:
To Review:
Static Analysis by Reviewer
The changes made to process Version Annotation Tasks and retrieve versions are working as intended - annotations rendered correctly.
To check this run the following commands:
Navigate to https://local.rosalution.cgds/rosalution/login. Login as developer. Click on any CPAM case, navigate to its Annotation view and ensure annotations are loading.