DO NOT MERGE: Update Runtime to work with Berkeley schema (meta PR) #581
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…reventing-runtime-from-booting-with-berkeley-schema Switch to "Berkeley schema" and eliminate broken references preventing application startup
38 tasks
`berkeley`: Merge `main` into `berkeley` (to trigger GHA workflow)
Updating to a berkeley schema valid biosample json file
Add type to DataObject.
Added missing comma for DataObject example
…berkeley-20240717 Merge `main` into `berkeley` (July 17)
…lid-biosample `berkeley`: Update `test_endpoints.py` to fix some failing tests
…r-to-use-first-typecode-when-pattern-contains-multiple-typecodes Update minter to use first typecode when pattern contains multiple typecodes
…le-merging-main-into-berkeley Merge `main` into `berkeley` (routine merge on August 9, 2024)
…ime (#634) * Documentation expectations regarding merging `main` into `berkeley` * Fix typo * Clarify expectation * Clarify sentence * Fix typo
…#637) * Get ORCID base URL (production vs. sandbox) from environment variable * style: reformat --------- Co-authored-by: github-actions <[email protected]>
…ctionary-is-not-compatible-with-orcid-sandbox-environment Use ORCID environment-specific JWKS values and clean up existing comments
* Update test_gold_translator.py to add `type` * Update test_gold_translator.py remove extra bracket * Update test_gold_translator.py syntax fixes * chore: format * fix: pass `type` to constructor closes #600 * fix: make test idempotent * feat: more resilient test data loading * fix: failing `test_get_samp_taxon_id` * fix: `test_get_collection_date` requires timestampvalue type * fix: add type to _get_quantity_value for gold & submission portal translators * fix:_get_text_value * update:test_get_controlled_term_value with comment * fix:test_get_lat_lon types * add types to _get_env_term_value * add types to submission portal translator * fix:broken neon translator tests * add types for submission portal translator * update doi getter * feat: clear test dbs on `make down-test` * fix: `test_get_doi` * fix: partial fix for `test_get_dataset` * add types to test data yaml * add more types * add credit assoc * add person, study * add type for env_package * add types for mock submission object * add types to translator * skip three remaining failing tests --------- Co-authored-by: Donny Winston <[email protected]> Co-authored-by: Jing <[email protected]>
* update /workflows/activities to /workflows/workflow_executions * modify test submit workflow executions * remove api/v1/workflows dir * remove unused files in `api/v1` * formatting * update endpoints * feat: refactor find endpoints * feat: reproduce deprecated interface and use `deprectated` kwarg * chore: docstring update * fix: `find_workflow_execution_by_id` add tests for /workflow_executions/* endpoints * fix: unskip `test_submit_workflow_executions` --------- Co-authored-by: Jing <[email protected]> Co-authored-by: Donny Winston <[email protected]>
Merge `main` into `berkeley` (routine, August 23, 2024)
commenting out pytest skip
Updating test_submit_workflow_activities
update POST endpoint for workflows
…682-documentation-updates-for-berkeley Restore hyperlinks to "Metadata" section and modernize Runtime description
…activities `berkeley`: Unskip `test_submit_workflow_activities` test and make it work with Berkeley schema
…iles-are-being-skipped-by-mistake `berkeley`: Restore tests that were being skipped by mistake (oops)
…st_gold_api_ops Quick fixes for GOLD API client tests in `tests/test_ops/test_gold_api_ops.py`
Merge `main` into `berkeley` (routine, September 19, 2024)
The previous code made the invalid assumption that a given collection could only store documents of a single type. That constraint does not exist in databases conforming to the Berkeley schema (nmdc-schema v11+).
…integrity-notebook 576 berkeley updates ref integrity notebook
…-ensure_alldocs-fails-with-assertionerror-1 `berkeley`: Determine class ancestry per-type value (within collection) instead of per-collection (when generating `alldocs`)
…-data_objectsstudystudy_id-not-returning-correct-results Update field name to be consistent with Berkeley schema
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I am closing this draft PR in order to see what effect closing it has on the symptoms described in issue #700. |
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