Update Runtime to work with Berkeley schema (i.e. nmdc-schema version v11.0.0)
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…reventing-runtime-from-booting-with-berkeley-schema Switch to "Berkeley schema" and eliminate broken references preventing application startup
`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)
…schema-dependency-to-latest-pre-release-1100rc20 `berkeley`: Update `nmdc-schema` to `11.0.0rc20` and sync transitive dependencies
Adding study id curie prefix.
applied_roles should be a list not a string
removing commented out skip pytests
Unskip and fix 3 tests that were being skipped in `test_metadata.py`
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Whoops! In the commit message of Update nmdc-schema package to 11.0.0 and synchronize transient deps, I used the word "transient" when I meant to use the word "transitive." |
eecavanna
requested review from
pkalita-lbl,
sujaypatil96,
dwinston,
aclum and
PeopleMakeCulture
eecavanna
commented
Oct 7, 2024
eecavanna
commented
Oct 7, 2024
pkalita-lbl
previously approved these changes
Oct 7, 2024
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In this branch, multiple team members made changes to multiple parts of the code base with the common goal of getting the Runtime to work with the so-called "Berkeley schema" (i.e.
nmdc-schemaversion 11). In this PR, we are requesting that those changed be merged into themainbranch of the repository, effectively making it so the Runtime stops being compatible with the legacy schema and starts being compatible with the Berkeley schema.