ensure no w3id.org loop; use data portal API #403
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PeopleMakeCulture
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dwinston
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* add stuff * Update json.dump() to json.dumps() in user.py * Mix in orcid jwt flow with client_credentials flow closes #333 * update .gitpod.yml * add sshproxy.sh for nersc tunneling * update make cmd * add gitpod affordance * add gitpod dockerfile * update gitpod stuff * rename * update Makefile * fix * gitpod: pull dev mdb * fix * fix make target * Separate dev and production deployments in GitHub workflow (#382) * Consolidate workflows for building docker images and deploying to Spin into one workflow * Remove docker-build.sh in favor of letting GitHub Actions handle Docker build and push * Update Release Process doc with info about initiating via GitHub Releases * Replace Rancher-Action with generic HTTP call * Replace release event with tag push event, which is required for semver metadata * Remove unnecessary pr event * Add more release instructions * fix: Handle `anyOf` in JSON Schema property (#379) * fix: Handle `anyOf` in JSON Schema property * Indicate function return value type * Refactor function and add comments * fix: Prefix class name with `nmdc:` * Implement helper function to process both single-ref and multi-ref specs * Document prefix functionality * Fix punctuation in comment * Update dictionary and function to accommodate multiple classes per collection * WIP: Update doc link maker to accommodate collections that map to multiple classes * Clarify variable names * Add comments in an attempt to clarify code * Delete commented-out code that doesn't accommodate multi-class collections * Add tests covering some corner cases * Fix inaccurate type hint * Clarify docstring * Replace reference to nonexistent dict and implement preliminary patch * Make the collection name bold on the search page * Update search page to account for collections mapping to multiple classes * Remove redundant type hints * style: black format * panic on no-type given * add script and api function * update script * Refactor runtime client methods to raise for status and parse and return results * handle omics processing records * update docstring * update to include correct prefix * update to use use new insdc_bioproject_identifiers slot on omics_processing * style: black format * add typecodes enpoint (#386) unauthenticated. closes #385 * update .gitpod.yml * add sshproxy.sh for nersc tunneling * update make cmd * add gitpod affordance * add gitpod dockerfile * update gitpod stuff * rename * update Makefile * fix * gitpod: pull dev mdb * fix * fix make target * Separate dev and production deployments in GitHub workflow (#382) * Consolidate workflows for building docker images and deploying to Spin into one workflow * Remove docker-build.sh in favor of letting GitHub Actions handle Docker build and push * Update Release Process doc with info about initiating via GitHub Releases * Replace Rancher-Action with generic HTTP call * Replace release event with tag push event, which is required for semver metadata * Remove unnecessary pr event * Add more release instructions * style: fix, and elaborate a bit * Revert stuff This reverts commit 1b2372d. * style: fix, and elaborate a bit --------- Co-authored-by: eecavanna <[email protected]> Co-authored-by: Donny Winston <[email protected]> Co-authored-by: Michael Thornton <[email protected]> Co-authored-by: Donny Winston <[email protected]> Co-authored-by: Jing Cao <[email protected]> Co-authored-by: Patrick Kalita <[email protected]> * Update build-and-release-to-spin.yml * fix: Update build-and-release-to-spin.yml * Replace illegal variable defined using other variable (#389) Co-authored-by: Donny Winston <[email protected]> * Do full depth checkout so setuptools-scm can detect version * Rever to using env context for variables * Use local path context when running docker build so that it knows about git tags * Actually push the docker image, but not if running in a fork * Fix use of boolean var * Env context only available in `steps.if` * Update .dockerignore * Update main.py to display scm version * Allow study metadata not captured in submission portal to be passed to SubmissionPortalTranslator * Allow passing doi category to SubmissionPortalTranslator, use dataset_doi by default * Connect additional study translator parameters to Dagster op inputs * Allow additional Biosample metadata to be passed in via external CSV file * Add PyPI URL and elaborate on manual publishing process * Add related links section to `README.md` * ensure no w3id.org loop; use data portal API (#403) closes #402 * Mix in orcid jwt flow with client_credentials flow closes #333 * style: rm print statement * style: add docstring * style: add commentary * style: rm print-debugging * fix: rm unneeded import --------- Co-authored-by: Jing Cao <[email protected]> Co-authored-by: Patrick Kalita <[email protected]> Co-authored-by: eecavanna <[email protected]> Co-authored-by: eecavanna <[email protected]> Co-authored-by: Michael Thornton <[email protected]>
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closes #402