microbiomedata nmdc-runtime issues

microbiomedata / nmdc-runtime

Runtime system for NMDC data management and orchestration

https://microbiomedata.github.io/nmdc-runtime/

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issues

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Cannot find or update documents by `_id` ObjectId via `/queries:run` endpoint

#575 mbthornton-lbl opened 1 day ago
1
Update notebook to use revised migrator (via newer `nmdc-schema` PyPI package)

#574 eecavanna closed 3 days ago
1
Migrations: Update `migrate_10_3_0_to_10_4_0.ipynb` notebook to use newer migrator

#573 eecavanna closed 3 days ago
0
Update `NmdcPortalApiClient` with new authentication scheme

#572 pkalita-lbl closed 4 days ago
0
Update `NmdcPortalApiClient` to use new Bearer token authentication

#571 pkalita-lbl closed 4 days ago
0
Runtime references `nmdc_schema_accepting_legacy_ids`, which is absent from `nmdc-schema` version `10.5.4`

#570 eecavanna opened 1 week ago
9
Standardize utils for mapping schema classes to mongo collections

#569 PeopleMakeCulture opened 1 week ago
0
Include `functional_annotation_agg` & `metap_gene_function_agg` collections (not defined in the schema) to referential integrity check

#568 PeopleMakeCulture opened 1 week ago
0
Authenticate as workflow triggerer instead of as repo owner

#566 eecavanna closed 1 week ago
1
Configure GitHub Actions to push container image to GitHub Container Registry (in addition to Docker Hub)

#565 eecavanna closed 1 week ago
1
Publish container images to GitHub Container Registry (GHCR)

#564 eecavanna closed 1 week ago
0
Replace custom build system with Poetry

#563 eecavanna opened 1 week ago
2
Bump migration notebooks' `pymongo` dependency to accommodate `nmdc-schema`

#562 eecavanna closed 1 week ago
1
Migration: Update notebook dependencies to accommodate `nmdc-schema` dependency requirements

#561 eecavanna closed 1 week ago
0
Bump `nmdc-schema` from `10.3.0` to `10.5.5`

#560 eecavanna closed 1 week ago
11
Bump schema version from `10.3.0` to `10.5.4`

#559 eecavanna closed 1 week ago
0
Implement migration notebook for `v10.3.0` to `v10.4.0`

#558 eecavanna closed 1 week ago
1
Add INSDC identifiers to NMDC studies on `insdc_bioproject_identifiers` slot

#557 sujaypatil96 opened 2 weeks ago
0
Migration: Implement notebook that runs migrator that appends version numbers to `nom_analysis_activity` `id`s

#556 eecavanna closed 1 week ago
0
Run Ref Integrity Notebook on post-re-iding Mongo

#555 PeopleMakeCulture closed 19 hours ago
4
Remove dependence upon schema variant that accepts legacy, pre-Napa IDs

#554 eecavanna closed 1 week ago
1
Implement notebook that migrates Mongo database to "Berkeley" schema

#553 eecavanna opened 2 weeks ago
0
nmdc-runtime should use materalized_pattern version of json schema

#552 aclum opened 2 weeks ago
2
Implementation of API endpoint for NMDC Database roll-up

#551 sujaypatil96 opened 3 weeks ago
1
Materialize mongo alldocs collection

#550 dwinston opened 3 weeks ago
1
Remove references to TerminusDB (without formatted unrelated code)

#549 eecavanna closed 3 weeks ago
1
Persist pared down `all_docs` collection in mongo

#548 PeopleMakeCulture closed 2 weeks ago
1
Inference of environmental package based on MIxS environmental context terms

#547 sujaypatil96 opened 3 weeks ago
0
Prep JAWS Presentation

#546 PeopleMakeCulture opened 3 weeks ago
0
Given a Biosample id we need to be able to retrieve the associated DataObjects

#545 sujaypatil96 closed 3 weeks ago
3
Two GitHub Actions workflows have the same name: "Python application"

#544 eecavanna opened 4 weeks ago
0
Materialize a version of `all_docs` collection in dev mongodb

#543 PeopleMakeCulture opened 4 weeks ago
2
[Clean-up] Remove references to `terminusdb`

#542 PeopleMakeCulture closed 3 weeks ago
13
`/queries:run` write errors yield a more informative error code and message

#541 dwinston opened 4 weeks ago
0
[Placeholder] Sync Runtime Auth with Data Portal Changes

#540 PeopleMakeCulture opened 1 month ago
1
Delete `read_based_analysis_activity_set` collection from production Mongo server

#539 aclum closed 1 month ago
2
Delete `read_QC_analysis_activity_set` collection from production Mongo server

#538 aclum closed 1 month ago
2
Expand minting service to append ID version for WorkflowExecutionActivity subclasses

#537 aclum closed 4 weeks ago
1
Consider deleting `tmp.json` file from code base

#536 eecavanna opened 1 month ago
0
Consider deleting `github_secrets_to_dotenv.sh` file from code base

#535 eecavanna opened 1 month ago
0
Consider deleting `guix-manifest.scm` file from code base

#534 eecavanna opened 1 month ago
0
Configure CORS to allow requests from clients hosted on GitHub Pages

#533 eecavanna closed 1 month ago
2
Implement API endpoint that returns name of collection containing document having a given `id`

#532 eecavanna closed 2 weeks ago
13
Implement API endpoint that accepts `id` value and returns its class name and collection name

#531 eecavanna closed 2 weeks ago
1
response to a request for a data object that a curator has determined should be removed

#530 dwinston opened 1 month ago
4
Mint & Validate versioned `WorkflowExecutionActivity` `nmdc:` IDs for workflows of same type and `OmicsProcessing`

#529 aclum opened 1 month ago
7
Remove banner saying that re-ID-ing will happen the week of May 13

#528 eecavanna closed 1 month ago
2
Update testing workflow name to pytest

#527 PeopleMakeCulture opened 1 month ago
0
Make CI Pipelines Faster

#526 PeopleMakeCulture opened 1 month ago
0
Upgrade to nmdc-schema 10.3.0

#525 pkalita-lbl closed 1 month ago
0