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microbiomedata
/
nmdc-runtime
Runtime system for NMDC data management and orchestration
https://microbiomedata.github.io/nmdc-runtime/
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Publish container images to GitHub Container Registry (GHCR)
#564
eecavanna
closed
3 months ago
0
Replace custom build system with Poetry
#563
eecavanna
opened
3 months ago
2
Bump migration notebooks' `pymongo` dependency to accommodate `nmdc-schema`
#562
eecavanna
closed
3 months ago
1
Migration: Update notebook dependencies to accommodate `nmdc-schema` dependency requirements
#561
eecavanna
closed
3 months ago
0
Bump `nmdc-schema` from `10.3.0` to `10.5.5`
#560
eecavanna
closed
3 months ago
11
Bump schema version from `10.3.0` to `10.5.4`
#559
eecavanna
closed
3 months ago
0
Implement migration notebook for `v10.3.0` to `v10.4.0`
#558
eecavanna
closed
3 months ago
1
Add INSDC identifiers to NMDC studies on `insdc_bioproject_identifiers` slot
#557
sujaypatil96
opened
3 months ago
0
Migration: Implement notebook that runs migrator that appends version numbers to `nom_analysis_activity` `id`s
#556
eecavanna
closed
3 months ago
0
Run Ref Integrity Notebook on post-re-iding Mongo
#555
PeopleMakeCulture
closed
3 months ago
4
Remove dependence upon schema variant that accepts legacy, pre-Napa IDs
#554
eecavanna
closed
3 months ago
1
Implement notebook that migrates Mongo database from "legacy" to "Berkeley" schema
#553
eecavanna
closed
1 month ago
4
nmdc-runtime should use materalized_pattern version of json schema
#552
aclum
opened
3 months ago
3
Implementation of API endpoint for NMDC Database roll-up
#551
sujaypatil96
opened
3 months ago
1
Materialize mongo alldocs collection
#550
dwinston
closed
2 months ago
4
Remove references to TerminusDB (without formatted unrelated code)
#549
eecavanna
closed
3 months ago
1
Persist pared down `all_docs` collection in mongo
#548
PeopleMakeCulture
closed
3 months ago
1
Inference of environmental package based on MIxS environmental context terms
#547
sujaypatil96
opened
3 months ago
0
Prep JAWS Presentation
#546
PeopleMakeCulture
opened
4 months ago
0
Given a Biosample id we need to be able to retrieve the associated DataObjects
#545
sujaypatil96
closed
3 months ago
3
Two GitHub Actions workflows have the same name: "Python application"
#544
eecavanna
opened
4 months ago
0
Materialize a version of `all_docs` collection in dev mongodb
#543
PeopleMakeCulture
closed
2 months ago
2
[Clean-up] Remove references to `terminusdb`
#542
PeopleMakeCulture
closed
3 months ago
13
`/queries:run` write errors yield a more informative error code and message
#541
dwinston
opened
4 months ago
0
[Placeholder] Sync Runtime Auth with Data Portal Changes
#540
PeopleMakeCulture
opened
4 months ago
1
Delete `read_based_analysis_activity_set` collection from production Mongo server
#539
aclum
closed
4 months ago
2
Delete `read_QC_analysis_activity_set` collection from production Mongo server
#538
aclum
closed
4 months ago
2
Expand minting service to append ID version for WorkflowExecutionActivity subclasses
#537
aclum
closed
4 months ago
1
Consider deleting `tmp.json` file from code base
#536
eecavanna
opened
4 months ago
0
Consider deleting `github_secrets_to_dotenv.sh` file from code base
#535
eecavanna
opened
4 months ago
0
Consider deleting `guix-manifest.scm` file from code base
#534
eecavanna
opened
4 months ago
0
Configure CORS to allow requests from clients hosted on GitHub Pages
#533
eecavanna
closed
4 months ago
2
Implement API endpoint that returns name of collection containing document having a given `id`
#532
eecavanna
closed
3 months ago
13
Implement API endpoint that accepts `id` value and returns its class name and collection name
#531
eecavanna
closed
3 months ago
1
response to a request for a data object that a curator has determined should be removed
#530
dwinston
opened
4 months ago
4
Mint & Validate versioned `WorkflowExecutionActivity` `nmdc:` IDs for workflows of same type and `OmicsProcessing`
#529
aclum
opened
4 months ago
7
Remove banner saying that re-ID-ing will happen the week of May 13
#528
eecavanna
closed
4 months ago
2
Update testing workflow name to pytest
#527
PeopleMakeCulture
opened
4 months ago
0
Make CI Pipelines Faster
#526
PeopleMakeCulture
opened
4 months ago
0
Upgrade to nmdc-schema 10.3.0
#525
pkalita-lbl
closed
4 months ago
0
`/metadata/json:validate` endpoint returns HTTP 500 error in Napa and prod (not dev)
#524
aclum
closed
4 months ago
6
Allow user to perform `$unset` operations via `/queries:run` endpoint
#523
aclum
opened
4 months ago
4
Mermaid reports "Parse error" and does not display diagram in Minter docs
#522
eecavanna
opened
4 months ago
0
[DRAFT] Merge jupyter notebooks for 1) mongo validation and ref integrity check && 2) RDF gen
#521
PeopleMakeCulture
closed
3 months ago
9
Minter responds with HTTP 500 and raw Python stack trace
#520
eecavanna
opened
4 months ago
0
Migrations: Implement notebook that runs all Berkeley schema migrators
#519
eecavanna
closed
1 month ago
7
Code for NMDC to NCBI export
#518
sujaypatil96
closed
3 months ago
4
Validation differs between `json:validate` and `json:submit` API endpoints
#517
aclum
opened
4 months ago
0
Update analytics middleware to log requests lacking a `user-agent` header
#516
eecavanna
closed
4 months ago
3
API returns HTTP 500 when request lacks `User-Agent` header (Analytics middleware raises `KeyError`)
#515
eecavanna
closed
4 months ago
3
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