Pinned issues
Issues
- 4
- 6
`berkeley`: Fix failing tests in GOLD, NEON, and submission portal translators
#600 opened by eecavanna - 5
`berkeley`: Update activity related endpoints
#593 opened by aclum - 0
- 0
GHA: Separate container `build` and `run` steps to simplify reading workflow logs
#640 opened by eecavanna - 1
`berkeley`: `ORCID_JWK` dictionary is not compatible with ORCID sandbox environment
#638 opened by eecavanna - 1
`berkeley`: Allow developer to switch between ORCID production and sandbox via environment variable
#636 opened by eecavanna - 1
- 0
`berkeley`: Update referential integrity notebook based upon assumption that `type` is required
#632 opened by eecavanna - 0
`berkeley`: Replace `designated_class ` with `type` (in `ncbi_xml_utils.py` script)
#630 opened by eecavanna - 0
`berkeley`: Replace `OmicsProcessing` with `DataGeneration` (in referential integrity checker notebook)
#629 opened by eecavanna - 0
`berkeley`: Replace `Activity` with `DataGeneration` (in referential integrity checker notebook)
#628 opened by eecavanna - 0
`berkeley`: Document expectations around merging `main` into `berkeley` branch over time
#626 opened by eecavanna - 0
`berkeley`: refactor `_get_instrument_name` in `nmdc_runtime/site/translation/gold_translator.py`
#622 opened by aclum - 0
`berkeley`: Validate or remove `_translate_omics_processing` function (in `neon_surface_water_translator.py`) that returned an `nmdc.OmicsProcessing`
#589 opened by eecavanna - 0
`berkeley`: Validate or remove `_translate_omics_processing` function (in `neon_benthic_translator.py`) that returned an `nmdc.OmicsProcessing`
#588 opened by eecavanna - 0
`berkeley`: Validate or remove `_translate_omics_processing` function (in `neon_soil_translator.py`) that returned an `nmdc.OmicsProcessing`
#587 opened by eecavanna - 0
`berkeley`: Validate or remove `_translate_omics_processing` function (in `gold_translator.py`) that returned an `nmdc.OmicsProcessing`
#586 opened by eecavanna - 0
`berkeley`: Update GHA workflow to publish container image from `berkeley` branch
#582 opened by eecavanna - 16
- 5
Dagster `apply_metadata_in` op fails to insert `functional_annotation_agg` documents
#611 opened by aclum - 1
ORCID Login does not work (sends user to `api.microbiomedata.org` page saying `Internal Server Error`)
#623 opened by eecavanna - 16
`load_changesheet` function tries to use Python `builtins` module to access non-Python (LinkML) data types
#616 opened by aclum - 3
`berkeley`: Dagster job `claim_and_run_apply_changesheet_jobs` fails to authenticate with Mongo server
#594 opened by aclum - 8
`berkeley`: Dagster does not insert data into Mongo despite `json:submit` returning success response
#595 opened by aclum - 0
Impossible to specify a bounding box filter query
#617 opened by cmungall - 1
Minter: Using multiple minter instances and discarding their databases can result in ID collisions
#615 opened by eecavanna - 2
- 3
Add documentation to "Referential integrity checker (prototype)" notebook (alldocs-based)
#604 opened by eecavanna - 1
Add Swagger documentation to `POST` `/sites/{site_id}:generateCredentials` API endpoint
#606 opened by eecavanna - 2
no longer have permission to generate site credentials
#605 opened by aclum - 8
Cannot find or update documents by `_id` ObjectId via `/queries:run` endpoint
#575 opened by mbthornton-lbl - 0
Refactor `validate_json`
#602 opened by PeopleMakeCulture - 2
`berkeley`: Update minter to use first typecode when pattern contains multiple typecodes
#592 opened by kheal - 0
`berkeley`: Fix failing test: `tests/test_api/test_metadata.py::test_ensure_data_object_type` (`DataObject` lacks `type` field)
#590 opened by eecavanna - 1
- 3
- 11
Runtime references to `nmdc_schema_accepting_legacy_ids`, which is absent from `nmdc-schema` version `10.5.4`
#570 opened by eecavanna - 1
`berkeley`: Fix type hint issue preventing Runtime from booting with Berkeley schema
#578 opened by eecavanna - 4
- 0
Migrations: Update `migrate_10_3_0_to_10_4_0.ipynb` notebook to use newer migrator
#573 opened by eecavanna - 0
- 0
Bump schema version from `10.3.0` to `10.5.4`
#559 opened by eecavanna - 1
- 0
Include `functional_annotation_agg` & `metap_gene_function_agg` collections (not defined in the schema) to referential integrity check
#568 opened by PeopleMakeCulture - 2
Replace custom build system with Poetry
#563 opened by eecavanna - 0
- 0
Migration: Update notebook dependencies to accommodate `nmdc-schema` dependency requirements
#561 opened by eecavanna - 0
Migration: Implement notebook that runs migrator that appends version numbers to `nom_analysis_activity` `id`s
#556 opened by eecavanna - 0
Add INSDC identifiers to NMDC studies on `insdc_bioproject_identifiers` slot
#557 opened by sujaypatil96