Issues

• biosample_submission_ingest reads the GOLD instrument mapping from the archived berkeley-schema-fy24 repo

  microbiomedata/nmdc-runtime#1657 · Filter by author turbomam opened on Oct 8, 2026

• Some API endpoints cannot omit superseded WFEs/DOs and failed PlannedProcess records

  bug
  microbiomedata/nmdc-runtime#1634 · Filter by author kheal opened on Sep 23, 2026
  1

  

• Include OrganismSample in runtime's provenance timestamp handling

  microbiomedata/nmdc-runtime#1632 · Filter by author turbomam opened on Sep 22, 2026

• Update synchronize_superseded_by_... Dagster op to log initial value alongside update statement

  Task

  microbiomedata/nmdc-runtime#1612 · Filter by author eecavanna opened on Sep 9, 2026
  1

  

• Harden id_prefix validation in the ontology reload jobs (defense-in-depth, not a bug)

  microbiomedata/nmdc-runtime#1600 · Filter by author turbomam opened on Aug 28, 2026

• Two changesheets applied to the same document race, and the later one silently discards the earlier one's changes

  microbiomedata/nmdc-runtime#1598 · Filter by author turbomam opened on Aug 28, 2026

• NCBI export raises AttributeError when a study has no principal_investigator name

  bug
  microbiomedata/nmdc-runtime#1596 · Filter by author turbomam opened on Aug 24, 2026
  2

  

• Changesheet validation gives every row the last row's linkml_class

  Bug

  microbiomedata/nmdc-runtime#1579 · Filter by author turbomam opened on Aug 12, 2026
  1

• changesheets:submit is documented as "applies"; the sheet is applied by a downstream job

  microbiomedata/nmdc-runtime#1577 · Filter by author turbomam opened on Aug 10, 2026
  1

• Mongo collection nmdc._runtime.analytics takes a long time to dump

  backlog
  microbiomedata/nmdc-runtime#1573 · Filter by author eecavanna opened on Jul 28, 2026

• Create GHA workflow that measures "cognitive complexity" (complexipy)

  Feature

  microbiomedata/nmdc-runtime#1567 · Filter by author eecavanna opened on Jul 23, 2026
  

• Reload / idempotency strategy for fast-initial ontology loads before enabling the NCBITaxon schedule

  task
  microbiomedata/nmdc-runtime#1565 · Filter by author turbomam opened on Jul 22, 2026
  2

• Decide indices for ontology_class_set and ontology_relation_set (loader builds none)

  task
  microbiomedata/nmdc-runtime#1564 · Filter by author turbomam opened on Jul 22, 2026
  3

• Decide which ancestry closure to compute per loaded ontology

  decision neededquestion
  microbiomedata/nmdc-runtime#1563 · Filter by author turbomam opened on Jul 22, 2026
  1

• Logic updates to Submission Portal to NMDC Mongo ingest ETL

  backlog
  microbiomedata/nmdc-runtime#1560 · Filter by author aclum opened on Jul 17, 2026
  1

  

• Update nmdc_runtime/site/export/ncbi_xml.py to use new LibraryPreparation values

  microbiomedata/nmdc-runtime#1549 · Filter by author aclum opened on Jun 24, 2026
  

• translate_metadata_submission_to_nmdc_schema_database dagster job does not populate infiltrations slot correctly

  bug
  microbiomedata/nmdc-runtime#1541 · Filter by author bmeluch opened on Jun 18, 2026
  6

  

• WorkflowExecution IDs minted by /pids/mint are not schema-compliant

  Bug

  microbiomedata/nmdc-runtime#1528 · Filter by author eecavanna opened on Jun 10, 2026
  

• User-facing parameter documentation for /pids/mint is not user friendly

  backlogdocumentation
  Bug

  microbiomedata/nmdc-runtime#1527 · Filter by author eecavanna opened on Jun 9, 2026

• Configure Dependabot to check for new versions of third-party GitHub Actions

  Feature

  microbiomedata/nmdc-runtime#1523 · Filter by author eecavanna opened on Jun 8, 2026

• Add NCBITaxon to the automated ontology-load schedule

  microbiomedata/nmdc-runtime#1516 · Filter by author turbomam opened on Jun 2, 2026
  1

  

• Bump ontology-loader pin and update the load_ontology op for the new controller API

  microbiomedata/nmdc-runtime#1515 · Filter by author turbomam opened on Jun 2, 2026
  1

  

• Health check failures coincide with DELETE /workflows/workflow_executions/ requests (dev and prod)

  Bug

  microbiomedata/nmdc-runtime#1491 · Filter by author eecavanna opened on May 16, 2026
  

• expand refscan to check for orphan data objects

  enhancement
  microbiomedata/nmdc-runtime#1490 · Filter by author aclum opened on May 15, 2026
  1

  

• Clarify role of operations documents within workflow automation subsystem

  Task

  microbiomedata/nmdc-runtime#1450 · Filter by author eecavanna opened on May 1, 2026