Skip to content

Expand evidence study-source vocabulary - #937

Open
realmarcin wants to merge 1 commit into
mainfrom
feat/evidence-assessment
Open

realmarcin wants to merge 1 commit into
mainfrom
feat/evidence-assessment

Conversation

@realmarcin

Copy link
Copy Markdown
Contributor

Extend the existing required EvidenceSourceEnum with EcoMech study types and DATABASE; retain all existing values and requiredness.

Use the five established support values and the fleet source vocabulary. Preserve existing citation formats, evidence types, required fields, and the legacy shared quotation-location field. No scientific records are changed or backfilled. Add usage documentation and closed-schema tests that reject conflating study type with curation method or quotation location.

Fleet rationale and contract: CultureBotAI/culturebotai-claw#448
Upstream: https://github.com/diatomsRcool/ecomech/blob/5d3f55467f3caaa6e88eb7f33037e4a8103873a7/docs/traitmech_integration.md

Validation

39 evidence tests passed, including all source types through the generated dataclass. Regenerated with pinned LinkML 1.9.3 and formatted with black.

All existing schema definitions compare unchanged after removing the newly added fields/enum members. Ruff and git diff --check pass. Vendored shared schema files are unchanged.

Copilot AI lite review requested due to automatic review settings September 17, 2026 07:42

Copilot AI left a comment

Copy link
Copy Markdown

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Copilot was unable to review this pull request because the user who requested the review has reached their quota limit.

@github-actions

Copy link
Copy Markdown

Network integrity findings

Warnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build.

Network Integrity Audit Report
================================================================================

0 error, 13 warning across 4 records with findings
Only error-severity findings fail the build.

Bacillus_G12_Y4_X25_Tobacco_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Bacillus_siamensis_vallismortis_HT_Masson_Pine_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Fusarium oxysporum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)

Total: 3 issues (0 error, 3 warning)

Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Space_Habitat_SevenMember_Stress_Tolerance_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acinetobacter radioresistens 50V1' has no interactions
  [warning] DISCONNECTED: Taxon 'Micrococcus luteus W4-Al-K1' has no interactions
  [warning] DISCONNECTED: Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas antarctica CMS 35T' has no interactions
  [warning] DISCONNECTED: Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptococcus halotolerans HTS9T' has no interactions

Total: 6 issues (0 error, 6 warning)

The full report is attached to the workflow run as an artifact.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants