Add schema-gap-analysis skill (CommunityMech-specific operational version)#68
Merged
Conversation
…sion) Copy-paste-runnable linkml-validate-based check for schema/data drift in CommunityMech YAMLs (kb/communities/ + data/isolates/). Three-axis classification (schema / instances / process); same methodology as the other Mechs but with CommunityMech paths baked in (so the user doesn't have to substitute placeholders from a cross-Mech table). Cross-Mech framework reference: https://github.com/CultureBotAI/culturebotai-claw/blob/main/.claude/skills/schema-gap-analysis/skill.md Smoke-tested 2026-05-17: kb/communities/*.yaml (261 records) validates with 0 errors. Force-added past .gitignore line 130 (`.claude/`) to match the existing pattern set by review-communities, evidence-curation, etc. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
There was a problem hiding this comment.
Pull request overview
Adds a CommunityMech-specific operational copy of the cross-Mech schema-gap-analysis skill, intended to be copy/paste runnable for validating CommunityMech YAML instances against the LinkML schema and for spotting generator drift.
Changes:
- Introduces a new
.claudeskill document with step-by-step commands for schema validation ofkb/communities/anddata/isolates/. - Adds simple post-processing (error histograms) and grep-based drift checks over
src/andscripts/. - Records a snapshot of validation status as of 2026-05-17.
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
- Step 2: drop the bogus `-C IsolateRecord` (no such class in the schema).
Per `data/isolates/README.md`, isolates use the same `MicrobialCommunity`
root as `kb/communities/`. Validate both with `-C MicrobialCommunity`.
- Steps 1/2/5: stop swallowing validator output to /dev/null — `tee` to
both stdout and log so startup errors are visible. Wrap `grep -c` with
`|| true` so a 0-error count doesn't break `set -e` recipes.
- Step 4: drop the dead `yaml.dump({"communities": ...})` grep (no
programmatic writers exist). Replace with broader greps that catch
`open()`, `Path.write_text()`, and `yaml.(safe_)?dump()` writes against
`kb/communities/` or `data/isolates/`.
- State table: populate `data/isolates/` row from a real run — 5 files,
4 missing required `id` slot.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
3 tasks
realmarcin
added a commit
that referenced
this pull request
May 19, 2026
The schema-gap-analysis skill (PR #68) flagged 4 of 5 files under data/isolates/ as missing the required `id` slot (`'id' is a required property`). The schema defines `id` on MicrobialCommunity as `identifier: true, required: true, pattern: "^CommunityMech:\\d{6}$"`. Assigned the next four available IDs (max in use was 000270): - Aspergillus_Indium_LED_Recovery.yaml → CommunityMech:000271 - BioModels_MODEL2204300002_Kefir_Rothia_Model → CommunityMech:000272 - Chromobacterium_Gold_Biocyanidation.yaml → CommunityMech:000273 - Methylobacterium_REE_Ewaste_Platform.yaml → CommunityMech:000274 All 5 isolates now validate clean under linkml-validate -C MicrobialCommunity Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Adds CommunityMech-specific operational version of the cross-Mech
schema-gap-analysisskill. Copy-paste-runnable: schema, kb/communities/, data/isolates/ all baked in (no need to substitute from a cross-Mech config table).Smoke-tested 2026-05-17:
kb/communities/*.yaml(261 records) validates cleanly with 0 errors.Cross-Mech framework reference: https://github.com/CultureBotAI/culturebotai-claw/blob/main/.claude/skills/schema-gap-analysis/skill.md
🤖 Generated with Claude Code