SciDEX — Task: [Exchange] Add mermaid pathway diagrams to top 10

Add mermaid pathway diagrams to hypothesis descriptions for the top 10 scoring hypotheses that don't have them yet. Each diagram should show the mechanistic pathway (gene -> protein interaction -> cellular process -> disease outcome). Update the description field in the hypotheses table. This enriches the hypothesis detail pages which render mermaid diagrams. ## REOPENED TASK — CRITICAL CONTEXT This task was previously marked 'done' but the audit could not verify the work actually landed on main. The original work may have been: - Lost to an orphan branch / failed push - Only a spec-file edit (no code changes) - Already addressed by other agents in the meantime - Made obsolete by subsequent work **Before doing anything else:** 1. **Re-evaluate the task in light of CURRENT main state.** Read the spec and the relevant files on origin/main NOW. The original task may have been written against a state of the code that no longer exists. 2. **Verify the task still advances SciDEX's aims.** If the system has evolved past the need for this work (different architecture, different priorities), close the task with reason "obsolete: " instead of doing it. 3. **Check if it's already done.** Run `git log --grep=''` and read the related commits. If real work landed, complete the task with `--no-sha-check --summary 'Already done in '`. 4. **Make sure your changes don't regress recent functionality.** Many agents have been working on this codebase. Before committing, run `git log --since='24 hours ago' -- ` to see what changed in your area, and verify you don't undo any of it. 5. **Stay scoped.** Only do what this specific task asks for. Do not refactor, do not "fix" unrelated issues, do not add features that weren't requested. Scope creep at this point is regression risk. If you cannot do this task safely (because it would regress, conflict with current direction, or the requirements no longer apply), escalate via `orchestra escalate` with a clear explanation instead of committing.

Completion Notes

Auto-completed by supervisor after successful deploy to main

Git Commits (2)

[Exchange] Update spec work log for mermaid task [task:33c114fa-1a5f-42ac-a50b-9c468cd5548d]2026-04-13

[Exchange] Add mermaid pathway diagrams to top 10 hypothesis descriptions [task:33c114fa-1a5f-42ac-a50b-9c468cd5548d]2026-04-13

Spec File

[Exchange] Add mermaid pathway diagrams to top 10 hypothesis descriptions

ID: 33c114fa-1a5 Priority: 95 Type: one_shot Status: open

Goal

Acceptance Criteria

☑ Concrete deliverables created

☑ Work log updated with timestamped entry

Work Log

2026-04-13 23:30 PT — Slot 0

Investigated current state: verified no prior commits for this task ID
Queried top hypotheses by composite_score, identified 10 without mermaid diagrams
Created scripts/add_mermaid_to_hypotheses.py with hypothesis-specific mechanistic pathways
Each diagram follows AGENTS.md mermaid rules: graph TD, quoted labels, max 20 nodes, color-coded by type
Ran script against live DB: updated 10 hypotheses with mermaid pathway sections
Verified via API: all 10 return 'graph TD' in description field
Committed script and pushed (ac276bbed)
Task complete: 10 hypothesis descriptions enriched with mechanistic pathway diagrams

Payload JSON

{
  "requirements": {
    "coding": 7,
    "reasoning": 7,
    "analysis": 8
  },
  "completion_shas": [
    "86af224b2345c60cb393fcc7aa27eb34e2bade96",
    "ac276bbeda744255afef431d00b585a049272956"
  ],
  "completion_shas_checked_at": "2026-04-13T23:21:13.670581+00:00"
}