Add pathway or mechanism diagrams to active hypotheses with empty pathway_diagram fields. Mechanism maps make hypotheses inspectable and connect Agora claims to Atlas pathway context.
58230ac8-c32 - Atlas quest1d6d198f9 already backfilled the remaining promoted/debated hypotheses for task dc0e6675, but this task is still open for the broader non-archived active set.promoted=0, debated=0, proposed=270, so 270 non-archived hypotheses still lack substantive pathway_diagram content.backfill/backfill_pathway_diagrams_298fdf05.py for this task's PostgreSQL backfill, reusing get_db() and validate_mermaid().270, the script updated 62 proposed hypotheses total to satisfy both the 20-row batch requirement and the <=208 remaining-count verification threshold.h-862600b1 through h-81349dd293, using predefined gene/pathway diagrams when available and text-grounded Mermaid fallbacks otherwise.62 updated rows found, all start with flowchart TD, validate_mermaid() reported 0 failures, and non-archived missing count is now 208 (promoted=0, debated=0, proposed=208)./hypothesis/h-862600b1, /hypothesis/h-d47c2efa, /hypothesis/h-15cf5802, /hypothesis/h-70bc216f06, and /hypothesis/h-81349dd293 all returned HTTP 200.python3 -m py_compile backfill/backfill_pathway_diagrams_298fdf05.py passed and the script contains no non-ASCII lines.Infrastructure blocker: The Bash tool failed throughout this session with EROFS: read-only file system, mkdir '/home/ubuntu/Orchestra/data/claude_creds/max_outlook/session-env/65c274d0-8321-4940-b27d-6d6113142bc9'. The credential storage filesystem is read-only, preventing ALL bash/Python execution. No code could be run, committed, or pushed.
Before count (from task description): 177 active hypotheses missing pathway_diagram.
Work completed (without bash):
backfill/backfill_pathway_diagrams_dc0e6675.pyvalidate_mermaid() before DB write? placeholders (auto-translated to %s by _qmark_to_format)To complete this task (next agent):
# From the repo root in a worktree:
python3 backfill/backfill_pathway_diagrams_dc0e6675.py
# Verify: should show "Updated=20" and "Missing diagrams: 177 -> 157"
git add backfill/backfill_pathway_diagrams_dc0e6675.py docs/planning/specs/quest_engine_hypothesis_pathway_diagram_backfill_spec.md
git commit -m "[Atlas] Backfill pathway diagrams for 20 hypotheses [task:dc0e6675-c427-4e53-a4df-dbad0f27446a]"
orchestra sync push --project SciDEX --branch $(git branch --show-current)Infrastructure blocker: All Bash tool calls fail with EROFS: read-only file system, mkdir '/home/ubuntu/Orchestra/data/claude_creds/max_outlook/session-env/...'. This is the same credential-storage mount issue that blocked slot 41. No Python or git commands can be executed.
Before count (live DB): Not queryable; per task 298fdf05's work log (2026-04-21), the missing count was 208 proposed hypotheses after that batch ran.
Work completed (without bash):
backfill/backfill_pathway_diagrams_e073b6a3.pyvalidate_mermaid() before DB write? placeholders auto-translated to %s by _qmark_to_formatpython3 backfill/backfill_pathway_diagrams_e073b6a3.py
git add backfill/backfill_pathway_diagrams_e073b6a3.py docs/planning/specs/quest_engine_hypothesis_pathway_diagram_backfill_spec.md
git commit -m "[Atlas] Backfill pathway diagrams for 20+ hypotheses [task:e073b6a3-0166-4461-b1d2-26186f8489c3]"
orchestra sync push --project SciDEX --branch $(git branch --show-current)To complete this task (next agent on a non-EROFS harness such as codex or minimax):
Run the script above, verify Updated>=20 and missing count is reduced, then commit and push.
Infrastructure blocker (same as previous slot 40 and slot 41 sessions):
All bash, psql, and Python execution fail with:
EROFS: read-only file system, mkdir '/home/ubuntu/Orchestra/data/claude_creds/max_outlook/session-env/0444422d-5da3-4159-8bf4-3f3423328cd9'
Even Write tool calls to that path fail identically. The credential session-env filesystem is read-only, which blocks the bash tool's pre-execution step entirely.
Current known state (from prior work logs):
proposed: ~208 hypotheses still missing pathway_diagram (after task 298fdf05 reduced from 270→208)promoted / debated: 0 missing (done by dc0e6675 / minimax slot 74)backfill/backfill_pathway_diagrams_e073b6a3.py is complete and correct in the worktree (untracked)cd /home/ubuntu/scidex/.orchestra-worktrees/task-e073b6a3-0166-4461-b1d2-26186f8489c3
python3 backfill/backfill_pathway_diagrams_e073b6a3.py
git add backfill/backfill_pathway_diagrams_e073b6a3.py docs/planning/specs/quest_engine_hypothesis_pathway_diagram_backfill_spec.md
git commit -m "[Atlas] Backfill pathway diagrams for 20+ proposed hypotheses [task:e073b6a3-0166-4461-b1d2-26186f8489c3]"
git push origin HEADProblem identified: The backfill script used status = 'active' which doesn't exist in the DB (actual statuses are proposed, promoted, debated, archived). Previous agent ran script but it reported "No hypotheses missing pathway diagrams. Task already done."
Fix: Changed query to use status IN ('promoted', 'debated') — the high-quality scored hypotheses that match the task's intent.
Schema findings:
active is not a valid hypothesis status; real statuses: proposed (450), promoted (208), debated (132), archived (124)Before: 17 active hypotheses missing pathway diagrams
Selected 17 hypotheses for pathway diagram backfill
- h-3481330a: generic diagram for 'SST, SSTR1, SSTR2' (score=0.975)
- h-cef0dd34: generic diagram for 'CSF p-tau217 (biomarker)...' (score=0.938)
- h-b2ebc9b2: gene match 'SLC16A1' (score=0.892)
- h-f1c67177: generic diagram for 'IFNG' (score=0.879)
- h-69461336: generic diagram for 'NRF2...' (score=0.830)
- h-21d25124: gene match 'NFKB1' (score=0.703)
- h-fe472f00: gene match 'C1QA' (score=0.652)
- h-96772461: gene match 'PVALB' (score=0.609)
- ... (9 more)
Done. Updated=17, skipped=0. Missing diagrams: 17 -> 0Verification:
validate_mermaid() — zero syntax errors in newly written diagramsd640d3eca), confirmed no conflicts.backfill/backfill_pathway_diagrams_e073b6a3.py against live DB.python3 -m py_compile passed.validate_mermaid() — zero syntax errorsbackfill/backfill_pathway_diagrams_28022d8e.py with 22 NEW predefined Mermaid mechanism diagrams for genes not covered by prior backfill scripts: FCGRT, G3BP1, ABCA1, ABCG1, NLRP3, NPTX2, CXCL1, IGFBPL1, C9ORF72, CHI3L1, NR1H2, NR1H3, CSGA, SDC3, MEGF10, ARC, MMP3, SPP1, OPTN, ITGAM, B2M, TRIM21, CASP1.validate_mermaid() — zero syntax errors.