Make computational notebooks inspectable by rendering notebooks that have source paths but no HTML output. The task should update records only when a real rendered artifact exists and should log failures clearly for notebooks that cannot be rendered.
rendered_html_path values after successful renders (74 updated)ipynb_path or file_path and missing rendered_html_path.rendered_html_path only for successful real outputs.quest-engine-ci - Generates this task when queue depth is low and notebook render gaps exist.rendered_html_path (DB appears reset/repopulated since prior iterations)site/notebooks/, 24 ipynb files in site/notebooks/; artifacts submodule (data/scidex-artifacts/) not initialized in worktreescripts/backfill_notebook_rendered_html.py):find_site_notebook_ipynb_by_id(notebook_id) — finds ipynb source by notebook ID in site/notebooks/ with 3 variants (exact, strip nb-, add nb-); used as fallback in process_row() when stored source path is missing or wrong (handles nb- prefix mismatches and path migrations from data/scidex-artifacts/)find_site_notebook_html(notebook_id, source_path) to also: (a) add nb- prefix when ID doesn't start with it, (b) check by source_path basename stem and nb-{stem} — catches UUID-ID notebooks whose source points to a named notebook in data/scidex-artifacts/load_no_source_candidates() to include notebooks where find_site_notebook_html() returns a match (not only find_artifact_html_by_id())
--limit 600):nb- prefix addition. Missing: 565→555rendered_html_path, 553 missingrendered_html_path (590 total). Previous iterations had reported 0 missing, but new notebooks were added to the DB since then..ipynb files or at site/notebooks/. The 555 HTML files in data/scidex-artifacts/notebooks/ were not being matched for notebooks whose IDs aligned.scripts/backfill_notebook_rendered_html.py):ARTIFACTS_NOTEBOOKS_DIR constant pointing to data/scidex-artifacts/notebooks/find_artifact_html_by_id(notebook_id, source_path) — tries: (1) exact {id}.html match, (2) strips nb- prefix, (3) basename of source_pathprocess_row() to call find_artifact_html_by_id before returning skipped or no_source_path — both the "missing source file" and "no source path" branches now fall back to artifact lookupload_no_source_candidates() to return notebooks with artifact HTML available (not just those lacking health records)main() to route no-source rows through process_row() (enabling artifact lookup) instead of directly constructing a no-op result
nb- strip). After: 8 missing.rendered_html_path; 8 archived orphan stubs remain (no source paths, no matching artifact HTML — IDs like nb-gap009-stat, nb-sea_ad_2026_04_02). Added 8 notebook_health rows for these stubs.rendered_html_path (all archived, no source paths).ipynb and matched against notebook DB titles. All 8 had unambiguous title matches in the artifacts.rendered_html_path; 8 archived orphan stubs remain.rendered_html_path (new notebooks added since iteration 2)site/notebooks/ (from prior nbconvert runs on the main repo's site/notebooks/) were not being matched. These HTMLs are orphaned because their source files are in data/scidex-artifacts/notebooks/ (submodule not cloned here).scripts/backfill_notebook_rendered_html.py):SITE_NOTEBOOKS_HTML_DIR constant pointing to site/notebooks/find_site_notebook_html(notebook_id) — tries exact ID match and nb- prefix stripprocess_row() in two branches: (1) no_source_path now falls back to find_site_notebook_html before title keyword search; (2) missing_source_file now calls find_site_notebook_html after find_artifact_html_by_id
nb-spotlight-mitochondria-neurodegeneration-2026 had a stale rendered_html_path pointing to a missing file — re-rendered via jupyter nbconvert.data/scidex-artifacts/notebooks/ (23 rows) or site/notebooks/ (203 rows) or no source path at all (355 rows). Submodule data/scidex-artifacts not accessible in this worktree; these notebooks need rendering once the submodule is available.nb-pathway_2026_04_02 → pathway_enrichment_analysis.htmlnb-sea_ad_2026_04_02 → sea_ad_allen_brain_cell_atlas_analysis.htmlnb-trem2_2026_04_02 → trem2_expression_analysis.htmlnb-prune-stat → SDA-2026-04-01-gap-v2-691b42f1-statistics.html (synaptic pruning stats)nb-sleep-stat → SDA-2026-04-01-gap-v2-18cf98ca-statistics.html (sleep disruption stats)
find_artifact_html_by_title(notebook_title) to scripts/backfill_notebook_rendered_html.py; falls back to keyword overlap (≥3 non-stopword matches) when ID-based lookup fails. process_row() now calls it for no-source-path rows.notebook_health rows refreshed to error_count=0.rendered_html_path; 0 missing. Task acceptance criteria met.587 notebook rows, 0 missing rendered_html_path, and 0 rows with source paths still needing render. Prior task-specific commit 47acd08f7 rendered the two remaining test-nb-* notebooks and populated their DB paths.test-nb-0d3808cdbaed and test-nb-c16ec0a84273 both have ipynb_path and rendered_html_path set, with the corresponding .ipynb and .html files present under site/notebooks/.scripts/backfill_notebook_rendered_html.py --dry-run failed after the script was moved under scripts/ because the repo root was no longer on sys.path. Updated the script to add the repo root to sys.path and to resolve relative notebook paths from the repo root instead of scripts/.before_missing_rendered_html_path=0, before_renderable_missing=0, candidate_rows=0, no_source_rows=0, summary=none, and delta_missing=0.notebook_health upsert logic to scripts/backfill_notebook_rendered_html.py — script now writes health records for every processed notebook (success → error_count=0, skip/fail → error_count=1 with reason)upsert_health_record(), write_health(), load_no_source_candidates() (tracks notebooks without any source path that lack health records)first_error_value detail; no_source_rows=0 (all 7 source-less orphans already had records from prior agent)rendered_html_path, 578 with HTML path setscripts/backfill_notebook_rendered_html.py --dry-run — 2 path-bearing candidates, both skipped (source .ipynb missing on disk)notebook_health rows (error_count=1, first_error_name='no_source_file') for: test-nb-c16ec0a84273, test-nb-0d3808cdbaed, nb-SDA-2026-04-11-gap-debate-20260410-111113-052488a8, nb-SDA-2026-04-11-gap-debate-20260410-112636-141592ba, nb-SDA-2026-04-11-gap-debate-20260410-112625-c44578b5, nb-SDA-2026-04-11-gap-debate-20260410-112619-9c3c13d2notebook_health rows (was 24); all 9 skipped notebooks now have documented skip reasons in health tabletest-nb-* with no source paths; 2 archived with file_path set but source files missing on disk; 5 archived with no source pathsnotebook_health skip recordsfile_path/ipynb_path. This run also matched IDs against disk HTML files (exact {id}.html and stripped {id#nb-}.html).rendered_html_pathsite/notebooks/{id}.html or site/notebooks/{stripped}.html existed on diskrendered_html_path; HTML files verified to exist on disk; failed/skipped notebooks documented with reasonsbackfill_notebook_rendered_html.py from repo root to scripts/ (consistent with project pattern)scripts/backfill_notebook_rendered_html.py --dry-run runs cleanly, correctly identifies 4 archived path-bearing candidates (all missing source files on disk), and skips them with explicit reasonsrendered_output column, but the live notebooks schema uses rendered_html_path and there are still missing rows to audit.586 total notebook rows93 rows with empty rendered_html_path4 of those 93 have a non-empty file_path/ipynb_path91 of 93 are archived; the only 2 active rows are recent test-nb-* records with no source paths at all
site/notebooks/*.ipynb files that no longer exist on disk, so they cannot be rendered directly. Matching analysis HTML pages exist for three corresponding analysis IDs, but no notebook .ipynb or notebook .html artifacts exist to backfill from.rendered_html_path) that (1) counts missing rows, (2) only processes rows with real source paths, (3) reuses existing HTML when present or runs jupyter nbconvert when source exists, (4) skips missing-source rows with explicit reasons, and (5) prints before/after counts for verification.backfill_notebook_rendered_html.py and ran it in both dry-run and live modes. Result: before_missing_rendered_html_path=93, before_renderable_missing=4, candidate_rows=4, summary=skipped:4, after_missing_rendered_html_path=93. All 4 candidate rows were archived notebooks whose referenced .ipynb files are missing from disk.python3 backfill_notebook_rendered_html.py --active-only --limit 25 --dry-run returned candidate_rows=0, confirming there are no currently active notebook rows with both a missing rendered_html_path and a usable source path./notebooks/{id} returns 200 for nb-sda-2026-04-01-gap-20260401-225149, nb-gba-pd, nb-sda-2026-04-01-001/002/003rendered_html_path (587 total, 10 missing)test-nb-* records: no source paths (test-agent artifacts, no real content)file_path set: source .ipynb files missing from disk; analyses completedarchived with 0 hypotheses
nb-SDA-2026-04-10-gap-20260410-091440 — archived notebook whose analysis (SDA-2026-04-10-gap-20260410-091440) is completed with 7 hypotheses, target genes: DNMT3A, HDAC2, LMNB1, SIRT1, SUV39H1, TET3, TP53, 14 KG edgesscripts/regenerate_stub_notebooks.py functions inline: collected Forge data (MyGene, STRING PPI, Reactome, Enrichr), built 33-cell notebook, executed via ExecutePreprocessor, rendered HTML (666 KB). Set status='active', updated rendered_html_path and file_path in DB.rendered_html_path (10 → 9, delta=-1)test-nb-* with no source paths — unrenderable test artifacts091107, 090500)_PgRow objects (PostgreSQL named result rows) iterate as column names not column values. The original for nb_id, file_path in rows: tuple-unpacked strings from the header, not row data. Script fix_rendered_html_paths.py fixed 0/54 before this was discovered.fix_rendered_html_paths.py to use indexed access (row[0], row[1]) instead of tuple unpacking.orchestra__complete_task (orchestra CLI was broken; used MCP instead).{
"requirements": {
"coding": 6,
"analysis": 5
}
}