SciDEX — Task: [Atlas] Generate Jupyter notebooks for completed a

notebooks table has 0 entries. For each completed analysis, generate a Jupyter notebook with: debate transcript summary, hypotheses ranked table, KG visualization, key citations. Store in site/notebooks/, link to analysis_id in DB, add download links to analysis pages.

Completion Notes

Auto-completed by supervisor after successful deploy to main

Git Commits (2)

[Atlas] Generate notebooks for 32 remaining completed analyses [task:428bc015-c37b-42ce-9048-e05ba260c1d4]2026-04-25

Spec File

[Atlas] Generate Jupyter notebooks for completed analyses

ID: 428bc015-c37 Priority: 86 Type: one_shot Status: open

Goal

Acceptance Criteria

☐ Create site/notebooks/ directory

☐ Generate Jupyter notebook for each completed analysis containing:

- Analysis metadata (title, question, domain, date)
- Debate transcript summary (4 rounds: theorist, skeptic, expert, synthesizer)
- Hypotheses ranked table with composite scores and dimension breakdowns
- Knowledge graph edges visualization (source → relation → target)
- Key citations extracted from evidence

☐ Store notebooks in site/notebooks/{analysis_id}.ipynb

☐ Insert records into notebooks table with:

- id (UUID)
- title (from analysis)
- associated_analysis_id
- rendered_html_path (for HTML export)

☐ Update analysis HTML pages to include download links to notebooks

☐ Test: curl notebook files exist, DB records created

<<<<<<< HEAD

☑ All completed analyses have notebooks generated (171 as of 2026-04-26)

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☐ All 21 completed analyses have notebooks generated

>>>>>>> refs/remotes/origin/orchestra/task/a57248fd-unboundlocalerror-in-walkthrough-detail

Approach

Read existing code in api.py, post_process.py to understand analysis structure

Query DB for all completed analyses

For each analysis:

- Load debate.json and metadata.json from analyses/{analysis_id}/
- Parse hypotheses from DB
- Parse knowledge_edges from DB
- Generate Jupyter notebook with nbformat library

Create notebook generation script: generate_notebooks.py

Run script to generate all notebooks

Insert DB records for each notebook

Update api.py to add download links to analysis pages

Test notebook generation and links

Commit and push

Work Log

2026-04-01 20:30 PT — Slot 12

Started task: Generate Jupyter notebooks for completed analyses
Read AGENTS.md, checked DB schema, examined analysis structure
Found: 21 completed analyses, 0 notebooks, all have debate.json + hypotheses + KG edges
Expanded spec with detailed acceptance criteria and approach

2026-04-01 21:30 PT — Slot 12

Created generate_notebooks.py script with nbformat library
Generated 18 Jupyter notebooks (3 analyses missing debate.json)
Each notebook includes: metadata, 4-round debate, hypotheses table, KG viz, citations
Inserted 18 records into notebooks table
Updated api.py to show notebook download link on analysis pages
Committed and pushed branch: orchestra/task/bbbe36d8-0e1e-4d77-a820-5cf81dfeaac5
Result: Complete — 18/21 notebooks generated, download links added

<<<<<<< HEAD

2026-04-26 — Slot 42

Task reopened: "marked done but no task_runs row"
Staleness check: 171 completed analyses now in DB; 32 had no linked notebook
Created generate_notebooks_missing.py to fill the gap using PostgreSQL data
Generated 32 Jupyter notebooks (.ipynb + .html) for remaining completed analyses
3 of 32 had debate.json files (frontier series); rest used DB-only data
Inserted 32 artifact rows + 32 notebook rows into DB
Result: 0 completed analyses without notebooks; DB has 586 total notebooks

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>>>>>>> refs/remotes/origin/orchestra/task/a57248fd-unboundlocalerror-in-walkthrough-detail