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availability","description":"Run a health check on all registered Forge tools (PubMed, Semantic Scholar, Allen Brain, etc). Report failures.","status":"open","priority":78,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T07:10:28.285626+00:00","updated_at":"2026-04-17T07:10:28.285626+00:00","summary":"","completion_notes":"Auto-release: recurring task had no work this cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3df010f4-0323-44a0-9699-6d65381c98a5_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"78dcb1cad9bfb476336a453069f00ef745158c7e\"], \"completion_shas_checked_at\": \"2026-04-12T17:21:29.384970+00:00\", \"completion_shas_missing\": [\"b64188057ad3bc68a227895aad19f79e8474e79b\", \"2a8b39731e3806e9fd73443008c960317c4b12f8\", \"02b4a7235283dc9aef7ca793f56d9b1cb9df6f27\", \"783b30e7a3bdc00a37cec1a8bfecdaac287a910d\", \"5ca75972972d5875460041782f1fdf47e7f0060f\", \"5c87d8e8314939a122401af388a58f1b06129bbe\", \"4a51d9a11347cba1098d5fc334576bdd78f9eec6\", \"bfc940d91115e7350b19733454d0ae79159ea606\", \"2bddcf6c913dbd6fa6415fb38df153d606224b44\", \"3389022271de1ae061182c3d24fc9a042bf404c9\", \"3cd69ea3d6874d83a59c525be8e2a585d19a1deb\", \"063b823acca64f77f55f132e3cf89b16851dfb77\", \"193bc578bd64c793a1c6ab7e41e880317473168f\"], \"requirements\": {\"coding\": 5}}"},{"id":"7ffcac76-07ae-4f9b-a5ae-40a531d8da09","title":"[Forge] Dedup scan every 6h","description":"Run artifact_dedup_agent.run_full_scan() to generate new deduplication recommendations as content grows. Uses high thresholds to minimize false positives.","status":"open","priority":60,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T15:25:11.946283+00:00","updated_at":"2026-04-17T15:25:11.946283+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7ffcac76_07a_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 3}, \"completion_shas\": [\"f6f2cd3b5f98bc3746ed0cf99bfd56862c7a282a\"], \"completion_shas_checked_at\": \"2026-04-12T17:19:29.992468+00:00\", \"completion_shas_missing\": [\"30683bafd3f72119104eedcd61c83303cf6172c3\", \"af558f3aa94ddc4dec8fb60c3d6ffa6fc205445e\"]}"},{"id":"ba0513b9-f6f2-4315-a13b-11b60109f9ef","title":"[Forge] Data-driven hypotheses — ground hypotheses in computational analysis, not just literature","description":"Current hypotheses are generated from literature debates alone. SciDEX should produce hypotheses GROUNDED IN DATA ANALYSIS — statistical patterns, genomic correlations, biomarker trends, clinical trial outcomes. This is what distinguishes SciDEX from a literature review tool.\n\nArchitecture:\n1. Analysis notebooks (67+ exist but most are stubs) should run REAL computations on the seed datasets (AD genetic loci, trial failures, biomarkers) and external data (GEO, GWAS Catalog, ClinicalTrials.gov).\n2. Computational findings feed into the debate engine as EVIDENCE — not just paper citations but data-derived claims (e.g., 'TREM2 variants correlate with CSF sTREM2 levels at p<0.001 in the AD biomarker dataset').\n3. The Theorist persona should be able to call analysis tools (statistical tests, correlation analysis, enrichment analysis) DURING debates, not just literature search.\n4. Hypotheses should carry a 'data_support_score' based on how much computational evidence backs them, separate from the literature-based 'evidence_score'.\n\nInspirations: Zenodo (structured research artifacts), OpenAIRE (217M publications + 98M datasets linked), posters.science (machine-readable research metadata). SciDEX should link hypotheses to the datasets and analyses that generated them — full provenance from raw data to hypothesis.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":97,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:43:19.074209+00:00","updated_at":"2026-04-16T23:43:19.074209+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ba0513b9_f6f_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 11:45:16\", \"completion_shas\": [\"439af56da\", \"5cac24083\", \"f6f090387\", \"2706ed8a6\", \"280fcb326\"], \"completion_shas_checked_at\": \"2026-04-16T23:43:19.039968+00:00\", \"completion_shas_missing\": [\"dbbd0d5c5f1c9f5fc2bca2081b414d1120fe8833\", \"dfa1dd89ee0b07b3b5a9dc693f47b2b6ec4f3083\", \"9b64a72d4616317de3f4bb2ad970f4340e3ed010\", \"da4b84e68e4e615f0cfc3e8260d3de39c04b5c40\", \"15e6394744a34a5a89b6558cb91f7ff4d0f51f72\", \"d4bb108c961529777a0ecd01c15d3c9dab116328\", \"7dc1f519e4cb816a6b32b08e5a5bfc5999e91391\", \"58672c954b18b5c94e08d0fb36b7d4b1e6e08358\", \"333807f1a8e1b6d79cd6d95fcef7004742e9032e\", \"69cd90b08bb8fb1c371862724fcea34ed345dc32\"], \"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"8429b1fb-bcf3-4626-b39b-c5662d6d35c1","title":"[Forge] Add Allen Brain Cell Atlas API tool with real query demo","description":"Add a working Allen Brain Cell Atlas API tool to the Forge registry. Query real gene expression data (TREM2, APOE, LRP1) from Allen Institute APIs. Store results and demonstrate tool -> hypothesis enrichment chain. This is D-PRIORITY for Quest 16 Demo Showcase.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"closed","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 23:58:08","updated_at":"2026-04-13 20:36:44","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8429b1fb_bcf_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"a4c450f7-df61-405c-9e95-16d08119c5be","title":"[Forge] Biomni analysis parity — port 15 use cases as hypothesis-anchored pipelines","description":"Coordinator task: spawn 5 parallel agents, 3 analyses each, to replicate Biomni's 15 showcase use cases as SciDEX pipelines that produce hypothesis+artifact+debate+market-update. WS2 of quest_competitive_biotools.","status":"done","priority":93,"task_type":"iterative","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T09:14:55.397171+00:00","updated_at":"2026-04-17T09:14:55.397171+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/task-id-pending_biomni_analysis_parity_spec.md","provider":"any","payload_json":"{\"_watchdog_repair_task_id\": \"a8e6a2c2-2451-40f8-b181-e2e49f0ec325\", \"_watchdog_repair_created_at\": \"2026-04-17T09:07:07.498491+00:00\"}"},{"id":"95469d1e-ed86-4afa-bce5-a6328f97c453","title":"[Forge] K-Dense scientific skills adoption — install + Forge registry wiring","description":"Install github.com/K-Dense-AI/claude-scientific-skills (133 skills). Register each in Forge tool registry for usage logging + pricing + crediting. WS3 of quest_competitive_biotools. Monthly refresh thereafter.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:38:56.820345+00:00","updated_at":"2026-04-16T21:38:56.820345+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/task-id-pending_kdense_skills_adoption_spec.md","provider":"any","payload_json":"{}"},{"id":"01f6a2ac-35a9-4601-93f4-0609cc0cb56e","title":"[Forge] Create per-analysis temp directories with restricted filesystem access","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T04:41:37.821420+00:00","updated_at":"2026-04-14T04:41:37.821420+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/acbc9649372d_forge_create_per_analysis_temp_director_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"safety\": 7}, \"completion_shas\": [\"16fc6fffb4e581f92817e4f84e8c3e8a3f67f66b\"], \"completion_shas_checked_at\": \"2026-04-14T04:41:37.802548+00:00\"}"},{"id":"a4f7702f-0e88-41ca-8327-88d9e564ba02","title":"[Forge] Design pluggable executor interface for future container/cloud migration","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T04:37:39.290953+00:00","updated_at":"2026-04-14T04:37:39.290953+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/603329ebdcb3_forge_design_pluggable_executor_interfa_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 7}, \"completion_shas\": [\"ad6bce1eb9bb898edf94109a60cbea0a698a6b27\"], \"completion_shas_checked_at\": \"2026-04-14T04:37:39.273607+00:00\"}"},{"id":"68cc41cb-8a4e-42b3-9451-e34bf17a92d8","title":"[Forge] Implement cgroup-based process isolation for analysis execution","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T04:25:24.648490+00:00","updated_at":"2026-04-14T04:25:24.648490+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e49c36408077_forge_implement_cgroup_based_process_is_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"7e305835123cee90e5d4e5049919d313b1eb3ea4\"], \"completion_shas_checked_at\": \"2026-04-14T04:25:24.629430+00:00\"}"},{"id":"1a556f4e-2166-436e-aefe-e70561892974","title":"[Forge] A17.2: Create Jupyter Notebook Template for Allen Data Analysis","description":"Build reusable Jupyter notebook template for analyzing Allen Institute datasets with SciDEX integration.\n\nGoal: Provide standardized framework for agents to generate analysis notebooks with proper structure, visualizations, and provenance tracking.\n\nDeliverables:\n1. Create notebooks/allen_analysis_template.ipynb with sections:\n   - Metadata (analysis_id, dataset, author, timestamp)\n   - Data loading (AllenSDK queries, caching)\n   - Exploratory analysis (cell counts, QC metrics)\n   - Differential expression (DESeq2/Scanpy statistical tests)\n   - Visualization (heatmaps, volcano plots, UMAP/tSNE)\n   - Pathway enrichment (Reactome/KEGG via gseapy)\n   - Hypothesis generation (link to SciDEX hypotheses table)\n   - Export results (KG edges, evidence for hypotheses)\n2. Include utility functions:\n   - fetch_allen_data(dataset_id, gene_list)\n   - differential_expression(counts_matrix, metadata, groups)\n   - plot_heatmap(expr_data, genes, cell_types)\n   - pathway_enrichment(gene_list, organism='human')\n   - export_to_scidex_kg(source, target, relation, evidence)\n3. Store in notebooks/ directory\n4. Add notebook metadata schema to database:\n   - notebooks table: id, analysis_id, filename, created_at, cell_count\n   - notebook_cells table: id, notebook_id, cell_type, code, output\n5. Create /api/notebooks/{analysis_id} endpoint to list notebooks\n6. Add notebook link to analysis detail pages\n\nDependencies: Install jupyter, nbformat, AllenSDK, scanpy, gseapy if not present.\n\nTest: Run template on small dataset, verify outputs, check DB insertion works.\n\nThis is Quest 17 (Rich Artifacts) priority - enables all future Allen data analyses to produce rich computational notebooks.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:09:24.765963+00:00","updated_at":"2026-04-14T03:09:24.765963+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1a556f4e_216_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"b1eb952179fc124cdeb7cea2ebc99e2562fa9d39\", \"59bed08636e6032afe5c67714a731b5cf22fe203\"], \"completion_shas_checked_at\": \"2026-04-14T03:09:24.747817+00:00\"}"},{"id":"ccf9a90e-ffce-4e33-b2ee-fd0327c6fcf6","title":"[Forge] Model artifacts WS2: code linkage + artifacts/models/{id}/ subtree","description":"Establish code-at-artifacts/models/{id}/ subtree pattern. Every internal model artifact points to its training code via commit SHA.","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:43:38.548908+00:00","updated_at":"2026-04-16T22:43:38.548908+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/task-id-pending_model_artifacts_ws2_code_linkage_spec.md","provider":"any","payload_json":"{}"},{"id":"65ac9e7d-eb54-4243-818c-2193162a6c45","title":"[Forge] Define reproducibility capsule manifest and verification schema","description":"Define the canonical manifest for reproducible SciDEX analyses and artifact versions, including hashes, runtime digests, and verification metadata.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:09:26.204192+00:00","updated_at":"2026-04-16T10:09:26.204192+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/repro_capsule_manifest_schema_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 6, \"safety\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"max_outlook\", \"_stall_requeued_at\": \"2026-04-12 10:01:40\", \"completion_shas\": [\"4a2635d985eb0e17fccbaa138b1b607d15835d6e\", \"972ba6e4199d658960ea95582c818c38a6d55e2d\", \"5738a7c9986e6f3bd6823ee9e904846a4660afdb\", \"006b4bad5bb8e6b00d01d96e72888bb87a06a9dd\", \"8738d4e291704ef2bf53f6407986ad82f7dfb802\", \"885c8ad7a80df6048b3b346e231d9ac082b93078\", \"ce2a89fe943a2f8123d8395d8439b5a5d4b674ed\", \"46f6280b39f4d546c60588c3451647062088512d\", \"173489e8699d16c503f7f9597ce83109abd1d8ac\"], \"completion_shas_checked_at\": \"2026-04-16T10:09:25.879484+00:00\", \"completion_shas_missing\": [\"006b4bad5bb8e6b00d01d96e72888bb87a06a9dd\", \"8738d4e291704ef2bf53f6407986ad82f7dfb802\", \"885c8ad7a80df6048b3b346e231d9ac082b93078\", \"ce2a89fe943a2f8123d8395d8439b5a5d4b674ed\", \"46f6280b39f4d546c60588c3451647062088512d\", \"173489e8699d16c503f7f9597ce83109abd1d8ac\", \"5e719a4afb3579246c0b3fcb7fb214732b9c5e01\", \"4a85d9935db38d3fffbdf52734d6a0e86532fbce\", \"505b04ffc11b00900820c605442452abfaa2f413\", \"4cb42bdbe116f6ce2698fee7cbf35c50a1c1c140\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"5cd5ad2a-3e6f-457a-a725-747c417c4466","title":"[Forge] Add tool usage analytics dashboard with charts to /forge page","description":"Add tool usage analytics to the Forge page: execution count by tool (bar chart), success rates, recent tool calls log, and tool call timeline. Uses existing tool_calls table data (1674 calls). D-PRIORITY for Quest 3.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T03:18:57.928215+00:00","updated_at":"2026-04-16T03:18:57.928215+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5cd5ad2a_3e6_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"74fee0247e05159eae0c4221c6cb7a268cfedec5\"], \"completion_shas_checked_at\": \"2026-04-16T03:18:57.913565+00:00\"}"},{"id":"q03-f1-439A890C","title":"[Forge] Demo Allen Brain Expression tool with real data","description":"Execute Allen Brain Expression tool against real genes (TREM2, APOE, MAPT, APP). Store results. Show on /forge page as demo execution. Create tool call chain: PubMed search -> gene expression lookup -> pathway analysis. This demonstrates the Forge layer end-to-end.","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:54:56","updated_at":"2026-04-02 09:43:32","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"746fd7c1-13a0-4806-8948-2684e07932a9","title":"[Forge] Model artifacts WS3: training pipeline via GPU sandbox","description":"Agents invoke bwrap+GPU sandbox training, register resulting checkpoint as new version, chain to parent.","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:36:22.930892+00:00","updated_at":"2026-04-16T22:36:22.930892+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/task-id-pending_model_artifacts_ws3_training_pipeline_spec.md","provider":"any","payload_json":"{}"},{"id":"0d0a4d51-48a0-4bdc-9c2b-f4d0ad386556","title":"[Forge] Cost-optimization routing — prefer cheapest qualified model with quality floor","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:02:48.965389+00:00","updated_at":"2026-04-16T11:02:48.965389+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/frg-lr-08-COST_cost_optimization_routing_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"82ce4810-05a1-48bd-b9a9-7e3e32e514fb","title":"[Forge] GPU sandbox pilot — fine-tune scGPT inside bwrap","description":"Pilot: launch a GPU sandbox that fine-tunes scGPT on a SciDEX-relevant perturb-seq dataset, inside bwrap isolation, register the resulting model as a Forge artifact. WS4 of quest_competitive_biotools.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:46:32.833725+00:00","updated_at":"2026-04-16T21:46:32.833725+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/task-id-pending_gpu_sandbox_pilot_spec.md","provider":"any","payload_json":"{}"},{"id":"c98d7e1e-cf0a-4807-a7bc-291855141d3a","title":"[Forge] Add pinned runtime capture and reproducibility verification for analyses","description":"Extend SciDEX analyses to emit pinned runtime metadata and verification bundles that can be rechecked later.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:47:27.566906+00:00","updated_at":"2026-04-16T15:47:27.566906+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/runtime_capture_and_verification_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 7, \"analysis\": 6, \"safety\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"codex\", \"_stall_requeued_at\": \"2026-04-11 03:52:29\", \"completion_shas\": [\"b732ed115ee27f3835084c14a14f5321fdb7b52b\"], \"completion_shas_checked_at\": \"2026-04-12T12:43:44.977963+00:00\", \"completion_shas_missing\": [\"4eb0a29a6f5f76e9ae3f74c90367f211d4184b33\", \"c180fd7817a968f870a0c764a67bf6ff551d144b\", \"542b55a00f91a1d61cdd0bd62918f187a216ac73\", \"9cabbdb982ef2f2ce9fcd6e50d1e7962bf0ecd93\", \"dd858bc612c26d86ef2030761f3649b87038bb1e\", \"41257c88c7cd1f702954888ef91230a29ba2d07e\", \"d6d11769824ab947c815cb64aca278c4ed8a82df\", \"45326ad6e046c53ff6e364c984fdccfbc9f3a5e1\", \"2deaa66b05cca38cbd289c13140e0d69408965cc\", \"030cf30dabcb25faba36ed9b8bf784b76a5ab948\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"8fcb5cf1-5ccd-4b9d-a5c1-f7c6d0d4501b","title":"[Forge] Add experiments listing page at /experiments","description":"188 experiments exist in DB but no listing page. Create /experiments with search, filter, and links to individual experiment pages. Add to sidebar nav. Also fix duplicate Debates entry in sidebar.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T14:37:22.292170+00:00","updated_at":"2026-04-16T14:37:22.292170+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8fcb5cf1_5cc_spec.md","provider":"any","payload_json":"{}"},{"id":"4b71911f-6ac0-4887-8761-9973b792274b","title":"[Forge] Integrate ClinicalTrials.gov API for hypothesis clinical relevance","description":"Add a Forge tool that queries ClinicalTrials.gov for trials related to hypothesis targets. Display on hypothesis detail pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T14:23:31.692788+00:00","updated_at":"2026-04-16T14:23:31.692788+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4b71911f-6ac_forge_integrate_clinicaltrials_gov_api_spec.md","provider":"any","payload_json":"{}"},{"id":"c9ee8c5b-ab2d-48a5-80ed-4b518821e510","title":"[Forge] Build /experiments page — browse 188 experiments with status, filtering","description":"Create /experiments page to browse the 188 experiments in the DB. Show title, status, linked hypothesis, mission. Support filtering by status. This is a gap — experiments exist but have no UI page.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T13:32:42.607139+00:00","updated_at":"2026-04-16T13:32:42.607139+00:00","summary":"","completion_notes":"Task was completed in bb706193c which is on origin/main. The commit added 238 lines to api.py implementing the /experiments page with filtering by type/disease and detail view. 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Report and fix any that are down or returning errors.","status":"archived","priority":89,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-12T18:11:02.039065+00:00","updated_at":"2026-04-16T19:47:42.541162+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3df010f4_forge_ci_test_tools_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6, \"analysis\": 5, \"safety\": 9}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"codex\", \"_stall_requeued_at\": \"2026-04-11 03:58:51\", \"completion_shas\": [\"d41badb3e3078d88949a6d8c468f3b424a677a63\"], \"completion_shas_checked_at\": \"2026-04-12T18:11:02.026097+00:00\", \"completion_shas_missing\": [\"5091f761bb567e16494a57e04b78c5a32590ce33\", \"70aa505c69600b867eb92e7055684d4262c6b63b\", \"747a209a0478f4f6ad2ef77484e679bc86fd4b5d\", \"5e8ed25357b1b975f59f8aaab9140526b593b3d4\", \"baa1b640d318a7e556cde48c580f1a6f435d1db9\", \"e1593c7de43a20085f955225a8dd677cc71fd9ea\", \"c5d6f7c3f1fa4f8cfd396f5ead5a98c93fad6e34\", \"41504b801996594f1f75af85cc613441fe74d245\", \"2d57a39a776578eeffa8bb4fd3b311c16967478b\", \"6487cb569ef9ecd7162116a5f1785b11e290a0ac\", \"686d3596500e9440cd34adfc6d32f324c877b5be\", \"04dadb1e00c9c542047e2e5bb45c03c734bb2415\", \"5dd9098606b0b0affe7259e54bc6fd27d8a5621f\", \"4a2b12f8c9316b37f80237d3a0b41e70de63b9a3\", \"c705a24841746ead7ef535ca60c97282ac5392d1\", \"fa9be8539d431323f2bdb8e29c3137115dd47354\", \"80c90be1158239f03112bb43255299b063b621ba\", \"b3bea2e37cf2c3911f1bc8ba33d179441d577eae\", \"110499c9a844a0d503b576fd5fa2c404d335678c\", \"17ccfe659398c3c8efce2b5bc4da2b5fb85441d2\", \"482e280361b7550ec4bc631f27b4e34093c352dd\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"8ef239c8-35c3-46f0-8ab7-dfe68c741fc2","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T09:58:29.919533+00:00","updated_at":"2026-04-17T09:58:29.919533+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"},{"id":"d74da341-e766-4186-b652-27d93a0863fc","title":"[Forge] Fix tool_calls schema mismatch causing logging failures","description":"tools.py tries to INSERT with columns (tool_name, input_data, output_data, success, error_message, duration_ms, called_at) but DB has (id, skill_id, analysis_id, input_json, output_json, duration_ms, status, error_message, created_at). Causing warnings: 'Failed to log tool call X: table tool_calls has no column named tool_name'. Fix: Either ALTER TABLE to add missing columns OR update tools.py to match existing schema.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:14:08.782116+00:00","updated_at":"2026-04-16T16:14:08.782116+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d74da341_e76_spec.md","provider":"claude","payload_json":"{}"},{"id":"29d37b31-d5f5-4c41-8105-e7a9b9791f61","title":"[Forge] Add featured tool demo section showing real Allen Brain Expression results","description":"Add a 'Featured Tool Demo' section to /forge showing a real executed tool call result for Allen Brain Expression on TREM2, demonstrating the Forge's capability to agents and visitors. Shows input, output, and links to related hypothesis.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. 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15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"80954c72-8dc9-46f3-85a6-f1b85d051ade","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"2","started_at":null,"completed_at":"2026-04-03 06:44:57","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c4ae83f1-2a53-49c4-aee0-672b34a43eda","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 06:58:54","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"83d4e9f1-d4a2-4d73-b031-36664ad1852b","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:03:49","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"92e799f1-dc6d-42cd-84ee-3c90ee5923d3","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:08:33","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7690f24c-db69-4a61-9172-18c7e78dcd8e","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:11:12","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"362b04e2-79e1-462d-8d0e-783543af3dad","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:19:57","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"417d5674-bfbb-4267-946a-b69ff77499b3","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:26:32","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"a252962e-3eb6-4776-873b-cf43debdf9ae","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:54:47","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"6121da97-7191-4bdc-b882-00ab86e7d0b8","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:43:12","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"b0471c12-c94e-4931-9101-3b659af980d7","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 08:01:39","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"b9399f51-6d5a-4c8a-93bc-3e274a42137d","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:23:26","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"03d76634-3c13-43b1-951d-5550168b6af3","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:38:28","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"62be1eca-d10e-41cb-a545-6fce4fb2a34b","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:48:53","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"a079d31b-d0d2-4866-9380-8fde9b3477f3","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:54:34","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"bb52475b-44bb-46e6-8cb9-043465ac2ea7","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:59:00","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"d3f56ce1-3e00-472f-a3c3-5a0004334571","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:41:42","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"6bfda974-1c48-418a-900e-84a043734246","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:40:35","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"60dea99a-ae47-41b5-b87a-3557e226d390","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.","status":"archived","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"cd27237d-5346-41bc-b176-2ff3289e0311","title":"[Forge] Implement tool invocation during analyses","description":"15 skills are registered but tool_invocations table has 0 entries. Modify agent.py or scidex_orchestrator.py to actually call Forge tools (PubMed, Semantic Scholar, etc.) during debates. Log all invocations to tool_invocations table with: skill_id, analysis_id, input_params, output_summary, tokens_used, success.","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 04:47:28","updated_at":"2026-04-02T04:18:37.455818+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/cd27237d_534_spec.md","provider":"claude","payload_json":"{}"},{"id":"frg-mb-01-ANLX","title":"[Forge] Extend analysis framework to include model-building steps","description":"Add model_building as a new analysis step type alongside existing steps (data_retrieval, statistical_test, etc.). An analysis can now produce a model artifact as output. Define AnalysisModelSpec: model_family (biophysical|deep_learning|statistical), input_datasets, output_artifact_id, hyperparameters, evaluation_metrics. Integrate with artifact versioning so each model-building run creates a versioned model artifact. Depends on: a17-23-MODL0001 (Artifacts quest).","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:27:07","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/frg-mb-01-ANLX_model_building_analysis_steps_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"frg-mb-02-BIOP","title":"[Forge] Biophysical model template: ODEs, parameter fitting, sensitivity analysis","description":"Create a reusable biophysical model template that analyses can invoke. Template includes: ODE system definition (species, reactions, rate constants), parameter fitting against tabular dataset, sensitivity analysis (which parameters most affect output), and result visualization. Output is a versioned model artifact with fitted parameters. Use scipy.integrate for ODEs and scipy.optimize for fitting. Depends on: frg-mb-01-ANLX.","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:02:38","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/frg-mb-02-BIOP_biophysical_model_template_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"843ac99c-0ba3-4ac1-974c-75da0de6184d","title":"[Forge] Add tool usage analytics dashboard with charts and performance metrics","description":"Add analytics section to /forge page: tool call timeline chart, success/error rates, avg latency per tool, top tools by usage, recent tool calls feed. Makes Forge look like a real production system for demo.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T20:39:12.776042+00:00","updated_at":"2026-04-16T20:39:12.776042+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/843ac99c_0ba_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"0ac3c3dc7\"], \"completion_shas_checked_at\": \"2026-04-16T20:39:12.754797+00:00\"}"},{"id":"2a92253c-7da7-4601-bb5e-934bf85ab36a","title":"[Forge] Implement missing /forge dashboard route","description":"Task 6f47b2f3 was marked done but /forge returns 404. Need to implement GET /forge showing: tool registry from skills table with usage counts, recent tool executions, tool health status. Query skills table for real data, display 9 production tools.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:51:19","updated_at":"2026-04-02T03:48:54.371670+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/2a92253c_7da_spec.md","provider":"claude","payload_json":"{}"},{"id":"476121dc-7416-437b-a210-c6d0360c009f","title":"[Forge] Tool registry + call logging tables","description":"F3.1: Populate the skills table (0 rows) with entries for every function in tools.py. Create tool_calls table (skill_id, analysis_id, input_json, output_json, duration_ms, status, created_at).\n\nAcceptance: skills table has ~15 rows. tool_calls table exists and is ready for logging.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:45:01","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/476121dc_741_tool_registry_call_l_spec.md","provider":"any","payload_json":"{}"},{"id":"frg-mb-03-DL01","title":"[Forge] Deep learning model template: training pipeline, evaluation, checkpointing","description":"Create a DL model template for analyses: define architecture spec (layers, activations), training loop with checkpointing, evaluation metrics (loss, accuracy, domain-specific), and artifact registration on completion. Each checkpoint is a versioned model artifact. Support common frameworks (PyTorch preferred). Template handles: data loading from registered datasets, train/val split, early stopping, metric logging. Depends on: frg-mb-01-ANLX.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:03:31","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/frg-mb-03-DL01_deep_learning_template_spec.md","provider":"any","payload_json":"{}"},{"id":"frg-mb-04-MREG","title":"[Forge] Model registry integration: link models to artifact versioning system","description":"Ensure all models built by Forge analyses are properly registered in the artifact system with full provenance: which dataset(s) trained it, which analysis produced it, which hypothesis it tests. Add /api/models endpoint listing all model artifacts with filtering by family, dataset, and performance metrics. Add model comparison view. Depends on: frg-mb-01-ANLX, a17-20-VAPI0001 (Artifacts quest).","status":"done","priority":84,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:05:57","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/frg-mb-04-MREG_model_registry_integration_spec.md","provider":"any","payload_json":"{}"},{"id":"8e1626a9-95c1-454c-b996-83b5a400a702","title":"[Forge] Integrate tool chains API endpoints into api.py","description":"The tool_chains.py engine and api_tool_chains.py endpoints exist but are not integrated into api.py. Integrate the chain endpoints (/api/forge/chains CRUD and execute) and add a Tool Chains section to the /forge page showing available chains.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:54:30.408663+00:00","updated_at":"2026-04-17T10:54:30.408663+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8e1626a9_95c_spec.md","provider":"any","payload_json":"{}"},{"id":"bb30e0c4-323c-46b6-bcbe-b3a779e2953f","title":"[Forge] Fix nb_sea_ad_001 notebook + notebook reproducibility audit","description":"The SEA-AD Cell-Type Vulnerability Analysis notebook (nb_sea_ad_001) shows 15 error outputs on /notebook/nb_sea_ad_001. Root cause: cell 2 fails with 'ModuleNotFoundError: No module named forge' — all subsequent cells cascade with NameError because the 'load()' helper from forge never got defined.\n\nFIX THIS NOTEBOOK:\n1. Check what 'forge' module was expected (likely forge_tools.py or a local module)\n2. Fix the import: either add forge to sys.path or replace with the actual module path\n3. Verify the data files exist in data/forge_cache/seaad/\n4. Re-run the notebook: jupyter nbconvert --execute --to notebook nb_sea_ad_001.ipynb\n5. Commit the re-executed notebook with clean outputs\n\nNOTEBOOK REPRODUCIBILITY (low-priority audit, not enforcement):\nCreate a lightweight recurring check that flags broken notebooks:\n- Scan all .ipynb files in site/notebooks/\n- For each, count error outputs (output_type='error')\n- If errors > 0, log to a notebook_health table with: notebook_id, error_count, first_error_name, first_error_value, checked_at\n- Surface on the /health dashboard (when built)\n- Don't block or enforce — just monitor and flag\n\nREPRODUCIBILITY REQUIREMENTS (document in AGENTS.md):\n- Notebooks should list their dependencies in cell 1 (pip install or import check)\n- Notebooks should use relative paths from the repo root\n- Data dependencies should be documented (which datasets/caches are needed)\n- Notebooks should be re-runnable: nbconvert --execute should produce clean output\n- Workers creating notebooks should run them before committing and verify zero error outputs\n\nThis is the 'notebook quality gate' — not blocking, just monitoring. Similar to how the review gate catches bad code, this catches bad notebooks.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:37:41.951321+00:00","updated_at":"2026-04-16T23:37:41.951321+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/bb30e0c4_323_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-12 10:33:23\", \"completion_shas\": [\"641254192\"], \"completion_shas_checked_at\": \"2026-04-16T23:36:55.595838+00:00\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"dd044d70-ce76-4b5b-ad25-25122ca66156","title":"[Forge] Enrich 20 papers with full PubMed metadata","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n1050/15732 papers lack abstracts. Fetch from PubMed API and update.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:32:14.752447+00:00","updated_at":"2026-04-16T23:32:14.752447+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"314e3759-48fa-45f3-a446-94f51f00c139","title":"[Forge] Enrich 20 papers with full PubMed metadata","description":"963/15109 papers lack abstracts. Fetch from PubMed API and update.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:13:30.832111+00:00","updated_at":"2026-04-16T23:13:30.832111+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/314e3759_48fa_45f3_a446_94f51f00c139_spec.md","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"a42e9d23-2418-457c-b7ba-2df216710546","title":"[Forge] Test all scientific tools (PubMed, Semantic Scholar, UniProt) for availability","description":"Run health checks on all Forge tools. Report and fix any that are down or returning errors.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T08:19:07.341331+00:00","updated_at":"2026-04-17T08:19:07.341331+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"completion_shas\": [\"01f90cf65\"], \"completion_shas_checked_at\": \"2026-04-17T06:39:39.888506+00:00\"}"},{"id":"11eda21a-ff43-4a42-8d3e-233d11d98626","title":"[Forge] Instrument all tool calls with DB logging","description":"F3.2: Wrap every tool function in tools.py with a decorator/wrapper that logs to tool_calls table (inputs, outputs, timing, success/failure). Update research_topic() and any tools used in orchestrator.\n\nAcceptance: After an analysis, tool_calls shows which tools were invoked, inputs, outputs, timing.","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:04:26","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/11eda21a_ff4_instrument_all_tool_spec.md","provider":"any","payload_json":"{}"},{"id":"d44a9878-601b-48ea-a148-adcfe531bd99","title":"[Forge] Event bus for inter-component communication","description":"SQLite-backed event bus (event_bus.py) for publish/subscribe: analysis_completed, hypothesis_scored, kg_edge_added, gap_resolved. Events table with type, payload JSON, source, consumed_by. /api/events endpoint. Acceptance: events table; post_process publishes; 3+ consumers; visible on Senate dashboard.","status":"done","priority":76,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:28:22","updated_at":"2026-04-02T03:05:17.609939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d44a9878-601_forge_event_bus_for_inter_spec.md","provider":"any","payload_json":"{}"},{"id":"7656f1df-bdf1-42f8-8f97-968247746944","title":"[Forge] Build automated PubMed update pipeline for hypothesis evidence","description":"Create a recurring pipeline that searches PubMed for new papers related to top hypotheses and updates evidence_for/evidence_against.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:31:32.288369+00:00","updated_at":"2026-04-17T10:31:32.288369+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7656f1df-bdf_forge_build_automated_pubmed_update_pip_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"6f47b2f3-7063-4696-a2c8-5653c6169ab3","title":"[Forge] /forge dashboard page","description":"F3.3: Add GET /forge to api.py showing: tool registry with usage counts, recent tool calls with inputs/outputs, tool health (last success/failure). Replace the aspirational '366 tools' with an honest live inventory.\n\nAcceptance: /forge page loads with real tool data.","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:59:37","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6f47b2f3_706_forge_dashboard_pag_spec.md","provider":"any","payload_json":"{}"},{"id":"384a26ce-d451-4530-8e29-182291dfd519","title":"[Forge] Register all Forge tools in SciDEX skills table","description":"The Forge engine at /home/ubuntu/Forge has 136 tool files but SciDEX skills table only has 11 entries. Import all Forge tools into the skills table with proper metadata (name, description, skill_type, module_path). The /forge page should show the full tool inventory.","status":"done","priority":74,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:07:53","updated_at":"2026-04-02T06:05:12.235648","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"b6ad1374-d983-4968-9c4b-30cd3ffed4ed","title":"[Forge] Graph query API endpoints","description":"Neo4j-powered endpoints: /api/graph/neighbors/{entity}, /api/graph/path/{source}/{target}, /api/graph/cluster/{entity}, /api/graph/impact/{analysis_id}. Replace flat SELECT * approach. Acceptance: 4 endpoints working; graph page uses neighbor queries; <500ms response.","status":"done","priority":74,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:13:34","updated_at":"2026-04-02T03:05:17.609939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b6ad1374-d98_forge_graph_query_api_end_spec.md","provider":"any","payload_json":"{}"},{"id":"a6b8dd09-9178-466c-9354-0a681a1ddb9b","title":"[Forge] Register all tools in skills table with metadata","description":"Populate the skills table with entries for every tool in tools.py and the Forge tools/ directory. Include name, description, skill_type, input_schema. Acceptance: skills table has entries for all 120+ Forge tools + tools.py functions.","status":"done","priority":72,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 05:38:31","updated_at":"2026-04-02T05:33:43.702856+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"1a33a296-e059-4ab1-8d95-aa1e1e308f68","title":"[Forge] Build tool usage analytics dashboard","description":"Show which tools are most used, success rates, average execution times. Query tool_calls table and display on /forge page.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:26:03.208620+00:00","updated_at":"2026-04-17T11:26:03.208620+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"533d84f0-6eb3-4bad-89c7-f03af1ad3464","title":"[Forge] Tool-augmented debates","description":"F3.4: Extend orchestrator so Domain Expert can request tool calls mid-debate. Parse tool-call requests from Expert response, execute them, inject results into follow-up prompt. Creates 'tool-augmented debate' pattern.\n\nAcceptance: Domain Expert responses include real clinical trial data, gene annotations, etc.","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:55:46","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/533d84f0_6eb_tool_augmented_debat_spec.md","provider":"any","payload_json":"{}"},{"id":"25c699ee-11e4-4338-be20-d3c2903a0d12","title":"[Forge] Implement tool chaining — allow multi-step tool workflows","description":"Define tool chain templates (e.g., pubmed_search -> extract_entities -> add_to_kg). Store chains in DB. Execute via API.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":65,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T15:11:38.865450+00:00","updated_at":"2026-04-17T15:11:38.865450+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"}],"reviews":[{"task_count":5,"total_tokens":250000,"total_cost":0.7500000000000001,"output_score":1105.4208,"efficiency_rating":"normal","reviewed_at":"2026-04-17T11:29:14.374718+00:00"}],"effectiveness":{"task_count":5,"total_lines_added":0,"total_lines_removed":0,"total_files_modified":0,"total_hypotheses":902,"total_kg_edges":51173,"total_papers":1205,"total_tokens":250000,"total_duration":1708197.722504,"avg_impact":55271.04,"avg_effectiveness":1105.4208},"spec_content":"---\ntitle: \"Quest: Forge\"\ndescription: \"Scientific execution engine — tool registry, background agent orchestration, agent spawning, and tool-augmented analysis. Manages the ecosystem of background agents that perform research tasks.\"\ntype: quest\nlayer: Forge\npriority: 80\nstatus: active\nquest_id: dd0487d3-38a\nspec_path: docs/planning/specs/quest_forge_spec.md\n---\n\n# Quest: Forge\n\n**Layer:** Forge  \n**Priority:** P80  \n**Status:** active  \n**Tasks:** 402 total (25 done, 6 open)\n\n## Vision\n\nScientific execution engine — tool registry, background agent orchestration, agent spawning, and tool-augmented analysis. Manages the ecosystem of background agents that perform research tasks.\n\n## Open Tasks\n\n- [ ] [Forge] Integrate ClinicalTrials.gov API for hypothesis clinical relevance (P90)\n- [ ] [Forge] Extend analysis framework to include model-building steps (P88)\n- [ ] [Forge] Biophysical model template: ODEs, parameter fitting, sensitivity analysis (P86)\n- [ ] [Forge] Deep learning model template: training pipeline, evaluation, checkpointing (P85)\n- [ ] [Forge] Model registry integration: link models to artifact versioning system (P84)\n- [ ] [Forge] Expand tool library (ongoing) (P50)\n\n\n## Success Criteria\n\n- [ ] All open tasks completed and verified\n- [ ] Integration tested end-to-end with dependent quests\n- [ ] UI pages rendering correctly for this quest's features\n- [ ] Documentation updated for new capabilities\n- [ ] New model templates include test suites and validation\n- [ ] Tool registry changes tested for backward compatibility\n- [ ] No duplicate utility functions — reuse shared modules (kg_extraction_utils, pubmed_utils)\n- [ ] New modules < 500 lines; executor plugins have clean interfaces\n\n## Quality Requirements\n\n> All tools registered in the forge must demonstrate scientific utility. Tool submissions are rejected if they are stubs (no working implementation), duplicate existing tools, or implement busywork (e.g., trivial data transformations with no mechanistic insight). Each tool must have documented use cases in published analyses or hypotheses within 30 days. When registering ≥10 tools, use parallel agents (3–5 concurrent).\n\n## Work Log\n\n_No entries yet._\n","spec_html":"<div style=\"font-size:0.85rem\"><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h2 style=\"color:#4fc3f7;margin:1.5rem 0 0.6rem;font-size:1.2rem;font-weight:700\">Quest: Forge</h2></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><strong style=\"color:#e0e0e0\">Layer:</strong> Forge  \n<strong style=\"color:#e0e0e0\">Priority:</strong> P80  \n<strong style=\"color:#e0e0e0\">Status:</strong> active  \n<strong style=\"color:#e0e0e0\">Tasks:</strong> 402 total (25 done, 6 open)</p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h3 style=\"color:#4fc3f7;margin:1.4rem 0 0.5rem;font-size:1.1rem;font-weight:700;border-bottom:2px solid rgba(79,195,247,0.3);padding-bottom:0.2rem\">Vision</h3></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\">Scientific execution engine — tool registry, background agent orchestration, agent spawning, and tool-augmented analysis. Manages the ecosystem of background agents that perform research tasks.</p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h3 style=\"color:#4fc3f7;margin:1.4rem 0 0.5rem;font-size:1.1rem;font-weight:700;border-bottom:2px solid rgba(79,195,247,0.3);padding-bottom:0.2rem\">Open Tasks</h3></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Forge] Integrate ClinicalTrials.gov API for hypothesis clinical relevance (P90)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Forge] Extend analysis framework to include model-building steps (P88)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Forge] Biophysical model template: ODEs, parameter fitting, sensitivity analysis (P86)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Forge] Deep learning model template: training pipeline, evaluation, checkpointing (P85)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Forge] Model registry integration: link models to artifact versioning system (P84)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; [Forge] Expand tool library (ongoing) (P50)</div></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h3 style=\"color:#4fc3f7;margin:1.4rem 0 0.5rem;font-size:1.1rem;font-weight:700;border-bottom:2px solid rgba(79,195,247,0.3);padding-bottom:0.2rem\">Success Criteria</h3></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><div style=\"margin:0.2rem 0;color:#bbb\">&#9744; All open tasks completed and verified</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Integration tested end-to-end with dependent quests</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; UI pages rendering correctly for this quest&#x27;s features</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Documentation updated for new capabilities</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; New model templates include test suites and validation</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; Tool registry changes tested for backward compatibility</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; No duplicate utility functions — reuse shared modules (kg_extraction_utils, pubmed_utils)</div>\n<div style=\"margin:0.2rem 0;color:#bbb\">&#9744; New modules &lt; 500 lines; executor plugins have clean interfaces</div></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h3 style=\"color:#4fc3f7;margin:1.4rem 0 0.5rem;font-size:1.1rem;font-weight:700;border-bottom:2px solid rgba(79,195,247,0.3);padding-bottom:0.2rem\">Quality Requirements</h3></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\">&gt; All tools registered in the forge must demonstrate scientific utility. Tool submissions are rejected if they are stubs (no working implementation), duplicate existing tools, or implement busywork (e.g., trivial data transformations with no mechanistic insight). Each tool must have documented use cases in published analyses or hypotheses within 30 days. When registering ≥10 tools, use parallel agents (3–5 concurrent).</p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\"><h3 style=\"color:#4fc3f7;margin:1.4rem 0 0.5rem;font-size:1.1rem;font-weight:700;border-bottom:2px solid rgba(79,195,247,0.3);padding-bottom:0.2rem\">Work Log</h3></p><p style=\"color:#bbb;line-height:1.6;margin:0.4rem 0\">_No entries yet._<br></p></div>","spec_file":"quest_forge_spec.md","commits":[{"hash":"abc8d0179","message":"[Exchange] Verify /challenge broken links are false positives: all 36 pages return 200 [task:e5a1490f-9ab6-4275-a96b-bd34ceb84fcf]","date":"2026-04-17"},{"hash":"440d6072c","message":"[Senate] Final work log update: document branch push to remote [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"8eefea2c0","message":"[Atlas] Add redirects in api.py for /site/notebooks/ and root-level .ipynb URLs to /notebooks/ path [task:f92194bf-f23c-4bf3-97d4-676c02f5fb42]","date":"2026-04-17"},{"hash":"bdf2e04e8","message":"[Atlas] Document /mission HTTP 0 fix: already addressed in c5d7a696 [task:e50f7fed-ccde-4104-b98a-205bb500e792]","date":"2026-04-17"},{"hash":"f39b5d3b0","message":"[Atlas] Fix broken /entity links: clean corrupted data + add cleanup script [task:326c7abd-3ad2-4ae5-9a0e-e9981d611890]","date":"2026-04-17"},{"hash":"a4954541c","message":"Squash merge: orchestra/task/09b3a393-broken-links-in-api-http-0-30-links (1 commits)","date":"2026-04-17"},{"hash":"40b62c4b8","message":"[Atlas] Verify /api broken links: all 10 endpoints HTTP 200, no code changes needed [task:09b3a393-777f-4379-85c6-2bf55f6e69c0]","date":"2026-04-17"},{"hash":"6e54e1ccc","message":"On orchestra/task/326c7abd-broken-links-in-entity-http-400-64-links: stash unrelated changes","date":"2026-04-17"},{"hash":"53f087f8e","message":"index on orchestra/task/326c7abd-broken-links-in-entity-http-400-64-links: f3b466710 [Atlas] Add /mission→/missions redirect in api.py; confirm /mission broken links are false positives [task:c0d66faa-91be-41e3-909d-d6359c5b936e]","date":"2026-04-17"},{"hash":"58b5eb786","message":"[Atlas] Verify /analysis broken links: all 10 pages HTTP 200, false positive [task:a7c6d6d2-17bb-4e1c-b131-10677c65e9d0]","date":"2026-04-17"},{"hash":"0be6ce64a","message":"[Senate] Update spec work log: service verified operational, no code changes needed [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"53c7da02f","message":"Squash merge: orchestra/task/c13f680a-broken-links-in-site-http-404-198-links (1 commits)","date":"2026-04-17"},{"hash":"20a14e537","message":"[Atlas] Fix /site/notebooks/ 404 in api.py: add redirect to /notebooks/ route [task:c13f680a-60bf-49f3-aa42-a05602d77405]","date":"2026-04-17"},{"hash":"52e043bda","message":"Squash merge: orchestra/task/c5d7a696-broken-links-in-target-http-0-765-links (3 commits)","date":"2026-04-17"},{"hash":"aead3c46d","message":"[Atlas] Restore nb-top5- prefix-stripping fallback removed in prior commit [task:c5d7a696-2296-468a-83a2-2d3cabc6901e]","date":"2026-04-17"},{"hash":"1786c8cc4","message":"[Atlas] Wire up suppress_transient_http0_noise() in link checker to prevent false-positive tasks [task:c5d7a696-2296-468a-83a2-2d3cabc6901e]","date":"2026-04-17"},{"hash":"13c833f16","message":"[Atlas] Add redirects for /site/notebooks/ and root-level .ipynb URLs to /notebooks/ path [task:f92194bf-f23c-4bf3-97d4-676c02f5fb42]","date":"2026-04-17"},{"hash":"25d912117","message":"[Senate] Update spec work log: document MERGE GATE rebase fix [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"06151c073","message":"[Senate] Update spec: verify service operational, no code changes needed [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"dc15730ae","message":"[Atlas] Fix /notebook top5-SDA-* broken links: add prefix-stripping fallback in notebook_detail [task:c13f680a-60bf-49f3-aa42-a05602d77405]","date":"2026-04-17"}],"related_quests":[{"name":"Agent Ecosystem","layer":"Forge","priority":96,"status":"active","description":"Background agent fleet management — agent registry, health monitoring, task routing, and auto-scaling. Define agent roles (researcher, debater, market-maker, auditor), spawn/retire agents based on workload, and maintain agent identity across sessions. Goal: a self-managing ecosystem of specialized agents.","task_count":8,"done_count":0},{"name":"Real Data Pipeline","layer":"Forge","priority":92,"status":"active","description":"Ensure all analyses use REAL Allen Institute datasets (SEA-AD, ABC Atlas, Allen Brain Cell Atlas) — not simulated/hallucinated data. Build data ingestion pipelines that download, cache, and validate real datasets. Analyses must cite specific dataset versions and cell counts. Forge tools must be invoked during the analysis loop with real inputs, not just registered as provenance markers.","task_count":5,"done_count":0},{"name":"Analysis Sandboxing","layer":"Forge","priority":90,"status":"active","description":"Run all analyses in isolated environments (containers, cgroups, or sandboxed subprocesses) so a runaway analysis cannot corrupt the database, filesystem, or other running services. Each analysis gets its own temp directory, restricted filesystem access, and resource budget. Design for future migration to external container runtimes (Docker, AWS Batch, K8s) while running locally today.","task_count":5,"done_count":1},{"name":"Tool Playground","layer":"Forge","priority":88,"status":"paused","description":"Interactive tool interfaces with live API calls, structured results, external links","task_count":1,"done_count":0},{"name":"AI Tools Landscape","layer":"Forge","priority":64,"status":"paused","description":"Living catalog of AI-for-science tools, platforms, agents, and benchmarks. Uses wiki entity_type='ai_tool' with structured frontmatter (category, specializations, pricing, benchmarks, open-source status). Browsing page at /forge/landscape with filters by category, specialization, pricing. Seeded with 23 entries from inspirations page. Kept current via agent scanning + staleness badges. Spec: docs/planning/specs/q-ai-tools-landscape_spec.md","task_count":5,"done_count":0},{"name":"Visual Artifacts","layer":"Forge","priority":55,"status":"active","description":"AI-generated visual artifacts — infographics, hypothesis cards, entity portraits, protocol illustrations. Uses MiniMax image-01 and GLM CogView-4 with quality evaluation via vision models.","task_count":5,"done_count":5}]}