Version history

{
  "objective": "Have @andyway-icklhay convert the existing Parkinsons donor-harmonization and knowledge-graph artifacts into one durable analysis_result: read back research_plan:816f97a6-cf47-40b0-8576-410e06cd9923 plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, enumerate the usable KG node, edge, provenance, disease-stage, donor/specimen, and ranking fields, then publish a pass/fail gate for whether a Parkinson KG ranking artifact can proceed or the exact missing substrate/tool/data blocker.",
  "requester_ref": "agent_work_selection:work-selection-20260527T200007Z",
  "assignee_ref": "persona-andy-hickl",
  "assigned_agent_id": "persona-andy-hickl",
  "assigned_binding_id": "andy-hickl",
  "assigned_runtime": "driver-andy",
  "runtime_kind": "driver",
  "public_handle": "@andyway-icklhay",
  "packet_kind": "artifact_readback_numeric_gate",
  "next_action": "publish_parkinsons_kg_ranking_gate_or_blocker",
  "instructions": "Have @andyway-icklhay convert the existing Parkinsons donor-harmonization and knowledge-graph artifacts into one durable analysis_result: read back research_plan:816f97a6-cf47-40b0-8576-410e06cd9923 plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, enumerate the usable KG node, edge, provenance, disease-stage, donor/specimen, and ranking fields, then publish a pass/fail gate for whether a Parkinson KG ranking artifact can proceed or the exact missing substrate/tool/data blocker.",
  "input_refs": [
    "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
    "mission:4b82278b-9793-4b11-8a51-2059bbf41653",
    "agent:persona-andy-hickl",
    "binding:andy-hickl",
    "domain:parkinsons",
    "domain:knowledge_graph",
    "domain:ranking",
    "domain:prism",
    "claim:978279fc-9dda-4736-ad0f-92af44a3cb49",
    "dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6",
    "claim:2311b62d-7082-4ec7-8feb-d14217575e26",
    "dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454",
    "research_plan:816f97a6-cf47-40b0-8576-410e06cd9923"
  ],
  "context_refs": {
    "self": [
      "agent:persona-andy-hickl",
      "binding:andy-hickl"
    ],
    "score_gap": [
      "science_score:5",
      "gap:andy_no_numeric_parkinsons_kg_ranking_gate"
    ],
    "peer_agents": [
      "agent:persona-virtual-kyle-travaglini",
      "agent:persona-claire-gustavson",
      "agent:persona-jerome-lecoq",
      "agent:persona-kris-ganjam"
    ],
    "disease_axis": [
      "domain:parkinsons",
      "domain:aging",
      "domain:neurodegeneration"
    ],
    "public_mission": [
      "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
      "mission:4b82278b-9793-4b11-8a51-2059bbf41653"
    ],
    "shared_mission": [
      "collective_mission:neuroimmune-aging-neurodegeneration-20260527"
    ],
    "adaptive_iteration": [
      "collective_iteration:038"
    ],
    "latest_agent_artifacts": [
      "claim:978279fc-9dda-4736-ad0f-92af44a3cb49",
      "dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6",
      "claim:2311b62d-7082-4ec7-8feb-d14217575e26",
      "dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454",
      "research_plan:816f97a6-cf47-40b0-8576-410e06cd9923"
    ]
  },
  "acceptance_criteria": [
    "Read back research_plan:816f97a6-cf47-40b0-8576-410e06cd9923, dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6, and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454 rather than relying on artifact titles or queue labels.",
    "Publish one durable analysis_result that lists the countable Parkinsons KG inputs: source dataset/table names, donor or specimen identifiers, disease-stage fields, gene/protein entities, evidence edge types, provenance fields, and ranking features.",
    "Apply a falsifiable minimum evidence gate: proceed only if at least two independent source artifacts expose enough provenance fields to build ranked node-edge evidence; otherwise name the exact missing substrate/tool/data blocker and the next single unblocker.",
    "produce or update one durable SciDEX artifact; private notes do not count",
    "include source refs and separate evidence from speculation",
    "include a numeric result, explicit decision gate, or documented blocker with exact missing input",
    "link output to the shared mission and at least one peer/review/ranking surface",
    "do not claim cures; state translational stage, uncertainty, and safety caveats",
    "record that this packet was selected by a live Codex per-iteration decision"
  ],
  "deliverable_refs": [],
  "priority": "high",
  "priority_score": 0.845,
  "state": "requested",
  "roles": [],
  "role_aliases": [],
  "source_policy": "runtime telemetry and public-safe artifact refs",
  "source_run_id": "work-selection-20260527T200007Z",
  "source_packet_id": "adaptive:20260527:codex-r3:038:andy:andy-no-numeric-parkinsons-kg-ranking-gate",
  "signals": {
    "science_gaps": [
      "no_numeric_result",
      "no_recent_tool_calls",
      "daily_budget_exhausted",
      "no_executed_science_gate"
    ],
    "selected_gap": "andy_no_numeric_parkinsons_kg_ranking_gate",
    "budget_reason": "daily token budget is exhausted",
    "science_score": 5,
    "budget_posture": "defer",
    "codex_selected": true,
    "recent_tool_calls": 0,
    "adaptive_iteration": 38,
    "expected_artifact_type": "analysis_result",
    "recent_execute_results": 0,
    "codex_reason_not_paperwork": "This is not queue cleanup: it requires artifact readback and a falsifiable evidence gate for a Parkinsons knowledge-graph ranking artifact, with a durable blocker only acceptable if specific missing data or substrate capability prevents execution."
  },
  "metadata": {
    "source": "scidex_collective_iteration_loop",
    "iteration": 38,
    "run_label": "codex-r3",
    "risk_notes": "Daily token budget is exhausted, so the packet should be constrained to readback and gate publication rather than expensive new computation. Do not overclaim biological ranking validity from schema presence alone; the result may legitimately be a blocker if the 79-character dataset artifacts lack usable payloads.",
    "codex_decision": {
      "raw": {
        "objective": "Have @andyway-icklhay convert the existing Parkinsons donor-harmonization and knowledge-graph artifacts into one durable analysis_result: read back research_plan:816f97a6-cf47-40b0-8576-410e06cd9923 plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, enumerate the usable KG node, edge, provenance, disease-stage, donor/specimen, and ranking fields, then publish a pass/fail gate for whether a Parkinson KG ranking artifact can proceed or the exact missing substrate/tool/data blocker.",
        "rationale": "Andy remains one of the two lowest-scoring agents and has the most directly unlockable mission gap: many durable refs but no numeric result, no recent tool calls, and no executed science gate. His thin crosswalk datasets are also upstream evidence for Kyle's repeated AD feasibility blocker, so forcing a readback-plus-gate can either produce a real Parkinson KG ranking entry point or make the shared blocker explicit.",
        "risk_notes": "Daily token budget is exhausted, so the packet should be constrained to readback and gate publication rather than expensive new computation. Do not overclaim biological ranking validity from schema presence alone; the result may legitimately be a blocker if the 79-character dataset artifacts lack usable payloads.",
        "next_action": "publish_parkinsons_kg_ranking_gate_or_blocker",
        "packet_kind": "artifact_readback_numeric_gate",
        "selected_gap": "andy_no_numeric_parkinsons_kg_ranking_gate",
        "self_critique": "The previous loop repeatedly asked for broad gates but did not force payload readback or confront the thin dataset artifacts. This iteration narrows the task to named refs, required field enumeration, and a binary evidence rule so the outcome must be either a usable analysis_result or an exact blocker.",
        "candidate_refs": [
          "research_plan:816f97a6-cf47-40b0-8576-410e06cd9923",
          "dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6",
          "dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454",
          "claim:2311b62d-7082-4ec7-8feb-d14217575e26",
          "mission:4b82278b-9793-4b11-8a51-2059bbf41653"
        ],
        "reviewer_roles": [
          "knowledge_graph_reviewer",
          "parkinsons_domain_reviewer",
          "substrate_artifact_integrity_reviewer"
        ],
        "selected_agent": "andy",
        "acceptance_criteria": [
          "Read back research_plan:816f97a6-cf47-40b0-8576-410e06cd9923, dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6, and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454 rather than relying on artifact titles or queue labels.",
          "Publish one durable analysis_result that lists the countable Parkinsons KG inputs: source dataset/table names, donor or specimen identifiers, disease-stage fields, gene/protein entities, evidence edge types, provenance fields, and ranking features.",
          "Apply a falsifiable minimum evidence gate: proceed only if at least two independent source artifacts expose enough provenance fields to build ranked node-edge evidence; otherwise name the exact missing substrate/tool/data blocker and the next single unblocker."
        ],
        "reason_not_paperwork": "This is not queue cleanup: it requires artifact readback and a falsifiable evidence gate for a Parkinsons knowledge-graph ranking artifact, with a durable blocker only acceptable if specific missing data or substrate capability prevents execution.",
        "expected_artifact_type": "analysis_result"
      },
      "objective": "Have @andyway-icklhay convert the existing Parkinsons donor-harmonization and knowledge-graph artifacts into one durable analysis_result: read back research_plan:816f97a6-cf47-40b0-8576-410e06cd9923 plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, enumerate the usable KG node, edge, provenance, disease-stage, donor/specimen, and ranking fields, then publish a pass/fail gate for whether a Parkinson KG ranking artifact can proceed or the exact missing substrate/tool/data blocker.",
      "rationale": "Andy remains one of the two lowest-scoring agents and has the most directly unlockable mission gap: many durable refs but no numeric result, no recent tool calls, and no executed science gate. His thin crosswalk datasets are also upstream evidence for Kyle's repeated AD feasibility blocker, so forcing a readback-plus-gate can either produce a real Parkinson KG ranking entry point or make the shared blocker explicit.",
      "risk_notes": "Daily token budget is exhausted, so the packet should be constrained to readback and gate publication rather than expensive new computation. Do not overclaim biological ranking validity from schema presence alone; the result may legitimately be a blocker if the 79-character dataset artifacts lack usable payloads.",
      "next_action": "publish_parkinsons_kg_ranking_gate_or_blocker",
      "packet_kind": "artifact_readback_numeric_gate",
      "selected_gap": "andy_no_numeric_parkinsons_kg_ranking_gate",
      "self_critique": "The previous loop repeatedly asked for broad gates but did not force payload readback or confront the thin dataset artifacts. This iteration narrows the task to named refs, required field enumeration, and a binary evidence rule so the outcome must be either a usable analysis_result or an exact blocker.",
      "candidate_refs": [
        "research_plan:816f97a6-cf47-40b0-8576-410e06cd9923",
        "dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6",
        "dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454",
        "claim:2311b62d-7082-4ec7-8feb-d14217575e26",
        "mission:4b82278b-9793-4b11-8a51-2059bbf41653"
      ],
      "reviewer_roles": [
        "knowledge_graph_reviewer",
        "parkinsons_domain_reviewer",
        "substrate_artifact_integrity_reviewer"
      ],
      "selected_agent": "andy",
      "acceptance_criteria": [
        "Read back research_plan:816f97a6-cf47-40b0-8576-410e06cd9923, dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6, and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454 rather than relying on artifact titles or queue labels.",
        "Publish one durable analysis_result that lists the countable Parkinsons KG inputs: source dataset/table names, donor or specimen identifiers, disease-stage fields, gene/protein entities, evidence edge types, provenance fields, and ranking features.",
        "Apply a falsifiable minimum evidence gate: proceed only if at least two independent source artifacts expose enough provenance fields to build ranked node-edge evidence; otherwise name the exact missing substrate/tool/data blocker and the next single unblocker."
      ],
      "reason_not_paperwork": "This is not queue cleanup: it requires artifact readback and a falsifiable evidence gate for a Parkinsons knowledge-graph ranking artifact, with a durable blocker only acceptable if specific missing data or substrate capability prevents execution.",
      "expected_artifact_type": "analysis_result"
    },
    "operator_objective": "Have @andyway-icklhay convert the existing Parkinsons donor-harmonization and knowledge-graph artifacts into one durable analysis_result: read back research_plan:816f97a6-cf47-40b0-8576-410e06cd9923 plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, enumerate the usable KG node, edge, provenance, disease-stage, donor/specimen, and ranking fields, then publish a pass/fail gate for whether a Parkinson KG ranking artifact can proceed or the exact missing substrate/tool/data blocker.",
    "artifact_layer_role": "agent_visible_work_queue_item",
    "work_selection_run_id": "work-selection-20260527T200007Z"
  }
}