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Invoke for investigations.json and current_investigation.json format reference. Defines the schema for claim investigations and query bundles.
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| name | write-investigation |
| description | Invoke for investigations.json and current_investigation.json format reference. Defines the schema for claim investigations and query bundles. |
Two files share the same investigation structure:
/workspace/run/investigations.json — cumulative record of all investigations. Root object with investigations array and active_investigation_id string./workspace/run/current_investigation.json — the investigation currently being executed. Single investigation object (same structure as one element of the investigations array). Overwritten each cycle.| Field | Type | Required | Description |
|---|---|---|---|
id | string | yes | Investigation identifier (I1, I2, ...) |
name | string | yes | Short label for the investigation |
phenomenon | string | yes | Full sentence describing the observed phenomenon being investigated |
adjudication_goal | string | yes | What this investigation aims to determine — stated as a question or judgment to be made |
pattern_ids | array of strings | yes | Pattern IDs this investigation addresses |
status | string | yes | One of: active, paused, resolved, retired, saturated |
cycle_id | integer | yes | Current cycle number for this investigation |
claims | array | yes | Claims being evaluated (see below) |
query_bundle | array | yes | Queries to execute (see below) |
active: currently being investigatedpaused: temporarily set aside, may resumeresolved: phenomenon explained, evidence sufficientretired: abandoned — artifact, low value, or merged with another investigationsaturated: diminishing returns, not fully resolved but not worth continuingclaims array)| Field | Type | Required | Description |
|---|---|---|---|
id | string | yes | Claim identifier (e.g. I1-claim1) |
text | string | yes | The claim statement |
role | string | yes | One of: main, alternative_explanation, artifact_check, robustness |
status | string | yes | One of: pending, supported, weakened, refuted, inconclusive |
confidence | number or null | yes | Judge's calibrated confidence (0-1), null if not yet evaluated |
supporting_evidence | array | yes | Experiment IDs that support this claim |
counter_evidence | array | yes | Experiment IDs that weaken or refute this claim |
main: the primary hypothesis about the phenomenonalternative_explanation: a competing explanation for the same phenomenonartifact_check: tests whether the phenomenon is an artifact of data processing, sampling, or annotationrobustness: tests whether the main finding holds under different conditions or parametersquery_bundle array)| Field | Type | Required | Description |
|---|---|---|---|
id | string | yes | Query identifier (e.g. I1-q1) |
claim_id | string | yes | Which claim this query tests |
text | string | yes | The specific analysis to perform |
role | string | yes | One of: observational, diagnostic, artifact_check |
expected_effect | string | yes | What the result would mean for the claim — how it discriminates between explanations |
result_ref | string or null | yes | Experiment ID that produced the result, null if not yet run |
depends_on | array of strings | yes | Query IDs that must complete before this one (empty array if independent) |
status | string | yes | One of: pending, running, done, failed, skipped |
| Field | Type | Required | Description |
|---|---|---|---|
active_investigation_id | string or null | yes | ID of the currently active investigation |
Invoke after experiment-runner completes an investigation's query bundle. Evaluates all claims in current_investigation.json and produces an investigation-level adjudication. Writes claim_scores.json.
Invoke after investigation-decomposition. Runs all queries in an investigation bundle using shared data preparation. Writes code and results.
Invoke after main agent writes L2 assessment. Reads epistemic state (L1/L2), patterns, and investigations to recommend next action. Writes strategy_recommendation.json.
Gene set enrichment analysis (GSEA, Enrichr, over-representation). Invoke when query mentions enrichment, pathway analysis, GO analysis, GSEA, or gene set.
Invoke before running experiments for an investigation. Reads current_investigation.json and task_packet.json, writes current_investigation_requirements.json with shared data preparation and per-query requirements.
Gene ID conversion and annotation. Invoke when you need to map between any gene identifier formats.