@inflexa-ai/harness 0.28.1 → 0.30.0

package/dist/schemas/data-profile-schemas.d.ts

@@ -1,22 +1,40 @@
 /**
- * Schemas for data profiling.
+ * The profiler's authoring contract.
  *
- * Defines the profiler structured output schema used by the data-profile
- * task and sandbox agent.
+ * What the agent submits is JUDGEMENT, never enumeration: operations on the scan's menu,
+ * what each resulting group means, and the dimensions it saw with the evidence it saw
+ * them in. Membership, counts, and display patterns are computed at resolution from the
+ * scanner's own templates, so no field here carries a count or a path pattern — those are
+ * unrepresentable rather than discouraged, because a discouraged field is a field that
+ * gets filled.
+ *
+ * Every array is bounded, and the bound is the enforcement: an over-long submission is a
+ * schema error the agent corrects, never a silent truncation. The governing invariant is
+ * that nothing the agent authors grows with the number of input files.
+ *
+ * The category enums are derived from the shipped vocabulary (`contracts/profile-vocabulary`),
+ * so the catalogue this validates against and the catalogue the prompt renders are one list.
  */
 import { z } from "zod";
-/** Per-file metadata — includes path so the agent can discover files itself. */
-export declare const ProfilerFileSchema: z.ZodObject<{
-    path: z.ZodString;
-    description: z.ZodString;
-    dataType: z.ZodString;
-    format: z.ZodString;
-    rows: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
-    cols: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
-    tags: z.ZodOptional<z.ZodArray<z.ZodString>>;
-    warnings: z.ZodOptional<z.ZodArray<z.ZodString>>;
-    metrics: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnion<readonly [z.ZodString, z.ZodNumber, z.ZodBoolean]>>>;
-}, z.core.$strip>;
+/** Operations one submission may carry — the menu's own bound. */
+export declare const MAX_OPERATIONS = 40;
+/** Groups one split may produce. A slot needing more is an identifier, and identifiers are never split. */
+export declare const MAX_SPLIT_GROUPS = 12;
+/** Slot values one split group may name. */
+export declare const MAX_SPLIT_VALUES = 50;
+export declare const MAX_MERGE_SETS = 12;
+/** Paths one explicit `group` may gather — the leftover aggregate, not the dataset. */
+export declare const MAX_EXPLICIT_PATHS = 50;
+/** Members of one group the agent may annotate individually. Never required to be exhaustive. */
+export declare const MAX_MEMBER_ANNOTATIONS = 25;
+/** Dataset-level dimensions. An experimental design with more varying dimensions is vanishingly rare. */
+export declare const MAX_DIMENSIONS = 12;
+export declare const MAX_OBSERVATIONS = 6;
+export declare const MAX_RECONCILIATIONS = 4;
+export declare const MAX_EXAMPLE_VALUES = 5;
+/** Files a `not-found` probe may name as searched — the probe-searchable set is bounded by design. */
+export declare const MAX_SEARCHED_FILES = 10;
+export declare const MAX_CAVEATS = 10;
 /**
  * Where an extracted subject fact came from. Used so downstream agents can
  * judge how much to trust a field and so this profiler can flag conflicts.
@@ -40,87 +58,935 @@ export declare const OrganismSchema: z.ZodObject<{
         inferred: "inferred";
     }>;
     confidence: z.ZodEnum<{
-        high: "high";
-        medium: "medium";
         low: "low";
+        medium: "medium";
+        high: "high";
     }>;
     notes: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>;
 export type Organism = z.infer<typeof OrganismSchema>;
-/** Kinds an output may carry. A tree needing more than this is not being grouped. */
-export declare const MAX_KINDS = 30;
-/** Axes an output may carry — an experimental design with more varying dimensions is vanishingly rare. */
-export declare const MAX_AXES = 8;
-/**
- * Individually described files an output may carry. `files` holds NOTABLE SINGLETONS
- * — the metadata sheet, the README, the paper, an outlier that fits no kind — not the
- * dataset's contents.
- */
-export declare const MAX_NOTABLE_FILES = 50;
+export declare const MemberAnnotationSchema: z.ZodObject<{
+    path: z.ZodString;
+    note: z.ZodString;
+}, z.core.$strict>;
+export type MemberAnnotation = z.infer<typeof MemberAnnotationSchema>;
 /**
- * A repeating set of files that are the same sort of thing.
- *
- * A kind is a claim about MEANING, so only the agent can author one: the input scan
- * reports shapes (these filenames differ only here) and cannot establish that the
- * files are the same sort of thing. Kinds need not correspond one-to-one with observed
- * shapes — one kind may span several shapes, and one shape may split into several
- * kinds.
+ * What a group IS, stated by the agent.
  *
- * A singleton is a kind of `count` 1. There is one concept with a count, not two
- * concepts with a threshold between them, so degenerate datasets need no special case.
+ * `.strict()` because the fields NOT here are the point: a count, a path pattern, and a
+ * member list are all computed at resolution from the operation's own membership, and a
+ * submission that carries one is rejected rather than quietly overridden.
  */
-export declare const KindSchema: z.ZodObject<{
+export declare const GroupAnnotationSchema: z.ZodObject<{
     name: z.ZodString;
     memberRepresents: z.ZodString;
     description: z.ZodString;
-    count: z.ZodNumber;
-    pathPattern: z.ZodString;
-    format: z.ZodOptional<z.ZodString>;
-    axisLabels: z.ZodOptional<z.ZodArray<z.ZodString>>;
-}, z.core.$strip>;
-export type ProfilerKind = z.infer<typeof KindSchema>;
+    role: z.ZodEnum<{
+        metadata: "metadata";
+        data: "data";
+        index: "index";
+        reference: "reference";
+        documentation: "documentation";
+    }>;
+    category: z.ZodEnum<{
+        other: "other";
+        code: "code";
+        document: "document";
+        manifest: "manifest";
+        "chemical-structures": "chemical-structures";
+        "sequencing-reads": "sequencing-reads";
+        alignment: "alignment";
+        "variant-calls": "variant-calls";
+        "copy-number": "copy-number";
+        "structural-variants": "structural-variants";
+        "association-results": "association-results";
+        "regions-signal": "regions-signal";
+        "expression-matrix": "expression-matrix";
+        "single-cell-matrix": "single-cell-matrix";
+        methylation: "methylation";
+        proteomics: "proteomics";
+        metabolomics: "metabolomics";
+        cytometry: "cytometry";
+        imaging: "imaging";
+        "clinical-table": "clinical-table";
+        "sample-annotation": "sample-annotation";
+        "reference-data": "reference-data";
+    }>;
+    categoryLabel: z.ZodOptional<z.ZodString>;
+    subtype: z.ZodOptional<z.ZodString>;
+    categoryReason: z.ZodOptional<z.ZodString>;
+    memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        path: z.ZodString;
+        note: z.ZodString;
+    }, z.core.$strict>>>;
+}, z.core.$strict>;
+export type GroupAnnotation = z.infer<typeof GroupAnnotationSchema>;
 /**
- * What varies across a kind's members.
+ * The four ways an agent expresses a grouping.
  *
- * The scan reports that a filename position varies and which values it takes; what the
- * variation IS — a subject, a timepoint, a treatment arm, a chromosome shard — is not
- * derivable from the values, so the label is required and agent-supplied. An axis
- * evident from a metadata sheet but not from filenames belongs here too.
+ * Operations, not freehand patterns: a mistyped value is a rejectable error at submit
+ * rather than a silent zero-match, and every run starts from the same menu, so two runs
+ * over one tree can only differ where the judgement differs.
  */
-export declare const AxisSchema: z.ZodObject<{
-    label: z.ZodString;
-    cardinality: z.ZodNumber;
-    exampleValues: z.ZodOptional<z.ZodArray<z.ZodString>>;
-    description: z.ZodOptional<z.ZodString>;
-}, z.core.$strip>;
-export type ProfilerAxis = z.infer<typeof AxisSchema>;
-export declare const ProfilerOutputSchema: z.ZodObject<{
-    files: z.ZodArray<z.ZodObject<{
-        path: z.ZodString;
+export declare const MenuOperationSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
+    op: z.ZodLiteral<"use">;
+    setId: z.ZodString;
+    group: z.ZodObject<{
+        name: z.ZodString;
+        memberRepresents: z.ZodString;
         description: z.ZodString;
-        dataType: z.ZodString;
-        format: z.ZodString;
-        rows: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
-        cols: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
-        tags: z.ZodOptional<z.ZodArray<z.ZodString>>;
-        warnings: z.ZodOptional<z.ZodArray<z.ZodString>>;
-        metrics: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnion<readonly [z.ZodString, z.ZodNumber, z.ZodBoolean]>>>;
-    }, z.core.$strip>>;
-    kinds: z.ZodArray<z.ZodObject<{
+        role: z.ZodEnum<{
+            metadata: "metadata";
+            data: "data";
+            index: "index";
+            reference: "reference";
+            documentation: "documentation";
+        }>;
+        category: z.ZodEnum<{
+            other: "other";
+            code: "code";
+            document: "document";
+            manifest: "manifest";
+            "chemical-structures": "chemical-structures";
+            "sequencing-reads": "sequencing-reads";
+            alignment: "alignment";
+            "variant-calls": "variant-calls";
+            "copy-number": "copy-number";
+            "structural-variants": "structural-variants";
+            "association-results": "association-results";
+            "regions-signal": "regions-signal";
+            "expression-matrix": "expression-matrix";
+            "single-cell-matrix": "single-cell-matrix";
+            methylation: "methylation";
+            proteomics: "proteomics";
+            metabolomics: "metabolomics";
+            cytometry: "cytometry";
+            imaging: "imaging";
+            "clinical-table": "clinical-table";
+            "sample-annotation": "sample-annotation";
+            "reference-data": "reference-data";
+        }>;
+        categoryLabel: z.ZodOptional<z.ZodString>;
+        subtype: z.ZodOptional<z.ZodString>;
+        categoryReason: z.ZodOptional<z.ZodString>;
+        memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+            path: z.ZodString;
+            note: z.ZodString;
+        }, z.core.$strict>>>;
+    }, z.core.$strict>;
+}, z.core.$strict>, z.ZodObject<{
+    op: z.ZodLiteral<"split">;
+    setId: z.ZodString;
+    by: z.ZodDiscriminatedUnion<[z.ZodObject<{
+        kind: z.ZodLiteral<"slot">;
+        slotId: z.ZodString;
+        group: z.ZodObject<{
+            name: z.ZodString;
+            memberRepresents: z.ZodString;
+            description: z.ZodString;
+            role: z.ZodEnum<{
+                metadata: "metadata";
+                data: "data";
+                index: "index";
+                reference: "reference";
+                documentation: "documentation";
+            }>;
+            category: z.ZodEnum<{
+                other: "other";
+                code: "code";
+                document: "document";
+                manifest: "manifest";
+                "chemical-structures": "chemical-structures";
+                "sequencing-reads": "sequencing-reads";
+                alignment: "alignment";
+                "variant-calls": "variant-calls";
+                "copy-number": "copy-number";
+                "structural-variants": "structural-variants";
+                "association-results": "association-results";
+                "regions-signal": "regions-signal";
+                "expression-matrix": "expression-matrix";
+                "single-cell-matrix": "single-cell-matrix";
+                methylation: "methylation";
+                proteomics: "proteomics";
+                metabolomics: "metabolomics";
+                cytometry: "cytometry";
+                imaging: "imaging";
+                "clinical-table": "clinical-table";
+                "sample-annotation": "sample-annotation";
+                "reference-data": "reference-data";
+            }>;
+            categoryLabel: z.ZodOptional<z.ZodString>;
+            subtype: z.ZodOptional<z.ZodString>;
+            categoryReason: z.ZodOptional<z.ZodString>;
+            memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                path: z.ZodString;
+                note: z.ZodString;
+            }, z.core.$strict>>>;
+        }, z.core.$strict>;
+    }, z.core.$strict>, z.ZodObject<{
+        kind: z.ZodLiteral<"values">;
+        slotId: z.ZodString;
+        groups: z.ZodArray<z.ZodObject<{
+            values: z.ZodArray<z.ZodString>;
+            group: z.ZodObject<{
+                name: z.ZodString;
+                memberRepresents: z.ZodString;
+                description: z.ZodString;
+                role: z.ZodEnum<{
+                    metadata: "metadata";
+                    data: "data";
+                    index: "index";
+                    reference: "reference";
+                    documentation: "documentation";
+                }>;
+                category: z.ZodEnum<{
+                    other: "other";
+                    code: "code";
+                    document: "document";
+                    manifest: "manifest";
+                    "chemical-structures": "chemical-structures";
+                    "sequencing-reads": "sequencing-reads";
+                    alignment: "alignment";
+                    "variant-calls": "variant-calls";
+                    "copy-number": "copy-number";
+                    "structural-variants": "structural-variants";
+                    "association-results": "association-results";
+                    "regions-signal": "regions-signal";
+                    "expression-matrix": "expression-matrix";
+                    "single-cell-matrix": "single-cell-matrix";
+                    methylation: "methylation";
+                    proteomics: "proteomics";
+                    metabolomics: "metabolomics";
+                    cytometry: "cytometry";
+                    imaging: "imaging";
+                    "clinical-table": "clinical-table";
+                    "sample-annotation": "sample-annotation";
+                    "reference-data": "reference-data";
+                }>;
+                categoryLabel: z.ZodOptional<z.ZodString>;
+                subtype: z.ZodOptional<z.ZodString>;
+                categoryReason: z.ZodOptional<z.ZodString>;
+                memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                    path: z.ZodString;
+                    note: z.ZodString;
+                }, z.core.$strict>>>;
+            }, z.core.$strict>;
+        }, z.core.$strict>>;
+        rest: z.ZodOptional<z.ZodObject<{
+            name: z.ZodString;
+            memberRepresents: z.ZodString;
+            description: z.ZodString;
+            role: z.ZodEnum<{
+                metadata: "metadata";
+                data: "data";
+                index: "index";
+                reference: "reference";
+                documentation: "documentation";
+            }>;
+            category: z.ZodEnum<{
+                other: "other";
+                code: "code";
+                document: "document";
+                manifest: "manifest";
+                "chemical-structures": "chemical-structures";
+                "sequencing-reads": "sequencing-reads";
+                alignment: "alignment";
+                "variant-calls": "variant-calls";
+                "copy-number": "copy-number";
+                "structural-variants": "structural-variants";
+                "association-results": "association-results";
+                "regions-signal": "regions-signal";
+                "expression-matrix": "expression-matrix";
+                "single-cell-matrix": "single-cell-matrix";
+                methylation: "methylation";
+                proteomics: "proteomics";
+                metabolomics: "metabolomics";
+                cytometry: "cytometry";
+                imaging: "imaging";
+                "clinical-table": "clinical-table";
+                "sample-annotation": "sample-annotation";
+                "reference-data": "reference-data";
+            }>;
+            categoryLabel: z.ZodOptional<z.ZodString>;
+            subtype: z.ZodOptional<z.ZodString>;
+            categoryReason: z.ZodOptional<z.ZodString>;
+            memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                path: z.ZodString;
+                note: z.ZodString;
+            }, z.core.$strict>>>;
+        }, z.core.$strict>>;
+    }, z.core.$strict>], "kind">;
+    reason: z.ZodString;
+}, z.core.$strict>, z.ZodObject<{
+    op: z.ZodLiteral<"merge">;
+    setIds: z.ZodArray<z.ZodString>;
+    group: z.ZodObject<{
         name: z.ZodString;
         memberRepresents: z.ZodString;
         description: z.ZodString;
-        count: z.ZodNumber;
-        pathPattern: z.ZodString;
-        format: z.ZodOptional<z.ZodString>;
-        axisLabels: z.ZodOptional<z.ZodArray<z.ZodString>>;
-    }, z.core.$strip>>;
-    axes: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        role: z.ZodEnum<{
+            metadata: "metadata";
+            data: "data";
+            index: "index";
+            reference: "reference";
+            documentation: "documentation";
+        }>;
+        category: z.ZodEnum<{
+            other: "other";
+            code: "code";
+            document: "document";
+            manifest: "manifest";
+            "chemical-structures": "chemical-structures";
+            "sequencing-reads": "sequencing-reads";
+            alignment: "alignment";
+            "variant-calls": "variant-calls";
+            "copy-number": "copy-number";
+            "structural-variants": "structural-variants";
+            "association-results": "association-results";
+            "regions-signal": "regions-signal";
+            "expression-matrix": "expression-matrix";
+            "single-cell-matrix": "single-cell-matrix";
+            methylation: "methylation";
+            proteomics: "proteomics";
+            metabolomics: "metabolomics";
+            cytometry: "cytometry";
+            imaging: "imaging";
+            "clinical-table": "clinical-table";
+            "sample-annotation": "sample-annotation";
+            "reference-data": "reference-data";
+        }>;
+        categoryLabel: z.ZodOptional<z.ZodString>;
+        subtype: z.ZodOptional<z.ZodString>;
+        categoryReason: z.ZodOptional<z.ZodString>;
+        memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+            path: z.ZodString;
+            note: z.ZodString;
+        }, z.core.$strict>>>;
+    }, z.core.$strict>;
+    reason: z.ZodString;
+}, z.core.$strict>, z.ZodObject<{
+    op: z.ZodLiteral<"group">;
+    paths: z.ZodArray<z.ZodString>;
+    group: z.ZodObject<{
+        name: z.ZodString;
+        memberRepresents: z.ZodString;
+        description: z.ZodString;
+        role: z.ZodEnum<{
+            metadata: "metadata";
+            data: "data";
+            index: "index";
+            reference: "reference";
+            documentation: "documentation";
+        }>;
+        category: z.ZodEnum<{
+            other: "other";
+            code: "code";
+            document: "document";
+            manifest: "manifest";
+            "chemical-structures": "chemical-structures";
+            "sequencing-reads": "sequencing-reads";
+            alignment: "alignment";
+            "variant-calls": "variant-calls";
+            "copy-number": "copy-number";
+            "structural-variants": "structural-variants";
+            "association-results": "association-results";
+            "regions-signal": "regions-signal";
+            "expression-matrix": "expression-matrix";
+            "single-cell-matrix": "single-cell-matrix";
+            methylation: "methylation";
+            proteomics: "proteomics";
+            metabolomics: "metabolomics";
+            cytometry: "cytometry";
+            imaging: "imaging";
+            "clinical-table": "clinical-table";
+            "sample-annotation": "sample-annotation";
+            "reference-data": "reference-data";
+        }>;
+        categoryLabel: z.ZodOptional<z.ZodString>;
+        subtype: z.ZodOptional<z.ZodString>;
+        categoryReason: z.ZodOptional<z.ZodString>;
+        memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+            path: z.ZodString;
+            note: z.ZodString;
+        }, z.core.$strict>>>;
+    }, z.core.$strict>;
+}, z.core.$strict>], "op">;
+export type MenuOperation = z.infer<typeof MenuOperationSchema>;
+export declare const ObservationSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
+    kind: z.ZodLiteral<"slot">;
+    setId: z.ZodString;
+    slotId: z.ZodString;
+    note: z.ZodOptional<z.ZodString>;
+}, z.core.$strict>, z.ZodObject<{
+    kind: z.ZodLiteral<"column">;
+    path: z.ZodString;
+    column: z.ZodString;
+    exampleValues: z.ZodArray<z.ZodString>;
+    distinctValues: z.ZodOptional<z.ZodNumber>;
+    checked: z.ZodOptional<z.ZodObject<{
+        matched: z.ZodNumber;
+        of: z.ZodNumber;
+    }, z.core.$strict>>;
+    checkedAgainst: z.ZodOptional<z.ZodString>;
+    note: z.ZodOptional<z.ZodString>;
+}, z.core.$strict>, z.ZodObject<{
+    kind: z.ZodLiteral<"document">;
+    path: z.ZodString;
+    citation: z.ZodString;
+    statesCardinality: z.ZodOptional<z.ZodNumber>;
+    checked: z.ZodOptional<z.ZodObject<{
+        matched: z.ZodNumber;
+        of: z.ZodNumber;
+    }, z.core.$strict>>;
+    checkedAgainst: z.ZodOptional<z.ZodString>;
+    note: z.ZodOptional<z.ZodString>;
+}, z.core.$strict>], "kind">;
+export type Observation = z.infer<typeof ObservationSchema>;
+/**
+ * A dataset-level thing that varies, with where it was seen.
+ *
+ * At least one observation, always: a dimension without one is a claim, and a claim is
+ * what this schema exists to make unwritable. A slot binding is the ONLY way a group
+ * links to a dimension — there is no freehand "this group varies by X" field, so a
+ * per-subject dimension attached to a group whose template has no such slot cannot be
+ * written down.
+ *
+ * Naming a slot is not the same as promoting a dimension. Technical, single-set slots
+ * (shards, callers, lanes, read pairs) stay on the set; this list is reserved for
+ * biological or cross-set variation and must read as the design at a glance. A value
+ * constant across the dataset is not a dimension — it is an identity field.
+ */
+export declare const DimensionSchema: z.ZodObject<{
+    label: z.ZodString;
+    category: z.ZodEnum<{
+        other: "other";
+        sex: "sex";
+        subject: "subject";
+        sample: "sample";
+        "organism-species": "organism-species";
+        "model-system": "model-system";
+        "cohort-arm": "cohort-arm";
+        "disease-state": "disease-state";
+        treatment: "treatment";
+        timepoint: "timepoint";
+        "tissue-site": "tissue-site";
+        "cell-type": "cell-type";
+        "genetic-perturbation": "genetic-perturbation";
+        "age-group": "age-group";
+        "developmental-stage": "developmental-stage";
+        environment: "environment";
+        "assay-modality": "assay-modality";
+        "assay-target": "assay-target";
+        "variant-origin": "variant-origin";
+        "sample-pairing": "sample-pairing";
+        "processing-level": "processing-level";
+        "assay-version": "assay-version";
+        batch: "batch";
+        replicate: "replicate";
+        "tool-variant": "tool-variant";
+        "library-prep": "library-prep";
+        "data-partition": "data-partition";
+    }>;
+    categoryLabel: z.ZodOptional<z.ZodString>;
+    scope: z.ZodOptional<z.ZodEnum<{
+        biological: "biological";
+        technical: "technical";
+    }>>;
+    description: z.ZodOptional<z.ZodString>;
+    observations: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
+        kind: z.ZodLiteral<"slot">;
+        setId: z.ZodString;
+        slotId: z.ZodString;
+        note: z.ZodOptional<z.ZodString>;
+    }, z.core.$strict>, z.ZodObject<{
+        kind: z.ZodLiteral<"column">;
+        path: z.ZodString;
+        column: z.ZodString;
+        exampleValues: z.ZodArray<z.ZodString>;
+        distinctValues: z.ZodOptional<z.ZodNumber>;
+        checked: z.ZodOptional<z.ZodObject<{
+            matched: z.ZodNumber;
+            of: z.ZodNumber;
+        }, z.core.$strict>>;
+        checkedAgainst: z.ZodOptional<z.ZodString>;
+        note: z.ZodOptional<z.ZodString>;
+    }, z.core.$strict>, z.ZodObject<{
+        kind: z.ZodLiteral<"document">;
+        path: z.ZodString;
+        citation: z.ZodString;
+        statesCardinality: z.ZodOptional<z.ZodNumber>;
+        checked: z.ZodOptional<z.ZodObject<{
+            matched: z.ZodNumber;
+            of: z.ZodNumber;
+        }, z.core.$strict>>;
+        checkedAgainst: z.ZodOptional<z.ZodString>;
+        note: z.ZodOptional<z.ZodString>;
+    }, z.core.$strict>], "kind">>;
+    reconciliations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        note: z.ZodString;
+        delta: z.ZodOptional<z.ZodNumber>;
+    }, z.core.$strict>>>;
+    nestsUnder: z.ZodOptional<z.ZodObject<{
+        dimension: z.ZodString;
+        evidence: z.ZodString;
+    }, z.core.$strict>>;
+    treatmentReason: z.ZodOptional<z.ZodString>;
+}, z.core.$strict>;
+export type ProfileDimension = z.infer<typeof DimensionSchema>;
+/**
+ * One outcome per probe. "Not found after looking" is a correct, complete answer — that
+ * is what removes the completeness pressure that otherwise invents dimensions. An
+ * attested find is prose-only evidence and can never justify a split.
+ */
+export declare const ProbeReportSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
+    probe: z.ZodEnum<{
+        subject: "subject";
+        sample: "sample";
+        "cohort-arm": "cohort-arm";
+        timepoint: "timepoint";
+        batch: "batch";
+    }>;
+    outcome: z.ZodLiteral<"found">;
+    dimension: z.ZodString;
+}, z.core.$strict>, z.ZodObject<{
+    probe: z.ZodEnum<{
+        subject: "subject";
+        sample: "sample";
+        "cohort-arm": "cohort-arm";
+        timepoint: "timepoint";
+        batch: "batch";
+    }>;
+    outcome: z.ZodLiteral<"not-found">;
+    searched: z.ZodArray<z.ZodString>;
+    reason: z.ZodString;
+}, z.core.$strict>, z.ZodObject<{
+    probe: z.ZodEnum<{
+        subject: "subject";
+        sample: "sample";
+        "cohort-arm": "cohort-arm";
+        timepoint: "timepoint";
+        batch: "batch";
+    }>;
+    outcome: z.ZodLiteral<"found-but-constant">;
+    value: z.ZodString;
+    evidence: z.ZodString;
+}, z.core.$strict>, z.ZodObject<{
+    probe: z.ZodEnum<{
+        subject: "subject";
+        sample: "sample";
+        "cohort-arm": "cohort-arm";
+        timepoint: "timepoint";
+        batch: "batch";
+    }>;
+    outcome: z.ZodLiteral<"attested">;
+    citation: z.ZodString;
+    path: z.ZodString;
+}, z.core.$strict>], "outcome">;
+export type ProbeReport = z.infer<typeof ProbeReportSchema>;
+export declare const ProfileSubmissionSchema: z.ZodObject<{
+    operations: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
+        op: z.ZodLiteral<"use">;
+        setId: z.ZodString;
+        group: z.ZodObject<{
+            name: z.ZodString;
+            memberRepresents: z.ZodString;
+            description: z.ZodString;
+            role: z.ZodEnum<{
+                metadata: "metadata";
+                data: "data";
+                index: "index";
+                reference: "reference";
+                documentation: "documentation";
+            }>;
+            category: z.ZodEnum<{
+                other: "other";
+                code: "code";
+                document: "document";
+                manifest: "manifest";
+                "chemical-structures": "chemical-structures";
+                "sequencing-reads": "sequencing-reads";
+                alignment: "alignment";
+                "variant-calls": "variant-calls";
+                "copy-number": "copy-number";
+                "structural-variants": "structural-variants";
+                "association-results": "association-results";
+                "regions-signal": "regions-signal";
+                "expression-matrix": "expression-matrix";
+                "single-cell-matrix": "single-cell-matrix";
+                methylation: "methylation";
+                proteomics: "proteomics";
+                metabolomics: "metabolomics";
+                cytometry: "cytometry";
+                imaging: "imaging";
+                "clinical-table": "clinical-table";
+                "sample-annotation": "sample-annotation";
+                "reference-data": "reference-data";
+            }>;
+            categoryLabel: z.ZodOptional<z.ZodString>;
+            subtype: z.ZodOptional<z.ZodString>;
+            categoryReason: z.ZodOptional<z.ZodString>;
+            memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                path: z.ZodString;
+                note: z.ZodString;
+            }, z.core.$strict>>>;
+        }, z.core.$strict>;
+    }, z.core.$strict>, z.ZodObject<{
+        op: z.ZodLiteral<"split">;
+        setId: z.ZodString;
+        by: z.ZodDiscriminatedUnion<[z.ZodObject<{
+            kind: z.ZodLiteral<"slot">;
+            slotId: z.ZodString;
+            group: z.ZodObject<{
+                name: z.ZodString;
+                memberRepresents: z.ZodString;
+                description: z.ZodString;
+                role: z.ZodEnum<{
+                    metadata: "metadata";
+                    data: "data";
+                    index: "index";
+                    reference: "reference";
+                    documentation: "documentation";
+                }>;
+                category: z.ZodEnum<{
+                    other: "other";
+                    code: "code";
+                    document: "document";
+                    manifest: "manifest";
+                    "chemical-structures": "chemical-structures";
+                    "sequencing-reads": "sequencing-reads";
+                    alignment: "alignment";
+                    "variant-calls": "variant-calls";
+                    "copy-number": "copy-number";
+                    "structural-variants": "structural-variants";
+                    "association-results": "association-results";
+                    "regions-signal": "regions-signal";
+                    "expression-matrix": "expression-matrix";
+                    "single-cell-matrix": "single-cell-matrix";
+                    methylation: "methylation";
+                    proteomics: "proteomics";
+                    metabolomics: "metabolomics";
+                    cytometry: "cytometry";
+                    imaging: "imaging";
+                    "clinical-table": "clinical-table";
+                    "sample-annotation": "sample-annotation";
+                    "reference-data": "reference-data";
+                }>;
+                categoryLabel: z.ZodOptional<z.ZodString>;
+                subtype: z.ZodOptional<z.ZodString>;
+                categoryReason: z.ZodOptional<z.ZodString>;
+                memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                    path: z.ZodString;
+                    note: z.ZodString;
+                }, z.core.$strict>>>;
+            }, z.core.$strict>;
+        }, z.core.$strict>, z.ZodObject<{
+            kind: z.ZodLiteral<"values">;
+            slotId: z.ZodString;
+            groups: z.ZodArray<z.ZodObject<{
+                values: z.ZodArray<z.ZodString>;
+                group: z.ZodObject<{
+                    name: z.ZodString;
+                    memberRepresents: z.ZodString;
+                    description: z.ZodString;
+                    role: z.ZodEnum<{
+                        metadata: "metadata";
+                        data: "data";
+                        index: "index";
+                        reference: "reference";
+                        documentation: "documentation";
+                    }>;
+                    category: z.ZodEnum<{
+                        other: "other";
+                        code: "code";
+                        document: "document";
+                        manifest: "manifest";
+                        "chemical-structures": "chemical-structures";
+                        "sequencing-reads": "sequencing-reads";
+                        alignment: "alignment";
+                        "variant-calls": "variant-calls";
+                        "copy-number": "copy-number";
+                        "structural-variants": "structural-variants";
+                        "association-results": "association-results";
+                        "regions-signal": "regions-signal";
+                        "expression-matrix": "expression-matrix";
+                        "single-cell-matrix": "single-cell-matrix";
+                        methylation: "methylation";
+                        proteomics: "proteomics";
+                        metabolomics: "metabolomics";
+                        cytometry: "cytometry";
+                        imaging: "imaging";
+                        "clinical-table": "clinical-table";
+                        "sample-annotation": "sample-annotation";
+                        "reference-data": "reference-data";
+                    }>;
+                    categoryLabel: z.ZodOptional<z.ZodString>;
+                    subtype: z.ZodOptional<z.ZodString>;
+                    categoryReason: z.ZodOptional<z.ZodString>;
+                    memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                        path: z.ZodString;
+                        note: z.ZodString;
+                    }, z.core.$strict>>>;
+                }, z.core.$strict>;
+            }, z.core.$strict>>;
+            rest: z.ZodOptional<z.ZodObject<{
+                name: z.ZodString;
+                memberRepresents: z.ZodString;
+                description: z.ZodString;
+                role: z.ZodEnum<{
+                    metadata: "metadata";
+                    data: "data";
+                    index: "index";
+                    reference: "reference";
+                    documentation: "documentation";
+                }>;
+                category: z.ZodEnum<{
+                    other: "other";
+                    code: "code";
+                    document: "document";
+                    manifest: "manifest";
+                    "chemical-structures": "chemical-structures";
+                    "sequencing-reads": "sequencing-reads";
+                    alignment: "alignment";
+                    "variant-calls": "variant-calls";
+                    "copy-number": "copy-number";
+                    "structural-variants": "structural-variants";
+                    "association-results": "association-results";
+                    "regions-signal": "regions-signal";
+                    "expression-matrix": "expression-matrix";
+                    "single-cell-matrix": "single-cell-matrix";
+                    methylation: "methylation";
+                    proteomics: "proteomics";
+                    metabolomics: "metabolomics";
+                    cytometry: "cytometry";
+                    imaging: "imaging";
+                    "clinical-table": "clinical-table";
+                    "sample-annotation": "sample-annotation";
+                    "reference-data": "reference-data";
+                }>;
+                categoryLabel: z.ZodOptional<z.ZodString>;
+                subtype: z.ZodOptional<z.ZodString>;
+                categoryReason: z.ZodOptional<z.ZodString>;
+                memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                    path: z.ZodString;
+                    note: z.ZodString;
+                }, z.core.$strict>>>;
+            }, z.core.$strict>>;
+        }, z.core.$strict>], "kind">;
+        reason: z.ZodString;
+    }, z.core.$strict>, z.ZodObject<{
+        op: z.ZodLiteral<"merge">;
+        setIds: z.ZodArray<z.ZodString>;
+        group: z.ZodObject<{
+            name: z.ZodString;
+            memberRepresents: z.ZodString;
+            description: z.ZodString;
+            role: z.ZodEnum<{
+                metadata: "metadata";
+                data: "data";
+                index: "index";
+                reference: "reference";
+                documentation: "documentation";
+            }>;
+            category: z.ZodEnum<{
+                other: "other";
+                code: "code";
+                document: "document";
+                manifest: "manifest";
+                "chemical-structures": "chemical-structures";
+                "sequencing-reads": "sequencing-reads";
+                alignment: "alignment";
+                "variant-calls": "variant-calls";
+                "copy-number": "copy-number";
+                "structural-variants": "structural-variants";
+                "association-results": "association-results";
+                "regions-signal": "regions-signal";
+                "expression-matrix": "expression-matrix";
+                "single-cell-matrix": "single-cell-matrix";
+                methylation: "methylation";
+                proteomics: "proteomics";
+                metabolomics: "metabolomics";
+                cytometry: "cytometry";
+                imaging: "imaging";
+                "clinical-table": "clinical-table";
+                "sample-annotation": "sample-annotation";
+                "reference-data": "reference-data";
+            }>;
+            categoryLabel: z.ZodOptional<z.ZodString>;
+            subtype: z.ZodOptional<z.ZodString>;
+            categoryReason: z.ZodOptional<z.ZodString>;
+            memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                path: z.ZodString;
+                note: z.ZodString;
+            }, z.core.$strict>>>;
+        }, z.core.$strict>;
+        reason: z.ZodString;
+    }, z.core.$strict>, z.ZodObject<{
+        op: z.ZodLiteral<"group">;
+        paths: z.ZodArray<z.ZodString>;
+        group: z.ZodObject<{
+            name: z.ZodString;
+            memberRepresents: z.ZodString;
+            description: z.ZodString;
+            role: z.ZodEnum<{
+                metadata: "metadata";
+                data: "data";
+                index: "index";
+                reference: "reference";
+                documentation: "documentation";
+            }>;
+            category: z.ZodEnum<{
+                other: "other";
+                code: "code";
+                document: "document";
+                manifest: "manifest";
+                "chemical-structures": "chemical-structures";
+                "sequencing-reads": "sequencing-reads";
+                alignment: "alignment";
+                "variant-calls": "variant-calls";
+                "copy-number": "copy-number";
+                "structural-variants": "structural-variants";
+                "association-results": "association-results";
+                "regions-signal": "regions-signal";
+                "expression-matrix": "expression-matrix";
+                "single-cell-matrix": "single-cell-matrix";
+                methylation: "methylation";
+                proteomics: "proteomics";
+                metabolomics: "metabolomics";
+                cytometry: "cytometry";
+                imaging: "imaging";
+                "clinical-table": "clinical-table";
+                "sample-annotation": "sample-annotation";
+                "reference-data": "reference-data";
+            }>;
+            categoryLabel: z.ZodOptional<z.ZodString>;
+            subtype: z.ZodOptional<z.ZodString>;
+            categoryReason: z.ZodOptional<z.ZodString>;
+            memberAnnotations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                path: z.ZodString;
+                note: z.ZodString;
+            }, z.core.$strict>>>;
+        }, z.core.$strict>;
+    }, z.core.$strict>], "op">>;
+    dimensions: z.ZodOptional<z.ZodArray<z.ZodObject<{
         label: z.ZodString;
-        cardinality: z.ZodNumber;
-        exampleValues: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        category: z.ZodEnum<{
+            other: "other";
+            sex: "sex";
+            subject: "subject";
+            sample: "sample";
+            "organism-species": "organism-species";
+            "model-system": "model-system";
+            "cohort-arm": "cohort-arm";
+            "disease-state": "disease-state";
+            treatment: "treatment";
+            timepoint: "timepoint";
+            "tissue-site": "tissue-site";
+            "cell-type": "cell-type";
+            "genetic-perturbation": "genetic-perturbation";
+            "age-group": "age-group";
+            "developmental-stage": "developmental-stage";
+            environment: "environment";
+            "assay-modality": "assay-modality";
+            "assay-target": "assay-target";
+            "variant-origin": "variant-origin";
+            "sample-pairing": "sample-pairing";
+            "processing-level": "processing-level";
+            "assay-version": "assay-version";
+            batch: "batch";
+            replicate: "replicate";
+            "tool-variant": "tool-variant";
+            "library-prep": "library-prep";
+            "data-partition": "data-partition";
+        }>;
+        categoryLabel: z.ZodOptional<z.ZodString>;
+        scope: z.ZodOptional<z.ZodEnum<{
+            biological: "biological";
+            technical: "technical";
+        }>>;
         description: z.ZodOptional<z.ZodString>;
-    }, z.core.$strip>>>;
+        observations: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
+            kind: z.ZodLiteral<"slot">;
+            setId: z.ZodString;
+            slotId: z.ZodString;
+            note: z.ZodOptional<z.ZodString>;
+        }, z.core.$strict>, z.ZodObject<{
+            kind: z.ZodLiteral<"column">;
+            path: z.ZodString;
+            column: z.ZodString;
+            exampleValues: z.ZodArray<z.ZodString>;
+            distinctValues: z.ZodOptional<z.ZodNumber>;
+            checked: z.ZodOptional<z.ZodObject<{
+                matched: z.ZodNumber;
+                of: z.ZodNumber;
+            }, z.core.$strict>>;
+            checkedAgainst: z.ZodOptional<z.ZodString>;
+            note: z.ZodOptional<z.ZodString>;
+        }, z.core.$strict>, z.ZodObject<{
+            kind: z.ZodLiteral<"document">;
+            path: z.ZodString;
+            citation: z.ZodString;
+            statesCardinality: z.ZodOptional<z.ZodNumber>;
+            checked: z.ZodOptional<z.ZodObject<{
+                matched: z.ZodNumber;
+                of: z.ZodNumber;
+            }, z.core.$strict>>;
+            checkedAgainst: z.ZodOptional<z.ZodString>;
+            note: z.ZodOptional<z.ZodString>;
+        }, z.core.$strict>], "kind">>;
+        reconciliations: z.ZodOptional<z.ZodArray<z.ZodObject<{
+            note: z.ZodString;
+            delta: z.ZodOptional<z.ZodNumber>;
+        }, z.core.$strict>>>;
+        nestsUnder: z.ZodOptional<z.ZodObject<{
+            dimension: z.ZodString;
+            evidence: z.ZodString;
+        }, z.core.$strict>>;
+        treatmentReason: z.ZodOptional<z.ZodString>;
+    }, z.core.$strict>>>;
+    probes: z.ZodOptional<z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
+        probe: z.ZodEnum<{
+            subject: "subject";
+            sample: "sample";
+            "cohort-arm": "cohort-arm";
+            timepoint: "timepoint";
+            batch: "batch";
+        }>;
+        outcome: z.ZodLiteral<"found">;
+        dimension: z.ZodString;
+    }, z.core.$strict>, z.ZodObject<{
+        probe: z.ZodEnum<{
+            subject: "subject";
+            sample: "sample";
+            "cohort-arm": "cohort-arm";
+            timepoint: "timepoint";
+            batch: "batch";
+        }>;
+        outcome: z.ZodLiteral<"not-found">;
+        searched: z.ZodArray<z.ZodString>;
+        reason: z.ZodString;
+    }, z.core.$strict>, z.ZodObject<{
+        probe: z.ZodEnum<{
+            subject: "subject";
+            sample: "sample";
+            "cohort-arm": "cohort-arm";
+            timepoint: "timepoint";
+            batch: "batch";
+        }>;
+        outcome: z.ZodLiteral<"found-but-constant">;
+        value: z.ZodString;
+        evidence: z.ZodString;
+    }, z.core.$strict>, z.ZodObject<{
+        probe: z.ZodEnum<{
+            subject: "subject";
+            sample: "sample";
+            "cohort-arm": "cohort-arm";
+            timepoint: "timepoint";
+            batch: "batch";
+        }>;
+        outcome: z.ZodLiteral<"attested">;
+        citation: z.ZodString;
+        path: z.ZodString;
+    }, z.core.$strict>], "outcome">>>;
     analysisSummary: z.ZodString;
     domain: z.ZodString;
     subtype: z.ZodOptional<z.ZodString>;
@@ -135,9 +1001,9 @@ export declare const ProfilerOutputSchema: z.ZodObject<{
             inferred: "inferred";
         }>;
         confidence: z.ZodEnum<{
-            high: "high";
-            medium: "medium";
             low: "low";
+            medium: "medium";
+            high: "high";
         }>;
         notes: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
@@ -146,9 +1012,6 @@ export declare const ProfilerOutputSchema: z.ZodObject<{
     condition: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     accessions: z.ZodOptional<z.ZodArray<z.ZodString>>;
     experimentalDesign: z.ZodOptional<z.ZodString>;
-    qualityAssessment: z.ZodOptional<z.ZodObject<{
-        concerns: z.ZodArray<z.ZodString>;
-        strengths: z.ZodArray<z.ZodString>;
-    }, z.core.$strip>>;
-}, z.core.$strip>;
-export type ProfilerOutput = z.infer<typeof ProfilerOutputSchema>;
+    caveats: z.ZodOptional<z.ZodArray<z.ZodString>>;
+}, z.core.$strict>;
+export type ProfileSubmission = z.infer<typeof ProfileSubmissionSchema>;