@inflexa-ai/harness 0.45.0 → 0.46.0

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

@@ -40,27 +40,27 @@ export declare const MAX_CAVEATS = 10;
  * judge how much to trust a field and so this profiler can flag conflicts.
  */
 export declare const SubjectSourceEnum: z.ZodEnum<{
-    metadata: "metadata";
     document: "document";
     filename: "filename";
-    "user-context": "user-context";
     inferred: "inferred";
+    metadata: "metadata";
+    "user-context": "user-context";
 }>;
 export type SubjectSource = z.infer<typeof SubjectSourceEnum>;
 export declare const OrganismSchema: z.ZodObject<{
     scientificName: z.ZodString;
     taxonId: z.ZodString;
     source: z.ZodEnum<{
-        metadata: "metadata";
         document: "document";
         filename: "filename";
-        "user-context": "user-context";
         inferred: "inferred";
+        metadata: "metadata";
+        "user-context": "user-context";
     }>;
     confidence: z.ZodEnum<{
+        high: "high";
         low: "low";
         medium: "medium";
-        high: "high";
     }>;
     notes: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>;
@@ -82,35 +82,35 @@ export declare const GroupAnnotationSchema: z.ZodObject<{
     memberRepresents: z.ZodString;
     description: z.ZodString;
     role: z.ZodEnum<{
-        metadata: "metadata";
         data: "data";
+        documentation: "documentation";
         index: "index";
+        metadata: "metadata";
         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";
+        "chemical-structures": "chemical-structures";
+        "clinical-table": "clinical-table";
+        code: "code";
+        "copy-number": "copy-number";
+        cytometry: "cytometry";
+        document: "document";
         "expression-matrix": "expression-matrix";
-        "single-cell-matrix": "single-cell-matrix";
+        imaging: "imaging";
+        manifest: "manifest";
+        metabolomics: "metabolomics";
         methylation: "methylation";
+        other: "other";
         proteomics: "proteomics";
-        metabolomics: "metabolomics";
-        cytometry: "cytometry";
-        imaging: "imaging";
-        "clinical-table": "clinical-table";
-        "sample-annotation": "sample-annotation";
         "reference-data": "reference-data";
+        "regions-signal": "regions-signal";
+        "sample-annotation": "sample-annotation";
+        "sequencing-reads": "sequencing-reads";
+        "single-cell-matrix": "single-cell-matrix";
+        "structural-variants": "structural-variants";
+        "variant-calls": "variant-calls";
     }>;
     categoryLabel: z.ZodOptional<z.ZodString>;
     subtype: z.ZodOptional<z.ZodString>;
@@ -136,35 +136,35 @@ export declare const MenuOperationSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
         memberRepresents: z.ZodString;
         description: z.ZodString;
         role: z.ZodEnum<{
-            metadata: "metadata";
             data: "data";
+            documentation: "documentation";
             index: "index";
+            metadata: "metadata";
             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";
+            "chemical-structures": "chemical-structures";
+            "clinical-table": "clinical-table";
+            code: "code";
+            "copy-number": "copy-number";
+            cytometry: "cytometry";
+            document: "document";
             "expression-matrix": "expression-matrix";
-            "single-cell-matrix": "single-cell-matrix";
+            imaging: "imaging";
+            manifest: "manifest";
+            metabolomics: "metabolomics";
             methylation: "methylation";
+            other: "other";
             proteomics: "proteomics";
-            metabolomics: "metabolomics";
-            cytometry: "cytometry";
-            imaging: "imaging";
-            "clinical-table": "clinical-table";
-            "sample-annotation": "sample-annotation";
             "reference-data": "reference-data";
+            "regions-signal": "regions-signal";
+            "sample-annotation": "sample-annotation";
+            "sequencing-reads": "sequencing-reads";
+            "single-cell-matrix": "single-cell-matrix";
+            "structural-variants": "structural-variants";
+            "variant-calls": "variant-calls";
         }>;
         categoryLabel: z.ZodOptional<z.ZodString>;
         subtype: z.ZodOptional<z.ZodString>;
@@ -185,35 +185,35 @@ export declare const MenuOperationSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
             memberRepresents: z.ZodString;
             description: z.ZodString;
             role: z.ZodEnum<{
-                metadata: "metadata";
                 data: "data";
+                documentation: "documentation";
                 index: "index";
+                metadata: "metadata";
                 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";
+                "chemical-structures": "chemical-structures";
+                "clinical-table": "clinical-table";
+                code: "code";
+                "copy-number": "copy-number";
+                cytometry: "cytometry";
+                document: "document";
                 "expression-matrix": "expression-matrix";
-                "single-cell-matrix": "single-cell-matrix";
+                imaging: "imaging";
+                manifest: "manifest";
+                metabolomics: "metabolomics";
                 methylation: "methylation";
+                other: "other";
                 proteomics: "proteomics";
-                metabolomics: "metabolomics";
-                cytometry: "cytometry";
-                imaging: "imaging";
-                "clinical-table": "clinical-table";
-                "sample-annotation": "sample-annotation";
                 "reference-data": "reference-data";
+                "regions-signal": "regions-signal";
+                "sample-annotation": "sample-annotation";
+                "sequencing-reads": "sequencing-reads";
+                "single-cell-matrix": "single-cell-matrix";
+                "structural-variants": "structural-variants";
+                "variant-calls": "variant-calls";
             }>;
             categoryLabel: z.ZodOptional<z.ZodString>;
             subtype: z.ZodOptional<z.ZodString>;
@@ -233,35 +233,35 @@ export declare const MenuOperationSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
                 memberRepresents: z.ZodString;
                 description: z.ZodString;
                 role: z.ZodEnum<{
-                    metadata: "metadata";
                     data: "data";
+                    documentation: "documentation";
                     index: "index";
+                    metadata: "metadata";
                     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";
+                    "chemical-structures": "chemical-structures";
+                    "clinical-table": "clinical-table";
+                    code: "code";
+                    "copy-number": "copy-number";
+                    cytometry: "cytometry";
+                    document: "document";
                     "expression-matrix": "expression-matrix";
-                    "single-cell-matrix": "single-cell-matrix";
+                    imaging: "imaging";
+                    manifest: "manifest";
+                    metabolomics: "metabolomics";
                     methylation: "methylation";
+                    other: "other";
                     proteomics: "proteomics";
-                    metabolomics: "metabolomics";
-                    cytometry: "cytometry";
-                    imaging: "imaging";
-                    "clinical-table": "clinical-table";
-                    "sample-annotation": "sample-annotation";
                     "reference-data": "reference-data";
+                    "regions-signal": "regions-signal";
+                    "sample-annotation": "sample-annotation";
+                    "sequencing-reads": "sequencing-reads";
+                    "single-cell-matrix": "single-cell-matrix";
+                    "structural-variants": "structural-variants";
+                    "variant-calls": "variant-calls";
                 }>;
                 categoryLabel: z.ZodOptional<z.ZodString>;
                 subtype: z.ZodOptional<z.ZodString>;
@@ -277,35 +277,35 @@ export declare const MenuOperationSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
             memberRepresents: z.ZodString;
             description: z.ZodString;
             role: z.ZodEnum<{
-                metadata: "metadata";
                 data: "data";
+                documentation: "documentation";
                 index: "index";
+                metadata: "metadata";
                 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";
+                "chemical-structures": "chemical-structures";
+                "clinical-table": "clinical-table";
+                code: "code";
+                "copy-number": "copy-number";
+                cytometry: "cytometry";
+                document: "document";
                 "expression-matrix": "expression-matrix";
-                "single-cell-matrix": "single-cell-matrix";
+                imaging: "imaging";
+                manifest: "manifest";
+                metabolomics: "metabolomics";
                 methylation: "methylation";
+                other: "other";
                 proteomics: "proteomics";
-                metabolomics: "metabolomics";
-                cytometry: "cytometry";
-                imaging: "imaging";
-                "clinical-table": "clinical-table";
-                "sample-annotation": "sample-annotation";
                 "reference-data": "reference-data";
+                "regions-signal": "regions-signal";
+                "sample-annotation": "sample-annotation";
+                "sequencing-reads": "sequencing-reads";
+                "single-cell-matrix": "single-cell-matrix";
+                "structural-variants": "structural-variants";
+                "variant-calls": "variant-calls";
             }>;
             categoryLabel: z.ZodOptional<z.ZodString>;
             subtype: z.ZodOptional<z.ZodString>;
@@ -325,35 +325,35 @@ export declare const MenuOperationSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
         memberRepresents: z.ZodString;
         description: z.ZodString;
         role: z.ZodEnum<{
-            metadata: "metadata";
             data: "data";
+            documentation: "documentation";
             index: "index";
+            metadata: "metadata";
             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";
+            "chemical-structures": "chemical-structures";
+            "clinical-table": "clinical-table";
+            code: "code";
+            "copy-number": "copy-number";
+            cytometry: "cytometry";
+            document: "document";
             "expression-matrix": "expression-matrix";
-            "single-cell-matrix": "single-cell-matrix";
+            imaging: "imaging";
+            manifest: "manifest";
+            metabolomics: "metabolomics";
             methylation: "methylation";
+            other: "other";
             proteomics: "proteomics";
-            metabolomics: "metabolomics";
-            cytometry: "cytometry";
-            imaging: "imaging";
-            "clinical-table": "clinical-table";
-            "sample-annotation": "sample-annotation";
             "reference-data": "reference-data";
+            "regions-signal": "regions-signal";
+            "sample-annotation": "sample-annotation";
+            "sequencing-reads": "sequencing-reads";
+            "single-cell-matrix": "single-cell-matrix";
+            "structural-variants": "structural-variants";
+            "variant-calls": "variant-calls";
         }>;
         categoryLabel: z.ZodOptional<z.ZodString>;
         subtype: z.ZodOptional<z.ZodString>;
@@ -372,35 +372,35 @@ export declare const MenuOperationSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
         memberRepresents: z.ZodString;
         description: z.ZodString;
         role: z.ZodEnum<{
-            metadata: "metadata";
             data: "data";
+            documentation: "documentation";
             index: "index";
+            metadata: "metadata";
             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";
+            "chemical-structures": "chemical-structures";
+            "clinical-table": "clinical-table";
+            code: "code";
+            "copy-number": "copy-number";
+            cytometry: "cytometry";
+            document: "document";
             "expression-matrix": "expression-matrix";
-            "single-cell-matrix": "single-cell-matrix";
+            imaging: "imaging";
+            manifest: "manifest";
+            metabolomics: "metabolomics";
             methylation: "methylation";
+            other: "other";
             proteomics: "proteomics";
-            metabolomics: "metabolomics";
-            cytometry: "cytometry";
-            imaging: "imaging";
-            "clinical-table": "clinical-table";
-            "sample-annotation": "sample-annotation";
             "reference-data": "reference-data";
+            "regions-signal": "regions-signal";
+            "sample-annotation": "sample-annotation";
+            "sequencing-reads": "sequencing-reads";
+            "single-cell-matrix": "single-cell-matrix";
+            "structural-variants": "structural-variants";
+            "variant-calls": "variant-calls";
         }>;
         categoryLabel: z.ZodOptional<z.ZodString>;
         subtype: z.ZodOptional<z.ZodString>;
@@ -459,33 +459,33 @@ export type Observation = z.infer<typeof ObservationSchema>;
 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";
+        "cell-type": "cell-type";
+        "cohort-arm": "cohort-arm";
+        "data-partition": "data-partition";
+        "developmental-stage": "developmental-stage";
+        "disease-state": "disease-state";
+        environment: "environment";
+        "genetic-perturbation": "genetic-perturbation";
+        "library-prep": "library-prep";
+        "model-system": "model-system";
+        "organism-species": "organism-species";
+        other: "other";
+        "processing-level": "processing-level";
         replicate: "replicate";
+        sample: "sample";
+        "sample-pairing": "sample-pairing";
+        sex: "sex";
+        subject: "subject";
+        timepoint: "timepoint";
+        "tissue-site": "tissue-site";
         "tool-variant": "tool-variant";
-        "library-prep": "library-prep";
-        "data-partition": "data-partition";
+        treatment: "treatment";
+        "variant-origin": "variant-origin";
     }>;
     categoryLabel: z.ZodOptional<z.ZodString>;
     scope: z.ZodOptional<z.ZodEnum<{
@@ -540,43 +540,43 @@ export type ProfileDimension = z.infer<typeof DimensionSchema>;
  */
 export declare const ProbeReportSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
     probe: z.ZodEnum<{
-        subject: "subject";
-        sample: "sample";
+        batch: "batch";
         "cohort-arm": "cohort-arm";
+        sample: "sample";
+        subject: "subject";
         timepoint: "timepoint";
-        batch: "batch";
     }>;
     outcome: z.ZodLiteral<"found">;
     dimension: z.ZodString;
 }, z.core.$strict>, z.ZodObject<{
     probe: z.ZodEnum<{
-        subject: "subject";
-        sample: "sample";
+        batch: "batch";
         "cohort-arm": "cohort-arm";
+        sample: "sample";
+        subject: "subject";
         timepoint: "timepoint";
-        batch: "batch";
     }>;
     outcome: z.ZodLiteral<"not-found">;
     searched: z.ZodArray<z.ZodString>;
     reason: z.ZodString;
 }, z.core.$strict>, z.ZodObject<{
     probe: z.ZodEnum<{
-        subject: "subject";
-        sample: "sample";
+        batch: "batch";
         "cohort-arm": "cohort-arm";
+        sample: "sample";
+        subject: "subject";
         timepoint: "timepoint";
-        batch: "batch";
     }>;
     outcome: z.ZodLiteral<"found-but-constant">;
     value: z.ZodString;
     evidence: z.ZodString;
 }, z.core.$strict>, z.ZodObject<{
     probe: z.ZodEnum<{
-        subject: "subject";
-        sample: "sample";
+        batch: "batch";
         "cohort-arm": "cohort-arm";
+        sample: "sample";
+        subject: "subject";
         timepoint: "timepoint";
-        batch: "batch";
     }>;
     outcome: z.ZodLiteral<"attested">;
     citation: z.ZodString;
@@ -592,35 +592,35 @@ export declare const ProfileSubmissionSchema: z.ZodObject<{
             memberRepresents: z.ZodString;
             description: z.ZodString;
             role: z.ZodEnum<{
-                metadata: "metadata";
                 data: "data";
+                documentation: "documentation";
                 index: "index";
+                metadata: "metadata";
                 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";
+                "chemical-structures": "chemical-structures";
+                "clinical-table": "clinical-table";
+                code: "code";
+                "copy-number": "copy-number";
+                cytometry: "cytometry";
+                document: "document";
                 "expression-matrix": "expression-matrix";
-                "single-cell-matrix": "single-cell-matrix";
+                imaging: "imaging";
+                manifest: "manifest";
+                metabolomics: "metabolomics";
                 methylation: "methylation";
+                other: "other";
                 proteomics: "proteomics";
-                metabolomics: "metabolomics";
-                cytometry: "cytometry";
-                imaging: "imaging";
-                "clinical-table": "clinical-table";
-                "sample-annotation": "sample-annotation";
                 "reference-data": "reference-data";
+                "regions-signal": "regions-signal";
+                "sample-annotation": "sample-annotation";
+                "sequencing-reads": "sequencing-reads";
+                "single-cell-matrix": "single-cell-matrix";
+                "structural-variants": "structural-variants";
+                "variant-calls": "variant-calls";
             }>;
             categoryLabel: z.ZodOptional<z.ZodString>;
             subtype: z.ZodOptional<z.ZodString>;
@@ -641,35 +641,35 @@ export declare const ProfileSubmissionSchema: z.ZodObject<{
                 memberRepresents: z.ZodString;
                 description: z.ZodString;
                 role: z.ZodEnum<{
-                    metadata: "metadata";
                     data: "data";
+                    documentation: "documentation";
                     index: "index";
+                    metadata: "metadata";
                     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";
+                    "chemical-structures": "chemical-structures";
+                    "clinical-table": "clinical-table";
+                    code: "code";
+                    "copy-number": "copy-number";
+                    cytometry: "cytometry";
+                    document: "document";
                     "expression-matrix": "expression-matrix";
-                    "single-cell-matrix": "single-cell-matrix";
+                    imaging: "imaging";
+                    manifest: "manifest";
+                    metabolomics: "metabolomics";
                     methylation: "methylation";
+                    other: "other";
                     proteomics: "proteomics";
-                    metabolomics: "metabolomics";
-                    cytometry: "cytometry";
-                    imaging: "imaging";
-                    "clinical-table": "clinical-table";
-                    "sample-annotation": "sample-annotation";
                     "reference-data": "reference-data";
+                    "regions-signal": "regions-signal";
+                    "sample-annotation": "sample-annotation";
+                    "sequencing-reads": "sequencing-reads";
+                    "single-cell-matrix": "single-cell-matrix";
+                    "structural-variants": "structural-variants";
+                    "variant-calls": "variant-calls";
                 }>;
                 categoryLabel: z.ZodOptional<z.ZodString>;
                 subtype: z.ZodOptional<z.ZodString>;
@@ -689,35 +689,35 @@ export declare const ProfileSubmissionSchema: z.ZodObject<{
                     memberRepresents: z.ZodString;
                     description: z.ZodString;
                     role: z.ZodEnum<{
-                        metadata: "metadata";
                         data: "data";
+                        documentation: "documentation";
                         index: "index";
+                        metadata: "metadata";
                         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";
+                        "chemical-structures": "chemical-structures";
+                        "clinical-table": "clinical-table";
+                        code: "code";
+                        "copy-number": "copy-number";
+                        cytometry: "cytometry";
+                        document: "document";
                         "expression-matrix": "expression-matrix";
-                        "single-cell-matrix": "single-cell-matrix";
+                        imaging: "imaging";
+                        manifest: "manifest";
+                        metabolomics: "metabolomics";
                         methylation: "methylation";
+                        other: "other";
                         proteomics: "proteomics";
-                        metabolomics: "metabolomics";
-                        cytometry: "cytometry";
-                        imaging: "imaging";
-                        "clinical-table": "clinical-table";
-                        "sample-annotation": "sample-annotation";
                         "reference-data": "reference-data";
+                        "regions-signal": "regions-signal";
+                        "sample-annotation": "sample-annotation";
+                        "sequencing-reads": "sequencing-reads";
+                        "single-cell-matrix": "single-cell-matrix";
+                        "structural-variants": "structural-variants";
+                        "variant-calls": "variant-calls";
                     }>;
                     categoryLabel: z.ZodOptional<z.ZodString>;
                     subtype: z.ZodOptional<z.ZodString>;
@@ -733,35 +733,35 @@ export declare const ProfileSubmissionSchema: z.ZodObject<{
                 memberRepresents: z.ZodString;
                 description: z.ZodString;
                 role: z.ZodEnum<{
-                    metadata: "metadata";
                     data: "data";
+                    documentation: "documentation";
                     index: "index";
+                    metadata: "metadata";
                     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";
+                    "chemical-structures": "chemical-structures";
+                    "clinical-table": "clinical-table";
+                    code: "code";
+                    "copy-number": "copy-number";
+                    cytometry: "cytometry";
+                    document: "document";
                     "expression-matrix": "expression-matrix";
-                    "single-cell-matrix": "single-cell-matrix";
+                    imaging: "imaging";
+                    manifest: "manifest";
+                    metabolomics: "metabolomics";
                     methylation: "methylation";
+                    other: "other";
                     proteomics: "proteomics";
-                    metabolomics: "metabolomics";
-                    cytometry: "cytometry";
-                    imaging: "imaging";
-                    "clinical-table": "clinical-table";
-                    "sample-annotation": "sample-annotation";
                     "reference-data": "reference-data";
+                    "regions-signal": "regions-signal";
+                    "sample-annotation": "sample-annotation";
+                    "sequencing-reads": "sequencing-reads";
+                    "single-cell-matrix": "single-cell-matrix";
+                    "structural-variants": "structural-variants";
+                    "variant-calls": "variant-calls";
                 }>;
                 categoryLabel: z.ZodOptional<z.ZodString>;
                 subtype: z.ZodOptional<z.ZodString>;
@@ -781,35 +781,35 @@ export declare const ProfileSubmissionSchema: z.ZodObject<{
             memberRepresents: z.ZodString;
             description: z.ZodString;
             role: z.ZodEnum<{
-                metadata: "metadata";
                 data: "data";
+                documentation: "documentation";
                 index: "index";
+                metadata: "metadata";
                 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";
+                "chemical-structures": "chemical-structures";
+                "clinical-table": "clinical-table";
+                code: "code";
+                "copy-number": "copy-number";
+                cytometry: "cytometry";
+                document: "document";
                 "expression-matrix": "expression-matrix";
-                "single-cell-matrix": "single-cell-matrix";
+                imaging: "imaging";
+                manifest: "manifest";
+                metabolomics: "metabolomics";
                 methylation: "methylation";
+                other: "other";
                 proteomics: "proteomics";
-                metabolomics: "metabolomics";
-                cytometry: "cytometry";
-                imaging: "imaging";
-                "clinical-table": "clinical-table";
-                "sample-annotation": "sample-annotation";
                 "reference-data": "reference-data";
+                "regions-signal": "regions-signal";
+                "sample-annotation": "sample-annotation";
+                "sequencing-reads": "sequencing-reads";
+                "single-cell-matrix": "single-cell-matrix";
+                "structural-variants": "structural-variants";
+                "variant-calls": "variant-calls";
             }>;
             categoryLabel: z.ZodOptional<z.ZodString>;
             subtype: z.ZodOptional<z.ZodString>;
@@ -828,35 +828,35 @@ export declare const ProfileSubmissionSchema: z.ZodObject<{
             memberRepresents: z.ZodString;
             description: z.ZodString;
             role: z.ZodEnum<{
-                metadata: "metadata";
                 data: "data";
+                documentation: "documentation";
                 index: "index";
+                metadata: "metadata";
                 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";
+                "chemical-structures": "chemical-structures";
+                "clinical-table": "clinical-table";
+                code: "code";
+                "copy-number": "copy-number";
+                cytometry: "cytometry";
+                document: "document";
                 "expression-matrix": "expression-matrix";
-                "single-cell-matrix": "single-cell-matrix";
+                imaging: "imaging";
+                manifest: "manifest";
+                metabolomics: "metabolomics";
                 methylation: "methylation";
+                other: "other";
                 proteomics: "proteomics";
-                metabolomics: "metabolomics";
-                cytometry: "cytometry";
-                imaging: "imaging";
-                "clinical-table": "clinical-table";
-                "sample-annotation": "sample-annotation";
                 "reference-data": "reference-data";
+                "regions-signal": "regions-signal";
+                "sample-annotation": "sample-annotation";
+                "sequencing-reads": "sequencing-reads";
+                "single-cell-matrix": "single-cell-matrix";
+                "structural-variants": "structural-variants";
+                "variant-calls": "variant-calls";
             }>;
             categoryLabel: z.ZodOptional<z.ZodString>;
             subtype: z.ZodOptional<z.ZodString>;
@@ -870,33 +870,33 @@ export declare const ProfileSubmissionSchema: z.ZodObject<{
     dimensions: z.ZodOptional<z.ZodArray<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";
+            "cell-type": "cell-type";
+            "cohort-arm": "cohort-arm";
+            "data-partition": "data-partition";
+            "developmental-stage": "developmental-stage";
+            "disease-state": "disease-state";
+            environment: "environment";
+            "genetic-perturbation": "genetic-perturbation";
+            "library-prep": "library-prep";
+            "model-system": "model-system";
+            "organism-species": "organism-species";
+            other: "other";
+            "processing-level": "processing-level";
             replicate: "replicate";
+            sample: "sample";
+            "sample-pairing": "sample-pairing";
+            sex: "sex";
+            subject: "subject";
+            timepoint: "timepoint";
+            "tissue-site": "tissue-site";
             "tool-variant": "tool-variant";
-            "library-prep": "library-prep";
-            "data-partition": "data-partition";
+            treatment: "treatment";
+            "variant-origin": "variant-origin";
         }>;
         categoryLabel: z.ZodOptional<z.ZodString>;
         scope: z.ZodOptional<z.ZodEnum<{
@@ -945,43 +945,43 @@ export declare const ProfileSubmissionSchema: z.ZodObject<{
     }, z.core.$strict>>>;
     probes: z.ZodOptional<z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
         probe: z.ZodEnum<{
-            subject: "subject";
-            sample: "sample";
+            batch: "batch";
             "cohort-arm": "cohort-arm";
+            sample: "sample";
+            subject: "subject";
             timepoint: "timepoint";
-            batch: "batch";
         }>;
         outcome: z.ZodLiteral<"found">;
         dimension: z.ZodString;
     }, z.core.$strict>, z.ZodObject<{
         probe: z.ZodEnum<{
-            subject: "subject";
-            sample: "sample";
+            batch: "batch";
             "cohort-arm": "cohort-arm";
+            sample: "sample";
+            subject: "subject";
             timepoint: "timepoint";
-            batch: "batch";
         }>;
         outcome: z.ZodLiteral<"not-found">;
         searched: z.ZodArray<z.ZodString>;
         reason: z.ZodString;
     }, z.core.$strict>, z.ZodObject<{
         probe: z.ZodEnum<{
-            subject: "subject";
-            sample: "sample";
+            batch: "batch";
             "cohort-arm": "cohort-arm";
+            sample: "sample";
+            subject: "subject";
             timepoint: "timepoint";
-            batch: "batch";
         }>;
         outcome: z.ZodLiteral<"found-but-constant">;
         value: z.ZodString;
         evidence: z.ZodString;
     }, z.core.$strict>, z.ZodObject<{
         probe: z.ZodEnum<{
-            subject: "subject";
-            sample: "sample";
+            batch: "batch";
             "cohort-arm": "cohort-arm";
+            sample: "sample";
+            subject: "subject";
             timepoint: "timepoint";
-            batch: "batch";
         }>;
         outcome: z.ZodLiteral<"attested">;
         citation: z.ZodString;
@@ -994,16 +994,16 @@ export declare const ProfileSubmissionSchema: z.ZodObject<{
         scientificName: z.ZodString;
         taxonId: z.ZodString;
         source: z.ZodEnum<{
-            metadata: "metadata";
             document: "document";
             filename: "filename";
-            "user-context": "user-context";
             inferred: "inferred";
+            metadata: "metadata";
+            "user-context": "user-context";
         }>;
         confidence: z.ZodEnum<{
+            high: "high";
             low: "low";
             medium: "medium";
-            high: "high";
         }>;
         notes: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
@@ -1015,3 +1015,48 @@ export declare const ProfileSubmissionSchema: z.ZodObject<{
     caveats: z.ZodOptional<z.ZodArray<z.ZodString>>;
 }, z.core.$strict>;
 export type ProfileSubmission = z.infer<typeof ProfileSubmissionSchema>;
+/**
+ * What `resolveProfileSubmission` resolves, as distinct from what an agent may submit.
+ *
+ * A replay (`src/tasks/data-profile-absorb.ts`) carries a persisted annotation through
+ * unchanged, so an id a retired vocabulary served can re-enter here. The agent-facing
+ * schemas above stay strict; the resolver reads `role` and `category` as opaque strings,
+ * so the input view widens exactly those fields.
+ */
+export type GroupAnnotationInput = Omit<GroupAnnotation, "role" | "category"> & {
+    role: string;
+    category: string;
+};
+export type ProfileDimensionInput = Omit<ProfileDimension, "category"> & {
+    category: string;
+};
+type WithInputAnnotation<T> = T extends {
+    group: GroupAnnotation;
+} ? Omit<T, "group"> & {
+    group: GroupAnnotationInput;
+} : T;
+type SplitBy = Extract<MenuOperation, {
+    op: "split";
+}>["by"];
+type SplitByInput = WithInputAnnotation<Extract<SplitBy, {
+    kind: "slot";
+}>> | (Omit<Extract<SplitBy, {
+    kind: "values";
+}>, "groups" | "rest"> & {
+    groups: WithInputAnnotation<Extract<SplitBy, {
+        kind: "values";
+    }>["groups"][number]>[];
+    rest?: GroupAnnotationInput;
+});
+export type MenuOperationInput = WithInputAnnotation<Extract<MenuOperation, {
+    op: "use" | "merge" | "group";
+}>> | (Omit<Extract<MenuOperation, {
+    op: "split";
+}>, "by"> & {
+    by: SplitByInput;
+});
+export type ProfileSubmissionInput = Omit<ProfileSubmission, "operations" | "dimensions"> & {
+    operations: MenuOperationInput[];
+    dimensions?: ProfileDimensionInput[];
+};
+export {};