@milaboratories/pl-model-common 1.48.0 → 1.49.0

package/dist/drivers/pframe/spec/selectors.d.ts

@@ -1,6 +1,7 @@
 import { AxisId, AxisValueType, Domain, PColumnSpec, ValueType } from "./spec.js";
 import { MultiColumnSelector } from "../spec_driver.js";
 import { PObjectSpec } from "../../../pool/spec.js";
+import "../../../pool/index.js";
 //#region src/drivers/pframe/spec/selectors.d.ts
 /**
  * Defines a pattern for matching axes within the PFrame data model.
@@ -19,7 +20,7 @@ import { PObjectSpec } from "../../../pool/spec.js";
  * stricter matching semantics (StringMatcher-based) and a unified approach
  * to working with columns, including domain and annotation matching.
  */
-interface LegacyAxisSelector {
+export interface LegacyAxisSelector {
   /**
    * Optional value type to match against.
    * When specified, only axes with this exact type will match.
@@ -47,7 +48,7 @@ interface LegacyAxisSelector {
   contextDomain?: Record<string, string>;
 }
 /** Single axis selector */
-interface SingleAxisSelector {
+export interface SingleAxisSelector {
   /** Axis name (required) */
   name: string;
   /** Axis type (optional) */
@@ -60,7 +61,7 @@ interface SingleAxisSelector {
   parentAxes?: SingleAxisSelector[];
 }
 /** Qualification applied to a single axis to make it compatible during integration. */
-interface AxisQualification {
+export interface AxisQualification {
   /** Axis selector identifying which axis is qualified. */
   readonly axis: SingleAxisSelector;
   /** Additional context domain entries applied to the axis. */
@@ -70,7 +71,7 @@ interface AxisQualification {
  * Reference to an axis by its numerical index within the anchor column's axes array
  * Format: [anchorId, axisIndex]
  */
-type AnchorAxisRefByIdx = {
+export type AnchorAxisRefByIdx = {
   anchor: string;
   idx: number;
 };
@@ -78,7 +79,7 @@ type AnchorAxisRefByIdx = {
  * Reference to an axis by its name within the anchor column
  * Format: [anchorId, axisName]
  */
-type AnchorAxisRefByName = {
+export type AnchorAxisRefByName = {
   anchor: string;
   name: string;
 };
@@ -86,41 +87,41 @@ type AnchorAxisRefByName = {
  * Reference to an axis using an AxisId matcher within the anchor
  * Format: [anchorId, axisMatcher]
  */
-type AnchorAxisRefByMatcher = {
+export type AnchorAxisRefByMatcher = {
   anchor: string;
   id: AxisId;
 };
 /**
  * Basic anchor axis reference that can be either by index or a direct AxisId
  */
-type AnchorAxisIdOrRefBasic = AnchorAxisRefByIdx | AxisId;
+export type AnchorAxisIdOrRefBasic = AnchorAxisRefByIdx | AxisId;
 /** Union of all possible ways to reference an axis in an anchored context  */
-type AnchorAxisRef = AnchorAxisRefByIdx | AnchorAxisRefByName | AnchorAxisRefByMatcher;
+export type AnchorAxisRef = AnchorAxisRefByIdx | AnchorAxisRefByName | AnchorAxisRefByMatcher;
 /** Reference to a domain value through an anchor */
-type AnchorDomainRef = {
+export type AnchorDomainRef = {
   anchor: string;
 };
 /**
  * Domain value that can be either a direct string value or a reference to a domain through an anchor
  * Used to establish domain context that can be resolved relative to other anchored columns
  */
-type ADomain = string | AnchorDomainRef;
+export type ADomain = string | AnchorDomainRef;
 /**
  * Axis identifier that can be either a direct AxisId or a reference to an axis through an anchor
  * Allows referring to axes in a way that can be resolved in different contexts
  */
-type AAxisSelector = LegacyAxisSelector | AnchorAxisRef;
+export type AAxisSelector = LegacyAxisSelector | AnchorAxisRef;
 /**
  * Match resolution strategy for PColumns
  * Specifies how to handle when multiple columns match the criteria
  * (default is "expectSingle")
  */
-type AnchoredColumnMatchStrategy = "expectSingle" | "expectMultiple" | "takeFirst";
+export type AnchoredColumnMatchStrategy = "expectSingle" | "expectMultiple" | "takeFirst";
 /**
  * Matcher for PColumns in an anchored context
  * Supports partial matching on axes, allowing for flexible column discovery
  */
-interface AnchoredPColumnSelector {
+export interface AnchoredPColumnSelector {
   /** Optional name of the column to match; can't be used together with namePattern */
   name?: string;
   /** Optional regexp pattern for column name matching; can't be used together with name */
@@ -151,7 +152,7 @@ interface AnchoredPColumnSelector {
 /**
  * Matcher for PColumns in a non-anchored context
  */
-interface PColumnSelector extends AnchoredPColumnSelector {
+export interface PColumnSelector extends AnchoredPColumnSelector {
   domainAnchor?: never;
   domain?: Record<string, string>;
   contextDomainAnchor?: never;
@@ -163,7 +164,7 @@ interface PColumnSelector extends AnchoredPColumnSelector {
  * Unlike APColumnMatcher, this requires exact matches on domain and axes
  * @deprecated This is part of the legacy column matching API. The new Columns API (see sdk/model/src/columns/) now handles column and axis
  */
-interface AnchoredPColumnId extends AnchoredPColumnSelector {
+export interface AnchoredPColumnId extends AnchoredPColumnSelector {
   /** Name is required for exact column identification */
   name: string;
   /** No namePattern in ID */
@@ -186,7 +187,7 @@ interface AnchoredPColumnId extends AnchoredPColumnSelector {
  * @param id - The value to check
  * @returns True if the value is an anchored column identifier, false otherwise
  */
-declare function isAnchoredPColumnId(id: unknown): id is AnchoredPColumnId;
+export declare function isAnchoredPColumnId(id: unknown): id is AnchoredPColumnId;
 /**
  * Determines if an axis ID matches an axis selector.
  *
@@ -194,7 +195,7 @@ declare function isAnchoredPColumnId(id: unknown): id is AnchoredPColumnId;
  * @param axis - The AxisId to check against the selector
  * @returns true if the AxisId matches all specified criteria in the selector, false otherwise
  */
-declare function matchAxis(selector: LegacyAxisSelector, axis: AxisId): boolean;
+export declare function matchAxis(selector: LegacyAxisSelector, axis: AxisId): boolean;
 /**
  * Determines if a given PColumnSpec matches a selector.
  *
@@ -202,21 +203,20 @@ declare function matchAxis(selector: LegacyAxisSelector, axis: AxisId): boolean;
  * @param selector - The selector criteria to match against
  * @returns true if the PColumnSpec matches all criteria in the selector, false otherwise
  */
-declare function matchPColumn(pcolumn: PColumnSpec, selector: PColumnSelector): boolean;
+export declare function matchPColumn(pcolumn: PColumnSpec, selector: PColumnSelector): boolean;
 /**
  * Convert a predicate or array of selectors to a single predicate function
  * @param predicateOrSelectors - Either a function that takes a PColumnSpec and returns a boolean,
  *                              or an array of PColumnSelectors, or a single PColumnSelector
  * @returns A function that takes a PColumnSpec and returns a boolean
  */
-declare function legacyColumnSelectorsToPredicate(predicateOrSelectors: PColumnSelector | PColumnSelector[]): (spec: PObjectSpec) => boolean;
+export declare function legacyColumnSelectorsToPredicate(predicateOrSelectors: PColumnSelector | PColumnSelector[]): (spec: PObjectSpec) => boolean;
 /** Match a {@link PColumnSpec} against a {@link MultiColumnSelector}. */
-declare function matchMultiColumnSelector(spec: PColumnSpec, selector: MultiColumnSelector): boolean;
+export declare function matchMultiColumnSelector(spec: PColumnSpec, selector: MultiColumnSelector): boolean;
 /**
  * Convert a {@link MultiColumnSelector} (or array; selectors OR-ed) to a predicate.
  * Non-PColumn specs always return false.
  */
-declare function multiColumnSelectorsToPredicate(selectors: MultiColumnSelector | MultiColumnSelector[]): (spec: PObjectSpec) => boolean;
+export declare function multiColumnSelectorsToPredicate(selectors: MultiColumnSelector | MultiColumnSelector[]): (spec: PObjectSpec) => boolean;
 //#endregion
-export { AAxisSelector, ADomain, AnchorAxisIdOrRefBasic, AnchorAxisRef, AnchorAxisRefByIdx, AnchorAxisRefByMatcher, AnchorAxisRefByName, AnchorDomainRef, AnchoredColumnMatchStrategy, AnchoredPColumnId, AnchoredPColumnSelector, AxisQualification, LegacyAxisSelector, PColumnSelector, SingleAxisSelector, isAnchoredPColumnId, legacyColumnSelectorsToPredicate, matchAxis, matchMultiColumnSelector, matchPColumn, multiColumnSelectorsToPredicate };
 //# sourceMappingURL=selectors.d.ts.map

package/dist/drivers/pframe/spec/selectors.d.ts.map

@@ -1 +1 @@
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package/dist/drivers/pframe/spec/spec.cjs

@@ -39,6 +39,36 @@ const Domain = {
 		ScClonotypeChain: { Index: "pl7.app/vdj/scClonotypeChain/index" }
 	}
 };
+/**
+* Domain keys whose value is the id of a block, rather than a qualifier of the data.
+*
+* Applying a template repoints these at the blocks of the project being built: an axis a block
+* produced names that block in its domain, so an axis left naming the exported-from project
+* resolves to nothing. Listing the keys is what makes that safe — a template's entry ids are
+* arbitrary non-empty strings, so a hand-written template may name an entry `closest`, and a
+* qualifier that happens to read `closest` must not be mistaken for a reference to it.
+*
+* A key absent from here is simply left alone, which is the behaviour from before relocation
+* reached domains at all. Adding one is therefore safe; omitting one costs only that a template
+* carrying it applies still pointing at the project it came from.
+*/
+const BlockScopedDomain = /* @__PURE__ */ new Set([
+	"pl7.app/blockId",
+	"pl7.app/block",
+	"pl7.app/redefined-by",
+	"pl7.app/annotationRunId",
+	"pl7.app/clonotypeAnnotationRunId",
+	"pl7.app/clustering/blockId",
+	"pl7.app/umap/blockId",
+	"pl7.app/peptide/extractionRunId",
+	"pl7.app/repertoire/extractionRunId",
+	"pl7.app/antibodyVariantDesigner/designRunId",
+	"pl7.app/vdj/clonotypingRunId",
+	"pl7.app/vdj/clustering/blockId",
+	"pl7.app/vdj/integration/blockId",
+	"pl7.app/vdj/spatiotemporalAnalysis/blockId",
+	"pl7.app/vdj/libraryId"
+]);
 const DomainJson = {};
 function readDomain(spec, key) {
 	return readMetadata(spec?.domain, key);
@@ -390,6 +420,7 @@ function isAxisId(id) {
 //#endregion
 exports.Annotation = Annotation;
 exports.AnnotationJson = AnnotationJson;
+exports.BlockScopedDomain = BlockScopedDomain;
 exports.Domain = Domain;
 exports.DomainJson = DomainJson;
 exports.PAxisName = PAxisName;

package/dist/drivers/pframe/spec/spec.cjs.map

@@ -1 +1 @@
-{"version":3,"file":"spec.cjs","names":["ensureError","z","canonicalizeJson"],"sources":["../../../../src/drivers/pframe/spec/spec.ts"],"sourcesContent":["import { ensureError } from \"../../../errors\";\nimport { canonicalizeJson, type CanonicalizedJson, type StringifiedJson } from \"../../../json\";\nimport type { PObject, PObjectId, PObjectSpec } from \"../../../pool\";\nimport { z } from \"zod\";\n\nexport const ValueType = {\n  Int: \"Int\",\n  Long: \"Long\",\n  Float: \"Float\",\n  Double: \"Double\",\n  String: \"String\",\n  Bytes: \"Bytes\",\n} as const;\n\nexport type AxisValueType = Extract<ValueType, \"Int\" | \"Long\" | \"String\">;\nexport type ColumnValueType = ValueType;\n\n/** PFrame columns and axes within them may store one of these types. */\nexport type ValueType = (typeof ValueType)[keyof typeof ValueType];\n\nexport type Metadata = Record<string, string>;\n\nexport function readMetadata<U extends Metadata, T extends keyof U = keyof U>(\n  metadata: Metadata | undefined,\n  key: T,\n): U[T] | undefined {\n  return (metadata as U | undefined)?.[key];\n}\n\ntype MetadataJsonImpl<M> = {\n  [P in keyof M as M[P] extends StringifiedJson ? P : never]: M[P] extends StringifiedJson<infer U>\n    ? z.ZodType<U>\n    : never;\n};\nexport type MetadataJson<M> = MetadataJsonImpl<Required<M>>;\n\nexport function readMetadataJsonOrThrow<M extends Metadata, T extends keyof MetadataJson<M>>(\n  metadata: Metadata | undefined,\n  metadataJson: MetadataJson<M>,\n  key: T,\n  methodNameInError: string = \"readMetadataJsonOrThrow\",\n): z.infer<MetadataJson<M>[T]> | undefined {\n  const json = readMetadata<M, T>(metadata, key);\n  if (json === undefined) return undefined;\n\n  const schema = metadataJson[key];\n  try {\n    const value = JSON.parse(json);\n    return schema.parse(value);\n  } catch (error: unknown) {\n    throw new Error(\n      `${methodNameInError} failed, ` +\n        `key: ${String(key)}, ` +\n        `value: ${json}, ` +\n        `error: ${ensureError(error)}`,\n    );\n  }\n}\n\nexport function readMetadataJson<M extends Metadata, T extends keyof MetadataJson<M>>(\n  metadata: Metadata | undefined,\n  metadataJson: MetadataJson<M>,\n  key: T,\n): z.infer<MetadataJson<M>[T]> | undefined {\n  try {\n    return readMetadataJsonOrThrow(metadata, metadataJson, key);\n  } catch {\n    return undefined; // treat invalid values as unset\n  }\n}\n\n/// Well-known domains\nexport const Domain = {\n  Alphabet: \"pl7.app/alphabet\",\n  BlockId: \"pl7.app/blockId\",\n  VDJ: {\n    Clustering: {\n      BlockId: \"pl7.app/vdj/clustering/blockId\",\n    },\n    ScClonotypeChain: {\n      Index: \"pl7.app/vdj/scClonotypeChain/index\",\n    },\n  },\n} as const;\n\nexport type Domain = Metadata &\n  Partial<{\n    [Domain.Alphabet]: \"nucleotide\" | \"aminoacid\" | (string & {});\n    [Domain.BlockId]: string;\n    [Domain.VDJ.ScClonotypeChain.Index]: \"primary\" | \"secondary\" | (string & {});\n  }>;\n\nexport type DomainJson = MetadataJson<Domain>;\nexport const DomainJson: DomainJson = {};\n\n/// Helper function for reading plain domain values\nexport function readDomain<T extends keyof Domain>(\n  spec: { domain?: Metadata | undefined } | undefined,\n  key: T,\n): Domain[T] | undefined {\n  return readMetadata<Domain, T>(spec?.domain, key);\n}\n\n/// Helper function for reading json-encoded domain values, throws on JSON parsing error\nexport function readDomainJsonOrThrow<T extends keyof DomainJson>(\n  spec: { domain?: Metadata | undefined } | undefined,\n  key: T,\n): z.infer<DomainJson[T]> | undefined {\n  return readMetadataJsonOrThrow<Domain, T>(spec?.domain, DomainJson, key, \"readDomainJsonOrThrow\");\n}\n\n/// Helper function for reading json-encoded domain values, returns undefined on JSON parsing error\nexport function readDomainJson<T extends keyof DomainJson>(\n  spec: { domain?: Metadata | undefined } | undefined,\n  key: T,\n): z.infer<DomainJson[T]> | undefined {\n  return readMetadataJson<Domain, T>(spec?.domain, DomainJson, key);\n}\n\n/// Well-known annotations\nexport const Annotation = {\n  AxisNature: \"pl7.app/axisNature\",\n  Alphabet: \"pl7.app/alphabet\",\n  Description: \"pl7.app/description\",\n  DataStatus: \"pl7.app/dataStatus\",\n  DiscreteValues: \"pl7.app/discreteValues\",\n  Format: \"pl7.app/format\",\n  Graph: {\n    Axis: {\n      HighCardinality: \"pl7.app/graph/axis/highCardinality\",\n      LowerLimit: \"pl7.app/graph/axis/lowerLimit\",\n      SymmetricRange: \"pl7.app/graph/axis/symmetricRange\",\n      UpperLimit: \"pl7.app/graph/axis/upperLimit\",\n    },\n    IsDenseAxis: \"pl7.app/graph/isDenseAxis\",\n    IsVirtual: \"pl7.app/graph/isVirtual\",\n    Palette: \"pl7.app/graph/palette\",\n    Thresholds: \"pl7.app/graph/thresholds\",\n    TreatAbsentValuesAs: \"pl7.app/graph/treatAbsentValuesAs\",\n  },\n  HideDataFromUi: \"pl7.app/hideDataFromUi\",\n  HideDataFromGraphs: \"pl7.app/hideDataFromGraphs\",\n  IsDiscreteFilter: \"pl7.app/isDiscreteFilter\",\n  IsAnchor: \"pl7.app/isAnchor\",\n  IsLinkerColumn: \"pl7.app/isLinkerColumn\",\n  IsScore: \"pl7.app/isScore\",\n  IsSubset: \"pl7.app/isSubset\",\n  Label: \"pl7.app/label\",\n  LinkLabel: \"pl7.app/linkLabel\",\n  Max: \"pl7.app/max\",\n  Min: \"pl7.app/min\",\n  MultipliesBy: \"pl7.app/multipliesBy\",\n  Parents: \"pl7.app/parents\",\n  Score: {\n    DefaultCutoff: \"pl7.app/score/defaultCutoff\",\n    RankingOrder: \"pl7.app/score/rankingOrder\",\n  },\n  Sequence: {\n    Annotation: {\n      Mapping: \"pl7.app/sequence/annotation/mapping\",\n    },\n    IsAnnotation: \"pl7.app/sequence/isAnnotation\",\n  },\n  Table: {\n    FontFamily: \"pl7.app/table/fontFamily\",\n    OrderPriority: \"pl7.app/table/orderPriority\",\n    Visibility: \"pl7.app/table/visibility\",\n    Info: \"pl7.app/table/info\",\n  },\n  Trace: \"pl7.app/trace\",\n  VDJ: {\n    IsAssemblingFeature: \"pl7.app/vdj/isAssemblingFeature\",\n    IsMainSequence: \"pl7.app/vdj/isMainSequence\",\n  },\n} as const;\n\nexport type AnnotationDataStatus =\n  | \"missing\"\n  | \"resolving\"\n  | \"absent\"\n  | \"computing\"\n  | \"ready\"\n  | \"error\";\n\nexport type Annotation = Metadata &\n  Partial<{\n    [Annotation.Alphabet]: \"nucleotide\" | \"aminoacid\" | (string & {});\n    [Annotation.AxisNature]: \"homogeneous\" | \"heterogeneous\" | \"scaleCompatible\" | (string & {});\n    [Annotation.Description]: string;\n    [Annotation.DataStatus]: AnnotationDataStatus;\n    [Annotation.DiscreteValues]: StringifiedJson<number[]> | StringifiedJson<string[]>;\n    [Annotation.Format]: string;\n    [Annotation.Graph.Axis.HighCardinality]: StringifiedJson<boolean>;\n    [Annotation.Graph.Axis.LowerLimit]: StringifiedJson<number>;\n    [Annotation.Graph.Axis.SymmetricRange]: StringifiedJson<boolean>;\n    [Annotation.Graph.Axis.UpperLimit]: StringifiedJson<number>;\n    [Annotation.Graph.IsDenseAxis]: StringifiedJson<boolean>;\n    [Annotation.Graph.IsVirtual]: StringifiedJson<boolean>;\n    [Annotation.Graph.Palette]: StringifiedJson<{ mapping: Record<string, number>; name: string }>;\n    [Annotation.Graph.Thresholds]: StringifiedJson<\n      { columnId: { valueType: ValueType; name: string }; value: number }[]\n    >;\n    [Annotation.Graph.TreatAbsentValuesAs]: StringifiedJson<number>;\n    [Annotation.HideDataFromGraphs]: StringifiedJson<boolean>;\n    [Annotation.HideDataFromUi]: StringifiedJson<boolean>;\n    [Annotation.IsDiscreteFilter]: StringifiedJson<boolean>;\n    [Annotation.IsLinkerColumn]: StringifiedJson<boolean>;\n    [Annotation.IsSubset]: StringifiedJson<boolean>;\n    [Annotation.Label]: string;\n    [Annotation.Max]: StringifiedJson<number>;\n    [Annotation.Min]: StringifiedJson<number>;\n    [Annotation.MultipliesBy]: StringifiedJson<AxisSpec[\"name\"][]>;\n    [Annotation.Parents]: StringifiedJson<AxisSpec[\"name\"][]>;\n    [Annotation.Sequence.Annotation.Mapping]: StringifiedJson<Record<string, string>>;\n    [Annotation.Sequence.IsAnnotation]: StringifiedJson<boolean>;\n    [Annotation.Table.FontFamily]: string;\n    [Annotation.Table.OrderPriority]: StringifiedJson<number>;\n    [Annotation.Table.Visibility]: \"hidden\" | \"optional\" | (string & {});\n    [Annotation.Table.Info]: string;\n    [Annotation.Trace]: StringifiedJson<Trace>;\n    [Annotation.VDJ.IsAssemblingFeature]: StringifiedJson<boolean>;\n  }>;\n\n/// One step in a column's derivation lineage. Only `type` and `label` are part\n/// of the typed public surface; writers may add fields (e.g. `id`, `importance`)\n/// passed through opaquely as `unknown`, accessed via explicit narrowing.\nconst TraceEntrySchema = z\n  .object({\n    type: z.string(),\n    label: z.string(),\n  })\n  .catchall(z.unknown());\n\nexport type TraceEntry = z.infer<typeof TraceEntrySchema>;\n\nexport type Trace = TraceEntry[];\n\n// export const AxisSpec = z.object({\n//   type: z.nativeEnum(ValueType),\n//   name: z.string(),\n//   domain: z.record(z.string(), z.string()).optional(),\n//   annotations: z.record(z.string(), z.string()).optional(),\n//   parentAxes: z.array(z.number()).optional(),\n// }).passthrough();\n//\n// type Expect<T extends true> = T;\n// type Equal<X, Y> =\n// (<T>() => T extends X ? 1 : 2) extends (<T>() => T extends Y ? 1 : 2) ? true : false;\n//\n// type _test = Expect<Equal<\n//   Readonly<z.infer<typeof AxisSpec>>,\n//   Readonly<AxisSpec & Record<string, unknown>>\n// >>;\n\nexport type AnnotationJson = MetadataJson<Annotation>;\n\nconst ValueTypeSchema = z.enum([\"Int\", \"Long\", \"Float\", \"Double\", \"String\"] as const);\nexport const AnnotationJson: AnnotationJson = {\n  [Annotation.DiscreteValues]: z.array(z.string()).or(z.array(z.number())),\n  [Annotation.Graph.Axis.HighCardinality]: z.boolean(),\n  [Annotation.Graph.Axis.LowerLimit]: z.number(),\n  [Annotation.Graph.Axis.UpperLimit]: z.number(),\n  [Annotation.Graph.Axis.SymmetricRange]: z.boolean(),\n  [Annotation.Graph.IsDenseAxis]: z.boolean(),\n  [Annotation.Graph.Palette]: z.object({ mapping: z.record(z.number()), name: z.string() }),\n  [Annotation.Graph.Thresholds]: z.array(\n    z.object({\n      columnId: z.object({ valueType: ValueTypeSchema, name: z.string() }),\n      value: z.number(),\n    }),\n  ),\n  [Annotation.Graph.TreatAbsentValuesAs]: z.number(),\n  [Annotation.Graph.IsVirtual]: z.boolean(),\n  [Annotation.HideDataFromUi]: z.boolean(),\n  [Annotation.HideDataFromGraphs]: z.boolean(),\n  [Annotation.IsDiscreteFilter]: z.boolean(),\n  [Annotation.IsLinkerColumn]: z.boolean(),\n  [Annotation.IsSubset]: z.boolean(),\n  [Annotation.Max]: z.number(),\n  [Annotation.Min]: z.number(),\n  [Annotation.MultipliesBy]: z.array(z.string()),\n  [Annotation.Parents]: z.array(z.string()),\n  [Annotation.Sequence.Annotation.Mapping]: z.record(z.string(), z.string()),\n  [Annotation.Sequence.IsAnnotation]: z.boolean(),\n  [Annotation.Table.OrderPriority]: z.number(),\n  [Annotation.Trace]: z.array(TraceEntrySchema),\n  [Annotation.VDJ.IsAssemblingFeature]: z.boolean(),\n};\n\n/// Helper function for reading plain annotation values\nexport function readAnnotation<T extends keyof Annotation>(\n  spec: { annotations?: Metadata | undefined } | undefined,\n  key: T,\n): Annotation[T] | undefined {\n  return readMetadata<Annotation, T>(spec?.annotations, key);\n}\n\n/// Helper function for reading json-encoded annotation values, throws on JSON parsing error\nexport function readAnnotationJsonOrThrow<T extends keyof AnnotationJson>(\n  spec: { annotations?: Metadata | undefined } | undefined,\n  key: T,\n): z.infer<AnnotationJson[T]> | undefined {\n  return readMetadataJsonOrThrow<Annotation, T>(\n    spec?.annotations,\n    AnnotationJson,\n    key,\n    \"readAnnotationJsonOrThrow\",\n  );\n}\n\n/// Helper function for reading json-encoded annotation values, returns undefined on JSON parsing error\nexport function readAnnotationJson<T extends keyof AnnotationJson>(\n  spec: { annotations?: Metadata | undefined } | undefined,\n  key: T,\n): z.infer<AnnotationJson[T]> | undefined {\n  return readMetadataJson<Annotation, T>(spec?.annotations, AnnotationJson, key);\n}\n\nexport function isLinkerColumn(column: PColumnSpec): boolean {\n  return !!readAnnotationJson(column, Annotation.IsLinkerColumn);\n}\n\n/**\n * Specification of an individual axis.\n *\n * Each axis is a part of a composite key that addresses data inside the PColumn.\n *\n * Each record inside a PColumn is addressed by a unique tuple of values set for\n * all the axes specified in the column spec.\n */\nexport type AxisSpec = {\n  /** Type of the axis value. Should not use non-key types like float or double. */\n  readonly type: AxisValueType;\n\n  /** Name of the axis */\n  readonly name: string;\n\n  /** Adds auxiliary information to the axis name, type and parents to form a\n   * unique identifier */\n  readonly domain?: Record<string, string>;\n\n  /** Context domain provides additional axis identity that is matched\n   * by kinship rules (subset/superset/overlap) rather than exact equality */\n  readonly contextDomain?: Record<string, string>;\n\n  /** Any additional information attached to the axis that does not affect its\n   * identifier */\n  readonly annotations?: Record<string, string>;\n\n  /**\n   * Parent axes provide contextual grouping for the axis in question, establishing\n   * a hierarchy where the current axis is dependent on one or more axes for its\n   * full definition and meaning. For instance, in a data structure where each\n   * \"container\" axis may contain multiple \"item\" axes, the `item` axis would\n   * list the index of the `container` axis in this field to denote its dependency.\n   *\n   * This means that the identity or significance of the `item` axis is only\n   * interpretable when combined with its parent `container` axis. An `item` axis\n   * index by itself may be non-unique and only gains uniqueness within the context\n   * of its parent `container`. Therefore, the `parentAxes` field is essential for\n   * mapping these relationships and ensuring data coherence across nested or\n   * multi-level data models.\n   *\n   * A list of zero-based indices of parent axes in the overall axes specification\n   * from the column spec. Each index corresponds to the position of a parent axis\n   * in the list that defines the structure of the data model.\n   */\n  readonly parentAxes?: number[];\n};\n\n/** Parents are specs, not indexes; normalized axis can be used considering its parents independently from column */\nexport interface AxisSpecNormalized extends Omit<AxisSpec, \"parentAxes\"> {\n  parentAxesSpec: AxisSpecNormalized[];\n}\n\n/** Tree: axis is a root, its parents are children */\nexport type AxisTree = {\n  axis: AxisSpecNormalized;\n  children: AxisTree[]; // parents\n};\n\nfunction makeAxisTree(axis: AxisSpecNormalized): AxisTree {\n  return { axis, children: [] };\n}\n\n/** Build tree by axis parents annotations */\nexport function getAxesTree(rootAxis: AxisSpecNormalized): AxisTree {\n  const root = makeAxisTree(rootAxis);\n  let nodesQ = [root];\n  while (nodesQ.length) {\n    const nextNodes: AxisTree[] = [];\n    for (const node of nodesQ) {\n      node.children = node.axis.parentAxesSpec.map(makeAxisTree);\n      nextNodes.push(...node.children);\n    }\n    nodesQ = nextNodes;\n  }\n  return root;\n}\n\n/** Get set of canonicalized axisIds from axisTree */\nexport function getSetFromAxisTree(tree: AxisTree): Set<CanonicalizedJson<AxisId>> {\n  const set = new Set([canonicalizeJson(getAxisId(tree.axis))]);\n  let nodesQ = [tree];\n  while (nodesQ.length) {\n    const nextNodes = [];\n    for (const node of nodesQ) {\n      for (const parent of node.children) {\n        set.add(canonicalizeJson(getAxisId(parent.axis)));\n        nextNodes.push(parent);\n      }\n    }\n    nodesQ = nextNodes;\n  }\n  return set;\n}\n\n/** Get array of axisSpecs from axisTree */\nexport function getArrayFromAxisTree(tree: AxisTree): AxisSpecNormalized[] {\n  const res = [tree.axis];\n  let nodesQ = [tree];\n  while (nodesQ.length) {\n    const nextNodes = [];\n    for (const node of nodesQ) {\n      for (const parent of node.children) {\n        res.push(parent.axis);\n        nextNodes.push(parent);\n      }\n    }\n    nodesQ = nextNodes;\n  }\n  return res;\n}\n\nexport function canonicalizeAxisWithParents(axis: AxisSpecNormalized) {\n  return canonicalizeJson(getArrayFromAxisTree(getAxesTree(axis)).map(getAxisId));\n}\n\nfunction normalizingAxesComparator(\n  axis1: AxisSpecNormalized,\n  axis2: AxisSpecNormalized,\n): 1 | -1 | 0 {\n  if (axis1.name !== axis2.name) {\n    return axis1.name < axis2.name ? 1 : -1;\n  }\n  if (axis1.type !== axis2.type) {\n    return axis1.type < axis2.type ? 1 : -1;\n  }\n  const domain1 = canonicalizeJson(axis1.domain ?? {});\n  const domain2 = canonicalizeJson(axis2.domain ?? {});\n  if (domain1 !== domain2) {\n    return domain1 < domain2 ? 1 : -1;\n  }\n\n  const contextDomain1 = canonicalizeJson(axis1.contextDomain ?? {});\n  const contextDomain2 = canonicalizeJson(axis2.contextDomain ?? {});\n  if (contextDomain1 !== contextDomain2) {\n    return contextDomain1 < contextDomain2 ? 1 : -1;\n  }\n\n  const parents1 = canonicalizeAxisWithParents(axis1);\n  const parents2 = canonicalizeAxisWithParents(axis2);\n\n  if (parents1 !== parents2) {\n    return parents1 < parents2 ? 1 : -1;\n  }\n\n  const annotation1 = canonicalizeJson(axis1.annotations ?? {});\n  const annotation2 = canonicalizeJson(axis2.annotations ?? {});\n  if (annotation1 !== annotation2) {\n    return annotation1 < annotation2 ? 1 : -1;\n  }\n  return 0;\n}\n\nfunction parseParentsFromAnnotations(axis: AxisSpec) {\n  const parentsList = readAnnotationJson(axis, Annotation.Parents);\n  if (parentsList === undefined) {\n    return [];\n  }\n  return parentsList;\n}\n\nfunction sortParentsDeep(axisSpec: AxisSpecNormalized) {\n  axisSpec.parentAxesSpec.forEach(sortParentsDeep);\n  axisSpec.parentAxesSpec.sort(normalizingAxesComparator);\n}\n\nfunction hasCycleOfParents(axisSpec: AxisSpecNormalized) {\n  const root = makeAxisTree(axisSpec);\n  let nodesQ = [root];\n  const ancestors = new Set(canonicalizeJson(getAxisId(axisSpec)));\n  while (nodesQ.length) {\n    const nextNodes: AxisTree[] = [];\n    const levelIds = new Set<CanonicalizedJson<AxisId>>();\n    for (const node of nodesQ) {\n      node.children = node.axis.parentAxesSpec.map(makeAxisTree);\n      for (const child of node.children) {\n        const childId = canonicalizeJson(getAxisId(child.axis));\n        if (!levelIds.has(childId)) {\n          nextNodes.push(child);\n          levelIds.add(childId);\n          if (ancestors.has(childId)) {\n            return true;\n          }\n          ancestors.add(childId);\n        }\n      }\n    }\n    nodesQ = nextNodes;\n  }\n  return false;\n}\n\n/** Create list of normalized axisSpec (parents are in array of specs, not indexes) */\nexport function getNormalizedAxesList(axes: AxisSpec[]): AxisSpecNormalized[] {\n  if (axes.length === 0) {\n    return [];\n  }\n  const modifiedAxes: AxisSpecNormalized[] = axes.map((axis) => {\n    const { parentAxes: _, ...copiedRest } = axis;\n    return { ...copiedRest, annotations: { ...copiedRest.annotations }, parentAxesSpec: [] };\n  });\n\n  axes.forEach((axis, idx) => {\n    const modifiedAxis = modifiedAxes[idx];\n    if (axis.parentAxes) {\n      // if we have parents by indexes then take from the list\n      modifiedAxis.parentAxesSpec = axis.parentAxes.map((idx) => modifiedAxes[idx]);\n    } else {\n      // else try to parse from annotation name\n      const parents = parseParentsFromAnnotations(axis).map((name) =>\n        modifiedAxes.find((axis) => axis.name === name),\n      );\n      modifiedAxis.parentAxesSpec = parents.some((p) => p === undefined)\n        ? []\n        : (parents as AxisSpecNormalized[]);\n    }\n  });\n\n  if (modifiedAxes.some(hasCycleOfParents)) {\n    // Axes list is broken\n    modifiedAxes.forEach((axis) => {\n      axis.parentAxesSpec = [];\n    });\n  } else {\n    modifiedAxes.forEach((axis) => {\n      sortParentsDeep(axis);\n    });\n  }\n\n  return modifiedAxes;\n}\n\n/** Create list of regular axisSpec from normalized (parents are indexes, inside of current axes list) */\nexport function getDenormalizedAxesList(axesSpec: AxisSpecNormalized[]): AxisSpec[] {\n  const idsList = axesSpec.map(canonicalizeAxisId);\n  return axesSpec.map((axisSpec) => {\n    const parentsIds = axisSpec.parentAxesSpec.map(canonicalizeAxisId);\n    const parentIdxs = parentsIds.map((id) => idsList.indexOf(id));\n    const { parentAxesSpec: _, ...copiedRest } = axisSpec;\n    if (parentIdxs.length) {\n      return { ...copiedRest, parentAxes: parentIdxs } as AxisSpec;\n    }\n    return copiedRest;\n  });\n}\n\n/**\n * Resolve annotation-based parents (`pl7.app/parents`) to numeric `parentAxes`\n * on a column spec. Returns the spec unchanged if all axes already use numeric\n * indices or have no parent annotations.\n */\nexport function resolveAnnotationParents(spec: PColumnSpec): PColumnSpec {\n  const hasAnnotationParents = spec.axesSpec.some(\n    (axis) => !!readAnnotationJson(axis, Annotation.Parents),\n  );\n  if (!hasAnnotationParents) return spec;\n\n  const normalized = getNormalizedAxesList(spec.axesSpec);\n  const denormalized = getDenormalizedAxesList(normalized);\n  return { ...spec, axesSpec: denormalized };\n}\n\n/** Common type representing spec for all the axes in a column */\nexport type AxesSpec = AxisSpec[];\n\n/// Well-known column names\nexport const PColumnName = {\n  Label: \"pl7.app/label\",\n  Table: {\n    RowSelection: \"pl7.app/table/row-selection\",\n  },\n  VDJ: {\n    LeadSelection: \"pl7.app/vdj/lead-selection\",\n    RankingOrder: \"pl7.app/vdj/ranking-order\",\n    Sequence: \"pl7.app/vdj/sequence\",\n  },\n} as const;\n\n/// Well-known axis names\nexport const PAxisName = {\n  SampleId: \"pl7.app/sampleId\",\n  VDJ: {\n    Assay: {\n      SequenceId: \"pl7.app/vdj/assay/sequenceId\",\n    },\n    ClusterId: \"pl7.app/vdj/clusterId\",\n    ClonotypeKey: \"pl7.app/vdj/clonotypeKey\",\n    ScClonotypeKey: \"pl7.app/vdj/scClonotypeKey\",\n  },\n} as const;\n\nexport function isLabelColumn(column: PColumnSpec) {\n  return column.axesSpec.length === 1 && column.name === PColumnName.Label;\n}\n\n/**\n * Full column specification including all axes specs and specs of the column\n * itself.\n *\n * A PColumn in its essence represents a mapping from a fixed size, explicitly\n * typed tuple to an explicitly typed value.\n *\n * (axis1Value1, axis2Value1, ...) -> columnValue\n *\n * Each element in tuple correspond to the axis having the same index in axesSpec.\n */\nexport type PUniversalColumnSpec = PObjectSpec & {\n  /** Defines specific type of BObject, the most generic type of unit of\n   * information in Platforma Project. */\n  readonly kind: \"PColumn\";\n\n  /** Type of column values */\n  readonly valueType: string;\n\n  /** Column name */\n  readonly name: string;\n\n  /** Adds auxiliary information to the axis name, type and parents to form a\n   * unique identifier */\n  readonly domain?: Record<string, string>;\n\n  /** Context domain provides additional column identity that is matched\n   * by kinship rules (subset/superset/overlap) rather than exact equality */\n  readonly contextDomain?: Record<string, string>;\n\n  /** Any additional information attached to the column that does not affect its\n   * identifier */\n  readonly annotations?: Record<string, string>;\n\n  /** A list of zero-based indices of parent axes from the {@link axesSpec} array. */\n  readonly parentAxes?: number[];\n\n  /** Axes specifications */\n  readonly axesSpec: AxesSpec;\n};\n\n/**\n * Specification of a data column.\n *\n * Data column is a specialized type of PColumn that stores only simple values (strings and numbers)\n * addressed by multiple keys. This is in contrast to other PColumn variants that can store more complex\n * values like files or other abstract data types. Data columns are optimized for storing and processing\n * basic tabular data.\n */\nexport type PDataColumnSpec = PUniversalColumnSpec & {\n  /** Type of column values */\n  readonly valueType: ValueType;\n};\n\n// @todo: change this to PUniversalColumnSpec\nexport type PColumnSpec = PDataColumnSpec;\n\n/** Unique PColumnSpec identifier */\nexport type PColumnSpecId = {\n  /** Defines specific type of BObject, the most generic type of unit of\n   * information in Platforma Project. */\n  readonly kind: \"PColumn\";\n\n  /** Type of column values */\n  readonly valueType: ValueType;\n\n  /** Column name */\n  readonly name: string;\n\n  /** Adds auxiliary information to the axis name, type and parents to form a\n   * unique identifier */\n  readonly domain?: Record<string, string>;\n\n  /** Context domain provides additional column identity that is matched\n   * by kinship rules (subset/superset/overlap) rather than exact equality */\n  readonly contextDomain?: Record<string, string>;\n\n  /** A list of zero-based indices of parent axes from the {@link axesSpec} array. */\n  readonly parentAxes?: number[];\n\n  /** Axes id */\n  readonly axesId: AxesId;\n};\n\nexport function getPColumnSpecId(spec: PColumnSpec): PColumnSpecId {\n  return {\n    kind: spec.kind,\n    valueType: spec.valueType,\n    name: spec.name,\n    domain: spec.domain,\n    contextDomain: spec.contextDomain,\n    parentAxes: spec.parentAxes,\n    axesId: getAxesId(spec.axesSpec),\n  };\n}\n\nexport interface PColumn<Data> extends PObject<Data> {\n  /** PColumn spec, allowing it to be found among other PObjects */\n  readonly spec: PColumnSpec;\n}\n\n/** Columns in a PFrame also have internal identifier, this object represents\n * combination of specs and such id */\nexport interface PColumnIdAndSpec {\n  /** Internal column id within the PFrame */\n  readonly columnId: PObjectId;\n\n  /** Column spec */\n  readonly spec: PColumnSpec;\n}\n\n/** Get column id and spec from a column */\nexport function getColumnIdAndSpec<Data>(column: PColumn<Data>): PColumnIdAndSpec {\n  return {\n    columnId: column.id,\n    spec: column.spec,\n  };\n}\n\nexport interface AxisId {\n  /** Type of the axis or column value. For an axis should not use non-key\n   * types like float or double. */\n  readonly type: AxisValueType;\n\n  /** Name of the axis or column */\n  readonly name: string;\n\n  /** Adds auxiliary information to the axis or column name and type to form a\n   * unique identifier */\n  readonly domain?: Record<string, string>;\n\n  /** Context domain provides additional axis identity that is matched\n   * by kinship rules (subset/superset/overlap) rather than exact equality */\n  readonly contextDomain?: Record<string, string>;\n}\n\n/** Array of axis ids */\nexport type AxesId = AxisId[];\n\n/** Extracts axis ids from axis spec */\nexport function getAxisId(spec: AxisSpec): AxisId {\n  const { type, name, domain, contextDomain } = spec;\n  const result: AxisId = { type, name };\n  if (domain && Object.entries(domain).length > 0) {\n    Object.assign(result, { domain });\n  }\n  if (contextDomain && Object.entries(contextDomain).length > 0) {\n    Object.assign(result, { contextDomain });\n  }\n  return result;\n}\n\n/** Extracts axes ids from axes spec array from column spec */\nexport function getAxesId(spec: AxesSpec): AxesId {\n  return spec.map(getAxisId);\n}\n\n/** Canonicalizes axis id */\nexport function canonicalizeAxisId(id: AxisId): CanonicalizedJson<AxisId> {\n  return canonicalizeJson(getAxisId(id));\n}\n\n/** Returns true if all domains from query are found in target */\nfunction matchDomain(query?: Record<string, string>, target?: Record<string, string>) {\n  if (query === undefined) return target === undefined;\n  if (target === undefined) return true;\n  for (const k in target) {\n    if (query[k] !== target[k]) return false;\n  }\n  return true;\n}\n\n/** Returns whether \"match\" axis id is compatible with the \"query\" */\nexport function matchAxisId(query: AxisId, target: AxisId): boolean {\n  return (\n    query.name === target.name &&\n    matchDomain(query.domain, target.domain) &&\n    matchDomain(query.contextDomain, target.contextDomain)\n  );\n}\n\nexport function getTypeFromPColumnOrAxisSpec(spec: PColumnSpec | AxisSpec): ValueType {\n  return \"valueType\" in spec ? spec.valueType : spec.type;\n}\n\nexport function isAxisId(id: unknown): id is AxisId {\n  return typeof id === \"object\" && id !== null && \"name\" in id && \"type\" in 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Adding one is therefore safe; omitting one costs only that a template\n * carrying it applies still pointing at the project it came from.\n */\nexport const BlockScopedDomain: ReadonlySet<string> = new Set<string>([\n  \"pl7.app/blockId\",\n  \"pl7.app/block\",\n  \"pl7.app/redefined-by\",\n  \"pl7.app/annotationRunId\",\n  \"pl7.app/clonotypeAnnotationRunId\",\n  \"pl7.app/clustering/blockId\",\n  \"pl7.app/umap/blockId\",\n  \"pl7.app/peptide/extractionRunId\",\n  \"pl7.app/repertoire/extractionRunId\",\n  \"pl7.app/antibodyVariantDesigner/designRunId\",\n  \"pl7.app/vdj/clonotypingRunId\",\n  \"pl7.app/vdj/clustering/blockId\",\n  \"pl7.app/vdj/integration/blockId\",\n  \"pl7.app/vdj/spatiotemporalAnalysis/blockId\",\n  \"pl7.app/vdj/libraryId\",\n]);\n\nexport type Domain = Metadata &\n  Partial<{\n    [Domain.Alphabet]: \"nucleotide\" | \"aminoacid\" | (string & {});\n    [Domain.BlockId]: string;\n    [Domain.VDJ.ScClonotypeChain.Index]: \"primary\" | \"secondary\" | (string & {});\n  }>;\n\nexport type DomainJson = MetadataJson<Domain>;\nexport const DomainJson: DomainJson = {};\n\n/// Helper function for reading plain domain values\nexport function readDomain<T extends keyof Domain>(\n  spec: { domain?: Metadata | undefined } | undefined,\n  key: T,\n): Domain[T] | undefined {\n  return readMetadata<Domain, T>(spec?.domain, key);\n}\n\n/// Helper function for reading json-encoded domain values, throws on JSON parsing error\nexport function readDomainJsonOrThrow<T extends keyof DomainJson>(\n  spec: { domain?: Metadata | undefined } | undefined,\n  key: T,\n): z.infer<DomainJson[T]> | undefined {\n  return readMetadataJsonOrThrow<Domain, T>(spec?.domain, DomainJson, key, \"readDomainJsonOrThrow\");\n}\n\n/// Helper function for reading json-encoded domain values, returns undefined on JSON parsing error\nexport function readDomainJson<T extends keyof DomainJson>(\n  spec: { domain?: Metadata | undefined } | undefined,\n  key: T,\n): z.infer<DomainJson[T]> | undefined {\n  return readMetadataJson<Domain, T>(spec?.domain, DomainJson, key);\n}\n\n/// Well-known annotations\nexport const Annotation = {\n  AxisNature: \"pl7.app/axisNature\",\n  Alphabet: \"pl7.app/alphabet\",\n  Description: \"pl7.app/description\",\n  DataStatus: \"pl7.app/dataStatus\",\n  DiscreteValues: \"pl7.app/discreteValues\",\n  Format: \"pl7.app/format\",\n  Graph: {\n    Axis: {\n      HighCardinality: \"pl7.app/graph/axis/highCardinality\",\n      LowerLimit: \"pl7.app/graph/axis/lowerLimit\",\n      SymmetricRange: \"pl7.app/graph/axis/symmetricRange\",\n      UpperLimit: \"pl7.app/graph/axis/upperLimit\",\n    },\n    IsDenseAxis: \"pl7.app/graph/isDenseAxis\",\n    IsVirtual: \"pl7.app/graph/isVirtual\",\n    Palette: \"pl7.app/graph/palette\",\n    Thresholds: \"pl7.app/graph/thresholds\",\n    TreatAbsentValuesAs: \"pl7.app/graph/treatAbsentValuesAs\",\n  },\n  HideDataFromUi: \"pl7.app/hideDataFromUi\",\n  HideDataFromGraphs: \"pl7.app/hideDataFromGraphs\",\n  IsDiscreteFilter: \"pl7.app/isDiscreteFilter\",\n  IsAnchor: \"pl7.app/isAnchor\",\n  IsLinkerColumn: \"pl7.app/isLinkerColumn\",\n  IsScore: \"pl7.app/isScore\",\n  IsSubset: \"pl7.app/isSubset\",\n  Label: \"pl7.app/label\",\n  LinkLabel: \"pl7.app/linkLabel\",\n  Max: \"pl7.app/max\",\n  Min: \"pl7.app/min\",\n  MultipliesBy: \"pl7.app/multipliesBy\",\n  Parents: \"pl7.app/parents\",\n  Score: {\n    DefaultCutoff: \"pl7.app/score/defaultCutoff\",\n    RankingOrder: \"pl7.app/score/rankingOrder\",\n  },\n  Sequence: {\n    Annotation: {\n      Mapping: \"pl7.app/sequence/annotation/mapping\",\n    },\n    IsAnnotation: \"pl7.app/sequence/isAnnotation\",\n  },\n  Table: {\n    FontFamily: \"pl7.app/table/fontFamily\",\n    OrderPriority: \"pl7.app/table/orderPriority\",\n    Visibility: \"pl7.app/table/visibility\",\n    Info: \"pl7.app/table/info\",\n  },\n  Trace: \"pl7.app/trace\",\n  VDJ: {\n    IsAssemblingFeature: \"pl7.app/vdj/isAssemblingFeature\",\n    IsMainSequence: \"pl7.app/vdj/isMainSequence\",\n  },\n} as const;\n\nexport type AnnotationDataStatus =\n  | \"missing\"\n  | \"resolving\"\n  | \"absent\"\n  | \"computing\"\n  | \"ready\"\n  | \"error\";\n\nexport type Annotation = Metadata &\n  Partial<{\n    [Annotation.Alphabet]: \"nucleotide\" | \"aminoacid\" | (string & {});\n    [Annotation.AxisNature]: \"homogeneous\" | \"heterogeneous\" | \"scaleCompatible\" | (string & {});\n    [Annotation.Description]: string;\n    [Annotation.DataStatus]: AnnotationDataStatus;\n    [Annotation.DiscreteValues]: StringifiedJson<number[]> | StringifiedJson<string[]>;\n    [Annotation.Format]: string;\n    [Annotation.Graph.Axis.HighCardinality]: StringifiedJson<boolean>;\n    [Annotation.Graph.Axis.LowerLimit]: StringifiedJson<number>;\n    [Annotation.Graph.Axis.SymmetricRange]: StringifiedJson<boolean>;\n    [Annotation.Graph.Axis.UpperLimit]: StringifiedJson<number>;\n    [Annotation.Graph.IsDenseAxis]: StringifiedJson<boolean>;\n    [Annotation.Graph.IsVirtual]: StringifiedJson<boolean>;\n    [Annotation.Graph.Palette]: StringifiedJson<{ mapping: Record<string, number>; name: string }>;\n    [Annotation.Graph.Thresholds]: StringifiedJson<\n      { columnId: { valueType: ValueType; name: string }; value: number }[]\n    >;\n    [Annotation.Graph.TreatAbsentValuesAs]: StringifiedJson<number>;\n    [Annotation.HideDataFromGraphs]: StringifiedJson<boolean>;\n    [Annotation.HideDataFromUi]: StringifiedJson<boolean>;\n    [Annotation.IsDiscreteFilter]: StringifiedJson<boolean>;\n    [Annotation.IsLinkerColumn]: StringifiedJson<boolean>;\n    [Annotation.IsSubset]: StringifiedJson<boolean>;\n    [Annotation.Label]: string;\n    [Annotation.Max]: StringifiedJson<number>;\n    [Annotation.Min]: StringifiedJson<number>;\n    [Annotation.MultipliesBy]: StringifiedJson<AxisSpec[\"name\"][]>;\n    [Annotation.Parents]: StringifiedJson<AxisSpec[\"name\"][]>;\n    [Annotation.Sequence.Annotation.Mapping]: StringifiedJson<Record<string, string>>;\n    [Annotation.Sequence.IsAnnotation]: StringifiedJson<boolean>;\n    [Annotation.Table.FontFamily]: string;\n    [Annotation.Table.OrderPriority]: StringifiedJson<number>;\n    [Annotation.Table.Visibility]: \"hidden\" | \"optional\" | (string & {});\n    [Annotation.Table.Info]: string;\n    [Annotation.Trace]: StringifiedJson<Trace>;\n    [Annotation.VDJ.IsAssemblingFeature]: StringifiedJson<boolean>;\n  }>;\n\n/// One step in a column's derivation lineage. Only `type` and `label` are part\n/// of the typed public surface; writers may add fields (e.g. `id`, `importance`)\n/// passed through opaquely as `unknown`, accessed via explicit narrowing.\nconst TraceEntrySchema = z\n  .object({\n    type: z.string(),\n    label: z.string(),\n  })\n  .catchall(z.unknown());\n\nexport type TraceEntry = z.infer<typeof TraceEntrySchema>;\n\nexport type Trace = TraceEntry[];\n\n// export const AxisSpec = z.object({\n//   type: z.nativeEnum(ValueType),\n//   name: z.string(),\n//   domain: z.record(z.string(), z.string()).optional(),\n//   annotations: z.record(z.string(), z.string()).optional(),\n//   parentAxes: z.array(z.number()).optional(),\n// }).passthrough();\n//\n// type Expect<T extends true> = T;\n// type Equal<X, Y> =\n// (<T>() => T extends X ? 1 : 2) extends (<T>() => T extends Y ? 1 : 2) ? true : false;\n//\n// type _test = Expect<Equal<\n//   Readonly<z.infer<typeof AxisSpec>>,\n//   Readonly<AxisSpec & Record<string, unknown>>\n// >>;\n\nexport type AnnotationJson = MetadataJson<Annotation>;\n\nconst ValueTypeSchema = z.enum([\"Int\", \"Long\", \"Float\", \"Double\", \"String\"] as const);\nexport const AnnotationJson: AnnotationJson = {\n  [Annotation.DiscreteValues]: z.array(z.string()).or(z.array(z.number())),\n  [Annotation.Graph.Axis.HighCardinality]: z.boolean(),\n  [Annotation.Graph.Axis.LowerLimit]: z.number(),\n  [Annotation.Graph.Axis.UpperLimit]: z.number(),\n  [Annotation.Graph.Axis.SymmetricRange]: z.boolean(),\n  [Annotation.Graph.IsDenseAxis]: z.boolean(),\n  [Annotation.Graph.Palette]: z.object({ mapping: z.record(z.number()), name: z.string() }),\n  [Annotation.Graph.Thresholds]: z.array(\n    z.object({\n      columnId: z.object({ valueType: ValueTypeSchema, name: z.string() }),\n      value: z.number(),\n    }),\n  ),\n  [Annotation.Graph.TreatAbsentValuesAs]: z.number(),\n  [Annotation.Graph.IsVirtual]: z.boolean(),\n  [Annotation.HideDataFromUi]: z.boolean(),\n  [Annotation.HideDataFromGraphs]: z.boolean(),\n  [Annotation.IsDiscreteFilter]: z.boolean(),\n  [Annotation.IsLinkerColumn]: z.boolean(),\n  [Annotation.IsSubset]: z.boolean(),\n  [Annotation.Max]: z.number(),\n  [Annotation.Min]: z.number(),\n  [Annotation.MultipliesBy]: z.array(z.string()),\n  [Annotation.Parents]: z.array(z.string()),\n  [Annotation.Sequence.Annotation.Mapping]: z.record(z.string(), z.string()),\n  [Annotation.Sequence.IsAnnotation]: z.boolean(),\n  [Annotation.Table.OrderPriority]: z.number(),\n  [Annotation.Trace]: z.array(TraceEntrySchema),\n  [Annotation.VDJ.IsAssemblingFeature]: z.boolean(),\n};\n\n/// Helper function for reading plain annotation values\nexport function readAnnotation<T extends keyof Annotation>(\n  spec: { annotations?: Metadata | undefined } | undefined,\n  key: T,\n): Annotation[T] | undefined {\n  return readMetadata<Annotation, T>(spec?.annotations, key);\n}\n\n/// Helper function for reading json-encoded annotation values, throws on JSON parsing error\nexport function readAnnotationJsonOrThrow<T extends keyof AnnotationJson>(\n  spec: { annotations?: Metadata | undefined } | undefined,\n  key: T,\n): z.infer<AnnotationJson[T]> | undefined {\n  return readMetadataJsonOrThrow<Annotation, T>(\n    spec?.annotations,\n    AnnotationJson,\n    key,\n    \"readAnnotationJsonOrThrow\",\n  );\n}\n\n/// Helper function for reading json-encoded annotation values, returns undefined on JSON parsing error\nexport function readAnnotationJson<T extends keyof AnnotationJson>(\n  spec: { annotations?: Metadata | undefined } | undefined,\n  key: T,\n): z.infer<AnnotationJson[T]> | undefined {\n  return readMetadataJson<Annotation, T>(spec?.annotations, AnnotationJson, key);\n}\n\nexport function isLinkerColumn(column: PColumnSpec): boolean {\n  return !!readAnnotationJson(column, Annotation.IsLinkerColumn);\n}\n\n/**\n * Specification of an individual axis.\n *\n * Each axis is a part of a composite key that addresses data inside the PColumn.\n *\n * Each record inside a PColumn is addressed by a unique tuple of values set for\n * all the axes specified in the column spec.\n */\nexport type AxisSpec = {\n  /** Type of the axis value. Should not use non-key types like float or double. */\n  readonly type: AxisValueType;\n\n  /** Name of the axis */\n  readonly name: string;\n\n  /** Adds auxiliary information to the axis name, type and parents to form a\n   * unique identifier */\n  readonly domain?: Record<string, string>;\n\n  /** Context domain provides additional axis identity that is matched\n   * by kinship rules (subset/superset/overlap) rather than exact equality */\n  readonly contextDomain?: Record<string, string>;\n\n  /** Any additional information attached to the axis that does not affect its\n   * identifier */\n  readonly annotations?: Record<string, string>;\n\n  /**\n   * Parent axes provide contextual grouping for the axis in question, establishing\n   * a hierarchy where the current axis is dependent on one or more axes for its\n   * full definition and meaning. For instance, in a data structure where each\n   * \"container\" axis may contain multiple \"item\" axes, the `item` axis would\n   * list the index of the `container` axis in this field to denote its dependency.\n   *\n   * This means that the identity or significance of the `item` axis is only\n   * interpretable when combined with its parent `container` axis. An `item` axis\n   * index by itself may be non-unique and only gains uniqueness within the context\n   * of its parent `container`. Therefore, the `parentAxes` field is essential for\n   * mapping these relationships and ensuring data coherence across nested or\n   * multi-level data models.\n   *\n   * A list of zero-based indices of parent axes in the overall axes specification\n   * from the column spec. Each index corresponds to the position of a parent axis\n   * in the list that defines the structure of the data model.\n   */\n  readonly parentAxes?: number[];\n};\n\n/** Parents are specs, not indexes; normalized axis can be used considering its parents independently from column */\nexport interface AxisSpecNormalized extends Omit<AxisSpec, \"parentAxes\"> {\n  parentAxesSpec: AxisSpecNormalized[];\n}\n\n/** Tree: axis is a root, its parents are children */\nexport type AxisTree = {\n  axis: AxisSpecNormalized;\n  children: AxisTree[]; // parents\n};\n\nfunction makeAxisTree(axis: AxisSpecNormalized): AxisTree {\n  return { axis, children: [] };\n}\n\n/** Build tree by axis parents annotations */\nexport function getAxesTree(rootAxis: AxisSpecNormalized): AxisTree {\n  const root = makeAxisTree(rootAxis);\n  let nodesQ = [root];\n  while (nodesQ.length) {\n    const nextNodes: AxisTree[] = [];\n    for (const node of nodesQ) {\n      node.children = node.axis.parentAxesSpec.map(makeAxisTree);\n      nextNodes.push(...node.children);\n    }\n    nodesQ = nextNodes;\n  }\n  return root;\n}\n\n/** Get set of canonicalized axisIds from axisTree */\nexport function getSetFromAxisTree(tree: AxisTree): Set<CanonicalizedJson<AxisId>> {\n  const set = new Set([canonicalizeJson(getAxisId(tree.axis))]);\n  let nodesQ = [tree];\n  while (nodesQ.length) {\n    const nextNodes = [];\n    for (const node of nodesQ) {\n      for (const parent of node.children) {\n        set.add(canonicalizeJson(getAxisId(parent.axis)));\n        nextNodes.push(parent);\n      }\n    }\n    nodesQ = nextNodes;\n  }\n  return set;\n}\n\n/** Get array of axisSpecs from axisTree */\nexport function getArrayFromAxisTree(tree: AxisTree): AxisSpecNormalized[] {\n  const res = [tree.axis];\n  let nodesQ = [tree];\n  while (nodesQ.length) {\n    const nextNodes = [];\n    for (const node of nodesQ) {\n      for (const parent of node.children) {\n        res.push(parent.axis);\n        nextNodes.push(parent);\n      }\n    }\n    nodesQ = nextNodes;\n  }\n  return res;\n}\n\nexport function canonicalizeAxisWithParents(axis: AxisSpecNormalized) {\n  return canonicalizeJson(getArrayFromAxisTree(getAxesTree(axis)).map(getAxisId));\n}\n\nfunction normalizingAxesComparator(\n  axis1: AxisSpecNormalized,\n  axis2: AxisSpecNormalized,\n): 1 | -1 | 0 {\n  if (axis1.name !== axis2.name) {\n    return axis1.name < axis2.name ? 1 : -1;\n  }\n  if (axis1.type !== axis2.type) {\n    return axis1.type < axis2.type ? 1 : -1;\n  }\n  const domain1 = canonicalizeJson(axis1.domain ?? {});\n  const domain2 = canonicalizeJson(axis2.domain ?? {});\n  if (domain1 !== domain2) {\n    return domain1 < domain2 ? 1 : -1;\n  }\n\n  const contextDomain1 = canonicalizeJson(axis1.contextDomain ?? {});\n  const contextDomain2 = canonicalizeJson(axis2.contextDomain ?? {});\n  if (contextDomain1 !== contextDomain2) {\n    return contextDomain1 < contextDomain2 ? 1 : -1;\n  }\n\n  const parents1 = canonicalizeAxisWithParents(axis1);\n  const parents2 = canonicalizeAxisWithParents(axis2);\n\n  if (parents1 !== parents2) {\n    return parents1 < parents2 ? 1 : -1;\n  }\n\n  const annotation1 = canonicalizeJson(axis1.annotations ?? {});\n  const annotation2 = canonicalizeJson(axis2.annotations ?? {});\n  if (annotation1 !== annotation2) {\n    return annotation1 < annotation2 ? 1 : -1;\n  }\n  return 0;\n}\n\nfunction parseParentsFromAnnotations(axis: AxisSpec) {\n  const parentsList = readAnnotationJson(axis, Annotation.Parents);\n  if (parentsList === undefined) {\n    return [];\n  }\n  return parentsList;\n}\n\nfunction sortParentsDeep(axisSpec: AxisSpecNormalized) {\n  axisSpec.parentAxesSpec.forEach(sortParentsDeep);\n  axisSpec.parentAxesSpec.sort(normalizingAxesComparator);\n}\n\nfunction hasCycleOfParents(axisSpec: AxisSpecNormalized) {\n  const root = makeAxisTree(axisSpec);\n  let nodesQ = [root];\n  const ancestors = new Set(canonicalizeJson(getAxisId(axisSpec)));\n  while (nodesQ.length) {\n    const nextNodes: AxisTree[] = [];\n    const levelIds = new Set<CanonicalizedJson<AxisId>>();\n    for (const node of nodesQ) {\n      node.children = node.axis.parentAxesSpec.map(makeAxisTree);\n      for (const child of node.children) {\n        const childId = canonicalizeJson(getAxisId(child.axis));\n        if (!levelIds.has(childId)) {\n          nextNodes.push(child);\n          levelIds.add(childId);\n          if (ancestors.has(childId)) {\n            return true;\n          }\n          ancestors.add(childId);\n        }\n      }\n    }\n    nodesQ = nextNodes;\n  }\n  return false;\n}\n\n/** Create list of normalized axisSpec (parents are in array of specs, not indexes) */\nexport function getNormalizedAxesList(axes: AxisSpec[]): AxisSpecNormalized[] {\n  if (axes.length === 0) {\n    return [];\n  }\n  const modifiedAxes: AxisSpecNormalized[] = axes.map((axis) => {\n    const { parentAxes: _, ...copiedRest } = axis;\n    return { ...copiedRest, annotations: { ...copiedRest.annotations }, parentAxesSpec: [] };\n  });\n\n  axes.forEach((axis, idx) => {\n    const modifiedAxis = modifiedAxes[idx];\n    if (axis.parentAxes) {\n      // if we have parents by indexes then take from the list\n      modifiedAxis.parentAxesSpec = axis.parentAxes.map((idx) => modifiedAxes[idx]);\n    } else {\n      // else try to parse from annotation name\n      const parents = parseParentsFromAnnotations(axis).map((name) =>\n        modifiedAxes.find((axis) => axis.name === name),\n      );\n      modifiedAxis.parentAxesSpec = parents.some((p) => p === undefined)\n        ? []\n        : (parents as AxisSpecNormalized[]);\n    }\n  });\n\n  if (modifiedAxes.some(hasCycleOfParents)) {\n    // Axes list is broken\n    modifiedAxes.forEach((axis) => {\n      axis.parentAxesSpec = [];\n    });\n  } else {\n    modifiedAxes.forEach((axis) => {\n      sortParentsDeep(axis);\n    });\n  }\n\n  return modifiedAxes;\n}\n\n/** Create list of regular axisSpec from normalized (parents are indexes, inside of current axes list) */\nexport function getDenormalizedAxesList(axesSpec: AxisSpecNormalized[]): AxisSpec[] {\n  const idsList = axesSpec.map(canonicalizeAxisId);\n  return axesSpec.map((axisSpec) => {\n    const parentsIds = axisSpec.parentAxesSpec.map(canonicalizeAxisId);\n    const parentIdxs = parentsIds.map((id) => idsList.indexOf(id));\n    const { parentAxesSpec: _, ...copiedRest } = axisSpec;\n    if (parentIdxs.length) {\n      return { ...copiedRest, parentAxes: parentIdxs } as AxisSpec;\n    }\n    return copiedRest;\n  });\n}\n\n/**\n * Resolve annotation-based parents (`pl7.app/parents`) to numeric `parentAxes`\n * on a column spec. Returns the spec unchanged if all axes already use numeric\n * indices or have no parent annotations.\n */\nexport function resolveAnnotationParents(spec: PColumnSpec): PColumnSpec {\n  const hasAnnotationParents = spec.axesSpec.some(\n    (axis) => !!readAnnotationJson(axis, Annotation.Parents),\n  );\n  if (!hasAnnotationParents) return spec;\n\n  const normalized = getNormalizedAxesList(spec.axesSpec);\n  const denormalized = getDenormalizedAxesList(normalized);\n  return { ...spec, axesSpec: denormalized };\n}\n\n/** Common type representing spec for all the axes in a column */\nexport type AxesSpec = AxisSpec[];\n\n/// Well-known column names\nexport const PColumnName = {\n  Label: \"pl7.app/label\",\n  Table: {\n    RowSelection: \"pl7.app/table/row-selection\",\n  },\n  VDJ: {\n    LeadSelection: \"pl7.app/vdj/lead-selection\",\n    RankingOrder: \"pl7.app/vdj/ranking-order\",\n    Sequence: \"pl7.app/vdj/sequence\",\n  },\n} as const;\n\n/// Well-known axis names\nexport const PAxisName = {\n  SampleId: \"pl7.app/sampleId\",\n  VDJ: {\n    Assay: {\n      SequenceId: \"pl7.app/vdj/assay/sequenceId\",\n    },\n    ClusterId: \"pl7.app/vdj/clusterId\",\n    ClonotypeKey: \"pl7.app/vdj/clonotypeKey\",\n    ScClonotypeKey: \"pl7.app/vdj/scClonotypeKey\",\n  },\n} as const;\n\nexport function isLabelColumn(column: PColumnSpec) {\n  return column.axesSpec.length === 1 && column.name === PColumnName.Label;\n}\n\n/**\n * Full column specification including all axes specs and specs of the column\n * itself.\n *\n * A PColumn in its essence represents a mapping from a fixed size, explicitly\n * typed tuple to an explicitly typed value.\n *\n * (axis1Value1, axis2Value1, ...) -> columnValue\n *\n * Each element in tuple correspond to the axis having the same index in axesSpec.\n */\nexport type PUniversalColumnSpec = PObjectSpec & {\n  /** Defines specific type of BObject, the most generic type of unit of\n   * information in Platforma Project. */\n  readonly kind: \"PColumn\";\n\n  /** Type of column values */\n  readonly valueType: string;\n\n  /** Column name */\n  readonly name: string;\n\n  /** Adds auxiliary information to the axis name, type and parents to form a\n   * unique identifier */\n  readonly domain?: Record<string, string>;\n\n  /** Context domain provides additional column identity that is matched\n   * by kinship rules (subset/superset/overlap) rather than exact equality */\n  readonly contextDomain?: Record<string, string>;\n\n  /** Any additional information attached to the column that does not affect its\n   * identifier */\n  readonly annotations?: Record<string, string>;\n\n  /** A list of zero-based indices of parent axes from the {@link axesSpec} array. */\n  readonly parentAxes?: number[];\n\n  /** Axes specifications */\n  readonly axesSpec: AxesSpec;\n};\n\n/**\n * Specification of a data column.\n *\n * Data column is a specialized type of PColumn that stores only simple values (strings and numbers)\n * addressed by multiple keys. This is in contrast to other PColumn variants that can store more complex\n * values like files or other abstract data types. Data columns are optimized for storing and processing\n * basic tabular data.\n */\nexport type PDataColumnSpec = PUniversalColumnSpec & {\n  /** Type of column values */\n  readonly valueType: ValueType;\n};\n\n// @todo: change this to PUniversalColumnSpec\nexport type PColumnSpec = PDataColumnSpec;\n\n/** Unique PColumnSpec identifier */\nexport type PColumnSpecId = {\n  /** Defines specific type of BObject, the most generic type of unit of\n   * information in Platforma Project. */\n  readonly kind: \"PColumn\";\n\n  /** Type of column values */\n  readonly valueType: ValueType;\n\n  /** Column name */\n  readonly name: string;\n\n  /** Adds auxiliary information to the axis name, type and parents to form a\n   * unique identifier */\n  readonly domain?: Record<string, string>;\n\n  /** Context domain provides additional column identity that is matched\n   * by kinship rules (subset/superset/overlap) rather than exact equality */\n  readonly contextDomain?: Record<string, string>;\n\n  /** A list of zero-based indices of parent axes from the {@link axesSpec} array. */\n  readonly parentAxes?: number[];\n\n  /** Axes id */\n  readonly axesId: AxesId;\n};\n\nexport function getPColumnSpecId(spec: PColumnSpec): PColumnSpecId {\n  return {\n    kind: spec.kind,\n    valueType: spec.valueType,\n    name: spec.name,\n    domain: spec.domain,\n    contextDomain: spec.contextDomain,\n    parentAxes: spec.parentAxes,\n    axesId: getAxesId(spec.axesSpec),\n  };\n}\n\nexport interface PColumn<Data> extends PObject<Data> {\n  /** PColumn spec, allowing it to be found among other PObjects */\n  readonly spec: PColumnSpec;\n}\n\n/** Columns in a PFrame also have internal identifier, this object represents\n * combination of specs and such id */\nexport interface PColumnIdAndSpec {\n  /** Internal column id within the PFrame */\n  readonly columnId: PObjectId;\n\n  /** Column spec */\n  readonly spec: PColumnSpec;\n}\n\n/** Get column id and spec from a column */\nexport function getColumnIdAndSpec<Data>(column: PColumn<Data>): PColumnIdAndSpec {\n  return {\n    columnId: column.id,\n    spec: column.spec,\n  };\n}\n\nexport interface AxisId {\n  /** Type of the axis or column value. For an axis should not use non-key\n   * types like float or double. */\n  readonly type: AxisValueType;\n\n  /** Name of the axis or column */\n  readonly name: string;\n\n  /** Adds auxiliary information to the axis or column name and type to form a\n   * unique identifier */\n  readonly domain?: Record<string, string>;\n\n  /** Context domain provides additional axis identity that is matched\n   * by kinship rules (subset/superset/overlap) rather than exact equality */\n  readonly contextDomain?: Record<string, string>;\n}\n\n/** Array of axis ids */\nexport type AxesId = AxisId[];\n\n/** Extracts axis ids from axis spec */\nexport function getAxisId(spec: AxisSpec): AxisId {\n  const { type, name, domain, contextDomain } = spec;\n  const result: AxisId = { type, name };\n  if (domain && Object.entries(domain).length > 0) {\n    Object.assign(result, { domain });\n  }\n  if (contextDomain && Object.entries(contextDomain).length > 0) {\n    Object.assign(result, { contextDomain });\n  }\n  return result;\n}\n\n/** Extracts axes ids from axes spec array from column spec */\nexport function getAxesId(spec: AxesSpec): AxesId {\n  return spec.map(getAxisId);\n}\n\n/** Canonicalizes axis id */\nexport function canonicalizeAxisId(id: AxisId): CanonicalizedJson<AxisId> {\n  return canonicalizeJson(getAxisId(id));\n}\n\n/** Returns true if all domains from query are found in target */\nfunction matchDomain(query?: Record<string, string>, target?: Record<string, string>) {\n  if (query === undefined) return target === undefined;\n  if (target === undefined) return true;\n  for (const k in target) {\n    if (query[k] !== target[k]) return false;\n  }\n  return true;\n}\n\n/** Returns whether \"match\" axis id is compatible with the \"query\" */\nexport function matchAxisId(query: AxisId, target: AxisId): boolean {\n  return (\n    query.name === target.name &&\n    matchDomain(query.domain, target.domain) &&\n    matchDomain(query.contextDomain, target.contextDomain)\n  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