@milaboratories/pl-model-common 1.24.0 → 1.24.1

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

@@ -43,6 +43,11 @@ function readMetadataJson(metadata, metadataJson, key) {
 const Domain = {
     Alphabet: 'pl7.app/alphabet',
     BlockId: 'pl7.app/blockId',
+    VDJ: {
+        ScClonotypeChain: {
+            Index: 'pl7.app/vdj/scClonotypeChain/index',
+        },
+    },
 };
 const DomainJson = {};
 /// Helper function for reading plain domain values
@@ -99,6 +104,9 @@ const Annotation = {
         Visibility: 'pl7.app/table/visibility',
     },
     Trace: 'pl7.app/trace',
+    VDJ: {
+        IsAssemblingFeature: 'pl7.app/vdj/isAssemblingFeature',
+    },
 };
 const ValueTypeSchema = zod.z.enum(['Int', 'Long', 'Float', 'Double', 'String']);
 const AnnotationJson = {
@@ -128,6 +136,7 @@ const AnnotationJson = {
     [Annotation.Sequence.IsAnnotation]: zod.z.boolean(),
     [Annotation.Table.OrderPriority]: zod.z.number(),
     [Annotation.Trace]: zod.z.record(zod.z.string(), zod.z.unknown()),
+    [Annotation.VDJ.IsAssemblingFeature]: zod.z.boolean(),
 };
 /// Helper function for reading plain annotation values
 function readAnnotation(spec, key) {
@@ -307,6 +316,18 @@ const PColumnName = {
     Table: {
         RowSelection: 'pl7.app/table/row-selection',
     },
+    VDJ: {
+        Sequence: 'pl7.app/vdj/sequence',
+    },
+};
+/// Well-known axis names
+const PAxisName = {
+    VDJ: {
+        Assay: {
+            SequenceId: 'pl7.app/vdj/assay/sequenceId',
+        },
+        ScClonotypeKey: 'pl7.app/vdj/scClonotypeKey',
+    },
 };
 function isLabelColumn(column) {
     return column.axesSpec.length === 1 && column.name === PColumnName.Label;
@@ -372,6 +393,7 @@ exports.Annotation = Annotation;
 exports.AnnotationJson = AnnotationJson;
 exports.Domain = Domain;
 exports.DomainJson = DomainJson;
+exports.PAxisName = PAxisName;
 exports.PColumnName = PColumnName;
 exports.ValueType = ValueType;
 exports.canonicalizeAxisId = canonicalizeAxisId;

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

@@ -1 +1 @@
-{"version":3,"file":"spec.cjs","sources":["../../../../src/drivers/pframe/spec/spec.ts"],"sourcesContent":["import { ensureError } from '../../../errors';\nimport {\n  canonicalizeJson,\n  type CanonicalizedJson,\n  type StringifiedJson,\n} from '../../../json';\nimport type {\n  PObject,\n  PObjectId,\n  PObjectSpec,\n} 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\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> ? z.ZodType<U> : 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} as const;\n\nexport type Domain = Metadata & Partial<{\n  [Domain.Alphabet]: 'nucleotide' | 'aminoacid' | string;\n  [Domain.BlockId]: 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  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  IsLinkerColumn: 'pl7.app/isLinkerColumn',\n  IsSubset: 'pl7.app/isSubset',\n  Label: 'pl7.app/label',\n  Max: 'pl7.app/max',\n  Min: 'pl7.app/min',\n  MultipliesBy: 'pl7.app/multipliesBy',\n  Parents: 'pl7.app/parents',\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  },\n  Trace: 'pl7.app/trace',\n} as const;\n\nexport type Annotation = Metadata & Partial<{\n  [Annotation.Alphabet]: 'nucleotide' | 'aminoacid' | string;\n  [Annotation.AxisNature]: 'homogeneous' | 'heterogeneous' | 'scaleCompatible' | string;\n  [Annotation.Description]: string;\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<{ columnId: { valueType: ValueType; name: string }; value: number }[]>;\n  [Annotation.Graph.TreatAbsentValuesAs]: StringifiedJson<number>;\n  [Annotation.HideDataFromUi]: StringifiedJson<boolean>;\n  [Annotation.HideDataFromGraphs]: 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.Trace]: StringifiedJson<Record<string, unknown>>;\n}>;\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.record(z.string(), z.unknown()),\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>(spec?.annotations, AnnotationJson, key, 'readAnnotationJsonOrThrow');\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: ValueType;\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  /** 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(axis1: AxisSpecNormalized, axis2: AxisSpecNormalized): 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 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) {\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) { // if we have parents by indexes then take from the list\n      modifiedAxis.parentAxesSpec = axis.parentAxes.map((idx) => modifiedAxes[idx]);\n    } else { // else try to parse from annotation name\n      const parents = parseParentsFromAnnotations(axis).map((name) => modifiedAxes.find((axis) => axis.name === name));\n      modifiedAxis.parentAxesSpec = parents.some((p) => p === undefined) ? [] : parents as AxisSpecNormalized[];\n\n      delete modifiedAxis.annotations?.[Annotation.Parents];\n    }\n  });\n\n  if (modifiedAxes.some(hasCycleOfParents)) { // 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((axisSpec) => canonicalizeJson(getAxisId(axisSpec)));\n  return axesSpec.map((axisSpec) => {\n    const parentsIds = axisSpec.parentAxesSpec.map((axisSpec) => canonicalizeJson(getAxisId(axisSpec)));\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/** 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} 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  /** 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  /** 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    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\nexport type PColumnLazy<T> = PColumn<() => T>;\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\n/** Information returned by {@link PFrame.listColumns} method */\nexport interface PColumnInfo extends PColumnIdAndSpec {\n  /** True if data was associated with this PColumn */\n  readonly hasData: boolean;\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: ValueType;\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\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 } = spec;\n  const result = { type, name };\n  if (domain && Object.entries(domain).length > 0) {\n    Object.assign(result, { domain });\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 query.name === target.name && matchDomain(query.domain, target.domain);\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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P : never)]: M[P] extends StringifiedJson<infer U> ? z.ZodType<U> : 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    ScClonotypeChain: {\n      Index: 'pl7.app/vdj/scClonotypeChain/index',\n    },\n  },\n} as const;\n\nexport type Domain = Metadata & 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  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  IsLinkerColumn: 'pl7.app/isLinkerColumn',\n  IsSubset: 'pl7.app/isSubset',\n  Label: 'pl7.app/label',\n  Max: 'pl7.app/max',\n  Min: 'pl7.app/min',\n  MultipliesBy: 'pl7.app/multipliesBy',\n  Parents: 'pl7.app/parents',\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  },\n  Trace: 'pl7.app/trace',\n  VDJ: {\n    IsAssemblingFeature: 'pl7.app/vdj/isAssemblingFeature',\n  },\n} as const;\n\nexport type Annotation = Metadata & Partial<{\n  [Annotation.Alphabet]: 'nucleotide' | 'aminoacid' | (string & {});\n  [Annotation.AxisNature]: 'homogeneous' | 'heterogeneous' | 'scaleCompatible' | (string & {});\n  [Annotation.Description]: string;\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<{ columnId: { valueType: ValueType; name: string }; value: number }[]>;\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.Trace]: StringifiedJson<Record<string, unknown>>;\n  [Annotation.VDJ.IsAssemblingFeature]: StringifiedJson<boolean>;\n}>;\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.record(z.string(), z.unknown()),\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>(spec?.annotations, AnnotationJson, key, 'readAnnotationJsonOrThrow');\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: ValueType;\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  /** 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(axis1: AxisSpecNormalized, axis2: AxisSpecNormalized): 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 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) {\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) { // if we have parents by indexes then take from the list\n      modifiedAxis.parentAxesSpec = axis.parentAxes.map((idx) => modifiedAxes[idx]);\n    } else { // else try to parse from annotation name\n      const parents = parseParentsFromAnnotations(axis).map((name) => modifiedAxes.find((axis) => axis.name === name));\n      modifiedAxis.parentAxesSpec = parents.some((p) => p === undefined) ? [] : parents as AxisSpecNormalized[];\n\n      delete modifiedAxis.annotations?.[Annotation.Parents];\n    }\n  });\n\n  if (modifiedAxes.some(hasCycleOfParents)) { // 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((axisSpec) => canonicalizeJson(getAxisId(axisSpec)));\n  return axesSpec.map((axisSpec) => {\n    const parentsIds = axisSpec.parentAxesSpec.map((axisSpec) => canonicalizeJson(getAxisId(axisSpec)));\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/** 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    Sequence: 'pl7.app/vdj/sequence',\n  },\n} as const;\n\n/// Well-known axis names\nexport const PAxisName = {\n  VDJ: {\n    Assay: {\n      SequenceId: 'pl7.app/vdj/assay/sequenceId',\n    },\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  /** 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  /** 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    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\nexport type PColumnLazy<T> = PColumn<() => T>;\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\n/** Information returned by {@link PFrame.listColumns} method */\nexport interface PColumnInfo extends PColumnIdAndSpec {\n  /** True if data was associated with this PColumn */\n  readonly hasData: boolean;\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: ValueType;\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\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 } = spec;\n  const result = { type, name };\n  if (domain && Object.entries(domain).length > 0) {\n    Object.assign(result, { domain });\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 query.name === target.name && matchDomain(query.domain, target.domain);\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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package/dist/drivers/pframe/spec/spec.d.ts

@@ -22,10 +22,16 @@ export declare function readMetadataJson<M extends Metadata, T extends keyof Met
 export declare const Domain: {
     readonly Alphabet: "pl7.app/alphabet";
     readonly BlockId: "pl7.app/blockId";
+    readonly VDJ: {
+        readonly ScClonotypeChain: {
+            readonly Index: "pl7.app/vdj/scClonotypeChain/index";
+        };
+    };
 };
 export type Domain = Metadata & Partial<{
-    [Domain.Alphabet]: 'nucleotide' | 'aminoacid' | string;
+    [Domain.Alphabet]: 'nucleotide' | 'aminoacid' | (string & {});
     [Domain.BlockId]: string;
+    [Domain.VDJ.ScClonotypeChain.Index]: 'primary' | 'secondary' | (string & {});
 }>;
 export type DomainJson = MetadataJson<Domain>;
 export declare const DomainJson: DomainJson;
@@ -79,10 +85,13 @@ export declare const Annotation: {
         readonly Visibility: "pl7.app/table/visibility";
     };
     readonly Trace: "pl7.app/trace";
+    readonly VDJ: {
+        readonly IsAssemblingFeature: "pl7.app/vdj/isAssemblingFeature";
+    };
 };
 export type Annotation = Metadata & Partial<{
-    [Annotation.Alphabet]: 'nucleotide' | 'aminoacid' | string;
-    [Annotation.AxisNature]: 'homogeneous' | 'heterogeneous' | 'scaleCompatible' | string;
+    [Annotation.Alphabet]: 'nucleotide' | 'aminoacid' | (string & {});
+    [Annotation.AxisNature]: 'homogeneous' | 'heterogeneous' | 'scaleCompatible' | (string & {});
     [Annotation.Description]: string;
     [Annotation.DiscreteValues]: StringifiedJson<number[]> | StringifiedJson<string[]>;
     [Annotation.Format]: string;
@@ -104,8 +113,8 @@ export type Annotation = Metadata & Partial<{
         value: number;
     }[]>;
     [Annotation.Graph.TreatAbsentValuesAs]: StringifiedJson<number>;
-    [Annotation.HideDataFromUi]: StringifiedJson<boolean>;
     [Annotation.HideDataFromGraphs]: StringifiedJson<boolean>;
+    [Annotation.HideDataFromUi]: StringifiedJson<boolean>;
     [Annotation.IsDiscreteFilter]: StringifiedJson<boolean>;
     [Annotation.IsLinkerColumn]: StringifiedJson<boolean>;
     [Annotation.IsSubset]: StringifiedJson<boolean>;
@@ -118,8 +127,9 @@ export type Annotation = Metadata & Partial<{
     [Annotation.Sequence.IsAnnotation]: StringifiedJson<boolean>;
     [Annotation.Table.FontFamily]: string;
     [Annotation.Table.OrderPriority]: StringifiedJson<number>;
-    [Annotation.Table.Visibility]: 'hidden' | 'optional' | string;
+    [Annotation.Table.Visibility]: 'hidden' | 'optional' | (string & {});
     [Annotation.Trace]: StringifiedJson<Record<string, unknown>>;
+    [Annotation.VDJ.IsAssemblingFeature]: StringifiedJson<boolean>;
 }>;
 export type AnnotationJson = MetadataJson<Annotation>;
 export declare const AnnotationJson: AnnotationJson;
@@ -201,6 +211,17 @@ export declare const PColumnName: {
     readonly Table: {
         readonly RowSelection: "pl7.app/table/row-selection";
     };
+    readonly VDJ: {
+        readonly Sequence: "pl7.app/vdj/sequence";
+    };
+};
+export declare const PAxisName: {
+    readonly VDJ: {
+        readonly Assay: {
+            readonly SequenceId: "pl7.app/vdj/assay/sequenceId";
+        };
+        readonly ScClonotypeKey: "pl7.app/vdj/scClonotypeKey";
+    };
 };
 export declare function isLabelColumn(column: PColumnSpec): boolean;
 /**

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

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

@@ -41,6 +41,11 @@ function readMetadataJson(metadata, metadataJson, key) {
 const Domain = {
     Alphabet: 'pl7.app/alphabet',
     BlockId: 'pl7.app/blockId',
+    VDJ: {
+        ScClonotypeChain: {
+            Index: 'pl7.app/vdj/scClonotypeChain/index',
+        },
+    },
 };
 const DomainJson = {};
 /// Helper function for reading plain domain values
@@ -97,6 +102,9 @@ const Annotation = {
         Visibility: 'pl7.app/table/visibility',
     },
     Trace: 'pl7.app/trace',
+    VDJ: {
+        IsAssemblingFeature: 'pl7.app/vdj/isAssemblingFeature',
+    },
 };
 const ValueTypeSchema = z.enum(['Int', 'Long', 'Float', 'Double', 'String']);
 const AnnotationJson = {
@@ -126,6 +134,7 @@ const AnnotationJson = {
     [Annotation.Sequence.IsAnnotation]: z.boolean(),
     [Annotation.Table.OrderPriority]: z.number(),
     [Annotation.Trace]: z.record(z.string(), z.unknown()),
+    [Annotation.VDJ.IsAssemblingFeature]: z.boolean(),
 };
 /// Helper function for reading plain annotation values
 function readAnnotation(spec, key) {
@@ -305,6 +314,18 @@ const PColumnName = {
     Table: {
         RowSelection: 'pl7.app/table/row-selection',
     },
+    VDJ: {
+        Sequence: 'pl7.app/vdj/sequence',
+    },
+};
+/// Well-known axis names
+const PAxisName = {
+    VDJ: {
+        Assay: {
+            SequenceId: 'pl7.app/vdj/assay/sequenceId',
+        },
+        ScClonotypeKey: 'pl7.app/vdj/scClonotypeKey',
+    },
 };
 function isLabelColumn(column) {
     return column.axesSpec.length === 1 && column.name === PColumnName.Label;
@@ -366,5 +387,5 @@ function isAxisId(id) {
     return typeof id === 'object' && id !== null && 'name' in id && 'type' in id;
 }
 
-export { Annotation, AnnotationJson, Domain, DomainJson, PColumnName, ValueType, canonicalizeAxisId, canonicalizeAxisWithParents, getArrayFromAxisTree, getAxesId, getAxesTree, getAxisId, getColumnIdAndSpec, getDenormalizedAxesList, getNormalizedAxesList, getPColumnSpecId, getSetFromAxisTree, getTypeFromPColumnOrAxisSpec, isAxisId, isLabelColumn, isLinkerColumn, matchAxisId, readAnnotation, readAnnotationJson, readAnnotationJsonOrThrow, readDomain, readDomainJson, readDomainJsonOrThrow, readMetadata, readMetadataJson, readMetadataJsonOrThrow };
+export { Annotation, AnnotationJson, Domain, DomainJson, PAxisName, PColumnName, ValueType, canonicalizeAxisId, canonicalizeAxisWithParents, getArrayFromAxisTree, getAxesId, getAxesTree, getAxisId, getColumnIdAndSpec, getDenormalizedAxesList, getNormalizedAxesList, getPColumnSpecId, getSetFromAxisTree, getTypeFromPColumnOrAxisSpec, isAxisId, isLabelColumn, isLinkerColumn, matchAxisId, readAnnotation, readAnnotationJson, readAnnotationJsonOrThrow, readDomain, readDomainJson, readDomainJsonOrThrow, readMetadata, readMetadataJson, readMetadataJsonOrThrow };
 //# sourceMappingURL=spec.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"spec.js","sources":["../../../../src/drivers/pframe/spec/spec.ts"],"sourcesContent":["import { ensureError } from '../../../errors';\nimport {\n  canonicalizeJson,\n  type CanonicalizedJson,\n  type StringifiedJson,\n} from '../../../json';\nimport type {\n  PObject,\n  PObjectId,\n  PObjectSpec,\n} 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\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> ? z.ZodType<U> : 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} as const;\n\nexport type Domain = Metadata & Partial<{\n  [Domain.Alphabet]: 'nucleotide' | 'aminoacid' | string;\n  [Domain.BlockId]: 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  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  IsLinkerColumn: 'pl7.app/isLinkerColumn',\n  IsSubset: 'pl7.app/isSubset',\n  Label: 'pl7.app/label',\n  Max: 'pl7.app/max',\n  Min: 'pl7.app/min',\n  MultipliesBy: 'pl7.app/multipliesBy',\n  Parents: 'pl7.app/parents',\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  },\n  Trace: 'pl7.app/trace',\n} as const;\n\nexport type Annotation = Metadata & Partial<{\n  [Annotation.Alphabet]: 'nucleotide' | 'aminoacid' | string;\n  [Annotation.AxisNature]: 'homogeneous' | 'heterogeneous' | 'scaleCompatible' | string;\n  [Annotation.Description]: string;\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<{ columnId: { valueType: ValueType; name: string }; value: number }[]>;\n  [Annotation.Graph.TreatAbsentValuesAs]: StringifiedJson<number>;\n  [Annotation.HideDataFromUi]: StringifiedJson<boolean>;\n  [Annotation.HideDataFromGraphs]: 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.Trace]: StringifiedJson<Record<string, unknown>>;\n}>;\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.record(z.string(), z.unknown()),\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>(spec?.annotations, AnnotationJson, key, 'readAnnotationJsonOrThrow');\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: ValueType;\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  /** 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(axis1: AxisSpecNormalized, axis2: AxisSpecNormalized): 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 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) {\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) { // if we have parents by indexes then take from the list\n      modifiedAxis.parentAxesSpec = axis.parentAxes.map((idx) => modifiedAxes[idx]);\n    } else { // else try to parse from annotation name\n      const parents = parseParentsFromAnnotations(axis).map((name) => modifiedAxes.find((axis) => axis.name === name));\n      modifiedAxis.parentAxesSpec = parents.some((p) => p === undefined) ? [] : parents as AxisSpecNormalized[];\n\n      delete modifiedAxis.annotations?.[Annotation.Parents];\n    }\n  });\n\n  if (modifiedAxes.some(hasCycleOfParents)) { // 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((axisSpec) => canonicalizeJson(getAxisId(axisSpec)));\n  return axesSpec.map((axisSpec) => {\n    const parentsIds = axisSpec.parentAxesSpec.map((axisSpec) => canonicalizeJson(getAxisId(axisSpec)));\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/** 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} 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  /** 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  /** 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    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\nexport type PColumnLazy<T> = PColumn<() => T>;\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\n/** Information returned by {@link PFrame.listColumns} method */\nexport interface PColumnInfo extends PColumnIdAndSpec {\n  /** True if data was associated with this PColumn */\n  readonly hasData: boolean;\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: ValueType;\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\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 } = spec;\n  const result = { type, name };\n  if (domain && Object.entries(domain).length > 0) {\n    Object.assign(result, { domain });\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 query.name === target.name && matchDomain(query.domain, target.domain);\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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P : never)]: M[P] extends StringifiedJson<infer U> ? z.ZodType<U> : 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    ScClonotypeChain: {\n      Index: 'pl7.app/vdj/scClonotypeChain/index',\n    },\n  },\n} as const;\n\nexport type Domain = Metadata & 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  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  IsLinkerColumn: 'pl7.app/isLinkerColumn',\n  IsSubset: 'pl7.app/isSubset',\n  Label: 'pl7.app/label',\n  Max: 'pl7.app/max',\n  Min: 'pl7.app/min',\n  MultipliesBy: 'pl7.app/multipliesBy',\n  Parents: 'pl7.app/parents',\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  },\n  Trace: 'pl7.app/trace',\n  VDJ: {\n    IsAssemblingFeature: 'pl7.app/vdj/isAssemblingFeature',\n  },\n} as const;\n\nexport type Annotation = Metadata & Partial<{\n  [Annotation.Alphabet]: 'nucleotide' | 'aminoacid' | (string & {});\n  [Annotation.AxisNature]: 'homogeneous' | 'heterogeneous' | 'scaleCompatible' | (string & {});\n  [Annotation.Description]: string;\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<{ columnId: { valueType: ValueType; name: string }; value: number }[]>;\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.Trace]: StringifiedJson<Record<string, unknown>>;\n  [Annotation.VDJ.IsAssemblingFeature]: StringifiedJson<boolean>;\n}>;\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.record(z.string(), z.unknown()),\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>(spec?.annotations, AnnotationJson, key, 'readAnnotationJsonOrThrow');\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: ValueType;\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  /** 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(axis1: AxisSpecNormalized, axis2: AxisSpecNormalized): 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 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) {\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) { // if we have parents by indexes then take from the list\n      modifiedAxis.parentAxesSpec = axis.parentAxes.map((idx) => modifiedAxes[idx]);\n    } else { // else try to parse from annotation name\n      const parents = parseParentsFromAnnotations(axis).map((name) => modifiedAxes.find((axis) => axis.name === name));\n      modifiedAxis.parentAxesSpec = parents.some((p) => p === undefined) ? [] : parents as AxisSpecNormalized[];\n\n      delete modifiedAxis.annotations?.[Annotation.Parents];\n    }\n  });\n\n  if (modifiedAxes.some(hasCycleOfParents)) { // 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((axisSpec) => canonicalizeJson(getAxisId(axisSpec)));\n  return axesSpec.map((axisSpec) => {\n    const parentsIds = axisSpec.parentAxesSpec.map((axisSpec) => canonicalizeJson(getAxisId(axisSpec)));\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/** 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    Sequence: 'pl7.app/vdj/sequence',\n  },\n} as const;\n\n/// Well-known axis names\nexport const PAxisName = {\n  VDJ: {\n    Assay: {\n      SequenceId: 'pl7.app/vdj/assay/sequenceId',\n    },\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  /** 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  /** 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    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\nexport type PColumnLazy<T> = PColumn<() => T>;\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\n/** Information returned by {@link PFrame.listColumns} method */\nexport interface PColumnInfo extends PColumnIdAndSpec {\n  /** True if data was associated with this PColumn */\n  readonly hasData: boolean;\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: ValueType;\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\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 } = spec;\n  const result = { type, name };\n  if (domain && Object.entries(domain).length > 0) {\n    Object.assign(result, { domain });\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 query.name === target.name && matchDomain(query.domain, target.domain);\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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package/dist/index.cjs

@@ -67,6 +67,7 @@ exports.Annotation = spec.Annotation;
 exports.AnnotationJson = spec.AnnotationJson;
 exports.Domain = spec.Domain;
 exports.DomainJson = spec.DomainJson;
+exports.PAxisName = spec.PAxisName;
 exports.PColumnName = spec.PColumnName;
 exports.ValueType = spec.ValueType;
 exports.canonicalizeAxisId = spec.canonicalizeAxisId;

package/dist/index.cjs.map

@@ -1 +1 @@
-{"version":3,"file":"index.cjs","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;"}
+{"version":3,"file":"index.cjs","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;"}

package/dist/index.js

@@ -7,7 +7,7 @@ export { isLiveLog } from './drivers/log.js';
 export { getFileNameFromHandle, getFilePathFromHandle, isImportFileHandleIndex, isImportFileHandleUpload } from './drivers/ls.js';
 export { dataInfoToEntries, entriesToDataInfo, isDataInfo, isDataInfoEntries, isPartitionedDataInfoEntries, mapDataInfo, mapDataInfoEntries, visitDataInfo } from './drivers/pframe/data_info.js';
 export { PTableAbsent, PTableNA, isPTableAbsent, isPTableNA, isPTableValueAxis, pTableValue, pTableValueBranded } from './drivers/pframe/data_types.js';
-export { Annotation, AnnotationJson, Domain, DomainJson, PColumnName, ValueType, canonicalizeAxisId, canonicalizeAxisWithParents, getArrayFromAxisTree, getAxesId, getAxesTree, getAxisId, getColumnIdAndSpec, getDenormalizedAxesList, getNormalizedAxesList, getPColumnSpecId, getSetFromAxisTree, getTypeFromPColumnOrAxisSpec, isAxisId, isLabelColumn, isLinkerColumn, matchAxisId, readAnnotation, readAnnotationJson, readAnnotationJsonOrThrow, readDomain, readDomainJson, readDomainJsonOrThrow, readMetadata, readMetadataJson, readMetadataJsonOrThrow } from './drivers/pframe/spec/spec.js';
+export { Annotation, AnnotationJson, Domain, DomainJson, PAxisName, PColumnName, ValueType, canonicalizeAxisId, canonicalizeAxisWithParents, getArrayFromAxisTree, getAxesId, getAxesTree, getAxisId, getColumnIdAndSpec, getDenormalizedAxesList, getNormalizedAxesList, getPColumnSpecId, getSetFromAxisTree, getTypeFromPColumnOrAxisSpec, isAxisId, isLabelColumn, isLinkerColumn, matchAxisId, readAnnotation, readAnnotationJson, readAnnotationJsonOrThrow, readDomain, readDomainJson, readDomainJsonOrThrow, readMetadata, readMetadataJson, readMetadataJsonOrThrow } from './drivers/pframe/spec/spec.js';
 export { mapJoinEntry, mapPTableDef } from './drivers/pframe/table_calculate.js';
 export { getPTableColumnId } from './drivers/pframe/table_common.js';
 export { AnchoredIdDeriver, resolveAnchors } from './drivers/pframe/spec/anchored.js';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@milaboratories/pl-model-common",
-  "version": "1.24.0",
+  "version": "1.24.1",
   "description": "Platforma SDK Model",
   "type": "module",
   "types": "./dist/index.d.ts",
@@ -26,10 +26,10 @@
     "typescript": "~5.6.3",
     "vitest": "^4.0.16",
     "@vitest/coverage-istanbul": "^4.0.16",
-    "@milaboratories/build-configs": "1.2.2",
     "@milaboratories/eslint-config": "1.0.5",
+    "@milaboratories/build-configs": "1.4.0",
     "@milaboratories/ts-configs": "1.2.0",
-    "@milaboratories/ts-builder": "1.2.2"
+    "@milaboratories/ts-builder": "1.2.4"
   },
   "scripts": {
     "type-check": "ts-builder types --target node",

package/src/drivers/pframe/spec/spec.ts

@@ -76,11 +76,17 @@ export function readMetadataJson<M extends Metadata, T extends keyof MetadataJso
 export const Domain = {
   Alphabet: 'pl7.app/alphabet',
   BlockId: 'pl7.app/blockId',
+  VDJ: {
+    ScClonotypeChain: {
+      Index: 'pl7.app/vdj/scClonotypeChain/index',
+    },
+  },
 } as const;
 
 export type Domain = Metadata & Partial<{
-  [Domain.Alphabet]: 'nucleotide' | 'aminoacid' | string;
+  [Domain.Alphabet]: 'nucleotide' | 'aminoacid' | (string & {});
   [Domain.BlockId]: string;
+  [Domain.VDJ.ScClonotypeChain.Index]: 'primary' | 'secondary' | (string & {});
 }>;
 
 export type DomainJson = MetadataJson<Domain>;
@@ -152,11 +158,14 @@ export const Annotation = {
     Visibility: 'pl7.app/table/visibility',
   },
   Trace: 'pl7.app/trace',
+  VDJ: {
+    IsAssemblingFeature: 'pl7.app/vdj/isAssemblingFeature',
+  },
 } as const;
 
 export type Annotation = Metadata & Partial<{
-  [Annotation.Alphabet]: 'nucleotide' | 'aminoacid' | string;
-  [Annotation.AxisNature]: 'homogeneous' | 'heterogeneous' | 'scaleCompatible' | string;
+  [Annotation.Alphabet]: 'nucleotide' | 'aminoacid' | (string & {});
+  [Annotation.AxisNature]: 'homogeneous' | 'heterogeneous' | 'scaleCompatible' | (string & {});
   [Annotation.Description]: string;
   [Annotation.DiscreteValues]: StringifiedJson<number[]> | StringifiedJson<string[]>;
   [Annotation.Format]: string;
@@ -169,8 +178,8 @@ export type Annotation = Metadata & Partial<{
   [Annotation.Graph.Palette]: StringifiedJson<{ mapping: Record<string, number>; name: string }>;
   [Annotation.Graph.Thresholds]: StringifiedJson<{ columnId: { valueType: ValueType; name: string }; value: number }[]>;
   [Annotation.Graph.TreatAbsentValuesAs]: StringifiedJson<number>;
-  [Annotation.HideDataFromUi]: StringifiedJson<boolean>;
   [Annotation.HideDataFromGraphs]: StringifiedJson<boolean>;
+  [Annotation.HideDataFromUi]: StringifiedJson<boolean>;
   [Annotation.IsDiscreteFilter]: StringifiedJson<boolean>;
   [Annotation.IsLinkerColumn]: StringifiedJson<boolean>;
   [Annotation.IsSubset]: StringifiedJson<boolean>;
@@ -183,8 +192,9 @@ export type Annotation = Metadata & Partial<{
   [Annotation.Sequence.IsAnnotation]: StringifiedJson<boolean>;
   [Annotation.Table.FontFamily]: string;
   [Annotation.Table.OrderPriority]: StringifiedJson<number>;
-  [Annotation.Table.Visibility]: 'hidden' | 'optional' | string;
+  [Annotation.Table.Visibility]: 'hidden' | 'optional' | (string & {});
   [Annotation.Trace]: StringifiedJson<Record<string, unknown>>;
+  [Annotation.VDJ.IsAssemblingFeature]: StringifiedJson<boolean>;
 }>;
 
 // export const AxisSpec = z.object({
@@ -236,6 +246,7 @@ export const AnnotationJson: AnnotationJson = {
   [Annotation.Sequence.IsAnnotation]: z.boolean(),
   [Annotation.Table.OrderPriority]: z.number(),
   [Annotation.Trace]: z.record(z.string(), z.unknown()),
+  [Annotation.VDJ.IsAssemblingFeature]: z.boolean(),
 };
 
 /// Helper function for reading plain annotation values
@@ -503,6 +514,19 @@ export const PColumnName = {
   Table: {
     RowSelection: 'pl7.app/table/row-selection',
   },
+  VDJ: {
+    Sequence: 'pl7.app/vdj/sequence',
+  },
+} as const;
+
+/// Well-known axis names
+export const PAxisName = {
+  VDJ: {
+    Assay: {
+      SequenceId: 'pl7.app/vdj/assay/sequenceId',
+    },
+    ScClonotypeKey: 'pl7.app/vdj/scClonotypeKey',
+  },
 } as const;
 
 export function isLabelColumn(column: PColumnSpec) {