@milaboratories/pl-model-common 1.24.3 → 1.24.4

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

@@ -5,17 +5,17 @@ var json = require('../../../json.cjs');
 var zod = require('zod');
 
 const ValueType = {
-    Int: 'Int',
-    Long: 'Long',
-    Float: 'Float',
-    Double: 'Double',
-    String: 'String',
-    Bytes: 'Bytes',
+    Int: "Int",
+    Long: "Long",
+    Float: "Float",
+    Double: "Double",
+    String: "String",
+    Bytes: "Bytes",
 };
 function readMetadata(metadata, key) {
     return metadata?.[key];
 }
-function readMetadataJsonOrThrow(metadata, metadataJson, key, methodNameInError = 'readMetadataJsonOrThrow') {
+function readMetadataJsonOrThrow(metadata, metadataJson, key, methodNameInError = "readMetadataJsonOrThrow") {
     const json = readMetadata(metadata, key);
     if (json === undefined)
         return undefined;
@@ -25,10 +25,10 @@ function readMetadataJsonOrThrow(metadata, metadataJson, key, methodNameInError
         return schema.parse(value);
     }
     catch (error) {
-        throw new Error(`${methodNameInError} failed, `
-            + `key: ${String(key)}, `
-            + `value: ${json}, `
-            + `error: ${errors.ensureError(error)}`);
+        throw new Error(`${methodNameInError} failed, ` +
+            `key: ${String(key)}, ` +
+            `value: ${json}, ` +
+            `error: ${errors.ensureError(error)}`);
     }
 }
 function readMetadataJson(metadata, metadataJson, key) {
@@ -41,11 +41,11 @@ function readMetadataJson(metadata, metadataJson, key) {
 }
 /// Well-known domains
 const Domain = {
-    Alphabet: 'pl7.app/alphabet',
-    BlockId: 'pl7.app/blockId',
+    Alphabet: "pl7.app/alphabet",
+    BlockId: "pl7.app/blockId",
     VDJ: {
         ScClonotypeChain: {
-            Index: 'pl7.app/vdj/scClonotypeChain/index',
+            Index: "pl7.app/vdj/scClonotypeChain/index",
         },
     },
 };
@@ -56,7 +56,7 @@ function readDomain(spec, key) {
 }
 /// Helper function for reading json-encoded domain values, throws on JSON parsing error
 function readDomainJsonOrThrow(spec, key) {
-    return readMetadataJsonOrThrow(spec?.domain, DomainJson, key, 'readDomainJsonOrThrow');
+    return readMetadataJsonOrThrow(spec?.domain, DomainJson, key, "readDomainJsonOrThrow");
 }
 /// Helper function for reading json-encoded domain values, returns undefined on JSON parsing error
 function readDomainJson(spec, key) {
@@ -64,51 +64,51 @@ function readDomainJson(spec, key) {
 }
 /// Well-known annotations
 const Annotation = {
-    AxisNature: 'pl7.app/axisNature',
-    Alphabet: 'pl7.app/alphabet',
-    Description: 'pl7.app/description',
-    DiscreteValues: 'pl7.app/discreteValues',
-    Format: 'pl7.app/format',
+    AxisNature: "pl7.app/axisNature",
+    Alphabet: "pl7.app/alphabet",
+    Description: "pl7.app/description",
+    DiscreteValues: "pl7.app/discreteValues",
+    Format: "pl7.app/format",
     Graph: {
         Axis: {
-            HighCardinality: 'pl7.app/graph/axis/highCardinality',
-            LowerLimit: 'pl7.app/graph/axis/lowerLimit',
-            SymmetricRange: 'pl7.app/graph/axis/symmetricRange',
-            UpperLimit: 'pl7.app/graph/axis/upperLimit',
+            HighCardinality: "pl7.app/graph/axis/highCardinality",
+            LowerLimit: "pl7.app/graph/axis/lowerLimit",
+            SymmetricRange: "pl7.app/graph/axis/symmetricRange",
+            UpperLimit: "pl7.app/graph/axis/upperLimit",
         },
-        IsDenseAxis: 'pl7.app/graph/isDenseAxis',
-        IsVirtual: 'pl7.app/graph/isVirtual',
-        Palette: 'pl7.app/graph/palette',
-        Thresholds: 'pl7.app/graph/thresholds',
-        TreatAbsentValuesAs: 'pl7.app/graph/treatAbsentValuesAs',
+        IsDenseAxis: "pl7.app/graph/isDenseAxis",
+        IsVirtual: "pl7.app/graph/isVirtual",
+        Palette: "pl7.app/graph/palette",
+        Thresholds: "pl7.app/graph/thresholds",
+        TreatAbsentValuesAs: "pl7.app/graph/treatAbsentValuesAs",
     },
-    HideDataFromUi: 'pl7.app/hideDataFromUi',
-    HideDataFromGraphs: 'pl7.app/hideDataFromGraphs',
-    IsDiscreteFilter: 'pl7.app/isDiscreteFilter',
-    IsLinkerColumn: 'pl7.app/isLinkerColumn',
-    IsSubset: 'pl7.app/isSubset',
-    Label: 'pl7.app/label',
-    Max: 'pl7.app/max',
-    Min: 'pl7.app/min',
-    MultipliesBy: 'pl7.app/multipliesBy',
-    Parents: 'pl7.app/parents',
+    HideDataFromUi: "pl7.app/hideDataFromUi",
+    HideDataFromGraphs: "pl7.app/hideDataFromGraphs",
+    IsDiscreteFilter: "pl7.app/isDiscreteFilter",
+    IsLinkerColumn: "pl7.app/isLinkerColumn",
+    IsSubset: "pl7.app/isSubset",
+    Label: "pl7.app/label",
+    Max: "pl7.app/max",
+    Min: "pl7.app/min",
+    MultipliesBy: "pl7.app/multipliesBy",
+    Parents: "pl7.app/parents",
     Sequence: {
         Annotation: {
-            Mapping: 'pl7.app/sequence/annotation/mapping',
+            Mapping: "pl7.app/sequence/annotation/mapping",
         },
-        IsAnnotation: 'pl7.app/sequence/isAnnotation',
+        IsAnnotation: "pl7.app/sequence/isAnnotation",
     },
     Table: {
-        FontFamily: 'pl7.app/table/fontFamily',
-        OrderPriority: 'pl7.app/table/orderPriority',
-        Visibility: 'pl7.app/table/visibility',
+        FontFamily: "pl7.app/table/fontFamily",
+        OrderPriority: "pl7.app/table/orderPriority",
+        Visibility: "pl7.app/table/visibility",
     },
-    Trace: 'pl7.app/trace',
+    Trace: "pl7.app/trace",
     VDJ: {
-        IsAssemblingFeature: 'pl7.app/vdj/isAssemblingFeature',
+        IsAssemblingFeature: "pl7.app/vdj/isAssemblingFeature",
     },
 };
-const ValueTypeSchema = zod.z.enum(['Int', 'Long', 'Float', 'Double', 'String']);
+const ValueTypeSchema = zod.z.enum(["Int", "Long", "Float", "Double", "String"]);
 const AnnotationJson = {
     [Annotation.DiscreteValues]: zod.z.array(zod.z.string()).or(zod.z.array(zod.z.number())),
     [Annotation.Graph.Axis.HighCardinality]: zod.z.boolean(),
@@ -144,7 +144,7 @@ function readAnnotation(spec, key) {
 }
 /// Helper function for reading json-encoded annotation values, throws on JSON parsing error
 function readAnnotationJsonOrThrow(spec, key) {
-    return readMetadataJsonOrThrow(spec?.annotations, AnnotationJson, key, 'readAnnotationJsonOrThrow');
+    return readMetadataJsonOrThrow(spec?.annotations, AnnotationJson, key, "readAnnotationJsonOrThrow");
 }
 /// Helper function for reading json-encoded annotation values, returns undefined on JSON parsing error
 function readAnnotationJson(spec, key) {
@@ -276,16 +276,21 @@ function getNormalizedAxesList(axes) {
     });
     axes.forEach((axis, idx) => {
         const modifiedAxis = modifiedAxes[idx];
-        if (axis.parentAxes) { // if we have parents by indexes then take from the list
+        if (axis.parentAxes) {
+            // if we have parents by indexes then take from the list
             modifiedAxis.parentAxesSpec = axis.parentAxes.map((idx) => modifiedAxes[idx]);
         }
-        else { // else try to parse from annotation name
+        else {
+            // else try to parse from annotation name
             const parents = parseParentsFromAnnotations(axis).map((name) => modifiedAxes.find((axis) => axis.name === name));
-            modifiedAxis.parentAxesSpec = parents.some((p) => p === undefined) ? [] : parents;
+            modifiedAxis.parentAxesSpec = parents.some((p) => p === undefined)
+                ? []
+                : parents;
             delete modifiedAxis.annotations?.[Annotation.Parents];
         }
     });
-    if (modifiedAxes.some(hasCycleOfParents)) { // Axes list is broken
+    if (modifiedAxes.some(hasCycleOfParents)) {
+        // Axes list is broken
         modifiedAxes.forEach((axis) => {
             axis.parentAxesSpec = [];
         });
@@ -312,21 +317,21 @@ function getDenormalizedAxesList(axesSpec) {
 }
 /// Well-known column names
 const PColumnName = {
-    Label: 'pl7.app/label',
+    Label: "pl7.app/label",
     Table: {
-        RowSelection: 'pl7.app/table/row-selection',
+        RowSelection: "pl7.app/table/row-selection",
     },
     VDJ: {
-        Sequence: 'pl7.app/vdj/sequence',
+        Sequence: "pl7.app/vdj/sequence",
     },
 };
 /// Well-known axis names
 const PAxisName = {
     VDJ: {
         Assay: {
-            SequenceId: 'pl7.app/vdj/assay/sequenceId',
+            SequenceId: "pl7.app/vdj/assay/sequenceId",
         },
-        ScClonotypeKey: 'pl7.app/vdj/scClonotypeKey',
+        ScClonotypeKey: "pl7.app/vdj/scClonotypeKey",
     },
 };
 function isLabelColumn(column) {
@@ -383,10 +388,10 @@ function matchAxisId(query, target) {
     return query.name === target.name && matchDomain(query.domain, target.domain);
 }
 function getTypeFromPColumnOrAxisSpec(spec) {
-    return 'valueType' in spec ? spec.valueType : spec.type;
+    return "valueType" in spec ? spec.valueType : spec.type;
 }
 function isAxisId(id) {
-    return typeof id === 'object' && id !== null && 'name' in id && 'type' in id;
+    return typeof id === "object" && id !== null && "name" in id && "type" in id;
 }
 
 exports.Annotation = Annotation;

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\nexport type AxisValueType = Extract<ValueType, 'Int' | 'Long' | 'String'>;\nexport type ColumnValueType = ValueType;\n\n/** PFrame columns and axes within them may store one of these types. */\nexport type ValueType = (typeof ValueType)[keyof typeof ValueType];\n\nexport type Metadata = Record<string, string>;\n\nexport function readMetadata<U extends Metadata, T extends keyof U = keyof U>(\n  metadata: Metadata | undefined,\n  key: T,\n): U[T] | undefined {\n  return (metadata as U | undefined)?.[key];\n}\n\ntype MetadataJsonImpl<M> = {\n  [P in keyof M as (M[P] extends StringifiedJson ? P : never)]: M[P] extends StringifiedJson<infer U> ? 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 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P : never]: M[P] extends StringifiedJson<infer U>\n    ? z.ZodType<U>\n    : never;\n};\nexport type MetadataJson<M> = MetadataJsonImpl<Required<M>>;\n\nexport function readMetadataJsonOrThrow<M extends Metadata, T extends keyof MetadataJson<M>>(\n  metadata: Metadata | undefined,\n  metadataJson: MetadataJson<M>,\n  key: T,\n  methodNameInError: string = \"readMetadataJsonOrThrow\",\n): z.infer<MetadataJson<M>[T]> | undefined {\n  const json = readMetadata<M, T>(metadata, key);\n  if (json === undefined) return undefined;\n\n  const schema = metadataJson[key];\n  try {\n    const value = JSON.parse(json);\n    return schema.parse(value);\n  } catch (error: unknown) {\n    throw new Error(\n      `${methodNameInError} failed, ` +\n        `key: ${String(key)}, ` +\n        `value: ${json}, ` +\n        `error: ${ensureError(error)}`,\n    );\n  }\n}\n\nexport function readMetadataJson<M extends Metadata, T extends keyof MetadataJson<M>>(\n  metadata: Metadata | undefined,\n  metadataJson: MetadataJson<M>,\n  key: T,\n): z.infer<MetadataJson<M>[T]> | undefined {\n  try {\n    return readMetadataJsonOrThrow(metadata, metadataJson, key);\n  } catch {\n    return undefined; // treat invalid values as unset\n  }\n}\n\n/// Well-known domains\nexport const Domain = {\n  Alphabet: \"pl7.app/alphabet\",\n  BlockId: \"pl7.app/blockId\",\n  VDJ: {\n    ScClonotypeChain: {\n      Index: \"pl7.app/vdj/scClonotypeChain/index\",\n    },\n  },\n} as const;\n\nexport type Domain = Metadata &\n  Partial<{\n    [Domain.Alphabet]: \"nucleotide\" | \"aminoacid\" | (string & {});\n    [Domain.BlockId]: string;\n    [Domain.VDJ.ScClonotypeChain.Index]: \"primary\" | \"secondary\" | (string & {});\n  }>;\n\nexport type DomainJson = MetadataJson<Domain>;\nexport const DomainJson: DomainJson = {};\n\n/// Helper function for reading plain domain values\nexport function readDomain<T extends keyof Domain>(\n  spec: { domain?: Metadata | undefined } | undefined,\n  key: T,\n): Domain[T] | undefined {\n  return readMetadata<Domain, T>(spec?.domain, key);\n}\n\n/// Helper function for reading json-encoded domain values, throws on JSON parsing error\nexport function readDomainJsonOrThrow<T extends keyof DomainJson>(\n  spec: { domain?: Metadata | undefined } | undefined,\n  key: T,\n): z.infer<DomainJson[T]> | undefined {\n  return readMetadataJsonOrThrow<Domain, T>(spec?.domain, DomainJson, key, \"readDomainJsonOrThrow\");\n}\n\n/// Helper function for reading json-encoded domain values, returns undefined on JSON parsing error\nexport function readDomainJson<T extends keyof DomainJson>(\n  spec: { domain?: Metadata | undefined } | undefined,\n  key: T,\n): z.infer<DomainJson[T]> | undefined {\n  return readMetadataJson<Domain, T>(spec?.domain, DomainJson, key);\n}\n\n/// Well-known annotations\nexport const Annotation = {\n  AxisNature: \"pl7.app/axisNature\",\n  Alphabet: \"pl7.app/alphabet\",\n  Description: \"pl7.app/description\",\n  DiscreteValues: 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{\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 &\n  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<\n      { columnId: { valueType: ValueType; name: string }; value: number }[]\n    >;\n    [Annotation.Graph.TreatAbsentValuesAs]: StringifiedJson<number>;\n    [Annotation.HideDataFromGraphs]: StringifiedJson<boolean>;\n    [Annotation.HideDataFromUi]: StringifiedJson<boolean>;\n    [Annotation.IsDiscreteFilter]: StringifiedJson<boolean>;\n    [Annotation.IsLinkerColumn]: StringifiedJson<boolean>;\n    [Annotation.IsSubset]: StringifiedJson<boolean>;\n    [Annotation.Label]: string;\n    [Annotation.Max]: StringifiedJson<number>;\n    [Annotation.Min]: StringifiedJson<number>;\n    [Annotation.MultipliesBy]: StringifiedJson<AxisSpec[\"name\"][]>;\n    [Annotation.Parents]: StringifiedJson<AxisSpec[\"name\"][]>;\n    [Annotation.Sequence.Annotation.Mapping]: StringifiedJson<Record<string, string>>;\n    [Annotation.Sequence.IsAnnotation]: StringifiedJson<boolean>;\n    [Annotation.Table.FontFamily]: string;\n    [Annotation.Table.OrderPriority]: StringifiedJson<number>;\n    [Annotation.Table.Visibility]: \"hidden\" | \"optional\" | (string & {});\n    [Annotation.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>(\n    spec?.annotations,\n    AnnotationJson,\n    key,\n    \"readAnnotationJsonOrThrow\",\n  );\n}\n\n/// Helper function for reading json-encoded annotation values, returns undefined on JSON parsing error\nexport function readAnnotationJson<T extends keyof AnnotationJson>(\n  spec: { annotations?: Metadata | undefined } | undefined,\n  key: T,\n): z.infer<AnnotationJson[T]> | undefined {\n  return readMetadataJson<Annotation, T>(spec?.annotations, AnnotationJson, key);\n}\n\nexport function isLinkerColumn(column: PColumnSpec): boolean {\n  return !!readAnnotationJson(column, Annotation.IsLinkerColumn);\n}\n\n/**\n * Specification of an individual axis.\n *\n * Each axis is a part of a composite key that addresses data inside the PColumn.\n *\n * Each record inside a PColumn is addressed by a unique tuple of values set for\n * all the axes specified in the column spec.\n */\nexport type AxisSpec = {\n  /** Type of the axis value. Should not use non-key types like float or double. */\n  readonly type: 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(\n  axis1: AxisSpecNormalized,\n  axis2: AxisSpecNormalized,\n): 1 | -1 | 0 {\n  if (axis1.name !== axis2.name) {\n    return axis1.name < axis2.name ? 1 : -1;\n  }\n  if (axis1.type !== axis2.type) {\n    return axis1.type < axis2.type ? 1 : -1;\n  }\n  const domain1 = canonicalizeJson(axis1.domain ?? {});\n  const domain2 = canonicalizeJson(axis2.domain ?? {});\n  if (domain1 !== domain2) {\n    return domain1 < domain2 ? 1 : -1;\n  }\n\n  const 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) {\n      // if we have parents by indexes then take from the list\n      modifiedAxis.parentAxesSpec = axis.parentAxes.map((idx) => modifiedAxes[idx]);\n    } else {\n      // else try to parse from annotation name\n      const parents = parseParentsFromAnnotations(axis).map((name) =>\n        modifiedAxes.find((axis) => axis.name === name),\n      );\n      modifiedAxis.parentAxesSpec = parents.some((p) => p === undefined)\n        ? []\n        : (parents as AxisSpecNormalized[]);\n\n      delete modifiedAxis.annotations?.[Annotation.Parents];\n    }\n  });\n\n  if (modifiedAxes.some(hasCycleOfParents)) {\n    // Axes list is broken\n    modifiedAxes.forEach((axis) => {\n      axis.parentAxesSpec = [];\n    });\n  } else {\n    modifiedAxes.forEach((axis) => {\n      sortParentsDeep(axis);\n    });\n  }\n\n  return modifiedAxes;\n}\n\n/** Create list of regular axisSpec from normalized (parents are indexes, inside of current axes list) */\nexport function getDenormalizedAxesList(axesSpec: AxisSpecNormalized[]): AxisSpec[] {\n  const idsList = axesSpec.map((axisSpec) => canonicalizeJson(getAxisId(axisSpec)));\n  return axesSpec.map((axisSpec) => {\n    const parentsIds = axisSpec.parentAxesSpec.map((axisSpec) =>\n      canonicalizeJson(getAxisId(axisSpec)),\n    );\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

@@ -1,6 +1,6 @@
-import { type CanonicalizedJson, type StringifiedJson } from '../../../json';
-import type { PObject, PObjectId, PObjectSpec } from '../../../pool';
-import { z } from 'zod';
+import { type CanonicalizedJson, type StringifiedJson } from "../../../json";
+import type { PObject, PObjectId, PObjectSpec } from "../../../pool";
+import { z } from "zod";
 export declare const ValueType: {
     readonly Int: "Int";
     readonly Long: "Long";
@@ -9,14 +9,14 @@ export declare const ValueType: {
     readonly String: "String";
     readonly Bytes: "Bytes";
 };
-export type AxisValueType = Extract<ValueType, 'Int' | 'Long' | 'String'>;
+export type AxisValueType = Extract<ValueType, "Int" | "Long" | "String">;
 export type ColumnValueType = ValueType;
 /** PFrame columns and axes within them may store one of these types. */
 export type ValueType = (typeof ValueType)[keyof typeof ValueType];
 export type Metadata = Record<string, string>;
 export declare function readMetadata<U extends Metadata, T extends keyof U = keyof U>(metadata: Metadata | undefined, key: T): U[T] | undefined;
 type MetadataJsonImpl<M> = {
-    [P in keyof M as (M[P] extends StringifiedJson ? P : never)]: M[P] extends StringifiedJson<infer U> ? z.ZodType<U> : never;
+    [P in keyof M as M[P] extends StringifiedJson ? P : never]: M[P] extends StringifiedJson<infer U> ? z.ZodType<U> : never;
 };
 export type MetadataJson<M> = MetadataJsonImpl<Required<M>>;
 export declare function readMetadataJsonOrThrow<M extends Metadata, T extends keyof MetadataJson<M>>(metadata: Metadata | undefined, metadataJson: MetadataJson<M>, key: T, methodNameInError?: string): z.infer<MetadataJson<M>[T]> | undefined;
@@ -31,9 +31,9 @@ export declare const Domain: {
     };
 };
 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 & {});
+    [Domain.VDJ.ScClonotypeChain.Index]: "primary" | "secondary" | (string & {});
 }>;
 export type DomainJson = MetadataJson<Domain>;
 export declare const DomainJson: DomainJson;
@@ -92,8 +92,8 @@ export declare const Annotation: {
     };
 };
 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;
@@ -123,13 +123,13 @@ export type Annotation = Metadata & Partial<{
     [Annotation.Label]: string;
     [Annotation.Max]: StringifiedJson<number>;
     [Annotation.Min]: StringifiedJson<number>;
-    [Annotation.MultipliesBy]: StringifiedJson<AxisSpec['name'][]>;
-    [Annotation.Parents]: StringifiedJson<AxisSpec['name'][]>;
+    [Annotation.MultipliesBy]: StringifiedJson<AxisSpec["name"][]>;
+    [Annotation.Parents]: StringifiedJson<AxisSpec["name"][]>;
     [Annotation.Sequence.Annotation.Mapping]: StringifiedJson<Record<string, string>>;
     [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>;
 }>;
@@ -185,7 +185,7 @@ export type AxisSpec = {
     readonly parentAxes?: number[];
 };
 /** Parents are specs, not indexes; normalized axis can be used considering its parents independently from column */
-export interface AxisSpecNormalized extends Omit<AxisSpec, 'parentAxes'> {
+export interface AxisSpecNormalized extends Omit<AxisSpec, "parentAxes"> {
     parentAxesSpec: AxisSpecNormalized[];
 }
 /** Tree: axis is a root, its parents are children */
@@ -240,7 +240,7 @@ export declare function isLabelColumn(column: PColumnSpec): boolean;
 export type PUniversalColumnSpec = PObjectSpec & {
     /** Defines specific type of BObject, the most generic type of unit of
      * information in Platforma Project. */
-    readonly kind: 'PColumn';
+    readonly kind: "PColumn";
     /** Type of column values */
     readonly valueType: string;
     /** Column name */
@@ -273,7 +273,7 @@ export type PColumnSpec = PDataColumnSpec;
 export type PColumnSpecId = {
     /** Defines specific type of BObject, the most generic type of unit of
      * information in Platforma Project. */
-    readonly kind: 'PColumn';
+    readonly kind: "PColumn";
     /** Type of column values */
     readonly valueType: ValueType;
     /** Column name */

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

@@ -1 +1 @@
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