@milaboratories/pl-model-common 1.48.0 → 1.50.0

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

@@ -1,9 +1,9 @@
 import { CanonicalizedJson, StringifiedJson } from "../../../json.js";
 import { PObject, PObjectId, PObjectSpec } from "../../../pool/spec.js";
+import "../../../pool/index.js";
 import { z } from "zod";
-
 //#region src/drivers/pframe/spec/spec.d.ts
-declare const ValueType: {
+export declare const ValueType: {
   readonly Int: "Int";
   readonly Long: "Long";
   readonly Float: "Float";
@@ -11,17 +11,17 @@ declare const ValueType: {
   readonly String: "String";
   readonly Bytes: "Bytes";
 };
-type AxisValueType = Extract<ValueType, "Int" | "Long" | "String">;
-type ColumnValueType = ValueType;
+export type AxisValueType = Extract<ValueType, "Int" | "Long" | "String">;
+export type ColumnValueType = ValueType;
 /** PFrame columns and axes within them may store one of these types. */
-type ValueType = (typeof ValueType)[keyof typeof ValueType];
-type Metadata = Record<string, string>;
-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 };
-type MetadataJson<M> = MetadataJsonImpl<Required<M>>;
-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;
-declare function readMetadataJson<M extends Metadata, T extends keyof MetadataJson<M>>(metadata: Metadata | undefined, metadataJson: MetadataJson<M>, key: T): z.infer<MetadataJson<M>[T]> | undefined;
-declare const Domain: {
+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; };
+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;
+export declare function readMetadataJson<M extends Metadata, T extends keyof MetadataJson<M>>(metadata: Metadata | undefined, metadataJson: MetadataJson<M>, key: T): z.infer<MetadataJson<M>[T]> | undefined;
+export declare const Domain: {
   readonly Alphabet: "pl7.app/alphabet";
   readonly BlockId: "pl7.app/blockId";
   readonly VDJ: {
@@ -33,23 +33,37 @@ declare const Domain: {
     };
   };
 };
-type Domain = Metadata & Partial<{
+/**
+ * Domain keys whose value is the id of a block, rather than a qualifier of the data.
+ *
+ * Applying a template repoints these at the blocks of the project being built: an axis a block
+ * produced names that block in its domain, so an axis left naming the exported-from project
+ * resolves to nothing. Listing the keys is what makes that safe — a template's entry ids are
+ * arbitrary non-empty strings, so a hand-written template may name an entry `closest`, and a
+ * qualifier that happens to read `closest` must not be mistaken for a reference to it.
+ *
+ * A key absent from here is simply left alone, which is the behaviour from before relocation
+ * reached domains at all. Adding one is therefore safe; omitting one costs only that a template
+ * carrying it applies still pointing at the project it came from.
+ */
+export declare const BlockScopedDomain: ReadonlySet<string>;
+export type Domain = Metadata & Partial<{
   [Domain.Alphabet]: "nucleotide" | "aminoacid" | (string & {});
   [Domain.BlockId]: string;
   [Domain.VDJ.ScClonotypeChain.Index]: "primary" | "secondary" | (string & {});
 }>;
-type DomainJson = MetadataJson<Domain>;
-declare const DomainJson: DomainJson;
-declare function readDomain<T extends keyof Domain>(spec: {
+export type DomainJson = MetadataJson<Domain>;
+export declare const DomainJson: DomainJson;
+export declare function readDomain<T extends keyof Domain>(spec: {
   domain?: Metadata | undefined;
 } | undefined, key: T): Domain[T] | undefined;
-declare function readDomainJsonOrThrow<T extends keyof DomainJson>(spec: {
+export declare function readDomainJsonOrThrow<T extends keyof DomainJson>(spec: {
   domain?: Metadata | undefined;
 } | undefined, key: T): z.infer<DomainJson[T]> | undefined;
-declare function readDomainJson<T extends keyof DomainJson>(spec: {
+export declare function readDomainJson<T extends keyof DomainJson>(spec: {
   domain?: Metadata | undefined;
 } | undefined, key: T): z.infer<DomainJson[T]> | undefined;
-declare const Annotation: {
+export declare const Annotation: {
   readonly AxisNature: "pl7.app/axisNature";
   readonly Alphabet: "pl7.app/alphabet";
   readonly Description: "pl7.app/description";
@@ -66,6 +80,7 @@ declare const Annotation: {
     readonly IsDenseAxis: "pl7.app/graph/isDenseAxis";
     readonly IsVirtual: "pl7.app/graph/isVirtual";
     readonly Palette: "pl7.app/graph/palette";
+    readonly Shape: "pl7.app/graph/shape";
     readonly Thresholds: "pl7.app/graph/thresholds";
     readonly TreatAbsentValuesAs: "pl7.app/graph/treatAbsentValuesAs";
   };
@@ -104,8 +119,8 @@ declare const Annotation: {
     readonly IsMainSequence: "pl7.app/vdj/isMainSequence";
   };
 };
-type AnnotationDataStatus = "missing" | "resolving" | "absent" | "computing" | "ready" | "error";
-type Annotation = Metadata & Partial<{
+export type AnnotationDataStatus = "missing" | "resolving" | "absent" | "computing" | "ready" | "error";
+export type Annotation = Metadata & Partial<{
   [Annotation.Alphabet]: "nucleotide" | "aminoacid" | (string & {});
   [Annotation.AxisNature]: "homogeneous" | "heterogeneous" | "scaleCompatible" | (string & {});
   [Annotation.Description]: string;
@@ -119,8 +134,15 @@ type Annotation = Metadata & Partial<{
   [Annotation.Graph.IsDenseAxis]: StringifiedJson<boolean>;
   [Annotation.Graph.IsVirtual]: StringifiedJson<boolean>;
   [Annotation.Graph.Palette]: StringifiedJson<{
-    mapping: Record<string, number>;
     name: string;
+    mapping?: Record<string, number>;
+    midPoint?: number;
+    min?: number;
+    max?: number;
+    log?: boolean;
+  }>;
+  [Annotation.Graph.Shape]: StringifiedJson<{
+    mapping: Record<string, string>;
   }>;
   [Annotation.Graph.Thresholds]: StringifiedJson<{
     columnId: {
@@ -159,20 +181,20 @@ declare const TraceEntrySchema: z.ZodObject<{
   type: z.ZodString;
   label: z.ZodString;
 }, z.ZodUnknown, "strip">>;
-type TraceEntry = z.infer<typeof TraceEntrySchema>;
-type Trace = TraceEntry[];
-type AnnotationJson = MetadataJson<Annotation>;
-declare const AnnotationJson: AnnotationJson;
-declare function readAnnotation<T extends keyof Annotation>(spec: {
+export type TraceEntry = z.infer<typeof TraceEntrySchema>;
+export type Trace = TraceEntry[];
+export type AnnotationJson = MetadataJson<Annotation>;
+export declare const AnnotationJson: AnnotationJson;
+export declare function readAnnotation<T extends keyof Annotation>(spec: {
   annotations?: Metadata | undefined;
 } | undefined, key: T): Annotation[T] | undefined;
-declare function readAnnotationJsonOrThrow<T extends keyof AnnotationJson>(spec: {
+export declare function readAnnotationJsonOrThrow<T extends keyof AnnotationJson>(spec: {
   annotations?: Metadata | undefined;
 } | undefined, key: T): z.infer<AnnotationJson[T]> | undefined;
-declare function readAnnotationJson<T extends keyof AnnotationJson>(spec: {
+export declare function readAnnotationJson<T extends keyof AnnotationJson>(spec: {
   annotations?: Metadata | undefined;
 } | undefined, key: T): z.infer<AnnotationJson[T]> | undefined;
-declare function isLinkerColumn(column: PColumnSpec): boolean;
+export declare function isLinkerColumn(column: PColumnSpec): boolean;
 /**
  * Specification of an individual axis.
  *
@@ -181,8 +203,10 @@ declare function isLinkerColumn(column: PColumnSpec): boolean;
  * Each record inside a PColumn is addressed by a unique tuple of values set for
  * all the axes specified in the column spec.
  */
-type AxisSpec = {
-  /** Type of the axis value. Should not use non-key types like float or double. */readonly type: AxisValueType; /** Name of the axis */
+export type AxisSpec = {
+  /** Type of the axis value. Should not use non-key types like float or double. */
+  readonly type: AxisValueType;
+  /** Name of the axis */
   readonly name: string;
   /** Adds auxiliary information to the axis name, type and parents to form a
    * unique identifier */
@@ -214,36 +238,36 @@ type AxisSpec = {
   readonly parentAxes?: number[];
 };
 /** Parents are specs, not indexes; normalized axis can be used considering its parents independently from column */
-interface AxisSpecNormalized extends Omit<AxisSpec, "parentAxes"> {
+export interface AxisSpecNormalized extends Omit<AxisSpec, "parentAxes"> {
   parentAxesSpec: AxisSpecNormalized[];
 }
 /** Tree: axis is a root, its parents are children */
-type AxisTree = {
+export type AxisTree = {
   axis: AxisSpecNormalized;
   children: AxisTree[];
 };
 /** Build tree by axis parents annotations */
-declare function getAxesTree(rootAxis: AxisSpecNormalized): AxisTree;
+export declare function getAxesTree(rootAxis: AxisSpecNormalized): AxisTree;
 /** Get set of canonicalized axisIds from axisTree */
-declare function getSetFromAxisTree(tree: AxisTree): Set<CanonicalizedJson<AxisId>>;
+export declare function getSetFromAxisTree(tree: AxisTree): Set<CanonicalizedJson<AxisId>>;
 /** Get array of axisSpecs from axisTree */
-declare function getArrayFromAxisTree(tree: AxisTree): AxisSpecNormalized[];
-declare function canonicalizeAxisWithParents(axis: AxisSpecNormalized): string & {
+export declare function getArrayFromAxisTree(tree: AxisTree): AxisSpecNormalized[];
+export declare function canonicalizeAxisWithParents(axis: AxisSpecNormalized): string & {
   __json_canonicalized: AxisId[];
 };
 /** Create list of normalized axisSpec (parents are in array of specs, not indexes) */
-declare function getNormalizedAxesList(axes: AxisSpec[]): AxisSpecNormalized[];
+export declare function getNormalizedAxesList(axes: AxisSpec[]): AxisSpecNormalized[];
 /** Create list of regular axisSpec from normalized (parents are indexes, inside of current axes list) */
-declare function getDenormalizedAxesList(axesSpec: AxisSpecNormalized[]): AxisSpec[];
+export declare function getDenormalizedAxesList(axesSpec: AxisSpecNormalized[]): AxisSpec[];
 /**
  * Resolve annotation-based parents (`pl7.app/parents`) to numeric `parentAxes`
  * on a column spec. Returns the spec unchanged if all axes already use numeric
  * indices or have no parent annotations.
  */
-declare function resolveAnnotationParents(spec: PColumnSpec): PColumnSpec;
+export declare function resolveAnnotationParents(spec: PColumnSpec): PColumnSpec;
 /** Common type representing spec for all the axes in a column */
-type AxesSpec = AxisSpec[];
-declare const PColumnName: {
+export type AxesSpec = AxisSpec[];
+export declare const PColumnName: {
   readonly Label: "pl7.app/label";
   readonly Table: {
     readonly RowSelection: "pl7.app/table/row-selection";
@@ -254,7 +278,7 @@ declare const PColumnName: {
     readonly Sequence: "pl7.app/vdj/sequence";
   };
 };
-declare const PAxisName: {
+export declare const PAxisName: {
   readonly SampleId: "pl7.app/sampleId";
   readonly VDJ: {
     readonly Assay: {
@@ -265,7 +289,7 @@ declare const PAxisName: {
     readonly ScClonotypeKey: "pl7.app/vdj/scClonotypeKey";
   };
 };
-declare function isLabelColumn(column: PColumnSpec): boolean;
+export declare function isLabelColumn(column: PColumnSpec): boolean;
 /**
  * Full column specification including all axes specs and specs of the column
  * itself.
@@ -277,11 +301,13 @@ declare function isLabelColumn(column: PColumnSpec): boolean;
  *
  * Each element in tuple correspond to the axis having the same index in axesSpec.
  */
-type PUniversalColumnSpec = PObjectSpec & {
+export type PUniversalColumnSpec = PObjectSpec & {
   /** Defines specific type of BObject, the most generic type of unit of
    * information in Platforma Project. */
-  readonly kind: "PColumn"; /** Type of column values */
-  readonly valueType: string; /** Column name */
+  readonly kind: "PColumn";
+  /** Type of column values */
+  readonly valueType: string;
+  /** Column name */
   readonly name: string;
   /** Adds auxiliary information to the axis name, type and parents to form a
    * unique identifier */
@@ -291,8 +317,10 @@ type PUniversalColumnSpec = PObjectSpec & {
   readonly contextDomain?: Record<string, string>;
   /** Any additional information attached to the column that does not affect its
    * identifier */
-  readonly annotations?: Record<string, string>; /** A list of zero-based indices of parent axes from the {@link axesSpec} array. */
-  readonly parentAxes?: number[]; /** Axes specifications */
+  readonly annotations?: Record<string, string>;
+  /** A list of zero-based indices of parent axes from the {@link axesSpec} array. */
+  readonly parentAxes?: number[];
+  /** Axes specifications */
   readonly axesSpec: AxesSpec;
 };
 /**
@@ -303,42 +331,47 @@ type PUniversalColumnSpec = PObjectSpec & {
  * values like files or other abstract data types. Data columns are optimized for storing and processing
  * basic tabular data.
  */
-type PDataColumnSpec = PUniversalColumnSpec & {
-  /** Type of column values */readonly valueType: ValueType;
+export type PDataColumnSpec = PUniversalColumnSpec & {
+  /** Type of column values */
+  readonly valueType: ValueType;
 };
-type PColumnSpec = PDataColumnSpec;
+export type PColumnSpec = PDataColumnSpec;
 /** Unique PColumnSpec identifier */
-type PColumnSpecId = {
+export type PColumnSpecId = {
   /** Defines specific type of BObject, the most generic type of unit of
    * information in Platforma Project. */
-  readonly kind: "PColumn"; /** Type of column values */
-  readonly valueType: ValueType; /** Column name */
+  readonly kind: "PColumn";
+  /** Type of column values */
+  readonly valueType: ValueType;
+  /** Column name */
   readonly name: string;
   /** Adds auxiliary information to the axis name, type and parents to form a
    * unique identifier */
   readonly domain?: Record<string, string>;
   /** Context domain provides additional column identity that is matched
    * by kinship rules (subset/superset/overlap) rather than exact equality */
-  readonly contextDomain?: Record<string, string>; /** A list of zero-based indices of parent axes from the {@link axesSpec} array. */
-  readonly parentAxes?: number[]; /** Axes id */
+  readonly contextDomain?: Record<string, string>;
+  /** A list of zero-based indices of parent axes from the {@link axesSpec} array. */
+  readonly parentAxes?: number[];
+  /** Axes id */
   readonly axesId: AxesId;
 };
-declare function getPColumnSpecId(spec: PColumnSpec): PColumnSpecId;
-interface PColumn<Data> extends PObject<Data> {
+export declare function getPColumnSpecId(spec: PColumnSpec): PColumnSpecId;
+export interface PColumn<Data> extends PObject<Data> {
   /** PColumn spec, allowing it to be found among other PObjects */
   readonly spec: PColumnSpec;
 }
 /** Columns in a PFrame also have internal identifier, this object represents
  * combination of specs and such id */
-interface PColumnIdAndSpec {
+export interface PColumnIdAndSpec {
   /** Internal column id within the PFrame */
   readonly columnId: PObjectId;
   /** Column spec */
   readonly spec: PColumnSpec;
 }
 /** Get column id and spec from a column */
-declare function getColumnIdAndSpec<Data>(column: PColumn<Data>): PColumnIdAndSpec;
-interface AxisId {
+export declare function getColumnIdAndSpec<Data>(column: PColumn<Data>): PColumnIdAndSpec;
+export interface AxisId {
   /** Type of the axis or column value. For an axis should not use non-key
    * types like float or double. */
   readonly type: AxisValueType;
@@ -352,17 +385,16 @@ interface AxisId {
   readonly contextDomain?: Record<string, string>;
 }
 /** Array of axis ids */
-type AxesId = AxisId[];
+export type AxesId = AxisId[];
 /** Extracts axis ids from axis spec */
-declare function getAxisId(spec: AxisSpec): AxisId;
+export declare function getAxisId(spec: AxisSpec): AxisId;
 /** Extracts axes ids from axes spec array from column spec */
-declare function getAxesId(spec: AxesSpec): AxesId;
+export declare function getAxesId(spec: AxesSpec): AxesId;
 /** Canonicalizes axis id */
-declare function canonicalizeAxisId(id: AxisId): CanonicalizedJson<AxisId>;
+export declare function canonicalizeAxisId(id: AxisId): CanonicalizedJson<AxisId>;
 /** Returns whether "match" axis id is compatible with the "query" */
-declare function matchAxisId(query: AxisId, target: AxisId): boolean;
-declare function getTypeFromPColumnOrAxisSpec(spec: PColumnSpec | AxisSpec): ValueType;
-declare function isAxisId(id: unknown): id is AxisId;
+export declare function matchAxisId(query: AxisId, target: AxisId): boolean;
+export declare function getTypeFromPColumnOrAxisSpec(spec: PColumnSpec | AxisSpec): ValueType;
+export declare function isAxisId(id: unknown): id is AxisId;
 //#endregion
-export { Annotation, AnnotationDataStatus, AnnotationJson, AxesId, AxesSpec, AxisId, AxisSpec, AxisSpecNormalized, AxisTree, AxisValueType, ColumnValueType, Domain, DomainJson, Metadata, MetadataJson, PAxisName, PColumn, PColumnIdAndSpec, PColumnName, PColumnSpec, PColumnSpecId, PDataColumnSpec, PUniversalColumnSpec, Trace, TraceEntry, 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, resolveAnnotationParents };
 //# sourceMappingURL=spec.d.ts.map

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

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

@@ -39,6 +39,36 @@ const Domain = {
 		ScClonotypeChain: { Index: "pl7.app/vdj/scClonotypeChain/index" }
 	}
 };
+/**
+* Domain keys whose value is the id of a block, rather than a qualifier of the data.
+*
+* Applying a template repoints these at the blocks of the project being built: an axis a block
+* produced names that block in its domain, so an axis left naming the exported-from project
+* resolves to nothing. Listing the keys is what makes that safe — a template's entry ids are
+* arbitrary non-empty strings, so a hand-written template may name an entry `closest`, and a
+* qualifier that happens to read `closest` must not be mistaken for a reference to it.
+*
+* A key absent from here is simply left alone, which is the behaviour from before relocation
+* reached domains at all. Adding one is therefore safe; omitting one costs only that a template
+* carrying it applies still pointing at the project it came from.
+*/
+const BlockScopedDomain = /* @__PURE__ */ new Set([
+	"pl7.app/blockId",
+	"pl7.app/block",
+	"pl7.app/redefined-by",
+	"pl7.app/annotationRunId",
+	"pl7.app/clonotypeAnnotationRunId",
+	"pl7.app/clustering/blockId",
+	"pl7.app/umap/blockId",
+	"pl7.app/peptide/extractionRunId",
+	"pl7.app/repertoire/extractionRunId",
+	"pl7.app/antibodyVariantDesigner/designRunId",
+	"pl7.app/vdj/clonotypingRunId",
+	"pl7.app/vdj/clustering/blockId",
+	"pl7.app/vdj/integration/blockId",
+	"pl7.app/vdj/spatiotemporalAnalysis/blockId",
+	"pl7.app/vdj/libraryId"
+]);
 const DomainJson = {};
 function readDomain(spec, key) {
 	return readMetadata(spec?.domain, key);
@@ -66,6 +96,7 @@ const Annotation = {
 		IsDenseAxis: "pl7.app/graph/isDenseAxis",
 		IsVirtual: "pl7.app/graph/isVirtual",
 		Palette: "pl7.app/graph/palette",
+		Shape: "pl7.app/graph/shape",
 		Thresholds: "pl7.app/graph/thresholds",
 		TreatAbsentValuesAs: "pl7.app/graph/treatAbsentValuesAs"
 	},
@@ -121,9 +152,14 @@ const AnnotationJson = {
 	[Annotation.Graph.Axis.SymmetricRange]: z.boolean(),
 	[Annotation.Graph.IsDenseAxis]: z.boolean(),
 	[Annotation.Graph.Palette]: z.object({
-		mapping: z.record(z.number()),
-		name: z.string()
+		name: z.string(),
+		mapping: z.record(z.coerce.number()).optional(),
+		midPoint: z.number().optional(),
+		min: z.number().optional(),
+		max: z.number().optional(),
+		log: z.boolean().optional()
 	}),
+	[Annotation.Graph.Shape]: z.object({ mapping: z.record(z.string()) }),
 	[Annotation.Graph.Thresholds]: z.array(z.object({
 		columnId: z.object({
 			valueType: ValueTypeSchema,
@@ -388,6 +424,6 @@ function isAxisId(id) {
 	return typeof id === "object" && id !== null && "name" in id && "type" in id;
 }
 //#endregion
-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, resolveAnnotationParents };
+export { Annotation, AnnotationJson, BlockScopedDomain, 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, resolveAnnotationParents };
 
 //# sourceMappingURL=spec.js.map