npm - @galaxy-tool-util/workflow-graph - Versions diffs - 1.0.0 → 1.15.0 - Mend

@galaxy-tool-util/workflow-graph 1.0.0 → 1.15.0

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Files changed (18) hide show

package/README.md +2 -12
package/dist/collection-type-variants.d.ts +12 -6
package/dist/collection-type-variants.d.ts.map +1 -1
package/dist/collection-type-variants.js +14 -8
package/dist/collection-type-variants.js.map +1 -1
package/dist/collection-type.d.ts +16 -2
package/dist/collection-type.d.ts.map +1 -1
package/dist/collection-type.js +57 -4
package/dist/collection-type.js.map +1 -1
package/dist/index.d.ts +2 -1
package/dist/index.d.ts.map +1 -1
package/dist/index.js +2 -1
package/dist/index.js.map +1 -1
package/dist/rules-dsl.d.ts +67 -0
package/dist/rules-dsl.d.ts.map +1 -0
package/dist/rules-dsl.js +477 -0
package/dist/rules-dsl.js.map +1 -0
package/package.json +8 -2

package/README.md CHANGED Viewed

@@ -1,15 +1,5 @@
 # @galaxy-tool-util/workflow-graph
-Pure collection-type algebra and datatype subtyping primitives extracted from Galaxy's workflow editor.
+Pure collection-type algebra, datatype subtyping primitives and the rule builder DSL, extracted from Galaxy. Its one runtime dependency, `pyre-to-regexp`, is the regex translator Galaxy's client uses.
-Consumed by:
-- Galaxy (re-exported from `client/src/components/Workflow/Editor/modules/` and
-  `client/src/components/Datatypes/`).
-- The TypeScript workflow connection validator in this monorepo.
-- Future tooling (CLI, VS Code plugin, gxwf-ui).
-No runtime dependencies. Pure TypeScript / ESM.
-See `TS_CONNECTION_REFACTOR_IN_GX_PLAN.md` and the `old/CONNECTION_VALIDATION.md`
-historical note for context on why these primitives were extracted.
+See the [workflow-graph package docs](https://jmchilton.github.io/galaxy-tool-util-ts/#/packages/workflow-graph) for the public API and TS-specific notes. The collection-type algebra itself is documented Galaxy-side in [`collection_semantics.yml`](https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/model/dataset_collections/types/collection_semantics.yml).

package/dist/collection-type-variants.d.ts CHANGED Viewed

@@ -4,19 +4,25 @@
  * Galaxy tools can declare `collection_types: string[]` on collection inputs,
  * meaning the input accepts any of several collection types. These helpers
  * mirror the inner loop of `InputCollectionTerminal._effectiveMapOver` in the
- * Galaxy editor and the Python port's `_split_collection_type` helper, minus
- * the sample_sheet asymmetry guard (which belongs in caller-side decision
- * logic — see D4 in the extraction plan).
+ * Galaxy editor and the Python port's `_split_collection_type` helper.
+ *
+ * sample_sheet asymmetry is enforced inside `CollectionTypeDescription.accepts`
+ * itself, so callers don't need to re-check it here for the simple
+ * `accepts(output)` cases. The Galaxy `InputCollectionTerminal.canAccept`
+ * still keeps a defense-in-depth re-check for compound effective types where
+ * the receiver's raw type can hide the guard from `accepts` — that remains a
+ * caller-side concern.
  */
 import type { CollectionTypeDescriptor } from "./collection-type.js";
 /**
- * True if `output`'s collection type matches any of the accepted `inputs`.
+ * True if any of the accepted `inputs` accepts `output` directly.
+ * Direction follows `input_type.accepts(output_type)`.
  */
-export declare function canMatchAny(output: CollectionTypeDescriptor, inputs: CollectionTypeDescriptor[]): boolean;
+export declare function acceptsAny(output: CollectionTypeDescriptor, inputs: CollectionTypeDescriptor[]): boolean;
 /**
  * Compute the effective map-over for an output connecting to a multi-accept
  * input. Mirrors `InputCollectionTerminal._effectiveMapOver`:
- * - If any accepted input directly matches the output, no map-over is needed
+ * - If any accepted input directly accepts the output, no map-over is needed
  *   (returns NULL).
  * - Otherwise, return the first non-null `output.effectiveMapOver(input)` for
  *   an input the output can map over.

package/dist/collection-type-variants.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"collection-type-variants.d.ts","sourceRoot":"","sources":["../src/collection-type-variants.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,KAAK,EAAE,wBAAwB,EAAE,MAAM,sBAAsB,CAAC;AAGrE;;;GAGG;AACH,wBAAgB,UAAU,CACxB,MAAM,EAAE,wBAAwB,EAChC,MAAM,EAAE,wBAAwB,EAAE,GACjC,OAAO,CAET;AAED;;;;;;;;GAQG;AACH,wBAAgB,mBAAmB,CACjC,MAAM,EAAE,wBAAwB,EAChC,MAAM,EAAE,wBAAwB,EAAE,GACjC,wBAAwB,CAa1B"}

package/dist/collection-type-variants.js CHANGED Viewed

@@ -4,28 +4,34 @@
  * Galaxy tools can declare `collection_types: string[]` on collection inputs,
  * meaning the input accepts any of several collection types. These helpers
  * mirror the inner loop of `InputCollectionTerminal._effectiveMapOver` in the
- * Galaxy editor and the Python port's `_split_collection_type` helper, minus
- * the sample_sheet asymmetry guard (which belongs in caller-side decision
- * logic — see D4 in the extraction plan).
+ * Galaxy editor and the Python port's `_split_collection_type` helper.
+ *
+ * sample_sheet asymmetry is enforced inside `CollectionTypeDescription.accepts`
+ * itself, so callers don't need to re-check it here for the simple
+ * `accepts(output)` cases. The Galaxy `InputCollectionTerminal.canAccept`
+ * still keeps a defense-in-depth re-check for compound effective types where
+ * the receiver's raw type can hide the guard from `accepts` — that remains a
+ * caller-side concern.
  */
 import { NULL_COLLECTION_TYPE_DESCRIPTION } from "./collection-type.js";
 /**
- * True if `output`'s collection type matches any of the accepted `inputs`.
+ * True if any of the accepted `inputs` accepts `output` directly.
+ * Direction follows `input_type.accepts(output_type)`.
  */
-export function canMatchAny(output, inputs) {
-    return inputs.some((input) => input.canMatch(output));
+export function acceptsAny(output, inputs) {
+    return inputs.some((input) => input.accepts(output));
 }
 /**
  * Compute the effective map-over for an output connecting to a multi-accept
  * input. Mirrors `InputCollectionTerminal._effectiveMapOver`:
- * - If any accepted input directly matches the output, no map-over is needed
+ * - If any accepted input directly accepts the output, no map-over is needed
  *   (returns NULL).
  * - Otherwise, return the first non-null `output.effectiveMapOver(input)` for
  *   an input the output can map over.
  * - Falls back to NULL when no variant accepts the output.
  */
 export function effectiveMapOverAny(output, inputs) {
-    if (inputs.some((input) => input.canMatch(output))) {
+    if (inputs.some((input) => input.accepts(output))) {
         return NULL_COLLECTION_TYPE_DESCRIPTION;
     }
     for (const input of inputs) {

package/dist/collection-type-variants.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"collection-type-variants.js","sourceRoot":"","sources":["../src/collection-type-variants.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAGH,OAAO,EAAE,gCAAgC,EAAE,MAAM,sBAAsB,CAAC;AAExE;;;GAGG;AACH,MAAM,UAAU,UAAU,CACxB,MAAgC,EAChC,MAAkC;IAElC,OAAO,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC;AACvD,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,mBAAmB,CACjC,MAAgC,EAChC,MAAkC;IAElC,IAAI,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC;QAClD,OAAO,gCAAgC,CAAC;IAC1C,CAAC;IACD,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;YAC7B,MAAM,SAAS,GAAG,MAAM,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAC;YACjD,IAAI,SAAS,KAAK,gCAAgC,EAAE,CAAC;gBACnD,OAAO,SAAS,CAAC;YACnB,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,gCAAgC,CAAC;AAC1C,CAAC"}

package/dist/collection-type.d.ts CHANGED Viewed

@@ -2,7 +2,8 @@ export interface CollectionTypeDescriptor {
     isCollection: boolean;
     collectionType: string | null;
     rank: number;
-    canMatch(other: CollectionTypeDescriptor): boolean;
+    accepts(other: CollectionTypeDescriptor): boolean;
+    compatible(other: CollectionTypeDescriptor): boolean;
     canMapOver(other: CollectionTypeDescriptor): boolean;
     append(other: CollectionTypeDescriptor): CollectionTypeDescriptor;
     equal(other: CollectionTypeDescriptor | null): boolean;
@@ -17,7 +18,20 @@ export declare class CollectionTypeDescription implements CollectionTypeDescript
     rank: number;
     constructor(collectionType: string);
     append(other: CollectionTypeDescriptor): CollectionTypeDescriptor;
-    canMatch(other: CollectionTypeDescriptor): boolean;
+    /**
+     * Asymmetric direct-edge check: does an input slot of type `this`
+     * accept an output of type `other`? Convention:
+     * `input_type.accepts(output_type)`. Used at workflow-editor edge
+     * validation.
+     */
+    accepts(other: CollectionTypeDescriptor): boolean;
+    /**
+     * Symmetric sibling-matching check: do `this` and `other` match such
+     * that they could drive a common map-over over sibling inputs of a
+     * single tool? Used for sibling map-over state checks where neither
+     * side is the declared input slot.
+     */
+    compatible(other: CollectionTypeDescriptor): boolean;
     canMapOver(other: CollectionTypeDescriptor): boolean;
     effectiveMapOver(other: CollectionTypeDescriptor): CollectionTypeDescriptor;
     equal(other: CollectionTypeDescriptor | null): boolean;

package/dist/collection-type.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"collection-type.d.ts","sourceRoot":"","sources":["../src/collection-type.ts"],"names":[],"mappings":"~~AAOA~~,MAAM,WAAW,wBAAwB;IACvC,YAAY,EAAE,OAAO,CAAC;IACtB,cAAc,EAAE,MAAM,GAAG,IAAI,CAAC;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,~~QAAQ~~,CAAC,KAAK,EAAE,wBAAwB,GAAG,OAAO,CAAC;~~IACnD~~,UAAU,CAAC,KAAK,EAAE,wBAAwB,GAAG,OAAO,CAAC;IACrD,MAAM,CAAC,KAAK,EAAE,wBAAwB,GAAG,wBAAwB,CAAC;IAClE,KAAK,CAAC,KAAK,EAAE,wBAAwB,GAAG,IAAI,GAAG,OAAO,CAAC;IACvD,QAAQ,IAAI,MAAM,CAAC;IACnB,gBAAgB,CAAC,KAAK,EAAE,wBAAwB,GAAG,wBAAwB,CAAC;CAC7E;AAED,eAAO,MAAM,gCAAgC,EAAE,~~wBAsB9C~~,CAAC;AAEF,eAAO,MAAM,+BAA+B,EAAE,~~wBAsB7C~~,CAAC;AAaF,qBAAa,yBAA0B,YAAW,wBAAwB;IACxE,cAAc,EAAE,MAAM,CAAC;IACvB,YAAY,EAAE,IAAI,CAAC;IACnB,IAAI,EAAE,MAAM,CAAC;gBAED,cAAc,EAAE,MAAM;IAKlC,MAAM,CAAC,KAAK,EAAE,wBAAwB,GAAG,wBAAwB;IASjE,~~QAAQ~~,CAAC,KAAK,EAAE,wBAAwB;~~IA2BxC~~,UAAU,CAAC,KAAK,EAAE,wBAAwB;~~IAuC1C~~,gBAAgB,CAAC,KAAK,EAAE,wBAAwB,GAAG,wBAAwB;IAkD3E,KAAK,CAAC,KAAK,EAAE,wBAAwB,GAAG,IAAI;IAM5C,QAAQ;IAGR,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM;CAGtC;AAKD,wBAAgB,wBAAwB,CAAC,cAAc,EAAE,MAAM,GAAG,SAAS,WAM1E"}
1	+ {"version":3,"file":"collection-type.d.ts","sourceRoot":"","sources":["../src/collection-type.ts"],"names":[],"mappings":"AAwBA,MAAM,WAAW,wBAAwB;IACvC,YAAY,EAAE,OAAO,CAAC;IACtB,cAAc,EAAE,MAAM,GAAG,IAAI,CAAC;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,CAAC,KAAK,EAAE,wBAAwB,GAAG,OAAO,CAAC;IAClD,UAAU,CAAC,KAAK,EAAE,wBAAwB,GAAG,OAAO,CAAC;IACrD,UAAU,CAAC,KAAK,EAAE,wBAAwB,GAAG,OAAO,CAAC;IACrD,MAAM,CAAC,KAAK,EAAE,wBAAwB,GAAG,wBAAwB,CAAC;IAClE,KAAK,CAAC,KAAK,EAAE,wBAAwB,GAAG,IAAI,GAAG,OAAO,CAAC;IACvD,QAAQ,IAAI,MAAM,CAAC;IACnB,gBAAgB,CAAC,KAAK,EAAE,wBAAwB,GAAG,wBAAwB,CAAC;CAC7E;AAED,eAAO,MAAM,gCAAgC,EAAE,wBAyB9C,CAAC;AAEF,eAAO,MAAM,+BAA+B,EAAE,wBAyB7C,CAAC;AAaF,qBAAa,yBAA0B,YAAW,wBAAwB;IACxE,cAAc,EAAE,MAAM,CAAC;IACvB,YAAY,EAAE,IAAI,CAAC;IACnB,IAAI,EAAE,MAAM,CAAC;gBAED,cAAc,EAAE,MAAM;IAKlC,MAAM,CAAC,KAAK,EAAE,wBAAwB,GAAG,wBAAwB;IASjE;;;;;OAKG;IACH,OAAO,CAAC,KAAK,EAAE,wBAAwB;IAqCvC;;;;;OAKG;IACH,UAAU,CAAC,KAAK,EAAE,wBAAwB;IAG1C,UAAU,CAAC,KAAK,EAAE,wBAAwB;IAgD1C,gBAAgB,CAAC,KAAK,EAAE,wBAAwB,GAAG,wBAAwB;IAkD3E,KAAK,CAAC,KAAK,EAAE,wBAAwB,GAAG,IAAI;IAM5C,QAAQ;IAGR,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM;CAGtC;AAKD,wBAAgB,wBAAwB,CAAC,cAAc,EAAE,MAAM,GAAG,SAAS,WAM1E"}

package/dist/collection-type.js CHANGED Viewed

@@ -1,4 +1,21 @@
-/* classes for reasoning about collection map over state
+/* Classes for reasoning about collection map-over state and the
+   compatibility algebra.
+   Two operations on collection types:
+   - accepts(other): asymmetric. input_type.accepts(output_type) is true
+     iff an output of type other can be connected to an input slot of
+     type this. Used at workflow-editor edge validation.
+   - compatible(other): symmetric. True iff this and other match such
+     that they could drive a common map-over over sibling inputs of one
+     tool. Used for sibling map-over state checks (neither side is the
+     input slot).
+   Mirrors the Python implementation in
+   lib/galaxy/model/dataset_collections/type_description.py — keep in sync.
+   See lib/galaxy/model/dataset_collections/types/collection_semantics.yml
+   "Type Compatibility Algebra" for the lattice diagram and worked examples.
+   Type variants:
    null: not a collection?
    NULL_COLLECTION_TYPE_DESCRIPTION: also not a collection. Is there any difference with null ?
    ANY_COLLECTION_TYPE_DESCRIPTION: collection, but will never be mapped over (input has no collection_type)
@@ -8,7 +25,10 @@ export const NULL_COLLECTION_TYPE_DESCRIPTION = {
     isCollection: false,
     collectionType: null,
     rank: 0,
-    canMatch: function (_other) {
+    accepts: function (_other) {
+        return false;
+    },
+    compatible: function (_other) {
         return false;
     },
     canMapOver: function () {
@@ -31,7 +51,10 @@ export const ANY_COLLECTION_TYPE_DESCRIPTION = {
     isCollection: true,
     collectionType: "any",
     rank: -1,
-    canMatch: function (other) {
+    accepts: function (other) {
+        return NULL_COLLECTION_TYPE_DESCRIPTION !== other;
+    },
+    compatible: function (other) {
         return NULL_COLLECTION_TYPE_DESCRIPTION !== other;
     },
     canMapOver: function () {
@@ -78,7 +101,13 @@ export class CollectionTypeDescription {
         }
         return new CollectionTypeDescription(`${this.collectionType}:${other.collectionType}`);
     }
-    canMatch(other) {
+    /**
+     * Asymmetric direct-edge check: does an input slot of type `this`
+     * accept an output of type `other`? Convention:
+     * `input_type.accepts(output_type)`. Used at workflow-editor edge
+     * validation.
+     */
+    accepts(other) {
         const otherCollectionType = other.collectionType;
         if (other === NULL_COLLECTION_TYPE_DESCRIPTION) {
             return false;
@@ -86,6 +115,14 @@ export class CollectionTypeDescription {
         if (other === ANY_COLLECTION_TYPE_DESCRIPTION) {
             return true;
         }
+        // sample_sheet asymmetry: a sample_sheet input needs column metadata
+        // that a plain-list output cannot provide. Check raw types before
+        // normalization (which otherwise equates the two).
+        if (this.collectionType.startsWith("sample_sheet") &&
+            otherCollectionType &&
+            !otherCollectionType.startsWith("sample_sheet")) {
+            return false;
+        }
         const normalizedThis = normalizeCollectionType(this.collectionType);
         const normalizedOther = otherCollectionType
             ? normalizeCollectionType(otherCollectionType)
@@ -105,10 +142,26 @@ export class CollectionTypeDescription {
         }
         return normalizedOther == normalizedThis;
     }
+    /**
+     * Symmetric sibling-matching check: do `this` and `other` match such
+     * that they could drive a common map-over over sibling inputs of a
+     * single tool? Used for sibling map-over state checks where neither
+     * side is the declared input slot.
+     */
+    compatible(other) {
+        return this.accepts(other) || other.accepts(this);
+    }
     canMapOver(other) {
         if (!other.collectionType || other.collectionType === "any") {
             return false;
         }
+        // sample_sheet asymmetry: a sample_sheet input requires sample_sheet
+        // column metadata; a plain-list output cannot be mapped over it.
+        // `this` is the output, `other` is the input.
+        if (other.collectionType.startsWith("sample_sheet") &&
+            !this.collectionType.startsWith("sample_sheet")) {
+            return false;
+        }
         const normalizedThis = normalizeCollectionType(this.collectionType);
         const normalizedOther = normalizeCollectionType(other.collectionType);
         if (this.rank <= other.rank) {

package/dist/collection-type.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/index.d.ts CHANGED Viewed

@@ -1,6 +1,7 @@
 export { ANY_COLLECTION_TYPE_DESCRIPTION, CollectionTypeDescription, NULL_COLLECTION_TYPE_DESCRIPTION, isValidCollectionTypeStr, type CollectionTypeDescriptor, } from "./collection-type.js";
-export { canMatchAny, effectiveMapOverAny } from "./collection-type-variants.js";
+export { acceptsAny, effectiveMapOverAny } from "./collection-type-variants.js";
 export type { DatatypesCombinedMap } from "./datatypes-combined-map.js";
 export { DatatypesMapperModel } from "./datatypes-mapper.js";
 export { ConnectionAcceptable, producesAcceptableDatatype } from "./connection-acceptable.js";
+export { RuleSet, RulesDSLError, SKIPPED_RULE_WARNING, applyRules, colHeadersFor, type ApplyRulesResult, type ClientRule, type Rule, type RuleMapping, type RuleRow, type RuleSetDict, type RuleSource, } from "./rules-dsl.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,+BAA+B,EAC/B,yBAAyB,EACzB,gCAAgC,EAChC,wBAAwB,EACxB,KAAK,wBAAwB,GAC9B,MAAM,sBAAsB,CAAC;AAC9B,OAAO,EAAE,~~WAAW~~,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;~~AACjF~~,YAAY,EAAE,oBAAoB,EAAE,MAAM,6BAA6B,CAAC;AACxE,OAAO,EAAE,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AAC7D,OAAO,EAAE,oBAAoB,EAAE,0BAA0B,EAAE,MAAM,4BAA4B,CAAC"}
1	+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,+BAA+B,EAC/B,yBAAyB,EACzB,gCAAgC,EAChC,wBAAwB,EACxB,KAAK,wBAAwB,GAC9B,MAAM,sBAAsB,CAAC;AAC9B,OAAO,EAAE,UAAU,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AAChF,YAAY,EAAE,oBAAoB,EAAE,MAAM,6BAA6B,CAAC;AACxE,OAAO,EAAE,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AAC7D,OAAO,EAAE,oBAAoB,EAAE,0BAA0B,EAAE,MAAM,4BAA4B,CAAC;AAC9F,OAAO,EACL,OAAO,EACP,aAAa,EACb,oBAAoB,EACpB,UAAU,EACV,aAAa,EACb,KAAK,gBAAgB,EACrB,KAAK,UAAU,EACf,KAAK,IAAI,EACT,KAAK,WAAW,EAChB,KAAK,OAAO,EACZ,KAAK,WAAW,EAChB,KAAK,UAAU,GAChB,MAAM,gBAAgB,CAAC"}

package/dist/index.js CHANGED Viewed

@@ -1,5 +1,6 @@
 export { ANY_COLLECTION_TYPE_DESCRIPTION, CollectionTypeDescription, NULL_COLLECTION_TYPE_DESCRIPTION, isValidCollectionTypeStr, } from "./collection-type.js";
-export { canMatchAny, effectiveMapOverAny } from "./collection-type-variants.js";
+export { acceptsAny, effectiveMapOverAny } from "./collection-type-variants.js";
 export { DatatypesMapperModel } from "./datatypes-mapper.js";
 export { ConnectionAcceptable, producesAcceptableDatatype } from "./connection-acceptable.js";
+export { RuleSet, RulesDSLError, SKIPPED_RULE_WARNING, applyRules, colHeadersFor, } from "./rules-dsl.js";
 //# sourceMappingURL=index.js.map

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,+BAA+B,EAC/B,yBAAyB,EACzB,gCAAgC,EAChC,wBAAwB,GAEzB,MAAM,sBAAsB,CAAC;AAC9B,OAAO,EAAE,~~WAAW~~,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;~~AAEjF~~,OAAO,EAAE,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AAC7D,OAAO,EAAE,oBAAoB,EAAE,0BAA0B,EAAE,MAAM,4BAA4B,CAAC"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,+BAA+B,EAC/B,yBAAyB,EACzB,gCAAgC,EAChC,wBAAwB,GAEzB,MAAM,sBAAsB,CAAC;AAC9B,OAAO,EAAE,UAAU,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AAEhF,OAAO,EAAE,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AAC7D,OAAO,EAAE,oBAAoB,EAAE,0BAA0B,EAAE,MAAM,4BAA4B,CAAC;AAC9F,OAAO,EACL,OAAO,EACP,aAAa,EACb,oBAAoB,EACpB,UAAU,EACV,aAAa,GAQd,MAAM,gBAAgB,CAAC"}

package/dist/rules-dsl.d.ts ADDED Viewed

@@ -0,0 +1,67 @@
+/**
+ * Port of Galaxy's rule builder DSL: `galaxy.util.rules_dsl.RuleSet` and the
+ * client's `RuleBuilder/rule-definitions.js` `applyRules`.
+ *
+ * Conformance is checked against Galaxy's `rules_dsl_spec.yml`, synced via
+ * `make sync-rules-dsl-spec`. Python `re` expressions go through
+ * `pyre-to-regexp`, as in Galaxy's client.
+ */
+export declare class RulesDSLError extends Error {
+    constructor(message: string);
+}
+export interface Rule {
+    type: string;
+    [key: string]: unknown;
+}
+export interface RuleMapping {
+    type: string;
+    columns: number[];
+    [key: string]: unknown;
+}
+export interface RuleSetDict {
+    rules: Rule[];
+    mapping?: RuleMapping[];
+}
+/** Collection element metadata a rule set reads from; tests also pass bare scalars. */
+export interface RuleSource {
+    identifiers?: string[];
+    indices?: number[];
+    tags?: string[];
+    columns?: unknown[];
+    hid?: unknown;
+    name?: unknown;
+    path?: unknown;
+    uri?: unknown;
+}
+export type RuleRow = unknown[];
+export declare class RuleSet {
+    readonly rules: Rule[];
+    readonly mapping: RuleMapping[];
+    constructor(ruleSet: RuleSetDict);
+    apply(data: RuleRow[], sources: unknown[]): [RuleRow[], unknown[]];
+    get hasErrors(): boolean;
+    get mappingAsDict(): Record<string, RuleMapping>;
+    get identifierColumns(): number[];
+    /** Collection type the mapping builds, e.g. `list:paired`; `""` when nothing is mapped. */
+    get collectionType(): string;
+}
+/** A rule as Galaxy's rule builder holds it; `applyRules` sets `error` and `warn`. */
+export interface ClientRule extends Rule {
+    error?: string | null;
+    warn?: string | null;
+}
+export interface ApplyRulesResult {
+    data: RuleRow[];
+    sources: unknown[];
+    columns: string[];
+    colHeadersPerRule: string[][];
+}
+export declare const SKIPPED_RULE_WARNING = "Skipped due to previous errors.";
+/** Spreadsheet-style headers (`A`, `B`, …) for the current table width. */
+export declare function colHeadersFor(data: RuleRow[], columns?: string[]): string[];
+/**
+ * Galaxy client's `applyRules`: runs rules without validating them, records a
+ * failing rule's message on `rule.error` and skips the rest with `rule.warn`.
+ */
+export declare function applyRules(data: RuleRow[], sources: unknown[], columns: string[], rules: ClientRule[], headersPerRule?: string[][]): ApplyRulesResult;
+//# sourceMappingURL=rules-dsl.d.ts.map

package/dist/rules-dsl.d.ts.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/rules-dsl.js ADDED Viewed

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+/**
+ * Port of Galaxy's rule builder DSL: `galaxy.util.rules_dsl.RuleSet` and the
+ * client's `RuleBuilder/rule-definitions.js` `applyRules`.
+ *
+ * Conformance is checked against Galaxy's `rules_dsl_spec.yml`, synced via
+ * `make sync-rules-dsl-spec`. Python `re` expressions go through
+ * `pyre-to-regexp`, as in Galaxy's client.
+ */
+import pyre from "pyre-to-regexp";
+export class RulesDSLError extends Error {
+    constructor(message) {
+        super(message);
+        this.name = "RulesDSLError";
+    }
+}
+const NEW_COLUMN = "new";
+const addsOneColumn = (_rule, columns) => [...columns, NEW_COLUMN];
+const removeColumns = (columns, targets) => columns.filter((_, index) => !targets.includes(index));
+const KEY_TYPE_CHECKS = {
+    int: (value) => Number.isInteger(value),
+    str: (value) => typeof value === "string",
+    bool: (value) => typeof value === "boolean",
+    list: (value) => Array.isArray(value),
+};
+function ensureRuleContainsKeys(rule, keys) {
+    for (const [key, keyType] of Object.entries(keys)) {
+        if (!(key in rule)) {
+            throw new RulesDSLError(`Rule of type [${rule.type}] does not contain key [${key}].`);
+        }
+        if (!KEY_TYPE_CHECKS[keyType](rule[key])) {
+            throw new RulesDSLError(`Rule of type [${rule.type}] does not contain correct value type for key [${key}].`);
+        }
+    }
+}
+function ensureKeyValueIn(rule, key, values) {
+    const value = rule[key];
+    if (!values.includes(value)) {
+        throw new RulesDSLError(`Invalid value [${String(value)}] for [${key}] encountered.`);
+    }
+}
+/** Compile a Python `re` pattern the way Galaxy's client does. */
+function compilePattern(expression) {
+    try {
+        return pyre(String(expression));
+    }
+    catch {
+        throw new RulesDSLError("Invalid regular expression specified.");
+    }
+}
+function applyRegex(regex, target, data, replacement, groupCount, allowUnmatched = false) {
+    const pattern = compilePattern(regex);
+    const groups = groupCount ? Number(groupCount) : 0;
+    let failedCount = 0;
+    const newData = data.map((row) => {
+        const match = pattern.exec(String(row[target]));
+        if (!match) {
+            if (!allowUnmatched) {
+                failedCount++;
+                return row;
+            }
+            return [...row, ...Array(replacement == null && groups ? groups : 1).fill("")];
+        }
+        if (replacement != null) {
+            return [...row, pattern.pyreReplace(match[0], replacement)];
+        }
+        if (groups) {
+            if (match.length - 1 !== groups) {
+                failedCount++;
+                return row;
+            }
+            return [...row, ...match.slice(1)];
+        }
+        return [...row, match[0]];
+    });
+    if (failedCount > 0) {
+        throw new RulesDSLError(`${failedCount} row(s) failed to match specified regular expression.`);
+    }
+    return newData;
+}
+function filterIndex(keep, items) {
+    return items.filter((_, index) => keep(index));
+}
+/** Python `float()` on a cell; throws instead of producing NaN. */
+function toFloat(value) {
+    const text = String(value).trim();
+    const result = Number(text);
+    if (text === "" || (Number.isNaN(result) && text.toLowerCase() !== "nan")) {
+        throw new RulesDSLError(`Could not convert [${text}] to a number.`);
+    }
+    return result;
+}
+function source(sources, index) {
+    return sources[index];
+}
+function metadataIndex(value, prefix) {
+    const index = Number(value.slice(prefix.length));
+    if (!Number.isInteger(index)) {
+        throw new RulesDSLError(`Invalid column metadata value [${value}].`);
+    }
+    return index;
+}
+/** Upload/history metadata only Galaxy's client reads; Python rejects these. */
+const CLIENT_METADATA = ["hid", "name", "path", "uri"];
+const RULES_DEFINITIONS = {
+    add_column_metadata: {
+        columns: addsOneColumn,
+        validate: (rule) => ensureRuleContainsKeys(rule, { value: "str" }),
+        apply: (rule, data, sources) => {
+            const value = rule.value;
+            let cell;
+            if (value.startsWith("identifier")) {
+                const identifierIndex = metadataIndex(value, "identifier");
+                cell = (index) => source(sources, index).identifiers[identifierIndex];
+            }
+            else if (value.startsWith("index")) {
+                const elementIndex = metadataIndex(value, "index");
+                cell = (index) => String(source(sources, index).indices[elementIndex]);
+            }
+            else if (value === "tags") {
+                cell = (index) => [...source(sources, index).tags].sort().join(",");
+            }
+            else if (CLIENT_METADATA.includes(value)) {
+                cell = (index) => source(sources, index)[value];
+            }
+            else {
+                throw new RulesDSLError(`Unknown metadata type [${value}]`);
+            }
+            return [data.map((row, index) => [...row, cell(index)]), sources];
+        },
+    },
+    add_column_group_tag_value: {
+        columns: addsOneColumn,
+        validate: (rule) => ensureRuleContainsKeys(rule, { value: "str" }),
+        apply: (rule, data, sources) => {
+            const tagPrefix = `group:${rule.value}:`;
+            const newRows = data.map((row, index) => {
+                const tag = [...source(sources, index).tags].sort().find((t) => t.startsWith(tagPrefix));
+                const value = tag === undefined ? (rule.default_value ?? "") : tag.slice(tagPrefix.length);
+                return [...row, value];
+            });
+            return [newRows, sources];
+        },
+    },
+    add_column_concatenate: {
+        columns: addsOneColumn,
+        validate: (rule) => ensureRuleContainsKeys(rule, { target_column_0: "int", target_column_1: "int" }),
+        apply: (rule, data, sources) => {
+            const column0 = rule.target_column_0;
+            const column1 = rule.target_column_1;
+            return [
+                data.map((row) => [...row, row[column0] + row[column1]]),
+                sources,
+            ];
+        },
+    },
+    add_column_basename: {
+        columns: addsOneColumn,
+        validate: (rule) => ensureRuleContainsKeys(rule, { target_column: "int" }),
+        apply: (rule, data, sources) => [
+            applyRegex("[^/]*$", rule.target_column, data),
+            sources,
+        ],
+    },
+    add_column_regex: {
+        columns: (rule, columns) => {
+            const added = rule.replacement == null && rule.group_count ? Number(rule.group_count) : 1;
+            return [...columns, ...Array(added).fill(NEW_COLUMN)];
+        },
+        validate: (rule) => {
+            ensureRuleContainsKeys(rule, { target_column: "int", expression: "str" });
+            compilePattern(rule.expression);
+        },
+        apply: (rule, data, sources) => {
+            let allowUnmatched = false;
+            if ("allow_unmatched" in rule) {
+                ensureRuleContainsKeys(rule, { allow_unmatched: "bool" });
+                allowUnmatched = rule.allow_unmatched;
+            }
+            const newData = applyRegex(rule.expression, rule.target_column, data, rule.replacement, rule.group_count, allowUnmatched);
+            return [newData, sources];
+        },
+    },
+    add_column_rownum: {
+        columns: addsOneColumn,
+        validate: (rule) => ensureRuleContainsKeys(rule, { start: "int" }),
+        apply: (rule, data, sources) => {
+            const start = rule.start;
+            return [data.map((row, index) => [...row, `${index + start}`]), sources];
+        },
+    },
+    add_column_value: {
+        columns: addsOneColumn,
+        validate: (rule) => ensureRuleContainsKeys(rule, { value: "str" }),
+        apply: (rule, data, sources) => [data.map((row) => [...row, String(rule.value)]), sources],
+    },
+    add_column_substr: {
+        columns: addsOneColumn,
+        validate: (rule) => {
+            ensureRuleContainsKeys(rule, { target_column: "int", length: "int", substr_type: "str" });
+            ensureKeyValueIn(rule, "substr_type", [
+                "keep_prefix",
+                "drop_prefix",
+                "keep_suffix",
+                "drop_suffix",
+            ]);
+        },
+        apply: (rule, data, sources) => {
+            const target = rule.target_column;
+            const length = rule.length;
+            const substrType = rule.substr_type;
+            const newRows = data.map((row) => {
+                const original = row[target];
+                let start = 0;
+                let end = original.length;
+                if (substrType === "keep_prefix") {
+                    end = length;
+                }
+                else if (substrType === "drop_prefix") {
+                    start = length;
+                }
+                else if (substrType === "keep_suffix") {
+                    start = Math.max(end - length, 0);
+                }
+                else {
+                    end = Math.max(end - length, 0);
+                }
+                return [...row, original.slice(start, end)];
+            });
+            return [newRows, sources];
+        },
+    },
+    add_column_from_sample_sheet_index: {
+        columns: addsOneColumn,
+        validate: (rule) => ensureRuleContainsKeys(rule, { value: "int" }),
+        apply: (rule, data, sources) => {
+            const columnIndex = rule.value;
+            return [
+                data.map((row, index) => [...row, source(sources, index).columns[columnIndex]]),
+                sources,
+            ];
+        },
+    },
+    remove_columns: {
+        columns: (rule, columns) => removeColumns(columns, rule.target_columns),
+        validate: (rule) => ensureRuleContainsKeys(rule, { target_columns: "list" }),
+        apply: (rule, data, sources) => {
+            const targetColumns = rule.target_columns;
+            return [data.map((row) => row.filter((_, index) => !targetColumns.includes(index))), sources];
+        },
+    },
+    add_filter_regex: {
+        validate: (rule) => {
+            ensureRuleContainsKeys(rule, { target_column: "int", invert: "bool", expression: "str" });
+            compilePattern(rule.expression);
+        },
+        apply: (rule, data, sources) => {
+            const pattern = compilePattern(rule.expression);
+            const invert = rule.invert;
+            const keep = (index) => pattern.test(String(data[index][rule.target_column])) ? !invert : invert;
+            return [filterIndex(keep, data), filterIndex(keep, sources)];
+        },
+    },
+    add_filter_count: {
+        validate: (rule) => {
+            ensureRuleContainsKeys(rule, { count: "int", invert: "bool", which: "str" });
+            ensureKeyValueIn(rule, "which", ["first", "last"]);
+        },
+        apply: (rule, data, sources) => {
+            const numRows = data.length;
+            const n = rule.count;
+            const invert = rule.invert;
+            const keep = (index) => {
+                const matches = rule.which === "first" ? index >= n : index < numRows - n;
+                return matches ? !invert : invert;
+            };
+            return [filterIndex(keep, data), filterIndex(keep, sources)];
+        },
+    },
+    add_filter_empty: {
+        validate: (rule) => ensureRuleContainsKeys(rule, { target_column: "int", invert: "bool" }),
+        apply: (rule, data, sources) => {
+            const invert = rule.invert;
+            const keep = (index) => data[index][rule.target_column].length !== 0 ? !invert : invert;
+            return [filterIndex(keep, data), filterIndex(keep, sources)];
+        },
+    },
+    add_filter_matches: {
+        validate: (rule) => ensureRuleContainsKeys(rule, { target_column: "int", invert: "bool", value: "str" }),
+        apply: (rule, data, sources) => {
+            const invert = rule.invert;
+            const keep = (index) => data[index][rule.target_column] === rule.value ? !invert : invert;
+            return [filterIndex(keep, data), filterIndex(keep, sources)];
+        },
+    },
+    add_filter_compare: {
+        validate: (rule) => {
+            ensureRuleContainsKeys(rule, { target_column: "int", value: "int", compare_type: "str" });
+            ensureKeyValueIn(rule, "compare_type", [
+                "less_than",
+                "less_than_equal",
+                "greater_than",
+                "greater_than_equal",
+            ]);
+        },
+        apply: (rule, data, sources) => {
+            const value = rule.value;
+            const keep = (index) => {
+                const target = toFloat(data[index][rule.target_column]);
+                switch (rule.compare_type) {
+                    case "less_than":
+                        return target < value;
+                    case "less_than_equal":
+                        return target <= value;
+                    case "greater_than":
+                        return target > value;
+                    default:
+                        return target >= value;
+                }
+            };
+            return [filterIndex(keep, data), filterIndex(keep, sources)];
+        },
+    },
+    sort: {
+        validate: (rule) => ensureRuleContainsKeys(rule, { target_column: "int", numeric: "bool" }),
+        apply: (rule, data, sources) => {
+            const target = rule.target_column;
+            const key = (row) => (rule.numeric ? toFloat(row[target]) : String(row[target]));
+            // Array.prototype.sort is stable, matching Python's sorted().
+            const sorted = data
+                .map((row, index) => ({ row, source: sources[index], key: key(row) }))
+                .sort((a, b) => (a.key < b.key ? -1 : a.key > b.key ? 1 : 0));
+            return [sorted.map((item) => item.row), sorted.map((item) => item.source)];
+        },
+    },
+    swap_columns: {
+        columns: (rule, columns) => {
+            const swapped = [...columns];
+            swapped[rule.target_column_0] = columns[rule.target_column_1];
+            swapped[rule.target_column_1] = columns[rule.target_column_0];
+            return swapped;
+        },
+        validate: (rule) => ensureRuleContainsKeys(rule, { target_column_0: "int", target_column_1: "int" }),
+        apply: (rule, data, sources) => {
+            const column0 = rule.target_column_0;
+            const column1 = rule.target_column_1;
+            const newRows = data.map((row) => {
+                const copy = [...row];
+                copy[column0] = row[column1];
+                copy[column1] = row[column0];
+                return copy;
+            });
+            return [newRows, sources];
+        },
+    },
+    split_columns: {
+        columns: (rule, columns) => removeColumns(columns, rule.target_columns_0),
+        validate: (rule) => ensureRuleContainsKeys(rule, { target_columns_0: "list", target_columns_1: "list" }),
+        apply: (rule, data, sources) => {
+            const columns0 = rule.target_columns_0;
+            const columns1 = rule.target_columns_1;
+            const newRows = data.flatMap((row) => {
+                const row0 = [];
+                const row1 = [];
+                row.forEach((cell, index) => {
+                    if (columns0.includes(index)) {
+                        row0.push(cell);
+                    }
+                    else if (columns1.includes(index)) {
+                        row1.push(cell);
+                    }
+                    else {
+                        row0.push(cell);
+                        row1.push(cell);
+                    }
+                });
+                return [row0, row1];
+            });
+            return [newRows, sources.flatMap((s) => [s, s])];
+        },
+    },
+};
+function ruleDefinition(rule) {
+    const definition = RULES_DEFINITIONS[rule.type];
+    if (!definition) {
+        throw new RulesDSLError(`Unknown rule type [${rule.type}].`);
+    }
+    return definition;
+}
+export class RuleSet {
+    rules;
+    mapping;
+    constructor(ruleSet) {
+        if (!Array.isArray(ruleSet.rules)) {
+            throw new RulesDSLError("Rule set does not contain [rules].");
+        }
+        this.rules = ruleSet.rules;
+        this.mapping = ruleSet.mapping ?? [];
+    }
+    apply(data, sources) {
+        for (const rule of this.rules) {
+            const definition = ruleDefinition(rule);
+            definition.validate(rule);
+            [data, sources] = definition.apply(rule, data, sources);
+        }
+        return [data, sources];
+    }
+    get hasErrors() {
+        try {
+            for (const rule of this.rules) {
+                ruleDefinition(rule).validate(rule);
+            }
+        }
+        catch {
+            return true;
+        }
+        return false;
+    }
+    get mappingAsDict() {
+        return Object.fromEntries(this.mapping.map((m) => [m.type, m]));
+    }
+    get identifierColumns() {
+        const mapping = this.mappingAsDict;
+        const columns = [...(mapping.list_identifiers?.columns ?? [])];
+        for (const type of ["paired_identifier", "paired_or_unpaired_identifier"]) {
+            if (mapping[type]) {
+                columns.push(mapping[type].columns[0]);
+            }
+        }
+        return columns;
+    }
+    /** Collection type the mapping builds, e.g. `list:paired`; `""` when nothing is mapped. */
+    get collectionType() {
+        const mapping = this.mappingAsDict;
+        const ranks = (mapping.list_identifiers?.columns ?? []).map(() => "list");
+        if (mapping.paired_identifier) {
+            ranks.push("paired");
+        }
+        if (mapping.paired_or_unpaired_identifier) {
+            ranks.push("paired_or_unpaired");
+        }
+        return ranks.join(":");
+    }
+}
+export const SKIPPED_RULE_WARNING = "Skipped due to previous errors.";
+/** Spreadsheet-style headers (`A`, `B`, …) for the current table width. */
+export function colHeadersFor(data, columns) {
+    const width = data.length === 0 ? (columns?.length ?? 0) : data[0].length;
+    return Array.from({ length: width }, (_, i) => String.fromCharCode(65 + i));
+}
+/**
+ * Galaxy client's `applyRules`: runs rules without validating them, records a
+ * failing rule's message on `rule.error` and skips the rest with `rule.warn`.
+ */
+export function applyRules(data, sources, columns, rules, headersPerRule = []) {
+    const colHeadersPerRule = Array.from(headersPerRule);
+    let hasRuleError = false;
+    rules.forEach((rule, ruleIndex) => {
+        colHeadersPerRule[ruleIndex] = colHeadersFor(data, columns);
+        rule.error = null;
+        rule.warn = null;
+        if (hasRuleError) {
+            rule.warn = SKIPPED_RULE_WARNING;
+            return;
+        }
+        try {
+            const definition = ruleDefinition(rule);
+            [data, sources] = definition.apply(rule, data, sources);
+            columns = definition.columns ? definition.columns(rule, columns) : columns;
+        }
+        catch (e) {
+            hasRuleError = true;
+            rule.error = e instanceof Error ? e.message : String(e);
+        }
+    });
+    return { data, sources, columns, colHeadersPerRule };
+}
+//# sourceMappingURL=rules-dsl.js.map

package/dist/rules-dsl.js.map ADDED Viewed

@@ -0,0 +1 @@

+ 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package/package.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "name": "@galaxy-tool-util/workflow-graph",
-  "version": "1.0.0",
-  "description": "Pure collection-type algebra and datatype subtyping primitives extracted from Galaxy's workflow editor",
+  "version": "1.15.0",
+  "description": "Pure collection-type algebra, datatype subtyping primitives and rule builder DSL extracted from Galaxy",
   "type": "module",
   "sideEffects": false,
   "exports": {
@@ -32,6 +32,12 @@
     "datatypes"
   ],
   "license": "MIT",
+  "devDependencies": {
+    "yaml": "^2.8.3"
+  },
+  "dependencies": {
+    "pyre-to-regexp": "0.0.6"
+  },
   "scripts": {
     "build": "tsc",
     "typecheck": "tsc --noEmit",