@apollo-annotation/shared 0.3.9 → 0.3.11

package/dist/Changes/AddFeatureChange.js

@@ -53,6 +53,11 @@ class AddFeatureChange extends common_1.FeatureChange {
         }
         let featureCnt = 0;
         logger.debug?.(`changes: ${JSON.stringify(changes)}`);
+        const { INDEXED_IDS } = process.env;
+        let idsToIndex;
+        if (INDEXED_IDS) {
+            idsToIndex = INDEXED_IDS.split(',');
+        }
         // Loop the changes
         for (const change of changes) {
             logger.debug?.(`change: ${JSON.stringify(change)}`);
@@ -67,12 +72,14 @@ class AddFeatureChange extends common_1.FeatureChange {
             }
             // CopyFeature is called from CopyFeature.tsx
             if (copyFeature) {
+                const indexedIds = this.getIndexedIds(addedFeature, idsToIndex);
                 // Add into Mongo
-                const [newFeatureDoc] = await featureModel.create([{ ...addedFeature, allIds, status: -1, user }], { session });
+                const [newFeatureDoc] = await featureModel.create([{ ...addedFeature, allIds, indexedIds, status: -1, user }], { session });
                 logger.debug?.(`Copied feature, docId "${newFeatureDoc._id}" to assembly "${assembly}"`);
                 featureCnt++;
             }
             else {
+                const indexedIds = this.getIndexedIds(addedFeature, idsToIndex);
                 // Adding new child feature
                 if (parentFeatureId) {
                     const topLevelFeature = await featureModel
@@ -89,12 +96,16 @@ class AddFeatureChange extends common_1.FeatureChange {
                     this.addChild(parentFeature, addedFeature);
                     const childIds = this.getChildFeatureIds(addedFeature);
                     topLevelFeature.allIds.push(_id, ...childIds);
+                    if (indexedIds.length > 0 && !topLevelFeature.indexedIds) {
+                        topLevelFeature.indexedIds = [];
+                    }
+                    topLevelFeature.indexedIds?.push(...indexedIds);
                     await topLevelFeature.save();
                 }
                 else {
                     const childIds = this.getChildFeatureIds(addedFeature);
                     const allIdsV2 = [_id, ...childIds];
-                    const [newFeatureDoc] = await featureModel.create([{ allIds: allIdsV2, status: 0, ...addedFeature }], { session });
+                    const [newFeatureDoc] = await featureModel.create([{ allIds: allIdsV2, indexedIds, status: 0, ...addedFeature }], { session });
                     logger.verbose?.(`Added docId "${newFeatureDoc._id}"`);
                 }
             }

package/dist/Changes/AddFeatureChange.js.map

@@ -1 +1 @@
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package/dist/Changes/DeleteFeatureChange.js

@@ -35,6 +35,11 @@ class DeleteFeatureChange extends common_1.FeatureChange {
     async executeOnServer(backend) {
         const { featureModel, session } = backend;
         const { changes, logger } = this;
+        const { INDEXED_IDS } = process.env;
+        let idsToIndex;
+        if (INDEXED_IDS) {
+            idsToIndex = INDEXED_IDS.split(',');
+        }
         // Loop the changes
         for (const change of changes) {
             const { deletedFeature, parentFeatureId } = change;
@@ -60,6 +65,20 @@ class DeleteFeatureChange extends common_1.FeatureChange {
             const deletedIds = findAndDeleteChildFeature(featureDoc, deletedFeature._id, this);
             deletedIds.push(deletedFeature._id);
             featureDoc.allIds = featureDoc.allIds.filter((id) => !deletedIds.includes(id));
+            const indexedIds = this.getIndexedIds(featureDoc, idsToIndex);
+            if (featureDoc.indexedIds) {
+                if (indexedIds.length > 0) {
+                    featureDoc.indexedIds = indexedIds;
+                }
+                else {
+                    delete featureDoc.indexedIds;
+                }
+            }
+            else {
+                if (indexedIds.length > 0) {
+                    featureDoc.indexedIds = indexedIds;
+                }
+            }
             // Save updated document in Mongo
             featureDoc.markModified('children'); // Mark as modified. Without this save() -method is not updating data in database
             try {

package/dist/Changes/DeleteFeatureChange.js.map

@@ -1 +1 @@
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+{"version":3,"file":"DeleteFeatureChange.js","sourceRoot":"","sources":["../../src/Changes/DeleteFeatureChange.ts"],"names":[],"mappings":";;;AAiMA,8DAwBC;AAED,sDAIC;AA/ND,qEAAqE;AACrE,qDAAqD;AACrD,gEAAgE;AAChE,sDAOkC;AAIlC,yDAAqD;AAwBrD,MAAa,mBAAoB,SAAQ,sBAAa;IACpD,QAAQ,GAAG,qBAA8B,CAAA;IACzC,OAAO,CAA8B;IAErC,YAAY,IAAmC,EAAE,OAAuB;QACtE,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAC1D,CAAC;IACD,2EAA2E;IAC3E,IAAI,YAAY;QACd,OAAO,8BAA8B,CAAA;IACvC,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,UAAU,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACxD,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,MAAM,CAAC,EAAE,cAAc,EAAE,eAAe,EAAE,CAAC,GAAG,OAAO,CAAA;YACrD,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,cAAc,EAAE,eAAe,EAAE,CAAA;QAC5E,CAAC;QACD,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAA;IACpD,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,eAAe,CAAC,OAAwB;QAC5C,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;QACzC,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QAEhC,MAAM,EAAE,WAAW,EAAE,GAAG,OAAO,CAAC,GAAG,CAAA;QACnC,IAAI,UAAgC,CAAA;QACpC,IAAI,WAAW,EAAE,CAAC;YAChB,UAAU,GAAG,WAAW,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QACrC,CAAC;QAED,mBAAmB;QACnB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,EAAE,cAAc,EAAE,eAAe,EAAE,GAAG,MAAM,CAAA;YAElD,iBAAiB;YACjB,MAAM,UAAU,GAAG,MAAM,YAAY;iBAClC,OAAO,CAAC,EAAE,MAAM,EAAE,cAAc,CAAC,GAAG,EAAE,CAAC;iBACvC,OAAO,CAAC,OAAO,CAAC;iBAChB,IAAI,EAAE,CAAA;YACT,IAAI,CAAC,UAAU,EAAE,CAAC;gBAChB,MAAM,MAAM,GAAG,kEAAkE,cAAc,CAAC,GAAG,GAAG,CAAA;gBACtG,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;gBACpB,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,CAAA;YACzB,CAAC;YAED,sHAAsH;YACtH,IAAI,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,cAAc,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC9C,IAAI,eAAe,EAAE,CAAC;oBACpB,MAAM,IAAI,KAAK,CACb,YAAY,cAAc,CAAC,GAAG,kDAAkD,CACjF,CAAA;gBACH,CAAC;gBACD,MAAM,YAAY,CAAC,iBAAiB,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;gBACpD,MAAM,CAAC,KAAK,EAAE,CACZ,YAAY,cAAc,CAAC,GAAG,4BAA4B,UAAU,CAAC,GAAG,4BAA4B,CACrG,CAAA;gBACD,SAAQ;YACV,CAAC;YAED,MAAM,UAAU,GAAG,yBAAyB,CAC1C,UAAU,EACV,cAAc,CAAC,GAAG,EAClB,IAAI,CACL,CAAA;YACD,UAAU,CAAC,IAAI,CAAC,cAAc,CAAC,GAAG,CAAC,CAAA;YACnC,UAAU,CAAC,MAAM,GAAG,UAAU,CAAC,MAAM,CAAC,MAAM,CAC1C,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,CAAC,CACjC,CAAA;YACD,MAAM,UAAU,GAAG,IAAI,CAAC,aAAa,CAAC,UAAU,EAAE,UAAU,CAAC,CAAA;YAC7D,IAAI,UAAU,CAAC,UAAU,EAAE,CAAC;gBAC1B,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;oBAC1B,UAAU,CAAC,UAAU,GAAG,UAAU,CAAA;gBACpC,CAAC;qBAAM,CAAC;oBACN,OAAO,UAAU,CAAC,UAAU,CAAA;gBAC9B,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;oBAC1B,UAAU,CAAC,UAAU,GAAG,UAAU,CAAA;gBACpC,CAAC;YACH,CAAC;YACD,iCAAiC;YACjC,UAAU,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA,CAAC,iFAAiF;YACrH,IAAI,CAAC;gBACH,MAAM,UAAU,CAAC,IAAI,EAAE,CAAA;YACzB,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,MAAM,CAAC,KAAK,EAAE,CAAC,eAAe,KAAK,EAAE,CAAC,CAAA;gBACtC,MAAM,KAAK,CAAA;YACb,CAAC;YAED,MAAM,CAAC,KAAK,EAAE,CACZ,YAAY,cAAc,CAAC,GAAG,4BAA4B,UAAU,CAAC,GAAG,GAAG,CAC5E,CAAA;QACH,CAAC;IACH,CAAC;IAED,KAAK,CAAC,kBAAkB,CAAC,QAA4B;QACnD,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAA;IACvD,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,SAA0B;QAC9C,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;QAClC,CAAC;QACD,KAAK,MAAM,MAAM,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC;YAClC,MAAM,EAAE,cAAc,EAAE,eAAe,EAAE,GAAG,MAAM,CAAA;YAClD,IAAI,eAAe,EAAE,CAAC;gBACpB,MAAM,aAAa,GAAG,SAAS,CAAC,UAAU,CAAC,eAAe,CAAC,CAAA;gBAC3D,IAAI,CAAC,aAAa,EAAE,CAAC;oBACnB,MAAM,IAAI,KAAK,CAAC,kCAAkC,eAAe,GAAG,CAAC,CAAA;gBACvE,CAAC;gBACD,aAAa,CAAC,WAAW,CAAC,cAAc,CAAC,GAAG,CAAC,CAAA;YAC/C,CAAC;iBAAM,CAAC;gBACN,IAAI,SAAS,CAAC,UAAU,CAAC,cAAc,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC7C,SAAS,CAAC,aAAa,CAAC,cAAc,CAAC,GAAG,CAAC,CAAA;gBAC7C,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,UAAU;QACR,MAAM,EAAE,QAAQ,EAAE,UAAU,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QACtD,MAAM,iBAAiB,GAAG,CAAC,GAAG,UAAU,CAAC,CAAC,OAAO,EAAE,CAAA;QACnD,MAAM,cAAc,GAAG,CAAC,GAAG,OAAO,CAAC;aAChC,OAAO,EAAE;aACT,GAAG,CAAC,CAAC,mBAAmB,EAAE,EAAE,CAAC,CAAC;YAC7B,YAAY,EAAE,mBAAmB,CAAC,cAAc;YAChD,eAAe,EAAE,mBAAmB,CAAC,eAAe;SACrD,CAAC,CAAC,CAAA;QACL,MAAM,CAAC,KAAK,EAAE,CAAC,mBAAmB,IAAI,CAAC,SAAS,CAAC,cAAc,CAAC,GAAG,CAAC,CAAA;QACpE,OAAO,IAAI,mCAAgB,CACzB;YACE,UAAU,EAAE,iBAAiB;YAC7B,QAAQ,EAAE,kBAAkB;YAC5B,OAAO,EAAE,cAAc;YACvB,QAAQ;SACT,EACD,EAAE,MAAM,EAAE,CACX,CAAA;IACH,CAAC;CACF;AAlJD,kDAkJC;AAED;;;;;;GAMG;AACH,SAAgB,yBAAyB,CACvC,OAAgB,EAChB,iBAAyB,EACzB,MAAqB;IAErB,IAAI,CAAC,OAAO,CAAC,QAAQ,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CAAC,WAAW,OAAO,CAAC,GAAG,kBAAkB,CAAC,CAAA;IAC3D,CAAC;IACD,MAAM,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,OAAO,CAAA;IACjC,MAAM,KAAK,GAAG,QAAQ,CAAC,GAAG,CAAC,iBAAiB,CAAC,CAAA;IAC7C,IAAI,KAAK,EAAE,CAAC;QACV,MAAM,UAAU,GAAG,MAAM,CAAC,kBAAkB,CAAC,KAAK,CAAC,CAAA;QACnD,QAAQ,CAAC,MAAM,CAAC,iBAAiB,CAAC,CAAA;QAClC,OAAO,UAAU,CAAA;IACnB,CAAC;IACD,KAAK,MAAM,CAAC,EAAE,YAAY,CAAC,IAAI,QAAQ,EAAE,CAAC;QACxC,IAAI,CAAC;YACH,OAAO,yBAAyB,CAAC,YAAY,EAAE,iBAAiB,EAAE,MAAM,CAAC,CAAA;QAC3E,CAAC;QAAC,MAAM,CAAC;YACP,OAAO;QACT,CAAC;IACH,CAAC;IAED,MAAM,IAAI,KAAK,CAAC,YAAY,iBAAiB,kBAAkB,GAAG,EAAE,CAAC,CAAA;AACvE,CAAC;AAED,SAAgB,qBAAqB,C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package/dist/Changes/FeatureAttributeChange.js

@@ -61,11 +61,22 @@ class FeatureAttributeChange extends common_1.FeatureChange {
             logger.debug?.(`*** Found feature: ${JSON.stringify(foundFeature)}`);
             featuresForChanges.push({ feature: foundFeature, topLevelFeature });
         }
+        const { INDEXED_IDS } = process.env;
+        let idsToIndex;
+        if (INDEXED_IDS) {
+            idsToIndex = INDEXED_IDS.split(',');
+        }
         // Let's update objects
         for (const [idx, change] of changes.entries()) {
             const { newAttributes } = change;
             const { feature, topLevelFeature } = featuresForChanges[idx];
+            const indexedIdsChanged = idsToIndex?.some((id) => id in newAttributes || id in (feature?.attributes ?? {}));
             feature.attributes = newAttributes;
+            if (indexedIdsChanged) {
+                const indexedIds = this.getIndexedIds(topLevelFeature, idsToIndex);
+                topLevelFeature.indexedIds = indexedIds;
+                topLevelFeature.markModified('indexedIds');
+            }
             if (topLevelFeature._id.equals(feature._id)) {
                 topLevelFeature.markModified('attributes'); // Mark as modified. Without this save() -method is not updating data in database
             }

package/dist/Changes/FeatureAttributeChange.js.map

@@ -1 +1 @@
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package/dist/Changes/FromFileBaseChange.d.ts

@@ -1,4 +1,5 @@
 import { AssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
 import { type FileDocument } from '@apollo-annotation/schemas';
 import { type GFF3Feature } from '@gmod/gff';
 export declare abstract class FromFileBaseChange extends AssemblySpecificChange {
@@ -6,4 +7,5 @@ export declare abstract class FromFileBaseChange extends AssemblySpecificChange
     private refSeqCache;
     removeExistingFeatures(backend: ServerDataStore): Promise<void>;
     addFeatureIntoDb(gff3Feature: GFF3Feature, backend: ServerDataStore): Promise<void>;
+    getAllIds(feature: AnnotationFeatureSnapshot): string[];
 }

package/dist/Changes/FromFileBaseChange.js

@@ -155,8 +155,13 @@ class FromFileBaseChange extends common_1.AssemblySpecificChange {
         }
     }
     async addFeatureIntoDb(gff3Feature, backend) {
-        const { featureModel, refSeqModel, user } = backend;
+        const { INDEXED_IDS } = process.env;
+        let idsToIndex;
+        if (INDEXED_IDS) {
+            idsToIndex = INDEXED_IDS.split(',');
+        }
         const { assembly, refSeqCache } = this;
+        const { featureModel, refSeqModel, user } = backend;
         const [{ seq_id: refName }] = gff3Feature;
         if (!refName) {
             throw new Error(`Valid seq_id not found in feature ${JSON.stringify(gff3Feature)}`);
@@ -173,15 +178,25 @@ class FromFileBaseChange extends common_1.AssemblySpecificChange {
         if (!refSeqDoc) {
             throw new Error(`RefSeq was not found by assembly "${assembly}" and seq_id "${refName}" not found`);
         }
-        // Let's add featureId to parent feature
-        const featureIds = [];
-        const newFeature = (0, GFF3_1.gff3ToAnnotationFeature)(gff3Feature, refSeqDoc._id, featureIds);
+        const newFeature = (0, GFF3_1.gff3ToAnnotationFeature)(gff3Feature, refSeqDoc._id);
+        const allIds = this.getAllIds(newFeature);
+        const indexedIds = this.getIndexedIds(newFeature, idsToIndex);
         // Add into Mongo
         // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
         await featureModel.create([
-            { allIds: featureIds, ...newFeature, user, status: -1 },
+            { allIds, indexedIds, ...newFeature, user, status: -1 },
         ]);
     }
+    getAllIds(feature) {
+        const allIds = [feature._id];
+        if (feature.children) {
+            for (const child of Object.values(feature.children)) {
+                const childIds = this.getAllIds(child);
+                allIds.push(...childIds);
+            }
+        }
+        return allIds;
+    }
 }
 exports.FromFileBaseChange = FromFileBaseChange;
 //# sourceMappingURL=FromFileBaseChange.js.map

package/dist/Changes/FromFileBaseChange.js.map

@@ -1 +1 @@
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package/dist/GFF3/annotationFeatureToGFF3.test.js

@@ -2,13 +2,27 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 /* eslint-disable prefer-destructuring */
 /* eslint-disable @typescript-eslint/no-floating-promises */
+const node_fs_1 = require("node:fs");
 const node_test_1 = require("node:test");
+const gff_1 = require("@gmod/gff");
 const chai_1 = require("chai");
 const annotationFeatureToGFF3_1 = require("./annotationFeatureToGFF3");
-const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test");
+const testUtil_1 = require("./testUtil");
+(0, node_test_1.describe)('Converts AnnotationFeatureSnapshot JSON to GFF3 when', () => {
+    for (const testCase of testUtil_1.testCases) {
+        const { filenameStem, description } = testCase;
+        (0, node_test_1.it)(description, () => {
+            const annotationFeatures = JSON.parse((0, node_fs_1.readFileSync)(`test_data/${filenameStem}.json`, 'utf8'));
+            const expectedGFF3 = (0, node_fs_1.readFileSync)(`test_data/${filenameStem}.gff3`, 'utf8');
+            const gffFeatures = annotationFeatures.map((annotationFeature) => (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature));
+            const gff3 = (0, gff_1.formatSync)(gffFeatures);
+            (0, chai_1.expect)(gff3).to.equal(expectedGFF3);
+        });
+    }
+});
 (0, node_test_1.describe)('annotationFeatureToGFF3', () => {
     (0, node_test_1.it)('Test mandatory columns', () => {
-        const annotationFeature = (0, gff3ToAnnotationFeature_test_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
+        const annotationFeature = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
         const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
         chai_1.assert.deepEqual(gff3Feature.seq_id, 'chr1');
         chai_1.assert.deepEqual(gff3Feature.type, 'gene');
@@ -88,7 +102,7 @@ const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test")
         chai_1.assert.deepEqual(gff3Feature.score, null);
     });
     (0, node_test_1.it)('Convert one gene test attributes', () => {
-        const annotationFeature = (0, gff3ToAnnotationFeature_test_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
+        const annotationFeature = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
         const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
         chai_1.assert.deepEqual(gff3Feature.attributes?.Name, ['EDEN']);
         chai_1.assert.deepEqual(gff3Feature.attributes?.testid, ['t001', 't003']);
@@ -107,7 +121,7 @@ const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test")
         chai_1.assert.deepEqual(gff3Feature.attributes?.Is_circular, ['true']);
     });
     (0, node_test_1.it)('Convert one gene test children', () => {
-        const annotationFeature = (0, gff3ToAnnotationFeature_test_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
+        const annotationFeature = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
         const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
         const [children] = gff3Feature.child_features;
         const [mrna] = children;
@@ -119,7 +133,7 @@ const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test")
         chai_1.assert.deepEqual(cds.attributes?.Parent, ['mRNA10001']);
     });
     (0, node_test_1.it)('Convert CDSs', () => {
-        const annotationFeature = (0, gff3ToAnnotationFeature_test_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
+        const annotationFeature = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
         const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
         const [children] = gff3Feature.child_features;
         const [mrna] = children;

package/dist/GFF3/annotationFeatureToGFF3.test.js.map

@@ -1 +1 @@
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package/dist/GFF3/gff3ToAnnotationFeature.d.ts

@@ -1,3 +1,3 @@
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
 import { type GFF3Feature } from '@gmod/gff';
-export declare function gff3ToAnnotationFeature(gff3Feature: GFF3Feature, refSeq?: string, featureIds?: string[]): AnnotationFeatureSnapshot;
+export declare function gff3ToAnnotationFeature(gff3Feature: GFF3Feature, refSeq?: string): AnnotationFeatureSnapshot;

package/dist/GFF3/gff3ToAnnotationFeature.js

@@ -5,7 +5,7 @@ const tslib_1 = require("tslib");
 const util_1 = require("@jbrowse/core/util");
 const bson_objectid_1 = tslib_1.__importDefault(require("bson-objectid"));
 const gffReservedKeys_1 = require("./gffReservedKeys");
-function gff3ToAnnotationFeature(gff3Feature, refSeq, featureIds) {
+function gff3ToAnnotationFeature(gff3Feature, refSeq) {
     const [firstFeature] = gff3Feature;
     const { end, seq_id: refName, start, strand, type } = firstFeature;
     if (!refName) {
@@ -21,7 +21,7 @@ function gff3ToAnnotationFeature(gff3Feature, refSeq, featureIds) {
         throw new Error(`feature does not have end: ${JSON.stringify(firstFeature)}`);
     }
     const [min, max] = getFeatureMinMax(gff3Feature);
-    const convertedChildren = convertChildren(gff3Feature, refSeq, featureIds);
+    const convertedChildren = convertChildren(gff3Feature, refSeq);
     const convertedAttributes = convertFeatureAttributes(gff3Feature);
     const feature = {
         _id: new bson_objectid_1.default().toHexString(),
@@ -47,9 +47,6 @@ function gff3ToAnnotationFeature(gff3Feature, refSeq, featureIds) {
     if (convertedAttributes) {
         feature.attributes = convertedAttributes;
     }
-    if (featureIds) {
-        featureIds.push(feature._id);
-    }
     return feature;
 }
 function getFeatureMinMax(gff3Feature) {
@@ -150,12 +147,12 @@ function convertChildren(gff3Feature, refSeq, featureIds) {
             cdsFeatures.push(childFeature);
         }
         else {
-            const child = gff3ToAnnotationFeature(childFeature, refSeq, featureIds);
+            const child = gff3ToAnnotationFeature(childFeature, refSeq);
             convertedChildren[child._id] = child;
         }
     }
     if (cdsFeatures.length > 0) {
-        const processedCDS = processCDS(cdsFeatures, refSeq, featureIds);
+        const processedCDS = processCDS(cdsFeatures, refSeq);
         for (const cds of processedCDS) {
             convertedChildren[cds._id] = cds;
         }
@@ -311,13 +308,13 @@ function mergeAnnotationFeatures(features) {
  * should be represented in our internal structure
  * @param cdsFeatures -
  */
-function processCDS(cdsFeatures, refSeq, featureIds) {
+function processCDS(cdsFeatures, refSeq) {
     const locationCounts = cdsFeatures.map((cds) => cds.length);
     // If any CDS have multiple locations, assume it really is multiple CDS
     // (e.g. the mRNA has multiple alternative translational start sites)
     // and process normally.
     if (locationCounts.some((count) => count > 1)) {
-        return cdsFeatures.map((cds) => gff3ToAnnotationFeature(cds, refSeq, featureIds));
+        return cdsFeatures.map((cds) => gff3ToAnnotationFeature(cds, refSeq));
     }
     // If all CDS have a single location, we guess that this GFF3 represented CDS
     // as multiple features instead of a single feature with multiple locations.
@@ -338,7 +335,7 @@ function processCDS(cdsFeatures, refSeq, featureIds) {
     });
     // If no overlaps, assume it's a single CDS feature
     if (!overlapping) {
-        return [gff3ToAnnotationFeature(sortedCDSLocations, refSeq, featureIds)];
+        return [gff3ToAnnotationFeature(sortedCDSLocations, refSeq)];
     }
     // Some CDS locations overlap, the best we can do is use the original order to
     // guess how to group the locations into features
@@ -360,6 +357,6 @@ function processCDS(cdsFeatures, refSeq, featureIds) {
             lastGroup.push(location);
         }
     }
-    return groupedLocations.map((group) => gff3ToAnnotationFeature(group, refSeq, featureIds));
+    return groupedLocations.map((group) => gff3ToAnnotationFeature(group, refSeq));
 }
 //# sourceMappingURL=gff3ToAnnotationFeature.js.map

package/dist/GFF3/gff3ToAnnotationFeature.js.map

@@ -1 +1 @@
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package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts

@@ -1,2 +1 @@
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-export declare function readAnnotationFeatureSnapshot(fn: string): AnnotationFeatureSnapshot;
+export {};