@apollo-annotation/shared 0.3.11 → 0.3.13
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/Changes/AddAssemblyAliasesChange.d.ts +1 -0
- package/dist/Changes/AddAssemblyAliasesChange.d.ts.map +1 -0
- package/dist/Changes/AddAssemblyAliasesChange.js +7 -9
- package/dist/Changes/AddAssemblyAliasesChange.js.map +1 -1
- package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.d.ts +5 -3
- package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.d.ts.map +1 -0
- package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js +31 -13
- package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map +1 -1
- package/dist/Changes/AddAssemblyFromExternalChange.d.ts +1 -0
- package/dist/Changes/AddAssemblyFromExternalChange.d.ts.map +1 -0
- package/dist/Changes/AddAssemblyFromExternalChange.js +13 -16
- package/dist/Changes/AddAssemblyFromExternalChange.js.map +1 -1
- package/dist/Changes/AddAssemblyFromFileChange.d.ts +3 -2
- package/dist/Changes/AddAssemblyFromFileChange.d.ts.map +1 -0
- package/dist/Changes/AddAssemblyFromFileChange.js +4 -8
- package/dist/Changes/AddAssemblyFromFileChange.js.map +1 -1
- package/dist/Changes/AddFeatureChange.d.ts +3 -2
- package/dist/Changes/AddFeatureChange.d.ts.map +1 -0
- package/dist/Changes/AddFeatureChange.js +6 -10
- package/dist/Changes/AddFeatureChange.js.map +1 -1
- package/dist/Changes/AddFeaturesFromFileChange.d.ts +5 -3
- package/dist/Changes/AddFeaturesFromFileChange.d.ts.map +1 -0
- package/dist/Changes/AddFeaturesFromFileChange.js +27 -14
- package/dist/Changes/AddFeaturesFromFileChange.js.map +1 -1
- package/dist/Changes/AddRefSeqAliasesChange.d.ts +1 -0
- package/dist/Changes/AddRefSeqAliasesChange.d.ts.map +1 -0
- package/dist/Changes/AddRefSeqAliasesChange.js +7 -8
- package/dist/Changes/AddRefSeqAliasesChange.js.map +1 -1
- package/dist/Changes/DeleteAssemblyChange.d.ts +1 -0
- package/dist/Changes/DeleteAssemblyChange.d.ts.map +1 -0
- package/dist/Changes/DeleteAssemblyChange.js +5 -8
- package/dist/Changes/DeleteAssemblyChange.js.map +1 -1
- package/dist/Changes/DeleteFeatureChange.d.ts +4 -3
- package/dist/Changes/DeleteFeatureChange.d.ts.map +1 -0
- package/dist/Changes/DeleteFeatureChange.js +6 -12
- package/dist/Changes/DeleteFeatureChange.js.map +1 -1
- package/dist/Changes/DeleteUserChange.d.ts +1 -0
- package/dist/Changes/DeleteUserChange.d.ts.map +1 -0
- package/dist/Changes/DeleteUserChange.js +2 -6
- package/dist/Changes/DeleteUserChange.js.map +1 -1
- package/dist/Changes/FeatureAttributeChange.d.ts +1 -0
- package/dist/Changes/FeatureAttributeChange.d.ts.map +1 -0
- package/dist/Changes/FeatureAttributeChange.js +3 -8
- package/dist/Changes/FeatureAttributeChange.js.map +1 -1
- package/dist/Changes/FromFileBaseChange.d.ts +4 -3
- package/dist/Changes/FromFileBaseChange.d.ts.map +1 -0
- package/dist/Changes/FromFileBaseChange.js +4 -10
- package/dist/Changes/FromFileBaseChange.js.map +1 -1
- package/dist/Changes/ImportJBrowseConfigChange.d.ts +1 -0
- package/dist/Changes/ImportJBrowseConfigChange.d.ts.map +1 -0
- package/dist/Changes/ImportJBrowseConfigChange.js +3 -8
- package/dist/Changes/ImportJBrowseConfigChange.js.map +1 -1
- package/dist/Changes/LocationEndChange.d.ts +1 -0
- package/dist/Changes/LocationEndChange.d.ts.map +1 -0
- package/dist/Changes/LocationEndChange.js +3 -8
- package/dist/Changes/LocationEndChange.js.map +1 -1
- package/dist/Changes/LocationStartChange.d.ts +1 -0
- package/dist/Changes/LocationStartChange.d.ts.map +1 -0
- package/dist/Changes/LocationStartChange.js +3 -8
- package/dist/Changes/LocationStartChange.js.map +1 -1
- package/dist/Changes/MergeExonsChange.d.ts +3 -2
- package/dist/Changes/MergeExonsChange.d.ts.map +1 -0
- package/dist/Changes/MergeExonsChange.js +9 -13
- package/dist/Changes/MergeExonsChange.js.map +1 -1
- package/dist/Changes/MergeTranscriptsChange.d.ts +4 -3
- package/dist/Changes/MergeTranscriptsChange.d.ts.map +1 -0
- package/dist/Changes/MergeTranscriptsChange.js +20 -24
- package/dist/Changes/MergeTranscriptsChange.js.map +1 -1
- package/dist/Changes/SplitExonChange.d.ts +3 -2
- package/dist/Changes/SplitExonChange.d.ts.map +1 -0
- package/dist/Changes/SplitExonChange.js +6 -10
- package/dist/Changes/SplitExonChange.js.map +1 -1
- package/dist/Changes/StrandChange.d.ts +1 -0
- package/dist/Changes/StrandChange.d.ts.map +1 -0
- package/dist/Changes/StrandChange.js +2 -6
- package/dist/Changes/StrandChange.js.map +1 -1
- package/dist/Changes/TypeChange.d.ts +1 -0
- package/dist/Changes/TypeChange.d.ts.map +1 -0
- package/dist/Changes/TypeChange.js +2 -6
- package/dist/Changes/TypeChange.js.map +1 -1
- package/dist/Changes/UndoMergeExonsChange.d.ts +3 -2
- package/dist/Changes/UndoMergeExonsChange.d.ts.map +1 -0
- package/dist/Changes/UndoMergeExonsChange.js +4 -8
- package/dist/Changes/UndoMergeExonsChange.js.map +1 -1
- package/dist/Changes/UndoMergeTranscriptsChange.d.ts +3 -2
- package/dist/Changes/UndoMergeTranscriptsChange.d.ts.map +1 -0
- package/dist/Changes/UndoMergeTranscriptsChange.js +4 -8
- package/dist/Changes/UndoMergeTranscriptsChange.js.map +1 -1
- package/dist/Changes/UndoSplitExonChange.d.ts +3 -2
- package/dist/Changes/UndoSplitExonChange.d.ts.map +1 -0
- package/dist/Changes/UndoSplitExonChange.js +6 -10
- package/dist/Changes/UndoSplitExonChange.js.map +1 -1
- package/dist/Changes/UserChange.d.ts +1 -0
- package/dist/Changes/UserChange.d.ts.map +1 -0
- package/dist/Changes/UserChange.js +2 -6
- package/dist/Changes/UserChange.js.map +1 -1
- package/dist/Changes/index.d.ts +47 -46
- package/dist/Changes/index.d.ts.map +1 -0
- package/dist/Changes/index.js +70 -74
- package/dist/Changes/index.js.map +1 -1
- package/dist/Checks/CDSCheck.d.ts +2 -1
- package/dist/Checks/CDSCheck.d.ts.map +1 -0
- package/dist/Checks/CDSCheck.js +17 -26
- package/dist/Checks/CDSCheck.js.map +1 -1
- package/dist/Checks/TranscriptCheck.d.ts +2 -1
- package/dist/Checks/TranscriptCheck.d.ts.map +1 -0
- package/dist/Checks/TranscriptCheck.js +11 -16
- package/dist/Checks/TranscriptCheck.js.map +1 -1
- package/dist/Checks/index.d.ts +3 -2
- package/dist/Checks/index.d.ts.map +1 -0
- package/dist/Checks/index.js +2 -5
- package/dist/Checks/index.js.map +1 -1
- package/dist/Checks/util.d.ts +2 -1
- package/dist/Checks/util.d.ts.map +1 -0
- package/dist/Checks/util.js +1 -4
- package/dist/Checks/util.js.map +1 -1
- package/dist/Common/index.d.ts +2 -1
- package/dist/Common/index.d.ts.map +1 -0
- package/dist/Common/index.js +1 -4
- package/dist/Common/index.js.map +1 -1
- package/dist/Common/jwtPayload.d.ts +1 -0
- package/dist/Common/jwtPayload.d.ts.map +1 -0
- package/dist/Common/jwtPayload.js +5 -10
- package/dist/Common/jwtPayload.js.map +1 -1
- package/dist/GFF3/annotationFeatureToGFF3.d.ts +3 -2
- package/dist/GFF3/annotationFeatureToGFF3.d.ts.map +1 -0
- package/dist/GFF3/annotationFeatureToGFF3.js +96 -93
- package/dist/GFF3/annotationFeatureToGFF3.js.map +1 -1
- package/dist/GFF3/annotationFeatureToGFF3.test.d.ts +1 -0
- package/dist/GFF3/annotationFeatureToGFF3.test.d.ts.map +1 -0
- package/dist/GFF3/annotationFeatureToGFF3.test.js +77 -79
- package/dist/GFF3/annotationFeatureToGFF3.test.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.d.ts +3 -2
- package/dist/GFF3/gff3ToAnnotationFeature.d.ts.map +1 -0
- package/dist/GFF3/gff3ToAnnotationFeature.js +30 -22
- package/dist/GFF3/gff3ToAnnotationFeature.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts +1 -0
- package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts.map +1 -0
- package/dist/GFF3/gff3ToAnnotationFeature.test.js +60 -63
- package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -1
- package/dist/GFF3/gffReservedKeys.d.ts +1 -0
- package/dist/GFF3/gffReservedKeys.d.ts.map +1 -0
- package/dist/GFF3/gffReservedKeys.js +12 -19
- package/dist/GFF3/gffReservedKeys.js.map +1 -1
- package/dist/GFF3/index.d.ts +4 -3
- package/dist/GFF3/index.d.ts.map +1 -0
- package/dist/GFF3/index.js +3 -6
- package/dist/GFF3/index.js.map +1 -1
- package/dist/GFF3/testUtil.d.ts +2 -1
- package/dist/GFF3/testUtil.d.ts.map +1 -0
- package/dist/GFF3/testUtil.js +8 -8
- package/dist/GFF3/testUtil.js.map +1 -1
- package/dist/Messages.d.ts +3 -2
- package/dist/Messages.d.ts.map +1 -0
- package/dist/Messages.js +1 -2
- package/dist/Operations/GetAssembliesOperation.d.ts +2 -3
- package/dist/Operations/GetAssembliesOperation.d.ts.map +1 -0
- package/dist/Operations/GetAssembliesOperation.js +2 -6
- package/dist/Operations/GetAssembliesOperation.js.map +1 -1
- package/dist/Operations/GetFeaturesOperation.d.ts +1 -0
- package/dist/Operations/GetFeaturesOperation.d.ts.map +1 -0
- package/dist/Operations/GetFeaturesOperation.js +2 -6
- package/dist/Operations/GetFeaturesOperation.js.map +1 -1
- package/dist/Operations/index.d.ts +5 -4
- package/dist/Operations/index.d.ts.map +1 -0
- package/dist/Operations/index.js +5 -9
- package/dist/Operations/index.js.map +1 -1
- package/dist/Validations/CoreValidation.d.ts +4 -3
- package/dist/Validations/CoreValidation.d.ts.map +1 -0
- package/dist/Validations/CoreValidation.js +6 -12
- package/dist/Validations/CoreValidation.js.map +1 -1
- package/dist/Validations/ParentChildValidation.d.ts +6 -5
- package/dist/Validations/ParentChildValidation.d.ts.map +1 -0
- package/dist/Validations/ParentChildValidation.js +6 -10
- package/dist/Validations/ParentChildValidation.js.map +1 -1
- package/dist/Validations/Validation.d.ts +6 -5
- package/dist/Validations/Validation.d.ts.map +1 -0
- package/dist/Validations/Validation.js +2 -7
- package/dist/Validations/Validation.js.map +1 -1
- package/dist/Validations/ValidationSet.d.ts +5 -4
- package/dist/Validations/ValidationSet.d.ts.map +1 -0
- package/dist/Validations/ValidationSet.js +3 -8
- package/dist/Validations/ValidationSet.js.map +1 -1
- package/dist/Validations/index.d.ts +5 -4
- package/dist/Validations/index.d.ts.map +1 -0
- package/dist/Validations/index.js +4 -7
- package/dist/Validations/index.js.map +1 -1
- package/dist/Validations/soSequenceTypes.d.ts +1 -0
- package/dist/Validations/soSequenceTypes.d.ts.map +1 -0
- package/dist/Validations/soSequenceTypes.js +1 -3
- package/dist/Validations/soSequenceTypes.js.map +1 -1
- package/dist/index.d.ts +9 -8
- package/dist/index.d.ts.map +1 -0
- package/dist/index.js +8 -11
- package/dist/index.js.map +1 -1
- package/dist/tsconfig.tsbuildinfo +1 -1
- package/dist/util.d.ts +3 -2
- package/dist/util.d.ts.map +1 -0
- package/dist/util.js +4 -10
- package/dist/util.js.map +1 -1
- package/package.json +16 -13
- package/src/Changes/AddAssemblyAliasesChange.ts +3 -1
- package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts +38 -16
- package/src/Changes/AddAssemblyFromExternalChange.ts +3 -2
- package/src/Changes/AddAssemblyFromFileChange.ts +11 -8
- package/src/Changes/AddFeatureChange.ts +3 -2
- package/src/Changes/AddFeaturesFromFileChange.ts +35 -18
- package/src/Changes/AddRefSeqAliasesChange.ts +3 -0
- package/src/Changes/DeleteAssemblyChange.ts +1 -0
- package/src/Changes/DeleteFeatureChange.ts +3 -3
- package/src/Changes/FeatureAttributeChange.ts +1 -1
- package/src/Changes/FromFileBaseChange.ts +4 -9
- package/src/Changes/LocationEndChange.ts +1 -1
- package/src/Changes/LocationStartChange.ts +1 -1
- package/src/Changes/MergeExonsChange.ts +4 -4
- package/src/Changes/MergeTranscriptsChange.ts +8 -8
- package/src/Changes/SplitExonChange.ts +3 -3
- package/src/Changes/StrandChange.ts +1 -1
- package/src/Changes/TypeChange.ts +1 -1
- package/src/Changes/UndoMergeExonsChange.ts +2 -2
- package/src/Changes/UndoMergeTranscriptsChange.ts +2 -2
- package/src/Changes/UndoSplitExonChange.ts +3 -3
- package/src/Changes/index.ts +46 -46
- package/src/Checks/CDSCheck.ts +8 -10
- package/src/Checks/TranscriptCheck.ts +4 -4
- package/src/Checks/index.ts +2 -2
- package/src/Checks/util.ts +1 -1
- package/src/Common/index.ts +1 -1
- package/src/GFF3/annotationFeatureToGFF3.test.ts +3 -3
- package/src/GFF3/annotationFeatureToGFF3.ts +105 -99
- package/src/GFF3/gff3ToAnnotationFeature.test.ts +3 -3
- package/src/GFF3/gff3ToAnnotationFeature.ts +29 -13
- package/src/GFF3/index.ts +3 -3
- package/src/GFF3/testUtil.ts +5 -1
- package/src/Messages.ts +2 -2
- package/src/Operations/index.ts +4 -4
- package/src/Validations/CoreValidation.ts +4 -4
- package/src/Validations/ParentChildValidation.ts +6 -6
- package/src/Validations/Validation.ts +5 -5
- package/src/Validations/ValidationSet.ts +4 -8
- package/src/Validations/index.ts +4 -4
- package/src/declare.d.ts +58 -0
- package/src/index.ts +8 -8
- package/src/util.ts +3 -3
- package/test_data/single_feature_mutliple_locations.gff3 +5 -0
- package/test_data/single_feature_mutliple_locations.json +76 -0
- package/tsconfig.json +6 -4
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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const tslib_1 = require("tslib");
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/* eslint-disable @typescript-eslint/no-floating-promises */
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import { readFileSync } from 'node:fs';
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import { describe, it } from 'node:test';
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import { parseStringSync } from '@gmod/gff';
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import { assert, use } from 'chai';
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import chaiExclude from 'chai-exclude';
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import { gff3ToAnnotationFeature } from './gff3ToAnnotationFeature.js';
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import { readAnnotationFeatureSnapshot, testCases } from './testUtil.js';
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use(chaiExclude);
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function childrenToArray(feature) {
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if (!children) {
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return { ...feature, children: childrenArray };
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function compareFeatures(feature1, feature2) {
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assert.deepEqualExcludingEvery(childrenToArray(feature1), childrenToArray(feature2), '_id');
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}
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for (const testCase of
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describe('Converts GFF3 to AnnotationFeatureSnapshot JSON when', () => {
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for (const testCase of testCases) {
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const { filenameStem, description } = testCase;
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const fileText =
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const gffFeatures =
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const annotationFeatures = gffFeatures.map((gff3Feature) =>
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const annotationFeaturesExpected = JSON.parse(
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it(description, () => {
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const fileText = readFileSync(`test_data/${filenameStem}.gff3`, 'utf8');
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const gffFeatures = parseStringSync(fileText, { parseSequences: false });
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const annotationFeatures = gffFeatures.map((gff3Feature) => gff3ToAnnotationFeature(gff3Feature));
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const annotationFeaturesExpected = JSON.parse(readFileSync(`test_data/${filenameStem}.json`, 'utf8'));
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for (const [i, annotationFeatureExpected,] of annotationFeaturesExpected.entries()) {
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compareFeatures(annotationFeature, annotationFeatureExpected);
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function readFeatureFile(fn) {
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const lines =
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const lines = readFileSync(fn).toString().split('\n');
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const feature = [];
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for (const line of lines) {
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feature.push(line);
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}
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}
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const inGff =
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const inGff = parseStringSync(feature.join('\n'));
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return inGff;
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}
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const [ex1, , ex2, , ex3, , ex4] = readFeatureFile('test_data/gene_representations.gff3');
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describe('gff3ToAnnotationFeature examples', () => {
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it('Convert one CDS', () => {
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const actual = gff3ToAnnotationFeature(readFeatureFile('test_data/one_cds.gff3')[0]);
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const expected = readAnnotationFeatureSnapshot('test_data/one_cds.json');
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compareFeatures(actual, expected);
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it('Convert example 1', () => {
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const actual = gff3ToAnnotationFeature(ex1);
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const txt = JSON.stringify(actual, null, 2);
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assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
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assert.equal(txt.match(/"type": "TF_binding_site"/g)?.length, 1);
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const expected = readAnnotationFeatureSnapshot('test_data/example01.json');
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compareFeatures(actual, expected);
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it('Convert example 2', () => {
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const actual = gff3ToAnnotationFeature(ex2);
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const expected = readAnnotationFeatureSnapshot('test_data/example02.json');
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compareFeatures(actual, expected);
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it('Convert example 3', () => {
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// NB: In example 3 (and in the other examples) mRNA10003 produces two proteins.
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// In example 3 instead each cds has a unique id so the two proteins are identified by the order they
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const actual = gff3ToAnnotationFeature(ex3);
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assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
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});
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it('Convert example 4', () => {
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-
|
|
87
|
-
const actual =
|
|
82
|
+
assert.equal(ft.match(/"type": "five_prime_UTR"/g)?.length, 6);
|
|
83
|
+
assert.equal(ft.match(/"type": "three_prime_UTR"/g)?.length, 3);
|
|
84
|
+
const actual = gff3ToAnnotationFeature(ex4);
|
|
88
85
|
const txt = JSON.stringify(actual, null, 2);
|
|
89
|
-
|
|
90
|
-
|
|
91
|
-
const expected =
|
|
86
|
+
assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
|
|
87
|
+
assert.equal(txt.match(/prime_UTR/g), null);
|
|
88
|
+
const expected = readAnnotationFeatureSnapshot('test_data/example04.json');
|
|
92
89
|
compareFeatures(actual, expected);
|
|
93
90
|
});
|
|
94
|
-
|
|
91
|
+
it('Convert braker gff', () => {
|
|
95
92
|
const [gffFeature] = readFeatureFile('test_data/braker.gff');
|
|
96
|
-
const actual =
|
|
93
|
+
const actual = gff3ToAnnotationFeature(gffFeature);
|
|
97
94
|
const txt = JSON.stringify(actual, null, 2);
|
|
98
|
-
|
|
99
|
-
|
|
95
|
+
assert.equal(txt.match(/intron/g), null);
|
|
96
|
+
assert.equal(txt.match(/_codon/g), null);
|
|
100
97
|
});
|
|
101
98
|
});
|
|
102
|
-
|
|
103
|
-
|
|
99
|
+
describe('CDS without exons', () => {
|
|
100
|
+
it('Convert mRNA with CDS but without exon', () => {
|
|
104
101
|
const [gffFeature] = readFeatureFile('test_data/cds_without_exon.gff');
|
|
105
|
-
const actual =
|
|
106
|
-
const expected =
|
|
102
|
+
const actual = gff3ToAnnotationFeature(gffFeature);
|
|
103
|
+
const expected = readAnnotationFeatureSnapshot('test_data/cds_without_exon.json');
|
|
107
104
|
compareFeatures(actual, expected);
|
|
108
105
|
});
|
|
109
|
-
|
|
106
|
+
it('Convert mRNA with CDS but without exon and spliced UTR', () => {
|
|
110
107
|
const [gffFeature] = readFeatureFile('test_data/cds_without_exon_spliced_utr.gff');
|
|
111
|
-
const actual =
|
|
112
|
-
const expected =
|
|
108
|
+
const actual = gff3ToAnnotationFeature(gffFeature);
|
|
109
|
+
const expected = readAnnotationFeatureSnapshot('test_data/cds_without_exon_spliced_utr.json');
|
|
113
110
|
compareFeatures(actual, expected);
|
|
114
111
|
});
|
|
115
|
-
|
|
112
|
+
it('Convert mRNA with one CDS, without exons non-adjacent UTR', () => {
|
|
116
113
|
const [gffFeature] = readFeatureFile('test_data/onecds_without_exon_spliced_utr.gff');
|
|
117
|
-
const actual =
|
|
118
|
-
const expected =
|
|
114
|
+
const actual = gff3ToAnnotationFeature(gffFeature);
|
|
115
|
+
const expected = readAnnotationFeatureSnapshot('test_data/onecds_without_exon_spliced_utr.json');
|
|
119
116
|
compareFeatures(actual, expected);
|
|
120
117
|
});
|
|
121
118
|
});
|
|
122
|
-
|
|
123
|
-
|
|
119
|
+
describe('Source and score', () => {
|
|
120
|
+
it('Convert score and source', () => {
|
|
124
121
|
const gffFeature = [
|
|
125
122
|
{
|
|
126
123
|
seq_id: 'chr1',
|
|
@@ -140,9 +137,9 @@ const [ex1, , ex2, , ex3, , ex4] = readFeatureFile('test_data/gene_representatio
|
|
|
140
137
|
derived_features: [],
|
|
141
138
|
},
|
|
142
139
|
];
|
|
143
|
-
const actual =
|
|
144
|
-
|
|
145
|
-
|
|
140
|
+
const actual = gff3ToAnnotationFeature(gffFeature);
|
|
141
|
+
assert.deepStrictEqual(actual.attributes?.gff_source?.at(0), 'mySource');
|
|
142
|
+
assert.deepStrictEqual(actual.attributes?.gff_score?.at(0), '0');
|
|
146
143
|
});
|
|
147
144
|
});
|
|
148
145
|
//# sourceMappingURL=gff3ToAnnotationFeature.test.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gff3ToAnnotationFeature.test.js","sourceRoot":"","sources":["../../src/GFF3/gff3ToAnnotationFeature.test.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"gff3ToAnnotationFeature.test.js","sourceRoot":"","sources":["../../src/GFF3/gff3ToAnnotationFeature.test.ts"],"names":[],"mappings":"AAAA,4DAA4D;AAC5D,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAA;AACtC,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,WAAW,CAAA;AAGxC,OAAO,EAAoB,eAAe,EAAE,MAAM,WAAW,CAAA;AAC7D,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,MAAM,CAAA;AAClC,OAAO,WAAW,MAAM,cAAc,CAAA;AAEtC,OAAO,EAAE,uBAAuB,EAAE,MAAM,8BAA8B,CAAA;AACtE,OAAO,EAAE,6BAA6B,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAExE,GAAG,CAAC,WAAW,CAAC,CAAA;AAOhB,SAAS,eAAe,CACtB,OAAkC;IAElC,MAAM,EAAE,QAAQ,EAAE,GAAG,OAAO,CAAA;IAC5B,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,OAAqD,CAAA;IAC9D,CAAC;IACD,MAAM,aAAa,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAC1D,eAAe,CAAC,KAAK,CAAC,CACvB,CAAA;IACD,OAAO,EAAE,GAAG,OAAO,EAAE,QAAQ,EAAE,aAAa,EAAE,CAAA;AAChD,CAAC;AAED,SAAS,eAAe,CACtB,QAAmC,EACnC,QAAmC;IAEnC,MAAM,CAAC,uBAAuB,CAC5B,eAAe,CAAC,QAAQ,CAAC,EACzB,eAAe,CAAC,QAAQ,CAAC,EACzB,KAAK,CACN,CAAA;AACH,CAAC;AAED,QAAQ,CAAC,sDAAsD,EAAE,GAAG,EAAE;IACpE,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE,CAAC;QACjC,MAAM,EAAE,YAAY,EAAE,WAAW,EAAE,GAAG,QAAQ,CAAA;QAC9C,EAAE,CAAC,WAAW,EAAE,GAAG,EAAE;YACnB,MAAM,QAAQ,GAAG,YAAY,CAAC,aAAa,YAAY,OAAO,EAAE,MAAM,CAAC,CAAA;YACvE,MAAM,WAAW,GAAG,eAAe,CAAC,QAAQ,EAAE,EAAE,cAAc,EAAE,KAAK,EAAE,CAAC,CAAA;YACxE,MAAM,kBAAkB,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,EAAE,CACzD,uBAAuB,CAAC,WAAW,CAAC,CACrC,CAAA;YACD,MAAM,0BAA0B,GAAG,IAAI,CAAC,KAAK,CAC3C,YAAY,CAAC,aAAa,YAAY,OAAO,EAAE,MAAM,CAAC,CACxB,CAAA;YAChC,KAAK,MAAM,CACT,CAAC,EACD,yBAAyB,EAC1B,IAAI,0BAA0B,CAAC,OAAO,EAAE,EAAE,CAAC;gBAC1C,MAAM,iBAAiB,GAAG,kBAAkB,CAAC,CAAC,CAAC,CAAA;gBAC/C,eAAe,CAAC,iBAAiB,EAAE,yBAAyB,CAAC,CAAA;YAC/D,CAAC;QACH,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC,CAAC,CAAA;AAEF,SAAS,eAAe,CAAC,EAAU;IACjC,MAAM,KAAK,GAAG,YAAY,CAAC,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IACrD,MAAM,OAAO,GAAa,EAAE,CAAA;IAC5B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAC1B,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,MAAM,KAAK,GAAG,eAAe,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAkB,CAAA;IAClE,OAAO,KAAK,CAAA;AACd,CAAC;AAED,MAAM,CAAC,GAAG,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,GAAG,CAAC,GAAG,eAAe,CAChD,qCAAqC,CACtC,CAAA;AAED,QAAQ,CAAC,kCAAkC,EAAE,GAAG,EAAE;IAChD,EAAE,CAAC,iBAAiB,EAAE,GAAG,EAAE;QACzB,MAAM,MAAM,GAAG,uBAAuB,CACpC,eAAe,CAAC,wBAAwB,CAAC,CAAC,CAAC,CAAC,CAC7C,CAAA;QACD,MAAM,QAAQ,GAAG,6BAA6B,CAAC,wBAAwB,CAAC,CAAA;QACxE,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,EAAE,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,MAAM,MAAM,GAAG,uBAAuB,CAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAE3C,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QACpD,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,4BAA4B,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAEhE,MAAM,QAAQ,GAAG,6BAA6B,CAAC,0BAA0B,CAAC,CAAA;QAC1E,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,EAAE,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,MAAM,MAAM,GAAG,uBAAuB,CAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QACpD,MAAM,QAAQ,GAAG,6BAA6B,CAAC,0BAA0B,CAAC,CAAA;QAC1E,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,EAAE,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,gFAAgF;QAChF,oFAAoF;QACpF,qGAAqG;QACrG,qBAAqB;QACrB,MAAM,MAAM,GAAG,uBAAuB,CAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAEpD,6EAA6E;QAC7E,oCAAoC;IACtC,CAAC,CAAC,CAAA;IACF,EAAE,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,MAAM,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QACvC,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,2BAA2B,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAC9D,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,4BAA4B,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAE/D,MAAM,MAAM,GAAG,uBAAuB,CAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QACpD,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,YAAY,CAAC,EAAE,IAAI,CAAC,CAAA;QAE3C,MAAM,QAAQ,GAAG,6BAA6B,CAAC,0BAA0B,CAAC,CAAA;QAC1E,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,EAAE,CAAC,oBAAoB,EAAE,GAAG,EAAE;QAC5B,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAAC,sBAAsB,CAAC,CAAA;QAC5D,MAAM,MAAM,GAAG,uBAAuB,CAAC,UAAU,CAAC,CAAA;QAClD,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,IAAI,CAAC,CAAA;QACxC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,IAAI,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,mBAAmB,EAAE,GAAG,EAAE;IACjC,EAAE,CAAC,wCAAwC,EAAE,GAAG,EAAE;QAChD,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAAC,gCAAgC,CAAC,CAAA;QACtE,MAAM,MAAM,GAAG,uBAAuB,CAAC,UAAU,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,6BAA6B,CAC5C,iCAAiC,CAClC,CAAA;QACD,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,EAAE,CAAC,wDAAwD,EAAE,GAAG,EAAE;QAChE,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAClC,4CAA4C,CAC7C,CAAA;QACD,MAAM,MAAM,GAAG,uBAAuB,CAAC,UAAU,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,6BAA6B,CAC5C,6CAA6C,CAC9C,CAAA;QACD,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,EAAE,CAAC,2DAA2D,EAAE,GAAG,EAAE;QACnE,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAClC,+CAA+C,CAChD,CAAA;QACD,MAAM,MAAM,GAAG,uBAAuB,CAAC,UAAU,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,6BAA6B,CAC5C,gDAAgD,CACjD,CAAA;QACD,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,kBAAkB,EAAE,GAAG,EAAE;IAChC,EAAE,CAAC,0BAA0B,EAAE,GAAG,EAAE;QAClC,MAAM,UAAU,GAAgB;YAC9B;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,UAAU;gBAClB,IAAI,EAAE,MAAM;gBACZ,KAAK,EAAE,IAAI;gBACX,GAAG,EAAE,IAAI;gBACT,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,IAAI;gBACX,UAAU,EAAE;oBACV,EAAE,EAAE,CAAC,WAAW,CAAC;oBACjB,IAAI,EAAE,CAAC,MAAM,CAAC;oBACd,MAAM,EAAE,CAAC,MAAM,CAAC;iBACjB;gBACD,cAAc,EAAE,EAAE;gBAClB,gBAAgB,EAAE,EAAE;aACrB;SACF,CAAA;QACD,MAAM,MAAM,GAAG,uBAAuB,CAAC,UAAU,CAAC,CAAA;QAClD,MAAM,CAAC,eAAe,CAAC,MAAM,CAAC,UAAU,EAAE,UAAU,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,UAAU,CAAC,CAAA;QACxE,MAAM,CAAC,eAAe,CAAC,MAAM,CAAC,UAAU,EAAE,SAAS,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;IAClE,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
|
|
@@ -10,3 +10,4 @@ export declare const gffColumnToInternal: Record<GFFColumn, GFFColumnInternal>;
|
|
|
10
10
|
export declare function isGFFColumn(attribute: string): attribute is GFFColumn;
|
|
11
11
|
export declare const gffInternalToColumn: Record<GFFColumnInternal, GFFColumn>;
|
|
12
12
|
export declare function isGFFColumnInternal(column: string): column is GFFColumnInternal;
|
|
13
|
+
//# sourceMappingURL=gffReservedKeys.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"gffReservedKeys.d.ts","sourceRoot":"","sources":["../../src/GFF3/gffReservedKeys.ts"],"names":[],"mappings":"AAAA,MAAM,MAAM,oBAAoB,GAC5B,IAAI,GACJ,MAAM,GACN,OAAO,GACP,QAAQ,GACR,QAAQ,GACR,KAAK,GACL,cAAc,GACd,MAAM,GACN,QAAQ,GACR,eAAe,GACf,aAAa,CAAA;AAEjB,MAAM,MAAM,oBAAoB,GAC5B,QAAQ,GACR,UAAU,GACV,WAAW,GACX,YAAY,GACZ,YAAY,GACZ,SAAS,GACT,kBAAkB,GAClB,UAAU,GACV,YAAY,GACZ,mBAAmB,GACnB,iBAAiB,CAAA;AAErB,eAAO,MAAM,aAAa,EAAE,MAAM,CAAC,oBAAoB,EAAE,oBAAoB,CAa1E,CAAA;AAEH,wBAAgB,sBAAsB,CACpC,SAAS,EAAE,MAAM,GAChB,SAAS,IAAI,oBAAoB,CAEnC;AAED,eAAO,MAAM,aAAa,EAAE,MAAM,CAAC,oBAAoB,EAAE,oBAAoB,CAa1E,CAAA;AAEH,wBAAgB,sBAAsB,CACpC,SAAS,EAAE,MAAM,GAChB,SAAS,IAAI,oBAAoB,CAEnC;AAED,MAAM,MAAM,SAAS,GAAG,OAAO,GAAG,QAAQ,CAAA;AAC1C,MAAM,MAAM,iBAAiB,GAAG,WAAW,GAAG,YAAY,CAAA;AAC1D,eAAO,MAAM,mBAAmB,EAAE,MAAM,CAAC,SAAS,EAAE,iBAAiB,CAGpE,CAAA;AACD,wBAAgB,WAAW,CAAC,SAAS,EAAE,MAAM,GAAG,SAAS,IAAI,SAAS,CAErE;AACD,eAAO,MAAM,mBAAmB,EAAE,MAAM,CAAC,iBAAiB,EAAE,SAAS,CAGpE,CAAA;AACD,wBAAgB,mBAAmB,CACjC,MAAM,EAAE,MAAM,GACb,MAAM,IAAI,iBAAiB,CAE7B"}
|
|
@@ -1,11 +1,4 @@
|
|
|
1
|
-
|
|
2
|
-
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.gffInternalToColumn = exports.gffColumnToInternal = exports.internalToGFF = exports.gffToInternal = void 0;
|
|
4
|
-
exports.isGFFReservedAttribute = isGFFReservedAttribute;
|
|
5
|
-
exports.isGFFInternalAttribute = isGFFInternalAttribute;
|
|
6
|
-
exports.isGFFColumn = isGFFColumn;
|
|
7
|
-
exports.isGFFColumnInternal = isGFFColumnInternal;
|
|
8
|
-
exports.gffToInternal = {
|
|
1
|
+
export const gffToInternal = {
|
|
9
2
|
ID: 'gff_id',
|
|
10
3
|
Name: 'gff_name',
|
|
11
4
|
Alias: 'gff_alias',
|
|
@@ -18,10 +11,10 @@ exports.gffToInternal = {
|
|
|
18
11
|
Ontology_term: 'gff_ontology_term',
|
|
19
12
|
Is_circular: 'gff_is_circular',
|
|
20
13
|
};
|
|
21
|
-
function isGFFReservedAttribute(attribute) {
|
|
22
|
-
return attribute in
|
|
14
|
+
export function isGFFReservedAttribute(attribute) {
|
|
15
|
+
return attribute in gffToInternal;
|
|
23
16
|
}
|
|
24
|
-
|
|
17
|
+
export const internalToGFF = {
|
|
25
18
|
gff_id: 'ID',
|
|
26
19
|
gff_name: 'Name',
|
|
27
20
|
gff_alias: 'Alias',
|
|
@@ -34,21 +27,21 @@ exports.internalToGFF = {
|
|
|
34
27
|
gff_ontology_term: 'Ontology_term',
|
|
35
28
|
gff_is_circular: 'Is_circular',
|
|
36
29
|
};
|
|
37
|
-
function isGFFInternalAttribute(attribute) {
|
|
38
|
-
return attribute in
|
|
30
|
+
export function isGFFInternalAttribute(attribute) {
|
|
31
|
+
return attribute in internalToGFF;
|
|
39
32
|
}
|
|
40
|
-
|
|
33
|
+
export const gffColumnToInternal = {
|
|
41
34
|
score: 'gff_score',
|
|
42
35
|
source: 'gff_source',
|
|
43
36
|
};
|
|
44
|
-
function isGFFColumn(attribute) {
|
|
45
|
-
return attribute in
|
|
37
|
+
export function isGFFColumn(attribute) {
|
|
38
|
+
return attribute in gffColumnToInternal;
|
|
46
39
|
}
|
|
47
|
-
|
|
40
|
+
export const gffInternalToColumn = {
|
|
48
41
|
gff_score: 'score',
|
|
49
42
|
gff_source: 'source',
|
|
50
43
|
};
|
|
51
|
-
function isGFFColumnInternal(column) {
|
|
52
|
-
return column in
|
|
44
|
+
export function isGFFColumnInternal(column) {
|
|
45
|
+
return column in gffInternalToColumn;
|
|
53
46
|
}
|
|
54
47
|
//# sourceMappingURL=gffReservedKeys.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gffReservedKeys.js","sourceRoot":"","sources":["../../src/GFF3/gffReservedKeys.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"gffReservedKeys.js","sourceRoot":"","sources":["../../src/GFF3/gffReservedKeys.ts"],"names":[],"mappings":"AA0BA,MAAM,CAAC,MAAM,aAAa,GACxB;IACE,EAAE,EAAE,QAAQ;IACZ,IAAI,EAAE,UAAU;IAChB,KAAK,EAAE,WAAW;IAClB,MAAM,EAAE,YAAY;IACpB,MAAM,EAAE,YAAY;IACpB,GAAG,EAAE,SAAS;IACd,YAAY,EAAE,kBAAkB;IAChC,IAAI,EAAE,UAAU;IAChB,MAAM,EAAE,YAAY;IACpB,aAAa,EAAE,mBAAmB;IAClC,WAAW,EAAE,iBAAiB;CAC/B,CAAA;AAEH,MAAM,UAAU,sBAAsB,CACpC,SAAiB;IAEjB,OAAO,SAAS,IAAI,aAAa,CAAA;AACnC,CAAC;AAED,MAAM,CAAC,MAAM,aAAa,GACxB;IACE,MAAM,EAAE,IAAI;IACZ,QAAQ,EAAE,MAAM;IAChB,SAAS,EAAE,OAAO;IAClB,UAAU,EAAE,QAAQ;IACpB,UAAU,EAAE,QAAQ;IACpB,OAAO,EAAE,KAAK;IACd,gBAAgB,EAAE,cAAc;IAChC,QAAQ,EAAE,MAAM;IAChB,UAAU,EAAE,QAAQ;IACpB,iBAAiB,EAAE,eAAe;IAClC,eAAe,EAAE,aAAa;CAC/B,CAAA;AAEH,MAAM,UAAU,sBAAsB,CACpC,SAAiB;IAEjB,OAAO,SAAS,IAAI,aAAa,CAAA;AACnC,CAAC;AAID,MAAM,CAAC,MAAM,mBAAmB,GAAyC;IACvE,KAAK,EAAE,WAAW;IAClB,MAAM,EAAE,YAAY;CACrB,CAAA;AACD,MAAM,UAAU,WAAW,CAAC,SAAiB;IAC3C,OAAO,SAAS,IAAI,mBAAmB,CAAA;AACzC,CAAC;AACD,MAAM,CAAC,MAAM,mBAAmB,GAAyC;IACvE,SAAS,EAAE,OAAO;IAClB,UAAU,EAAE,QAAQ;CACrB,CAAA;AACD,MAAM,UAAU,mBAAmB,CACjC,MAAc;IAEd,OAAO,MAAM,IAAI,mBAAmB,CAAA;AACtC,CAAC"}
|
package/dist/GFF3/index.d.ts
CHANGED
|
@@ -1,3 +1,4 @@
|
|
|
1
|
-
export * from './annotationFeatureToGFF3';
|
|
2
|
-
export * from './gffReservedKeys';
|
|
3
|
-
export * from './gff3ToAnnotationFeature';
|
|
1
|
+
export * from './annotationFeatureToGFF3.js';
|
|
2
|
+
export * from './gffReservedKeys.js';
|
|
3
|
+
export * from './gff3ToAnnotationFeature.js';
|
|
4
|
+
//# sourceMappingURL=index.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/GFF3/index.ts"],"names":[],"mappings":"AAAA,cAAc,8BAA8B,CAAA;AAC5C,cAAc,sBAAsB,CAAA;AACpC,cAAc,8BAA8B,CAAA"}
|
package/dist/GFF3/index.js
CHANGED
|
@@ -1,7 +1,4 @@
|
|
|
1
|
-
|
|
2
|
-
|
|
3
|
-
|
|
4
|
-
tslib_1.__exportStar(require("./annotationFeatureToGFF3"), exports);
|
|
5
|
-
tslib_1.__exportStar(require("./gffReservedKeys"), exports);
|
|
6
|
-
tslib_1.__exportStar(require("./gff3ToAnnotationFeature"), exports);
|
|
1
|
+
export * from './annotationFeatureToGFF3.js';
|
|
2
|
+
export * from './gffReservedKeys.js';
|
|
3
|
+
export * from './gff3ToAnnotationFeature.js';
|
|
7
4
|
//# sourceMappingURL=index.js.map
|
package/dist/GFF3/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GFF3/index.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GFF3/index.ts"],"names":[],"mappings":"AAAA,cAAc,8BAA8B,CAAA;AAC5C,cAAc,sBAAsB,CAAA;AACpC,cAAc,8BAA8B,CAAA"}
|
package/dist/GFF3/testUtil.d.ts
CHANGED
|
@@ -1,6 +1,7 @@
|
|
|
1
|
-
import {
|
|
1
|
+
import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
|
|
2
2
|
export declare function readAnnotationFeatureSnapshot(fn: string): AnnotationFeatureSnapshot;
|
|
3
3
|
export declare const testCases: {
|
|
4
4
|
filenameStem: string;
|
|
5
5
|
description: string;
|
|
6
6
|
}[];
|
|
7
|
+
//# sourceMappingURL=testUtil.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"testUtil.d.ts","sourceRoot":"","sources":["../../src/GFF3/testUtil.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,yBAAyB,EAAE,MAAM,wBAAwB,CAAA;AAEvE,wBAAgB,6BAA6B,CAC3C,EAAE,EAAE,MAAM,GACT,yBAAyB,CAG3B;AAED,eAAO,MAAM,SAAS,EAAE;IAAE,YAAY,EAAE,MAAM,CAAC;IAAC,WAAW,EAAE,MAAM,CAAA;CAAE,EAiBpE,CAAA"}
|
package/dist/GFF3/testUtil.js
CHANGED
|
@@ -1,13 +1,9 @@
|
|
|
1
|
-
|
|
2
|
-
|
|
3
|
-
|
|
4
|
-
exports.readAnnotationFeatureSnapshot = readAnnotationFeatureSnapshot;
|
|
5
|
-
const node_fs_1 = require("node:fs");
|
|
6
|
-
function readAnnotationFeatureSnapshot(fn) {
|
|
7
|
-
const lines = (0, node_fs_1.readFileSync)(fn).toString();
|
|
1
|
+
import { readFileSync } from 'node:fs';
|
|
2
|
+
export function readAnnotationFeatureSnapshot(fn) {
|
|
3
|
+
const lines = readFileSync(fn).toString();
|
|
8
4
|
return JSON.parse(lines);
|
|
9
5
|
}
|
|
10
|
-
|
|
6
|
+
export const testCases = [
|
|
11
7
|
{
|
|
12
8
|
filenameStem: 'single_feature_no_children',
|
|
13
9
|
description: 'there is a single feature with no children',
|
|
@@ -20,5 +16,9 @@ exports.testCases = [
|
|
|
20
16
|
filenameStem: 'gene_with_two_cds',
|
|
21
17
|
description: 'Gene with two CDS',
|
|
22
18
|
},
|
|
19
|
+
{
|
|
20
|
+
filenameStem: 'single_feature_mutliple_locations',
|
|
21
|
+
description: 'A single top-level feature has multiple locations',
|
|
22
|
+
},
|
|
23
23
|
];
|
|
24
24
|
//# sourceMappingURL=testUtil.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"testUtil.js","sourceRoot":"","sources":["../../src/GFF3/testUtil.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"testUtil.js","sourceRoot":"","sources":["../../src/GFF3/testUtil.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAA;AAItC,MAAM,UAAU,6BAA6B,CAC3C,EAAU;IAEV,MAAM,KAAK,GAAG,YAAY,CAAC,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;IACzC,OAAO,IAAI,CAAC,KAAK,CAAC,KAAK,CAA8B,CAAA;AACvD,CAAC;AAED,MAAM,CAAC,MAAM,SAAS,GAAoD;IACxE;QACE,YAAY,EAAE,4BAA4B;QAC1C,WAAW,EAAE,4CAA4C;KAC1D;IACD;QACE,YAAY,EAAE,6BAA6B;QAC3C,WAAW,EAAE,6CAA6C;KAC3D;IACD;QACE,YAAY,EAAE,mBAAmB;QACjC,WAAW,EAAE,mBAAmB;KACjC;IACD;QACE,YAAY,EAAE,mCAAmC;QACjD,WAAW,EAAE,mDAAmD;KACjE;CACF,CAAA"}
|
package/dist/Messages.d.ts
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import {
|
|
2
|
-
import {
|
|
1
|
+
import type { SerializedChange } from '@apollo-annotation/common';
|
|
2
|
+
import type { CheckResultSnapshot } from '@apollo-annotation/mst';
|
|
3
3
|
interface BaseMessage {
|
|
4
4
|
channel: string;
|
|
5
5
|
userName: string;
|
|
@@ -26,3 +26,4 @@ export interface RequestUserInformationMessage extends BaseMessage {
|
|
|
26
26
|
readonly reqType: 'CURRENT_LOCATION';
|
|
27
27
|
}
|
|
28
28
|
export {};
|
|
29
|
+
//# sourceMappingURL=Messages.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"Messages.d.ts","sourceRoot":"","sources":["../src/Messages.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AACjE,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,wBAAwB,CAAA;AAEjE,UAAU,WAAW;IACnB,OAAO,EAAE,MAAM,CAAA;IACf,QAAQ,EAAE,MAAM,CAAA;IAChB,aAAa,EAAE,MAAM,CAAA;CACtB;AAED,MAAM,WAAW,aAAc,SAAQ,WAAW;IAChD,UAAU,EAAE,gBAAgB,CAAA;IAC5B,cAAc,EAAE,MAAM,CAAA;CACvB;AACD,MAAM,WAAW,iBAAkB,SAAQ,WAAW;IACpD,WAAW,EAAE,mBAAmB,CAAA;IAChC,OAAO,CAAC,EAAE,OAAO,CAAA;CAClB;AAED,MAAM,WAAW,YAAY;IAC3B,UAAU,EAAE,MAAM,CAAA;IAClB,MAAM,EAAE,MAAM,CAAA;IACd,KAAK,EAAE,MAAM,CAAA;IACb,GAAG,EAAE,MAAM,CAAA;CACZ;AAED,MAAM,WAAW,mBAAoB,SAAQ,WAAW;IACtD,SAAS,EAAE,YAAY,EAAE,CAAA;CAC1B;AAED,MAAM,WAAW,6BAA8B,SAAQ,WAAW;IAChE,QAAQ,CAAC,OAAO,EAAE,kBAAkB,CAAA;CACrC"}
|
package/dist/Messages.js
CHANGED
|
@@ -5,9 +5,8 @@ interface SerializedGetAssembliesOperation extends SerializedOperation {
|
|
|
5
5
|
export declare class GetAssembliesOperation extends Operation {
|
|
6
6
|
typeName: "GetAssembliesOperation";
|
|
7
7
|
toJSON(): SerializedGetAssembliesOperation;
|
|
8
|
-
executeOnServer(backend: ServerDataStore): Promise<
|
|
9
|
-
_id: import("mongoose").Types.ObjectId;
|
|
10
|
-
}, never>)[]>;
|
|
8
|
+
executeOnServer(backend: ServerDataStore): Promise<any[]>;
|
|
11
9
|
executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
|
|
12
10
|
}
|
|
13
11
|
export {};
|
|
12
|
+
//# sourceMappingURL=GetAssembliesOperation.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"GetAssembliesOperation.d.ts","sourceRoot":"","sources":["../../src/Operations/GetAssembliesOperation.ts"],"names":[],"mappings":"AACA,OAAO,EACL,KAAK,kBAAkB,EACvB,SAAS,EACT,KAAK,mBAAmB,EACxB,KAAK,eAAe,EACrB,MAAM,2BAA2B,CAAA;AAElC,UAAU,gCAAiC,SAAQ,mBAAmB;IACpE,QAAQ,EAAE,wBAAwB,CAAA;CACnC;AAED,qBAAa,sBAAuB,SAAQ,SAAS;IACnD,QAAQ,2BAAoC;IAE5C,MAAM,IAAI,gCAAgC;IAK1C,eAAe,CAAC,OAAO,EAAE,eAAe;IAIlC,kBAAkB,CAAC,QAAQ,EAAE,kBAAkB;CAGtD"}
|
|
@@ -1,9 +1,6 @@
|
|
|
1
|
-
"use strict";
|
|
2
|
-
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.GetAssembliesOperation = void 0;
|
|
4
1
|
/* eslint-disable @typescript-eslint/require-await */
|
|
5
|
-
|
|
6
|
-
class GetAssembliesOperation extends
|
|
2
|
+
import { Operation, } from '@apollo-annotation/common';
|
|
3
|
+
export class GetAssembliesOperation extends Operation {
|
|
7
4
|
typeName = 'GetAssembliesOperation';
|
|
8
5
|
toJSON() {
|
|
9
6
|
const { typeName } = this;
|
|
@@ -16,5 +13,4 @@ class GetAssembliesOperation extends common_1.Operation {
|
|
|
16
13
|
throw new Error('executeOnLocalGFF3 not implemented');
|
|
17
14
|
}
|
|
18
15
|
}
|
|
19
|
-
exports.GetAssembliesOperation = GetAssembliesOperation;
|
|
20
16
|
//# sourceMappingURL=GetAssembliesOperation.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"GetAssembliesOperation.js","sourceRoot":"","sources":["../../src/Operations/GetAssembliesOperation.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"GetAssembliesOperation.js","sourceRoot":"","sources":["../../src/Operations/GetAssembliesOperation.ts"],"names":[],"mappings":"AAAA,qDAAqD;AACrD,OAAO,EAEL,SAAS,GAGV,MAAM,2BAA2B,CAAA;AAMlC,MAAM,OAAO,sBAAuB,SAAQ,SAAS;IACnD,QAAQ,GAAG,wBAAiC,CAAA;IAE5C,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACzB,OAAO,EAAE,QAAQ,EAAE,CAAA;IACrB,CAAC;IAED,eAAe,CAAC,OAAwB;QACtC,OAAO,OAAO,CAAC,aAAa,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,CAAA;IACzD,CAAC;IAED,KAAK,CAAC,kBAAkB,CAAC,QAA4B;QACnD,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAA;IACvD,CAAC;CACF"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"GetFeaturesOperation.d.ts","sourceRoot":"","sources":["../../src/Operations/GetFeaturesOperation.ts"],"names":[],"mappings":"AACA,OAAO,EACL,KAAK,kBAAkB,EACvB,SAAS,EACT,KAAK,gBAAgB,EACrB,KAAK,mBAAmB,EACxB,KAAK,eAAe,EACrB,MAAM,2BAA2B,CAAA;AAElC,UAAU,8BAA+B,SAAQ,mBAAmB;IAClE,QAAQ,EAAE,sBAAsB,CAAA;IAChC,MAAM,EAAE,MAAM,CAAA;IACd,KAAK,EAAE,MAAM,CAAA;IACb,GAAG,EAAE,MAAM,CAAA;CACZ;AAED,qBAAa,oBAAqB,SAAQ,SAAS;IACjD,QAAQ,yBAAkC;IAC1C,MAAM,EAAE,MAAM,CAAA;IACd,KAAK,EAAE,MAAM,CAAA;IACb,GAAG,EAAE,MAAM,CAAA;gBAGT,IAAI,EAAE,8BAA8B,EACpC,OAAO,CAAC,EAAE,gBAAgB;IAQ5B,MAAM,IAAI,8BAA8B;IAKxC;;;;;OAKG;IACH,eAAe,CAAC,OAAO,EAAE,eAAe;;;IAWlC,kBAAkB,CAAC,QAAQ,EAAE,kBAAkB;CAGtD"}
|
|
@@ -1,9 +1,6 @@
|
|
|
1
|
-
"use strict";
|
|
2
|
-
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.GetFeaturesOperation = void 0;
|
|
4
1
|
/* eslint-disable @typescript-eslint/require-await */
|
|
5
|
-
|
|
6
|
-
class GetFeaturesOperation extends
|
|
2
|
+
import { Operation, } from '@apollo-annotation/common';
|
|
3
|
+
export class GetFeaturesOperation extends Operation {
|
|
7
4
|
typeName = 'GetFeaturesOperation';
|
|
8
5
|
refSeq;
|
|
9
6
|
start;
|
|
@@ -38,5 +35,4 @@ class GetFeaturesOperation extends common_1.Operation {
|
|
|
38
35
|
throw new Error('executeOnLocalGFF3 not implemented');
|
|
39
36
|
}
|
|
40
37
|
}
|
|
41
|
-
exports.GetFeaturesOperation = GetFeaturesOperation;
|
|
42
38
|
//# sourceMappingURL=GetFeaturesOperation.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"GetFeaturesOperation.js","sourceRoot":"","sources":["../../src/Operations/GetFeaturesOperation.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"GetFeaturesOperation.js","sourceRoot":"","sources":["../../src/Operations/GetFeaturesOperation.ts"],"names":[],"mappings":"AAAA,qDAAqD;AACrD,OAAO,EAEL,SAAS,GAIV,MAAM,2BAA2B,CAAA;AASlC,MAAM,OAAO,oBAAqB,SAAQ,SAAS;IACjD,QAAQ,GAAG,sBAA+B,CAAA;IAC1C,MAAM,CAAQ;IACd,KAAK,CAAQ;IACb,GAAG,CAAQ;IAEX,YACE,IAAoC,EACpC,OAA0B;QAE1B,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;QACvB,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,GAAG,CAAA;IACrB,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QAC7C,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,CAAA;IACzC,CAAC;IAED;;;;;OAKG;IACH,eAAe,CAAC,OAAwB;QACtC,OAAO,OAAO,CAAC,YAAY;aACxB,IAAI,CAAC;YACJ,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,GAAG,EAAE,EAAE,IAAI,EAAE,IAAI,CAAC,GAAG,EAAE;YACvB,GAAG,EAAE,EAAE,IAAI,EAAE,IAAI,CAAC,KAAK,EAAE;YACzB,MAAM,EAAE,CAAC;SACV,CAAC;aACD,IAAI,EAAE,CAAA;IACX,CAAC;IAED,KAAK,CAAC,kBAAkB,CAAC,QAA4B;QACnD,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAA;IACvD,CAAC;CACF"}
|
|
@@ -1,8 +1,9 @@
|
|
|
1
|
-
import { GetAssembliesOperation } from './GetAssembliesOperation';
|
|
2
|
-
import { GetFeaturesOperation } from './GetFeaturesOperation';
|
|
1
|
+
import { GetAssembliesOperation } from './GetAssembliesOperation.js';
|
|
2
|
+
import { GetFeaturesOperation } from './GetFeaturesOperation.js';
|
|
3
3
|
export declare const operations: {
|
|
4
4
|
GetAssembliesOperation: typeof GetAssembliesOperation;
|
|
5
5
|
GetFeaturesOperation: typeof GetFeaturesOperation;
|
|
6
6
|
};
|
|
7
|
-
export * from './GetAssembliesOperation';
|
|
8
|
-
export * from './GetFeaturesOperation';
|
|
7
|
+
export * from './GetAssembliesOperation.js';
|
|
8
|
+
export * from './GetFeaturesOperation.js';
|
|
9
|
+
//# sourceMappingURL=index.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/Operations/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAA;AACpE,OAAO,EAAE,oBAAoB,EAAE,MAAM,2BAA2B,CAAA;AAEhE,eAAO,MAAM,UAAU;;;CAAmD,CAAA;AAC1E,cAAc,6BAA6B,CAAA;AAC3C,cAAc,2BAA2B,CAAA"}
|
package/dist/Operations/index.js
CHANGED
|
@@ -1,10 +1,6 @@
|
|
|
1
|
-
|
|
2
|
-
|
|
3
|
-
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
const GetFeaturesOperation_1 = require("./GetFeaturesOperation");
|
|
7
|
-
exports.operations = { GetAssembliesOperation: GetAssembliesOperation_1.GetAssembliesOperation, GetFeaturesOperation: GetFeaturesOperation_1.GetFeaturesOperation };
|
|
8
|
-
tslib_1.__exportStar(require("./GetAssembliesOperation"), exports);
|
|
9
|
-
tslib_1.__exportStar(require("./GetFeaturesOperation"), exports);
|
|
1
|
+
import { GetAssembliesOperation } from './GetAssembliesOperation.js';
|
|
2
|
+
import { GetFeaturesOperation } from './GetFeaturesOperation.js';
|
|
3
|
+
export const operations = { GetAssembliesOperation, GetFeaturesOperation };
|
|
4
|
+
export * from './GetAssembliesOperation.js';
|
|
5
|
+
export * from './GetFeaturesOperation.js';
|
|
10
6
|
//# sourceMappingURL=index.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Operations/index.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Operations/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAA;AACpE,OAAO,EAAE,oBAAoB,EAAE,MAAM,2BAA2B,CAAA;AAEhE,MAAM,CAAC,MAAM,UAAU,GAAG,EAAE,sBAAsB,EAAE,oBAAoB,EAAE,CAAA;AAC1E,cAAc,6BAA6B,CAAA;AAC3C,cAAc,2BAA2B,CAAA"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import {
|
|
2
|
-
import {
|
|
3
|
-
import { Validation } from './Validation';
|
|
1
|
+
import type { Change } from '@apollo-annotation/common';
|
|
2
|
+
import type { TypeChange } from '../Changes/index.js';
|
|
3
|
+
import { Validation } from './Validation.js';
|
|
4
4
|
export declare function isTypeChange(thing: Change): thing is TypeChange;
|
|
5
5
|
export declare class CoreValidation extends Validation {
|
|
6
6
|
name: "Core";
|
|
@@ -15,3 +15,4 @@ export declare class CoreValidation extends Validation {
|
|
|
15
15
|
}>;
|
|
16
16
|
possibleValues(key: string): Promise<string[] | undefined>;
|
|
17
17
|
}
|
|
18
|
+
//# sourceMappingURL=CoreValidation.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"CoreValidation.d.ts","sourceRoot":"","sources":["../../src/Validations/CoreValidation.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,2BAA2B,CAAA;AAEvD,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAA;AAErD,OAAO,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAA;AAG5C,wBAAgB,YAAY,CAAC,KAAK,EAAE,MAAM,GAAG,KAAK,IAAI,UAAU,CAE/D;AAED,qBAAa,cAAe,SAAQ,UAAU;IAC5C,IAAI,SAAkB;IAEhB,mBAAmB,CAAC,MAAM,EAAE,MAAM;;;;;;;;;IAgBlC,cAAc,CAAC,GAAG,EAAE,MAAM;CAMjC"}
|
|
@@ -1,19 +1,14 @@
|
|
|
1
|
-
|
|
2
|
-
|
|
3
|
-
|
|
4
|
-
exports.isTypeChange = isTypeChange;
|
|
5
|
-
const tslib_1 = require("tslib");
|
|
6
|
-
const Validation_1 = require("./Validation");
|
|
7
|
-
const soSequenceTypes_1 = tslib_1.__importDefault(require("./soSequenceTypes"));
|
|
8
|
-
function isTypeChange(thing) {
|
|
1
|
+
import { Validation } from './Validation.js';
|
|
2
|
+
import soSequenceTypes from './soSequenceTypes.js';
|
|
3
|
+
export function isTypeChange(thing) {
|
|
9
4
|
return 'oldType' in thing && 'newType' in thing;
|
|
10
5
|
}
|
|
11
|
-
class CoreValidation extends
|
|
6
|
+
export class CoreValidation extends Validation {
|
|
12
7
|
name = 'Core';
|
|
13
8
|
async frontendPreValidate(change) {
|
|
14
9
|
if (isTypeChange(change)) {
|
|
15
10
|
for (const subChange of change.changes) {
|
|
16
|
-
if (!
|
|
11
|
+
if (!soSequenceTypes.includes(subChange.newType)) {
|
|
17
12
|
return {
|
|
18
13
|
validationName: this.name,
|
|
19
14
|
error: {
|
|
@@ -27,10 +22,9 @@ class CoreValidation extends Validation_1.Validation {
|
|
|
27
22
|
}
|
|
28
23
|
async possibleValues(key) {
|
|
29
24
|
if (key === 'type') {
|
|
30
|
-
return
|
|
25
|
+
return soSequenceTypes;
|
|
31
26
|
}
|
|
32
27
|
return;
|
|
33
28
|
}
|
|
34
29
|
}
|
|
35
|
-
exports.CoreValidation = CoreValidation;
|
|
36
30
|
//# sourceMappingURL=CoreValidation.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"CoreValidation.js","sourceRoot":"","sources":["../../src/Validations/CoreValidation.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"CoreValidation.js","sourceRoot":"","sources":["../../src/Validations/CoreValidation.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAA;AAC5C,OAAO,eAAe,MAAM,sBAAsB,CAAA;AAElD,MAAM,UAAU,YAAY,CAAC,KAAa;IACxC,OAAO,SAAS,IAAI,KAAK,IAAI,SAAS,IAAI,KAAK,CAAA;AACjD,CAAC;AAED,MAAM,OAAO,cAAe,SAAQ,UAAU;IAC5C,IAAI,GAAG,MAAe,CAAA;IAEtB,KAAK,CAAC,mBAAmB,CAAC,MAAc;QACtC,IAAI,YAAY,CAAC,MAAM,CAAC,EAAE,CAAC;YACzB,KAAK,MAAM,SAAS,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;gBACvC,IAAI,CAAC,eAAe,CAAC,QAAQ,CAAC,SAAS,CAAC,OAAO,CAAC,EAAE,CAAC;oBACjD,OAAO;wBACL,cAAc,EAAE,IAAI,CAAC,IAAI;wBACzB,KAAK,EAAE;4BACL,OAAO,EAAE,IAAI,SAAS,CAAC,OAAO,2CAA2C;yBAC1E;qBACF,CAAA;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,EAAE,cAAc,EAAE,IAAI,CAAC,IAAI,EAAE,CAAA;IACtC,CAAC;IAED,KAAK,CAAC,cAAc,CAAC,GAAW;QAC9B,IAAI,GAAG,KAAK,MAAM,EAAE,CAAC;YACnB,OAAO,eAAe,CAAA;QACxB,CAAC;QACD,OAAM;IACR,CAAC;CACF"}
|