Arno Kaimbacher
c049b22723
- fix: Update API routes to include DOI URL handling and improve route organization - chore: Add ORCID preload rule file and ensure proper registration - docs: Add MIT License to the project for open-source compliance - feat: Implement command to detect and fix missing dataset cross-references - feat: Create command for updating DataCite DOI records with detailed logging and error handling - docs: Add comprehensive documentation for dataset indexing command - docs: Create detailed documentation for DataCite update command with usage examples and error handling
317 lines
14 KiB
TypeScript
317 lines
14 KiB
TypeScript
/*
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|--------------------------------------------------------------------------
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| node ace make:command fix-dataset-cross-references
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| DONE: create commands/fix_dataset_cross_references.ts
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|--------------------------------------------------------------------------
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*/
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import { BaseCommand, flags } from '@adonisjs/core/ace';
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import type { CommandOptions } from '@adonisjs/core/types/ace';
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import Dataset from '#models/dataset';
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import DatasetReference from '#models/dataset_reference';
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// import env from '#start/env';
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interface MissingCrossReference {
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sourceDatasetId: number;
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targetDatasetId: number;
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sourcePublishId: number | null;
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targetPublishId: number | null;
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referenceType: string;
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relation: string;
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doi: string | null;
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reverseRelation: string;
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}
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export default class DetectMissingCrossReferences extends BaseCommand {
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static commandName = 'detect:missing-cross-references';
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static description = 'Detect missing bidirectional cross-references between versioned datasets';
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public static needsApplication = true;
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@flags.boolean({ alias: 'f', description: 'Fix missing cross-references automatically' })
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public fix: boolean = false;
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@flags.boolean({ alias: 'v', description: 'Verbose output' })
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public verbose: boolean = false;
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public static options: CommandOptions = {
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startApp: true,
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staysAlive: false,
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};
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async run() {
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this.logger.info('🔍 Detecting missing cross-references...');
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try {
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const missingReferences = await this.findMissingCrossReferences();
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if (missingReferences.length === 0) {
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this.logger.success('All cross-references are properly linked!');
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return;
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}
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this.logger.warning(`Found ${missingReferences.length} missing cross-reference(s):`);
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for (const missing of missingReferences) {
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this.logger.info(
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`Dataset ${missing.sourceDatasetId} references ${missing.targetDatasetId}, but reverse reference is missing`,
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);
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if (this.verbose) {
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this.logger.info(` - Reference type: ${missing.referenceType}`);
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this.logger.info(` - Relation: ${missing.relation}`);
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this.logger.info(` - DOI: ${missing.doi}`);
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}
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}
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if (this.fix) {
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await this.fixMissingReferences(missingReferences);
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this.logger.success('All missing cross-references have been fixed!');
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} else {
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this.printMissingReferencesList(missingReferences);
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this.logger.info('💡 Run with --fix flag to automatically create missing cross-references');
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}
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} catch (error) {
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this.logger.error('Error detecting missing cross-references:', error);
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process.exit(1);
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}
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}
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private async findMissingCrossReferences(): Promise<MissingCrossReference[]> {
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const missingReferences: {
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sourceDatasetId: number;
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targetDatasetId: number;
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sourcePublishId: number | null;
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targetPublishId: number | null;
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referenceType: string;
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relation: string;
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doi: string | null;
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reverseRelation: string;
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}[] = [];
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this.logger.info('📊 Querying dataset references...');
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// Find all references that point to Tethys datasets (DOI or URL containing tethys DOI)
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// Only from datasets that are published
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const tethysReferences = await DatasetReference.query()
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.whereIn('type', ['DOI', 'URL'])
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.where((query) => {
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query.where('value', 'like', '%doi.org/10.24341/tethys.%').orWhere('value', 'like', '%tethys.at/dataset/%');
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})
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.preload('dataset', (datasetQuery) => {
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datasetQuery.where('server_state', 'published');
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})
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.whereHas('dataset', (datasetQuery) => {
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datasetQuery.where('server_state', 'published');
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});
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this.logger.info(`🔗 Found ${tethysReferences.length} Tethys references from published datasets`);
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let processedCount = 0;
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for (const reference of tethysReferences) {
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processedCount++;
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if (this.verbose && processedCount % 10 === 0) {
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this.logger.info(`📈 Processed ${processedCount}/${tethysReferences.length} references...`);
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}
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// Extract dataset publish_id from DOI or URL
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const targetDatasetPublish = this.extractDatasetPublishIdFromReference(reference.value);
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if (!targetDatasetPublish) {
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if (this.verbose) {
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this.logger.warning(`⚠️ Could not extract publish ID from: ${reference.value}`);
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}
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continue;
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}
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// Check if target dataset exists and is published
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const targetDataset = await Dataset.query()
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.where('publish_id', targetDatasetPublish)
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.where('server_state', 'published')
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.first();
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if (!targetDataset) {
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if (this.verbose) {
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this.logger.warning(`⚠️ Target dataset with publish_id ${targetDatasetPublish} not found or not published`);
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}
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continue;
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}
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// Ensure we have a valid source dataset with proper preloading
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if (!reference.dataset) {
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this.logger.warning(`⚠️ Source dataset ${reference.document_id} not properly loaded, skipping...`);
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continue;
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}
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// Check if reverse reference exists
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const reverseReferenceExists = await this.checkReverseReferenceExists(
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targetDataset.id,
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reference.document_id,
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reference.relation,
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);
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if (!reverseReferenceExists) {
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missingReferences.push({
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sourceDatasetId: reference.document_id,
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targetDatasetId: targetDataset.id,
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sourcePublishId: reference.dataset.publish_id || null,
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targetPublishId: targetDataset.publish_id || null,
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referenceType: reference.type,
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relation: reference.relation,
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doi: reference.value,
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reverseRelation: this.getReverseRelation(reference.relation),
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});
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}
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}
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this.logger.info(`✅ Processed all ${processedCount} references`);
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return missingReferences;
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}
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private extractDatasetPublishIdFromReference(value: string): number | null {
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// Extract from DOI: https://doi.org/10.24341/tethys.107 -> 107
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const doiMatch = value.match(/10\.24341\/tethys\.(\d+)/);
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if (doiMatch) {
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return parseInt(doiMatch[1]);
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}
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// Extract from URL: https://tethys.at/dataset/107 -> 107
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const urlMatch = value.match(/tethys\.at\/dataset\/(\d+)/);
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if (urlMatch) {
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return parseInt(urlMatch[1]);
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}
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return null;
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}
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private async checkReverseReferenceExists(
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sourceDatasetId: number,
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targetDatasetId: number,
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originalRelation: string,
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): Promise<boolean> {
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const reverseRelation = this.getReverseRelation(originalRelation);
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// Only check for reverse references where the source dataset is also published
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const reverseReference = await DatasetReference.query()
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.where('document_id', sourceDatasetId)
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.where('related_document_id', targetDatasetId)
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.where('relation', reverseRelation)
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.whereHas('dataset', (datasetQuery) => {
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datasetQuery.where('server_state', 'published');
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})
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.first();
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return !!reverseReference;
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}
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private getReverseRelation(relation: string): string {
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const relationMap: Record<string, string> = {
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IsNewVersionOf: 'IsPreviousVersionOf',
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IsPreviousVersionOf: 'IsNewVersionOf',
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IsVersionOf: 'HasVersion',
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HasVersion: 'IsVersionOf',
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Compiles: 'IsCompiledBy',
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IsCompiledBy: 'Compiles',
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IsVariantFormOf: 'IsOriginalFormOf',
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IsOriginalFormOf: 'IsVariantFormOf',
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IsPartOf: 'HasPart',
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HasPart: 'IsPartOf',
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IsSupplementTo: 'IsSupplementedBy',
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IsSupplementedBy: 'IsSupplementTo',
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Continues: 'IsContinuedBy',
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IsContinuedBy: 'Continues',
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};
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// to catch relation types like 'compiles' or 'IsVariantFormOf' that are not in the map mark reverse as 'HasVersion'
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return relationMap[relation] || 'HasVersion'; // Default fallback
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}
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private printMissingReferencesList(missingReferences: MissingCrossReference[]) {
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console.log('┌─────────────────────────────────────────────────────────────────────────────────┐');
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console.log('│ MISSING CROSS-REFERENCES REPORT │');
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console.log('│ (Published Datasets Only) │');
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console.log('└─────────────────────────────────────────────────────────────────────────────────┘');
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console.log();
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missingReferences.forEach((missing, index) => {
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console.log(
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`${index + 1}. Dataset ${missing.sourceDatasetId} (Publish ID: ${missing.sourcePublishId}) → Dataset ${missing.targetDatasetId} (Publish ID: ${missing.targetPublishId})`,
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);
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console.log(` ├─ Current relation: "${missing.relation}"`);
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console.log(` ├─ Missing reverse relation: "${missing.reverseRelation}"`);
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console.log(` ├─ Reference type: ${missing.referenceType}`);
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console.log(` └─ DOI/URL: ${missing.doi}`);
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console.log();
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});
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console.log('┌─────────────────────────────────────────────────────────────────────────────────┐');
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console.log(`│ SUMMARY: ${missingReferences.length} missing reverse reference(s) detected │`);
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console.log('└─────────────────────────────────────────────────────────────────────────────────┘');
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}
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private async fixMissingReferences(missingReferences: MissingCrossReference[]) {
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this.logger.info('🔧 Creating missing cross-references in database...');
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let fixedCount = 0;
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let errorCount = 0;
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for (const [index, missing] of missingReferences.entries()) {
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try {
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// Get the source dataset to create proper reference - ensure it's published
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const sourceDataset = await Dataset.query()
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.where('id', missing.sourceDatasetId)
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.where('server_state', 'published')
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.preload('identifier')
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.first();
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if (!sourceDataset) {
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this.logger.warning(`⚠️ Source dataset ${missing.sourceDatasetId} not found or not published, skipping...`);
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errorCount++;
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continue;
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}
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// Create the reverse reference
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const reverseReference = new DatasetReference();
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reverseReference.document_id = missing.targetDatasetId;
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reverseReference.related_document_id = missing.sourceDatasetId;
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reverseReference.type = 'DOI';
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reverseReference.relation = missing.reverseRelation;
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// Use the source dataset's DOI for the value
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if (sourceDataset.identifier?.value) {
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reverseReference.value = `https://doi.org/${sourceDataset.identifier.value}`;
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} else {
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// Fallback to dataset URL if no DOI
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reverseReference.value = `https://tethys.at/dataset/${sourceDataset.publish_id || missing.sourceDatasetId}`;
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}
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// Use the source dataset's main title for the label
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reverseReference.label = sourceDataset.mainTitle || `Dataset ${missing.sourceDatasetId}`;
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await reverseReference.save();
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fixedCount++;
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if (this.verbose) {
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this.logger.info(
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`✅ [${index + 1}/${missingReferences.length}] Created reverse reference: Dataset ${missing.targetDatasetId} -> ${missing.sourceDatasetId}`,
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);
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} else if ((index + 1) % 10 === 0) {
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this.logger.info(`📈 Fixed ${fixedCount}/${missingReferences.length} references...`);
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}
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} catch (error) {
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this.logger.error(
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`❌ Error creating reverse reference for datasets ${missing.targetDatasetId} -> ${missing.sourceDatasetId}:`,
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error,
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);
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errorCount++;
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}
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}
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this.logger.info(`📊 Fix completed: ${fixedCount} created, ${errorCount} errors`);
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}
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}
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