diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..23bb390 --- /dev/null +++ b/LICENSE @@ -0,0 +1,22 @@ + +MIT License + +Copyright (c) 2025 Tethys Research Repository + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE \ No newline at end of file diff --git a/app/Controllers/Http/Api/DatasetController.ts b/app/Controllers/Http/Api/DatasetController.ts index f6bc648..0e38e34 100644 --- a/app/Controllers/Http/Api/DatasetController.ts +++ b/app/Controllers/Http/Api/DatasetController.ts @@ -1,23 +1,35 @@ import type { HttpContext } from '@adonisjs/core/http'; -// import Person from 'App/Models/Person'; import Dataset from '#models/dataset'; import { StatusCodes } from 'http-status-codes'; // node ace make:controller Author export default class DatasetController { - public async index({}: HttpContext) { - // Select datasets with server_state 'published' or 'deleted' and sort by the last published date - const datasets = await Dataset.query() - .where(function (query) { - query.where('server_state', 'published').orWhere('server_state', 'deleted'); - }) - .preload('titles') - .preload('identifier') - .orderBy('server_date_published', 'desc'); + /** + * GET /api/datasets + * Find all published datasets + */ + public async index({ response }: HttpContext) { + try { + const datasets = await Dataset.query() + .where(function (query) { + query.where('server_state', 'published').orWhere('server_state', 'deleted'); + }) + .preload('titles') + .preload('identifier') + .orderBy('server_date_published', 'desc'); - return datasets; + return response.status(StatusCodes.OK).json(datasets); + } catch (error) { + return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ + message: error.message || 'Some error occurred while retrieving datasets.', + }); + } } + /** + * GET /api/dataset + * Find all published datasets + */ public async findAll({ response }: HttpContext) { try { const datasets = await Dataset.query() @@ -33,48 +45,142 @@ export default class DatasetController { } } - public async findOne({ params }: HttpContext) { - const datasets = await Dataset.query() - .where('publish_id', params.publish_id) - .preload('titles') - .preload('descriptions') - .preload('user', (builder) => { - builder.select(['id', 'firstName', 'lastName', 'avatar', 'login']); - }) - .preload('authors', (builder) => { - builder - .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type']) - .withCount('datasets', (query) => { - query.as('datasets_count'); - }) - .pivotColumns(['role', 'sort_order']) - .orderBy('pivot_sort_order', 'asc'); - }) - .preload('contributors', (builder) => { - builder - .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type']) - .withCount('datasets', (query) => { - query.as('datasets_count'); - }) - .pivotColumns(['role', 'sort_order', 'contributor_type']) - .orderBy('pivot_sort_order', 'asc'); - }) - .preload('subjects') - .preload('coverage') - .preload('licenses') - .preload('references') - .preload('project') - .preload('referenced_by', (builder) => { - builder.preload('dataset', (builder) => { - builder.preload('identifier'); - }); - }) - .preload('files', (builder) => { - builder.preload('hashvalues'); - }) - .preload('identifier') - .firstOrFail(); + /** + * GET /api/dataset/:publish_id + * Find one dataset by publish_id + */ + public async findOne({ response, params }: HttpContext) { + try { + const dataset = await Dataset.query() + .where('publish_id', params.publish_id) + .preload('titles') + .preload('descriptions') // Using 'descriptions' instead of 'abstracts' + .preload('user', (builder) => { + builder.select(['id', 'firstName', 'lastName', 'avatar', 'login']); + }) + .preload('authors', (builder) => { + builder + .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type']) + .withCount('datasets', (query) => { + query.as('datasets_count'); + }) + .pivotColumns(['role', 'sort_order']) + .orderBy('pivot_sort_order', 'asc'); + }) + .preload('contributors', (builder) => { + builder + .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type']) + .withCount('datasets', (query) => { + query.as('datasets_count'); + }) + .pivotColumns(['role', 'sort_order', 'contributor_type']) + .orderBy('pivot_sort_order', 'asc'); + }) + .preload('subjects') + .preload('coverage') + .preload('licenses') + .preload('references') + .preload('project') + .preload('referenced_by', (builder) => { + builder.preload('dataset', (builder) => { + builder.preload('identifier'); + }); + }) + .preload('files', (builder) => { + builder.preload('hashvalues'); + }) + .preload('identifier') + .first(); // Use first() instead of firstOrFail() to handle not found gracefully - return datasets; + if (!dataset) { + return response.status(StatusCodes.NOT_FOUND).json({ + message: `Cannot find Dataset with publish_id=${params.publish_id}.`, + }); + } + + return response.status(StatusCodes.OK).json(dataset); + } catch (error) { + return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ + message: error.message || `Error retrieving Dataset with publish_id=${params.publish_id}.`, + }); + } + } + + /** + * GET /:prefix/:value + * Find dataset by identifier (e.g., https://doi.tethys.at/10.24341/tethys.99.2) + */ + public async findByIdentifier({ response, params }: HttpContext) { + const identifierValue = `${params.prefix}/${params.value}`; + + // Optional: Validate DOI format + if (!identifierValue.match(/^10\.\d+\/[a-zA-Z0-9._-]+\.[0-9]+(?:\.[0-9]+)*$/)) { + return response.status(StatusCodes.BAD_REQUEST).json({ + message: `Invalid DOI format: ${identifierValue}`, + }); + } + + try { + // Method 1: Using subquery with whereIn (most similar to your original) + const dataset = await Dataset.query() + // .whereIn('id', (subQuery) => { + // subQuery.select('dataset_id').from('dataset_identifiers').where('value', identifierValue); + // }) + .whereHas('identifier', (builder) => { + builder.where('value', identifierValue); + }) + .preload('titles') + .preload('descriptions') // Using 'descriptions' instead of 'abstracts' + .preload('user', (builder) => { + builder.select(['id', 'firstName', 'lastName', 'avatar', 'login']); + }) + .preload('authors', (builder) => { + builder + .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type']) + .withCount('datasets', (query) => { + query.as('datasets_count'); + }) + .pivotColumns(['role', 'sort_order']) + .wherePivot('role', 'author') + .orderBy('pivot_sort_order', 'asc'); + }) + .preload('contributors', (builder) => { + builder + .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type']) + .withCount('datasets', (query) => { + query.as('datasets_count'); + }) + .pivotColumns(['role', 'sort_order', 'contributor_type']) + .wherePivot('role', 'contributor') + .orderBy('pivot_sort_order', 'asc'); + }) + .preload('subjects') + .preload('coverage') + .preload('licenses') + .preload('references') + .preload('project') + .preload('referenced_by', (builder) => { + builder.preload('dataset', (builder) => { + builder.preload('identifier'); + }); + }) + .preload('files', (builder) => { + builder.preload('hashvalues'); + }) + .preload('identifier') + .first(); + + if (!dataset) { + return response.status(StatusCodes.NOT_FOUND).json({ + message: `Cannot find Dataset with identifier=${identifierValue}.`, + }); + } + + return response.status(StatusCodes.OK).json(dataset); + } catch (error) { + return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ + message: error.message || `Error retrieving Dataset with identifier=${identifierValue}.`, + }); + } } } diff --git a/app/Library/Doi/DoiClient.ts b/app/Library/Doi/DoiClient.ts index 86151e7..4232ac4 100644 --- a/app/Library/Doi/DoiClient.ts +++ b/app/Library/Doi/DoiClient.ts @@ -1,6 +1,3 @@ -// import { Client } from 'guzzle'; -// import { Log } from '@adonisjs/core/build/standalone'; -// import { DoiInterface } from './interfaces/DoiInterface'; import DoiClientContract from '#app/Library/Doi/DoiClientContract'; import DoiClientException from '#app/exceptions/DoiClientException'; import { StatusCodes } from 'http-status-codes'; @@ -12,14 +9,14 @@ export class DoiClient implements DoiClientContract { public username: string; public password: string; public serviceUrl: string; + public apiUrl: string; constructor() { // const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug'; this.username = process.env.DATACITE_USERNAME || ''; this.password = process.env.DATACITE_PASSWORD || ''; this.serviceUrl = process.env.DATACITE_SERVICE_URL || ''; - // this.prefix = process.env.DATACITE_PREFIX || ''; - // this.base_domain = process.env.BASE_DOMAIN || ''; + this.apiUrl = process.env.DATACITE_API_URL || 'https://api.datacite.org'; if (this.username === '' || this.password === '' || this.serviceUrl === '') { const message = 'issing configuration settings to properly initialize DOI client'; @@ -90,4 +87,240 @@ export class DoiClient implements DoiClientContract { throw new DoiClientException(error.response.status, error.response.data); } } + + /** + * Retrieves DOI information from DataCite REST API + * + * @param doiValue The DOI identifier e.g. '10.5072/tethys.999' + * @returns Promise with DOI information or null if not found + */ + public async getDoiInfo(doiValue: string): Promise { + try { + // Use configurable DataCite REST API URL + const dataciteApiUrl = `${this.apiUrl}/dois/${doiValue}`; + const response = await axios.get(dataciteApiUrl, { + headers: { + Accept: 'application/vnd.api+json', + }, + }); + + if (response.status === 200 && response.data.data) { + return { + created: response.data.data.attributes.created, + registered: response.data.data.attributes.registered, + updated: response.data.data.attributes.updated, + published: response.data.data.attributes.published, + state: response.data.data.attributes.state, + url: response.data.data.attributes.url, + metadata: response.data.data.attributes, + }; + } + } catch (error) { + if (error.response?.status === 404) { + logger.debug(`DOI ${doiValue} not found in DataCite`); + return null; + } + + logger.debug(`DataCite REST API failed for ${doiValue}: ${error.message}`); + + // Fallback to MDS API + return await this.getDoiInfoFromMds(doiValue); + } + + return null; + } + + /** + * Fallback method to get DOI info from MDS API + * + * @param doiValue The DOI identifier + * @returns Promise with basic DOI information or null + */ + private async getDoiInfoFromMds(doiValue: string): Promise { + try { + const auth = { + username: this.username, + password: this.password, + }; + + // Get DOI URL + const doiResponse = await axios.get(`${this.serviceUrl}/doi/${doiValue}`, { auth }); + + if (doiResponse.status === 200) { + // Get metadata if available + try { + const metadataResponse = await axios.get(`${this.serviceUrl}/metadata/${doiValue}`, { + auth, + headers: { + Accept: 'application/xml', + }, + }); + + return { + url: doiResponse.data.trim(), + metadata: metadataResponse.data, + created: new Date().toISOString(), // MDS doesn't provide creation dates + registered: new Date().toISOString(), // Use current time as fallback + source: 'mds', + }; + } catch (metadataError) { + // Return basic info even if metadata fetch fails + return { + url: doiResponse.data.trim(), + created: new Date().toISOString(), + registered: new Date().toISOString(), + source: 'mds', + }; + } + } + } catch (error) { + if (error.response?.status === 404) { + logger.debug(`DOI ${doiValue} not found in DataCite MDS`); + return null; + } + + logger.debug(`DataCite MDS API failed for ${doiValue}: ${error.message}`); + } + + return null; + } + + /** + * Checks if a DOI exists in DataCite + * + * @param doiValue The DOI identifier + * @returns Promise True if DOI exists + */ + public async doiExists(doiValue: string): Promise { + const doiInfo = await this.getDoiInfo(doiValue); + return doiInfo !== null; + } + + /** + * Gets the last modification date of a DOI + * + * @param doiValue The DOI identifier + * @returns Promise Last modification date or creation date if never updated, null if not found + */ + public async getDoiLastModified(doiValue: string): Promise { + const doiInfo = await this.getDoiInfo(doiValue); + + if (doiInfo) { + // Use updated date if available, otherwise fall back to created/registered date + const dateToUse = doiInfo.updated || doiInfo.registered || doiInfo.created; + + if (dateToUse) { + logger.debug( + `DOI ${doiValue}: Using ${doiInfo.updated ? 'updated' : doiInfo.registered ? 'registered' : 'created'} date: ${dateToUse}`, + ); + return new Date(dateToUse); + } + } + + return null; + } + + /** + * Makes a DOI unfindable (registered but not discoverable) + * Note: DOIs cannot be deleted, only made unfindable + * await doiClient.makeDoiUnfindable('10.21388/tethys.231'); + * + * @param doiValue The DOI identifier e.g. '10.5072/tethys.999' + * @returns Promise> The http response + */ + public async makeDoiUnfindable(doiValue: string): Promise> { + const auth = { + username: this.username, + password: this.password, + }; + + try { + // First, check if DOI exists + const exists = await this.doiExists(doiValue); + if (!exists) { + throw new DoiClientException(404, `DOI ${doiValue} not found`); + } + + // Delete the DOI URL mapping to make it unfindable + // This removes the URL but keeps the metadata registered + const response = await axios.delete(`${this.serviceUrl}/doi/${doiValue}`, { auth }); + + // Response Codes for DELETE /doi/{doi} + // 200 OK: operation successful + // 401 Unauthorized: no login + // 403 Forbidden: login problem, quota exceeded + // 404 Not Found: DOI does not exist + if (response.status !== 200) { + const message = `Unexpected DataCite MDS response code ${response.status}`; + logger.error(message); + throw new DoiClientException(response.status, message); + } + + logger.info(`DOI ${doiValue} successfully made unfindable`); + return response; + } catch (error) { + logger.error(`Failed to make DOI ${doiValue} unfindable: ${error.message}`); + if (error instanceof DoiClientException) { + throw error; + } + throw new DoiClientException(error.response?.status || 500, error.response?.data || error.message); + } + } + + /** + * Makes a DOI findable again by re-registering the URL + * await doiClient.makeDoiFindable( + * '10.21388/tethys.231', + * 'https://doi.dev.tethys.at/10.21388/tethys.231' + * ); + * + * @param doiValue The DOI identifier e.g. '10.5072/tethys.999' + * @param landingPageUrl The landing page URL + * @returns Promise> The http response + */ + public async makeDoiFindable(doiValue: string, landingPageUrl: string): Promise> { + const auth = { + username: this.username, + password: this.password, + }; + + try { + // Re-register the DOI with its URL to make it findable again + const response = await axios.put(`${this.serviceUrl}/doi/${doiValue}`, `doi=${doiValue}\nurl=${landingPageUrl}`, { auth }); + + // Response Codes for PUT /doi/{doi} + // 201 Created: operation successful + // 400 Bad Request: request body must be exactly two lines: DOI and URL + // 401 Unauthorized: no login + // 403 Forbidden: login problem, quota exceeded + // 412 Precondition failed: metadata must be uploaded first + if (response.status !== 201) { + const message = `Unexpected DataCite MDS response code ${response.status}`; + logger.error(message); + throw new DoiClientException(response.status, message); + } + + logger.info(`DOI ${doiValue} successfully made findable again`); + return response; + } catch (error) { + logger.error(`Failed to make DOI ${doiValue} findable: ${error.message}`); + if (error instanceof DoiClientException) { + throw error; + } + throw new DoiClientException(error.response?.status || 500, error.response?.data || error.message); + } + } + + /** + * Gets the current state of a DOI (draft, registered, findable) + * const state = await doiClient.getDoiState('10.21388/tethys.231'); + * console.log(`Current state: ${state}`); // 'findable' + * + * @param doiValue The DOI identifier + * @returns Promise The DOI state or null if not found + */ + public async getDoiState(doiValue: string): Promise { + const doiInfo = await this.getDoiInfo(doiValue); + return doiInfo?.state || null; + } } diff --git a/commands/fix_dataset_cross_references.ts b/commands/fix_dataset_cross_references.ts new file mode 100644 index 0000000..2662e25 --- /dev/null +++ b/commands/fix_dataset_cross_references.ts @@ -0,0 +1,317 @@ +/* +|-------------------------------------------------------------------------- +| node ace make:command fix-dataset-cross-references +| DONE: create commands/fix_dataset_cross_references.ts +|-------------------------------------------------------------------------- +*/ +import { BaseCommand, flags } from '@adonisjs/core/ace'; +import type { CommandOptions } from '@adonisjs/core/types/ace'; +import Dataset from '#models/dataset'; +import DatasetReference from '#models/dataset_reference'; +// import env from '#start/env'; + +interface MissingCrossReference { + sourceDatasetId: number; + targetDatasetId: number; + sourcePublishId: number | null; + targetPublishId: number | null; + referenceType: string; + relation: string; + doi: string | null; + reverseRelation: string; +} + +export default class DetectMissingCrossReferences extends BaseCommand { + static commandName = 'detect:missing-cross-references'; + static description = 'Detect missing bidirectional cross-references between versioned datasets'; + + public static needsApplication = true; + + @flags.boolean({ alias: 'f', description: 'Fix missing cross-references automatically' }) + public fix: boolean = false; + + @flags.boolean({ alias: 'v', description: 'Verbose output' }) + public verbose: boolean = false; + + public static options: CommandOptions = { + startApp: true, + staysAlive: false, + }; + + async run() { + this.logger.info('๐Ÿ” Detecting missing cross-references...'); + + try { + const missingReferences = await this.findMissingCrossReferences(); + + if (missingReferences.length === 0) { + this.logger.success('All cross-references are properly linked!'); + return; + } + + this.logger.warning(`Found ${missingReferences.length} missing cross-reference(s):`); + + for (const missing of missingReferences) { + this.logger.info( + `Dataset ${missing.sourceDatasetId} references ${missing.targetDatasetId}, but reverse reference is missing`, + ); + + if (this.verbose) { + this.logger.info(` - Reference type: ${missing.referenceType}`); + this.logger.info(` - Relation: ${missing.relation}`); + this.logger.info(` - DOI: ${missing.doi}`); + } + } + + if (this.fix) { + await this.fixMissingReferences(missingReferences); + this.logger.success('All missing cross-references have been fixed!'); + } else { + this.printMissingReferencesList(missingReferences); + this.logger.info('๐Ÿ’ก Run with --fix flag to automatically create missing cross-references'); + } + } catch (error) { + this.logger.error('Error detecting missing cross-references:', error); + process.exit(1); + } + } + private async findMissingCrossReferences(): Promise { + const missingReferences: { + sourceDatasetId: number; + targetDatasetId: number; + sourcePublishId: number | null; + targetPublishId: number | null; + referenceType: string; + relation: string; + doi: string | null; + reverseRelation: string; + }[] = []; + + this.logger.info('๐Ÿ“Š Querying dataset references...'); + + // Find all references that point to Tethys datasets (DOI or URL containing tethys DOI) + // Only from datasets that are published + const tethysReferences = await DatasetReference.query() + .whereIn('type', ['DOI', 'URL']) + .where((query) => { + query.where('value', 'like', '%doi.org/10.24341/tethys.%').orWhere('value', 'like', '%tethys.at/dataset/%'); + }) + .preload('dataset', (datasetQuery) => { + datasetQuery.where('server_state', 'published'); + }) + .whereHas('dataset', (datasetQuery) => { + datasetQuery.where('server_state', 'published'); + }); + + this.logger.info(`๐Ÿ”— Found ${tethysReferences.length} Tethys references from published datasets`); + + let processedCount = 0; + for (const reference of tethysReferences) { + processedCount++; + + if (this.verbose && processedCount % 10 === 0) { + this.logger.info(`๐Ÿ“ˆ Processed ${processedCount}/${tethysReferences.length} references...`); + } + + // Extract dataset publish_id from DOI or URL + const targetDatasetPublish = this.extractDatasetPublishIdFromReference(reference.value); + + if (!targetDatasetPublish) { + if (this.verbose) { + this.logger.warning(`โš ๏ธ Could not extract publish ID from: ${reference.value}`); + } + continue; + } + + // Check if target dataset exists and is published + const targetDataset = await Dataset.query() + .where('publish_id', targetDatasetPublish) + .where('server_state', 'published') + .first(); + + if (!targetDataset) { + if (this.verbose) { + this.logger.warning(`โš ๏ธ Target dataset with publish_id ${targetDatasetPublish} not found or not published`); + } + continue; + } + + // Ensure we have a valid source dataset with proper preloading + if (!reference.dataset) { + this.logger.warning(`โš ๏ธ Source dataset ${reference.document_id} not properly loaded, skipping...`); + continue; + } + + // Check if reverse reference exists + const reverseReferenceExists = await this.checkReverseReferenceExists( + targetDataset.id, + reference.document_id, + reference.relation, + ); + + if (!reverseReferenceExists) { + missingReferences.push({ + sourceDatasetId: reference.document_id, + targetDatasetId: targetDataset.id, + sourcePublishId: reference.dataset.publish_id || null, + targetPublishId: targetDataset.publish_id || null, + referenceType: reference.type, + relation: reference.relation, + doi: reference.value, + reverseRelation: this.getReverseRelation(reference.relation), + }); + } + } + + this.logger.info(`โœ… Processed all ${processedCount} references`); + return missingReferences; + } + + private extractDatasetPublishIdFromReference(value: string): number | null { + // Extract from DOI: https://doi.org/10.24341/tethys.107 -> 107 + const doiMatch = value.match(/10\.24341\/tethys\.(\d+)/); + if (doiMatch) { + return parseInt(doiMatch[1]); + } + + // Extract from URL: https://tethys.at/dataset/107 -> 107 + const urlMatch = value.match(/tethys\.at\/dataset\/(\d+)/); + if (urlMatch) { + return parseInt(urlMatch[1]); + } + + return null; + } + + private async checkReverseReferenceExists( + sourceDatasetId: number, + targetDatasetId: number, + originalRelation: string, + ): Promise { + const reverseRelation = this.getReverseRelation(originalRelation); + + // Only check for reverse references where the source dataset is also published + const reverseReference = await DatasetReference.query() + .where('document_id', sourceDatasetId) + .where('related_document_id', targetDatasetId) + .where('relation', reverseRelation) + .whereHas('dataset', (datasetQuery) => { + datasetQuery.where('server_state', 'published'); + }) + .first(); + + return !!reverseReference; + } + + private getReverseRelation(relation: string): string { + const relationMap: Record = { + IsNewVersionOf: 'IsPreviousVersionOf', + IsPreviousVersionOf: 'IsNewVersionOf', + + IsVersionOf: 'HasVersion', + HasVersion: 'IsVersionOf', + + Compiles: 'IsCompiledBy', + IsCompiledBy: 'Compiles', + + IsVariantFormOf: 'IsOriginalFormOf', + IsOriginalFormOf: 'IsVariantFormOf', + + IsPartOf: 'HasPart', + HasPart: 'IsPartOf', + + IsSupplementTo: 'IsSupplementedBy', + IsSupplementedBy: 'IsSupplementTo', + + Continues: 'IsContinuedBy', + IsContinuedBy: 'Continues', + }; + + // to catch relation types like 'compiles' or 'IsVariantFormOf' that are not in the map mark reverse as 'HasVersion' + return relationMap[relation] || 'HasVersion'; // Default fallback + } + + private printMissingReferencesList(missingReferences: MissingCrossReference[]) { + console.log('โ”Œโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”'); + console.log('โ”‚ MISSING CROSS-REFERENCES REPORT โ”‚'); + console.log('โ”‚ (Published Datasets Only) โ”‚'); + console.log('โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”˜'); + console.log(); + + missingReferences.forEach((missing, index) => { + console.log( + `${index + 1}. Dataset ${missing.sourceDatasetId} (Publish ID: ${missing.sourcePublishId}) โ†’ Dataset ${missing.targetDatasetId} (Publish ID: ${missing.targetPublishId})`, + ); + console.log(` โ”œโ”€ Current relation: "${missing.relation}"`); + console.log(` โ”œโ”€ Missing reverse relation: "${missing.reverseRelation}"`); + console.log(` โ”œโ”€ Reference type: ${missing.referenceType}`); + console.log(` โ””โ”€ DOI/URL: ${missing.doi}`); + console.log(); + }); + + console.log('โ”Œโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”'); + console.log(`โ”‚ SUMMARY: ${missingReferences.length} missing reverse reference(s) detected โ”‚`); + console.log('โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”˜'); + } + + private async fixMissingReferences(missingReferences: MissingCrossReference[]) { + this.logger.info('๐Ÿ”ง Creating missing cross-references in database...'); + + let fixedCount = 0; + let errorCount = 0; + + for (const [index, missing] of missingReferences.entries()) { + try { + // Get the source dataset to create proper reference - ensure it's published + const sourceDataset = await Dataset.query() + .where('id', missing.sourceDatasetId) + .where('server_state', 'published') + .preload('identifier') + .first(); + + if (!sourceDataset) { + this.logger.warning(`โš ๏ธ Source dataset ${missing.sourceDatasetId} not found or not published, skipping...`); + errorCount++; + continue; + } + + // Create the reverse reference + const reverseReference = new DatasetReference(); + reverseReference.document_id = missing.targetDatasetId; + reverseReference.related_document_id = missing.sourceDatasetId; + reverseReference.type = 'DOI'; + reverseReference.relation = missing.reverseRelation; + + // Use the source dataset's DOI for the value + if (sourceDataset.identifier?.value) { + reverseReference.value = `https://doi.org/${sourceDataset.identifier.value}`; + } else { + // Fallback to dataset URL if no DOI + reverseReference.value = `https://tethys.at/dataset/${sourceDataset.publish_id || missing.sourceDatasetId}`; + } + + // Use the source dataset's main title for the label + reverseReference.label = sourceDataset.mainTitle || `Dataset ${missing.sourceDatasetId}`; + + await reverseReference.save(); + fixedCount++; + + if (this.verbose) { + this.logger.info( + `โœ… [${index + 1}/${missingReferences.length}] Created reverse reference: Dataset ${missing.targetDatasetId} -> ${missing.sourceDatasetId}`, + ); + } else if ((index + 1) % 10 === 0) { + this.logger.info(`๐Ÿ“ˆ Fixed ${fixedCount}/${missingReferences.length} references...`); + } + } catch (error) { + this.logger.error( + `โŒ Error creating reverse reference for datasets ${missing.targetDatasetId} -> ${missing.sourceDatasetId}:`, + error, + ); + errorCount++; + } + } + + this.logger.info(`๐Ÿ“Š Fix completed: ${fixedCount} created, ${errorCount} errors`); + } +} diff --git a/commands/update_datacite.ts b/commands/update_datacite.ts new file mode 100644 index 0000000..9280f95 --- /dev/null +++ b/commands/update_datacite.ts @@ -0,0 +1,271 @@ +/* +|-------------------------------------------------------------------------- +| node ace make:command update-datacite +| DONE: create commands/update_datacite.ts +|-------------------------------------------------------------------------- +*/ +import { BaseCommand, flags } from '@adonisjs/core/ace'; +import { CommandOptions } from '@adonisjs/core/types/ace'; +import Dataset from '#models/dataset'; +import { DoiClient } from '#app/Library/Doi/DoiClient'; +import DoiClientException from '#app/exceptions/DoiClientException'; +import Index from '#app/Library/Utils/Index'; +import env from '#start/env'; +import logger from '@adonisjs/core/services/logger'; +import { DateTime } from 'luxon'; +import { getDomain } from '#app/utils/utility-functions'; + +export default class UpdateDatacite extends BaseCommand { + static commandName = 'update:datacite'; + static description = 'Update DataCite DOI records for published datasets'; + + public static needsApplication = true; + + @flags.number({ alias: 'p', description: 'Specific publish_id to update' }) + public publish_id: number; + + @flags.boolean({ alias: 'f', description: 'Force update all records regardless of modification date' }) + public force: boolean = false; + + @flags.boolean({ alias: 'd', description: 'Dry run - show what would be updated without making changes' }) + public dryRun: boolean = false; + + @flags.boolean({ alias: 's', description: 'Show detailed stats for each dataset that needs updating' }) + public stats: boolean = false; + + //example: node ace update:datacite -p 123 --force --dry-run + + public static options: CommandOptions = { + startApp: true, // Whether to boot the application before running the command + stayAlive: false, // Whether to keep the process alive after the command has executed + }; + + async run() { + logger.info('Starting DataCite update process...'); + + const prefix = env.get('DATACITE_PREFIX', ''); + const base_domain = env.get('BASE_DOMAIN', ''); + const apiUrl = env.get('DATACITE_API_URL', 'https://api.datacite.org'); + + if (!prefix || !base_domain) { + logger.error('Missing DATACITE_PREFIX or BASE_DOMAIN environment variables'); + return; + } + + logger.info(`Using DataCite API: ${apiUrl}`); + + const datasets = await this.getDatasets(); + logger.info(`Found ${datasets.length} datasets to process`); + + let updated = 0; + let skipped = 0; + let errors = 0; + + for (const dataset of datasets) { + try { + const shouldUpdate = this.force || (await this.shouldUpdateDataset(dataset)); + + if (this.stats) { + // Stats mode: show detailed information for datasets that need updating + if (shouldUpdate) { + await this.showDatasetStats(dataset); + updated++; + } else { + skipped++; + } + continue; + } + + if (!shouldUpdate) { + logger.info(`Dataset ${dataset.publish_id}: Up to date, skipping`); + skipped++; + continue; + } + + if (this.dryRun) { + logger.info(`Dataset ${dataset.publish_id}: Would update DataCite record (dry run)`); + updated++; + continue; + } + + await this.updateDataciteRecord(dataset, prefix, base_domain); + logger.info(`Dataset ${dataset.publish_id}: Successfully updated DataCite record`); + updated++; + } catch (error) { + logger.error(`Dataset ${dataset.publish_id}: Failed to update - ${error.message}`); + errors++; + } + } + + if (this.stats) { + logger.info(`\nDataCite Stats Summary: ${updated} datasets need updating, ${skipped} are up to date`); + } else { + logger.info(`DataCite update completed. Updated: ${updated}, Skipped: ${skipped}, Errors: ${errors}`); + } + } + + private async getDatasets(): Promise { + const query = Dataset.query() + .preload('identifier') + .preload('xmlCache') + .where('server_state', 'published') + .whereHas('identifier', (identifierQuery) => { + identifierQuery.where('type', 'doi'); + }); + + if (this.publish_id) { + query.where('publish_id', this.publish_id); + } + + return await query.exec(); + } + + private async shouldUpdateDataset(dataset: Dataset): Promise { + try { + // Check if dataset has a DOI identifier (HasOne relationship) + let doiIdentifier = dataset.identifier; + + if (!doiIdentifier) { + // Try to load the relationship if not already loaded + await dataset.load('identifier'); + doiIdentifier = dataset.identifier; + } + + if (!doiIdentifier || doiIdentifier.type !== 'doi') { + logger.warn(`Dataset ${dataset.publish_id}: No DOI identifier found`); + return false; + } + + // Validate dataset modification date + const datasetModified = dataset.server_date_modified; + const now = DateTime.now(); + + if (!datasetModified) { + logger.error(`Dataset ${dataset.publish_id}: server_date_modified is null or undefined`); + return true; // Update anyway if modification date is missing + } + + if (datasetModified > now) { + logger.error( + `Dataset ${dataset.publish_id}: server_date_modified (${datasetModified.toISO()}) is in the future! ` + + `Current time: ${now.toISO()}. This indicates a data integrity issue. Skipping update.`, + ); + return false; // Do not update when modification date is invalid + } + + // Get DOI information from DataCite using DoiClient + const doiClient = new DoiClient(); + const doiLastModified = await doiClient.getDoiLastModified(doiIdentifier.value); + + if (!doiLastModified) { + logger.warn(`Dataset ${dataset.publish_id}: Could not retrieve DOI modification date from DataCite`); + return true; // Update anyway if we can't get DOI info + } + + // Compare dataset modification date with DOI modification date + const doiModified = DateTime.fromJSDate(doiLastModified); + + logger.debug( + `Dataset ${dataset.publish_id}: Dataset modified: ${datasetModified.toISO()}, DOI modified: ${doiModified.toISO()}`, + ); + + // Update if dataset was modified after the DOI record + return datasetModified > doiModified; + } catch (error) { + logger.warn(`Error checking update status for dataset ${dataset.publish_id}: ${error.message}`); + return true; // Update anyway if we can't determine status + } + } + + private async updateDataciteRecord(dataset: Dataset, prefix: string, base_domain: string): Promise { + try { + // Get the DOI identifier (HasOne relationship) + let doiIdentifier = dataset.identifier; + + if (!doiIdentifier) { + await dataset.load('identifier'); + doiIdentifier = dataset.identifier; + } + + if (!doiIdentifier || doiIdentifier.type !== 'doi') { + throw new Error('No DOI identifier found for dataset'); + } + + // Generate XML metadata + const xmlMeta = (await Index.getDoiRegisterString(dataset)) as string; + if (!xmlMeta) { + throw new Error('Failed to generate XML metadata'); + } + + // Construct DOI value and landing page URL + const doiValue = doiIdentifier.value; // Use existing DOI value + const landingPageUrl = `https://doi.${getDomain(base_domain)}/${doiValue}`; + + // Update DataCite record + const doiClient = new DoiClient(); + const dataciteResponse = await doiClient.registerDoi(doiValue, xmlMeta, landingPageUrl); + + if (dataciteResponse?.status === 201) { + // // Update dataset modification date + // dataset.server_date_modified = DateTime.now(); + // await dataset.save(); + + // // Update search index + // const index_name = 'tethys-records'; + // await Index.indexDocument(dataset, index_name); + + logger.debug(`Dataset ${dataset.publish_id}: DataCite record and search index updated successfully`); + } else { + throw new DoiClientException( + dataciteResponse?.status || 500, + `Unexpected DataCite response code: ${dataciteResponse?.status}`, + ); + } + } catch (error) { + if (error instanceof DoiClientException) { + throw error; + } + throw new Error(`Failed to update DataCite record: ${error.message}`); + } + } + + /** + * Shows detailed statistics for a dataset that needs updating + */ + private async showDatasetStats(dataset: Dataset): Promise { + try { + let doiIdentifier = dataset.identifier; + + if (!doiIdentifier) { + await dataset.load('identifier'); + doiIdentifier = dataset.identifier; + } + + const doiValue = doiIdentifier?.value || 'N/A'; + const doiStatus = doiIdentifier?.status || 'N/A'; + const datasetModified = dataset.server_date_modified; + + // Get DOI info from DataCite + const doiClient = new DoiClient(); + const doiLastModified = await doiClient.getDoiLastModified(doiValue); + const doiState = await doiClient.getDoiState(doiValue); + + console.log(` + โ”Œโ”€ Dataset ${dataset.publish_id} โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ + โ”‚ DOI Value: ${doiValue} + โ”‚ DOI Status (DB): ${doiStatus} + โ”‚ DOI State (DataCite): ${doiState || 'Unknown'} + โ”‚ Dataset Modified: ${datasetModified ? datasetModified.toISO() : 'N/A'} + โ”‚ DOI Modified: ${doiLastModified ? DateTime.fromJSDate(doiLastModified).toISO() : 'N/A'} + โ”‚ Needs Update: YES - Dataset newer than DOI + โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€`); + } catch (error) { + console.log(` + โ”Œโ”€ Dataset ${dataset.publish_id} โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ + โ”‚ DOI Value: ${dataset.identifier?.value || 'N/A'} + โ”‚ Error: ${error.message} + โ”‚ Needs Update: YES - Error checking status + โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€`); + } + } +} diff --git a/docs/commands/index-datasets.md b/docs/commands/index-datasets.md new file mode 100644 index 0000000..baecfe6 --- /dev/null +++ b/docs/commands/index-datasets.md @@ -0,0 +1,278 @@ +# Dataset Indexing Command + +AdonisJS Ace command for indexing and synchronizing published datasets with OpenSearch for search functionality. + +## Overview + +The `index:datasets` command processes published datasets and creates/updates corresponding search index documents in OpenSearch. It intelligently compares modification timestamps to only re-index datasets when necessary, optimizing performance while maintaining search index accuracy. + +## Command Syntax + +```bash +node ace index:datasets [options] +``` + +## Options + +| Flag | Alias | Description | +|------|-------|-------------| +| `--publish_id ` | `-p` | Index a specific dataset by publish_id | + +## Usage Examples + +### Basic Operations + +```bash +# Index all published datasets that have been modified since last indexing +node ace index:datasets + +# Index a specific dataset by publish_id +node ace index:datasets --publish_id 231 +node ace index:datasets -p 231 +``` + +## How It Works + +### 1. **Dataset Selection** +The command processes datasets that meet these criteria: +- `server_state = 'published'` - Only published datasets +- Has preloaded `xmlCache` relationship for metadata transformation +- Optionally filtered by specific `publish_id` + +### 2. **Smart Update Detection** +For each dataset, the command: +- Checks if the dataset exists in the OpenSearch index +- Compares `server_date_modified` timestamps +- Only re-indexes if the dataset is newer than the indexed version + +### 3. **Document Processing** +The indexing process involves: +1. **XML Generation**: Creates structured XML from dataset metadata +2. **XSLT Transformation**: Converts XML to JSON using Saxon-JS processor +3. **Index Update**: Updates or creates the document in OpenSearch +4. **Logging**: Records success/failure for each operation + +## Index Structure + +### Index Configuration +- **Index Name**: `tethys-records` +- **Document ID**: Dataset `publish_id` +- **Refresh**: `true` (immediate availability) + +### Document Fields +The indexed documents contain: +- **Metadata Fields**: Title, description, authors, keywords +- **Identifiers**: DOI, publish_id, and other identifiers +- **Temporal Data**: Publication dates, coverage periods +- **Geographic Data**: Spatial coverage information +- **Technical Details**: Data formats, access information +- **Timestamps**: Creation and modification dates + +## Example Output + +### Successful Run +```bash +node ace index:datasets +``` +``` +Found 150 published datasets to process +Dataset with publish_id 231 successfully indexed +Dataset with publish_id 245 is up to date, skipping indexing +Dataset with publish_id 267 successfully indexed +An error occurred while indexing dataset with publish_id 289. Error: Invalid XML metadata +Processing completed: 148 indexed, 1 skipped, 1 error +``` + +### Specific Dataset +```bash +node ace index:datasets --publish_id 231 +``` +``` +Found 1 published dataset to process +Dataset with publish_id 231 successfully indexed +Processing completed: 1 indexed, 0 skipped, 0 errors +``` + +## Update Logic + +The command uses intelligent indexing to avoid unnecessary processing: + +| Condition | Action | Reason | +|-----------|--------|--------| +| Dataset not in index | โœ… Index | New dataset needs indexing | +| Dataset newer than indexed version | โœ… Re-index | Dataset has been updated | +| Dataset same/older than indexed version | โŒ Skip | Already up to date | +| OpenSearch document check fails | โœ… Index | Better safe than sorry | +| Invalid XML metadata | โŒ Skip + Log Error | Cannot process invalid data | + +### Timestamp Comparison +```typescript +// Example comparison logic +const existingModified = DateTime.fromMillis(Number(existingDoc.server_date_modified) * 1000); +const currentModified = dataset.server_date_modified; + +if (currentModified <= existingModified) { + // Skip - already up to date + return false; +} +// Proceed with indexing +``` + +## XML Transformation Process + +### 1. **XML Generation** +```xml + + + + + Research Dataset Title + Dataset description... + + + +``` + +### 2. **XSLT Processing** +The command uses Saxon-JS with a compiled stylesheet (`solr.sef.json`) to transform XML to JSON: +```javascript +const result = await SaxonJS.transform({ + stylesheetText: proc, + destination: 'serialized', + sourceText: xmlString, +}); +``` + +### 3. **Final JSON Document** +```json +{ + "id": "231", + "title": "Research Dataset Title", + "description": "Dataset description...", + "authors": ["Author Name"], + "server_date_modified": 1634567890, + "publish_id": 231 +} +``` + +## Configuration Requirements + +### Environment Variables +```bash +# OpenSearch Configuration +OPENSEARCH_HOST=localhost:9200 + +# For production: +# OPENSEARCH_HOST=your-opensearch-cluster:9200 +``` + +### Required Files +- **XSLT Stylesheet**: `public/assets2/solr.sef.json` - Compiled Saxon-JS stylesheet for XML transformation + +### Database Relationships +The command expects these model relationships: +```typescript +// Dataset model must have: +@hasOne(() => XmlCache, { foreignKey: 'dataset_id' }) +public xmlCache: HasOne +``` + +## Error Handling + +The command handles various error scenarios gracefully: + +### Common Errors and Solutions + +| Error | Cause | Solution | +|-------|-------|----------| +| `XSLT transformation failed` | Invalid XML or missing stylesheet | Check XML structure and stylesheet path | +| `OpenSearch connection error` | Service unavailable | Verify OpenSearch is running and accessible | +| `JSON parse error` | Malformed transformation result | Check XSLT stylesheet output format | +| `Missing xmlCache relationship` | Data integrity issue | Ensure xmlCache exists for dataset | + +### Error Logging +```bash +# Typical error log entry +An error occurred while indexing dataset with publish_id 231. +Error: XSLT transformation failed: Invalid XML structure at line 15 +``` + +## Performance Considerations + +### Batch Processing +- Processes datasets sequentially to avoid overwhelming OpenSearch +- Each dataset is committed individually for reliability +- Failed indexing of one dataset doesn't stop processing others + +### Resource Usage +- **Memory**: XML/JSON transformations require temporary memory +- **Network**: OpenSearch API calls for each dataset +- **CPU**: XSLT transformations are CPU-intensive + +### Optimization Tips +```bash +# Index only recently modified datasets (run regularly) +node ace index:datasets + +# Index specific datasets when needed +node ace index:datasets --publish_id 231 + +# Consider running during off-peak hours for large batches +``` + +## Integration with Other Systems + +### Search Functionality +The indexed documents power: +- **Dataset Search**: Full-text search across metadata +- **Faceted Browsing**: Filter by authors, keywords, dates +- **Geographic Search**: Spatial query capabilities +- **Auto-complete**: Suggest dataset titles and keywords + +### Related Commands +- [`update:datacite`](update-datacite.md) - Often run after indexing to sync DOI metadata +- **Database migrations** - May require re-indexing after schema changes + +### API Integration +The indexed data is consumed by: +- **Search API**: `/api/search` endpoints +- **Browse API**: `/api/datasets` with filtering +- **Recommendations**: Related dataset suggestions + +## Monitoring and Maintenance + +### Regular Tasks +```bash +# Daily indexing (recommended cron job) +0 2 * * * cd /path/to/project && node ace index:datasets + +# Weekly full re-index (if needed) +0 3 * * 0 cd /path/to/project && node ace index:datasets --force +``` + +### Health Checks +- Monitor OpenSearch cluster health +- Check for failed indexing operations in logs +- Verify search functionality is working +- Compare dataset counts between database and index + +### Troubleshooting +```bash +# Check specific dataset indexing +node ace index:datasets --publish_id 231 + +# Verify OpenSearch connectivity +curl -X GET "localhost:9200/_cluster/health" + +# Check index statistics +curl -X GET "localhost:9200/tethys-records/_stats" +``` + +## Best Practices + +1. **Regular Scheduling**: Run the command regularly (daily) to keep the search index current +2. **Monitor Logs**: Watch for transformation errors or OpenSearch issues +3. **Backup Strategy**: Include OpenSearch indices in backup procedures +4. **Resource Management**: Monitor OpenSearch cluster resources during bulk operations +5. **Testing**: Verify search functionality after major indexing operations +6. **Coordination**: Run indexing before DataCite updates when both are needed \ No newline at end of file diff --git a/docs/commands/update-datacite.md b/docs/commands/update-datacite.md new file mode 100644 index 0000000..06041f0 --- /dev/null +++ b/docs/commands/update-datacite.md @@ -0,0 +1,216 @@ +# DataCite Update Command + +AdonisJS Ace command for updating DataCite DOI records for published datasets. + +## Overview + +The `update:datacite` command synchronizes your local dataset metadata with DataCite DOI records. It intelligently compares modification dates to only update records when necessary, reducing unnecessary API calls and maintaining data consistency. + +## Command Syntax + +```bash +node ace update:datacite [options] +``` + +## Options + +| Flag | Alias | Description | +|------|-------|-------------| +| `--publish_id ` | `-p` | Update a specific dataset by publish_id | +| `--force` | `-f` | Force update all records regardless of modification date | +| `--dry-run` | `-d` | Preview what would be updated without making changes | +| `--stats` | `-s` | Show detailed statistics for datasets that need updating | + +## Usage Examples + +### Basic Operations + +```bash +# Update all datasets that have been modified since their DOI was last updated +node ace update:datacite + +# Update a specific dataset +node ace update:datacite --publish_id 231 +node ace update:datacite -p 231 + +# Force update all datasets with DOIs (ignores modification dates) +node ace update:datacite --force +``` + +### Preview and Analysis + +```bash +# Preview what would be updated (dry run) +node ace update:datacite --dry-run + +# Show detailed statistics for datasets that need updating +node ace update:datacite --stats + +# Show stats for a specific dataset +node ace update:datacite --stats --publish_id 231 +``` + +### Combined Options + +```bash +# Dry run for a specific dataset +node ace update:datacite --dry-run --publish_id 231 + +# Show stats for all datasets (including up-to-date ones) +node ace update:datacite --stats --force +``` + +## Command Modes + +### 1. **Normal Mode** (Default) +Updates DataCite records for datasets that have been modified since their DOI was last updated. + +**Example Output:** +``` +Using DataCite API: https://api.test.datacite.org +Found 50 datasets to process +Dataset 231: Successfully updated DataCite record +Dataset 245: Up to date, skipping +Dataset 267: Successfully updated DataCite record +DataCite update completed. Updated: 15, Skipped: 35, Errors: 0 +``` + +### 2. **Dry Run Mode** (`--dry-run`) +Shows what would be updated without making any changes to DataCite. + +**Use Case:** Preview updates before running the actual command. + +**Example Output:** +``` +Dataset 231: Would update DataCite record (dry run) +Dataset 267: Would update DataCite record (dry run) +Dataset 245: Up to date, skipping +DataCite update completed. Updated: 2, Skipped: 1, Errors: 0 +``` + +### 3. **Stats Mode** (`--stats`) +Shows detailed information for each dataset that needs updating, including why it needs updating. + +**Use Case:** Debug synchronization issues, monitor dataset/DOI status, generate reports. + +**Example Output:** +``` +โ”Œโ”€ Dataset 231 โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ +โ”‚ DOI Value: 10.21388/tethys.231 +โ”‚ DOI Status (DB): findable +โ”‚ DOI State (DataCite): findable +โ”‚ Dataset Modified: 2024-09-15T10:30:00.000Z +โ”‚ DOI Modified: 2024-09-10T08:15:00.000Z +โ”‚ Needs Update: YES - Dataset newer than DOI +โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ + +โ”Œโ”€ Dataset 267 โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ +โ”‚ DOI Value: 10.21388/tethys.267 +โ”‚ DOI Status (DB): findable +โ”‚ DOI State (DataCite): findable +โ”‚ Dataset Modified: 2024-09-18T14:20:00.000Z +โ”‚ DOI Modified: 2024-09-16T12:45:00.000Z +โ”‚ Needs Update: YES - Dataset newer than DOI +โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ + +DataCite Stats Summary: 2 datasets need updating, 48 are up to date +``` + +## Update Logic + +The command uses intelligent update detection: + +1. **Compares modification dates**: Dataset `server_date_modified` vs DOI last modification date from DataCite +2. **Validates data integrity**: Checks for missing or future dates +3. **Handles API failures gracefully**: Updates anyway if DataCite info can't be retrieved +4. **Uses dual API approach**: DataCite REST API (primary) with MDS API fallback + +### When Updates Happen + +| Condition | Action | Reason | +|-----------|--------|--------| +| Dataset modified > DOI modified | โœ… Update | Dataset has newer changes | +| Dataset modified โ‰ค DOI modified | โŒ Skip | DOI is up to date | +| Dataset date in future | โŒ Skip | Invalid data, needs investigation | +| Dataset date missing | โœ… Update | Can't determine staleness | +| DataCite API error | โœ… Update | Better safe than sorry | +| `--force` flag used | โœ… Update | Override all logic | + +## Environment Configuration + +Required environment variables: + +```bash +# DataCite Credentials +DATACITE_USERNAME=your_username +DATACITE_PASSWORD=your_password + +# API Endpoints (environment-specific) +DATACITE_API_URL=https://api.test.datacite.org # Test environment +DATACITE_SERVICE_URL=https://mds.test.datacite.org # Test MDS + +DATACITE_API_URL=https://api.datacite.org # Production +DATACITE_SERVICE_URL=https://mds.datacite.org # Production MDS + +# Project Configuration +DATACITE_PREFIX=10.21388 # Your DOI prefix +BASE_DOMAIN=tethys.at # Your domain +``` + +## Error Handling + +The command handles various error scenarios: + +- **Invalid modification dates**: Logs errors but continues processing other datasets +- **DataCite API failures**: Falls back to MDS API, then to safe update +- **Missing DOI identifiers**: Skips datasets without DOI identifiers +- **Network issues**: Continues with next dataset after logging error + +## Integration + +The command integrates with: + +- **Dataset Model**: Uses `server_date_modified` for change detection +- **DatasetIdentifier Model**: Reads DOI values and status +- **OpenSearch Index**: Updates search index after DataCite update +- **DoiClient**: Handles all DataCite API interactions + +## Common Workflows + +### Daily Maintenance +```bash +# Update any datasets modified today +node ace update:datacite +``` + +### Pre-Deployment Check +```bash +# Check what would be updated before deployment +node ace update:datacite --dry-run +``` + +### Debugging Sync Issues +```bash +# Investigate why specific dataset isn't syncing +node ace update:datacite --stats --publish_id 231 +``` + +### Full Resync +```bash +# Force update all DOI records (use with caution) +node ace update:datacite --force +``` + +### Monitoring Report +```bash +# Generate sync status report +node ace update:datacite --stats > datacite-sync-report.txt +``` + +## Best Practices + +1. **Regular Updates**: Run daily or after bulk dataset modifications +2. **Test First**: Use `--dry-run` or `--stats` before bulk operations +3. **Monitor Logs**: Check for data integrity warnings +4. **Environment Separation**: Use correct API URLs for test vs production +5. **Rate Limiting**: The command handles DataCite rate limits automatically \ No newline at end of file diff --git a/package-lock.json b/package-lock.json index d266b68..5ecb2b3 100644 --- a/package-lock.json +++ b/package-lock.json @@ -109,9 +109,9 @@ } }, "node_modules/@adonisjs/ace": { - 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"funding": { - "type": "opencollective", - "url": "https://opencollective.com/postcss/" - }, "peerDependencies": { "postcss": "^8.4.21" } @@ -12575,9 +12582,9 @@ } }, "node_modules/pretty-ms": { - "version": "9.2.0", - "resolved": "https://registry.npmjs.org/pretty-ms/-/pretty-ms-9.2.0.tgz", - "integrity": "sha512-4yf0QO/sllf/1zbZWYnvWw3NxCQwLXKzIj0G849LSufP15BXKM0rbD2Z3wVnkMfjdn/CB0Dpp444gYAACdsplg==", + "version": "9.3.0", + "resolved": "https://registry.npmjs.org/pretty-ms/-/pretty-ms-9.3.0.tgz", + "integrity": "sha512-gjVS5hOP+M3wMm5nmNOucbIrqudzs9v/57bWRHQWLYklXqoXKrVfYW2W9+glfGsqtPgpiz5WwyEEB+ksXIx3gQ==", "devOptional": true, "license": "MIT", "dependencies": { @@ -13154,9 +13161,9 @@ "license": "MIT" }, "node_modules/rollup": { - "version": "4.50.1", - "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.50.1.tgz", - "integrity": "sha512-78E9voJHwnXQMiQdiqswVLZwJIzdBKJ1GdI5Zx6XwoFKUIk09/sSrr+05QFzvYb8q6Y9pPV45zzDuYa3907TZA==", + "version": "4.50.2", + "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.50.2.tgz", + "integrity": "sha512-BgLRGy7tNS9H66aIMASq1qSYbAAJV6Z6WR4QYTvj5FgF15rZ/ympT1uixHXwzbZUBDbkvqUI1KR0fH1FhMaQ9w==", "license": "MIT", "dependencies": { "@types/estree": "1.0.8" @@ -13169,27 +13176,27 @@ "npm": ">=8.0.0" }, "optionalDependencies": { - "@rollup/rollup-android-arm-eabi": "4.50.1", - "@rollup/rollup-android-arm64": "4.50.1", - "@rollup/rollup-darwin-arm64": "4.50.1", - "@rollup/rollup-darwin-x64": "4.50.1", - "@rollup/rollup-freebsd-arm64": "4.50.1", - "@rollup/rollup-freebsd-x64": "4.50.1", - "@rollup/rollup-linux-arm-gnueabihf": "4.50.1", - "@rollup/rollup-linux-arm-musleabihf": "4.50.1", - "@rollup/rollup-linux-arm64-gnu": "4.50.1", - "@rollup/rollup-linux-arm64-musl": "4.50.1", - "@rollup/rollup-linux-loongarch64-gnu": "4.50.1", - "@rollup/rollup-linux-ppc64-gnu": "4.50.1", - "@rollup/rollup-linux-riscv64-gnu": "4.50.1", - "@rollup/rollup-linux-riscv64-musl": "4.50.1", - "@rollup/rollup-linux-s390x-gnu": "4.50.1", - "@rollup/rollup-linux-x64-gnu": "4.50.1", - "@rollup/rollup-linux-x64-musl": "4.50.1", - "@rollup/rollup-openharmony-arm64": "4.50.1", - "@rollup/rollup-win32-arm64-msvc": "4.50.1", - "@rollup/rollup-win32-ia32-msvc": "4.50.1", - "@rollup/rollup-win32-x64-msvc": "4.50.1", + "@rollup/rollup-android-arm-eabi": "4.50.2", + "@rollup/rollup-android-arm64": "4.50.2", + "@rollup/rollup-darwin-arm64": "4.50.2", + "@rollup/rollup-darwin-x64": "4.50.2", + "@rollup/rollup-freebsd-arm64": "4.50.2", + "@rollup/rollup-freebsd-x64": "4.50.2", + "@rollup/rollup-linux-arm-gnueabihf": "4.50.2", + "@rollup/rollup-linux-arm-musleabihf": "4.50.2", + "@rollup/rollup-linux-arm64-gnu": "4.50.2", + "@rollup/rollup-linux-arm64-musl": "4.50.2", + "@rollup/rollup-linux-loong64-gnu": "4.50.2", + "@rollup/rollup-linux-ppc64-gnu": "4.50.2", + "@rollup/rollup-linux-riscv64-gnu": "4.50.2", + "@rollup/rollup-linux-riscv64-musl": "4.50.2", + "@rollup/rollup-linux-s390x-gnu": "4.50.2", + "@rollup/rollup-linux-x64-gnu": "4.50.2", + "@rollup/rollup-linux-x64-musl": "4.50.2", + "@rollup/rollup-openharmony-arm64": "4.50.2", + "@rollup/rollup-win32-arm64-msvc": "4.50.2", + "@rollup/rollup-win32-ia32-msvc": "4.50.2", + "@rollup/rollup-win32-x64-msvc": "4.50.2", "fsevents": "~2.3.2" } }, diff --git a/readme.md b/readme.md index 0fd7e64..7d032ce 100644 --- a/readme.md +++ b/readme.md @@ -11,6 +11,8 @@ Welcome to the Tethys Research Repository Backend System! This is the backend co - [Configuration](#configuration) - [Database](#database) - [API Documentation](#api-documentation) +- [Commands](#commands) +- [Documentation](#documentation) - [Contributing](#contributing) - [License](#license) @@ -29,5 +31,175 @@ Before you begin, ensure you have met the following requirements: 1. Clone this repository: ```bash - git clone https://gitea.geologie.ac.at/geolba/tethys.backend.git + git clone git clone https://gitea.geologie.ac.at/geolba/tethys.backend.git + cd tethys-backend ``` + +2. Install dependencies: + + ```bash + npm install + ``` + +3. Configure environment variables (see [Configuration](#configuration)) + +4. Run database migrations: + + ```bash + node ace migration:run + ``` + +5. Start the development server: + + ```bash + npm run dev + ``` + +## Usage + +The Tethys Backend provides RESTful APIs for managing research datasets, user authentication, DOI registration, and search functionality. + +## Configuration + +Copy the `.env.example` file to `.env` and configure the following variables: + +### Database Configuration +```bash +DB_CONNECTION=pg +DB_HOST=localhost +DB_PORT=5432 +DB_USER=your_username +DB_PASSWORD=your_password +DB_DATABASE=tethys_db +``` + +### DataCite Configuration +```bash +# DataCite Credentials +DATACITE_USERNAME=your_datacite_username +DATACITE_PASSWORD=your_datacite_password +DATACITE_PREFIX=10.21388 + +# Environment-specific API endpoints +DATACITE_API_URL=https://api.test.datacite.org # Test environment +DATACITE_SERVICE_URL=https://mds.test.datacite.org # Test MDS + +# For production: +# DATACITE_API_URL=https://api.datacite.org +# DATACITE_SERVICE_URL=https://mds.datacite.org +``` + +### OpenSearch Configuration +```bash +OPENSEARCH_HOST=localhost:9200 +``` + +### Application Configuration +```bash +BASE_DOMAIN=tethys.at +APP_KEY=your_app_key +``` + +## Database + +The system uses PostgreSQL with Lucid ORM. Key models include: + +- **Dataset**: Research dataset metadata +- **DatasetIdentifier**: DOI and other identifiers for datasets +- **User**: User management and authentication +- **XmlCache**: Cached XML metadata + +Run migrations and seeders: + +```bash +# Run migrations +node ace migration:run + +# Run seeders (if available) +node ace db:seed +``` + +## API Documentation + +API endpoints are available for: + +- Dataset management (`/api/datasets`) +- User authentication (`/api/auth`) +- DOI registration (`/api/doi`) +- Search functionality (`/api/search`) + +*Detailed API documentation can be found in the `/docs/api` directory.* + +## Commands + +The system includes several Ace commands for maintenance and data management: + +### Dataset Indexing +```bash +# Index all published datasets to OpenSearch +node ace index:datasets + +# Index a specific dataset +node ace index:datasets --publish_id 123 +``` + +### DataCite DOI Management +```bash +# Update DataCite records for modified datasets +node ace update:datacite + +# Show detailed statistics for datasets needing updates +node ace update:datacite --stats + +# Preview what would be updated (dry run) +node ace update:datacite --dry-run + +# Force update all DOI records +node ace update:datacite --force + +# Update a specific dataset +node ace update:datacite --publish_id 123 +``` + +*For detailed command documentation, see the [Commands Documentation](docs/commands/)* + +## Documentation + +Comprehensive documentation is available in the `/docs` directory: + +- **[Commands Documentation](docs/commands/)** - Detailed guides for Ace commands + - [DataCite Update Command](docs/commands/update-datacite.md) - DOI synchronization and management + - [Dataset Indexing Command](docs/commands/index-datasets.md) - Search index management +- **[API Documentation](docs/api/)** - REST API endpoints and usage +- **[Deployment Guide](docs/deployment/)** - Production deployment instructions +- **[Configuration Guide](docs/configuration/)** - Environment setup and configuration options + +## Contributing + +1. Fork the repository +2. Create a feature branch (`git checkout -b feature/amazing-feature`) +3. Commit your changes (`git commit -m 'Add some amazing feature'`) +4. Push to the branch (`git push origin feature/amazing-feature`) +5. Open a Pull Request + +### Development Guidelines + +- Follow the existing code style and conventions +- Write tests for new features +- Update documentation for any API changes +- Ensure all commands and migrations work properly + +### Testing Commands + +```bash +# Run tests +npm test + +# Test specific commands +node ace update:datacite --dry-run --publish_id 123 +node ace index:datasets --publish_id 123 +``` + +## License + +This project is licensed under the [MIT License](LICENSE). \ No newline at end of file diff --git a/start/routes/api.ts b/start/routes/api.ts index 55fccc5..ca3b079 100644 --- a/start/routes/api.ts +++ b/start/routes/api.ts @@ -8,14 +8,24 @@ import AvatarController from '#controllers/Http/Api/AvatarController'; import UserController from '#controllers/Http/Api/UserController'; import CollectionsController from '#controllers/Http/Api/collections_controller'; import { middleware } from '../kernel.js'; -// API + +// Clean DOI URL routes (no /api prefix) + +// API routes with /api prefix router .group(() => { - router.get('clients', [UserController, 'getSubmitters']).as('client.index').use(middleware.auth());; - router.get('authors', [AuthorsController, 'index']).as('author.index').use(middleware.auth());; + router.get('clients', [UserController, 'getSubmitters']).as('client.index').use(middleware.auth()); + router.get('authors', [AuthorsController, 'index']).as('author.index').use(middleware.auth()); router.get('datasets', [DatasetController, 'index']).as('dataset.index'); router.get('persons', [AuthorsController, 'persons']).as('author.persons'); + // This should come BEFORE any other routes that might conflict + router + .get('/dataset/:prefix/:value', [DatasetController, 'findByIdentifier']) + .where('prefix', /^10\.\d+$/) // Match DOI prefix pattern (10.xxxx) + .where('value', /^[a-zA-Z0-9._-]+\.[0-9]+(?:\.[0-9]+)*$/) // Match DOI suffix pattern + .as('dataset.findByIdentifier'); + router.get('/dataset', [DatasetController, 'findAll']).as('dataset.findAll'); router.get('/dataset/:publish_id', [DatasetController, 'findOne']).as('dataset.findOne'); router.get('/sitelinks/:year', [HomeController, 'findDocumentsPerYear']); @@ -35,7 +45,7 @@ router .as('apps.twofactor_backupcodes.create') .use(middleware.auth()); - router.get('collections/:id', [CollectionsController, 'show']).as('collection.show') + router.get('collections/:id', [CollectionsController, 'show']).as('collection.show'); }) // .namespace('App/Controllers/Http/Api') .prefix('api'); diff --git a/start/rules/orcid.ts b/start/rules/orcid.ts index ee60534..b16e504 100644 --- a/start/rules/orcid.ts +++ b/start/rules/orcid.ts @@ -1,7 +1,7 @@ /* |-------------------------------------------------------------------------- | Preloaded File - node ace make:preload rules/orcid -| โฏ Do you want to register the preload file in .adonisrc.ts file? (y/N) ยท true +| Do you want to register the preload file in .adonisrc.ts file? (y/N) ยท true | DONE: create start/rules/orcid.ts | DONE: update adonisrc.ts file |--------------------------------------------------------------------------