From cf859ba4025d1c00c59fd014676898d68d64e8d1 Mon Sep 17 00:00:00 2001 From: Arno Kaimbacher Date: Tue, 17 Oct 2023 15:45:41 +0200 Subject: [PATCH] - remove VOLUME assignments from DOXKERFILE - add package @opensearch-project/opensearch for manipulating opensearch index - index tethys datasets via new command IndexDatasets, callable node ace index:datasets or node ace index:datasets -p 193 - add mapping file for opensearch index in public/records.json - added solr.xslt for transforming Datset model to json for opensearch adding in opensearch - added route /editor/ dataset/:id/update (beginning of editor/DatasetController.ts - npm updates --- Dockerfile | 2 +- ace-manifest.json | 12 + .../Http/Editor/DatasetsController.ts | 175 ++++++ app/Library/XmlModel.ts | 4 +- app/Models/BaseModel.ts | 4 +- app/Models/Collection.ts | 1 - app/Models/Traits/DatasetExtension.ts | 3 +- commands/IndexDatasets.ts | 115 ++++ config/database.ts | 3 +- package-lock.json | 577 ++++++++++-------- package.json | 8 +- public/assets2/datasetxml2oai.sef.json | 2 +- public/assets2/solr.sef.json | 1 + public/assets2/solr.xslt | 553 +++++++++++++++++ public/records.json | 146 +++++ resources/js/Components/FormInput.vue | 4 +- resources/js/Pages/App.vue | 10 +- resources/js/Pages/Auth/Register.vue | 4 +- .../js/Pages/Submitter/Dataset/Release.vue | 1 + .../register-view/register-view-component.ts | 4 +- start/routes.ts | 8 + 21 files changed, 1357 insertions(+), 280 deletions(-) create mode 100644 app/Controllers/Http/Editor/DatasetsController.ts create mode 100644 commands/IndexDatasets.ts create mode 100644 public/assets2/solr.sef.json create mode 100644 public/assets2/solr.xslt create mode 100644 public/records.json diff --git a/Dockerfile b/Dockerfile index 0975855..7184d96 100644 --- a/Dockerfile +++ b/Dockerfile @@ -44,7 +44,7 @@ USER node # initial update of av databases RUN freshclam -VOLUME /var/lib/clamav +# VOLUME /var/lib/clamav COPY --chown=node:clamav docker-entrypoint.sh /home/node/app/docker-entrypoint.sh RUN chmod +x /home/node/app/docker-entrypoint.sh ENV TZ="Europe/Vienna" diff --git a/ace-manifest.json b/ace-manifest.json index 485d3b5..3a4ec65 100644 --- a/ace-manifest.json +++ b/ace-manifest.json @@ -1,5 +1,17 @@ { "commands": { + "index:datasets": { + "settings": { + "loadApp": true, + "stayAlive": false + }, + "commandPath": "./commands/IndexDatasets", + "commandName": "index:datasets", + "description": "", + "args": [], + "aliases": [], + "flags": [] + }, "validate:checksum": { "settings": { "loadApp": true, diff --git a/app/Controllers/Http/Editor/DatasetsController.ts b/app/Controllers/Http/Editor/DatasetsController.ts new file mode 100644 index 0000000..f30dff9 --- /dev/null +++ b/app/Controllers/Http/Editor/DatasetsController.ts @@ -0,0 +1,175 @@ +import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext'; +import { Client } from '@opensearch-project/opensearch'; +import Dataset from 'App/Models/Dataset'; +import XmlModel from 'App/Library/XmlModel'; +import { XMLBuilder } from 'xmlbuilder2/lib/interfaces'; +import { create } from 'xmlbuilder2'; +import { readFileSync } from 'fs'; +import { transform } from 'saxon-js'; + +// Create a new instance of the client +const client = new Client({ node: 'http://localhost:9200' }); // replace with your OpenSearch endpoint + +export default class DatasetsController { + private proc; + + constructor() { + this.proc = readFileSync('public/assets2/solr.sef.json'); + // Load the XSLT file + // this.proc = readFileSync('public/assets2/datasetxml2oai.sef.json'); + } + + public async index({}: HttpContextContract) {} + + public async create({}: HttpContextContract) {} + + public async store({}: HttpContextContract) {} + + public async show({}: HttpContextContract) {} + + public async edit({}: HttpContextContract) {} + + // public async update({}: HttpContextContract) {} + public async update({ request, response }) { + const id = 273; //request.param('id'); + const dataset = await Dataset.query().preload('xmlCache').where('id', id).firstOrFail(); + // add xml elements + let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, ''); + const datasetNode = xml.root().ele('Dataset'); + await this.createXmlRecord(dataset, datasetNode); + // const domNode = await this.getDatasetXmlDomNode(dataset); + // const xmlString = xml.end({ prettyPrint: true }); + + // const data = request.only(['field1', 'field2']); // get it from xslt + + // Create an index with non-default settings. + var index_name = 'tethys-features'; + + const xmlString = xml.end({ prettyPrint: false }); + let doc = ''; + try { + const result = await transform({ + // stylesheetFileName: `${config.TMP_BASE_DIR}/data-quality/rules/iati.sef.json`, + stylesheetText: this.proc, + destination: 'serialized', + // sourceFileName: sourceFile, + sourceText: xmlString, + // stylesheetParams: xsltParameter, + // logLevel: 10, + }); + doc = result.principalResult; + } catch (error) { + return response.status(500).json({ + message: 'An error occurred while creating the user', + error: error.message, + }); + } + + // var settings = { + // settings: { + // index: { + // number_of_shards: 4, + // number_of_replicas: 3, + // }, + // }, + // }; + // var test = await client.indices.create({ + // index: index_name, + // body: settings, + // }); + + // var document = { + // title: 'Sample Document', + // authors: [ + // { + // first_name: 'John', + // last_name: 'Doe', + // }, + // { + // first_name: 'Jane', + // last_name: 'Smith', + // }, + // ], + // year: '2018', + // genre: 'Crime fiction', + // }; + + // http://localhost:9200/datastets/_doc/1 + + // var id = '1'; + + try { + // console.log(doc); + let document = JSON.parse(`${doc}`); + + // https://opensearch.org/docs/2.1/opensearch/supported-field-types/geo-shape/ + // Define the new document + // const document = { + // title: 'Your Document Name', + // id: dataset.publish_id, + // doctype: 'GIS', + // // "location" : { + // // "type" : "point", + // // "coordinates" : [74.00, 40.71] + // // }, + // geo_location: { + // type: 'linestring', + // coordinates: [ + // [-77.03653, 38.897676], + // [-77.009051, 38.889939], + // ], + // }, + // // geo_location: 'BBOX (71.0589, 74.0060, 42.3601, 40.7128)' + // // geo_location: { + // // type: 'envelope', + // // coordinates: [ + // // [13.0, 53.0], + // // [14.0, 52.0], + // // ], // Define your BBOX coordinates + // // }, + // }; + + // Update the document + var test = await client.index({ + id: dataset.publish_id, + index: index_name, + body: document, + refresh: true, + }); + + // Return the result + return response.json(test.body); + } catch (error) { + // Handle any errors + console.error(error); + return response.status(500).json({ error: 'An error occurred while updating the data.' }); + } + } + + public async destroy({}: HttpContextContract) {} + + public async syncOpensearch({}: HttpContextContract) {} + + private async createXmlRecord(dataset: Dataset, datasetNode: XMLBuilder) { + const domNode = await this.getDatasetXmlDomNode(dataset); + if (domNode) { + datasetNode.import(domNode); + } + } + + private async getDatasetXmlDomNode(dataset: Dataset) { + const xmlModel = new XmlModel(dataset); + // xmlModel.setModel(dataset); + xmlModel.excludeEmptyFields(); + xmlModel.caching = true; + // const cache = dataset.xmlCache ? dataset.xmlCache : null; + // dataset.load('xmlCache'); + if (dataset.xmlCache) { + xmlModel.xmlCache = dataset.xmlCache; + } + + // return cache.getDomDocument(); + const domDocument: XMLBuilder | null = await xmlModel.getDomDocument(); + return domDocument; + } +} diff --git a/app/Library/XmlModel.ts b/app/Library/XmlModel.ts index df15916..96ca60f 100644 --- a/app/Library/XmlModel.ts +++ b/app/Library/XmlModel.ts @@ -85,7 +85,7 @@ export default class XmlModel { this.cache = this.cache || new DocumentXmlCache(); this.cache.document_id = dataset.id; this.cache.xml_version = 1; // (int)$this->strategy->getVersion(); - this.cache.server_date_modified = dataset.server_date_modified.toFormat("yyyy-MM-dd HH:mm:ss"); + this.cache.server_date_modified = dataset.server_date_modified.toFormat('yyyy-MM-dd HH:mm:ss'); this.cache.xml_data = domDocument.end(); await this.cache.save(); } @@ -97,7 +97,7 @@ export default class XmlModel { false, true, )?.node; - if(node != undefined) { + if (node != undefined) { domDocument = builder({ version: '1.0', encoding: 'UTF-8', standalone: true }, node); } } diff --git a/app/Models/BaseModel.ts b/app/Models/BaseModel.ts index 5954db6..324d59e 100644 --- a/app/Models/BaseModel.ts +++ b/app/Models/BaseModel.ts @@ -13,7 +13,6 @@ import { BaseModel as LucidBaseModel } from '@ioc:Adonis/Lucid/Orm'; // } // } - /** * Helper to find if value is a valid Object or * not @@ -22,7 +21,7 @@ export function isObject(value: any): boolean { return value !== null && typeof value === 'object' && !Array.isArray(value); } -export default class BaseModel extends LucidBaseModel { +export default class BaseModel extends LucidBaseModel { /** * When `fill` method is called, then we may have a situation where it * removed the values which exists in `original` and hence the dirty @@ -117,7 +116,6 @@ export default class BaseModel extends LucidBaseModel { return this; } - } // export class DatasetRelatedBaseModel extends LucidBaseModel { diff --git a/app/Models/Collection.ts b/app/Models/Collection.ts index 0d67be3..e8a0c79 100644 --- a/app/Models/Collection.ts +++ b/app/Models/Collection.ts @@ -49,5 +49,4 @@ export default class Collection extends BaseModel { foreignKey: 'role_id', }) public collectionRole: BelongsTo; - } diff --git a/app/Models/Traits/DatasetExtension.ts b/app/Models/Traits/DatasetExtension.ts index 926f14c..0403014 100644 --- a/app/Models/Traits/DatasetExtension.ts +++ b/app/Models/Traits/DatasetExtension.ts @@ -30,7 +30,6 @@ export type DatasetRelatedModel = | typeof DatasetIdentifier | typeof File; - export default abstract class DatasetExtension extends LucidBaseModel { public abstract id; public externalFields: Record = this.getExternalFields(); @@ -323,7 +322,7 @@ export default abstract class DatasetExtension extends LucidBaseModel { private convertColumnToFieldname(columnName: string): string { return columnName .split(/[-_]/) - .map((word) => (word.charAt(0).toUpperCase() + word.slice(1))) + .map((word) => word.charAt(0).toUpperCase() + word.slice(1)) .join(''); } } diff --git a/commands/IndexDatasets.ts b/commands/IndexDatasets.ts new file mode 100644 index 0000000..6044af4 --- /dev/null +++ b/commands/IndexDatasets.ts @@ -0,0 +1,115 @@ +import { BaseCommand, flags } from '@adonisjs/core/build/standalone'; +import Logger from '@ioc:Adonis/Core/Logger'; +import { XMLBuilder } from 'xmlbuilder2/lib/interfaces'; +import { create } from 'xmlbuilder2'; +import Dataset from 'App/Models/Dataset'; +import XmlModel from 'App/Library/XmlModel'; +import { readFileSync } from 'fs'; +import { transform } from 'saxon-js'; +import { Client } from '@opensearch-project/opensearch'; + +const client = new Client({ node: 'http://localhost:9200' }); // replace with your OpenSearch endpoint + +export default class IndexDatasets extends BaseCommand { + public static commandName = 'index:datasets'; + public static description = 'Index datasets based on publish_id'; + + @flags.number({ alias: 'p' }) + public publish_id: number; + + public static settings = { + /** + * Set the following value to true, if you want to load the application + * before running the command. Don't forget to call `node ace generate:manifest` + * afterwards. + */ + loadApp: true, + + /** + * Set the following value to true, if you want this command to keep running until + * you manually decide to exit the process. Don't forget to call + * `node ace generate:manifest` afterwards. + */ + stayAlive: false, + }; + + public async run() { + this.logger.info('Hello world!'); + // const { default: Dataset } = await import('App/Models/Dataset'); + const datasets = await this.getDatasets(); + const proc = readFileSync('public/assets2/solr.sef.json'); + const index_name = 'tethys-records'; + + for (var dataset of datasets) { + // Logger.info(`File publish_id ${dataset.publish_id}`); + const jsonString = await this.getJsonString(dataset, proc); + // console.log(jsonString); + await this.indexDocument(dataset, index_name, jsonString); + } + } + + private async getDatasets(): Promise { + const query = Dataset.query().preload('xmlCache').where('server_state', 'published'); + if (this.publish_id) { + query.where('publish_id', this.publish_id); + } + return await query; + } + + private async getJsonString(dataset, proc) { + let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, ''); + const datasetNode = xml.root().ele('Dataset'); + await this.createXmlRecord(dataset, datasetNode); + const xmlString = xml.end({ prettyPrint: false }); + + try { + const result = await transform({ + stylesheetText: proc, + destination: 'serialized', + sourceText: xmlString, + }); + return result.principalResult; + } catch (error) { + Logger.error(`An error occurred while creating the user, error: ${error.message},`); + return ''; + } + } + + private async indexDocument(dataset: Dataset, index_name: string, doc: string): Promise { + try { + let document = JSON.parse(doc); + await client.index({ + id: dataset.publish_id?.toString(), + index: index_name, + body: document, + refresh: true, + }); + Logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`); + } catch (error) { + Logger.error(`An error occurred while uindexing datsaet with publish_id ${dataset.publish_id}.`); + } + } + + private async createXmlRecord(dataset: Dataset, datasetNode: XMLBuilder): Promise { + const domNode = await this.getDatasetXmlDomNode(dataset); + if (domNode) { + datasetNode.import(domNode); + } + } + + private async getDatasetXmlDomNode(dataset: Dataset): Promise { + const xmlModel = new XmlModel(dataset); + // xmlModel.setModel(dataset); + xmlModel.excludeEmptyFields(); + xmlModel.caching = true; + // const cache = dataset.xmlCache ? dataset.xmlCache : null; + // dataset.load('xmlCache'); + if (dataset.xmlCache) { + xmlModel.xmlCache = dataset.xmlCache; + } + + // return cache.getDomDocument(); + const domDocument: XMLBuilder | null = await xmlModel.getDomDocument(); + return domDocument; + } +} diff --git a/config/database.ts b/config/database.ts index 0952a45..36a1748 100644 --- a/config/database.ts +++ b/config/database.ts @@ -48,8 +48,7 @@ const databaseConfig: DatabaseConfig = { }, healthCheck: false, debug: false, - pool: { min: 1, max: 100 }, - + pool: { min: 1, max: 100 }, }, }, }; diff --git a/package-lock.json b/package-lock.json index b092ca3..0041ef5 100644 --- a/package-lock.json +++ b/package-lock.json @@ -21,6 +21,7 @@ "@fontsource/inter": "^5.0.1", "@inertiajs/inertia": "^0.11.1", "@inertiajs/vue3": "^1.0.0", + "@opensearch-project/opensearch": "^2.4.0", "bcryptjs": "^2.4.3", "clamscan": "^2.1.2", "crypto": "^1.0.1", @@ -46,8 +47,8 @@ "@babel/plugin-transform-runtime": "^7.19.6", "@babel/preset-env": "^7.20.2", "@babel/preset-typescript": "^7.18.6", - "@japa/preset-adonis": "^1.0.16", - "@japa/runner": "^2.0.8", + "@japa/preset-adonis": "^1.2.0", + "@japa/runner": "^2.5.1", "@mdi/js": "^7.1.96", "@symfony/webpack-encore": "^4.2.0", "@tailwindcss/forms": "^0.5.2", @@ -65,7 +66,7 @@ "eslint-config-prettier": "^9.0.0", "eslint-plugin-adonis": "^2.1.1", "eslint-plugin-prettier": "^5.0.0-alpha.2", - "naive-ui": "^2.34.3", + "naive-ui": "^2.35.0", "numeral": "^2.0.6", "pinia": "^2.0.30", "pino-pretty": "^10.0.0", @@ -150,9 +151,9 @@ } }, "node_modules/@adonisjs/assembler": { - 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xlink=http://www.w3.org/1999/xlink gmd=http://www.isotc211.org/2005/gmd gco=http://www.isotc211.org/2005/gco json=http://www.w3.org/2013/XSL/json ","role":"select","line":"382"}]}]},{"N":"fn","name":"string","sType":"1AS ","C":[{"N":"dot"}]}]},{"N":"str","sType":"1AS ","val":" "}]}]},{"N":"valueOf","sType":"1NT ","C":[{"N":"str","sType":"1AS ","val":"]"}]},{"N":"valueOf","sType":"1NT ","C":[{"N":"str","sType":"1AS ","val":"}"}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]},{"N":"overridden"},{"N":"output","C":[{"N":"property","name":"Q{http://saxon.sf.net/}stylesheet-version","value":"30"},{"N":"property","name":"method","value":"text"}]},{"N":"decimalFormat"}],"Σ":"b8107a64"} \ No newline at end of file diff --git a/public/assets2/solr.xslt b/public/assets2/solr.xslt new file mode 100644 index 0000000..d4cac24 --- /dev/null +++ b/public/assets2/solr.xslt @@ -0,0 +1,553 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + { + "id": " + + ", + + + + + + + + + + + + + "year": " + + ", + + + + + "year_inverted": " + + ", + + + + + "server_date_published": " + + ", + + + + + "server_date_modified": " + + ", + + + + + "language": " + + ", + + + + "title": " + + ", + + "title_output": " + + ", + + + + + + + " + + + " + , + + + "abstract": [ + + ], + + + + + + + + " + + + , + + " + , + + + "author": [ + + ], + + + + + + + "doctype": " + + ", + + + + + " + + " + , + + + "subjects": [ + + ], + + + "belongs_to_bibliography": + + + true + + + false + + + , + + + + + + + + " + + " + + , + + + + "title_sub": [ + + ], + + + + + + " + + + " + + , + + + + "title_additional": [ + + ], + + + + + " + + " + + , + + + + "abstract_additional": [ + + ], + + + + "licence": " + + ", + + + + + "creating_corporation": " + + ", + + + + + "contributing_corporation": " + + ", + + + + + "publisher_name": " + + ", + + + + + "publisher_place": " + + ", + + + + + + + "geo_location": + "BBOX ( + + )", + + "bbox_xmin": + + , + "bbox_xmax": + + , + "bbox_ymin": + + , + "bbox_ymax": + + , + + + + + + + " + + " + + , + + + + "identifier": [ + + ], + + + + + " + + " + + , + + + + "reference": [ + + ] + + + + } + + + + + + + + + + + + + + + + fulltext + + + + + + + has_fulltext + + + + + + + fulltext_id_success + + + + + + + + fulltext_id_failure + + + + + + + + referee + + + + + + + + + + + persons + + + + + + + + + + + + + + + + + + + + + project + + + + app_area + + + + + + institute + + + + + + + collection_ids + + + + + + + + + + + + + + series_ids + + + + + + series_number_for_id_ + + + + + + + + doc_sort_order_for_seriesid_ + + + + + + + + + + + + + + + + + + geo_location + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/public/records.json b/public/records.json new file mode 100644 index 0000000..9a19ede --- /dev/null +++ b/public/records.json @@ -0,0 +1,146 @@ +{ + "settings": { + "analysis": { + "analyzer": { + "pathAnalyzer": { + "tokenizer": "pathTokenizer" + } + }, + "tokenizer": { + "pathTokenizer": { + "type": "path_hierarchy", + "delimiter": "/", + "replacement": "/", + "skip": 0, + "reverse": false + } + } + } + }, + "mappings": { + "properties": { + "id": { + "type": "keyword" + }, + "year": { + "type": "integer" + }, + "year_iverted": { + "type": "double" + }, + "server_date_published": { + "type": "double" + }, + "server_date_modified": { + "type": "double" + }, + "language": { + "type": "keyword" + }, + "title": { + "type": "text" + }, + "title_output": { + "type": "keyword", + "index": false + }, + "abstract": { + "type": "text" + }, + "abstract_output": { + "type": "keyword", + "index": false + }, + "author": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "doctype": { + "type": "keyword" + }, + "subjects": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "belongs_to_bibliography": { + "type": "boolean" + }, + "title_additional": { + "type": "text", + "index": false, + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "abstract_additional": { + "type": "text", + "index": false, + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "licence": { + "type": "text", + "index": false, + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "creating_corporation": { + "type": "text" + }, + "contributing_corporation": { + "type": "text" + }, + "publisher_name": { + "type": "text" + }, + "publisher_place": { + "type": "text" + }, + + "geo_location": { + "type": "geo_shape", + "tree": "quadtree", + "precision": "10km" + }, + "bbox_xmin": { + "type": "float" + }, + "bbox_xmax": { + "type": "float" + }, + "bbox_ymin": { + "type": "float" + }, + "bbox_ymax": { + "type": "float" + }, + + + + "status": { + "type": "keyword" + } + } + } +} diff --git a/resources/js/Components/FormInput.vue b/resources/js/Components/FormInput.vue index cf81bb8..302780b 100644 --- a/resources/js/Components/FormInput.vue +++ b/resources/js/Components/FormInput.vue @@ -2,7 +2,7 @@
{{ errors.join(', ') }} @@ -12,7 +12,7 @@ diff --git a/resources/js/Pages/register-view/register-view-component.ts b/resources/js/Pages/register-view/register-view-component.ts index 1d90c94..19fa6fe 100644 --- a/resources/js/Pages/register-view/register-view-component.ts +++ b/resources/js/Pages/register-view/register-view-component.ts @@ -1,7 +1,7 @@ import { Component, Vue, Prop } from 'vue-facing-decorator'; import AuthLayout from '@/Layouts/Auth.vue'; // import { Inertia } from '@inertiajs/inertia'; -import { NButton } from 'naive-ui'; +// import { NButton } from 'naive-ui'; import { useForm, InertiaForm, router } from '@inertiajs/vue3'; import FormInput from '@/Components/FormInput.vue'; // @/Components/FormInput.vue' // import { defineComponent, reactive } from 'vue'; @@ -42,7 +42,7 @@ export interface IErrorMessage { }, name: 'RegisterViewComponent', components: { - NButton, + // NButton, FormInput, }, }) diff --git a/start/routes.ts b/start/routes.ts index ce04ffa..11d88a1 100644 --- a/start/routes.ts +++ b/start/routes.ts @@ -183,3 +183,11 @@ Route.group(() => { .prefix('submitter'); // .middleware(['auth', 'can:dataset-list,dataset-publish']); // .middleware(['auth', 'is:submitter']); + +Route.group(() => { + Route.put('/dataset/:id/update', 'DatasetsController.update') + .as('editor.dataset.update') + .middleware(['auth', 'can:dataset-submit']); +}) +.namespace('App/Controllers/Http/Editor') +.prefix('editor'); \ No newline at end of file