barmar/tethys.backend
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- added new class CollectionRole.ts

Browse Source 
- added relation 'collectionRole' to Collection.ts class
- added 'ListSets' and  =GetRecord request for OaiController.ts
- npm updates
- added utility-functions.ts
This commit is contained in:
Kaimbacher 2023-09-28 22:43:46 +02:00
parent ebb24cc75c
commit 2a7480d2ed
9 changed files with 349 additions and 91 deletions
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2
Dockerfile
View File

@ -85,7 +85,7 @@ RUN npm ci --omit=dev
# Copy files to the working directory from the build folder the user
COPY --chown=node:node --from=build /home/node/app/build .
# Expose port
EXPOSE $PORT
EXPOSE 3333
ENTRYPOINT ["/home/node/app/docker-entrypoint.sh"]
# Run the command to start the server using "dumb-init"
CMD [ "dumb-init", "node", "server.js" ]

227
app/Controllers/Http/Oai/OaiController.ts
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@ -10,7 +10,11 @@ import { StatusCodes } from 'http-status-codes';
import { transform } from 'saxon-js';
// import { Xslt, xmlParse } from 'xslt-processor'
import { OaiErrorCodes, OaiModelError } from 'App/Exceptions/OaiErrorCodes';
import { OaiModelException } from 'App/Exceptions/OaiModelException';
import { OaiModelException, BadOaiModelException } from 'App/Exceptions/OaiModelException';
import Dataset from 'App/Models/Dataset';
import Collection from 'App/Models/Collection';
import { getDomain } from 'App/Utils/utility-functions';
import XmlModel from 'App/Library/XmlModel';
interface XslTParameter {
[key: string]: any;
@ -21,9 +25,12 @@ interface Dictionary {
}
export default class OaiController {
// private deliveringDocumentStates = ["published", "deleted"];
private deliveringDocumentStates = ['published', 'deleted'];
// private sampleRegEx = /^[A-Za-zäüÄÜß0-9\-_.!~]+$/;
private xsltParameter: XslTParameter;
// private configuration: Configuration;
// private tokenWorker: TokenWorker;
/**
* Holds xml representation of document information to be processed.
*
@ -61,7 +68,7 @@ export default class OaiController {
}
// const oaiRequest: OaiParameter = request.body;
try {
this.handleRequest(oaiRequest, request);
await this.handleRequest(oaiRequest, request);
} catch (error) {
if (error instanceof OaiModelException) {
const code = error.oaiCode;
@ -106,7 +113,7 @@ export default class OaiController {
response.status(StatusCodes.OK).send(xmlOutput);
}
protected handleRequest(oaiRequest: Dictionary, request: RequestContract) {
protected async handleRequest(oaiRequest: Dictionary, request: RequestContract) {
// Setup stylesheet
// $this->loadStyleSheet('datasetxml2oai-pmh.xslt');
@ -130,17 +137,17 @@ export default class OaiController {
this.handleIdentify();
} else if (verb === 'ListMetadataFormats') {
this.handleListMetadataFormats();
} else if (verb == 'GetRecord') {
await this.handleGetRecord(oaiRequest);
}
// else if (verb == "GetRecord") {
// await this.handleGetRecord(oaiRequest);
// } else if (verb == "ListRecords") {
// else if (verb == "ListRecords") {
// await this.handleListRecords(oaiRequest);
// } else if (verb == "ListIdentifiers") {
// await this.handleListIdentifiers(oaiRequest);
// } else if (verb == "ListSets") {
// await this.handleListSets();
// }
else {
else if (verb == 'ListSets') {
await this.handleListSets();
} else {
this.handleIllegalVerb();
}
} else {
@ -182,6 +189,206 @@ export default class OaiController {
this.xml.root().ele('Datasets');
}
protected async handleListSets() {
const repIdentifier = 'tethys.at';
this.xsltParameter['repIdentifier'] = repIdentifier;
const datasetElement = this.xml.root().ele('Datasets');
const sets: { [key: string]: string } = {
'open_access': 'Set for open access licenses',
'doc-type:ResearchData': 'Set for document type ResearchData',
// ...(await this.getSetsForDatasetTypes()),
...(await this.getSetsForCollections()),
// ... await this.getSetsForProjects(),
} as Dictionary;
for (const [key, value] of Object.entries(sets)) {
const setElement = datasetElement.ele('Rdr_Sets');
setElement.att('Type', key);
setElement.att('TypeName', value);
}
}
protected async handleGetRecord(oaiRequest: Dictionary) {
const repIdentifier = 'tethys.at';
this.xsltParameter['repIdentifier'] = repIdentifier;
const dataId = this.validateAndGetIdentifier(oaiRequest);
const dataset = await Dataset.query().where('publish_id', dataId).preload('xmlCache').preload('collections').first();
if (!dataset || !dataset.publish_id) {
throw new OaiModelException(
StatusCodes.INTERNAL_SERVER_ERROR,
'The value of the identifier argument is unknown or illegal in this repository.',
OaiErrorCodes.IDDOESNOTEXIST,
);
}
const metadataPrefix = this.validateAndGetMetadataPrefix(oaiRequest);
this.xsltParameter['oai_metadataPrefix'] = metadataPrefix;
// do not deliver datasets which are restricted by document state defined in deliveringStates
this.validateDatasetState(dataset);
// add xml elements
const datasetNode = this.xml.root().ele('Datasets');
await this.createXmlRecord(dataset, datasetNode);
}
private validateAndGetIdentifier(oaiRequest: Dictionary): number {
// Identifier references metadata Urn, not plain Id!
// Currently implemented as 'oai:foo.bar.de:{docId}' or 'urn:nbn...-123'
if (!('identifier' in oaiRequest)) {
throw new BadOaiModelException('The prefix of the identifier argument is unknown.');
}
const dataId = Number(this.getDocumentIdByIdentifier(oaiRequest.identifier));
if (isNaN(dataId)) {
throw new OaiModelException(
StatusCodes.INTERNAL_SERVER_ERROR,
'The value of the identifier argument is illegal in this repository.',
OaiErrorCodes.BADARGUMENT,
);
}
return dataId;
}
private validateAndGetMetadataPrefix(oaiRequest: Dictionary): string {
let metadataPrefix = '';
if ('metadataPrefix' in oaiRequest) {
metadataPrefix = oaiRequest['metadataPrefix'];
} else {
throw new OaiModelException(
StatusCodes.INTERNAL_SERVER_ERROR,
'The prefix of the metadata argument is unknown.',
OaiErrorCodes.BADARGUMENT,
);
}
return metadataPrefix;
}
private validateDatasetState(dataset: Dataset): void {
if (dataset.server_state == null || !this.deliveringDocumentStates.includes(dataset.server_state)) {
throw new OaiModelException(
StatusCodes.INTERNAL_SERVER_ERROR,
'Document is not available for OAI export!',
OaiErrorCodes.NORECORDSMATCH,
);
}
}
private async createXmlRecord(dataset: Dataset, datasetNode: XMLBuilder) {
const domNode = await this.getDatasetXmlDomNode(dataset);
if (domNode) {
// add frontdoor url and data-type
dataset.publish_id && this.addLandingPageAttribute(domNode, dataset.publish_id.toString());
this.addSpecInformation(domNode, 'data-type:' + dataset.type);
// if (dataset.collections) {
// for (const coll of dataset.collections) {
// const collRole = await coll.getCollectionRole();
// this.addSpecInformation(domNode, collRole.oai_name + ':' + coll.number);
// }
// }
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;
}
private addSpecInformation(domNode: XMLBuilder, information: string) {
domNode.ele('SetSpec').att('Value', information);
}
private addLandingPageAttribute(domNode: XMLBuilder, dataid: string) {
const baseDomain = process.env.BASE_DOMAIN || 'localhost';
const url = 'https://' + getDomain(baseDomain) + '/dataset/' + dataid;
// add attribute du dataset xml element
domNode.att('landingpage', url);
}
private getDocumentIdByIdentifier(oaiIdentifier: string): string {
const identifierParts: string[] = oaiIdentifier.split(':'); // explode(":", $oaiIdentifier);
const dataId: string = identifierParts[2];
// switch (identifierParts[0]) {
// case 'oai':
// if (isset($identifierParts[2])) {
// $dataId = $identifierParts[2];
// }
// break;
// default:
// throw new OaiModelException(
// 'The prefix of the identifier argument is unknown.',
// OaiModelError::BADARGUMENT
// );
// break;
// }
// if (empty($dataId) or !preg_match('/^\d+$/', $dataId)) {
// throw new OaiModelException(
// 'The value of the identifier argument is unknown or illegal in this repository.',
// OaiModelError::IDDOESNOTEXIST
// );
return dataId;
}
private async getSetsForCollections(): Promise<Dictionary> {
const sets: { [key: string]: string } = {} as Dictionary;
const collections = await Collection.query()
.select('name', 'number', 'role_id')
.whereHas('collectionRole', (query) => {
query.where('visible_oai', true);
})
.preload('collectionRole');
collections.forEach((collection) => {
// if collection has a collection role (classification like ddc):
if (collection.number) {
// collection.load('collectionRole');
const setSpec = collection.collectionRole?.oai_name + ':' + collection.number;
sets[setSpec] = `Set ${collection.number} '${collection.name}'`;
}
});
return sets;
}
// private async getSetsForDatasetTypes(): Promise<IDictionary> {
// const sets: { [key: string]: string } = {} as IDictionary;
// const datasets: Array<Dataset> = await Dataset.findAll({
// attributes: ["type"],
// where: { server_state: { [Sequelize.Op.eq]: "published" } },
// });
// datasets.forEach((dataset) => {
// if (dataset.type && false == preg_match(this.sampleRegEx, dataset.type)) {
// const msg = `Invalid SetSpec (data-type='${dataset.type}').
// Allowed characters are [${this.sampleRegEx}].`;
// Logger.err(`OAI: ${msg}`);
// // Log::error("OAI-PMH: $msg");
// return;
// }
// const setSpec = "data-type:" + dataset.type;
// sets[setSpec] = `Set for document type '${dataset.type}'`;
// });
// return sets;
// }
private handleIllegalVerb() {
this.xsltParameter['oai_error_code'] = 'badVerb';
this.xsltParameter['oai_error_message'] = 'The verb provided in the request is illegal.';

21
app/Controllers/Http/Submitter/DatasetController.ts
View File

@ -33,8 +33,8 @@ import ClamScan from 'clamscan';
import { ValidationException } from '@ioc:Adonis/Core/Validator';
import Drive from '@ioc:Adonis/Core/Drive';
import { Exception } from '@adonisjs/core/build/standalone';
import XmlModel from 'App/Library/XmlModel';
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces';
// import XmlModel from 'App/Library/XmlModel';
// import { XMLBuilder } from 'xmlbuilder2/lib/interfaces';
export default class DatasetController {
public async index({ auth, request, inertia }: HttpContextContract) {
@ -579,23 +579,6 @@ export default class DatasetController {
'files.extnames': 'file extension is not supported',
};
private async getDatasetXmlDomNode(dataset: Dataset) {
// dataset.fetchValues();
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;
}
// public async release({ params, view }) {
public async release({ request, inertia, response }: HttpContextContract) {
const id = request.param('id');

9
app/Models/Collection.ts
View File

@ -1,6 +1,7 @@
import { column, SnakeCaseNamingStrategy, manyToMany, ManyToMany } from '@ioc:Adonis/Lucid/Orm';
import { column, SnakeCaseNamingStrategy, manyToMany, ManyToMany, belongsTo, BelongsTo } from '@ioc:Adonis/Lucid/Orm';
import Dataset from './Dataset';
import BaseModel from './BaseModel';
import CollectionRole from './CollectionRole';
export default class Collection extends BaseModel {
public static namingStrategy = new SnakeCaseNamingStrategy();
@ -43,4 +44,10 @@ export default class Collection extends BaseModel {
pivotTable: 'link_documents_collections',
})
public datasets: ManyToMany<typeof Dataset>;
@belongsTo(() => CollectionRole, {
foreignKey: 'role_id',
})
public collectionRole: BelongsTo<typeof CollectionRole>;
}

38
app/Models/CollectionRole.ts Normal file
View File

@ -0,0 +1,38 @@
import { column, SnakeCaseNamingStrategy, hasMany, HasMany } from '@ioc:Adonis/Lucid/Orm';
import BaseModel from './BaseModel';
import Collection from './Collection';
export default class CollectionRole extends BaseModel {
public static namingStrategy = new SnakeCaseNamingStrategy();
public static primaryKey = 'id';
public static table = 'collections_roles';
public static fillable: string[] = ['name', 'oai_name', 'visible'];
@column({
isPrimary: true,
})
public id: number;
@column({})
public name: string;
@column({})
public oai_name?: string;
@column({})
public position: number;
@column({})
public visible: boolean;
@column({})
public visible_frontdoor: boolean;
@column({})
public visible_oai: boolean;
@hasMany(() => Collection, {
foreignKey: 'role_id',
})
public collections: HasMany<typeof Collection>;
}

1
app/Models/DocumentXmlCache.ts
View File

@ -3,7 +3,6 @@ import Dataset from './Dataset';
import { builder, create } from 'xmlbuilder2';
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces';
import Database from '@ioc:Adonis/Lucid/Database';
import dayjs from 'dayjs';
import { DateTime } from 'luxon';
export default class DocumentXmlCache extends BaseModel {

21
app/Utils/utility-functions.ts Normal file
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@ -0,0 +1,21 @@
export function sum(a: number, b: number): number {
return a + b;
}
export function getDomain(host: string): string {
// $myhost = strtolower(trim($host));
let myHost: string = host.trim().toLocaleLowerCase();
// $count = substr_count($myhost, '.');
const count: number = myHost.split(',').length - 1;
if (count == 2) {
const words = myHost.split('.');
if (words[1].length > 3) {
myHost = myHost.split('.', 2)[1];
}
} else if (count > 2) {
myHost = getDomain(myHost.split('.', 2)[1]);
}
myHost = myHost.replace(new RegExp(/^.*:\/\//i, 'g'), '');
return myHost;
}

119
package-lock.json generated
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@ -2677,9 +2677,9 @@
}
},
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"dev": true,
"engines": {
"node": "^12.0.0 || ^14.0.0 || >=16.0.0"
@ -2832,9 +2832,9 @@
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"follow-redirects": "^1.15.0",
"form-data": "^4.0.0",
@ -3966,9 +3966,9 @@
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},
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"dev": true,
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@ -4026,14 +4026,14 @@
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"dev": true
},
"node_modules/@types/minimatch": {
@ -4043,9 +4043,9 @@
"dev": true
},
"node_modules/@types/node": {
"version": "20.7.0",
"resolved": "https://registry.npmjs.org/@types/node/-/node-20.7.0.tgz",
"integrity": "sha512-zI22/pJW2wUZOVyguFaUL1HABdmSVxpXrzIqkjsHmyUjNhPoWM1CKfvVuXfetHhIok4RY573cqS0mZ1SJEnoTg=="
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},
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"version": "6.3.12",
@ -4092,9 +4092,9 @@
"dev": true
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"node_modules/@types/range-parser": {
"version": "1.2.4",
"resolved": "https://registry.npmjs.org/@types/range-parser/-/range-parser-1.2.4.tgz",
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"dev": true
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@ -4168,9 +4168,9 @@
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},
"node_modules/@types/ws": {
"version": "8.5.6",
@ -5868,9 +5868,9 @@
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"dev": true,
"funding": [
{
@ -5887,8 +5887,8 @@
}
],
"dependencies": {
"caniuse-lite": "^1.0.30001538",
"electron-to-chromium": "^1.4.526",
"caniuse-lite": "^1.0.30001541",
"electron-to-chromium": "^1.4.535",
"node-releases": "^2.0.13",
"update-browserslist-db": "^1.0.13"
},
@ -6085,9 +6085,9 @@
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},
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"dev": true,
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@ -6128,18 +6128,18 @@
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"dev": true,
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"deep-eql": "^4.1.2",
"get-func-name": "^2.0.0",
"loupe": "^2.3.1",
"check-error": "^1.0.3",
"deep-eql": "^4.1.3",
"get-func-name": "^2.0.2",
"loupe": "^2.3.6",
"pathval": "^1.1.1",
"type-detect": "^4.0.5"
"type-detect": "^4.0.8"
},
"engines": {
"node": ">=4"
@ -6208,10 +6208,13 @@
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},
"node_modules/check-error": {
"version": "1.0.2",
"resolved": "https://registry.npmjs.org/check-error/-/check-error-1.0.2.tgz",
"integrity": "sha512-BrgHpW9NURQgzoNyjfq0Wu6VFO6D7IZEmJNdtgNqpzGG8RuNFHt2jQxWlAs4HMe119chBnv+34syEZtc6IhLtA==",
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"dev": true,
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},
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@ -7970,9 +7973,9 @@
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"resolved": "https://registry.npmjs.org/electron-to-chromium/-/electron-to-chromium-1.4.529.tgz",
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@ -9213,9 +9216,9 @@
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@ -10793,9 +10796,9 @@
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"resolved": "https://registry.npmjs.org/@types/istanbul-reports/-/istanbul-reports-3.0.1.tgz",
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@ -12983,9 +12986,9 @@
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@ -16763,9 +16766,9 @@
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"dev": true,
"peerDependencies": {
"vue": "^3.0.0"

2
tests/functional/dataset_controller.spec.ts
View File

@ -28,7 +28,7 @@ test.group('DatasetController', (group) => {
const dataset = new Dataset();
dataset.type = 'analysisdata';
dataset.creatingCorporation = 'Tethys RDR';
dataset.creating_corporation = 'Tethys RDR';
dataset.language = 'de';
dataset.server_state = 'inprogress'; // Set the desired server state here
await dataset.save();