feat: Enhance background job settings UI and functionality
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- Updated BackgroundJob.vue to improve the display of background job statuses, including missing cross-references and current job mode.
- Added auto-refresh functionality for background job status.
- Introduced success toast notifications for successful status refreshes.
- Modified the XML serialization process in DatasetXmlSerializer for better caching and performance.
- Implemented a new RuleProvider for managing custom validation rules.
- Improved error handling in routes for loading background job settings.
- Enhanced ClamScan configuration with socket support for virus scanning.
- Refactored dayjs utility to streamline locale management.
This commit is contained in:
Kaimbacher 2025-10-14 12:19:09 +02:00
commit b5bbe26ec2
27 changed files with 1221 additions and 603 deletions

View file

@ -11,11 +11,12 @@ RUN apt-get update \
dumb-init \
clamav \
clamav-daemon \
clamdscan \
ca-certificates \
&& rm -rf /var/lib/apt/lists/* \
# Creating folders and changing ownerships
&& mkdir -p /home/node/app \
&& mkdir -p /var/lib/clamav \
&& mkdir -p /var/lib/clamav \
&& mkdir /usr/local/share/clamav \
&& mkdir /var/run/clamav \
&& mkdir -p /var/log/clamav \
@ -24,38 +25,37 @@ RUN apt-get update \
# Set ownership and permissions
&& chown node:node /home/node/app \
# && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav /var/run/clamav \
&& chown -R clamav:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav /var/run/clamav /var/log/clamav \
&& chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav /var/run/clamav /var/log/clamav \
&& chown -R node:clamav /etc/clamav \
&& chmod 755 /tmp/clamav-logs \
&& chmod 750 /var/run/clamav \
&& chmod 755 /var/lib/clamav \
&& chmod 755 /var/log/clamav \
# Add node user to clamav group and allow sudo for clamav commands
&& usermod -a -G clamav node \
&& chmod g+w /var/run/clamav /var/lib/clamav /var/log/clamav /tmp/clamav-logs
&& usermod -a -G clamav node
# && chmod 666 /var/run/clamav/clamd.socket
# Make directories group-writable so node (as member of clamav group) can access them
# && chmod 750 /var/run/clamav /var/lib/clamav /var/log/clamav /tmp/clamav-logs
# Configure ClamAV - copy config files before switching user
# COPY --chown=node:clamav ./*.conf /etc/clamav/
COPY --chown=clamav:clamav ./*.conf /etc/clamav/
COPY --chown=node:clamav ./*.conf /etc/clamav/
# Copy entrypoint script
COPY --chown=node:node docker-entrypoint.sh /home/node/app/docker-entrypoint.sh
RUN chmod +x /home/node/app/docker-entrypoint.sh
ENV TZ="Europe/Vienna"
# Setting the working directory
WORKDIR /home/node/app
# Changing the current active user to "node"
# Download initial ClamAV database as root before switching users
USER root
USER node
RUN freshclam --quiet || echo "Initial database download failed - will retry at runtime"
USER node
# Initial update of AV databases (moved after USER directive)
# RUN freshclam || true
# Copy entrypoint script
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"
################## Second Stage - Installing dependencies ##########
@ -82,7 +82,7 @@ RUN node ace build --ignore-ts-errors
# In this final stage, we will start running the application
FROM base AS production
# Here, we include all the required environment variables
ENV NODE_ENV=production
# ENV NODE_ENV=production
# ENV PORT=$PORT
# ENV HOST=0.0.0.0
@ -93,7 +93,8 @@ 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 3310
EXPOSE 3333
ENTRYPOINT ["/home/node/app/docker-entrypoint.sh"]
# Run the command to start the server using "dumb-init"
CMD [ "node", "bin/server.js" ]
CMD [ "dumb-init", "node", "bin/server.js" ]

View file

@ -27,17 +27,17 @@ export default defineConfig({
() => import('./start/routes.js'),
() => import('./start/kernel.js'),
() => import('#start/validator'),
() => import('#start/rules/unique'),
() => import('#start/rules/translated_language'),
() => import('#start/rules/unique_person'),
// () => import('#start/rules/file_length'),
// () => import('#start/rules/file_scan'),
// () => import('#start/rules/allowed_extensions_mimetypes'),
() => import('#start/rules/dependent_array_min_length'),
() => import('#start/rules/referenceValidation'),
() => import('#start/rules/valid_mimetype'),
() => import('#start/rules/array_contains_types'),
() => import('#start/rules/orcid'),
// () => import('#start/rules/unique'),
// () => import('#start/rules/translated_language'),
// () => import('#start/rules/unique_person'),
// // () => import('#start/rules/file_length'),
// // () => import('#start/rules/file_scan'),
// // () => import('#start/rules/allowed_extensions_mimetypes'),
// () => import('#start/rules/dependent_array_min_length'),
// () => import('#start/rules/referenceValidation'),
// () => import('#start/rules/valid_mimetype'),
// () => import('#start/rules/array_contains_types'),
// () => import('#start/rules/orcid'),
],
/*
|--------------------------------------------------------------------------
@ -72,7 +72,7 @@ export default defineConfig({
() => import('#providers/stardust_provider'),
() => import('#providers/query_builder_provider'),
() => import('#providers/token_worker_provider'),
// () => import('#providers/validator_provider'),
() => import('#providers/rule_provider'),
// () => import('#providers/drive/provider/drive_provider'),
() => import('@adonisjs/drive/drive_provider'),
// () => import('@adonisjs/core/providers/vinejs_provider'),

View file

@ -1,6 +1,7 @@
import type { HttpContext } from '@adonisjs/core/http';
import Dataset from '#models/dataset';
import { StatusCodes } from 'http-status-codes';
import DatasetReference from '#models/dataset_reference';
// node ace make:controller Author
export default class DatasetController {
@ -81,11 +82,11 @@ export default class DatasetController {
.preload('licenses')
.preload('references')
.preload('project')
.preload('referenced_by', (builder) => {
builder.preload('dataset', (builder) => {
builder.preload('identifier');
});
})
// .preload('referenced_by', (builder) => {
// builder.preload('dataset', (builder) => {
// builder.preload('identifier');
// });
// })
.preload('files', (builder) => {
builder.preload('hashvalues');
})
@ -98,7 +99,17 @@ export default class DatasetController {
});
}
return response.status(StatusCodes.OK).json(dataset);
// Build the version chain
const versionChain = await this.buildVersionChain(dataset);
// Add version chain to response
const responseData = {
...dataset.toJSON(),
versionChain: versionChain,
};
// return response.status(StatusCodes.OK).json(dataset);
return response.status(StatusCodes.OK).json(responseData);
} catch (error) {
return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({
message: error.message || `Error retrieving Dataset with publish_id=${params.publish_id}.`,
@ -159,11 +170,11 @@ export default class DatasetController {
.preload('licenses')
.preload('references')
.preload('project')
.preload('referenced_by', (builder) => {
builder.preload('dataset', (builder) => {
builder.preload('identifier');
});
})
// .preload('referenced_by', (builder) => {
// builder.preload('dataset', (builder) => {
// builder.preload('identifier');
// });
// })
.preload('files', (builder) => {
builder.preload('hashvalues');
})
@ -175,12 +186,139 @@ export default class DatasetController {
message: `Cannot find Dataset with identifier=${identifierValue}.`,
});
}
// Build the version chain
const versionChain = await this.buildVersionChain(dataset);
return response.status(StatusCodes.OK).json(dataset);
// Add version chain to response
const responseData = {
...dataset.toJSON(),
versionChain: versionChain,
};
// return response.status(StatusCodes.OK).json(dataset);
return response.status(StatusCodes.OK).json(responseData);
} catch (error) {
return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({
message: error.message || `Error retrieving Dataset with identifier=${identifierValue}.`,
});
}
}
/**
* Build the complete version chain for a dataset
* Traverses both backwards (previous versions) and forwards (newer versions)
*/
private async buildVersionChain(dataset: Dataset) {
const versionChain = {
current: {
id: dataset.id,
publish_id: dataset.publish_id,
doi: dataset.identifier?.value || null,
main_title: dataset.mainTitle || null,
server_date_published: dataset.server_date_published,
},
previousVersions: [] as any[],
newerVersions: [] as any[],
};
// Get all previous versions (going backwards in time)
versionChain.previousVersions = await this.getPreviousVersions(dataset.id);
// Get all newer versions (going forwards in time)
versionChain.newerVersions = await this.getNewerVersions(dataset.id);
return versionChain;
}
/**
* Recursively get all previous versions
*/
private async getPreviousVersions(datasetId: number, visited: Set<number> = new Set()): Promise<any[]> {
// Prevent infinite loops
if (visited.has(datasetId)) {
return [];
}
visited.add(datasetId);
const previousVersions: any[] = [];
// Find references where this dataset "IsNewVersionOf" another dataset
const previousRefs = await DatasetReference.query()
.where('document_id', datasetId)
.where('relation', 'IsNewVersionOf')
.whereNotNull('related_document_id');
for (const ref of previousRefs) {
if (!ref.related_document_id) continue;
const previousDataset = await Dataset.query()
.where('id', ref.related_document_id)
.preload('identifier')
.preload('titles')
.first();
if (previousDataset) {
const versionInfo = {
id: previousDataset.id,
publish_id: previousDataset.publish_id,
doi: previousDataset.identifier?.value || null,
main_title: previousDataset.mainTitle || null,
server_date_published: previousDataset.server_date_published,
relation: 'IsPreviousVersionOf', // From perspective of current dataset
};
previousVersions.push(versionInfo);
// Recursively get even older versions
const olderVersions = await this.getPreviousVersions(previousDataset.id, visited);
previousVersions.push(...olderVersions);
}
}
return previousVersions;
}
/**
* Recursively get all newer versions
*/
private async getNewerVersions(datasetId: number, visited: Set<number> = new Set()): Promise<any[]> {
// Prevent infinite loops
if (visited.has(datasetId)) {
return [];
}
visited.add(datasetId);
const newerVersions: any[] = [];
// Find references where this dataset "IsPreviousVersionOf" another dataset
const newerRefs = await DatasetReference.query()
.where('document_id', datasetId)
.where('relation', 'IsPreviousVersionOf')
.whereNotNull('related_document_id');
for (const ref of newerRefs) {
if (!ref.related_document_id) continue;
const newerDataset = await Dataset.query().where('id', ref.related_document_id).preload('identifier').preload('titles').first();
if (newerDataset) {
const versionInfo = {
id: newerDataset.id,
publish_id: newerDataset.publish_id,
doi: newerDataset.identifier?.value || null,
main_title: newerDataset.mainTitle || null,
server_date_published: newerDataset.server_date_published,
relation: 'IsNewVersionOf', // From perspective of current dataset
};
newerVersions.push(versionInfo);
// Recursively get even newer versions
const evenNewerVersions = await this.getNewerVersions(newerDataset.id, visited);
newerVersions.push(...evenNewerVersions);
}
}
return newerVersions;
}
}

View file

@ -25,10 +25,10 @@ export default class FileController {
const dataset = file.dataset;
// Files from unpublished datasets are now blocked
if (dataset.server_state !== 'published') {
return response.status(StatusCodes.FORBIDDEN).send({
message: `File access denied: Dataset is not published.`,
});
}
return response.status(StatusCodes.FORBIDDEN).send({
message: `File access denied: Dataset is not published.`,
});
}
if (dataset && this.isUnderEmbargo(dataset.embargo_date)) {
return response.status(StatusCodes.FORBIDDEN).send({
message: `File is under embargo until ${dataset.embargo_date?.toFormat('yyyy-MM-dd')}`,
@ -39,9 +39,23 @@ export default class FileController {
const filePath = '/storage/app/data/' + file.pathName;
const fileExt = file.filePath.split('.').pop() || '';
// const fileName = file.label + fileExt;
const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`)
? file.label
: `${file.label}.${fileExt}`;
const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) ? file.label : `${file.label}.${fileExt}`;
// Determine if file can be previewed inline in browser
const canPreviewInline = (mimeType: string): boolean => {
const type = mimeType.toLowerCase();
return (
type === 'application/pdf' ||
type.startsWith('image/') ||
type.startsWith('text/') ||
type === 'application/json' ||
type === 'application/xml' ||
// Uncomment if you want video/audio inline
type.startsWith('video/') ||
type.startsWith('audio/')
);
};
const disposition = canPreviewInline(file.mimeType) ? 'inline' : 'attachment';
try {
fs.accessSync(filePath, fs.constants.R_OK); //| fs.constants.W_OK);
@ -51,7 +65,7 @@ export default class FileController {
.header('Cache-Control', 'no-cache private')
.header('Content-Description', 'File Transfer')
.header('Content-Type', file.mimeType)
.header('Content-Disposition', 'inline; filename=' + fileName)
.header('Content-Disposition', `${disposition}; filename="${fileName}"`)
.header('Content-Transfer-Encoding', 'binary')
.header('Access-Control-Allow-Origin', '*')
.header('Access-Control-Allow-Methods', 'GET');

View file

@ -3,7 +3,7 @@ import { Client } from '@opensearch-project/opensearch';
import User from '#models/user';
import Dataset from '#models/dataset';
import DatasetIdentifier from '#models/dataset_identifier';
import XmlModel from '#app/Library/XmlModel';
import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer';
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
import { create } from 'xmlbuilder2';
import { readFileSync } from 'fs';
@ -574,55 +574,88 @@ export default class DatasetsController {
public async doiStore({ request, response }: HttpContext) {
const dataId = request.param('publish_id');
const dataset = await Dataset.query()
// .preload('xmlCache')
.where('publish_id', dataId)
.firstOrFail();
// Load dataset with minimal required relationships
const dataset = await Dataset.query().where('publish_id', dataId).firstOrFail();
const prefix = process.env.DATACITE_PREFIX || '';
const base_domain = process.env.BASE_DOMAIN || '';
// Generate DOI metadata XML
const xmlMeta = (await Index.getDoiRegisterString(dataset)) as string;
let prefix = '';
let base_domain = '';
// const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug';
prefix = process.env.DATACITE_PREFIX || '';
base_domain = process.env.BASE_DOMAIN || '';
// Prepare DOI registration data
const doiValue = `${prefix}/tethys.${dataset.publish_id}`; //'10.21388/tethys.213'
const landingPageUrl = `https://doi.${getDomain(base_domain)}/${prefix}/tethys.${dataset.publish_id}`; //https://doi.dev.tethys.at/10.21388/tethys.213
// register DOI:
const doiValue = prefix + '/tethys.' + dataset.publish_id; //'10.21388/tethys.213'
const landingPageUrl = 'https://doi.' + getDomain(base_domain) + '/' + prefix + '/tethys.' + dataset.publish_id; //https://doi.dev.tethys.at/10.21388/tethys.213
// Register DOI with DataCite
const doiClient = new DoiClient();
const dataciteResponse = await doiClient.registerDoi(doiValue, xmlMeta, landingPageUrl);
if (dataciteResponse?.status === 201) {
// if response OK 201; save the Identifier value into db
const doiIdentifier = new DatasetIdentifier();
doiIdentifier.value = doiValue;
doiIdentifier.dataset_id = dataset.id;
doiIdentifier.type = 'doi';
doiIdentifier.status = 'findable';
// save updated dataset to db an index to OpenSearch
try {
// save modified date of datset for re-caching model in db an update the search index
dataset.server_date_modified = DateTime.now();
// autoUpdate: true only triggers when dataset.save() is called, not when saving a related model like below
await dataset.save();
await dataset.related('identifier').save(doiIdentifier);
const index_name = 'tethys-records';
await Index.indexDocument(dataset, index_name);
} catch (error) {
logger.error(`${__filename}: Indexing document ${dataset.id} failed: ${error.message}`);
// Log the error or handle it as needed
throw new HttpException(error.message);
}
return response.toRoute('editor.dataset.list').flash('message', 'You have successfully created a DOI for the dataset!');
} else {
if (dataciteResponse?.status !== 201) {
const message = `Unexpected DataCite MDS response code ${dataciteResponse?.status}`;
// Log the error or handle it as needed
throw new DoiClientException(dataciteResponse?.status, message);
}
// DOI registration successful - persist and index
try {
// Save identifier
await this.persistDoiAndIndex(dataset, doiValue);
return response.toRoute('editor.dataset.list').flash('message', 'You have successfully created a DOI for the dataset!');
} catch (error) {
logger.error(`${__filename}: Failed to persist DOI and index dataset ${dataset.id}: ${error.message}`);
throw new HttpException(error.message);
}
// return response.toRoute('editor.dataset.list').flash('message', xmlMeta);
}
/**
* Persist DOI identifier and update search index
* Handles cache invalidation to ensure fresh indexing
*/
private async persistDoiAndIndex(dataset: Dataset, doiValue: string): Promise<void> {
// Create DOI identifier
const doiIdentifier = new DatasetIdentifier();
doiIdentifier.value = doiValue;
doiIdentifier.dataset_id = dataset.id;
doiIdentifier.type = 'doi';
doiIdentifier.status = 'findable';
// Save identifier (this will trigger database insert)
await dataset.related('identifier').save(doiIdentifier);
// Update dataset modification timestamp to reflect the change
dataset.server_date_modified = DateTime.now();
await dataset.save();
// Invalidate stale XML cache
await this.invalidateDatasetCache(dataset);
// Reload dataset with fresh state for indexing
const freshDataset = await Dataset.query().where('id', dataset.id).preload('identifier').preload('xmlCache').firstOrFail();
// Index to OpenSearch with fresh data
const index_name = process.env.OPENSEARCH_INDEX || 'tethys-records';
await Index.indexDocument(freshDataset, index_name);
logger.info(`Successfully created DOI ${doiValue} and indexed dataset ${dataset.id}`);
}
/**
* Invalidate XML cache for dataset
* Ensures fresh cache generation on next access
*/
private async invalidateDatasetCache(dataset: Dataset): Promise<void> {
await dataset.load('xmlCache');
if (dataset.xmlCache) {
await dataset.xmlCache.delete();
logger.debug(`Invalidated XML cache for dataset ${dataset.id}`);
}
}
public async show({}: HttpContext) {}
public async edit({ request, inertia, response }: HttpContext) {
@ -1124,14 +1157,14 @@ export default class DatasetsController {
// Set the response headers and download the file
response
.header('Cache-Control', 'no-cache private')
.header('Content-Description', 'File Transfer')
.header('Content-Type', file.mime_type || 'application/octet-stream')
// .header('Content-Disposition', 'inline; filename=' + fileName)
.header('Content-Transfer-Encoding', 'binary')
.header('Access-Control-Allow-Origin', '*')
.header('Access-Control-Allow-Methods', 'GET');
response.attachment(fileName);
.header('Cache-Control', 'no-cache private')
.header('Content-Description', 'File Transfer')
.header('Content-Type', file.mime_type || 'application/octet-stream')
// .header('Content-Disposition', 'inline; filename=' + fileName)
.header('Content-Transfer-Encoding', 'binary')
.header('Access-Control-Allow-Origin', '*')
.header('Access-Control-Allow-Methods', 'GET');
response.attachment(fileName);
return response.download(filePath);
}
@ -1144,19 +1177,18 @@ export default class DatasetsController {
}
}
private async getDatasetXmlDomNode(dataset: Dataset) {
const xmlModel = new XmlModel(dataset);
private async getDatasetXmlDomNode(dataset: Dataset): Promise<XMLBuilder | null> {
const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields();
// xmlModel.setModel(dataset);
xmlModel.excludeEmptyFields();
xmlModel.caching = true;
// const cache = dataset.xmlCache ? dataset.xmlCache : null;
// dataset.load('xmlCache');
// Load existing cache if available
await dataset.load('xmlCache');
if (dataset.xmlCache) {
xmlModel.xmlCache = dataset.xmlCache;
serializer.setCache(dataset.xmlCache);
}
// return cache.getDomDocument();
const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
return domDocument;
const xmlDocument : XMLBuilder | null = await serializer.toXmlDocument();
return xmlDocument;
}
}

View file

@ -15,7 +15,7 @@ import { OaiModelException, BadOaiModelException } from '#app/exceptions/OaiMode
import Dataset from '#models/dataset';
import Collection from '#models/collection';
import { getDomain, preg_match } from '#app/utils/utility-functions';
import XmlModel from '#app/Library/XmlModel';
import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer';
import logger from '@adonisjs/core/services/logger';
import ResumptionToken from '#app/Library/Oai/ResumptionToken';
// import Config from '@ioc:Adonis/Core/Config';
@ -292,7 +292,7 @@ export default class OaiController {
this.xsltParameter['repIdentifier'] = repIdentifier;
const datasetNode = this.xml.root().ele('Datasets');
const paginationParams: PagingParameter ={
const paginationParams: PagingParameter = {
cursor: 0,
totalLength: 0,
start: maxRecords + 1,
@ -347,16 +347,20 @@ export default class OaiController {
finder: ModelQueryBuilderContract<typeof Dataset, Dataset>,
paginationParams: PagingParameter,
oaiRequest: Dictionary,
maxRecords: number
maxRecords: number,
) {
const totalResult = await finder
.clone()
.count('* as total')
.first()
.then((res) => res?.$extras.total);
paginationParams.totalLength = Number(totalResult);
paginationParams.totalLength = Number(totalResult);
const combinedRecords: Dataset[] = await finder.select('publish_id').orderBy('publish_id').offset(0).limit(maxRecords*2);
const combinedRecords: Dataset[] = await finder
.select('publish_id')
.orderBy('publish_id')
.offset(0)
.limit(maxRecords * 2);
paginationParams.activeWorkIds = combinedRecords.slice(0, 100).map((dat) => Number(dat.publish_id));
paginationParams.nextDocIds = combinedRecords.slice(100).map((dat) => Number(dat.publish_id));
@ -602,19 +606,17 @@ export default class OaiController {
}
private async getDatasetXmlDomNode(dataset: Dataset) {
const xmlModel = new XmlModel(dataset);
// xmlModel.setModel(dataset);
xmlModel.excludeEmptyFields();
xmlModel.caching = true;
const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields();
// const cache = dataset.xmlCache ? dataset.xmlCache : null;
// dataset.load('xmlCache');
if (dataset.xmlCache) {
xmlModel.xmlCache = dataset.xmlCache;
serializer.setCache(dataset.xmlCache);
}
// return cache.getDomDocument();
const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
return domDocument;
// return cache.toXmlDocument();
const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument();
return xmlDocument;
}
private addSpecInformation(domNode: XMLBuilder, information: string) {

View file

@ -0,0 +1,231 @@
import DocumentXmlCache from '#models/DocumentXmlCache';
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
import Dataset from '#models/dataset';
import Strategy from './Strategy.js';
import { builder } from 'xmlbuilder2';
import logger from '@adonisjs/core/services/logger';
/**
* Configuration for XML serialization
*
* @interface XmlSerializationConfig
*/
export interface XmlSerializationConfig {
/** The dataset model to serialize */
model: Dataset;
/** DOM representation (if available) */
dom?: XMLBuilder;
/** Fields to exclude from serialization */
excludeFields: Array<string>;
/** Whether to exclude empty fields */
excludeEmpty: boolean;
/** Base URI for xlink:ref elements */
baseUri: string;
}
/**
* Options for controlling serialization behavior
*/
export interface SerializationOptions {
/** Enable XML caching */
enableCaching?: boolean;
/** Exclude empty fields from output */
excludeEmptyFields?: boolean;
/** Custom base URI */
baseUri?: string;
/** Fields to exclude */
excludeFields?: string[];
}
/**
* DatasetXmlSerializer
*
* Handles XML serialization of Dataset models with intelligent caching.
* Generates XML representations and manages cache lifecycle to optimize performance.
*
* @example
* ```typescript
* const serializer = new DatasetXmlSerializer(dataset);
* serializer.enableCaching();
* serializer.excludeEmptyFields();
*
* const xmlDocument = await serializer.toXmlDocument();
* ```
*/
export default class DatasetXmlSerializer {
private readonly config: XmlSerializationConfig;
private readonly strategy: Strategy;
private cache: DocumentXmlCache | null = null;
private cachingEnabled = false;
constructor(dataset: Dataset, options: SerializationOptions = {}) {
this.config = {
model: dataset,
excludeEmpty: options.excludeEmptyFields ?? false,
baseUri: options.baseUri ?? '',
excludeFields: options.excludeFields ?? [],
};
this.strategy = new Strategy({
excludeEmpty: options.excludeEmptyFields ?? false,
baseUri: options.baseUri ?? '',
excludeFields: options.excludeFields ?? [],
model: dataset,
});
if (options.enableCaching) {
this.cachingEnabled = true;
}
}
/**
* Enable caching for XML generation
* When enabled, generated XML is stored in database for faster retrieval
*/
public enableCaching(): this {
this.cachingEnabled = true;
return this;
}
/**
* Disable caching for XML generation
*/
public disableCaching(): this {
this.cachingEnabled = false;
return this;
}
set model(model: Dataset) {
this.config.model = model;
}
/**
* Configure to exclude empty fields from XML output
*/
public excludeEmptyFields(): this {
this.config.excludeEmpty = true;
return this;
}
/**
* Set the cache instance directly (useful when preloading)
* @param cache - The DocumentXmlCache instance
*/
public setCache(cache: DocumentXmlCache): this {
this.cache = cache;
return this;
}
/**
* Get the current cache instance
*/
public getCache(): DocumentXmlCache | null {
return this.cache;
}
/**
* Get DOM document with intelligent caching
* Returns cached version if valid, otherwise generates new document
*/
public async toXmlDocument(): Promise<XMLBuilder | null> {
const dataset = this.config.model;
// Try to get from cache first
let cachedDocument: XMLBuilder | null = await this.retrieveFromCache();
if (cachedDocument) {
logger.debug(`Using cached XML for dataset ${dataset.id}`);
return cachedDocument;
}
// Generate fresh document
logger.debug(`[DatasetXmlSerializer] Cache miss - generating fresh XML for dataset ${dataset.id}`);
const freshDocument = await this.strategy.createDomDocument();
if (!freshDocument) {
logger.error(`[DatasetXmlSerializer] Failed to generate XML for dataset ${dataset.id}`);
return null;
}
// Cache if caching is enabled
if (this.cachingEnabled) {
await this.persistToCache(freshDocument, dataset);
}
// Extract the dataset-specific node
return this.extractDatasetNode(freshDocument);
}
/**
* Generate XML string representation
* Convenience method that converts XMLBuilder to string
*/
public async toXmlString(): Promise<string | null> {
const document = await this.toXmlDocument();
return document ? document.end({ prettyPrint: false }) : null;
}
/**
* Persist generated XML document to cache
* Non-blocking - failures are logged but don't interrupt the flow
*/
private async persistToCache(domDocument: XMLBuilder, dataset: Dataset): Promise<void> {
try {
this.cache = this.cache || new DocumentXmlCache();
this.cache.document_id = dataset.id;
this.cache.xml_version = 1;
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();
logger.debug(`Cached XML for dataset ${dataset.id}`);
} catch (error) {
logger.error(`Failed to cache XML for dataset ${dataset.id}: ${error.message}`);
// Don't throw - caching failure shouldn't break the flow
}
}
/**
* Extract the Rdr_Dataset node from full document
*/
private extractDatasetNode(domDocument: XMLBuilder): XMLBuilder | null {
const node = domDocument.find((n) => n.node.nodeName === 'Rdr_Dataset', false, true)?.node;
if (node) {
return builder({ version: '1.0', encoding: 'UTF-8', standalone: true }, node);
}
return domDocument;
}
/**
* Attempt to retrieve valid cached XML document
* Returns null if cache doesn't exist or is stale
*/
private async retrieveFromCache(): Promise<XMLBuilder | null> {
const dataset: Dataset = this.config.model;
if (!this.cache) {
return null;
}
// Check if cache is still valid
const actuallyCached = await DocumentXmlCache.hasValidEntry(dataset.id, dataset.server_date_modified);
if (!actuallyCached) {
logger.debug(`Cache invalid for dataset ${dataset.id}`);
return null;
}
//cache is actual return cached document
try {
if (this.cache) {
return this.cache.getDomDocument();
} else {
return null;
}
} catch (error) {
logger.error(`Failed to retrieve cached document for dataset ${dataset.id}: ${error.message}`);
return null;
}
}
}

View file

@ -2,7 +2,7 @@ import Dataset from '#models/dataset';
import { Client } from '@opensearch-project/opensearch';
import { create } from 'xmlbuilder2';
import SaxonJS from 'saxon-js';
import XmlModel from '#app/Library/XmlModel';
import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer';
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
import logger from '@adonisjs/core/services/logger';
import { readFileSync } from 'fs';
@ -72,31 +72,42 @@ export default {
}
},
/**
* Index a dataset document to OpenSearch/Elasticsearch
*/
async indexDocument(dataset: Dataset, index_name: string): Promise<void> {
try {
const proc = readFileSync('public/assets2/solr.sef.json');
const doc: string = await this.getTransformedString(dataset, proc);
// Load XSLT transformation file
const xsltProc = readFileSync('public/assets2/solr.sef.json');
let document = JSON.parse(doc);
// Transform dataset to JSON document
const jsonDoc: string = await this.getTransformedString(dataset, xsltProc);
const document = JSON.parse(jsonDoc);
// Index document to OpenSearch with doument json body
await this.client.index({
id: dataset.publish_id?.toString(),
index: index_name,
body: document,
refresh: true,
refresh: true, // make immediately searchable
});
logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`);
logger.info(`Dataset ${dataset.publish_id} successfully indexed to ${index_name}`);
} catch (error) {
logger.error(`An error occurred while indexing datsaet with publish_id ${dataset.publish_id}.`);
logger.error(`Failed to index dataset ${dataset.publish_id}: ${error.message}`);
throw error; // Re-throw to allow caller to handle
}
},
/**
* Transform dataset XML to JSON using XSLT
*/
async getTransformedString(dataset: Dataset, proc: Buffer): Promise<string> {
let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
const datasetNode = xml.root().ele('Dataset');
await createXmlRecord(dataset, datasetNode);
const xmlString = xml.end({ prettyPrint: false });
// Generate XML string from dataset
const xmlString = await this.generateDatasetXml(dataset);
try {
// Apply XSLT transformation
const result = await SaxonJS.transform({
stylesheetText: proc,
destination: 'serialized',
@ -108,6 +119,18 @@ export default {
return '';
}
},
/**
* Generate XML string from dataset model
*/
async generateDatasetXml(dataset: Dataset): Promise<string> {
const xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
const datasetNode = xml.root().ele('Dataset');
await createXmlRecord(dataset, datasetNode);
return xml.end({ prettyPrint: false });
},
};
/**
* Return the default global focus trap stack
@ -115,74 +138,49 @@ export default {
* @return {import('focus-trap').FocusTrap[]}
*/
// export const indexDocument = async (dataset: Dataset, index_name: string, proc: Buffer): Promise<void> => {
// try {
// const doc = await getJsonString(dataset, proc);
// 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 indexing datsaet with publish_id ${dataset.publish_id}.`);
// }
// };
// const getJsonString = async (dataset, proc): Promise<string> => {
// let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
// const datasetNode = xml.root().ele('Dataset');
// await 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 '';
// }
// };
/**
* Create complete XML record for dataset
* Handles caching and metadata enrichment
*/
const createXmlRecord = async (dataset: Dataset, datasetNode: XMLBuilder): Promise<void> => {
const domNode = await getDatasetXmlDomNode(dataset);
if (domNode) {
// add frontdoor url and data-type
dataset.publish_id && addLandingPageAttribute(domNode, dataset.publish_id.toString());
addSpecInformation(domNode, 'data-type:' + dataset.type);
if (dataset.collections) {
for (const coll of dataset.collections) {
const collRole = coll.collectionRole;
addSpecInformation(domNode, collRole.oai_name + ':' + coll.number);
}
}
datasetNode.import(domNode);
if (!domNode) {
throw new Error(`Failed to generate XML DOM node for dataset ${dataset.id}`);
}
// Enrich with landing page URL
if (dataset.publish_id) {
addLandingPageAttribute(domNode, dataset.publish_id.toString());
}
// Add data type specification
addSpecInformation(domNode, `data-type:${dataset.type}`);
// Add collection information
if (dataset.collections) {
for (const coll of dataset.collections) {
const collRole = coll.collectionRole;
addSpecInformation(domNode, `${collRole.oai_name}:${coll.number}`);
}
}
datasetNode.import(domNode);
};
const getDatasetXmlDomNode = async (dataset: Dataset): Promise<XMLBuilder | null> => {
const xmlModel = new XmlModel(dataset);
const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields();
// xmlModel.setModel(dataset);
xmlModel.excludeEmptyFields();
xmlModel.caching = true;
// const cache = dataset.xmlCache ? dataset.xmlCache : null;
// dataset.load('xmlCache');
// Load cache relationship if not already loaded
await dataset.load('xmlCache');
if (dataset.xmlCache) {
xmlModel.xmlCache = dataset.xmlCache;
serializer.setCache(dataset.xmlCache);
}
// return cache.getDomDocument();
const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
return domDocument;
// Generate or retrieve cached DOM document
const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument();
return xmlDocument;
};
const addLandingPageAttribute = (domNode: XMLBuilder, dataid: string) => {
@ -192,6 +190,6 @@ const addLandingPageAttribute = (domNode: XMLBuilder, dataid: string) => {
domNode.att('landingpage', url);
};
const addSpecInformation= (domNode: XMLBuilder, information: string) => {
const addSpecInformation = (domNode: XMLBuilder, information: string) => {
domNode.ele('SetSpec').att('Value', information);
};

View file

@ -1,129 +0,0 @@
import DocumentXmlCache from '#models/DocumentXmlCache';
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
import Dataset from '#models/dataset';
import Strategy from './Strategy.js';
import { DateTime } from 'luxon';
import { builder } from 'xmlbuilder2';
/**
* This is the description of the interface
*
* @interface Conf
* @member {Model} model holds the current dataset model
* @member {XMLBuilder} dom holds the current DOM representation
* @member {Array<string>} excludeFields List of fields to skip on serialization.
* @member {boolean} excludeEmpty True, if empty fields get excluded from serialization.
* @member {string} baseUri Base URI for xlink:ref elements
*/
export interface Conf {
model: Dataset;
dom?: XMLBuilder;
excludeFields: Array<string>;
excludeEmpty: boolean;
baseUri: string;
}
export default class XmlModel {
private config: Conf;
// private strategy = null;
private cache: DocumentXmlCache | null = null;
private _caching = false;
private strategy: Strategy;
constructor(dataset: Dataset) {
// $this->strategy = new Strategy();// Opus_Model_Xml_Version1;
// $this->config = new Conf();
// $this->strategy->setup($this->config);
this.config = {
excludeEmpty: false,
baseUri: '',
excludeFields: [],
model: dataset,
};
this.strategy = new Strategy({
excludeEmpty: true,
baseUri: '',
excludeFields: [],
model: dataset,
});
}
set model(model: Dataset) {
this.config.model = model;
}
public excludeEmptyFields(): void {
this.config.excludeEmpty = true;
}
get xmlCache(): DocumentXmlCache | null {
return this.cache;
}
set xmlCache(cache: DocumentXmlCache) {
this.cache = cache;
}
get caching(): boolean {
return this._caching;
}
set caching(caching: boolean) {
this._caching = caching;
}
public async getDomDocument(): Promise<XMLBuilder | null> {
const dataset = this.config.model;
let domDocument: XMLBuilder | null = await this.getDomDocumentFromXmlCache();
if (domDocument == null) {
domDocument = await this.strategy.createDomDocument();
// domDocument = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
if (this._caching) {
// caching is desired:
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.xml_data = domDocument.end();
await this.cache.save();
}
const node = domDocument.find(
(n) => {
const test = n.node.nodeName == 'Rdr_Dataset';
return test;
},
false,
true,
)?.node;
if (node != undefined) {
domDocument = builder({ version: '1.0', encoding: 'UTF-8', standalone: true }, node);
}
}
return domDocument;
}
private async getDomDocumentFromXmlCache(): Promise<XMLBuilder | null> {
const dataset: Dataset = this.config.model;
if (!this.cache) {
return null;
}
//.toFormat('YYYY-MM-DD HH:mm:ss');
let date: DateTime = dataset.server_date_modified;
const actuallyCached: boolean = await DocumentXmlCache.hasValidEntry(dataset.id, date);
if (!actuallyCached) {
return null;
}
//cache is actual return it for oai:
try {
if (this.cache) {
return this.cache.getDomDocument();
} else {
return null;
}
} catch (error) {
return null;
}
}
}

View file

@ -4,7 +4,8 @@ import { builder, create } from 'xmlbuilder2';
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
import db from '@adonisjs/lucid/services/db';
import { DateTime } from 'luxon';
import type { BelongsTo } from "@adonisjs/lucid/types/relations";
import type { BelongsTo } from '@adonisjs/lucid/types/relations';
import logger from '@adonisjs/core/services/logger';
export default class DocumentXmlCache extends BaseModel {
public static namingStrategy = new SnakeCaseNamingStrategy();
@ -66,33 +67,38 @@ export default class DocumentXmlCache extends BaseModel {
}
/**
* Check if a dataset in a specific xml version is already cached or not.
* Check if a valid (non-stale) cache entry exists
* Cache is valid only if it was created AFTER the dataset's last modification
*
* @param mixed datasetId
* @param mixed serverDateModified
* @returns {Promise<boolean>} Returns true on cached hit else false.
* @param datasetId - The dataset ID to check
* @param datasetServerDateModified - The dataset's last modification timestamp
* @returns true if valid cache exists, false otherwise
*/
// public static async hasValidEntry(datasetId: number, datasetServerDateModified: DateTime): Promise<boolean> {
// // const formattedDate = dayjs(datasetServerDateModified).format('YYYY-MM-DD HH:mm:ss');
// const query = Database.from(this.table)
// .where('document_id', datasetId)
// .where('server_date_modified', '2023-08-17 16:51:03')
// .first();
// const row = await query;
// return !!row;
// }
// Assuming 'DocumentXmlCache' has a table with a 'server_date_modified' column in your database
public static async hasValidEntry(datasetId: number, datasetServerDateModified: DateTime): Promise<boolean> {
const serverDateModifiedString: string = datasetServerDateModified.toFormat('yyyy-MM-dd HH:mm:ss'); // Convert DateTime to ISO string
const query = db.from(this.table)
const row = await db
.from(this.table)
.where('document_id', datasetId)
.where('server_date_modified', '>=', serverDateModifiedString) // Check if server_date_modified is newer or equal
.where('server_date_modified', '>', serverDateModifiedString) // Check if server_date_modified is newer or equal
.first();
const row = await query;
return !!row;
const isValid = !!row;
if (isValid) {
logger.debug(`Valid cache found for dataset ${datasetId}`);
} else {
logger.debug(`No valid cache for dataset ${datasetId} (dataset modified: ${serverDateModifiedString})`);
}
return isValid;
}
/**
* Invalidate (delete) cache entry
*/
public async invalidate(): Promise<void> {
await this.delete();
logger.debug(`Invalidated cache for document ${this.document_id}`);
}
}

View file

@ -55,8 +55,8 @@ export const createDatasetValidator = vine.compile(
.translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
}),
)
// .minLength(1),
.arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }),
// .minLength(1),
.arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }),
authors: vine
.array(
vine.object({
@ -160,7 +160,8 @@ export const createDatasetValidator = vine.compile(
.fileScan({ removeInfected: true }),
)
.minLength(1),
}),);
}),
);
/**
* Validates the dataset's update action
@ -309,11 +310,13 @@ export const updateDatasetValidator = vine.compile(
.fileScan({ removeInfected: true }),
)
.dependentArrayMinLength({ dependentArray: 'fileInputs', min: 1 }),
fileInputs: vine.array(
vine.object({
label: vine.string().trim().maxLength(100),
}),
).optional(),
fileInputs: vine
.array(
vine.object({
label: vine.string().trim().maxLength(100),
}),
)
.optional(),
}),
);
@ -501,7 +504,7 @@ let messagesProvider = new SimpleMessagesProvider({
'files.array.minLength': 'At least {{ min }} file upload is required.',
'files.*.size': 'file size is to big',
'files.*.extnames': 'file extension is not supported',
'embargo_date.date.afterOrEqual': `Embargo date must be on or after ${dayjs().add(10, 'day').format('DD.MM.YYYY')}`,
'embargo_date.date.afterOrEqual': `Embargo date must be on or after ${dayjs().add(10, 'day').format('DD.MM.YYYY')}`,
});
createDatasetValidator.messagesProvider = messagesProvider;

View file

@ -8,20 +8,20 @@ export const createRoleValidator = vine.compile(
vine.object({
name: vine
.string()
.isUnique({ table: 'roles', column: 'name' })
.trim()
.minLength(3)
.maxLength(255)
.regex(/^[a-zA-Z0-9]+$/), //Must be alphanumeric with hyphens or underscores
.isUnique({ table: 'roles', column: 'name' })
.regex(/^[a-zA-Z0-9]+$/), // Must be alphanumeric
display_name: vine
.string()
.isUnique({ table: 'roles', column: 'display_name' })
.trim()
.minLength(3)
.maxLength(255)
.isUnique({ table: 'roles', column: 'display_name' })
.regex(/^[a-zA-Z0-9]+$/),
description: vine.string().trim().escape().minLength(3).maxLength(255).optional(),
permissions: vine.array(vine.number()).minLength(1), // define at least one permission for the new role
permissions: vine.array(vine.number()).minLength(1), // At least one permission required
}),
);
@ -29,21 +29,28 @@ export const updateRoleValidator = vine.withMetaData<{ roleId: number }>().compi
vine.object({
name: vine
.string()
// .unique(async (db, value, field) => {
// const result = await db.from('roles').select('id').whereNot('id', field.meta.roleId).where('name', value).first();
// return result.length ? false : true;
// })
.trim()
.minLength(3)
.maxLength(255)
.isUnique({
table: 'roles',
column: 'name',
whereNot: (field) => field.meta.roleId,
})
.regex(/^[a-zA-Z0-9]+$/),
display_name: vine
.string()
.trim()
.minLength(3)
.maxLength(255),
.maxLength(255)
.isUnique({
table: 'roles',
column: 'display_name',
whereNot: (field) => field.meta.roleId,
})
.regex(/^[a-zA-Z0-9]+$/),
description: vine.string().trim().escape().minLength(3).maxLength(255).optional(),
permissions: vine.array(vine.number()).minLength(1), // define at least one permission for the new role
permissions: vine.array(vine.number()).minLength(1), // At least one permission required
}),
);

View file

@ -5,7 +5,23 @@ LogSyslog no
LogVerbose yes
DatabaseDirectory /var/lib/clamav
LocalSocket /var/run/clamav/clamd.socket
# LocalSocketMode 666
# Optional: allow multiple threads
MaxThreads 20
# Disable TCP socket
# TCPSocket 0
# TCP port address.
# Default: no
# TCPSocket 3310
# TCP address.
# By default we bind to INADDR_ANY, probably not wise.
# Enable the following to provide some degree of protection
# from the outside world.
# Default: no
# TCPAddr 127.0.0.1
Foreground no
PidFile /var/run/clamav/clamd.pid
LocalSocketGroup node
User node
# LocalSocketGroup node # Changed from 'clamav'
# User node # Changed from 'clamav' - clamd runs as clamav user

View file

@ -9,6 +9,7 @@ import type { CommandOptions } from '@adonisjs/core/types/ace';
import { DateTime } from 'luxon';
import Dataset from '#models/dataset';
import DatasetReference from '#models/dataset_reference';
import AppConfig from '#models/appconfig';
// import env from '#start/env';
interface MissingCrossReference {
@ -22,6 +23,7 @@ interface MissingCrossReference {
relation: string;
doi: string | null;
reverseRelation: string;
sourceReferenceLabel: string | null;
}
export default class DetectMissingCrossReferences extends BaseCommand {
@ -50,7 +52,17 @@ export default class DetectMissingCrossReferences extends BaseCommand {
};
// Define the allowed relations that we want to process
private readonly ALLOWED_RELATIONS = ['IsNewVersionOf', 'IsPreviousVersionOf', 'IsVariantFormOf', 'IsOriginalFormOf'];
private readonly ALLOWED_RELATIONS = [
'IsNewVersionOf',
'IsPreviousVersionOf',
'IsVariantFormOf',
'IsOriginalFormOf',
'Continues',
'IsContinuedBy',
'HasPart',
'IsPartOf',
];
// private readonly ALLOWED_RELATIONS = ['IsPreviousVersionOf', 'IsOriginalFormOf'];
async run() {
this.logger.info('🔍 Detecting missing cross-references...');
@ -63,9 +75,18 @@ export default class DetectMissingCrossReferences extends BaseCommand {
try {
const missingReferences = await this.findMissingCrossReferences();
// Store count in AppConfig if not fixing and count >= 1
if (!this.fix && missingReferences.length >= 1) {
await this.storeMissingCrossReferencesCount(missingReferences.length);
}
if (missingReferences.length === 0) {
const filterMsg = this.publish_id ? ` for publish_id ${this.publish_id}` : '';
this.logger.success(`All cross-references are properly linked for the specified relations${filterMsg}!`);
// Clear the count if no missing references
if (!this.fix) {
await this.storeMissingCrossReferencesCount(0);
}
return;
}
@ -96,6 +117,8 @@ export default class DetectMissingCrossReferences extends BaseCommand {
if (this.fix) {
await this.fixMissingReferences(missingReferences);
// Clear the count after fixing
await this.storeMissingCrossReferencesCount(0);
this.logger.success('All missing cross-references have been fixed!');
} else {
if (this.verbose) {
@ -112,6 +135,24 @@ export default class DetectMissingCrossReferences extends BaseCommand {
}
}
private async storeMissingCrossReferencesCount(count: number): Promise<void> {
try {
await AppConfig.updateOrCreate(
{
appid: 'commands',
configkey: 'missing_cross_references_count',
},
{
configvalue: count.toString(),
},
);
this.logger.info(`📊 Stored missing cross-references count in database: ${count}`);
} catch (error) {
this.logger.error('Failed to store missing cross-references count:', error);
}
}
private async findMissingCrossReferences(): Promise<MissingCrossReference[]> {
const missingReferences: {
sourceDatasetId: number;
@ -124,6 +165,7 @@ export default class DetectMissingCrossReferences extends BaseCommand {
relation: string;
doi: string | null;
reverseRelation: string;
sourceReferenceLabel: string | null;
}[] = [];
this.logger.info('📊 Querying dataset references...');
@ -158,9 +200,9 @@ export default class DetectMissingCrossReferences extends BaseCommand {
for (const reference of tethysReferences) {
processedCount++;
if (this.verbose && processedCount % 10 === 0) {
this.logger.info(`📈 Processed ${processedCount}/${tethysReferences.length} references...`);
}
// if (this.verbose && processedCount % 10 === 0) {
// this.logger.info(`📈 Processed ${processedCount}/${tethysReferences.length} references...`);
// }
// Double-check that this relation is in our allowed list (safety check)
if (!this.ALLOWED_RELATIONS.includes(reference.relation)) {
@ -172,25 +214,41 @@ export default class DetectMissingCrossReferences extends BaseCommand {
}
// Extract dataset publish_id from DOI or URL
const targetDatasetPublish = this.extractDatasetPublishIdFromReference(reference.value);
// const targetDatasetPublish = this.extractDatasetPublishIdFromReference(reference.value);
// Extract DOI from reference URL
const doi = this.extractDoiFromReference(reference.value);
if (!targetDatasetPublish) {
// if (!targetDatasetPublish) {
// if (this.verbose) {
// this.logger.warning(`Could not extract publish ID from: ${reference.value}`);
// }
// continue;
// }
if (!doi) {
if (this.verbose) {
this.logger.warning(`⚠️ Could not extract publish ID from: ${reference.value}`);
this.logger.warning(`Could not extract DOI from: ${reference.value}`);
}
continue;
}
// Check if target dataset exists and is published
// // Check if target dataset exists and is published
// const targetDataset = await Dataset.query()
// .where('publish_id', targetDatasetPublish)
// .where('server_state', 'published')
// .preload('identifier')
// .first();
// Check if target dataset exists and is published by querying via identifier
const targetDataset = await Dataset.query()
.where('publish_id', targetDatasetPublish)
.where('server_state', 'published')
.whereHas('identifier', (query) => {
query.where('value', doi);
})
.preload('identifier')
.first();
if (!targetDataset) {
if (this.verbose) {
this.logger.warning(`⚠️ Target dataset with publish_id ${targetDatasetPublish} not found or not published`);
this.logger.warning(`⚠️ Target dataset with publish_id ${doi} not found or not published`);
}
continue;
}
@ -204,8 +262,9 @@ export default class DetectMissingCrossReferences extends BaseCommand {
// Check if reverse reference exists
const reverseReferenceExists = await this.checkReverseReferenceExists(
targetDataset.id,
// reference.document_id,
reference.document_id,
reference.relation,
reference.dataset.identifier.value
);
if (!reverseReferenceExists) {
@ -223,6 +282,7 @@ export default class DetectMissingCrossReferences extends BaseCommand {
reverseRelation: reverseRelation,
sourceDoi: reference.dataset.identifier ? reference.dataset.identifier.value : null,
targetDoi: targetDataset.identifier ? targetDataset.identifier.value : null,
sourceReferenceLabel: reference.label || null,
});
}
}
@ -232,6 +292,18 @@ export default class DetectMissingCrossReferences extends BaseCommand {
return missingReferences;
}
private extractDoiFromReference(reference: string): string | null {
// Match DOI pattern, with or without URL prefix
const doiPattern = /(?:https?:\/\/)?(?:doi\.org\/)?(.+)/i;
const match = reference.match(doiPattern);
if (match && match[1]) {
return match[1]; // Returns just "10.24341/tethys.99.2"
}
return null;
}
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+)/);
@ -248,7 +320,12 @@ export default class DetectMissingCrossReferences extends BaseCommand {
return null;
}
private async checkReverseReferenceExists(targetDatasetId: number, originalRelation: string): Promise<boolean> {
private async checkReverseReferenceExists(
targetDatasetId: number,
sourceDatasetId: number,
originalRelation: string,
sourceDatasetIdentifier: string | null,
): Promise<boolean> {
const reverseRelation = this.getReverseRelation(originalRelation);
if (!reverseRelation) {
@ -258,9 +335,10 @@ export default class DetectMissingCrossReferences extends BaseCommand {
// Only check for reverse references where the source dataset is also published
const reverseReference = await DatasetReference.query()
// We don't filter by source document_id here to find any incoming reference from any published dataset
// .where('document_id', sourceDatasetId)
.where('related_document_id', targetDatasetId)
.where('document_id', targetDatasetId)
// .where('related_document_id', sourceDatasetId) // Ensure it's an incoming reference
.where('relation', reverseRelation)
.where('value', 'like', `%${sourceDatasetIdentifier}`) // Basic check to ensure it points back to source dataset
.first();
return !!reverseReference;
@ -272,6 +350,10 @@ export default class DetectMissingCrossReferences extends BaseCommand {
IsPreviousVersionOf: 'IsNewVersionOf',
IsVariantFormOf: 'IsOriginalFormOf',
IsOriginalFormOf: 'IsVariantFormOf',
Continues: 'IsContinuedBy',
IsContinuedBy: 'Continues',
HasPart: 'IsPartOf',
IsPartOf: 'HasPart',
};
// Only return reverse relation if it exists in our map, otherwise return null
@ -316,6 +398,7 @@ export default class DetectMissingCrossReferences extends BaseCommand {
.where('id', missing.sourceDatasetId)
.where('server_state', 'published')
.preload('identifier')
.preload('titles') // Preload titles to get mainTitle
.first();
const targetDataset = await Dataset.query().where('id', missing.targetDatasetId).where('server_state', 'published').first();
@ -332,12 +415,27 @@ export default class DetectMissingCrossReferences extends BaseCommand {
continue;
}
// **NEW: Update the original reference if related_document_id is missing**
const originalReference = await DatasetReference.query()
.where('document_id', missing.sourceDatasetId)
.where('relation', missing.relation)
.where('value', 'like', `%${missing.targetDoi}%`)
.first();
if (originalReference && !originalReference.related_document_id) {
originalReference.related_document_id = missing.targetDatasetId;
await originalReference.save();
if (this.verbose) {
this.logger.info(`🔗 Updated original reference with related_document_id: ${missing.targetDatasetId}`);
}
}
// Create the reverse reference using the referenced_by relationship
// Example: If Dataset 297 IsNewVersionOf Dataset 144
// We create an incoming reference for Dataset 144 that shows Dataset 297 IsPreviousVersionOf it
const reverseReference = new DatasetReference();
// Don't set document_id - this creates an incoming reference via related_document_id
reverseReference.related_document_id = missing.targetDatasetId; // 144 (dataset receiving the incoming reference)
reverseReference.document_id = missing.targetDatasetId; //
reverseReference.related_document_id = missing.sourceDatasetId;
reverseReference.type = 'DOI';
reverseReference.relation = missing.reverseRelation;
@ -350,8 +448,12 @@ export default class DetectMissingCrossReferences extends BaseCommand {
}
// Use the source dataset's main title for the label
reverseReference.label = sourceDataset.mainTitle || `Dataset ${missing.sourceDatasetId}`;
//reverseReference.label = sourceDataset.mainTitle || `Dataset ${missing.sourceDatasetId}`;
// get label of forward reference
reverseReference.label = missing.sourceReferenceLabel || sourceDataset.mainTitle || `Dataset ${missing.sourceDatasetId}`;
// reverseReference.notes = `Auto-created by detect:missing-cross-references command on ${DateTime.now().toISO()} to fix missing bidirectional reference.`;
// Save the new reverse reference
// Also save 'server_date_modified' on target dataset to trigger any downstream updates (e.g. search index)
targetDataset.server_date_modified = DateTime.now();
await targetDataset.save();

View file

@ -4,7 +4,7 @@
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
import { create } from 'xmlbuilder2';
import Dataset from '#models/dataset';
import XmlModel from '#app/Library/XmlModel';
import XmlModel from '#app/Library/DatasetXmlSerializer';
import { readFileSync } from 'fs';
import SaxonJS from 'saxon-js';
import { Client } from '@opensearch-project/opensearch';
@ -151,19 +151,16 @@ export default class IndexDatasets extends BaseCommand {
}
private async getDatasetXmlDomNode(dataset: Dataset): Promise<XMLBuilder | null> {
const xmlModel = new XmlModel(dataset);
const serializer = new XmlModel(dataset).enableCaching().excludeEmptyFields();
// 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;
serializer.setCache(dataset.xmlCache);
}
// return cache.getDomDocument();
const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
return domDocument;
// return cache.toXmlDocument();
const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument();
return xmlDocument;
}
private addSpecInformation(domNode: XMLBuilder, information: string) {

View file

@ -1,38 +1,45 @@
#!/bin/bash
set -e
set -m
echo "Starting ClamAV services..."
# Try to download database if missing
if [ ! "$(ls -A /var/lib/clamav 2>/dev/null)" ]; then
echo "Downloading ClamAV database (this may take a while)..."
# if [ ! "$(ls -A /var/lib/clamav 2>/dev/null)" ]; then
# echo "Downloading ClamAV database (this may take a while)..."
# Simple freshclam run without complex config
if sg clamav -c "freshclam --datadir=/var/lib/clamav --quiet"; then
echo "✓ Database downloaded successfully"
else
echo "⚠ Database download failed - creating minimal setup"
# Create a dummy file so clamd doesn't immediately fail
sg clamav -c "touch /var/lib/clamav/.dummy"
fi
fi
# # Simple freshclam run without complex config
# if freshclam --datadir=/var/lib/clamav --quiet; then
# echo "✓ Database downloaded successfully"
# else
# echo "⚠ Database download failed - creating minimal setup"
# # Create a dummy file so clamd doesn't immediately fail
# touch /var/lib/clamav/.dummy
# fi
# fi
# Start freshclam daemon for automatic updates
echo "Starting freshclam daemon for automatic updates..."
sg clamav -c "freshclam -d" &
# sg clamav -c "freshclam -d" &
# Added --daemon-notify to freshclam - This notifies clamd when the database updates
freshclam -d --daemon-notify=/etc/clamav/clamd.conf &
#freshclam -d &
# /etc/init.d/clamav-freshclam start &
# Start clamd in background
# Start clamd in foreground (so dumb-init can supervise it)
# /etc/init.d/clamav-daemon start &
# Give freshclam a moment to start
sleep 2
# Start clamd daemon in background using sg
echo "Starting ClamAV daemon..."
# sg clamav -c "clamd" &
# Use sg to run clamd with proper group permissions
# sg clamav -c "clamd" &
sg clamav -c "clamd --config-file=/etc/clamav/clamd.conf" &
# clamd --config-file=/etc/clamav/clamd.conf &
clamd &
# Give services time to start
@ -53,9 +60,15 @@ else
echo "⚠ Freshclam daemon status uncertain, but continuing..."
fi
# # change back to CMD of dockerfile
# exec "$@"
# # Optional: Test socket connectivity
# if [ -S /var/run/clamav/clamd.socket ]; then
# echo "✓ ClamAV socket exists"
# else
# echo "⚠ WARNING: ClamAV socket not found - services may still be starting"
# fi
# # change back to CMD of dockerfile
echo "✓ ClamAV setup complete"
echo "Starting main application..."
exec dumb-init -- "$@"
# exec dumb-init -- "$@"
exec "$@"

View file

@ -10,14 +10,14 @@ DatabaseDirectory /var/lib/clamav
# Basic logging settings
LogTime yes
LogVerbose no
LogVerbose yes
LogSyslog no
# PID file location
PidFile /var/run/clamav/freshclam.pid
# Database owner
DatabaseOwner clamav
DatabaseOwner node
# Mirror settings for Austria
DatabaseMirror db.at.clamav.net

92
package-lock.json generated
View file

@ -10,7 +10,7 @@
"dependencies": {
"@adonisjs/auth": "^9.2.4",
"@adonisjs/bodyparser": "^10.0.1",
"@adonisjs/core": "^6.17.0",
"@adonisjs/core": "6.17.2",
"@adonisjs/cors": "^2.2.1",
"@adonisjs/drive": "^3.2.0",
"@adonisjs/inertia": "^2.1.3",
@ -30,7 +30,6 @@
"@phc/format": "^1.0.0",
"@poppinss/manager": "^5.0.2",
"@vinejs/vine": "^3.0.0",
"argon2": "^0.43.0",
"axios": "^1.7.9",
"bcrypt": "^5.1.1",
"bcryptjs": "^2.4.3",
@ -48,9 +47,7 @@
"node-2fa": "^2.0.3",
"node-exceptions": "^4.0.1",
"notiwind": "^2.0.0",
"p-limit": "^7.1.1",
"pg": "^8.9.0",
"pino-pretty": "^13.0.0",
"qrcode": "^1.5.3",
"redis": "^5.0.0",
"reflect-metadata": "^0.2.1",
@ -94,6 +91,7 @@
"hot-hook": "^0.4.0",
"numeral": "^2.0.6",
"pinia": "^3.0.2",
"pino-pretty": "^13.0.0",
"postcss-loader": "^8.1.1",
"prettier": "^3.4.2",
"supertest": "^6.3.3",
@ -259,31 +257,31 @@
}
},
"node_modules/@adonisjs/core": {
"version": "6.19.0",
"resolved": "https://registry.npmjs.org/@adonisjs/core/-/core-6.19.0.tgz",
"integrity": "sha512-qwGuapvMLYPna89Qji/MuD9xx6qqcqc/aLrSGgoFbOzBmd8Ycc9391w7sFrrGuJpHiNLBmf1NJsY3YS2AwyX0A==",
"version": "6.17.2",
"resolved": "https://registry.npmjs.org/@adonisjs/core/-/core-6.17.2.tgz",
"integrity": "sha512-POT5COID8Z3j37+Dd7Y1EfG01Q6+HPY/tGcSb0Y97W2VIPkFjqcW2ooTE4wFT09u7coNohtXJa19a0feMz9ncw==",
"license": "MIT",
"dependencies": {
"@adonisjs/ace": "^13.3.0",
"@adonisjs/application": "^8.4.1",
"@adonisjs/bodyparser": "^10.1.0",
"@adonisjs/config": "^5.0.3",
"@adonisjs/application": "^8.3.1",
"@adonisjs/bodyparser": "^10.0.3",
"@adonisjs/config": "^5.0.2",
"@adonisjs/encryption": "^6.0.2",
"@adonisjs/env": "^6.2.0",
"@adonisjs/env": "^6.1.1",
"@adonisjs/events": "^9.0.2",
"@adonisjs/fold": "^10.2.0",
"@adonisjs/hash": "^9.1.1",
"@adonisjs/fold": "^10.1.3",
"@adonisjs/hash": "^9.0.5",
"@adonisjs/health": "^2.0.0",
"@adonisjs/http-server": "^7.7.0",
"@adonisjs/logger": "^6.0.6",
"@adonisjs/http-server": "^7.4.0",
"@adonisjs/logger": "^6.0.5",
"@adonisjs/repl": "^4.1.0",
"@antfu/install-pkg": "^1.1.0",
"@antfu/install-pkg": "^1.0.0",
"@paralleldrive/cuid2": "^2.2.2",
"@poppinss/colors": "^4.1.4",
"@poppinss/dumper": "^0.6.3",
"@poppinss/dumper": "^0.6.2",
"@poppinss/macroable": "^1.0.4",
"@poppinss/utils": "^6.10.0",
"@sindresorhus/is": "^7.0.2",
"@poppinss/utils": "^6.9.2",
"@sindresorhus/is": "^7.0.1",
"@types/he": "^1.2.3",
"error-stack-parser-es": "^1.0.5",
"he": "^1.2.0",
@ -302,8 +300,8 @@
"peerDependencies": {
"@adonisjs/assembler": "^7.8.0",
"@vinejs/vine": "^2.1.0 || ^3.0.0",
"argon2": "^0.31.2 || ^0.41.0 || ^0.43.0",
"bcrypt": "^5.1.1 || ^6.0.0",
"argon2": "^0.31.2 || ^0.41.0",
"bcrypt": "^5.1.1",
"edge.js": "^6.2.0"
},
"peerDependenciesMeta": {
@ -6098,15 +6096,17 @@
"license": "MIT"
},
"node_modules/argon2": {
"version": "0.43.1",
"resolved": "https://registry.npmjs.org/argon2/-/argon2-0.43.1.tgz",
"integrity": "sha512-TfOzvDWUaQPurCT1hOwIeFNkgrAJDpbBGBGWDgzDsm11nNhImc13WhdGdCU6K7brkp8VpeY07oGtSex0Wmhg8w==",
"version": "0.41.1",
"resolved": "https://registry.npmjs.org/argon2/-/argon2-0.41.1.tgz",
"integrity": "sha512-dqCW8kJXke8Ik+McUcMDltrbuAWETPyU6iq+4AhxqKphWi7pChB/Zgd/Tp/o8xRLbg8ksMj46F/vph9wnxpTzQ==",
"hasInstallScript": true,
"license": "MIT",
"optional": true,
"peer": true,
"dependencies": {
"@phc/format": "^1.0.0",
"node-addon-api": "^8.4.0",
"node-gyp-build": "^4.8.4"
"node-addon-api": "^8.1.0",
"node-gyp-build": "^4.8.1"
},
"engines": {
"node": ">=16.17.0"
@ -7399,6 +7399,7 @@
"version": "4.6.3",
"resolved": "https://registry.npmjs.org/dateformat/-/dateformat-4.6.3.tgz",
"integrity": "sha512-2P0p0pFGzHS5EMnhdxQi7aJN+iMheud0UhG4dlE1DLAlvL8JHjJJTX/CSm4JXwV0Ka5nGk3zC5mcb5bUQUxxMA==",
"dev": true,
"license": "MIT",
"engines": {
"node": "*"
@ -7904,6 +7905,7 @@
"version": "1.4.5",
"resolved": "https://registry.npmjs.org/end-of-stream/-/end-of-stream-1.4.5.tgz",
"integrity": "sha512-ooEGc6HP26xXq/N+GCGOT0JKCLDGrq2bQUZrQ7gyrJiZANJ/8YDTxTpQBXGMn+WbIQXNVpyWymm7KYVICQnyOg==",
"dev": true,
"license": "MIT",
"dependencies": {
"once": "^1.4.0"
@ -8559,6 +8561,7 @@
"version": "3.0.2",
"resolved": "https://registry.npmjs.org/fast-copy/-/fast-copy-3.0.2.tgz",
"integrity": "sha512-dl0O9Vhju8IrcLndv2eU4ldt1ftXMqqfgN4H1cpmGV7P6jeB9FwpN9a2c8DPGE1Ys88rNUJVYDHq73CGAGOPfQ==",
"dev": true,
"license": "MIT"
},
"node_modules/fast-deep-equal": {
@ -8631,6 +8634,7 @@
"version": "2.1.1",
"resolved": "https://registry.npmjs.org/fast-safe-stringify/-/fast-safe-stringify-2.1.1.tgz",
"integrity": "sha512-W+KJc2dmILlPplD/H4K9l9LcAHAfPtP6BY84uVLXQ6Evcz9Lcg33Y2z1IVblT6xdY54PXYVHEv+0Wpq8Io6zkA==",
"dev": true,
"license": "MIT"
},
"node_modules/fast-uri": {
@ -9664,6 +9668,7 @@
"version": "5.0.0",
"resolved": "https://registry.npmjs.org/help-me/-/help-me-5.0.0.tgz",
"integrity": "sha512-7xgomUX6ADmcYzFik0HzAxh/73YlKR9bmFzf51CZwR+b6YtzU2m0u49hQCqV6SvlqIqsaxovfwdvbnsw3b/zpg==",
"dev": true,
"license": "MIT"
},
"node_modules/hookable": {
@ -10428,6 +10433,7 @@
"version": "3.1.1",
"resolved": "https://registry.npmjs.org/joycon/-/joycon-3.1.1.tgz",
"integrity": "sha512-34wB/Y7MW7bzjKRjUKTa46I2Z7eV62Rkhva+KkopW7Qvv/OSWBqvkSY7vusOPrNuZcUG3tApvdVgNB8POj3SPw==",
"dev": true,
"license": "MIT",
"engines": {
"node": ">=10"
@ -11154,6 +11160,7 @@
"version": "1.2.8",
"resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.8.tgz",
"integrity": "sha512-2yyAR8qBkN3YuheJanUpWC5U3bb5osDywNB8RzDVlDwDHbocAJveqqj1u8+SVD7jkWT4yvsHCpWqqWqAxb0zCA==",
"dev": true,
"license": "MIT",
"funding": {
"url": "https://github.com/sponsors/ljharb"
@ -11324,6 +11331,8 @@
"resolved": "https://registry.npmjs.org/node-addon-api/-/node-addon-api-8.5.0.tgz",
"integrity": "sha512-/bRZty2mXUIFY/xU5HLvveNHlswNJej+RnxBjOMkidWfwZzgTbPG1E3K5TOxRLOR+5hX7bSofy8yf1hZevMS8A==",
"license": "MIT",
"optional": true,
"peer": true,
"engines": {
"node": "^18 || ^20 || >= 21"
}
@ -11369,6 +11378,8 @@
"resolved": "https://registry.npmjs.org/node-gyp-build/-/node-gyp-build-4.8.4.tgz",
"integrity": "sha512-LA4ZjwlnUblHVgq0oBF3Jl/6h/Nvs5fzBLwdEF4nuxnFdsfajde4WfxtJr3CaiH+F6ewcIB/q4jQ4UzPyid+CQ==",
"license": "MIT",
"optional": true,
"peer": true,
"bin": {
"node-gyp-build": "bin.js",
"node-gyp-build-optional": "optional.js",
@ -11711,15 +11722,15 @@
}
},
"node_modules/p-limit": {
"version": "7.1.1",
"resolved": "https://registry.npmjs.org/p-limit/-/p-limit-7.1.1.tgz",
"integrity": "sha512-i8PyM2JnsNChVSYWLr2BAjNoLi0BAYC+wecOnZnVV+YSNJkzP7cWmvI34dk0WArWfH9KwBHNoZI3P3MppImlIA==",
"version": "4.0.0",
"resolved": "https://registry.npmjs.org/p-limit/-/p-limit-4.0.0.tgz",
"integrity": "sha512-5b0R4txpzjPWVw/cXXUResoD4hb6U/x9BH08L7nw+GN1sezDzPdxeRvpc9c433fZhBan/wusjbCsqwqm4EIBIQ==",
"license": "MIT",
"dependencies": {
"yocto-queue": "^1.2.1"
"yocto-queue": "^1.0.0"
},
"engines": {
"node": ">=20"
"node": "^12.20.0 || ^14.13.1 || >=16.0.0"
},
"funding": {
"url": "https://github.com/sponsors/sindresorhus"
@ -11740,21 +11751,6 @@
"url": "https://github.com/sponsors/sindresorhus"
}
},
"node_modules/p-locate/node_modules/p-limit": {
"version": "4.0.0",
"resolved": "https://registry.npmjs.org/p-limit/-/p-limit-4.0.0.tgz",
"integrity": "sha512-5b0R4txpzjPWVw/cXXUResoD4hb6U/x9BH08L7nw+GN1sezDzPdxeRvpc9c433fZhBan/wusjbCsqwqm4EIBIQ==",
"license": "MIT",
"dependencies": {
"yocto-queue": "^1.0.0"
},
"engines": {
"node": "^12.20.0 || ^14.13.1 || >=16.0.0"
},
"funding": {
"url": "https://github.com/sponsors/sindresorhus"
}
},
"node_modules/p-map": {
"version": "7.0.3",
"resolved": "https://registry.npmjs.org/p-map/-/p-map-7.0.3.tgz",
@ -12174,6 +12170,7 @@
"version": "13.1.1",
"resolved": "https://registry.npmjs.org/pino-pretty/-/pino-pretty-13.1.1.tgz",
"integrity": "sha512-TNNEOg0eA0u+/WuqH0MH0Xui7uqVk9D74ESOpjtebSQYbNWJk/dIxCXIxFsNfeN53JmtWqYHP2OrIZjT/CBEnA==",
"dev": true,
"license": "MIT",
"dependencies": {
"colorette": "^2.0.7",
@ -12198,6 +12195,7 @@
"version": "4.0.0",
"resolved": "https://registry.npmjs.org/secure-json-parse/-/secure-json-parse-4.0.0.tgz",
"integrity": "sha512-dxtLJO6sc35jWidmLxo7ij+Eg48PM/kleBsxpC8QJE0qJICe+KawkDQmvCMZUr9u7WKVHgMW6vy3fQ7zMiFZMA==",
"dev": true,
"funding": [
{
"type": "github",
@ -12214,6 +12212,7 @@
"version": "5.0.3",
"resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-5.0.3.tgz",
"integrity": "sha512-1tB5mhVo7U+ETBKNf92xT4hrQa3pm0MZ0PQvuDnWgAAGHDsfp4lPSpiS6psrSiet87wyGPh9ft6wmhOMQ0hDiw==",
"dev": true,
"license": "MIT",
"engines": {
"node": ">=14.16"
@ -12665,6 +12664,7 @@
"version": "3.0.3",
"resolved": "https://registry.npmjs.org/pump/-/pump-3.0.3.tgz",
"integrity": "sha512-todwxLMY7/heScKmntwQG8CXVkWUOdYxIvY2s0VWAAMh/nd8SoYiRaKjlr7+iCs984f2P8zvrfWcDDYVb73NfA==",
"dev": true,
"license": "MIT",
"dependencies": {
"end-of-stream": "^1.1.0",

View file

@ -59,6 +59,7 @@
"hot-hook": "^0.4.0",
"numeral": "^2.0.6",
"pinia": "^3.0.2",
"pino-pretty": "^13.0.0",
"postcss-loader": "^8.1.1",
"prettier": "^3.4.2",
"supertest": "^6.3.3",
@ -76,7 +77,7 @@
"dependencies": {
"@adonisjs/auth": "^9.2.4",
"@adonisjs/bodyparser": "^10.0.1",
"@adonisjs/core": "^6.17.0",
"@adonisjs/core": "6.17.2",
"@adonisjs/cors": "^2.2.1",
"@adonisjs/drive": "^3.2.0",
"@adonisjs/inertia": "^2.1.3",
@ -96,7 +97,6 @@
"@phc/format": "^1.0.0",
"@poppinss/manager": "^5.0.2",
"@vinejs/vine": "^3.0.0",
"argon2": "^0.43.0",
"axios": "^1.7.9",
"bcrypt": "^5.1.1",
"bcryptjs": "^2.4.3",
@ -114,9 +114,7 @@
"node-2fa": "^2.0.3",
"node-exceptions": "^4.0.1",
"notiwind": "^2.0.0",
"p-limit": "^7.1.1",
"pg": "^8.9.0",
"pino-pretty": "^13.0.0",
"qrcode": "^1.5.3",
"redis": "^5.0.0",
"reflect-metadata": "^0.2.1",

View file

@ -0,0 +1,34 @@
import { ApplicationService } from '@adonisjs/core/types';
export default class RuleProvider {
constructor(protected app: ApplicationService) {}
public register() {
// Register your own bindings
}
public async boot() {
// IoC container is ready
// await import("../src/rules/index.js");
await import('#start/rules/unique');
await import('#start/rules/translated_language');
await import('#start/rules/unique_person');
// () => import('#start/rules/file_length'),
// () => import('#start/rules/file_scan'),
// () => import('#start/rules/allowed_extensions_mimetypes'),
await import('#start/rules/dependent_array_min_length');
await import('#start/rules/referenceValidation');
await import('#start/rules/valid_mimetype');
await import('#start/rules/array_contains_types');
await import('#start/rules/orcid');
}
public async ready() {
// App is ready
}
public async shutdown() {
// Cleanup, since app is going down
}
}

File diff suppressed because one or more lines are too long

View file

@ -207,7 +207,8 @@
<!--17 +18 uncontrolled subject (swd) -->
<xsl:variable name="subjects">
<xsl:for-each select="Subject[@Type = 'Uncontrolled']">
<!-- <xsl:for-each select="Subject[@Type = 'Uncontrolled']"> -->
<xsl:for-each select="Subject[@Type = 'Uncontrolled' or @Type = 'Geoera']">
<xsl:text>"</xsl:text>
<xsl:value-of select="fn:escapeQuotes(@Value)"/>
<xsl:text>"</xsl:text>

View file

@ -1,21 +1,41 @@
<template>
<NcSettingsSection :name="t('settings', 'Background jobs')" :description="t(
'settings',
`For the server to work properly, it\'s important to configure background jobs correctly. Cron is the recommended setting. Please see the documentation for more information.`,
)" :doc-url="backgroundJobsDocUrl">
<template v-if="lastCron !== 0">
<NcNoteCard v-if="oldExecution" type="danger">
{{ t('settings', `Last job execution ran {time}. Something seems wrong.`, {
time: relativeTime,
timestamp: lastCron
}) }}
<NcSettingsSection
:name="t('settings', 'Background jobs')"
:description="
t(
'settings',
`For the server to work properly, it's important to configure background jobs correctly. Cron is the recommended setting. Please see the documentation for more information.`,
)
"
:doc-url="backgroundJobsDocUrl"
>
<template v-if="lastCronTimestamp">
<NcNoteCard v-if="isExecutionTooOld" type="danger">
{{
t(
'settings',
`Last job execution ran {time}. Something seems wrong.
Timestamp of last cron: {timestamp} `,
{
time: relativeTime,
timestamp: lastCronTimestamp,
},
)
}}
</NcNoteCard>
<!-- <NcNoteCard v-else-if="longExecutionCron" type="warning">
{{ t('settings', `Some jobs have not been executed since {maxAgeRelativeTime}. Please consider increasing the execution frequency.`, {maxAgeRelativeTime}) }}
</NcNoteCard> -->
<NcNoteCard v-else-if="isLongExecutionCron" type="warning">
{{
t(
'settings',
`Some jobs have not been executed since {maxAgeRelativeTime}. Please consider increasing the execution
frequency.`,
{
maxAgeRelativeTime,
},
)
}}
</NcNoteCard>
<NcNoteCard v-else type="success">
{{ t('settings', 'Last job ran {relativeTime}.', { relativeTime }) }}
@ -23,147 +43,180 @@
</template>
<NcNoteCard v-else type="danger">
'Background job did not run yet!'
{{ t('settings', 'Background job did not run yet!') }}
</NcNoteCard>
<!-- Missing Cross References Warning -->
<NcNoteCard v-if="missingCrossReferencesCount >= 1" type="warning">
{{
t('settings', 'Found {count} missing dataset cross-reference(s). You can fix this by running: node ace detect:missing-cross-references --fix', {
count: missingCrossReferencesCount,
})
}}
</NcNoteCard>
<!-- Background Jobs Status Display -->
<div class="background-jobs-mode">
<h3>{{ t('settings', 'Background Jobs Mode') }}</h3>
<div class="current-mode">
<span class="mode-label">{{ t('settings', 'Current mode:') }}</span>
<span class="mode-value">{{ getCurrentModeLabel() }}</span>
</div>
<!-- <div class="mode-description" v-if="backgroundJobsMode === 'cron'" v-html="cronLabel"></div> -->
</div>
<!-- Refresh Button -->
<div class="actions">
<button type="button" class="primary" @click="refreshStatus" :disabled="isRefreshing">
{{ isRefreshing ? t('settings', 'Refreshing...') : t('settings', 'Refresh Status') }}
</button>
</div>
</NcSettingsSection>
</template>
<script lang="ts">
import { usePage } from '@inertiajs/vue3';
<script setup lang="ts">
import { ref, computed, onMounted, onUnmounted } from 'vue';
import { usePage, router } from '@inertiajs/vue3';
import { loadState } from '@/utils/initialState';
import { showError } from '@/utils/toast';
// import { generateOcsUrl } from '@nextcloud/router';
// import { confirmPassword } from '@nextcloud/password-confirmation';
import axios from 'axios';
import { showError, showSuccess } from '@/utils/toast';
import dayjs from '@/utils/dayjs';
import NcNoteCard from '@/Components/NCNoteCard.vue';
import NcSettingsSection from '@/Components/NcSettingsSection.vue';
import { translate as t } from '@/utils/tethyscloud-l10n';
// import { useLocaleStore } from '@/Stores/locale';
// import '@nextcloud/password-confirmation/dist/style.css';
// Props and reactive data
const cronMaxAge =ref<number>(loadState('settings', 'cronMaxAge', 1758824778));
const backgroundJobsMode = ref<string>(loadState('settings', 'backgroundJobsMode', 'cron'));
const cliBasedCronPossible = ref<boolean>(loadState('settings', 'cliBasedCronPossible', true));
const cliBasedCronUser = ref<string>(loadState('settings', 'cliBasedCronUser', 'www-data'));
const backgroundJobsDocUrl = ref<string>(loadState('settings', 'backgroundJobsDocUrl', ''));
const isRefreshing = ref<boolean>(false);
// const lastCron: number = 1723807502; //loadState('settings', 'lastCron'); //1723788607
const cronMaxAge: number = 1724046901;//loadState('settings', 'cronMaxAge', 0); //''
const backgroundJobsMode: string = loadState('settings', 'backgroundJobsMode', 'cron'); //cron
const cliBasedCronPossible = loadState('settings', 'cliBasedCronPossible', true); //true
const cliBasedCronUser = loadState('settings', 'cliBasedCronUser', 'www-data'); //www-data
const backgroundJobsDocUrl: string = loadState('settings', 'backgroundJobsDocUrl'); //https://docs.nextcloud.com/server/29/go.php?to=admin-background-jobs
// Use reactive page reference
const page = usePage();
// await loadTranslations('settings');
// Auto-refresh timer
let refreshTimer: NodeJS.Timeout | null = null;
const AUTO_REFRESH_INTERVAL = 30000; // 30 seconds
export default {
name: 'BackgroundJob',
// Computed properties
const missingCrossReferencesCount = computed((): number => {
const count = page.props.missingCrossReferencesCount as string | number;
return typeof count === 'string' ? parseInt(count) || 0 : count || 0;
});
components: {
NcSettingsSection,
NcNoteCard,
},
const lastCronTimestamp = computed((): number => {
const lastCron = page.props.lastCron as string | number;
return typeof lastCron === 'string' ? parseInt(lastCron) || 0 : lastCron || 0;
});
data() {
return {
// lastCron: 0,
cronMaxAge: cronMaxAge,
backgroundJobsMode: backgroundJobsMode,
cliBasedCronPossible: cliBasedCronPossible,
cliBasedCronUser: cliBasedCronUser,
backgroundJobsDocUrl: backgroundJobsDocUrl,
// relativeTime: dayjs(this.lastCron * 1000).fromNow(),
// maxAgeRelativeTime: dayjs(cronMaxAge * 1000).fromNow(),
t: t,
};
},
computed: {
lastCron(): number {
return usePage().props.lastCron as number;
const relativeTime = computed((): string => {
if (!lastCronTimestamp.value) return '';
// Reference currentTime.value to make this reactive to time changes
let intermValue = page.props.lastCron as string | number;
intermValue = typeof intermValue === 'string' ? parseInt(intermValue) || 0 : intermValue || 0;
return dayjs.unix(intermValue).fromNow();
});
},
relativeTime() {
return dayjs.unix(this.lastCron).fromNow(); // Calculate relative time for lastCron
},
maxAgeRelativeTime() {
return dayjs.unix(this.cronMaxAge).fromNow(); // Calculate relative time for cronMaxAge
},
cronLabel() {
let desc = 'Use system cron service to call the cron.php file every 5 minutes.';
if (this.cliBasedCronPossible) {
desc +=
'<br>' +
'The cron.php needs to be executed by the system account "{user}".', { user: this.cliBasedCronUser };
} else {
desc +=
'<br>' +
const maxAgeRelativeTime = computed((): string => {
return dayjs.unix(cronMaxAge).fromNow();
});
'The PHP POSIX extension is required. See {linkstart}PHP documentation{linkend} for more details.',
{
linkstart:
'<a target="_blank" rel="noreferrer nofollow" class="external" href="https://www.php.net/manual/en/book.posix.php">',
linkend: '</a>',
}
}
return desc;
},
oldExecution() {
return (dayjs().unix() - this.lastCron) > 600; // older than 10 minutes
},
const cronLabel = computed((): string => {
let desc = t('settings', 'Use system cron service to call the cron.php file every 5 minutes.');
longExecutionCron() {
//type of cron job and greater than 24h
// let test = dayjs.unix(this.cronMaxAge).format('YYYY-MM-DD HH:mm:ss');
return (dayjs().unix() - this.cronMaxAge) > 24 * 3600 && this.backgroundJobsMode === 'cron';
},
},
methods: {
async onBackgroundJobModeChanged(backgroundJobsMode: string) {
const url = generateOcsUrl('/apps/provisioning_api/api/v1/config/apps/{appId}/{key}', {
appId: 'core',
key: 'backgroundjobs_mode',
if (cliBasedCronPossible.value) {
desc +=
'<br>' +
t('settings', 'The cron.php needs to be executed by the system account "{user}".', {
user: cliBasedCronUser.value,
});
// await confirmPassword();
try {
const { data } = await axios.post(url, {
value: backgroundJobsMode,
});
this.handleResponse({
status: data.ocs?.meta?.status,
});
} catch (e) {
this.handleResponse({
errorMessage: t('settings', 'Unable to update background job mode'),
error: e,
});
}
},
async handleResponse({ status, errorMessage, error }) {
if (status === 'ok') {
await this.deleteError();
} else {
showError(errorMessage);
console.error(errorMessage, error);
}
},
async deleteError() {
// clear cron errors on background job mode change
const url = generateOcsUrl('/apps/provisioning_api/api/v1/config/apps/{appId}/{key}', {
appId: 'core',
key: 'cronErrors',
} else {
desc +=
'<br>' +
t('settings', 'The PHP POSIX extension is required. See {linkstart}PHP documentation{linkend} for more details.', {
linkstart:
'<a target="_blank" rel="noreferrer nofollow" class="external" href="https://www.php.net/manual/en/book.posix.php">',
linkend: '</a>',
});
}
// await confirmPassword();
return desc;
});
try {
await axios.delete(url);
} catch (error) {
console.error(error);
}
},
},
const isExecutionTooOld = computed((): boolean => {
if (!lastCronTimestamp.value) return false;
return dayjs().unix() - lastCronTimestamp.value > 600; // older than 10 minutes
});
const isLongExecutionCron = computed((): boolean => {
return dayjs().unix() - cronMaxAge > 24 * 3600 && backgroundJobsMode.value === 'cron';
});
// Methods
const getCurrentModeLabel = (): string => {
switch (backgroundJobsMode.value) {
case 'cron':
return t('settings', 'Cron (Recommended)');
case 'webcron':
return t('settings', 'Webcron');
case 'ajax':
return t('settings', 'AJAX');
default:
return t('settings', 'Unknown');
}
};
const refreshStatus = async (): Promise<void> => {
isRefreshing.value = true;
try {
// Use Inertia to refresh the current page data
router.reload({
only: ['lastCron', 'cronMaxAge', 'missingCrossReferencesCount'], // Also reload missing cross references count
onSuccess: () => {
showSuccess(t('settings', 'Background job status refreshed'));
},
onError: () => {
showError(t('settings', 'Failed to refresh status'));
},
onFinish: () => {
isRefreshing.value = false;
},
});
} catch (error) {
console.error('Failed to refresh status:', error);
showError(t('settings', 'Failed to refresh status'));
isRefreshing.value = false;
}
};
const startAutoRefresh = (): void => {
refreshTimer = setInterval(() => {
if (!isRefreshing.value) {
router.reload({ only: ['lastCron', 'cronMaxAge', 'missingCrossReferencesCount'] });
}
}, AUTO_REFRESH_INTERVAL);
};
const stopAutoRefresh = (): void => {
if (refreshTimer) {
clearInterval(refreshTimer);
refreshTimer = null;
}
};
// Lifecycle hooks
onMounted(() => {
startAutoRefresh();
});
onUnmounted(() => {
stopAutoRefresh();
});
</script>
<style lang="css" scoped>
@ -185,7 +238,76 @@ export default {
width: initial;
}
.ajaxSwitch {
.background-jobs-mode {
margin-top: 1rem;
}
.background-jobs-mode h3 {
margin-bottom: 0.5rem;
font-weight: 600;
}
.current-mode {
display: flex;
align-items: center;
gap: 0.5rem;
margin-bottom: 1rem;
}
.mode-label {
font-weight: 500;
color: var(--color-text-light);
}
.mode-value {
font-weight: 600;
color: var(--color-main-text);
padding: 0.25rem 0.5rem;
background-color: var(--color-background-hover);
border-radius: var(--border-radius);
}
.mode-description {
color: var(--color-text-maxcontrast);
font-size: 0.9rem;
line-height: 1.4;
margin-top: 0.5rem;
}
.actions {
margin-top: 1rem;
display: flex;
gap: 0.5rem;
}
.actions button {
padding: 0.5rem 1rem;
border: none;
border-radius: var(--border-radius);
cursor: pointer;
font-weight: 500;
transition: all 0.2s ease;
}
.actions button.primary {
background-color: var(--color-primary-element);
color: var(--color-primary-element-text);
}
.actions button.primary:hover:not(:disabled) {
background-color: var(--color-primary-element-hover);
}
.actions button.primary:disabled {
opacity: 0.6;
cursor: not-allowed;
}
@media (max-width: 768px) {
.current-mode {
flex-direction: column;
align-items: flex-start;
gap: 0.25rem;
}
}
</style>

View file

@ -4,13 +4,13 @@ import relativeTime from 'dayjs/plugin/relativeTime';
import 'dayjs/locale/de';
import 'dayjs/locale/en';
const extendedDayjs = dayjs.extend(relativeTime);
dayjs.extend(relativeTime);
export const setDayjsLocale = (locale: string) => {
extendedDayjs.locale(locale);
dayjs.locale(locale);
};
// // Set a default locale initially
// setDayjsLocale('en');
export default extendedDayjs;
export default dayjs;

View file

@ -160,6 +160,16 @@ export function showError(text: string, options?: ToastOptions): Toast {
return showMessage(text, { ...options, type: ToastType.ERROR })
}
/**
* Show a toast message with success styling
*
* @param text Message to be shown in the toast, any HTML is removed by default
* @param options
*/
export function showSuccess(text: string, options?: ToastOptions): Toast {
return showMessage(text, { ...options, type: ToastType.SUCCESS });
}
export default {
updatableNotification: null,

View file

@ -127,15 +127,33 @@ router
.group(() => {
router
.get('/settings', async ({ inertia }: HttpContext) => {
const updatedConfigValue = await db
.from('appconfigs')
.select('configvalue')
.where('appid', 'backgroundjob')
.where('configkey', 'lastjob')
.first();
return inertia.render('Admin/Settings', {
lastCron: updatedConfigValue?.configvalue || '',
});
try {
const [lastJobConfig, missingCrossReferencesConfig] = await Promise.all([
db.from('appconfigs').select('configvalue').where('appid', 'backgroundjob').where('configkey', 'lastjob').first(),
db
.from('appconfigs')
.select('configvalue')
.where('appid', 'commands')
.where('configkey', 'missing_cross_references_count')
.first(),
]);
return inertia.render('Admin/Settings', {
lastCron: lastJobConfig?.configvalue || 0,
missingCrossReferencesCount: parseInt(missingCrossReferencesConfig?.configvalue || '0'),
// Add timestamp for cache busting
lastUpdated: Date.now(),
});
} catch (error) {
console.error('Failed to load background job settings:', error);
return inertia.render('Admin/Settings', {
lastCron: 0,
cronMaxAge: 0,
backgroundJobsMode: 'cron',
missingCrossReferencesCount: 0,
error: 'Failed to load background job settings',
});
}
})
.as('overview');

View file

@ -43,10 +43,14 @@ async function scanFileForViruses(filePath: string | undefined, options: Options
scanRecursively: true, // If true, deep scan folders recursively
clamdscan: {
active: true, // If true, this module will consider using the clamdscan binary
host: options.host,
port: options.port,
host: options.host, // IP of host to connect to TCP interface,
port: options.port, // Port of host to use when connecting to TCP interface
socket: '/var/run/clamav/clamd.socket', // Socket file for connecting via socket
localFallback: false, // Use local clamscan binary if socket/tcp fails
// port: options.port,
multiscan: true, // Scan using all available cores! Yay!
},
preference: 'clamdscan', // If clamdscan is found and active, it will be used by default over clamscan
};
const clamscan = await new ClamScan().init(opts);