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elichadelichad
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Merge pull request #78 from workflowhub-eu/fix-vis
Correct run script so blueprint config can be generated
2 parents c6ff9cb + 7087862 commit 23fa445

19 files changed

Lines changed: 930 additions & 11 deletions

‎vis/blueprint-ui-config-initializer/lib/actions.js‎

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import oxigraph from 'oxigraph';
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import * as queries from './queries.js';
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import { prettify } from './prettyprint.js';
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import { runGraphQuery, parametrizeQuery, writeDataToFile, readClassesFromFile, loadTurtleFileIntoStore } from './glue.js';
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import chalk from 'chalk';
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import createDebug from 'debug';
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const debug_sparql = createDebug('sparql');
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async function fetchClasses(options) {
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console.log(`output filename: ${options.output}`);
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const data = await runGraphQuery(queries.constructCandidateClasses, 'constructCandidateClasses');
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if (data) {
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writeDataToFile(options.output, data);
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}
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}
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async function fetchLinks(options) {
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console.log(`classes filename: ${options.classes}`);
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console.log(`output filename: ${options.output}`);
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const classes = await readClassesFromFile(options.classes);
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if (classes === undefined) {
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return console.error(chalk.red(`Aborting`));
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} else if (classes.size === 0) {
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return console.error(chalk.red(`Aborting. No classes found in file ${options.classes}`));
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}
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const query = parametrizeQuery(queries.constructCandidateLinks, ["%%values-cls%%", "%%values-linktype%%"], classes);
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const data = await runGraphQuery(query, 'constructCandidateLinks');
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const prettyTurtle = await prettify(data);
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if (prettyTurtle) {
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writeDataToFile(options.output, prettyTurtle);
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}
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}
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async function fetchDetails(options) {
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console.log(`classes filename: ${options.classes}`);
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console.log(`output filename: ${options.output}`);
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const classes = await readClassesFromFile(options.classes);
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if (classes === undefined) {
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return console.error(chalk.red(`Aborting`));
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} else if (classes.size === 0) {
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return console.error(chalk.red(`Aborting. No classes found in file ${options.classes}`));
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}
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const query = parametrizeQuery(queries.constructCandidateDetails, ["%%values-cls%%"], classes);
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const data = await runGraphQuery(query, 'constructCandidateDetails');
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const prettyTurtle = await prettify(data);
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if (prettyTurtle) {
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writeDataToFile(options.output, prettyTurtle);
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}
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}
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async function generateConfig(options) {
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console.log(`classes filename: ${options.classes}`);
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console.log(`links filename: ${options.links}`);
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console.log(`details filename: ${options.details}`);
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console.log(`output filename: ${options.output}`);
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console.log(chalk.blue(`Combining the files and generating the config ...`));
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const inMemoryStore = new oxigraph.Store();
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let loadingOK = true;
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loadingOK &= loadTurtleFileIntoStore(options.classes, inMemoryStore);
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loadingOK &= loadTurtleFileIntoStore(options.links, inMemoryStore);
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loadingOK &= loadTurtleFileIntoStore(options.details, inMemoryStore);
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if (!loadingOK) {
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return console.error(chalk.red(`Aborting`));
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}
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const query = queries.constructConfig;
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debug_sparql(query);
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const blueprintConfig = new oxigraph.Store(inMemoryStore.query(query));
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const data = blueprintConfig.dump({format: "application/trig"});
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const prettyTurtle = await prettify(data);
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if (prettyTurtle) {
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writeDataToFile(options.output, prettyTurtle);
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}
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}
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export {
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fetchClasses,
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fetchLinks,
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fetchDetails,
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generateConfig
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}

‎vis/blueprint-ui-config-initializer/lib/glue.js‎

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import SparqlClient from 'sparql-http-client/SimpleClient.js';
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import fs from 'fs';
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import rdfEnv from './rdf-env.js'
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import chalk from 'chalk';
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import createDebug from 'debug';
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const debug_sparql = createDebug('sparql');
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const clientOptions = {
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endpointUrl: process.env.SPARQL_ENDPOINT,
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user: process.env.SPARQL_USER,
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password: process.env.SPARQL_PASS
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};
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function createSparqlClient() {
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logENV();
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return new SparqlClient(clientOptions);
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}
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const queryOptions = { operation: 'postDirect', headers: { 'Accept': 'text/turtle' } };
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function logENV() {
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console.log(`SPARQL_ENDPOINT: ${process.env.SPARQL_ENDPOINT}`);
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console.log(`SPARQL_USER: ${process.env.SPARQL_USER}`);
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console.log(`SPARQL_PASS: ${process.env.SPARQL_PASS !== undefined ? '********' : undefined}`);
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}
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function parametrizeQuery(queryTemplate, placeholders, classes) {
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if (classes === undefined) {
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return undefined;
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}
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const valuesString = Array.from(classes)
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.map(iri => `\n<${iri}>`)
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.sort()
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.join('');
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let query = queryTemplate;
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placeholders.forEach(x => {
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query = query.replaceAll(x, valuesString);
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});
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return query;
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}
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async function runGraphQuery(query, queryId) {
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const client = createSparqlClient();
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console.log(chalk.blue(`Running graph query '${queryId}' ...`));
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debug_sparql(query);
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try {
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const res = await client.query.construct(query, queryOptions);
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if (!res.ok) {
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return console.error(chalk.red(`Failed to run graph query '${queryId}': HTTP status ${res.status} ${res.statusText}`));
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}
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return await res.text();
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} catch (err) {
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return console.error(chalk.red(`Failed to run graph query: ${err}`));
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}
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}
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function writeDataToFile(file, data) {
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try {
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fs.writeFileSync(file, data, 'utf8');
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console.log(chalk.green(`File ${file} has been written`));
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} catch (err) {
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console.error(chalk.red(`Failed to write file ${file}: ${err}`));
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}
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}
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async function readClassesFromFile(file) {
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try {
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const dataset = await rdfEnv.dataset().import(rdfEnv.fromFile(file));
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const classes = new Set();
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dataset.filter(matchClassDeclaration)
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.forEach(quad => classes.add(quad.subject.value));
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return classes;
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} catch (err) {
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return console.error(chalk.red(`Failed to read classes from file ${file}: ${err}`));
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}
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}
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function matchClassDeclaration(quad) {
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return quad.predicate.value === 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'
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&& quad.object.value === 'http://schema.example.org/blueprint-ui-config-initializer/Class'
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}
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function loadTurtleFileIntoStore(file, store) {
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try {
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const ttlString = fs.readFileSync(file, 'utf8');
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store.load(ttlString, { format: "text/turtle" });
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return true;
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} catch (err) {
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return console.error(chalk.red(`Failed to load turtle from file ${file} into in-memory-store: ${err}`));
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}
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}
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export {
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runGraphQuery,
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parametrizeQuery,
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writeDataToFile,
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readClassesFromFile,
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loadTurtleFileIntoStore
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}

‎vis/blueprint-ui-config-initializer/lib/prettyprint.js‎

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import rdfEnv from './rdf-env.js'
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import formats from '@rdfjs-elements/formats-pretty'
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import { TurtleSerializer } from '@rdfjs-elements/formats-pretty'
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import { Readable } from 'readable-stream'
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import getStream from 'get-stream'
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const sink = new TurtleSerializer({
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prefixes: {
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'': 'http://schema.example.org/blueprint-ui-config-initializer/',
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rdf: 'http://www.w3.org/1999/02/22-rdf-syntax-ns#',
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rdfs: 'http://www.w3.org/2000/01/rdf-schema#',
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sh: 'http://www.w3.org/ns/shacl#',
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blueprintMetaShapes: 'https://ld.flux.zazuko.com/shapes/metadata/',
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blueprintMetaLink: 'https://ld.flux.zazuko.com/link/metadata/',
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blueprint: 'https://flux.described.at/',
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}
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})
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async function prettify(uglyTurtle) {
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if (uglyTurtle === undefined) {
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return undefined;
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}
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const inQuadStream = formats.parsers.import('text/turtle', Readable.from(uglyTurtle))
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const dataset = await rdfEnv.dataset().import(inQuadStream)
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const outStream = sink.import(dataset.toStream())
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const result = await getStream(outStream)
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return result
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}
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export {
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prettify
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}

‎vis/blueprint-ui-config-initializer/lib/queries-refactored/construct-candidate-classes.rq‎

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PREFIX schema: <http://schema.org/>
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PREFIX : <http://schema.example.org/blueprint-ui-config-initializer/>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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PREFIX owl: <http://www.w3.org/2002/07/owl#>
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CONSTRUCT {
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?cls a :Class ;
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:label ?localName ;
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:icon ?icon;
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:colorIndex ?colorIndex ;
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:searchPrio 1 .
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}
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WHERE {
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{
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SELECT DISTINCT ?cls ?localName ?icon ?colorIndex WHERE {
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?subject a ?cls .
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bind(replace(str(?cls), "^.*[/#]", "") AS ?localName)
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# Assigning an icon and color to the type
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BIND(IF(STR(?cls) = "http://schema.org/Person", "fas fa-user", "fas fa-circle") AS ?icon)
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BIND(IF(STR(?cls) = "http://schema.org/Person", 2, 1) AS ?colorIndex)
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# Filtering out well-known types that are less relevant
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MINUS {
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VALUES ?cls {
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schema:Property
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schema:URL
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schema:Thing
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schema:DefinedTerm
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# -----------------------------------
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rdf:Property
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owl:TransitiveProperty
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owl:SymmetricProperty
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rdf:List
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rdfs:Class
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rdfs:Datatype
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rdfs:ContainerMembershipProperty
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# -----------------------------------
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<https://flux.described.at/Detail>
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<https://flux.described.at/Link>
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<https://flux.described.at/CompositionToNodeLink>
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<https://flux.described.at/Aggregate>
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<https://flux.described.at/Composition>
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<https://flux.described.at/Hierarchy>
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<https://flux.described.at/Container>
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<https://flux.described.at/ConnectionPoint>
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# -----------------------------------
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<https://ld.flux.zazuko.com/shapes/metadata/ClassShape>
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<https://ld.flux.zazuko.com/shapes/metadata/ClassMetadataShape>
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<https://ld.flux.zazuko.com/shapes/metadata/ClassDetailShape>
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}
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}
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}
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ORDER BY ?localName ?cls
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}
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}

‎vis/blueprint-ui-config-initializer/lib/queries-refactored/construct-candidate-details.rq‎

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PREFIX schema: <http://schema.org/>
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PREFIX : <http://schema.example.org/blueprint-ui-config-initializer/>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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CONSTRUCT {
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?cls :detailGroup ?detailGroup .
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?detailGroup :label "Info" ;
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:order 0 ;
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:detail [
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:label ?label ;
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:path ?property ;
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:order 0
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] .
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}
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WHERE {
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{
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SELECT DISTINCT ?detailGroup ?cls ?label ?property WHERE {
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?subject a ?cls .
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?subject ?property ?object .
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FILTER(isLiteral(?object))
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# Only consider schema.org types and properties
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#FILTER (?cls IN (schema:Person, schema:Organization, schema:Event))
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#FILTER (?property IN (schema:familyName, schema:givenName, schema:jobTitle))
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# Bind the local names and detail group URIs
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BIND(REPLACE(STR(?property), "^.*[/#]", "") AS ?propertyLocalName)
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BIND(REPLACE(STR(?cls), "^.*[/#]", "") AS ?clsLocalName)
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BIND(CONCAT(?clsLocalName, "-info-", ENCODE_FOR_URI(STR(?cls))) AS ?localDetailGroupId)
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BIND(IRI(CONCAT("http://data.example.org/blueprint-ui-config-initializer/detailgroup/", ?localDetailGroupId)) AS ?detailGroup)
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# Bind the label
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OPTIONAL {
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?property rdfs:label ?propertyLabel
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}
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# Otherwise, generate a label from the property's local name
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BIND(COALESCE(?propertyLabel, ?propertyLocalName) AS ?label)
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}
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ORDER BY ?cls ?label
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}
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}

‎vis/blueprint-ui-config-initializer/lib/queries-refactored/construct-candidate-links.rq‎

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PREFIX schema: <http://schema.org/>
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PREFIX : <http://schema.example.org/blueprint-ui-config-initializer/>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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CONSTRUCT {
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?cls :link [
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:label ?label ;
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:to ?linkType ;
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:path ?property
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]
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}
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WHERE {
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{
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SELECT DISTINCT ?cls ?property ?linkType ?label WHERE {
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?subject a ?cls .
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?subject ?property ?object .
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?object a ?linkType .
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# Bind local names for better readability
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BIND(REPLACE(STR(?cls), "^.*[/#]", "") AS ?clsLocalName)
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BIND(REPLACE(STR(?property), "^.*[/#]", "") AS ?propertyLocalName)
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# Filter to only include schema.org types and properties
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# FILTER (?cls IN (schema:Person, schema:Organization, schema:Event))
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# FILTER (?linkType IN (schema:Person, schema:Organization, schema:Event))
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# Optional: Get labels for properties if available
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OPTIONAL {
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?property rdfs:label ?propertyLabel
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}
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# Otherwise, generate a label from the property's local name
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BIND(COALESCE(?propertyLabel, ?propertyLocalName) AS ?label)
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}
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order by ?clsLocalName ?cls ?propertyLocalName ?property ?linkType
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}
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}

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