larsgw/Attempts at running ShEx validation.md

## Attempts at running ShEx validation.md

      
    Raw
  

              Attempts at running ShEx validation.md
            
          
    Validating linked data from the Library of Identification resources (https://doi.org/10.5281/zenodo.15552611).
shex.js

node ./tools/validate-shex.js
shex-validate -x docs/linked-data/shape.shex -d data.nq -n "https://purl.org/identification-resources/catalog/B1"

rudof

rudof shex-validate -s docs/linked-data/shape_rudof.shex -n "<https://purl.org/identification-resources/catalog/B1>" -t nquads -r json data.nq

jena-shex

node ./tools/validate-shex.groovy


## shape_rudof.shex
PREFIX ac: <http://rs.tdwg.org/ac/terms/>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
PREFIX dwciri: <http://rs.tdwg.org/dwc/iri/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX schema: <https://schema.org/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

start=@<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#work>

<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#work> IRI CLOSED {
  a [bibo:BookSection bibo:AcademicArticle bibo:Website bibo:Book];
  dcterms:title rdf:langString+;
  dcterms:language [<http://id.loc.gov/vocabulary/iso639-1/~>]+;
  dcterms:hasPart [<https://purl.org/identification-resources/catalog/~>]*;
  dcterms:isPartOf [<https://purl.org/identification-resources/catalog/~>]*;
  dcterms:references [<https://purl.org/identification-resources/catalog/~>]*;
  dcterms:isReferencedBy [<https://purl.org/identification-resources/catalog/~>]*;
  dcterms:isVersionOf [<https://purl.org/identification-resources/catalog/~>]*;
  dcterms:hasPart [<https://purl.org/identification-resources/resource/~>]*;
  bibo:annotates [<https://purl.org/identification-resources/catalog/~>]*;
  bibo:cites [<https://purl.org/identification-resources/catalog/~>]*;
  bibo:citedBy [<https://purl.org/identification-resources/catalog/~>]*;
  bibo:translationOf [<https://purl.org/identification-resources/catalog/~>]*;

  dcterms:creator [<https://purl.org/identification-resources/author/~>]*;
  dcterms:issued xsd:date OR xsd:gYearMonth OR xsd:gYear OR LITERAL?;
  dcterms:publisher [<https://purl.org/identification-resources/publisher/~>]*;
  dcterms:rights LITERAL*;
  dcterms:rights [<https://spdx.org/licenses/~>]*;

  schema:url IRI?;
  schema:encoding @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#file>*;
  schema:archivedAt IRI*;

  bibo:authorList @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#authors>?;
  bibo:handle IRI?;
  bibo:issn LITERAL?;
  bibo:isbn LITERAL*;
  bibo:isbn10 LITERAL*;
  bibo:isbn13 LITERAL*;
  bibo:uri [<http://www.wikidata.org/entity/~>]?;
  bibo:doi LITERAL?;
  bibo:volume LITERAL?;
  bibo:issue LITERAL?;
  bibo:pages LITERAL?;
  bibo:pageStart LITERAL?;
  bibo:pageEnd LITERAL?;
  bibo:numPages xsd:integer?;
  bibo:edition LITERAL?
}

<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#authors> BNODE CLOSED {
  rdf:first [<https://purl.org/identification-resources/author/~>];
  rdf:rest [rdf:nil] OR @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#authors>
}

<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#author> IRI CLOSED {
  a [foaf:Person];
  foaf:name LITERAL;
  owl:sameAs [<http://www.wikidata.org/entity/~>]?
}

<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#publisher> IRI CLOSED {
  a [foaf:Organization];
  foaf:name LITERAL;
  owl:sameAs [<http://www.wikidata.org/entity/~>]?
}

<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#file> BNODE CLOSED {
  a [schema:MediaObject];
  schema:contentUrl IRI
}

<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#resource> IRI CLOSED {
  a [bibo:DocumentPart];
  dcterms:isPartOf [<https://purl.org/identification-resources/catalog/~>];
  dcterms:type [
    <http://purl.org/dc/dcmitype/Software>
    <http://purl.org/dc/dcmitype/Text>
    <http://purl.org/dc/dcmitype/Collection>
  ];
  dcterms:spatial @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#place>*;
  dcterms:subject @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#scientificName>*;

  ac:subtype [<http://rs.tdwg.org/acsubtype/values/IdentificationKey>]?;
  ( ac:taxonCoverage @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#taxon> | ac:taxonCoverage [<https://gbif.org/species/~>]? );
  ac:tag LITERAL*;
  ac:taxonCount xsd:integer?;
  ac:subjectPart [<http://rs.tdwg.org/acpart/values/~>]*;
  ac:subjectPartLiteral LITERAL*;

  dwc:taxonID @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#taxon>*;
  dwciri:lifeStage [<http://rs.gbif.org/vocabulary/gbif/life_stage/~>]*;
  dwciri:sex [<http://rs.gbif.org/vocabulary/gbif/sex/~>]*;
  dwc:caste LITERAL*;

  dcterms:title rdf:langString*;
  dcterms:language [<http://id.loc.gov/vocabulary/iso639-1/~>]*;
  dcterms:hasPart [<https://purl.org/identification-resources/resource/~>]*;
  dcterms:isPartOf [<https://purl.org/identification-resources/resource/~>]*;
  dcterms:references [<https://purl.org/identification-resources/resource/~>]*;
  dcterms:isReferencedBy [<https://purl.org/identification-resources/resource/~>]*;
  dcterms:isVersionOf [<https://purl.org/identification-resources/resource/~>]*;
  dcterms:hasPart [<https://purl.org/identification-resources/resource/~>]*;
  bibo:annotates [<https://purl.org/identification-resources/resource/~>]*;
  bibo:cites [<https://purl.org/identification-resources/resource/~>]*;
  bibo:citedBy [<https://purl.org/identification-resources/resource/~>]*;
  bibo:translationOf [<https://purl.org/identification-resources/resource/~>]*;

  dcterms:creator [<https://purl.org/identification-resources/author/~>]*;
  dcterms:issued xsd:date OR xsd:gYearMonth OR xsd:gYear OR LITERAL?;
  dcterms:publisher [<https://purl.org/identification-resources/publisher/~>]*;
  dcterms:rights LITERAL*;
  dcterms:rights [<https://spdx.org/licenses/~>]*;

  schema:url IRI?;
  schema:encoding @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#file>*;
  schema:archivedAt IRI*;

  bibo:authorList @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#authors>?;
  bibo:handle IRI?;
  bibo:issn LITERAL?;
  bibo:isbn LITERAL*;
  bibo:isbn10 LITERAL*;
  bibo:isbn13 LITERAL*;
  bibo:uri [<http://www.wikidata.org/entity/~>]?;
  bibo:doi LITERAL?;
  bibo:volume LITERAL?;
  bibo:issue LITERAL?;
  bibo:pages LITERAL?;
  bibo:pageStart LITERAL?;
  bibo:pageEnd LITERAL?;
  bibo:numPages xsd:integer?;
  bibo:edition LITERAL?
}

<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#taxon> IRI /^https:\/\/purl\.org\/identification-resources\/taxon\/T[1-9][0-9]*$/ CLOSED {
  a [dwc:Taxon];
  dwc:scientificname LITERAL?;
  dwc:taxonRank [<http://rs.gbif.org/vocabulary/gbif/rank/~>]?;
  dwc:parentNameUsageID @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#taxon>?;
  owl:sameAs [<http://www.wikidata.org/entity/~>]?;
  owl:sameAs [<https://gbif.org/species/~>]?
}

<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#place> IRI /^https:\/\/purl\.org\/identification-resources\/place\/G[1-9][0-9]*$/ CLOSED {
  a [dcterms:Location];
  dcterms:title LITERAL;
  owl:sameAs [<http://www.wikidata.org/entity/~>]?
}

<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#scientificName> IRI /^https:\/\/purl\.org\/identification-resources\/resource\/B[1-9][0-9]*:[1-9][0-9]*#B[1-9][0-9]*:[1-9][0-9]*:[1-9][0-9]*$/ CLOSED {
  a [dwc:Taxon];
  dwc:scientificName LITERAL;
  dwc:scientificNameAuthorship LITERAL?;
  dwc:genericName LITERAL?;
  dwc:infragenericEpithet LITERAL?;
  dwc:specificEpithet LITERAL?;
  dwc:infraspecificEpithet LITERAL?;
  dwc:taxonRemarks LITERAL?;
  dwc:verbatimIdentification LITERAL;
  (
    dwc:taxonRank [<http://rs.gbif.org/vocabulary/gbif/rank/~>]
    |
    dwc:taxonRank LITERAL
  );
  dwc:taxonomicStatus [<http://rs.gbif.org/vocabulary/gbif/taxonomicStatus/~>];
  dwc:acceptedNameUsageID @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#scientificName>?;
  dwc:parentNameUsageID @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#scientificName>?;

  dwc:taxonID [<https://gbif.org/species/~>]?;
  dwc:taxonID [<https://www.checklistbank.org/dataset/309120/taxon/~>]?
}

## validate-shex.groovy
@Grab(group='io.github.egonw.bacting', module='managers-rdf', version='0.3.2')

import org.apache.jena.shex.ShexStatus

rdf = new net.bioclipse.managers.RDFManager("./");
store = rdf.createInMemoryStore(true)
store = rdf.importFile(store, "data.ttl", "TURTLE")
report = rdf.validateAllOfType(
  store,
  "docs/linked-data/shape.shex",
  "file:///home/loir/catalog/docs/linked-data/work",
  "http://purl.org/ontology/bibo/BookSection"
)

total = 0
fails = 0

report.forEachReport { reportEntry ->
  total++
  switch (reportEntry.status) {
    case ShexStatus.nonconformant :
      fails++
      System.err.println "failed on ${reportEntry.focus}, reason: \"${reportEntry.reason}\""
  }
}

System.err.println "success for ${total - fails}/${total} nodes"

if (fails > 0) {
  System.exit(1)
}

## validate-shex.js
const { promises: fs } = require('fs')
const path = require('path')

const ShExParser = require('@shexjs/parser')
const ShExTerm = require('@shexjs/term')
const { ctor: RdfJsDb } = require('@shexjs/neighborhood-rdfjs')
const { ShExValidator } = require('@shexjs/validator')
const { Parser: N3Parser, Store: N3Store } = require('n3')

const BASE = 'http://raw.githubusercontent.com/identification-resources/main/docs/linked-data/'
const SHAPE_MAP = {
  // TODO
  'http://purl.org/ontology/bibo/BookSection': 'work',
  'http://purl.org/ontology/bibo/AcademicArticle': 'work',
  'http://purl.org/ontology/bibo/Website': 'work',
  'http://purl.org/ontology/bibo/Book': 'work',
  // 'http://xmlns.com/foaf/0.1/Person': 'author',
  // 'http://xmlns.com/foaf/0.1/Organization': 'publisher'
}

async function parseTurtle (file) {
  return new Promise(function (resolve, reject) {
    const store = new N3Store()
    new N3Parser().parse(file, function (error, quad, _prefixes) {
      if (error) {
        reject(error)
      } else if (quad) {
        store.addQuad(quad)
      } else {
        resolve(store)
      }
    })
  })
}

class DebugTracker {
  depth = 0;

  _log (...args) {
    console.error('  '.repeat(this.depth), ...args)
  }

  recurse (_rec) { }
  known (_res) { }
  shapeDecl (f, s) {
    // this._log(f.id || f.value, JSON.stringify(s))
  }

  enter (_term, _shapeLabel) {
    this._log('{', _term.id || _term.value, _shapeLabel.slice(BASE.length))
    ++this.depth
  }
  exit (_term, _shapeLabel, _res) {
    --this.depth
    this._log('}')
  }
}

async function main () {
  const shexc = await fs.readFile(path.join(__dirname, '../docs/linked-data/shape.shex'), 'utf8')
  const turtle = await fs.readFile(path.join(__dirname, '../data.ttl'), 'utf8') // TODO

  const schema = ShExParser.construct(BASE).parse(shexc)
  const store = await parseTurtle(turtle)
  const validator = new ShExValidator(schema, RdfJsDb(store))

  const shapeMap = []
  for (const quad of store.readQuads(null, 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', null, null)) {
    const type = quad.object.id
    if (type in SHAPE_MAP) {
      shapeMap.push({
        node: quad.subject.id,
        shape: BASE + SHAPE_MAP[type]
      })
    }
  }

  // TODO
  {
    const _old = validator.validateShapeExpr
    validator.validateShapeExpr = function (focus, shapeExpr, ctx) {
      ctx.tracker.shapeDecl(focus, shapeExpr)
      return _old.call(this, focus, shapeExpr, ctx)
    }
  }
  const tracker = new DebugTracker()

  let passed = 0
  for (const { node, shape } of shapeMap) {
    console.error('==', node, '==') // TODO
    console.time('validation')
    const report = validator.validateNodeShapePair(ShExTerm.ld2RdfJsTerm(node), shape, tracker)
    console.timeEnd('validation')
    if ('errors' in report) {
      console.error(require('util').inspect(report.errors, { depth: Infinity, colors: true }))
    } else {
      passed++
    }
  }

  console.error(`${passed}/${shapeMap.length} nodes passed`)
  process.exit(passed === shapeMap.length ? 0 : 1)
}

main().catch(console.error)
	PREFIX ac: <http://rs.tdwg.org/ac/terms/>
	PREFIX bibo: <http://purl.org/ontology/bibo/>
	PREFIX dcterms: <http://purl.org/dc/terms/>
	PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
	PREFIX dwciri: <http://rs.tdwg.org/dwc/iri/>
	PREFIX foaf: <http://xmlns.com/foaf/0.1/>
	PREFIX owl: <http://www.w3.org/2002/07/owl#>
	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
	PREFIX schema: <https://schema.org/>
	PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

	start=@<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#work>

	<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#work> IRI CLOSED {
	a [bibo:BookSection bibo:AcademicArticle bibo:Website bibo:Book];
	dcterms:title rdf:langString+;
	dcterms:language [<http://id.loc.gov/vocabulary/iso639-1/~>]+;
	dcterms:hasPart [<https://purl.org/identification-resources/catalog/~>]*;
	dcterms:isPartOf [<https://purl.org/identification-resources/catalog/~>]*;
	dcterms:references [<https://purl.org/identification-resources/catalog/~>]*;
	dcterms:isReferencedBy [<https://purl.org/identification-resources/catalog/~>]*;
	dcterms:isVersionOf [<https://purl.org/identification-resources/catalog/~>]*;
	dcterms:hasPart [<https://purl.org/identification-resources/resource/~>]*;
	bibo:annotates [<https://purl.org/identification-resources/catalog/~>]*;
	bibo:cites [<https://purl.org/identification-resources/catalog/~>]*;
	bibo:citedBy [<https://purl.org/identification-resources/catalog/~>]*;
	bibo:translationOf [<https://purl.org/identification-resources/catalog/~>]*;

	dcterms:creator [<https://purl.org/identification-resources/author/~>]*;
	dcterms:issued xsd:date OR xsd:gYearMonth OR xsd:gYear OR LITERAL?;
	dcterms:publisher [<https://purl.org/identification-resources/publisher/~>]*;
	dcterms:rights LITERAL*;
	dcterms:rights [<https://spdx.org/licenses/~>]*;

	schema:url IRI?;
	schema:encoding @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#file>*;
	schema:archivedAt IRI*;

	bibo:authorList @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#authors>?;
	bibo:handle IRI?;
	bibo:issn LITERAL?;
	bibo:isbn LITERAL*;
	bibo:isbn10 LITERAL*;
	bibo:isbn13 LITERAL*;
	bibo:uri [<http://www.wikidata.org/entity/~>]?;
	bibo:doi LITERAL?;
	bibo:volume LITERAL?;
	bibo:issue LITERAL?;
	bibo:pages LITERAL?;
	bibo:pageStart LITERAL?;
	bibo:pageEnd LITERAL?;
	bibo:numPages xsd:integer?;
	bibo:edition LITERAL?
	}

	<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#authors> BNODE CLOSED {
	rdf:first [<https://purl.org/identification-resources/author/~>];
	rdf:rest [rdf:nil] OR @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#authors>
	}

	<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#author> IRI CLOSED {
	a [foaf:Person];
	foaf:name LITERAL;
	owl:sameAs [<http://www.wikidata.org/entity/~>]?
	}

	<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#publisher> IRI CLOSED {
	a [foaf:Organization];
	foaf:name LITERAL;
	owl:sameAs [<http://www.wikidata.org/entity/~>]?
	}

	<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#file> BNODE CLOSED {
	a [schema:MediaObject];
	schema:contentUrl IRI
	}

	<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#resource> IRI CLOSED {
	a [bibo:DocumentPart];
	dcterms:isPartOf [<https://purl.org/identification-resources/catalog/~>];
	dcterms:type [
	<http://purl.org/dc/dcmitype/Software>
	<http://purl.org/dc/dcmitype/Text>
	<http://purl.org/dc/dcmitype/Collection>
	];
	dcterms:spatial @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#place>*;
	dcterms:subject @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#scientificName>*;

	ac:subtype [<http://rs.tdwg.org/acsubtype/values/IdentificationKey>]?;
	( ac:taxonCoverage @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#taxon> \| ac:taxonCoverage [<https://gbif.org/species/~>]? );
	ac:tag LITERAL*;
	ac:taxonCount xsd:integer?;
	ac:subjectPart [<http://rs.tdwg.org/acpart/values/~>]*;
	ac:subjectPartLiteral LITERAL*;

	dwc:taxonID @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#taxon>*;
	dwciri:lifeStage [<http://rs.gbif.org/vocabulary/gbif/life_stage/~>]*;
	dwciri:sex [<http://rs.gbif.org/vocabulary/gbif/sex/~>]*;
	dwc:caste LITERAL*;

	dcterms:title rdf:langString*;
	dcterms:language [<http://id.loc.gov/vocabulary/iso639-1/~>]*;
	dcterms:hasPart [<https://purl.org/identification-resources/resource/~>]*;
	dcterms:isPartOf [<https://purl.org/identification-resources/resource/~>]*;
	dcterms:references [<https://purl.org/identification-resources/resource/~>]*;
	dcterms:isReferencedBy [<https://purl.org/identification-resources/resource/~>]*;
	dcterms:isVersionOf [<https://purl.org/identification-resources/resource/~>]*;
	dcterms:hasPart [<https://purl.org/identification-resources/resource/~>]*;
	bibo:annotates [<https://purl.org/identification-resources/resource/~>]*;
	bibo:cites [<https://purl.org/identification-resources/resource/~>]*;
	bibo:citedBy [<https://purl.org/identification-resources/resource/~>]*;
	bibo:translationOf [<https://purl.org/identification-resources/resource/~>]*;

	dcterms:creator [<https://purl.org/identification-resources/author/~>]*;
	dcterms:issued xsd:date OR xsd:gYearMonth OR xsd:gYear OR LITERAL?;
	dcterms:publisher [<https://purl.org/identification-resources/publisher/~>]*;
	dcterms:rights LITERAL*;
	dcterms:rights [<https://spdx.org/licenses/~>]*;

	schema:url IRI?;
	schema:encoding @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#file>*;
	schema:archivedAt IRI*;

	bibo:authorList @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#authors>?;
	bibo:handle IRI?;
	bibo:issn LITERAL?;
	bibo:isbn LITERAL*;
	bibo:isbn10 LITERAL*;
	bibo:isbn13 LITERAL*;
	bibo:uri [<http://www.wikidata.org/entity/~>]?;
	bibo:doi LITERAL?;
	bibo:volume LITERAL?;
	bibo:issue LITERAL?;
	bibo:pages LITERAL?;
	bibo:pageStart LITERAL?;
	bibo:pageEnd LITERAL?;
	bibo:numPages xsd:integer?;
	bibo:edition LITERAL?
	}

	<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#taxon> IRI /^https:\/\/purl\.org\/identification-resources\/taxon\/T[1-9][0-9]*$/ CLOSED {
	a [dwc:Taxon];
	dwc:scientificname LITERAL?;
	dwc:taxonRank [<http://rs.gbif.org/vocabulary/gbif/rank/~>]?;
	dwc:parentNameUsageID @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#taxon>?;
	owl:sameAs [<http://www.wikidata.org/entity/~>]?;
	owl:sameAs [<https://gbif.org/species/~>]?
	}

	<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#place> IRI /^https:\/\/purl\.org\/identification-resources\/place\/G[1-9][0-9]*$/ CLOSED {
	a [dcterms:Location];
	dcterms:title LITERAL;
	owl:sameAs [<http://www.wikidata.org/entity/~>]?
	}

	<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#scientificName> IRI /^https:\/\/purl\.org\/identification-resources\/resource\/B[1-9][0-9]:[1-9][0-9]#B[1-9][0-9]:[1-9][0-9]:[1-9][0-9]*$/ CLOSED {
	a [dwc:Taxon];
	dwc:scientificName LITERAL;
	dwc:scientificNameAuthorship LITERAL?;
	dwc:genericName LITERAL?;
	dwc:infragenericEpithet LITERAL?;
	dwc:specificEpithet LITERAL?;
	dwc:infraspecificEpithet LITERAL?;
	dwc:taxonRemarks LITERAL?;
	dwc:verbatimIdentification LITERAL;
	(
	dwc:taxonRank [<http://rs.gbif.org/vocabulary/gbif/rank/~>]
	\|
	dwc:taxonRank LITERAL
	);
	dwc:taxonomicStatus [<http://rs.gbif.org/vocabulary/gbif/taxonomicStatus/~>];
	dwc:acceptedNameUsageID @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#scientificName>?;
	dwc:parentNameUsageID @<https://github.com/identification-resources/catalog/blob/main/docs/linked-data/shape.shex#scientificName>?;

	dwc:taxonID [<https://gbif.org/species/~>]?;
	dwc:taxonID [<https://www.checklistbank.org/dataset/309120/taxon/~>]?
	}
	@Grab(group='io.github.egonw.bacting', module='managers-rdf', version='0.3.2')

	import org.apache.jena.shex.ShexStatus

	rdf = new net.bioclipse.managers.RDFManager("./");
	store = rdf.createInMemoryStore(true)
	store = rdf.importFile(store, "data.ttl", "TURTLE")
	report = rdf.validateAllOfType(
	store,
	"docs/linked-data/shape.shex",
	"file:///home/loir/catalog/docs/linked-data/work",
	"http://purl.org/ontology/bibo/BookSection"
	)

	total = 0
	fails = 0

	report.forEachReport { reportEntry ->
	total++
	switch (reportEntry.status) {
	case ShexStatus.nonconformant :
	fails++
	System.err.println "failed on ${reportEntry.focus}, reason: \"${reportEntry.reason}\""
	}
	}

	System.err.println "success for ${total - fails}/${total} nodes"

	if (fails > 0) {
	System.exit(1)
	}
	const { promises: fs } = require('fs')
	const path = require('path')

	const ShExParser = require('@shexjs/parser')
	const ShExTerm = require('@shexjs/term')
	const { ctor: RdfJsDb } = require('@shexjs/neighborhood-rdfjs')
	const { ShExValidator } = require('@shexjs/validator')
	const { Parser: N3Parser, Store: N3Store } = require('n3')

	const BASE = 'http://raw.githubusercontent.com/identification-resources/main/docs/linked-data/'
	const SHAPE_MAP = {
	// TODO
	'http://purl.org/ontology/bibo/BookSection': 'work',
	'http://purl.org/ontology/bibo/AcademicArticle': 'work',
	'http://purl.org/ontology/bibo/Website': 'work',
	'http://purl.org/ontology/bibo/Book': 'work',
	// 'http://xmlns.com/foaf/0.1/Person': 'author',
	// 'http://xmlns.com/foaf/0.1/Organization': 'publisher'
	}

	async function parseTurtle (file) {
	return new Promise(function (resolve, reject) {
	const store = new N3Store()
	new N3Parser().parse(file, function (error, quad, _prefixes) {
	if (error) {
	reject(error)
	} else if (quad) {
	store.addQuad(quad)
	} else {
	resolve(store)
	}
	})
	})
	}

	class DebugTracker {
	depth = 0;

	_log (...args) {
	console.error(' '.repeat(this.depth), ...args)
	}

	recurse (_rec) { }
	known (_res) { }
	shapeDecl (f, s) {
	// this._log(f.id \|\| f.value, JSON.stringify(s))
	}

	enter (_term, _shapeLabel) {
	this._log('{', _term.id \|\| _term.value, _shapeLabel.slice(BASE.length))
	++this.depth
	}
	exit (_term, _shapeLabel, _res) {
	--this.depth
	this._log('}')
	}
	}

	async function main () {
	const shexc = await fs.readFile(path.join(__dirname, '../docs/linked-data/shape.shex'), 'utf8')
	const turtle = await fs.readFile(path.join(__dirname, '../data.ttl'), 'utf8') // TODO

	const schema = ShExParser.construct(BASE).parse(shexc)
	const store = await parseTurtle(turtle)
	const validator = new ShExValidator(schema, RdfJsDb(store))

	const shapeMap = []
	for (const quad of store.readQuads(null, 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', null, null)) {
	const type = quad.object.id
	if (type in SHAPE_MAP) {
	shapeMap.push({
	node: quad.subject.id,
	shape: BASE + SHAPE_MAP[type]
	})
	}
	}

	// TODO
	{
	const _old = validator.validateShapeExpr
	validator.validateShapeExpr = function (focus, shapeExpr, ctx) {
	ctx.tracker.shapeDecl(focus, shapeExpr)
	return _old.call(this, focus, shapeExpr, ctx)
	}
	}
	const tracker = new DebugTracker()

	let passed = 0
	for (const { node, shape } of shapeMap) {
	console.error('==', node, '==') // TODO
	console.time('validation')
	const report = validator.validateNodeShapePair(ShExTerm.ld2RdfJsTerm(node), shape, tracker)
	console.timeEnd('validation')
	if ('errors' in report) {
	console.error(require('util').inspect(report.errors, { depth: Infinity, colors: true }))
	} else {
	passed++
	}
	}

	console.error(`${passed}/${shapeMap.length} nodes passed`)
	process.exit(passed === shapeMap.length ? 0 : 1)
	}

	main().catch(console.error)