@larsgw/formica 0.8.4 → 0.8.6

package/lib/bin/generate-linked-data.js

@@ -1,16 +1,5 @@
 #!/usr/bin/env node
 "use strict";
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -53,55 +42,19 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
 };
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g = Object.create((typeof Iterator === "function" ? Iterator : Object).prototype);
-    return g.next = verb(0), g["throw"] = verb(1), g["return"] = verb(2), typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (g && (g = 0, op[0] && (_ = 0)), _) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
-    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
-        if (ar || !(i in from)) {
-            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
-            ar[i] = from[i];
-        }
-    }
-    return to.concat(ar || Array.prototype.slice.call(from));
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-var fs_1 = require("fs");
-var path = __importStar(require("path"));
-var util = __importStar(require("util"));
-var jsonld = __importStar(require("jsonld"));
-var N3 = __importStar(require("n3"));
-var index_1 = require("../index");
-var resource_1 = require("../resources/resource");
-var csv_1 = require("../csv");
-var SHEETS = ['catalog', 'authors', 'places', 'publishers', 'taxa'];
-var PREFIX = 'https://purl.org/identification-resources/';
-var HANDLE_PREFIX = 'https://hdl.handle.net/';
-var SCOPES = {
+const fs_1 = require("fs");
+const path = __importStar(require("path"));
+const util = __importStar(require("util"));
+const jsonld = __importStar(require("jsonld"));
+const N3 = __importStar(require("n3"));
+const index_1 = require("../index");
+const resource_1 = require("../resources/resource");
+const csv_1 = require("../csv");
+const SHEETS = ['catalog', 'authors', 'places', 'publishers', 'taxa'];
+const PREFIX = 'https://purl.org/identification-resources/';
+const HANDLE_PREFIX = 'https://hdl.handle.net/';
+const SCOPES = {
     // animal life stage
     'adults': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/adult'],
     'pupae': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/pupa'],
@@ -126,6 +79,7 @@ var SCOPES = {
     // sex
     'females': ['dwciri:sex', 'http://rs.gbif.org/vocabulary/gbif/sex/female'],
     'males': ['dwciri:sex', 'http://rs.gbif.org/vocabulary/gbif/sex/male'],
+    'male': ['dwciri:sex', 'http://rs.gbif.org/vocabulary/gbif/sex/male'],
     // caste
     'queens': ['dwc:caste', 'queen'],
     'workers': ['dwc:caste', 'worker'],
@@ -143,7 +97,7 @@ var SCOPES = {
     'bones (upper jaws)': ['ac:subjectPart', 'http://rs.tdwg.org/acpart/values/p0028'],
     'bones (lower jaws)': ['ac:subjectPart', 'http://rs.tdwg.org/acpart/values/p0029'],
 };
-var PREFIXES = {
+const PREFIXES = {
     'ac': 'http://rs.tdwg.org/ac/terms/',
     'bibo': 'http://purl.org/ontology/bibo/',
     'dcterms': 'http://purl.org/dc/terms/',
@@ -155,7 +109,7 @@ var PREFIXES = {
     'schema': 'https://schema.org/',
     'xsd': 'http://www.w3.org/2001/XMLSchema#',
 };
-var DWC_FIELDS = {
+const DWC_FIELDS = {
     scientificName: 'dwc:scientificName',
     scientificNameAuthorship: 'dwc:scientificNameAuthorship',
     genericName: 'dwc:genericName',
@@ -167,30 +121,29 @@ var DWC_FIELDS = {
     taxonomicStatus: 'dwc:taxonomicStatus',
     verbatimIdentification: 'dwc:verbatimIdentification',
 };
-var GBIF_RANKS = ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species', 'subspecies'];
-var GBIF_VOCAB_RANKS = ['domain', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'superclass', 'class', 'subclass', 'supercohort', 'cohort', 'subcohort', 'superorder', 'order', 'suborder', 'infraorder', 'superfamily', 'family', 'subfamily', 'tribe', 'subtribe', 'genus', 'subgenus', 'section', 'subsection', 'series', 'subseries', 'speciesAggregate', 'species', 'subspecificAggregate', 'subspecies', 'variety', 'subvariety', 'form', 'subform', 'cultivarGroup', 'cultivar', 'strain'];
-var STATUSES = {
+const GBIF_RANKS = ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species', 'subspecies'];
+const GBIF_VOCAB_RANKS = ['domain', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'superclass', 'class', 'subclass', 'supercohort', 'cohort', 'subcohort', 'superorder', 'order', 'suborder', 'infraorder', 'superfamily', 'family', 'subfamily', 'tribe', 'subtribe', 'genus', 'subgenus', 'section', 'subsection', 'series', 'subseries', 'speciesAggregate', 'species', 'subspecificAggregate', 'subspecies', 'variety', 'subvariety', 'form', 'subform', 'cultivarGroup', 'cultivar', 'strain'];
+const STATUSES = {
     'accepted': 'http://rs.gbif.org/vocabulary/gbif/taxonomicStatus/accepted',
     'heterotypic synonym': 'http://rs.gbif.org/vocabulary/gbif/taxonomicStatus/heterotypicSynonym',
     'synonym': 'http://rs.gbif.org/vocabulary/gbif/taxonomicStatus/synonym',
 };
 function getCoveringTaxon(taxa) {
     if (taxa.length === 1 && !taxa[0].has('gbif')) {
-        return "".concat(PREFIX, "taxon/").concat(taxa[0].get('id'));
+        return `${PREFIX}taxon/${taxa[0].get('id')}`;
     }
     function getAncestors(taxon) {
         var _a;
-        var parents = ((_a = taxon.get('parent_taxa')) !== null && _a !== void 0 ? _a : []).slice(0);
+        const [...parents] = ((_a = taxon.get('parent_taxa')) !== null && _a !== void 0 ? _a : []);
         if (taxon.has('gbif')) {
             parents.push(taxon.get('gbif'));
         }
         return parents;
     }
-    var ancestors = getAncestors(taxa[0]);
-    for (var _i = 0, _a = taxa.slice(1); _i < _a.length; _i++) {
-        var taxon = _a[_i];
-        var otherAncestors = getAncestors(taxon);
-        for (var i = 0; i < ancestors.length; i++) {
+    const ancestors = getAncestors(taxa[0]);
+    for (const taxon of taxa.slice(1)) {
+        const otherAncestors = getAncestors(taxon);
+        for (let i = 0; i < ancestors.length; i++) {
             if (ancestors[i] !== otherAncestors[i]) {
                 ancestors.splice(i);
             }
@@ -199,40 +152,36 @@ function getCoveringTaxon(taxa) {
     return ancestors.length ? makeGbifUri(ancestors[ancestors.length - 1])['@id'] : null;
 }
 function mapEntities(names, entities) {
-    var result = [];
-    var _loop_1 = function (name_1) {
-        var entity = entities.find(function (entity) {
-            var values = entity.get('name');
-            return Array.isArray(values) ? values.includes(name_1) : values === name_1;
+    const result = [];
+    for (const name of names) {
+        const entity = entities.find(entity => {
+            const values = entity.get('name');
+            return Array.isArray(values) ? values.includes(name) : values === name;
         });
         if (!entity) {
-            console.error('Unmapped entity:', name_1);
-            return "continue";
+            console.error('Unmapped entity:', name);
+            continue;
         }
         result.push(entity);
-    };
-    for (var _i = 0, names_1 = names; _i < names_1.length; _i++) {
-        var name_1 = names_1[_i];
-        _loop_1(name_1);
     }
     return result;
 }
 function makeWikidataUri(qid) {
-    return { '@id': "http://www.wikidata.org/entity/".concat(qid) };
+    return { '@id': `http://www.wikidata.org/entity/${qid}` };
 }
 function makeGbifUri(id) {
-    return { '@id': "https://gbif.org/species/".concat(id) };
+    return { '@id': `https://gbif.org/species/${id}` };
 }
 function makeWorkUri(id) {
-    return { '@id': "".concat(PREFIX, "catalog/").concat(id) };
+    return { '@id': `${PREFIX}catalog/${id}` };
 }
 function makeScientificNameUri(id) {
-    var resource = id.split(':').slice(0, -1).join(':');
-    return { '@id': "".concat(PREFIX, "resource/").concat(resource, "#").concat(id) };
+    const resource = id.split(':').slice(0, -1).join(':');
+    return { '@id': `${PREFIX}resource/${resource}#${id}` };
 }
 function makeTaxonRankUri(rank) {
     if (GBIF_VOCAB_RANKS.includes(rank)) {
-        return { '@id': "http://rs.gbif.org/vocabulary/gbif/rank/".concat(rank) };
+        return { '@id': `http://rs.gbif.org/vocabulary/gbif/rank/${rank}` };
     }
     else {
         return rank;
@@ -242,8 +191,8 @@ function makeTaxonomicStatusUri(status) {
     return { '@id': STATUSES[status] };
 }
 function makeLinkedDataForAuthor(author) {
-    var node = {
-        '@id': "".concat(PREFIX, "author/").concat(author.get('id')),
+    const node = {
+        '@id': `${PREFIX}author/${author.get('id')}`,
         '@type': 'foaf:Person',
         'foaf:name': author.get('display_name')
     };
@@ -253,8 +202,8 @@ function makeLinkedDataForAuthor(author) {
     return node;
 }
 function makeLinkedDataForPlace(place) {
-    var node = {
-        '@id': "".concat(PREFIX, "place/").concat(place.get('id')),
+    const node = {
+        '@id': `${PREFIX}place/${place.get('id')}`,
         '@type': 'dcterms:Location',
         'dcterms:title': place.get('display_name'),
     };
@@ -264,8 +213,8 @@ function makeLinkedDataForPlace(place) {
     return node;
 }
 function makeLinkedDataForPublisher(publisher) {
-    var node = {
-        '@id': "".concat(PREFIX, "publisher/").concat(publisher.get('id')),
+    const node = {
+        '@id': `${PREFIX}publisher/${publisher.get('id')}`,
         '@type': 'foaf:Organization',
         'foaf:name': publisher.get('display_name')
     };
@@ -275,15 +224,15 @@ function makeLinkedDataForPublisher(publisher) {
     return node;
 }
 function makeLinkedDataForTaxon(taxon) {
-    var node = {
-        '@id': "".concat(PREFIX, "taxon/").concat(taxon.get('id')),
+    const node = {
+        '@id': `${PREFIX}taxon/${taxon.get('id')}`,
         '@type': 'dwc:Taxon',
-        'dwc:scientificName': taxon.get('display_name'),
+        'dwc:scientificName': taxon.get('name'),
     };
     if (taxon.has('rank')) {
         node['dwc:taxonRank'] = makeTaxonRankUri(taxon.get('rank'));
     }
-    var ids = [];
+    const ids = [];
     if (taxon.has('qid')) {
         ids.push(makeWikidataUri(taxon.get('qid')));
     }
@@ -297,39 +246,37 @@ function makeLinkedDataForTaxon(taxon) {
 }
 function makeLinkedDataForTaxa(files) {
     var _a;
-    var nodes = [];
-    var gbifTaxa = {};
-    for (var _i = 0, _b = files.taxa.entities; _i < _b.length; _i++) {
-        var taxon = _b[_i];
-        var node = makeLinkedDataForTaxon(taxon);
-        var ancestors = (_a = taxon.get('ancestors_gbif')) !== null && _a !== void 0 ? _a : [];
+    const nodes = [];
+    const gbifTaxa = {};
+    for (const taxon of files.taxa.entities) {
+        const node = makeLinkedDataForTaxon(taxon);
+        const ancestors = (_a = taxon.get('ancestors_gbif')) !== null && _a !== void 0 ? _a : [];
         if (ancestors.length) {
             node['dwc:parentNameUsageID'] = makeGbifUri(ancestors[ancestors.length - 1]);
         }
         else if (taxon.get('id') !== 'T141') {
-            node['dwc:parentNameUsageID'] = { '@id': "".concat(PREFIX, "taxon/T141") };
+            node['dwc:parentNameUsageID'] = { '@id': `${PREFIX}taxon/T141` };
         }
-        for (var i = 0; i < ancestors.length; i++) {
-            gbifTaxa[ancestors[i]] = __assign(__assign({}, makeGbifUri(ancestors[i])), { 'dwc:taxonRank': makeTaxonRankUri(GBIF_RANKS[i]), 'dwc:parentNameUsageID': i ? makeGbifUri(ancestors[i - 1]) : { '@id': "".concat(PREFIX, "taxon/T141") } });
+        for (let i = 0; i < ancestors.length; i++) {
+            gbifTaxa[ancestors[i]] = Object.assign(Object.assign({}, makeGbifUri(ancestors[i])), { 'dwc:taxonRank': makeTaxonRankUri(GBIF_RANKS[i]), 'dwc:parentNameUsageID': i ? makeGbifUri(ancestors[i - 1]) : { '@id': `${PREFIX}taxon/T141` } });
         }
         if (taxon.has('children_gbif')) {
-            var children = taxon.get('children_gbif');
+            const children = taxon.get('children_gbif');
             node['@reverse'] = { 'dwc:parentNameUsageID': children.map(makeGbifUri) };
-            var childRank = GBIF_RANKS[ancestors.length];
-            for (var _c = 0, children_1 = children; _c < children_1.length; _c++) {
-                var child = children_1[_c];
-                gbifTaxa[child] = __assign(__assign({}, makeGbifUri(child)), { 'dwc:taxonRank': makeTaxonRankUri(childRank) });
+            const childRank = GBIF_RANKS[ancestors.length];
+            for (const child of children) {
+                gbifTaxa[child] = Object.assign(Object.assign({}, makeGbifUri(child)), { 'dwc:taxonRank': makeTaxonRankUri(childRank) });
             }
         }
         nodes.push(node);
     }
-    nodes.push.apply(nodes, Object.values(gbifTaxa));
+    nodes.push(...Object.values(gbifTaxa));
     return nodes;
 }
 function makeLinkedDataForScientificName(name) {
-    var node = __assign(__assign({}, makeScientificNameUri(name.scientificNameID)), { '@type': 'dwc:Taxon' });
-    for (var field in DWC_FIELDS) {
-        var value = name[field];
+    const node = Object.assign(Object.assign({}, makeScientificNameUri(name.scientificNameID)), { '@type': 'dwc:Taxon' });
+    for (const field in DWC_FIELDS) {
+        const value = name[field];
         if (value) {
             node[DWC_FIELDS[field]] = value;
         }
@@ -346,12 +293,12 @@ function makeLinkedDataForScientificName(name) {
     if (name.parentNameUsageID) {
         node['dwc:parentNameUsageID'] = makeScientificNameUri(name.parentNameUsageID);
     }
-    var identifiers = [];
+    const identifiers = [];
     if (name.gbifTaxonID) {
         identifiers.push(makeGbifUri(name.gbifTaxonID));
     }
     if (name.colTaxonID) {
-        identifiers.push({ '@id': "https://www.checklistbank.org/dataset/309120/taxon/".concat(name.colTaxonID) });
+        identifiers.push({ '@id': `https://www.checklistbank.org/dataset/309120/taxon/${name.colTaxonID}` });
     }
     if (identifiers.length) {
         node['dwc:taxonID'] = identifiers;
@@ -360,9 +307,9 @@ function makeLinkedDataForScientificName(name) {
 }
 function makeLinkedDataForResource(work, files, resourceId) {
     var _a, _b, _c, _d, _e, _f, _g, _h;
-    var resource = new resource_1.WorkResource({});
+    const resource = new resource_1.WorkResource({});
     if (!resourceId) {
-        resourceId = "".concat(work.get('id'), ":0");
+        resourceId = `${work.get('id')}:0`;
     }
     if (files.resources[resourceId] && files.resources[resourceId].metadata.catalog) {
         resource.fields = files.resources[resourceId].metadata.catalog;
@@ -370,9 +317,9 @@ function makeLinkedDataForResource(work, files, resourceId) {
     if (!resource.has('language')) {
         resource.fields.language = work.get('language');
     }
-    var node = __assign(__assign({}, makeLinkedDataForWork(resource, files)), { '@id': "".concat(PREFIX, "resource/").concat(resourceId), '@type': 'bibo:DocumentPart' });
-    var types = (_b = (_a = resource.get('key_type')) !== null && _a !== void 0 ? _a : work.get('key_type')) !== null && _b !== void 0 ? _b : [];
-    if (types.includes('matrix')) {
+    const node = Object.assign(Object.assign({}, makeLinkedDataForWork(resource, files)), { '@id': `${PREFIX}resource/${resourceId}`, '@type': 'bibo:DocumentPart' });
+    const types = (_b = (_a = resource.get('key_type')) !== null && _a !== void 0 ? _a : work.get('key_type')) !== null && _b !== void 0 ? _b : [];
+    if (types.includes('matrix') || types.includes('algorithm')) {
         node['dcterms:type'] = { '@id': 'http://purl.org/dc/dcmitype/Software' };
     }
     else if (types.includes('key') || types.includes('reference') || types.includes('supplement')) {
@@ -381,32 +328,33 @@ function makeLinkedDataForResource(work, files, resourceId) {
     else if (types.includes('gallery') || types.includes('collection')) {
         node['dcterms:type'] = { '@id': 'http://purl.org/dc/dcmitype/Collection' };
     }
+    else if (types.includes('checklist')) {
+        node['dcterms:type'] = { '@id': 'http://purl.org/dc/dcmitype/Dataset' };
+    }
     if (types.includes('key') || types.includes('matrix')) {
         node['ac:subtype'] = { '@id': 'http://rs.tdwg.org/acsubtype/values/IdentificationKey' };
     }
-    var taxonNames = (_c = resource.get('taxon')) !== null && _c !== void 0 ? _c : work.get('taxon');
+    const taxonNames = (_c = resource.get('taxon')) !== null && _c !== void 0 ? _c : work.get('taxon');
     if (taxonNames) {
-        var taxa = mapEntities(taxonNames, files.taxa.entities);
-        var coveringTaxon = taxa.length ? getCoveringTaxon(taxa) : null;
+        const taxa = mapEntities(taxonNames, files.taxa.entities);
+        const coveringTaxon = taxa.length ? getCoveringTaxon(taxa) : null;
         if (coveringTaxon !== null) {
             node['ac:taxonCoverage'] = { '@id': coveringTaxon };
         }
-        node['dwc:taxonID'] = taxa.map(function (taxon) { return ({ '@id': "".concat(PREFIX, "taxon/").concat(taxon.get('id')) }); });
+        node['dwc:taxonID'] = taxa.map(taxon => ({ '@id': `${PREFIX}taxon/${taxon.get('id')}` }));
     }
-    var scopes = (_d = resource.get('scope')) !== null && _d !== void 0 ? _d : work.get('scope');
+    const scopes = (_d = resource.get('scope')) !== null && _d !== void 0 ? _d : work.get('scope');
     if (scopes) {
-        for (var _i = 0, _j = scopes; _i < _j.length; _i++) {
-            var scope = _j[_i];
+        for (const scope of scopes) {
             if (!SCOPES[scope]) {
                 console.error('Unmapped scope:', scope);
                 continue;
             }
-            var _k = SCOPES[scope], property = _k[0], values = _k.slice(1);
+            const [property, ...values] = SCOPES[scope];
             if (!Array.isArray(node[property])) {
                 node[property] = [];
             }
-            for (var _l = 0, values_1 = values; _l < values_1.length; _l++) {
-                var value = values_1[_l];
+            for (const value of values) {
                 if (value.startsWith('http')) {
                     node[property].push({ '@id': value });
                 }
@@ -416,34 +364,33 @@ function makeLinkedDataForResource(work, files, resourceId) {
             }
         }
     }
-    var region = (_e = resource.get('region')) !== null && _e !== void 0 ? _e : work.get('region');
+    const region = (_e = resource.get('region')) !== null && _e !== void 0 ? _e : work.get('region');
     if (region) {
-        var places = mapEntities(region, files.places.entities).map(function (place) { return ({ '@id': "".concat(PREFIX, "place/").concat(place.get('id')) }); });
+        const places = mapEntities(region, files.places.entities).map(place => ({ '@id': `${PREFIX}place/${place.get('id')}` }));
         node['dcterms:spatial'] = places;
     }
-    var tags = [];
-    var taxonScopes = (_f = resource.get('taxon_scope')) !== null && _f !== void 0 ? _f : work.get('taxon_scope');
+    const tags = [];
+    const taxonScopes = (_f = resource.get('taxon_scope')) !== null && _f !== void 0 ? _f : work.get('taxon_scope');
     if (taxonScopes) {
-        tags.push.apply(tags, taxonScopes);
+        tags.push(...taxonScopes);
     }
     else if (((_g = resource.get('complete')) !== null && _g !== void 0 ? _g : work.get('complete')) === 'FALSE') {
         tags.push('not intended to be complete');
     }
-    var targetTaxa = (_h = resource.get('target_taxa')) !== null && _h !== void 0 ? _h : work.get('target_taxa');
+    const targetTaxa = (_h = resource.get('target_taxa')) !== null && _h !== void 0 ? _h : work.get('target_taxa');
     if (targetTaxa) {
-        var first = targetTaxa.slice(0, -1).map(function (rank) { return rank + ','; });
-        var last = targetTaxa[targetTaxa.length - 1];
-        var list = first.length ? first.join('') + ' or ' + last : last;
-        tags.push("for identification to ".concat(list));
+        const first = targetTaxa.slice(0, -1).map(rank => rank + ',');
+        const last = targetTaxa[targetTaxa.length - 1];
+        const list = first.length ? first.join('') + ' or ' + last : last;
+        tags.push(`for identification to ${list}`);
     }
     if (tags.length) {
         node['ac:tag'] = tags;
     }
     if (files.resources[resourceId].taxa) {
-        var leafs = new Set(files.resources[resourceId].taxa.map(function (taxon) { return taxon.scientificNameID; }));
-        var taxa = [];
-        for (var _m = 0, _o = files.resources[resourceId].taxa; _m < _o.length; _m++) {
-            var taxon = _o[_m];
+        const leafs = new Set(files.resources[resourceId].taxa.map(taxon => taxon.scientificNameID));
+        const taxa = [];
+        for (const taxon of files.resources[resourceId].taxa) {
             taxa.push(makeLinkedDataForScientificName(taxon));
             if (taxon.parentNameUsageID) {
                 leafs.delete(taxon.parentNameUsageID);
@@ -455,20 +402,20 @@ function makeLinkedDataForResource(work, files, resourceId) {
     return node;
 }
 function makeLinkedDataForWork(work, files) {
-    var id = work.get('id');
-    var node = makeWorkUri(id);
-    var languages = work.get('language');
-    node['dcterms:language'] = languages.map(function (language) { return ({ '@id': "http://id.loc.gov/vocabulary/iso639-1/".concat(language) }); });
+    const id = work.get('id');
+    const node = makeWorkUri(id);
+    const languages = work.get('language');
+    node['dcterms:language'] = languages.map(language => ({ '@id': `http://id.loc.gov/vocabulary/iso639-1/${language}` }));
     if (work.has('title')) {
-        var title = work.get('title');
+        const title = work.get('title');
         if (title.length > languages.length) {
             title.splice(0, title.length, title.join('; '));
         }
-        node['dcterms:title'] = title.map(function (value, i) { return ({ '@value': value, '@language': languages[i] }); });
+        node['dcterms:title'] = title.map((value, i) => ({ '@value': value, '@language': languages[i] }));
     }
     if (work.has('pages') && work.get('pages').includes('-')) {
-        var containers = work.has('part_of') ? work.get('part_of').map(function (id) { return files.catalog.get(id); }) : [];
-        if (containers.find(function (container) { return container.get('entry_type') === 'online'; })) {
+        const containers = work.has('part_of') ? work.get('part_of').map(id => files.catalog.get(id)) : [];
+        if (containers.find(container => container.get('entry_type') === 'online')) {
             node['@type'] = 'bibo:BookSection';
         }
         else {
@@ -482,28 +429,28 @@ function makeLinkedDataForWork(work, files) {
         node['@type'] = 'bibo:Book';
     }
     if (work.has('author')) {
-        var authors = mapEntities(work.get('author'), files.authors.entities).map(function (author) { return ({ '@id': "".concat(PREFIX, "author/").concat(author.get('id')) }); });
+        const authors = mapEntities(work.get('author'), files.authors.entities).map(author => ({ '@id': `${PREFIX}author/${author.get('id')}` }));
         node['bibo:authorList'] = { '@list': authors };
         node['dcterms:creator'] = authors;
     }
     if (work.has('url')) {
-        var urls = work.get('url');
-        var handle = urls.find(function (url) { return url.startsWith(HANDLE_PREFIX); });
+        const urls = work.get('url');
+        const handle = urls.find(url => url.startsWith(HANDLE_PREFIX));
         if (handle) {
             node['bibo:handle'] = { '@id': handle.slice(HANDLE_PREFIX.length) };
         }
-        node['schema:url'] = urls.map(function (url) { return ({ '@id': url }); });
+        node['schema:url'] = urls.map(url => ({ '@id': url }));
     }
     if (work.has('fulltext_url')) {
-        var urls = work.get('fulltext_url');
-        node['schema:encoding'] = urls.map(function (url) { return ({ '@type': 'schema:MediaObject', 'schema:contentUrl': { '@id': url } }); });
+        const urls = work.get('fulltext_url');
+        node['schema:encoding'] = urls.map(url => ({ '@type': 'schema:MediaObject', 'schema:contentUrl': { '@id': url } }));
     }
     if (work.has('archive_url')) {
-        node['schema:archivedAt'] = work.get('archive_url').map(function (url) { return ({ '@id': url }); });
+        node['schema:archivedAt'] = work.get('archive_url').map(url => ({ '@id': url }));
     }
     if (work.has('date')) {
-        var date = work.get('date');
-        var dateType = 'rdfs:Literal';
+        const date = work.get('date');
+        let dateType = 'rdfs:Literal';
         if (date.match(/^\d{4}-\d{2}-\d{2}$/)) {
             dateType = 'xsd:date';
         }
@@ -516,16 +463,15 @@ function makeLinkedDataForWork(work, files) {
         node['dcterms:issued'] = { '@value': work.get('date'), '@type': dateType };
     }
     if (work.has('publisher')) {
-        var publishers = mapEntities(work.get('publisher'), files.publishers.entities).map(function (publisher) { return ({ '@id': "".concat(PREFIX, "publisher/").concat(publisher.get('id')) }); });
+        const publishers = mapEntities(work.get('publisher'), files.publishers.entities).map(publisher => ({ '@id': `${PREFIX}publisher/${publisher.get('id')}` }));
         node['dcterms:publisher'] = publishers;
     }
     if (work.has('ISSN')) {
         node['bibo:issn'] = work.get('ISSN');
     }
     if (work.has('ISBN')) {
-        var isbns = work.get('ISBN');
-        for (var _i = 0, isbns_1 = isbns; _i < isbns_1.length; _i++) {
-            var isbn = isbns_1[_i];
+        const isbns = work.get('ISBN');
+        for (const isbn of isbns) {
             if (isbn.length === 13) {
                 node['bibo:isbn13'] = isbn;
             }
@@ -550,14 +496,14 @@ function makeLinkedDataForWork(work, files) {
         node['bibo:issue'] = work.get('issue');
     }
     if (work.has('pages')) {
-        var pages = work.get('pages');
-        var range = pages.split('-');
+        const pages = work.get('pages');
+        const range = pages.split('-');
         if (pages.match(/^\d+$/)) {
             node['bibo:numPages'] = parseInt(pages);
         }
         else if (range.length === 2) {
             node['bibo:pages'] = pages;
-            var _a = range.map(function (part) { return parseInt(part); }), start = _a[0], end = _a[1];
+            const [start, end] = range.map(part => parseInt(part));
             if (!isNaN(start)) {
                 node['bibo:pageStart'] = start;
             }
@@ -576,38 +522,36 @@ function makeLinkedDataForWork(work, files) {
         node['bibo:edition'] = work.get('edition');
     }
     if (work.has('license')) {
-        var licenses = work.get('license');
-        node['dcterms:rights'] = licenses.map(function (license) {
+        const licenses = work.get('license');
+        node['dcterms:rights'] = licenses.map(license => {
             if (license === '<public domain>' || license.match(/^<.+\?>$/)) {
                 return license.slice(1, -1);
             }
             else {
-                return { '@id': "https://spdx.org/licenses/".concat(license, ".html") };
+                return { '@id': `https://spdx.org/licenses/${license}.html` };
             }
         });
     }
     return node;
 }
 function makeLinkedDataForWorks(files) {
-    var nodes = {};
-    var works = files.catalog;
-    for (var _i = 0, _a = works.entities; _i < _a.length; _i++) {
-        var work = _a[_i];
+    const nodes = {};
+    const works = files.catalog;
+    for (const work of works.entities) {
         nodes[work.get('id')] = makeLinkedDataForWork(work, files);
     }
-    var _loop_2 = function (work) {
-        var id = work.get('id');
-        var node = nodes[id];
-        var language = work.get('language');
+    for (const work of works.entities) {
+        const id = work.get('id');
+        const node = nodes[id];
+        const language = work.get('language');
         if (work.has('part_of')) {
-            var containers = work.get('part_of');
+            const containers = work.get('part_of');
             if (work.get('key_type').includes('supplement')) {
                 node['bibo:annotates'] = containers.map(makeWorkUri);
             }
             else {
                 node['dcterms:isPartOf'] = containers.map(makeWorkUri);
-                for (var _d = 0, containers_1 = containers; _d < containers_1.length; _d++) {
-                    var container = containers_1[_d];
+                for (const container of containers) {
                     if (!Array.isArray(nodes[container]['dcterms:hasPart'])) {
                         nodes[container]['dcterms:hasPart'] = [];
                     }
@@ -616,170 +560,107 @@ function makeLinkedDataForWorks(files) {
             }
         }
         if (work.has('listed_in')) {
-            var referers = work.get('listed_in');
+            const referers = work.get('listed_in');
             node['bibo:citedBy'] = node['dcterms:isReferencedBy'] = referers.map(makeWorkUri);
-            for (var _e = 0, referers_1 = referers; _e < referers_1.length; _e++) {
-                var referer = referers_1[_e];
+            for (const referer of referers) {
                 nodes[referer]['bibo:cites'] = nodes[referer]['dcterms:references'] = makeWorkUri(id);
             }
         }
         if (work.has('version_of')) {
-            var originals = work.get('version_of');
-            var originalLanguages_1 = originals.map(function (id) { return works.get(id).get('language').join(); });
-            node['bibo:translationOf'] = originals.filter(function (_, i) { return originalLanguages_1[i] !== language.join(); }).map(makeWorkUri);
-            node['dcterms:isVersionOf'] = originals.filter(function (id) { return work.get('id') !== id; }).map(makeWorkUri);
-        }
-        var resourceIndex = 1;
-        var resourceId = void 0;
-        while ((resourceId = "".concat(id, ":").concat(resourceIndex++)) in files.resources) {
-            var resource = makeLinkedDataForResource(work, files, resourceId);
+            const originals = work.get('version_of');
+            const originalLanguages = originals.map(id => works.get(id).get('language').join());
+            node['bibo:translationOf'] = originals.filter((_, i) => originalLanguages[i] !== language.join()).map(makeWorkUri);
+            node['dcterms:isVersionOf'] = originals.filter(id => work.get('id') !== id).map(makeWorkUri);
+        }
+        let resourceIndex = 1;
+        let resourceId;
+        while ((resourceId = `${id}:${resourceIndex++}`) in files.resources) {
+            const resource = makeLinkedDataForResource(work, files, resourceId);
             if (!Array.isArray(node['dcterms:hasPart'])) {
                 node['dcterms:hasPart'] = [];
             }
             node['dcterms:hasPart'].push(resource);
-            if (!Array.isArray(resource['dcterms:isPartof'])) {
-                resource['dcterms:isPartof'] = [];
+            if (!Array.isArray(resource['dcterms:isPartOf'])) {
+                resource['dcterms:isPartOf'] = [];
             }
-            resource['dcterms:isPartof'].push({ '@id': node['@id'] });
+            resource['dcterms:isPartOf'].push({ '@id': node['@id'] });
         }
-    };
-    for (var _b = 0, _c = works.entities; _b < _c.length; _b++) {
-        var work = _c[_b];
-        _loop_2(work);
     }
     return Object.values(nodes);
 }
 function writeOutput(document_1) {
-    return __awaiter(this, arguments, void 0, function (document, format) {
-        var nquads, parser, writer;
-        if (format === void 0) { format = 'jsonld'; }
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    if (format === 'jsonld') {
-                        process.stdout.write(JSON.stringify(document, null, 2));
-                        return [2 /*return*/];
-                    }
-                    return [4 /*yield*/, jsonld.toRDF(document, { format: 'application/n-quads' })];
-                case 1:
-                    nquads = _a.sent();
-                    if (format === 'nquads') {
-                        process.stdout.write(nquads);
-                        return [2 /*return*/];
-                    }
-                    parser = new N3.StreamParser();
-                    writer = new N3.StreamWriter({ prefixes: PREFIXES });
-                    parser.write(nquads);
-                    parser.pipe(writer);
-                    writer.pipe(process.stdout);
-                    return [2 /*return*/];
-            }
-        });
+    return __awaiter(this, arguments, void 0, function* (document, format = 'jsonld') {
+        if (format === 'jsonld') {
+            process.stdout.write(JSON.stringify(document, null, 2));
+            return;
+        }
+        const nquads = yield jsonld.toRDF(document, { format: 'application/n-quads' });
+        if (format === 'nquads') {
+            process.stdout.write(nquads);
+            return;
+        }
+        const parser = new N3.StreamParser();
+        const writer = new N3.StreamWriter({ prefixes: PREFIXES });
+        parser.write(nquads);
+        parser.pipe(writer);
+        writer.pipe(process.stdout);
     });
 }
 function main() {
-    return __awaiter(this, void 0, void 0, function () {
-        var args, directory, files, _i, SHEETS_1, sheet, filePath, file, resources, _a, _b, _loop_3, _c, _d, _e, _f, id, graph, _g, _h, entity, _j, _k, entity, _l, _m, entity, document;
-        return __generator(this, function (_o) {
-            switch (_o.label) {
-                case 0:
-                    args = util.parseArgs({
-                        allowPositionals: true,
-                        options: {
-                            format: {
-                                type: 'string',
-                                short: 'f',
-                                default: 'jsonld',
-                            }
-                        },
-                    });
-                    directory = path.resolve(args.positionals[0]);
-                    files = {};
-                    _i = 0, SHEETS_1 = SHEETS;
-                    _o.label = 1;
-                case 1:
-                    if (!(_i < SHEETS_1.length)) return [3 /*break*/, 4];
-                    sheet = SHEETS_1[_i];
-                    filePath = path.join(directory, "".concat(sheet, ".csv"));
-                    if (!(0, fs_1.existsSync)(filePath)) {
-                        throw new Error("File \"".concat(sheet, ".csv\" must be provided"));
-                    }
-                    return [4 /*yield*/, fs_1.promises.readFile(filePath, 'utf8')];
-                case 2:
-                    file = _o.sent();
-                    files[sheet] = index_1.catalog.loadData(file, sheet);
-                    _o.label = 3;
-                case 3:
-                    _i++;
-                    return [3 /*break*/, 1];
-                case 4:
-                    files.resources = {};
-                    _b = (_a = JSON).parse;
-                    return [4 /*yield*/, fs_1.promises.readFile(path.join(directory, 'resources', 'index.json'), 'utf8')];
-                case 5:
-                    resources = _b.apply(_a, [_o.sent()]);
-                    _loop_3 = function (id) {
-                        var filePath, file, _p, header, rows, taxa;
-                        return __generator(this, function (_q) {
-                            switch (_q.label) {
-                                case 0:
-                                    filePath = path.join(directory, 'resources', 'dwc', id.split(':').join('-') + '.csv');
-                                    return [4 /*yield*/, fs_1.promises.readFile(filePath, 'utf8')];
-                                case 1:
-                                    file = _q.sent();
-                                    _p = (0, csv_1.parseCsv)(file), header = _p[0], rows = _p.slice(1);
-                                    taxa = rows.map(function (row) { return row.reduce(function (object, value, index) {
-                                        object[header[index]] = value;
-                                        return object;
-                                    }, {}); });
-                                    files.resources[id] = { metadata: resources[id], taxa: taxa };
-                                    return [2 /*return*/];
-                            }
-                        });
-                    };
-                    _c = resources;
-                    _d = [];
-                    for (_e in _c)
-                        _d.push(_e);
-                    _f = 0;
-                    _o.label = 6;
-                case 6:
-                    if (!(_f < _d.length)) return [3 /*break*/, 9];
-                    _e = _d[_f];
-                    if (!(_e in _c)) return [3 /*break*/, 8];
-                    id = _e;
-                    return [5 /*yield**/, _loop_3(id)];
-                case 7:
-                    _o.sent();
-                    _o.label = 8;
-                case 8:
-                    _f++;
-                    return [3 /*break*/, 6];
-                case 9:
-                    graph = __spreadArray(__spreadArray([], makeLinkedDataForWorks(files), true), makeLinkedDataForTaxa(files), true);
-                    for (_g = 0, _h = files.authors.entities; _g < _h.length; _g++) {
-                        entity = _h[_g];
-                        graph.push(makeLinkedDataForAuthor(entity));
-                    }
-                    for (_j = 0, _k = files.places.entities; _j < _k.length; _j++) {
-                        entity = _k[_j];
-                        graph.push(makeLinkedDataForPlace(entity));
-                    }
-                    for (_l = 0, _m = files.publishers.entities; _l < _m.length; _l++) {
-                        entity = _m[_l];
-                        graph.push(makeLinkedDataForPublisher(entity));
-                    }
-                    document = {
-                        '@context': PREFIXES,
-                        '@graph': graph
-                    };
-                    writeOutput(document, args.values.format);
-                    return [2 /*return*/];
-            }
+    return __awaiter(this, void 0, void 0, function* () {
+        const args = util.parseArgs({
+            allowPositionals: true,
+            options: {
+                format: {
+                    type: 'string',
+                    short: 'f',
+                    default: 'jsonld',
+                }
+            },
         });
+        const directory = path.resolve(args.positionals[0]);
+        const files = {};
+        for (const sheet of SHEETS) {
+            const filePath = path.join(directory, `${sheet}.csv`);
+            if (!(0, fs_1.existsSync)(filePath)) {
+                throw new Error(`File "${sheet}.csv" must be provided`);
+            }
+            const file = yield fs_1.promises.readFile(filePath, 'utf8');
+            files[sheet] = index_1.catalog.loadData(file, sheet);
+        }
+        files.resources = {};
+        const resources = JSON.parse(yield fs_1.promises.readFile(path.join(directory, 'resources', 'index.json'), 'utf8'));
+        for (const id in resources) {
+            const filePath = path.join(directory, 'resources', 'dwc', id.split(':').join('-') + '.csv');
+            const file = yield fs_1.promises.readFile(filePath, 'utf8');
+            const [header, ...rows] = (0, csv_1.parseCsv)(file);
+            const taxa = rows.map(row => row.reduce((object, value, index) => {
+                object[header[index]] = value;
+                return object;
+            }, {}));
+            files.resources[id] = { metadata: resources[id], taxa };
+        }
+        const graph = [
+            ...makeLinkedDataForWorks(files),
+            ...makeLinkedDataForTaxa(files),
+        ];
+        for (const entity of files.authors.entities) {
+            graph.push(makeLinkedDataForAuthor(entity));
+        }
+        for (const entity of files.places.entities) {
+            graph.push(makeLinkedDataForPlace(entity));
+        }
+        for (const entity of files.publishers.entities) {
+            graph.push(makeLinkedDataForPublisher(entity));
+        }
+        const document = {
+            '@context': PREFIXES,
+            '@graph': graph
+        };
+        writeOutput(document, args.values.format);
     });
 }
-main().catch(function (error) {
+main().catch((error) => {
     console.error(error);
     process.exit(1);
 });