@larsgw/formica 0.10.4 → 0.10.5

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

@@ -161,7 +161,7 @@ function getCoveringTaxon(taxa, allTaxa) {
         }
     }
     if (!ancestors.length) {
-        return null;
+        return makeTaxonUri('T141')['@id'];
     }
     const ancestor = ancestors[ancestors.length - 1];
     const ancestorEntity = allTaxa.find(taxon => taxon.get('col') === ancestor);
@@ -197,6 +197,9 @@ function makeColUri(id) {
 function makeWorkUri(id) {
     return { '@id': `${PREFIX}catalog/${id}` };
 }
+function makeResourceUri(id) {
+    return { '@id': `${PREFIX}resource/${id}` };
+}
 function makeTaxonUri(id) {
     return { '@id': `${PREFIX}taxon/${id}` };
 }
@@ -400,12 +403,13 @@ function makeLinkedDataForResource(work, files, resourceId) {
         resourceId = `${work.get('id')}:0`;
     }
     if (files.resources[resourceId] && files.resources[resourceId].metadata.catalog) {
-        resource.fields = files.resources[resourceId].metadata.catalog;
+        resource.fields = Object.assign({}, files.resources[resourceId].metadata.catalog);
     }
     if (!resource.has('language')) {
         resource.fields.language = work.get('language');
     }
-    const node = Object.assign(Object.assign({}, makeLinkedDataForWork(resource, files)), { '@id': `${PREFIX}resource/${resourceId}`, '@type': 'bibo:DocumentPart' });
+    resource.fields.id = resourceId;
+    const node = Object.assign(Object.assign({}, makeLinkedDataForWork(resource, files, makeResourceUri)), { '@type': 'bibo:DocumentPart' });
     const types = (_b = (_a = resource.get('key_type')) !== null && _a !== void 0 ? _a : work.get('key_type')) !== null && _b !== void 0 ? _b : [];
     if (types.includes('matrix') || types.includes('algorithm')) {
         node['dcterms:type'] = { '@id': 'http://purl.org/dc/dcmitype/Software' };
@@ -489,9 +493,9 @@ function makeLinkedDataForResource(work, files, resourceId) {
     }
     return node;
 }
-function makeLinkedDataForWork(work, files) {
+function makeLinkedDataForWork(work, files, makeUri = makeWorkUri) {
     const id = work.get('id');
-    const node = makeWorkUri(id);
+    const node = makeUri(id);
     node['@reverse'] = {};
     const languages = work.get('language');
     node['dcterms:language'] = languages.map(language => ({ '@id': `http://id.loc.gov/vocabulary/iso639-1/${language}` }));
@@ -624,30 +628,30 @@ function makeLinkedDataForWork(work, files) {
     if (work.has('part_of')) {
         const containers = work.get('part_of');
         if (work.get('key_type').includes('supplement')) {
-            node['bibo:annotates'] = containers.map(makeWorkUri);
+            node['bibo:annotates'] = containers.map(makeUri);
         }
         else {
-            node['dcterms:isPartOf'] = containers.map(makeWorkUri);
+            node['dcterms:isPartOf'] = containers.map(makeUri);
             for (const container of containers) {
                 if (!Array.isArray(node['@reverse']['dcterms:hasPart'])) {
                     node['@reverse']['dcterms:hasPart'] = [];
                 }
-                node['@reverse']['dcterms:hasPart'].push(makeWorkUri(container));
+                node['@reverse']['dcterms:hasPart'].push(makeUri(container));
             }
         }
     }
     if (work.has('listed_in')) {
         const referers = work.get('listed_in');
-        node['bibo:citedBy'] = node['dcterms:isReferencedBy'] = referers.map(makeWorkUri);
+        node['bibo:citedBy'] = node['dcterms:isReferencedBy'] = referers.map(makeUri);
         for (const referer of referers) {
             if (!Array.isArray(node['@reverse']['bibo:cites'])) {
                 node['@reverse']['bibo:cites'] = [];
             }
-            node['@reverse']['bibo:cites'].push(makeWorkUri(referer));
+            node['@reverse']['bibo:cites'].push(makeUri(referer));
             if (!Array.isArray(node['@reverse']['dcterms:references'])) {
                 node['@reverse']['dcterms:references'] = [];
             }
-            node['@reverse']['dcterms:references'].push(makeWorkUri(referer));
+            node['@reverse']['dcterms:references'].push(makeUri(referer));
         }
     }
     if (work.has('version_of')) {
@@ -665,8 +669,8 @@ function makeLinkedDataForWork(work, files) {
             }
             return language;
         });
-        node['bibo:translationOf'] = originals.filter((_, i) => originalLanguages[i] !== languages.join()).map(makeWorkUri);
-        node['dcterms:isVersionOf'] = originals.filter(id => work.get('id') !== id).map(makeWorkUri);
+        node['bibo:translationOf'] = originals.filter((_, i) => originalLanguages[i] !== languages.join()).map(makeUri);
+        node['dcterms:isVersionOf'] = originals.filter(id => work.get('id') !== id).map(makeUri);
     }
     return node;
 }
@@ -733,6 +737,12 @@ class Writer {
         if (this.format === 'jsonld') {
             process.stdout.write('    null\n  ]\n}\n');
         }
+        else if (this.format === 'nquads') {
+            // no ending required
+        }
+        else {
+            this.n3parser.end();
+        }
     }
 }
 function main() {

package/lib/bin/validate-linked-data.d.ts

@@ -0,0 +1,2 @@
+#!/usr/bin/env node
+export {};

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

@@ -0,0 +1,132 @@
+#!/usr/bin/env node
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const path = __importStar(require("path"));
+const fs_1 = require("fs");
+const n3_1 = __importDefault(require("n3"));
+const shape_map_1 = require("shape-map");
+const shex_1 = __importDefault(require("shex"));
+const neighborhood_rdfjs_1 = require("@shexjs/neighborhood-rdfjs");
+const ShExParser = __importStar(require("@shexjs/parser"));
+const SCHEMA_PATH = 'docs/linked-data/shape.shex';
+const SHAPEMAP_PATH = 'docs/linked-data/shapeMap.sm';
+const BASE = 'https://identification-resources.github.io/assets/data/';
+const SCHEMA_BASE = BASE + SCHEMA_PATH;
+const SHAPEMAP_BASE = BASE + SHAPEMAP_PATH;
+const DATA_BASE = BASE;
+function loadData(path) {
+    return __awaiter(this, void 0, void 0, function* () {
+        const parser = new n3_1.default.Parser();
+        const file = yield fs_1.promises.readFile(path, 'utf8');
+        const data = new n3_1.default.Store(parser.parse(file));
+        return (0, neighborhood_rdfjs_1.ctor)(data);
+    });
+}
+function loadSchema(path) {
+    return __awaiter(this, void 0, void 0, function* () {
+        const parser = ShExParser.construct(SCHEMA_BASE);
+        const file = yield fs_1.promises.readFile(path, 'utf8');
+        const schema = parser.parse(file, SCHEMA_BASE);
+        return schema;
+    });
+}
+function loadShapeMap(path) {
+    return __awaiter(this, void 0, void 0, function* () {
+        const parser = shape_map_1.Parser.construct(SHAPEMAP_BASE, { base: SCHEMA_BASE }, { base: DATA_BASE });
+        const file = yield fs_1.promises.readFile(path, 'utf8');
+        const shapeMap = parser.parse(file);
+        return shapeMap;
+    });
+}
+function resolveShapeMap(shapeMap, db) {
+    var _a;
+    const pairs = [];
+    for (const part of shapeMap) {
+        if (typeof part.node === 'string') {
+            pairs.push(part);
+        }
+        else if (part.node.type === 'TriplePattern') {
+            const focusSubject = typeof part.node.subject === 'object' && ((_a = part.node.subject) === null || _a === void 0 ? void 0 : _a.term) === shape_map_1.Focus.term;
+            const subject = typeof part.node.subject === 'string' ? part.node.subject : null;
+            const object = typeof part.node.object === 'string' ? part.node.object : null;
+            const quads = db.getQuads(subject, part.node.predicate, object, null);
+            for (const quad of quads) {
+                pairs.push({
+                    node: focusSubject ? quad.subject.id : quad.object.id,
+                    shape: part.shape
+                });
+            }
+        }
+        else {
+            throw new Error(`Shape map type not supported: "${part.node.type}"`);
+        }
+    }
+    return pairs;
+}
+function main(args) {
+    return __awaiter(this, void 0, void 0, function* () {
+        const [base, data] = args.map(arg => path.resolve(arg));
+        const db = yield loadData(data);
+        const schema = yield loadSchema(path.join(base, SCHEMA_PATH));
+        const shapeMap = yield loadShapeMap(path.join(base, SHAPEMAP_PATH));
+        const nodePairs = resolveShapeMap(shapeMap, db);
+        const validator = new shex_1.default.Validator(schema, db);
+        const results = validator.validateShapeMap(nodePairs);
+        let successes = 0;
+        for (const result of results) {
+            if (!result.appinfo.errors) {
+                successes++;
+                continue;
+            }
+            console.error('===', result.node, '===');
+            console.error(JSON.stringify(result.appinfo, null, 2));
+        }
+        console.error(`Success: ${successes}/${nodePairs.length}`);
+    });
+}
+main(process.argv.slice(2));

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@larsgw/formica",
-  "version": "0.10.4",
+  "version": "0.10.5",
   "description": "SDK and tools for data from the Library of Identification Resources",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",
@@ -11,6 +11,7 @@
     "loir-validate-catalog": "lib/bin/validate-catalog.js",
     "loir-validate-resources": "lib/bin/validate-resources-text.js",
     "loir-validate-integrity": "lib/bin/validate-integrity.js",
+    "loir-validate-linked-data": "lib/bin/validate-linked-data.js",
     "loir-resources-process": "lib/bin/process-resources.js",
     "loir-resources-index": "lib/bin/process-resources-index.js",
     "loir-resources-check-diff": "lib/bin/check-resources-diff.js",
@@ -40,6 +41,7 @@
     "js-yaml": "^5.2.1",
     "jsonld": "^9.0.0",
     "n3": "^2.1.1",
+    "shex": "^1.0.0-alpha.30",
     "spdx-license-list": "^6.6.0"
   },
   "devDependencies": {