@larsgw/formica 0.10.2 → 0.10.3

package/README.md

@@ -20,6 +20,8 @@ Run locally:
   - `loir-validate-resources [./B1234.txt]`:
     Validate the `.txt` files containing information on the taxonomic scope of keys
     ([documentation](https://github.com/identification-resources/catalog/blob/main/docs/resources-txt.md)).
+  - `loir-validate-integrity .`:
+    Check if all values are mapped as expected.
   - `loir-resources-process [./resources]`:
     Interactive tool to convert the aforementioned `.txt` files to Darwin Core archives
     ([documentation](https://github.com/identification-resources/catalog/blob/main/docs/resources-dwc.md)),

package/lib/bin/validate-integrity.d.ts

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

package/lib/bin/validate-integrity.js

@@ -0,0 +1,133 @@
+#!/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());
+    });
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const fs_1 = require("fs");
+const path = __importStar(require("path"));
+const index_1 = require("../index");
+function loadCatalogFile(file, base) {
+    return __awaiter(this, void 0, void 0, function* () {
+        const contents = yield fs_1.promises.readFile(path.join(base, `${file}.csv`), 'utf8');
+        return index_1.catalog.loadData(contents, file);
+    });
+}
+function loadResourcesIndex(base) {
+    return __awaiter(this, void 0, void 0, function* () {
+        const contents = yield fs_1.promises.readFile(path.join(base, 'resources', 'index.json'), 'utf8');
+        return JSON.parse(contents);
+    });
+}
+function getAll(entity, field) {
+    const value = entity.get(field);
+    if (Array.isArray(value)) {
+        return value;
+    }
+    else if (value) {
+        return [value];
+    }
+    else {
+        return [];
+    }
+}
+function checkIntegrity(catalog, resources, field, sheet) {
+    const errors = [];
+    const index = new Set();
+    for (const entity of sheet) {
+        for (const value of getAll(entity, 'name')) {
+            index.add(value);
+        }
+    }
+    for (const entity of catalog) {
+        const id = entity.get('id');
+        for (const value of getAll(entity, field)) {
+            if (!index.has(value)) {
+                errors.push({
+                    entity: id,
+                    field: field,
+                    error: `Value "${value}" not mapped`
+                });
+            }
+        }
+    }
+    for (const id in resources) {
+        const resource = resources[id];
+        if (!resource.catalog || !Object.prototype.hasOwnProperty.call(resource.catalog, field)) {
+            continue;
+        }
+        const value = resource.catalog[field];
+        const values = Array.isArray(value) ? value : [value];
+        for (const value of values) {
+            if (!index.has(value)) {
+                errors.push({
+                    entity: id,
+                    field: field,
+                    error: `Value "${value}" is not mapped`
+                });
+            }
+        }
+    }
+    return errors;
+}
+function main(args) {
+    return __awaiter(this, void 0, void 0, function* () {
+        const base = path.resolve(args[0]);
+        const [catalog, authors, places, publishers, taxa, resources] = yield Promise.all([
+            loadCatalogFile('catalog', base),
+            loadCatalogFile('authors', base),
+            loadCatalogFile('places', base),
+            loadCatalogFile('publishers', base),
+            loadCatalogFile('taxa', base),
+            loadResourcesIndex(base)
+        ]);
+        const errors = [
+            ...checkIntegrity(catalog, resources, 'author', authors),
+            ...checkIntegrity(catalog, resources, 'publisher', publishers),
+            ...checkIntegrity(catalog, resources, 'taxon', taxa),
+            ...checkIntegrity(catalog, resources, 'region', places)
+        ];
+        console.table(errors);
+        process.exit(errors.length ? 1 : 0);
+    });
+}
+main(process.argv.slice(2));

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@larsgw/formica",
-  "version": "0.10.2",
+  "version": "0.10.3",
   "description": "SDK and tools for data from the Library of Identification Resources",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",
@@ -10,6 +10,7 @@
   "bin": {
     "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-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",