@larsgw/formica 0.1.0

package/.eslintrc.js

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+module.exports = {
+  extends: ['eslint:recommended', 'plugin:@typescript-eslint/recommended'],
+  parser: '@typescript-eslint/parser',
+  plugins: ['@typescript-eslint'],
+  root: true,
+
+  rules: {
+    indent: ['error', 4, { SwitchCase: 1 }],
+    'no-unused-vars': 'off',
+    '@typescript-eslint/no-unused-vars': ['warn', {
+      argsIgnorePattern: '^_',
+      varsIgnorePattern: '^_',
+      caughtErrorsIgnorePattern: '^_'
+    }]
+  }
+}

package/LICENSE

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+MIT License
+
+Copyright (c) 2023 Lars Willighagen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# Formica
+
+**Formica** is an SDK and a collection of tools for the data in the Library of
+Identification Resources.
+
+## Tools
+
+  - `loir-validate-catalog [./catalog.csv ./authors.csv ./places.csv ./publishers.csv]`:
+    Validate the CSV files containing metadata ([schema](https://github.com/identification-resources/catalog/blob/main/docs/tools-resources.md)).
+  - `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-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)),
+    and link the taxa to GBIF and Catalogue of Life identifiers. Use the `-u` or
+    `--update` flag in a Git repo to update existing Darwin Core files while keeping
+    the identifiers stable (in most cases).
+  - `loir-resources-index [./resources]`: Create indices of the Darwin Core archives.

package/lib/bin/process-resources-index.d.ts

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+export {};

package/lib/bin/process-resources-index.js

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+"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 __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 __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;
+    return g = { next: verb(0), "throw": verb(1), "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 };
+    }
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var fs_1 = require("fs");
+var path = require("path");
+var index_1 = require("../index");
+var util_1 = require("./util");
+/* eslint-disable @typescript-eslint/no-explicit-any */
+function sortObject(object) {
+    var sorted = {};
+    for (var _i = 0, _a = Object.keys(object).sort(util_1.numericSort); _i < _a.length; _i++) {
+        var key = _a[_i];
+        sorted[key] = object[key];
+    }
+    return sorted;
+}
+/* eslint-enable @typescript-eslint/no-explicit-any */
+function main(args) {
+    return __awaiter(this, void 0, void 0, function () {
+        var REPO_ROOT, files, gbifIndex, resourceIndex;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    REPO_ROOT = path.resolve(args[0]);
+                    return [4 /*yield*/, fs_1.promises.readdir(path.join(REPO_ROOT, 'txt'))];
+                case 1:
+                    files = _a.sent();
+                    gbifIndex = {};
+                    resourceIndex = {};
+                    return [4 /*yield*/, Promise.all(files.map(function (fileName) {
+                            return __awaiter(this, void 0, void 0, function () {
+                                var id, file;
+                                return __generator(this, function (_a) {
+                                    switch (_a.label) {
+                                        case 0:
+                                            if (!fileName.endsWith('.txt')) {
+                                                return [2 /*return*/];
+                                            }
+                                            id = fileName.slice(0, -4);
+                                            return [4 /*yield*/, fs_1.promises.readFile(path.join(REPO_ROOT, 'txt', fileName), 'utf-8')];
+                                        case 1:
+                                            file = _a.sent();
+                                            return [2 /*return*/, Promise.all(index_1.resources.parseTextFileHeader(file).map(function (resource, index) {
+                                                    return __awaiter(this, void 0, void 0, function () {
+                                                        var amendedResource, dwcFile, _a, _header, dwc, _b, _c, _i, dwc_1, taxon, gbifId;
+                                                        return __generator(this, function (_d) {
+                                                            switch (_d.label) {
+                                                                case 0:
+                                                                    amendedResource = __assign(__assign({}, resource), { id: "".concat(id, ":").concat(index + 1), taxonCount: 0 });
+                                                                    dwcFile = path.join(REPO_ROOT, 'dwc', "".concat(id, "-").concat(index + 1, ".csv"));
+                                                                    if (!(0, fs_1.existsSync)(dwcFile)) {
+                                                                        return [2 /*return*/];
+                                                                    }
+                                                                    _c = (_b = index_1.csv).parseCsv;
+                                                                    return [4 /*yield*/, fs_1.promises.readFile(dwcFile, 'utf-8')];
+                                                                case 1:
+                                                                    _a = _c.apply(_b, [_d.sent()]), _header = _a[0], dwc = _a.slice(1);
+                                                                    for (_i = 0, dwc_1 = dwc; _i < dwc_1.length; _i++) {
+                                                                        taxon = dwc_1[_i];
+                                                                        gbifId = taxon[25];
+                                                                        if (gbifId) {
+                                                                            if (!(gbifId in gbifIndex)) {
+                                                                                gbifIndex[gbifId] = [];
+                                                                            }
+                                                                            gbifIndex[gbifId].push(taxon[0]);
+                                                                            gbifIndex[gbifId].sort(util_1.numericSort);
+                                                                        }
+                                                                        amendedResource.taxonCount += 1;
+                                                                    }
+                                                                    resourceIndex[amendedResource.id] = amendedResource;
+                                                                    return [2 /*return*/];
+                                                            }
+                                                        });
+                                                    });
+                                                }))];
+                                    }
+                                });
+                            });
+                        }))];
+                case 2:
+                    _a.sent();
+                    return [4 /*yield*/, Promise.all([
+                            fs_1.promises.writeFile(path.join(REPO_ROOT, 'gbif.index.json'), JSON.stringify(sortObject(gbifIndex), null, 2)),
+                            fs_1.promises.writeFile(path.join(REPO_ROOT, 'index.json'), JSON.stringify(sortObject(resourceIndex), null, 2))
+                        ])];
+                case 3:
+                    _a.sent();
+                    return [2 /*return*/];
+            }
+        });
+    });
+}
+main(process.argv.slice(2)).catch(function (error) {
+    console.error(error);
+    process.exit(1);
+});

package/lib/bin/process-resources.d.ts

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+export {};