@larsgw/formica 0.9.2 → 0.10.1

package/lib/bin/download-place-shapes.js

@@ -1,188 +0,0 @@
-#!/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 __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 };
-    }
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-var fs_1 = require("fs");
-var path = __importStar(require("path"));
-var index_1 = require("../index");
-function loadPlaces(directory) {
-    return __awaiter(this, void 0, void 0, function () {
-        var filePath, file;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    filePath = path.join(path.resolve(directory), 'places.csv');
-                    return [4 /*yield*/, fs_1.promises.readFile(filePath, 'utf8')];
-                case 1:
-                    file = _a.sent();
-                    return [2 /*return*/, index_1.catalog.loadData(file, path.basename(filePath, '.csv'))];
-            }
-        });
-    });
-}
-function getInatIds(places) {
-    return __awaiter(this, void 0, void 0, function () {
-        var values, query, url, response, data;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    values = places.entities
-                        .filter(function (place) { return place.has('qid'); })
-                        .map(function (place) { return "(wd:".concat(place.get('qid'), " \"").concat(place.get('id'), "\")"); })
-                        .join(' ');
-                    query = "SELECT ?name ?id WHERE {\n    VALUES (?qid ?name) { ".concat(values, " }\n    ?qid wdt:P7471 ?id .\n}");
-                    url = "https://query.wikidata.org/sparql?query=".concat(encodeURIComponent(query));
-                    return [4 /*yield*/, fetch(url, { headers: { accept: 'application/json', 'user-agent': 'Formica (https://github.com/identification-resources/formica)' } })];
-                case 1:
-                    response = _a.sent();
-                    if (response.status >= 400) {
-                        throw new Error("Fetching iNaturalist IDs for places: ".concat(response.status));
-                    }
-                    return [4 /*yield*/, response.json()];
-                case 2:
-                    data = _a.sent();
-                    return [2 /*return*/, data.results.bindings];
-            }
-        });
-    });
-}
-function getInatShapes(places) {
-    return __awaiter(this, void 0, void 0, function () {
-        var values, url, response, data;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    values = Object.keys(places).join(',');
-                    url = "https://api.inaturalist.org/v1/places/".concat(values);
-                    return [4 /*yield*/, fetch(url, { headers: { accept: 'application/json' } })];
-                case 1:
-                    response = _a.sent();
-                    if (response.status >= 400) {
-                        throw new Error("Fetching iNaturalist data for places: ".concat(response.status));
-                    }
-                    return [4 /*yield*/, response.json()];
-                case 2:
-                    data = _a.sent();
-                    return [2 /*return*/, data.results];
-            }
-        });
-    });
-}
-function main(args) {
-    return __awaiter(this, void 0, void 0, function () {
-        var directory, places, inatMap, _i, _a, _b, name_1, id, _c, _d, _e, inatId, geometry_geojson, id;
-        return __generator(this, function (_f) {
-            switch (_f.label) {
-                case 0:
-                    directory = path.resolve(args[0]);
-                    return [4 /*yield*/, loadPlaces(directory)];
-                case 1:
-                    places = _f.sent();
-                    inatMap = {};
-                    _i = 0;
-                    return [4 /*yield*/, getInatIds(places)];
-                case 2:
-                    _a = _f.sent();
-                    _f.label = 3;
-                case 3:
-                    if (!(_i < _a.length)) return [3 /*break*/, 5];
-                    _b = _a[_i], name_1 = _b.name, id = _b.id;
-                    inatMap[id.value] = places.get(name_1.value);
-                    _f.label = 4;
-                case 4:
-                    _i++;
-                    return [3 /*break*/, 3];
-                case 5:
-                    _c = 0;
-                    return [4 /*yield*/, getInatShapes(inatMap)];
-                case 6:
-                    _d = _f.sent();
-                    _f.label = 7;
-                case 7:
-                    if (!(_c < _d.length)) return [3 /*break*/, 10];
-                    _e = _d[_c], inatId = _e.id, geometry_geojson = _e.geometry_geojson;
-                    id = inatMap[inatId].get('id');
-                    return [4 /*yield*/, fs_1.promises.writeFile(path.join(directory, 'maps', id + '.json'), JSON.stringify(geometry_geojson))];
-                case 8:
-                    _f.sent();
-                    _f.label = 9;
-                case 9:
-                    _c++;
-                    return [3 /*break*/, 7];
-                case 10: return [2 /*return*/];
-            }
-        });
-    });
-}
-main(process.argv.slice(2)).catch(function (error) {
-    console.error(error);
-    process.exit(1);
-});

package/lib/bin/index-place-shapes.js

@@ -1,115 +0,0 @@
-#!/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 __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 };
-    }
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-var fs_1 = require("fs");
-var path = __importStar(require("path"));
-function main(args) {
-    return __awaiter(this, void 0, void 0, function () {
-        var rootDirectory, directory, files, index, _i, files_1, file, id, json;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    rootDirectory = path.resolve(args[0]);
-                    directory = path.join(rootDirectory, 'maps');
-                    return [4 /*yield*/, fs_1.promises.readdir(directory)];
-                case 1:
-                    files = _a.sent();
-                    index = {};
-                    _i = 0, files_1 = files;
-                    _a.label = 2;
-                case 2:
-                    if (!(_i < files_1.length)) return [3 /*break*/, 5];
-                    file = files_1[_i];
-                    id = path.basename(file, '.json');
-                    if (!id.match(/^G[1-9][0-9]*$/)) {
-                        return [3 /*break*/, 4];
-                    }
-                    return [4 /*yield*/, fs_1.promises.readFile(path.join(directory, file), 'utf8')];
-                case 3:
-                    json = _a.sent();
-                    index[id] = JSON.parse(json);
-                    _a.label = 4;
-                case 4:
-                    _i++;
-                    return [3 /*break*/, 2];
-                case 5: return [4 /*yield*/, fs_1.promises.writeFile(path.join(directory, 'index.json'), JSON.stringify(index))];
-                case 6:
-                    _a.sent();
-                    return [2 /*return*/];
-            }
-        });
-    });
-}
-main(process.argv.slice(2)).catch(function (error) {
-    console.error(error);
-    process.exit(1);
-});

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

@@ -1,177 +0,0 @@
-#!/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 __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 util = require("util");
-var index_1 = require("../index");
-var GBIF_RANKS = [
-    'kingdom',
-    'phyllum',
-    'class',
-    'order',
-    'family',
-    'genus',
-    'species',
-    'subspecies',
-    'variety'
-];
-var DISPLAY_FIELDS = [
-    'scientificNameID',
-    'taxonRank',
-    'scientificName',
-    'taxonomicStatus',
-    'taxonRemarks',
-    'colTaxonID',
-    'gbifTaxonID'
-];
-var ResourceProblemsProcessor = /** @class */ (function () {
-    function ResourceProblemsProcessor(collectionPath) {
-        this.DIR_ROOT = path.resolve(collectionPath);
-        this.DIR_DWC = path.join(this.DIR_ROOT, 'dwc');
-        this.FILE_INDEX = path.join(this.DIR_ROOT, 'index.json');
-        this.FILE_PROBLEMS = path.join(this.DIR_ROOT, 'problems.csv');
-    }
-    ResourceProblemsProcessor.prototype.run = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var problems, _a, _b, resources, _c, _d, _i, problems_1, problem, _work, resourceId, _problemText, resource, missing;
-            return __generator(this, function (_e) {
-                switch (_e.label) {
-                    case 0:
-                        _b = (_a = index_1.csv).parseCsv;
-                        return [4 /*yield*/, fs_1.promises.readFile(this.FILE_PROBLEMS, 'utf8')];
-                    case 1:
-                        problems = _b.apply(_a, [_e.sent()]).slice(1);
-                        _d = (_c = JSON).parse;
-                        return [4 /*yield*/, fs_1.promises.readFile(this.FILE_INDEX, 'utf8')];
-                    case 2:
-                        resources = _d.apply(_c, [_e.sent()]);
-                        _i = 0, problems_1 = problems;
-                        _e.label = 3;
-                    case 3:
-                        if (!(_i < problems_1.length)) return [3 /*break*/, 6];
-                        problem = problems_1[_i];
-                        _work = problem[0], resourceId = problem[1], _problemText = problem[2];
-                        return [4 /*yield*/, this.readAmendedResource(resourceId, resources)];
-                    case 4:
-                        resource = _e.sent();
-                        missing = this.getMissingMappings(resource);
-                        if (missing.length === 0) {
-                            this.removeProblem(resourceId);
-                        }
-                        _e.label = 5;
-                    case 5:
-                        _i++;
-                        return [3 /*break*/, 3];
-                    case 6: return [2 /*return*/];
-                }
-            });
-        });
-    };
-    ResourceProblemsProcessor.prototype.readAmendedResource = function (resourceId, resources) {
-        return __awaiter(this, void 0, void 0, function () {
-            var resource, resourceFileId, resourceFile, _a, header, taxonRows, _b, _c, taxa, _i, taxonRows_1, row, taxon;
-            return __generator(this, function (_d) {
-                switch (_d.label) {
-                    case 0:
-                        resource = resources[resourceId];
-                        resourceFileId = resourceId.split(':').join('-');
-                        resourceFile = path.join(this.DIR_DWC, "".concat(resourceFileId, ".csv"));
-                        _c = (_b = index_1.csv).parseCsv;
-                        return [4 /*yield*/, fs_1.promises.readFile(resourceFile, 'utf8')];
-                    case 1:
-                        _a = _c.apply(_b, [_d.sent()]), header = _a[0], taxonRows = _a.slice(1);
-                        taxa = {};
-                        for (_i = 0, taxonRows_1 = taxonRows; _i < taxonRows_1.length; _i++) {
-                            row = taxonRows_1[_i];
-                            taxon = row.reduce(function (taxon, value, index) {
-                                taxon[header[index]] = value;
-                                return taxon;
-                            }, {});
-                            taxa[taxon.scientificNameID] = taxon;
-                        }
-                        return [2 /*return*/, __assign(__assign({}, resource), { taxa: taxa })];
-                }
-            });
-        });
-    };
-    ResourceProblemsProcessor.prototype.getMissingMappings = function (resource) {
-        var missing = [];
-        for (var id in resource.taxa) {
-            var taxon = resource.taxa[id];
-            if (taxon.taxonomicStatus !== 'accepted') {
-                continue;
-            }
-            var missingCol = false; // !taxon.colTaxonID
-            var missingGbif = GBIF_RANKS.includes(taxon.taxonRank) && !taxon.gbifTaxonID;
-            if (missingCol || missingGbif) {
-                missing.push(taxon);
-            }
-        }
-        return missing;
-    };
-    ResourceProblemsProcessor.prototype.removeProblem = function (resourceId) {
-        resourceId;
-        //
-    };
-    return ResourceProblemsProcessor;
-}());
-function main() {
-    var args = util.parseArgs({ allowPositionals: true });
-    var processor = new ResourceProblemsProcessor(args.positionals[0]);
-    process.on('exit', function () {
-        process.stdout.write('\n');
-    });
-    processor.run().catch(function (error) {
-        console.error(error);
-        process.exit(1);
-    });
-}
-main();

package/lib/resources/content/clavis.js

@@ -1,10 +0,0 @@
-// interface Key {
-//     $schema: Url,
-//     title: LocalizedString,
-//     media?: Url,
-//     description: LocalizedString
-// }
-//
-// type Url = string
-// type LocalizedString = string|Record<Locale,string>
-// type Locale = string