@larsgw/formica 0.8.1 → 0.8.3

package/CHANGELOG.md

@@ -1,3 +1,22 @@
+## [0.8.3](https://github.com/identification-resources/formica/compare/v0.8.2...v0.8.3) (2025-07-15)
+
+
+### Features
+
+* **catalog:** add catalog field key_characteristics ([6529cfa](https://github.com/identification-resources/formica/commit/6529cfab81f759f926b81bdd9d5a36e84b526284))
+
+
+
+## [0.8.2](https://github.com/identification-resources/formica/compare/v0.8.1...v0.8.2) (2025-06-26)
+
+
+### Bug Fixes
+
+* **resources:** add support for documented flag ([6cb89e4](https://github.com/identification-resources/formica/commit/6cb89e428bde8665b7e8f03b5c7f47a44e15f58e))
+* **resources:** allow hyphens in biname pattern ([6a58a77](https://github.com/identification-resources/formica/commit/6a58a77757b8b6ae8c2d7d01440775776d183d05))
+
+
+
 ## [0.8.1](https://github.com/identification-resources/formica/compare/v0.8.0...v0.8.1) (2025-05-30)
 
 

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

@@ -0,0 +1,188 @@
+#!/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

@@ -0,0 +1,115 @@
+#!/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/catalog/tables/work.js

@@ -48,6 +48,7 @@ var Work = /** @class */ (function (_super) {
             scope: { required: false, multiple: true },
             region: { required: true, multiple: true },
             complete: { required: false, multiple: false, format: value_1.FORMATS.COMPLETE },
+            key_characteristics: { required: false, multiple: true },
             target_taxa: { required: false, multiple: true },
             listed_in: { required: false, multiple: true, format: value_1.FORMATS.WORK_ID },
             part_of: { required: false, multiple: true, format: value_1.FORMATS.WORK_ID },

package/lib/resources/parse-text.js

@@ -102,7 +102,8 @@ var DWC_RANKS = [
 var FLAGS = [
     'MISSING_TAXA',
     'MISSING_PARENT_TAXA',
-    'MISSING_SYNONYMS'
+    'MISSING_SYNONYMS',
+    'MISSING_AUTHORSHIP'
 ];
 var TAXONOMIC_STATUS = {
     '>': 'incorrect',
@@ -164,12 +165,12 @@ var NAME_PATTERN = new RegExp('^' +
  *   $1 genus+subgenus (+ trailing space): (?:([A-Z]\S+) (?:\(([A-Z]\S+?)\) )?)?
  *     $1.1 genus: ((?:x )?[A-Z]\S+)
  *     $1.2 subgenus: (?:\(([A-Z]\S+?)\) )?
- *   $2 species: (x [a-z]+|[a-z][^\s.]+(?: x [a-z]+)?|[A-Z][a-z]+_[a-z]+ x [A-Z][a-z]+_[a-z]+)
- *     $2a: x [a-z]+
- *     $2b hybrid: [a-z][^\s.]+(?: x [a-z]+)?
- *     $2c intergeneric hybrid: [A-Z][a-z]+_[a-z]+ x [A-Z][a-z]+_[a-z]+
+ *   $2 species: (x [a-z-]+|[a-z-][^\s.]+(?: x [a-z-]+)?|[A-Z][a-z]+_[a-z-]+ x [A-Z][a-z]+_[a-z-]+)
+ *     $2a: x [a-z-]+
+ *     $2b hybrid: [a-z-][^\s.]+(?: x [a-z-]+)?
+ *     $2c intergeneric hybrid: [A-Z][a-z]+_[a-z-]+ x [A-Z][a-z]+_[a-z-]+
  */
-var BINAME_PATTERN = /^(?:((?:x )?[A-Z]\S+) (?:\(([A-Z]\S+?)\) )?)?(x [a-z]+|[a-z][^\s.]+(?: x [a-z]+)?|[A-Z][a-z]+_[a-z]+ x [A-Z][a-z]+_[a-z]+)(?= |$)/;
+var BINAME_PATTERN = /^(?:((?:x )?[A-Z]\S+) (?:\(([A-Z]\S+?)\) )?)?(x [a-z-]+|[a-z-][^\s.]+(?: x [a-z-]+)?|[A-Z][a-z]+_[a-z-]+ x [A-Z][a-z]+_[a-z-]+)(?= |$)/;
 function compareRanks(a, b) {
     return RANKS.indexOf(a) - RANKS.indexOf(b);
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@larsgw/formica",
-  "version": "0.8.1",
+  "version": "0.8.3",
   "description": "SDK and tools for data from the Library of Identification Resources",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",

package/src/catalog/tables/work.ts

@@ -30,6 +30,7 @@ export class Work extends Entity {
             scope: { required: false, multiple: true },
             region: { required: true, multiple: true },
             complete: { required: false, multiple: false, format: FORMATS.COMPLETE },
+            key_characteristics: { required: false, multiple: true },
             target_taxa: { required: false, multiple: true },
             listed_in: { required: false, multiple: true, format: FORMATS.WORK_ID },
             part_of: { required: false, multiple: true, format: FORMATS.WORK_ID },

package/src/resources/parse-text.ts

@@ -58,7 +58,8 @@ const DWC_RANKS: DwcRank[] = [
 const FLAGS: ResourceFlag[] = [
     'MISSING_TAXA',
     'MISSING_PARENT_TAXA',
-    'MISSING_SYNONYMS'
+    'MISSING_SYNONYMS',
+    'MISSING_AUTHORSHIP'
 ]
 
 const TAXONOMIC_STATUS: Record<string, TaxonStatus> = {
@@ -130,12 +131,12 @@ const NAME_PATTERN = new RegExp(
  *   $1 genus+subgenus (+ trailing space): (?:([A-Z]\S+) (?:\(([A-Z]\S+?)\) )?)?
  *     $1.1 genus: ((?:x )?[A-Z]\S+)
  *     $1.2 subgenus: (?:\(([A-Z]\S+?)\) )?
- *   $2 species: (x [a-z]+|[a-z][^\s.]+(?: x [a-z]+)?|[A-Z][a-z]+_[a-z]+ x [A-Z][a-z]+_[a-z]+)
- *     $2a: x [a-z]+
- *     $2b hybrid: [a-z][^\s.]+(?: x [a-z]+)?
- *     $2c intergeneric hybrid: [A-Z][a-z]+_[a-z]+ x [A-Z][a-z]+_[a-z]+
+ *   $2 species: (x [a-z-]+|[a-z-][^\s.]+(?: x [a-z-]+)?|[A-Z][a-z]+_[a-z-]+ x [A-Z][a-z]+_[a-z-]+)
+ *     $2a: x [a-z-]+
+ *     $2b hybrid: [a-z-][^\s.]+(?: x [a-z-]+)?
+ *     $2c intergeneric hybrid: [A-Z][a-z]+_[a-z-]+ x [A-Z][a-z]+_[a-z-]+
  */
-const BINAME_PATTERN = /^(?:((?:x )?[A-Z]\S+) (?:\(([A-Z]\S+?)\) )?)?(x [a-z]+|[a-z][^\s.]+(?: x [a-z]+)?|[A-Z][a-z]+_[a-z]+ x [A-Z][a-z]+_[a-z]+)(?= |$)/
+const BINAME_PATTERN = /^(?:((?:x )?[A-Z]\S+) (?:\(([A-Z]\S+?)\) )?)?(x [a-z-]+|[a-z-][^\s.]+(?: x [a-z-]+)?|[A-Z][a-z]+_[a-z-]+ x [A-Z][a-z]+_[a-z-]+)(?= |$)/
 
 function compareRanks (a: Rank, b: Rank): number {
     return RANKS.indexOf(a) - RANKS.indexOf(b)