@larsgw/formica 0.8.5 → 0.8.7

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

@@ -1,16 +1,5 @@
 #!/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 __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -53,45 +42,17 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         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");
-var util_1 = require("./util");
+const fs_1 = require("fs");
+const path = __importStar(require("path"));
+const index_1 = require("../index");
+const util_1 = require("./util");
 function alphabeticSort(a, b) {
     return a > b ? 1 : a < b ? -1 : 0;
 }
 function sortObject(object, sorter) {
-    var sorted = {};
-    for (var _i = 0, _a = Object.keys(object).sort(sorter !== null && sorter !== void 0 ? sorter : util_1.numericSort); _i < _a.length; _i++) {
-        var key = _a[_i];
+    const sorted = {};
+    for (const key of Object.keys(object).sort(sorter !== null && sorter !== void 0 ? sorter : util_1.numericSort)) {
         sorted[key] = object[key];
     }
     return sorted;
@@ -104,93 +65,61 @@ function addTaxon(index, id, taxon) {
     index[id].sort(util_1.numericSort);
 }
 function main(args) {
-    return __awaiter(this, void 0, void 0, function () {
-        var REPO_ROOT, files, gbifIndex, colIndex, 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 = {};
-                    colIndex = {};
-                    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, gbifColumn, gbifAcceptedColumn, colColumn, colAcceptedColumn, _i, dwc_1, taxon, gbifId, colId;
-                                                        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);
-                                                                    gbifColumn = header.indexOf('gbifTaxonID');
-                                                                    gbifAcceptedColumn = header.indexOf('gbifAcceptedTaxonID');
-                                                                    colColumn = header.indexOf('colTaxonID');
-                                                                    colAcceptedColumn = header.indexOf('colAcceptedTaxonID');
-                                                                    for (_i = 0, dwc_1 = dwc; _i < dwc_1.length; _i++) {
-                                                                        taxon = dwc_1[_i];
-                                                                        gbifId = taxon[gbifColumn];
-                                                                        if (gbifId) {
-                                                                            addTaxon(gbifIndex, gbifId, taxon);
-                                                                            if (taxon[gbifAcceptedColumn] !== taxon[gbifColumn]) {
-                                                                                addTaxon(gbifIndex, taxon[gbifAcceptedColumn], taxon);
-                                                                            }
-                                                                        }
-                                                                        colId = taxon[colColumn];
-                                                                        if (colId) {
-                                                                            addTaxon(colIndex, colId, taxon);
-                                                                            if (taxon[colAcceptedColumn] !== taxon[colColumn]) {
-                                                                                addTaxon(colIndex, taxon[colAcceptedColumn], taxon);
-                                                                            }
-                                                                        }
-                                                                        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, 'col.index.json'), JSON.stringify(sortObject(colIndex, alphabeticSort), 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*/];
-            }
-        });
+    return __awaiter(this, void 0, void 0, function* () {
+        const REPO_ROOT = path.resolve(args[0]);
+        const files = yield fs_1.promises.readdir(path.join(REPO_ROOT, 'txt'));
+        const gbifIndex = {};
+        const colIndex = {};
+        const resourceIndex = {};
+        yield Promise.all(files.map(function (fileName) {
+            return __awaiter(this, void 0, void 0, function* () {
+                if (!fileName.endsWith('.txt')) {
+                    return;
+                }
+                const id = fileName.slice(0, -4);
+                const file = yield fs_1.promises.readFile(path.join(REPO_ROOT, 'txt', fileName), 'utf-8');
+                return Promise.all(index_1.resources.parseTextFileHeader(file).map(function (resource, index) {
+                    return __awaiter(this, void 0, void 0, function* () {
+                        const amendedResource = Object.assign(Object.assign({}, resource), { id: `${id}:${index + 1}`, taxonCount: 0 });
+                        const dwcFile = path.join(REPO_ROOT, 'dwc', `${id}-${index + 1}.csv`);
+                        if (!(0, fs_1.existsSync)(dwcFile)) {
+                            return;
+                        }
+                        const [header, ...dwc] = index_1.csv.parseCsv(yield fs_1.promises.readFile(dwcFile, 'utf-8'));
+                        const gbifColumn = header.indexOf('gbifTaxonID');
+                        const gbifAcceptedColumn = header.indexOf('gbifAcceptedTaxonID');
+                        const colColumn = header.indexOf('colTaxonID');
+                        const colAcceptedColumn = header.indexOf('colAcceptedTaxonID');
+                        for (const taxon of dwc) {
+                            const gbifId = taxon[gbifColumn];
+                            if (gbifId) {
+                                addTaxon(gbifIndex, gbifId, taxon);
+                                if (taxon[gbifAcceptedColumn] !== taxon[gbifColumn]) {
+                                    addTaxon(gbifIndex, taxon[gbifAcceptedColumn], taxon);
+                                }
+                            }
+                            const colId = taxon[colColumn];
+                            if (colId) {
+                                addTaxon(colIndex, colId, taxon);
+                                if (taxon[colAcceptedColumn] !== taxon[colColumn]) {
+                                    addTaxon(colIndex, taxon[colAcceptedColumn], taxon);
+                                }
+                            }
+                            amendedResource.taxonCount += 1;
+                        }
+                        resourceIndex[amendedResource.id] = amendedResource;
+                    });
+                }));
+            });
+        }));
+        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, 'col.index.json'), JSON.stringify(sortObject(colIndex, alphabeticSort), null, 2)),
+            fs_1.promises.writeFile(path.join(REPO_ROOT, 'index.json'), JSON.stringify(sortObject(resourceIndex), null, 2))
+        ]);
     });
 }
-main(process.argv.slice(2)).catch(function (error) {
+main(process.argv.slice(2)).catch(error => {
     console.error(error);
     process.exit(1);
 });