@larsgw/formica 0.5.1 → 0.6.0

package/CHANGELOG.md

@@ -1,3 +1,21 @@
+# [0.6.0](https://github.com/identification-resources/formica/compare/v0.5.2...v0.6.0) (2024-01-05)
+
+
+### Features
+
+* **catalog:** add entry type, key type values ([ed6e4fb](https://github.com/identification-resources/formica/commit/ed6e4fb545e09cddb5d466f602bffb8a8483f043))
+
+
+
+## [0.5.2](https://github.com/identification-resources/formica/compare/v0.5.1...v0.5.2) (2023-11-27)
+
+
+### Bug Fixes
+
+* **resources:** fix GBIF index generation ([c88e2d2](https://github.com/identification-resources/formica/commit/c88e2d2b306b930ca0b00b978e3eb89b8adfb656))
+
+
+
 ## [0.5.1](https://github.com/identification-resources/formica/compare/v0.5.0...v0.5.1) (2023-11-03)
 
 

package/README.md

@@ -3,7 +3,17 @@
 **Formica** is an SDK and a collection of tools for the data in the Library of
 Identification Resources.
 
-## Tools
+## Install
+
+Install globally:
+
+    npm install --global @larsgw/formica
+
+Run locally:
+
+    npx --package @larsgw/formica -- ...
+
+## CLI
 
   - `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)).
@@ -17,3 +27,12 @@ Identification Resources.
     `--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.
+
+## API
+
+```js
+const Formica = require('@larsgw/formica')
+
+// Load catalog data
+const catalog = Formica.catalog.loadData(`...`, 'catalog')
+```

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

@@ -96,7 +96,7 @@ function main(args) {
                                             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;
+                                                        var amendedResource, dwcFile, _a, header, dwc, _b, _c, gbifColumn, gbifAcceptedColumn, _i, dwc_1, taxon, gbifId;
                                                         return __generator(this, function (_d) {
                                                             switch (_d.label) {
                                                                 case 0:
@@ -108,14 +108,16 @@ function main(args) {
                                                                     _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);
+                                                                    _a = _c.apply(_b, [_d.sent()]), header = _a[0], dwc = _a.slice(1);
+                                                                    gbifColumn = header.indexOf('gbifTaxonID');
+                                                                    gbifAcceptedColumn = header.indexOf('gbifAcceptedTaxonID');
                                                                     for (_i = 0, dwc_1 = dwc; _i < dwc_1.length; _i++) {
                                                                         taxon = dwc_1[_i];
-                                                                        gbifId = taxon[25];
+                                                                        gbifId = taxon[gbifColumn];
                                                                         if (gbifId) {
                                                                             addTaxon(gbifIndex, gbifId, taxon);
-                                                                            if (taxon[27] !== taxon[25]) {
-                                                                                addTaxon(gbifIndex, taxon[27], taxon);
+                                                                            if (taxon[gbifAcceptedColumn] !== taxon[gbifColumn]) {
+                                                                                addTaxon(gbifIndex, taxon[gbifAcceptedColumn], taxon);
                                                                             }
                                                                         }
                                                                         amendedResource.taxonCount += 1;

package/lib/catalog/value.js

@@ -7,8 +7,8 @@ var spdxLicenseList = require("spdx-license-list");
 var ietfTagListFactory = require("ietf-language-tag-regex");
 var ietfTagList = ietfTagListFactory();
 exports.FORMATS = {
-    ENTRY_TYPE: ['print', 'online', 'cd'],
-    KEY_TYPE: ['key', 'matrix', 'reference', 'gallery', 'checklist', 'supplement', 'collection'],
+    ENTRY_TYPE: ['print', 'online', 'cd', 'application'],
+    KEY_TYPE: ['key', 'matrix', 'reference', 'gallery', 'checklist', 'supplement', 'collection', 'algorithm'],
     COMPLETE: ['TRUE', 'FALSE'],
     ID: /^B\d+$/,
     EDTF_0: /^(\d{4}(-\d{2}(-\d{2}(T\d{2}:\d{2}:\d{2}(Z|[-+]\d{2}(:\d{2})?))?)?)?|\d{4}(-\d{2}(-\d{2})?)?\/(\d{4}(-\d{2}(-\d{2})?)?|\.\.))$/,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@larsgw/formica",
-  "version": "0.5.1",
+  "version": "0.6.0",
   "description": "SDK and tools for data from the Library of Identification Resources",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",

package/src/bin/process-resources-index.ts

@@ -54,13 +54,15 @@ async function main (args: string[]): Promise<void> {
                 return
             }
 
-            const [_header, ...dwc] = csv.parseCsv(await fs.readFile(dwcFile, 'utf-8'))
+            const [header, ...dwc] = csv.parseCsv(await fs.readFile(dwcFile, 'utf-8'))
+            const gbifColumn = header.indexOf('gbifTaxonID')
+            const gbifAcceptedColumn = header.indexOf('gbifAcceptedTaxonID')
             for (const taxon of dwc) {
-                const gbifId = taxon[25]
+                const gbifId = taxon[gbifColumn]
                 if (gbifId) {
                     addTaxon(gbifIndex, gbifId, taxon)
-                    if (taxon[27] !== taxon[25]) {
-                        addTaxon(gbifIndex, taxon[27], taxon)
+                    if (taxon[gbifAcceptedColumn] !== taxon[gbifColumn]) {
+                        addTaxon(gbifIndex, taxon[gbifAcceptedColumn], taxon)
                     }
                 }
                 amendedResource.taxonCount += 1

package/src/catalog/value.ts

@@ -6,8 +6,8 @@ import ietfTagListFactory = require('ietf-language-tag-regex')
 const ietfTagList = ietfTagListFactory()
 
 export const FORMATS = {
-    ENTRY_TYPE: ['print', 'online', 'cd'],
-    KEY_TYPE: ['key', 'matrix', 'reference', 'gallery', 'checklist', 'supplement', 'collection'],
+    ENTRY_TYPE: ['print', 'online', 'cd', 'application'],
+    KEY_TYPE: ['key', 'matrix', 'reference', 'gallery', 'checklist', 'supplement', 'collection', 'algorithm'],
     COMPLETE: ['TRUE', 'FALSE'],
 
     ID: /^B\d+$/,