@larsgw/formica 0.10.0 → 0.10.1

package/lib/bin/validate-catalog.js

@@ -47,37 +47,38 @@ const fs_1 = require("fs");
 const path = __importStar(require("path"));
 const index_1 = require("../index");
 class TaxaValidator {
-    constructor(taxa) {
-        this.taxa = Array.from(taxa).filter(taxon => taxon.has('ancestors_gbif'));
+    constructor(taxa, fields) {
+        this.taxa = Array.from(taxa).filter(taxon => taxon.has(fields.ancestors));
+        this.fields = fields;
         this.errors = [];
         this.parentIndex = {};
     }
     validate() {
         for (const taxon of this.taxa) {
-            const parents = taxon.get('ancestors_gbif');
+            const parents = taxon.get(this.fields.ancestors);
             if (parents.length > 1) {
                 const id = taxon.get('id');
                 for (let i = 1; i < parents.length; i++) {
-                    this.addToIndex(id, 'ancestors_gbif', parents[i], parents[i - 1]);
+                    this.addToIndex(id, this.fields.ancestors, parents[i], parents[i - 1]);
                 }
             }
         }
         for (const taxon of this.taxa) {
-            if (taxon.has('gbif')) {
+            if (taxon.has(this.fields.id)) {
                 const id = taxon.get('id');
-                const parents = taxon.get('ancestors_gbif');
+                const parents = taxon.get(this.fields.ancestors);
                 const parent = parents[parents.length - 1];
-                this.addToIndex(id, 'gbif', taxon.get('gbif'), parent);
+                this.addToIndex(id, this.fields.id, taxon.get(this.fields.id), parent);
             }
         }
         for (const taxon of this.taxa) {
-            if (taxon.has('children_gbif')) {
+            if (taxon.has(this.fields.children)) {
                 const id = taxon.get('id');
-                const parents = taxon.get('ancestors_gbif');
+                const parents = taxon.get(this.fields.ancestors);
                 const parent = parents[parents.length - 1];
-                const childIds = taxon.get('children_gbif');
+                const childIds = taxon.get(this.fields.children);
                 for (const childId of childIds) {
-                    this.addToIndex(id, 'gbif', childId, parent);
+                    this.addToIndex(id, this.fields.id, childId, parent);
                 }
             }
         }
@@ -94,6 +95,24 @@ class TaxaValidator {
         }
     }
 }
+class GbifTaxaValidator extends TaxaValidator {
+    constructor(taxa) {
+        super(taxa, {
+            id: 'gbif',
+            children: 'children_gbif',
+            ancestors: 'ancestors_gbif'
+        });
+    }
+}
+class ColTaxaValidator extends TaxaValidator {
+    constructor(taxa) {
+        super(taxa, {
+            id: 'col',
+            children: 'children_col',
+            ancestors: 'ancestors_col'
+        });
+    }
+}
 function validateFile(arg) {
     return __awaiter(this, void 0, void 0, function* () {
         const filePath = path.resolve(arg);
@@ -116,8 +135,10 @@ function validateFile(arg) {
             }
         }
         if (sheet === 'taxa') {
-            const validator = new TaxaValidator(entities);
-            errors.push(...validator.validate());
+            // const colValidator = new ColTaxaValidator(entities)
+            // errors.push(...colValidator.validate())
+            const gbifValidator = new GbifTaxaValidator(entities);
+            errors.push(...gbifValidator.validate());
         }
         return errors;
     });

package/lib/catalog/tables/taxon.js

@@ -10,6 +10,10 @@ class Taxon extends entity_1.Entity {
             id: { required: true, multiple: false, format: value_1.FORMATS.TAXON_ID },
             qid: { required: false, multiple: false, format: value_1.FORMATS.QID },
             rank: { required: false, multiple: false },
+            col: { required: false, multiple: false, format: value_1.FORMATS.COL_ID },
+            accepted_col: { required: false, multiple: false, format: value_1.FORMATS.COL_ID },
+            children_col: { required: false, multiple: true, format: value_1.FORMATS.COL_ID },
+            ancestors_col: { required: false, multiple: true, format: value_1.FORMATS.COL_ID },
             gbif: { required: false, multiple: false, format: value_1.FORMATS.INTEGER },
             children_gbif: { required: false, multiple: true, format: value_1.FORMATS.INTEGER },
             ancestors_gbif: { required: false, multiple: true, format: value_1.FORMATS.INTEGER },

package/lib/catalog/value.d.ts

@@ -14,6 +14,7 @@ export declare const FORMATS: {
     QID: RegExp;
     URL: RegExp;
     INTEGER: RegExp;
+    COL_ID: RegExp;
     LICENSE(value: SingleValue): true;
     LANGUAGE(value: SingleValue): boolean;
 };

package/lib/catalog/value.js

@@ -24,6 +24,7 @@ exports.FORMATS = {
     QID: /^Q[1-9][0-9]*$/,
     URL: /^(ftp|http|https):\/\/((?:[a-z0-9][a-z0-9-_]*?[a-z0-9]?\.)+(?:xn--)?[a-z0-9]+)(:\d*)?((?:\/(?:%\d\d|[!$&'()*+,\-.0-9";=@A-Z_a-z~])*)*)(\?(?:%\d\d|[!$&'()*+,\-./0-9:;=?@A-Z_a-z~])*)?(#(?:%\d\d|[!$&'()*+,\-./0-9:;=?@A-Z_a-z~])*)?/i,
     INTEGER: /^(0|[1-9]\d*)$/,
+    COL_ID: /^(0|[1-9A-Z][0-9A-Z]*)$/,
     LICENSE(value) { return /^<(public domain|.+\?)>$/.test(value) || !!spdx_license_list_1.default[value]; },
     LANGUAGE(value) { return ietfTagList.test(value); }
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@larsgw/formica",
-  "version": "0.10.0",
+  "version": "0.10.1",
   "description": "SDK and tools for data from the Library of Identification Resources",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",