@larsgw/formica 0.1.1 → 0.2.0

package/lib/catalog/tables/work.js

@@ -44,6 +44,7 @@ var Work = /** @class */ (function (_super) {
             license: { required: false, multiple: true, format: value_1.FORMATS.LICENSE },
             key_type: { required: true, multiple: true, format: value_1.FORMATS.KEY_TYPE },
             taxon: { required: true, multiple: true },
+            taxon_scope: { required: false, multiple: true },
             scope: { required: false, multiple: true },
             region: { required: true, multiple: true },
             complete: { required: false, multiple: false, format: value_1.FORMATS.COMPLETE },

package/lib/resources/parse-text.js

@@ -362,6 +362,14 @@ function parseResource(resource) {
         var line = (content.slice(0, offset).match(/\n/g) || []).length + 1;
         throw new SyntaxError("Too much indentation at ".concat(line, ":0\n").concat(content.slice(offset).split('\n', 1), "\n^"));
     }
+    // Check for missing leaf taxa
+    var missingLeafTaxa = new RegExp("^(  ){0,".concat(config.levels.length - 2, "}(?![+=>] ).*\\n(?!\\1  )"), 'm');
+    var missingLeafTaxaMatch = content.match(missingLeafTaxa);
+    if (missingLeafTaxaMatch !== null) {
+        var offset = missingLeafTaxaMatch.index;
+        var line = (content.slice(0, offset).match(/\n/g) || []).length + 1;
+        throw new SyntaxError("Missing leaf taxon at ".concat(line, ":0\n").concat(content.slice(offset).split('\n', 1), "\n^"));
+    }
     return [config, content];
 }
 function parseResourceContent(content, resource, oldIds) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@larsgw/formica",
-  "version": "0.1.1",
+  "version": "0.2.0",
   "description": "SDK and tools for data from the Library of Identification Resources",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",
@@ -11,6 +11,7 @@
     "loir-resources-index": "./lib/bin/process-resources-index.js"
   },
   "scripts": {
+    "test": "node --test --test-reporter spec",
     "lint": "eslint src",
     "build": "tsc -d",
     "preversion": "npm run lint",

package/src/catalog/tables/work.ts

@@ -26,6 +26,7 @@ export class Work extends Entity {
             license: { required: false, multiple: true, format: FORMATS.LICENSE },
             key_type: { required: true, multiple: true, format: FORMATS.KEY_TYPE },
             taxon: { required: true, multiple: true },
+            taxon_scope: { required: false, multiple: true },
             scope: { required: false, multiple: true },
             region: { required: true, multiple: true },
             complete: { required: false, multiple: false, format: FORMATS.COMPLETE },

package/src/resources/parse-text.ts

@@ -376,6 +376,17 @@ ${content.slice(offset).split('\n', 1)}
 ^`)
     }
 
+    // Check for missing leaf taxa
+    const missingLeafTaxa = new RegExp(`^(  ){0,${config.levels.length - 2}}(?![+=>] ).*\\n(?!\\1  )`, 'm')
+    const missingLeafTaxaMatch = content.match(missingLeafTaxa)
+    if (missingLeafTaxaMatch !== null) {
+        const offset = missingLeafTaxaMatch.index
+        const line = (content.slice(0, offset).match(/\n/g) || []).length + 1
+        throw new SyntaxError(`Missing leaf taxon at ${line}:0
+${content.slice(offset).split('\n', 1)}
+^`)
+    }
+
     return [config, content]
 }
 

package/test/resources.js

@@ -0,0 +1,19 @@
+const test = require('node:test')
+const assert = require('assert')
+
+const { resources } = require('../lib')
+
+test('resources', async (t) => {
+    await t.test('missing leaf taxa', (t) => {
+        assert.throws(() => {
+            resources.parseTextFile(`---
+levels: [family, genus, species]
+---
+
+Cydnidae
+Cydnidae
+  Legnotus
+    limbosus`, 'T1')
+        })
+    })
+})

package/lib/types.d.ts

@@ -1,62 +0,0 @@
-type Value = string[] | string;
-type SingleValue = string;
-interface FieldError {
-    field: string;
-    error: string;
-}
-interface WorkError extends FieldError {
-    entity: WorkId;
-}
-type Rank = string;
-type DwcRank = Rank;
-type TaxonStatus = string;
-type TaxonId = string;
-type ResourceId = string;
-type WorkId = string;
-interface WorkingTaxon {
-    scientificNameID?: TaxonId;
-    scientificName?: string;
-    scientificNameAuthorship?: string;
-    genericName?: string;
-    infragenericEpithet?: string;
-    specificEpithet?: string;
-    intraspecificEpithet?: string;
-    taxonRank?: Rank;
-    taxonRemarks?: string;
-    collectionCode?: ResourceId;
-    taxonomicStatus?: TaxonStatus;
-    acceptedNameUsageID?: TaxonId;
-    acceptedNameUsage?: string;
-    parentNameUsageID?: TaxonId;
-    parentNameUsage?: string;
-    kingdom?: string;
-    phylum?: string;
-    class?: string;
-    order?: string;
-    family?: string;
-    subfamily?: string;
-    genus?: string;
-    subgenus?: string;
-    higherClassification?: string;
-    scientificNameOnly?: string;
-    incorrect?: WorkingTaxon;
-}
-interface Taxon extends WorkingTaxon {
-    scientificNameID: TaxonId;
-    scientificName: string;
-    taxonRank: Rank;
-    collectionCode: ResourceId;
-    taxonomicStatus: string;
-}
-interface ResourceMetadata {
-    levels: Rank[];
-    scope: string[];
-    catalog?: object;
-}
-interface Resource {
-    id: string;
-    file: string;
-    workId: string;
-    metadata: ResourceMetadata;
-    taxa: Record<TaxonId, Taxon>;
-}