@larsgw/formica 0.3.0 → 0.3.1

package/CHANGELOG.md

@@ -1,3 +1,14 @@
+## [0.3.1](https://github.com/identification-resources/formica/compare/v0.3.0...v0.3.1) (2023-09-04)
+
+
+### Bug Fixes
+
+* **resources:** allow correction of synonyms of lowest taxa ([c737d5b](https://github.com/identification-resources/formica/commit/c737d5b09d5e5b24f4cc2c8cff88c9ada8d0ab7b))
+* **resources:** fix regression in c737d5b ([d4e52e9](https://github.com/identification-resources/formica/commit/d4e52e95ed1a35dabbd80b9f9aace1a824fdae98))
+* **resources:** handle corrections to synonyms ([21ed9b7](https://github.com/identification-resources/formica/commit/21ed9b79f77e1e6d0639d96ed9822d5212a85a2e)), closes [#4](https://github.com/identification-resources/formica/issues/4)
+
+
+
 # [0.3.0](https://github.com/identification-resources/formica/compare/v0.2.1...v0.3.0) (2023-08-20)
 
 

package/lib/resources/parse-text.js

@@ -361,7 +361,7 @@ function parseHeader(header) {
 }
 function validateResource(config, content) {
     // Check for too much indentation
-    var longerIndent = new RegExp("^(  ){".concat(config.levels.length - 1, "}(?!  [+=>] ) "), 'm');
+    var longerIndent = new RegExp("^(  ){".concat(config.levels.length - 1, "}(?!  [+=>] |    > ) "), 'm');
     var longerIndentMatch = content.match(longerIndent);
     if (longerIndentMatch !== null) {
         var offset = longerIndentMatch.index;
@@ -402,8 +402,8 @@ function parseResourceContent(content, resource, oldIds) {
         }
         var lineIndent = line.match(/^ */)[0].length;
         if (lineIndent > groupIndent) {
-            // Do not count synonyms as parents
-            if (data[previousId] && data[previousId].taxonomicStatus === 'accepted') {
+            // Do not count synonyms as parents (unless this is correcting a typo in the synonym)
+            if (data[previousId] && data[previousId].taxonomicStatus === 'accepted' || /^( {2})+> /.test(line)) {
                 parents.push(previousId);
             }
             else {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@larsgw/formica",
-  "version": "0.3.0",
+  "version": "0.3.1",
   "description": "SDK and tools for data from the Library of Identification Resources",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",

package/src/resources/parse-text.ts

@@ -372,7 +372,7 @@ function parseHeader (header: string): ResourceMetadata {
 
 function validateResource (config: ResourceMetadata, content: string) {
     // Check for too much indentation
-    const longerIndent = new RegExp(`^(  ){${config.levels.length - 1}}(?!  [+=>] ) `, 'm')
+    const longerIndent = new RegExp(`^(  ){${config.levels.length - 1}}(?!  [+=>] |    > ) `, 'm')
     const longerIndentMatch = content.match(longerIndent)
     if (longerIndentMatch !== null) {
         const offset = longerIndentMatch.index
@@ -425,8 +425,8 @@ function parseResourceContent (content: ResourceDiff, resource: Resource, oldIds
         const lineIndent = (line.match(/^ */) as string[])[0].length
 
         if (lineIndent > groupIndent) {
-            // Do not count synonyms as parents
-            if (data[previousId] && data[previousId].taxonomicStatus === 'accepted') {
+            // Do not count synonyms as parents (unless this is correcting a typo in the synonym)
+            if (data[previousId] && data[previousId].taxonomicStatus === 'accepted' || /^( {2})+> /.test(line)) {
                 parents.push(previousId)
             } else {
                 parents.push(null)

package/test/resources.js

@@ -4,7 +4,33 @@ const assert = require('assert')
 const { resources } = require('../lib')
 
 test('resources', async (t) => {
-    await t.test('missing leaf taxa', (t) => {
+    await t.test('parses author with initials', (t) => {
+        const [resource] = resources.parseTextFile(`---
+levels: [family, genus, species]
+---
+
+    Dolichurus haemorrhous A. Costa, 1886
+  Dolichurus A. Costa, 1886
+    Dolichurus indet.
+Sphecidae A. Costa, 1886
+    Sphecidae indet.
+`, 'T1')
+        assert.deepStrictEqual(Object.values(resource.taxa).map(taxon => taxon.scientificNameAuthorship), Array(3).fill('A. Costa, 1886'))
+    })
+
+    await t.test('does not validate name with correction', (t) => {
+        const [resource] = resources.parseTextFile(`---
+levels: [species]
+---
+
+Clytochrysus lapidarius (Panzer, 1804)
+  = Crabo chrysostomus Lepeletier & Brullé, 1835
+    > Crabro chrysostomus Lepeletier & Brullé, 1835
+`, 'T1')
+        assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Clytochrysus lapidarius (Panzer, 1804)')
+    })
+
+    await t.test('errors for missing leaf taxa', (t) => {
         assert.throws(() => {
             resources.parseTextFile(`---
 levels: [family, genus, species]