@larsgw/formica 0.8.6 → 0.8.7

package/CHANGELOG.md

@@ -1,3 +1,12 @@
+## [0.8.7](https://github.com/identification-resources/formica/compare/v0.8.6...v0.8.7) (2025-11-01)
+
+
+### Bug Fixes
+
+* **resources:** fix handling of corrections ([49c05b4](https://github.com/identification-resources/formica/commit/49c05b499262e64514b832313360d1e6a4cc6378))
+
+
+
 ## [0.8.6](https://github.com/identification-resources/formica/compare/v0.8.5...v0.8.6) (2025-10-28)
 
 

package/lib/resources/parse-text.js

@@ -255,6 +255,10 @@ function parseResourceContent(content, resource, oldIds, offsetLine) {
         }
         // Amend "parent" with corrections, exit
         if (item.taxonomicStatus === 'incorrect') {
+            if (parent.taxonomicStatus !== 'accepted') {
+                // Remove corrected synonym from parentage
+                parents[parents.length - 1] = null;
+            }
             if (parent.incorrect) {
                 errors.push(makeParseError('Cannot apply a correction to a previous correction', lineNumber));
                 continue;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@larsgw/formica",
-  "version": "0.8.6",
+  "version": "0.8.7",
   "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

@@ -243,6 +243,11 @@ function parseResourceContent (content: ResourceDiff, resource: Resource, oldIds
 
         // Amend "parent" with corrections, exit
         if (item.taxonomicStatus === 'incorrect') {
+            if (parent.taxonomicStatus !== 'accepted') {
+                // Remove corrected synonym from parentage
+                parents[parents.length - 1] = null
+            }
+
             if (parent.incorrect) {
                 errors.push(makeParseError('Cannot apply a correction to a previous correction', lineNumber))
                 continue

package/test/resources.js

@@ -3,8 +3,8 @@ const assert = require('assert')
 
 const { catalog, resources } = require('../lib')
 
-suite('catalog', async (t) => {
-    await test('reports missing required fields', (t) => {
+suite('catalog', () => {
+    test('reports missing required fields', () => {
         const errors = catalog.loadData(`id
 B1`, 'catalog').validate()
         assert.deepStrictEqual(errors, [
@@ -18,8 +18,8 @@ B1`, 'catalog').validate()
     })
 })
 
-suite('resources', async (t) => {
-    await test('parses author with initials', (t) => {
+suite('resources', () => {
+    test('parses author with initials', () => {
         const [resource] = resources.parseTextFile(`---
 levels: [family, genus, species]
 ---
@@ -33,32 +33,7 @@ Sphecidae A. Costa, 1886
         assert.deepStrictEqual(Object.values(resource.taxa).map(taxon => taxon.scientificNameAuthorship), Array(3).fill('A. Costa, 1886'))
     })
 
-    await 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 test('errors for missing leaf taxa', (t) => {
-        assert.throws(() => {
-            resources.parseTextFile(`---
-levels: [family, genus, species]
----
-
-Cydnidae
-Cydnidae
-  Legnotus
-    limbosus`, 'T1')
-        })
-    })
-
-    await test('parses synonyms starting with intraspecific ranks', (t) => {
+    test('parses synonyms starting with intraspecific ranks', () => {
         const [resource] = resources.parseTextFile(`---
 levels: [species]
 ---
@@ -69,7 +44,7 @@ Lygaeus equestris (Linnaeus, 1758)
         assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Lygaeus equestris f. lactans Horváth, 1899')
     })
 
-    await test('parses accepted taxa starting with intraspecific ranks', (t) => {
+    test('parses accepted taxa starting with intraspecific ranks', () => {
         const [resource] = resources.parseTextFile(`---
 levels: [species, form]
 ---
@@ -80,18 +55,7 @@ Lygaeus equestris (Linnaeus, 1758)
         assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Lygaeus equestris f. lactans Horváth, 1899')
     })
 
-    await test('does not validate "indet." lines', (t) => {
-        const [resource] = resources.parseTextFile(`---
-levels: [genus, species]
----
-
-Drymus
-  [indet]
-`, 'T1')
-        assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Drymus')
-    })
-
-    await test('parses names containing non-ASCII characters', (t) => {
+    test('parses names containing non-ASCII characters', () => {
         const [resource] = resources.parseTextFile(`---
 levels: [species]
 ---
@@ -101,7 +65,7 @@ Nematus fåhraei Thomson
         assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Nematus fåhraei Thomson')
     })
 
-    await test('parses synonyms in different genera', (t) => {
+    test('parses synonyms in different genera', () => {
         const [resource] = resources.parseTextFile(`---
 levels: [species]
 ---
@@ -113,7 +77,7 @@ Katamenes arbustorum subsp. burlinii
         assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Eumenes arbustorum var. burlinii')
     })
 
-    await test('parses species without generic names', (t) => {
+    test('parses species without generic names', () => {
         const [resource] = resources.parseTextFile(`---
 levels: [genus, subgenus, species]
 ---
@@ -125,7 +89,7 @@ Microdynerus Thomson, 1874
         assert.strictEqual(resource.taxa['T1:1:3'].scientificName, 'Microdynerus microdynerus (Dalla Torre, 1889)')
     })
 
-    await test('parses hybrids', (t) => {
+    test('parses hybrids', () => {
         const [resource] = resources.parseTextFile(`---
 levels: [species]
 ---
@@ -137,20 +101,7 @@ Tilia x vulgaris
         assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Tilia ×vulgaris')
     })
 
-    await test('outputs corrected generic names', (t) => {
-        const [resource] = resources.parseTextFile(`---
-levels: [genus, species]
----
-
-Bogdania Kerzhner, 1964
-  > Bogdiana Kerzhner, 1964
-  myrmica Kerzhner, 1964
-`, 'T1')
-        assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Bogdiana Kerzhner, 1964')
-        assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Bogdiana myrmica Kerzhner, 1964')
-    })
-
-    await test('parses cross-genus hybrids', (t) => {
+    test('parses cross-genus hybrids', () => {
         const [resource] = resources.parseTextFile(`---
 levels: [genus, species]
 ---
@@ -165,7 +116,7 @@ x Festulpia
         assert.strictEqual(resource.taxa['T1:1:3'].scientificName, '×Festulpia Festuca rubra×Vulpia bromoides')
     })
 
-    await test('parses cross-genus hybrids without parent context', (t) => {
+    test('parses cross-genus hybrids without parent context', () => {
         const [resource] = resources.parseTextFile(`---
 levels: [species]
 ---
@@ -176,7 +127,7 @@ x Festulpia Festuca_rubra x Vulpia_bromoides
         assert.strictEqual(resource.taxa['T1:1:1'].verbatimIdentification, '× Festulpia Festuca rubra × Vulpia bromoides')
     })
 
-    await test('handles skips in ranks', (t) => {
+    test('handles skips in ranks', () => {
         const [resource] = resources.parseTextFile(`---
 levels: [family, genus, species]
 ---
@@ -189,8 +140,59 @@ Apidae
         assert.strictEqual(resource.taxa['T1:1:2'].taxonRank, 'species')
     })
 
-    await test('synonyms do not break recognition of missing leaf taxa (1)', (t) => {
+    test('parses genera with subgenus-rank synonyms', () => {
         const [resource] = resources.parseTextFile(`---
+levels: [genus]
+---
+
+Ectemnius Dahlbom
+  = Crabro (Ectemnius) Dahlbom
+`, 'T1')
+        assert.strictEqual(resource.taxa['T1:1:2'].taxonRank, 'subgenus')
+        assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Ectemnius Dahlbom')
+        assert.strictEqual(resource.taxa['T1:1:2'].genericName, 'Crabro')
+    })
+
+    test('parses genera with like-name subgenera', () => {
+        const [resource] = resources.parseTextFile(`---
+levels: [genus, subgenus]
+---
+
+Polistes Latreille, 1802
+  Polistes Latreille, 1802
+`, 'T1')
+        assert.strictEqual(resource.taxa['T1:1:2'].taxonRank, 'subgenus')
+        assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Polistes Latreille, 1802')
+        assert.strictEqual(resource.taxa['T1:1:2'].genericName, 'Polistes')
+    })
+
+    suite('leaf taxa checks', () => {
+        test('errors for missing leaf taxa', () => {
+            assert.throws(() => {
+                resources.parseTextFile(`---
+levels: [family, genus, species]
+---
+
+Cydnidae
+Cydnidae
+  Legnotus
+    limbosus`, 'T1')
+            })
+        })
+
+        test('does not validate "indet." lines', () => {
+            const [resource] = resources.parseTextFile(`---
+levels: [genus, species]
+---
+
+Drymus
+  [indet]
+`, 'T1')
+            assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Drymus')
+        })
+
+        test('synonyms do not break recognition of missing leaf taxa (1)', () => {
+            const [resource] = resources.parseTextFile(`---
 levels: [genus, subgenus, species]
 ---
 
@@ -199,12 +201,12 @@ Bombus
   Bombus
     pascuorum
 `, 'T1')
-        assert.strictEqual(resource.taxa['T1:1:4'].scientificName, 'Bombus pascuorum')
-    })
+            assert.strictEqual(resource.taxa['T1:1:4'].scientificName, 'Bombus pascuorum')
+        })
 
-    await test('synonyms do not break recognition of missing leaf taxa (2)', (t) => {
-        assert.throws(() => {
-          resources.parseTextFile(`---
+        test('synonyms do not break recognition of missing leaf taxa (2)', () => {
+            assert.throws(() => {
+            resources.parseTextFile(`---
 levels: [genus, subgenus, species]
 ---
 
@@ -214,12 +216,12 @@ Bombus
   Bombus
     pascuorum
 `, 'T1')
+            })
         })
-    })
 
-    await test('synonyms do not break recognition of missing leaf taxa (3)', (t) => {
-        assert.throws(() => {
-            resources.parseTextFile(`---
+        test('synonyms do not break recognition of missing leaf taxa (3)', () => {
+            assert.throws(() => {
+                resources.parseTextFile(`---
 levels: [family, genus, species]
 ---
 
@@ -229,50 +231,51 @@ Cydnidae
   Legnotus
     limbosus
 `, 'T1')
+            })
         })
     })
 
-    await test('parses genera with subgenus-rank synonyms', (t) => {
-        const [resource] = resources.parseTextFile(`---
-levels: [genus]
+    suite('corrections', () => {
+        test('outputs corrected generic names', () => {
+            const [resource] = resources.parseTextFile(`---
+levels: [genus, species]
 ---
 
-Ectemnius Dahlbom
-  = Crabro (Ectemnius) Dahlbom
+Bogdania Kerzhner, 1964
+  > Bogdiana Kerzhner, 1964
+  myrmica Kerzhner, 1964
 `, 'T1')
-        assert.strictEqual(resource.taxa['T1:1:2'].taxonRank, 'subgenus')
-        assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Ectemnius Dahlbom')
-        assert.strictEqual(resource.taxa['T1:1:2'].genericName, 'Crabro')
-    })
+            assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Bogdiana Kerzhner, 1964')
+            assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Bogdiana myrmica Kerzhner, 1964')
+        })
 
-    await test('parses genera with like-name subgenera', (t) => {
-        const [resource] = resources.parseTextFile(`---
-levels: [genus, subgenus]
+        test('does not validate name with correction', () => {
+            const [resource] = resources.parseTextFile(`---
+levels: [species]
 ---
 
-Polistes Latreille, 1802
-  Polistes Latreille, 1802
+Clytochrysus lapidarius (Panzer, 1804)
+  = Crabo chrysostomus Lepeletier & Brullé, 1835
+    > Crabro chrysostomus Lepeletier & Brullé, 1835
 `, 'T1')
-        assert.strictEqual(resource.taxa['T1:1:2'].taxonRank, 'subgenus')
-        assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Polistes Latreille, 1802')
-        assert.strictEqual(resource.taxa['T1:1:2'].genericName, 'Polistes')
-    })
+            assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Clytochrysus lapidarius (Panzer, 1804)')
+        })
 
-    await test('parses invalid but corrected name', (t) => {
-        const [resource] = resources.parseTextFile(`---
+        test('parses invalid but corrected name', () => {
+            const [resource] = resources.parseTextFile(`---
 levels: [species]
 ---
 
 Crabro Kiesenwetteri A. Morawitz. 1866
   > Crabro kiesenwetteri A. Morawitz. 1866
 `, 'T1')
-        assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Crabro kiesenwetteri A. Morawitz. 1866')
-        assert.strictEqual(resource.taxa['T1:1:1'].scientificNameAuthorship, 'A. Morawitz. 1866')
-        assert.strictEqual(resource.taxa['T1:1:1'].verbatimIdentification, 'Crabro Kiesenwetteri A. Morawitz. 1866')
-    })
+            assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Crabro kiesenwetteri A. Morawitz. 1866')
+            assert.strictEqual(resource.taxa['T1:1:1'].scientificNameAuthorship, 'A. Morawitz. 1866')
+            assert.strictEqual(resource.taxa['T1:1:1'].verbatimIdentification, 'Crabro Kiesenwetteri A. Morawitz. 1866')
+        })
 
-    await test('parses children of invalid but corrected name', (t) => {
-        const [resource] = resources.parseTextFile(`---
+        test('parses children of invalid but corrected name', () => {
+            const [resource] = resources.parseTextFile(`---
 levels: [genus, species]
 ---
 
@@ -283,40 +286,68 @@ Pirus L.
   Pirus aria Ehrh.
     > Pyrus aria Ehrh.
 `, 'T1')
-        assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Pyrus aucuparia Gaertn.')
-        assert.strictEqual(resource.taxa['T1:1:3'].scientificName, 'Pyrus domestica Sm.')
-        assert.strictEqual(resource.taxa['T1:1:4'].scientificName, 'Pyrus aria Ehrh.')
-    })
+            assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Pyrus aucuparia Gaertn.')
+            assert.strictEqual(resource.taxa['T1:1:3'].scientificName, 'Pyrus domestica Sm.')
+            assert.strictEqual(resource.taxa['T1:1:4'].scientificName, 'Pyrus aria Ehrh.')
+        })
 
-    await test('does not keep parts of invalid but corrected name', (t) => {
-        const [resource] = resources.parseTextFile(`---
+        test('does not keep parts of invalid but corrected name', () => {
+            const [resource] = resources.parseTextFile(`---
 levels: [species]
 ---
 
 Scolia 5-punctata FABRICIUS, 1781
   > Scolia quinquepunctata FABRICIUS, 1781
 `, 'T1')
-        assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Scolia quinquepunctata Fabricius, 1781')
-        assert.strictEqual(resource.taxa['T1:1:1'].verbatimIdentification, 'Scolia 5-punctata FABRICIUS, 1781')
-    })
+            assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Scolia quinquepunctata Fabricius, 1781')
+            assert.strictEqual(resource.taxa['T1:1:1'].verbatimIdentification, 'Scolia 5-punctata FABRICIUS, 1781')
+        })
 
-    await test('make correct diff when last line changes', (t) => {
-        const newText = `---
+        test('make correct diff when last line changes', () => {
+            const newText = `---
 levels: [species]
 ---
 
 Bittacus Hageni Brauer
   > Bittacus hageni Brauer
 `
-        const oldText = `---
+            const oldText = `---
 levels: [genus, species]
 ---
 
 Bittacus hageni Brauer
 `
 
-        const [resource] = resources.parseTextFile(newText, 'T1', { txt: oldText, dwc: [[null, ['T:1:1'], ['T:1:2']]] })
-        assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Bittacus hageni Brauer')
-        assert.strictEqual(resource.taxa['T1:1:1'].verbatimIdentification, 'Bittacus Hageni Brauer')
+            const [resource] = resources.parseTextFile(newText, 'T1', { txt: oldText, dwc: [[null, ['T:1:1'], ['T:1:2']]] })
+            assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Bittacus hageni Brauer')
+            assert.strictEqual(resource.taxa['T1:1:1'].verbatimIdentification, 'Bittacus Hageni Brauer')
+        })
+
+        test('corrections of synonyms are correctly applied', () => {
+            const [resource] = resources.parseTextFile(`---
+levels: [genus, subgenus, species]
+---
+
+Lasius F.
+  = Domisthorpea Mor. & Drnt., 1915
+    > Donisthorpea Mor. & Drnt., 1915
+    fuliginosus Latr.
+`, 'T1')
+            assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Donisthorpea Mor. & Drnt., 1915')
+            assert.strictEqual(resource.taxa['T1:1:3'].scientificName, 'Lasius fuliginosus Latr.')
+        })
+
+        test('corrections are correctly applied', () => {
+            const [resource] = resources.parseTextFile(`---
+levels: [genus, species]
+---
+
+Neopachygaster Austin, 1901
+  > Neopachygaster Austen, 1901
+  meromelas (Dufour, 1841)
+`, 'T1')
+            assert.strictEqual(resource.taxa['T1:1:1'].scientificName, 'Neopachygaster Austen, 1901')
+            assert.strictEqual(resource.taxa['T1:1:2'].scientificName, 'Neopachygaster meromelas (Dufour, 1841)')
+        })
     })
 })