@larsgw/formica 0.3.0 → 0.4.0

package/CHANGELOG.md

@@ -1,3 +1,29 @@
+# [0.4.0](https://github.com/identification-resources/formica/compare/v0.3.1...v0.4.0) (2023-09-07)
+
+
+### Bug Fixes
+
+* **catalog:** validation checks for unknown fields ([5fe5cf0](https://github.com/identification-resources/formica/commit/5fe5cf0b8cf4db7c4af50a897821077e410a1e09))
+* **catalog:** verify if required fields are missing ([c327ae4](https://github.com/identification-resources/formica/commit/c327ae458a80567aac34dd03f3970dcf9d575479))
+
+
+### Features
+
+* **catalog:** add duplicate_of field ([e4a8bbe](https://github.com/identification-resources/formica/commit/e4a8bbecef9c6a40d0f2cc5d4e8bb67685a453ff))
+
+
+
+## [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/catalog/entity.js

@@ -1,4 +1,15 @@
 "use strict";
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.Entity = void 0;
 var value_1 = require("./value");
@@ -6,7 +17,7 @@ var Entity = /** @class */ (function () {
     function Entity(values, schema) {
         this.fields = {};
         for (var key in values) {
-            var value = (0, value_1.parseValue)(values[key], !!schema[key].multiple);
+            var value = (0, value_1.parseValue)(values[key], !!schema[key] && !!schema[key].multiple);
             if (value !== null) {
                 this.fields[key] = value;
             }
@@ -31,7 +42,7 @@ var Entity = /** @class */ (function () {
     };
     Entity.prototype.validate = function () {
         var errors = [];
-        for (var field in this.fields) {
+        for (var field in __assign(__assign({}, this.fields), this.schema)) {
             for (var _i = 0, _a = this._validateField(field); _i < _a.length; _i++) {
                 var error = _a[_i];
                 errors.push({ field: field, error: error });
@@ -41,6 +52,10 @@ var Entity = /** @class */ (function () {
     };
     Entity.prototype._validateField = function (field) {
         var errors = [];
+        if (!(field in this.schema)) {
+            errors.push('Field unknown');
+            return errors;
+        }
         if (!(field in this.fields)) {
             if (this.schema[field].required) {
                 errors.push('Value(s) required but missing');

package/lib/catalog/tables/work.js

@@ -51,7 +51,8 @@ var Work = /** @class */ (function (_super) {
             target_taxa: { required: false, multiple: true },
             listed_in: { required: false, multiple: true, format: value_1.FORMATS.ID },
             part_of: { required: false, multiple: true, format: value_1.FORMATS.ID },
-            version_of: { required: false, multiple: true, format: value_1.FORMATS.ID }
+            version_of: { required: false, multiple: true, format: value_1.FORMATS.ID },
+            // duplicate_of: { required: false, multiple: false, format: FORMATS.ID }
         }) || this;
     }
     Work.prototype.deriveFields = function () {

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": "0.4.0",
   "description": "SDK and tools for data from the Library of Identification Resources",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",

package/src/catalog/entity.ts

@@ -8,7 +8,7 @@ export class Entity {
     constructor (values: Record<string, string>, schema: Schema) {
         this.fields = {}
         for (const key in values) {
-            const value = parseValue(values[key], !!schema[key].multiple)
+            const value = parseValue(values[key], !!schema[key] && !!schema[key].multiple)
             if (value !== null) {
                 this.fields[key] = value
             }
@@ -37,7 +37,7 @@ export class Entity {
 
     validate (): FieldError[] {
         const errors = []
-        for (const field in this.fields) {
+        for (const field in { ...this.fields, ...this.schema }) {
             for (const error of this._validateField(field)) {
                 errors.push({ field, error })
             }
@@ -48,6 +48,11 @@ export class Entity {
     _validateField (field: string) {
         const errors = []
 
+        if (!(field in this.schema)) {
+            errors.push('Field unknown')
+            return errors
+        }
+
         if (!(field in this.fields)) {
             if (this.schema[field].required) {
                 errors.push('Value(s) required but missing')

package/src/catalog/tables/work.ts

@@ -33,7 +33,8 @@ export class Work extends Entity {
             target_taxa: { required: false, multiple: true },
             listed_in: { required: false, multiple: true, format: FORMATS.ID },
             part_of: { required: false, multiple: true, format: FORMATS.ID },
-            version_of: { required: false, multiple: true, format: FORMATS.ID }
+            version_of: { required: false, multiple: true, format: FORMATS.ID },
+            // duplicate_of: { required: false, multiple: false, format: FORMATS.ID }
         })
     }
 

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

@@ -1,10 +1,51 @@
 const test = require('node:test')
 const assert = require('assert')
 
-const { resources } = require('../lib')
+const { catalog, resources } = require('../lib')
+
+test('catalog', async (t) => {
+    await t.test('reports missing required fields', (t) => {
+        const errors = catalog.loadData(`id
+B1`, 'catalog').validate()
+        assert.deepStrictEqual(errors, [
+            { entity: 'B1', field: 'title', error: 'Value(s) required but missing' },
+            { entity: 'B1', field: 'entry_type', error: 'Value(s) required but missing' },
+            { entity: 'B1', field: 'language', error: 'Value(s) required but missing' },
+            { entity: 'B1', field: 'key_type', error: 'Value(s) required but missing' },
+            { entity: 'B1', field: 'taxon', error: 'Value(s) required but missing' },
+            { entity: 'B1', field: 'region', error: 'Value(s) required but missing' }
+        ])
+    })
+})
 
 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]