@larsgw/formica 0.6.4 → 0.6.6

package/CHANGELOG.md

@@ -1,3 +1,23 @@
+## [0.6.6](https://github.com/identification-resources/formica/compare/v0.6.5...v0.6.6) (2025-02-16)
+
+
+### Features
+
+* **resources:** allow other resources in version_of ([85947b0](https://github.com/identification-resources/formica/commit/85947b0dcfbdb4bfd6537c628b34087a6e6326f7))
+
+
+
+## [0.6.5](https://github.com/identification-resources/formica/compare/v0.6.4...v0.6.5) (2024-12-20)
+
+
+### Bug Fixes
+
+* **resources:** ignore empty lines in diff mode ([3fb027e](https://github.com/identification-resources/formica/commit/3fb027e8968196910fff2e574e700ac0abee996c))
+* **resources:** improve (ICBN) author parsing ([d3e3faf](https://github.com/identification-resources/formica/commit/d3e3faf411d1a7dccd528a5ee78bd0823a5883b4)), closes [#13](https://github.com/identification-resources/formica/issues/13) [#14](https://github.com/identification-resources/formica/issues/14)
+* **resources:** support "et al." in author name ([82993bf](https://github.com/identification-resources/formica/commit/82993bffac5e7f3ed00d00c28c836f347b264a43))
+
+
+
 ## [0.6.4](https://github.com/identification-resources/formica/compare/v0.6.3...v0.6.4) (2024-12-16)
 
 

package/lib/bin/process-resources.js

@@ -454,8 +454,8 @@ var ResourceProcessor = /** @class */ (function () {
                                 }
                                 return name_2 === a.matchedName ? -1 : name_2 === b.matchedName ? 1 : 0;
                             });
-                            for (var _o = 0, matches_1 = matches; _o < matches_1.length; _o++) {
-                                var match = matches_1[_o];
+                            for (var _o = 0, _p = matches; _o < _p.length; _o++) {
+                                var match = _p[_o];
                                 var source = match.dataSourceId;
                                 var currentRank = match.classificationRanks.split('|').pop();
                                 if (match.scoreDetails.cardinalityScore === 0) {
@@ -466,8 +466,8 @@ var ResourceProcessor = /** @class */ (function () {
                                     // GBIF species like "Nomada spec"
                                     continue;
                                 }
-                                for (var _p = 0, _q = taxonNames[name_2]; _p < _q.length; _p++) {
-                                    var loirId = _q[_p];
+                                for (var _q = 0, _r = taxonNames[name_2]; _q < _r.length; _q++) {
+                                    var loirId = _r[_q];
                                     var taxon = resource.taxa[loirId];
                                     if (source === 11 && !GBIF_RANKS.includes(taxon.taxonRank)) {
                                         // Exclude GBIF matches for ranks that are not in GBIF

package/lib/resources/parse-text.js

@@ -13,7 +13,7 @@ var __assign = (this && this.__assign) || function () {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseFileHeader = exports.parseFile = void 0;
 var yaml = require("js-yaml");
-var work_1 = require("../catalog/tables/work");
+var resource_1 = require("./resource");
 var diff_resource_1 = require("./diff-resource");
 var RANKS = [
     'phylum',
@@ -93,6 +93,18 @@ var RANK_LABELS_REVERSE = {
     'ssp': 'subspecies',
     'subsp': 'subspecies'
 };
+/**
+ *   1. Any number of
+ *      - capitalized words
+ *      - "&"
+ *      - " in "
+ *      - " ex "
+ *      - lowercase name particles
+ *   2. Followed by a capitalized word
+ *   3. Optionally, followed by "et al."
+ */
+var LOWERCASE_NAME_PARTICLES = ['y', 'der', 'den', 'de', 'van'].join('|');
+var SIMPLE_AUTHOR_PATTERN = '(?:(?:\\p{Lu}\\S*|&|in|ex|' + LOWERCASE_NAME_PARTICLES + ')\\s*)*\\p{Lu}\\S+(?:\\s+et\\s+al\\.)?';
 var NAME_PATTERN = new RegExp('^' +
     // $1 main name part
     '(\\S+)' +
@@ -101,20 +113,14 @@ var NAME_PATTERN = new RegExp('^' +
     // but not auct(t)., etc.
     '(?!auctt?\\.|(?:syn|comb|sp|spec)\\. n(?:ov)?\\.|s(?:ens[.u]|\\.))' +
     '(' +
-    // $2.1 anything in parentheses
-    '\\(.+?\\)' +
+    // $2.1 anything in parentheses, followed by optional revising author(s)
+    '\\(.+?\\)(?:\\s+' + SIMPLE_AUTHOR_PATTERN + ')?' +
     '|' +
     // $2.2 anything followed by a year
     '.+?\\d{4}\\)?' +
     '|' +
-    // $2.3 name(, name)* & name
-    '.+(?:, .+)* & \\S+' +
-    '|' +
-    // $2.4 name y name
-    '\\S+ [yY] \\S+' +
-    '|' +
-    // $2.5 name( in name)
-    '\\p{Lu}\\S*(?: in \\S+)?' +
+    // $2.3 author(s)
+    SIMPLE_AUTHOR_PATTERN +
     '))?' +
     // $3 optional notes
     '(?:,? (.+))?' +
@@ -364,6 +370,9 @@ function parseHeader(header) {
     var metadata = { levels: levels };
     if ('catalog' in config && typeof config.catalog === 'object' && config.catalog !== null) {
         var catalog = {};
+        if ('id' in config.catalog) {
+            throw new SyntaxError('"catalog" should not contain id');
+        }
         for (var key in config.catalog) {
             var value = config.catalog[key];
             if (typeof value === 'number') {
@@ -376,7 +385,7 @@ function parseHeader(header) {
                 throw new SyntaxError("\"catalog\" should contain only strings (\"".concat(key, "\")"));
             }
         }
-        var work = new work_1.Work(catalog);
+        var work = new resource_1.WorkResource(catalog);
         var errors = work.validate().filter(function (_a) {
             var error = _a.error;
             return error !== 'Value(s) required but missing';
@@ -541,6 +550,8 @@ function parseFile(file, id, old) {
         var diff;
         if (oldResources[index]) {
             diff = (0, diff_resource_1.createDiff)(content, parseResource(oldResources[index])[1]);
+            // Ignore empty lines
+            diff = diff.filter(function (line) { return line.text !== ''; });
         }
         else {
             diff = (0, diff_resource_1.createDiff)(content, content);

package/lib/resources/resource.d.ts

@@ -0,0 +1,4 @@
+import { Work } from '../catalog/tables/work';
+export declare class WorkResource extends Work {
+    constructor(values: Record<string, string>);
+}

package/lib/resources/resource.js

@@ -0,0 +1,30 @@
+"use strict";
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.WorkResource = void 0;
+var work_1 = require("../catalog/tables/work");
+var WorkResource = /** @class */ (function (_super) {
+    __extends(WorkResource, _super);
+    function WorkResource(values) {
+        var _this = _super.call(this, values) || this;
+        _this.schema.version_of.format = /^B[1-9]\d*:[1-9]\d*$/;
+        _this.schema.duplicate_of.format = /^B[1-9]\d*:[1-9]\d*$/;
+        return _this;
+    }
+    return WorkResource;
+}(work_1.Work));
+exports.WorkResource = WorkResource;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@larsgw/formica",
-  "version": "0.6.4",
+  "version": "0.6.6",
   "description": "SDK and tools for data from the Library of Identification Resources",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",
@@ -16,7 +16,7 @@
     "lint": "eslint src",
     "build": "tsc -d",
     "changelog": "conventional-changelog -p angular -i CHANGELOG.md -s -r 0",
-    "preversion": "npm run lint",
+    "preversion": "npm run lint && npm test",
     "version": "npm run changelog && git add CHANGELOG.md",
     "prepublishOnly": "npm run build"
   },

package/src/bin/process-resources.ts

@@ -287,6 +287,22 @@ class ResourceProcessor {
 
         const result = await runGnverifier(Array.from(names).join('\n'))
         for (const results of result.trim().split('\n')) {
+            interface MatchScoreDetails {
+                cardinalityScore: number;
+            }
+
+            interface Match {
+                currentRecordId: string;
+                dataSourceId: number;
+                matchedName: string;
+                recordId: string;
+                sortScore: number;
+                isSynonym: boolean;
+                classificationPath: string;
+                classificationRanks: string;
+                scoreDetails: MatchScoreDetails;
+            }
+
             const { name, results: matches } = JSON.parse(results)
 
             if (!matches) {
@@ -294,7 +310,7 @@ class ResourceProcessor {
             }
 
             // Fix author scoring for some species, see https://github.com/gnames/gnverifier/issues/129
-            matches.sort((a: Record<string, any>, b: Record<string, any>) => {
+            matches.sort((a: Match, b: Match) => {
                 if (a.sortScore !== b.sortScore) {
                     return b.sortScore - a.sortScore
                 }
@@ -302,7 +318,7 @@ class ResourceProcessor {
                 return name === a.matchedName ? -1 : name === b.matchedName ? 1 : 0
             })
 
-            for (const match of matches) {
+            for (const match of matches as Match[]) {
                 const source = match.dataSourceId
                 const currentRank = match.classificationRanks.split('|').pop()
 

package/src/resources/parse-text.ts

@@ -1,5 +1,5 @@
 import * as yaml from 'js-yaml'
-import { Work } from '../catalog/tables/work'
+import { WorkResource } from './resource'
 import { createDiff, ResourceDiffType } from './diff-resource'
 
 const RANKS: Rank[] = [
@@ -87,6 +87,19 @@ const RANK_LABELS_REVERSE: Record<string, Rank> = {
     'subsp': 'subspecies'
 }
 
+/**
+ *   1. Any number of
+ *      - capitalized words
+ *      - "&"
+ *      - " in "
+ *      - " ex "
+ *      - lowercase name particles
+ *   2. Followed by a capitalized word
+ *   3. Optionally, followed by "et al."
+ */
+const LOWERCASE_NAME_PARTICLES = ['y', 'der', 'den', 'de', 'van'].join('|')
+const SIMPLE_AUTHOR_PATTERN = '(?:(?:\\p{Lu}\\S*|&|in|ex|' + LOWERCASE_NAME_PARTICLES + ')\\s*)*\\p{Lu}\\S+(?:\\s+et\\s+al\\.)?'
+
 const NAME_PATTERN = new RegExp(
     '^' +
         // $1 main name part
@@ -96,20 +109,14 @@ const NAME_PATTERN = new RegExp(
             // but not auct(t)., etc.
             '(?!auctt?\\.|(?:syn|comb|sp|spec)\\. n(?:ov)?\\.|s(?:ens[.u]|\\.))' +
         '(' +
-            // $2.1 anything in parentheses
-            '\\(.+?\\)' +
+            // $2.1 anything in parentheses, followed by optional revising author(s)
+            '\\(.+?\\)(?:\\s+' + SIMPLE_AUTHOR_PATTERN + ')?' +
         '|' +
             // $2.2 anything followed by a year
             '.+?\\d{4}\\)?' +
         '|' +
-            // $2.3 name(, name)* & name
-            '.+(?:, .+)* & \\S+' +
-        '|' +
-            // $2.4 name y name
-            '\\S+ [yY] \\S+' +
-        '|' +
-            // $2.5 name( in name)
-            '\\p{Lu}\\S*(?: in \\S+)?' +
+            // $2.3 author(s)
+            SIMPLE_AUTHOR_PATTERN +
         '))?' +
         // $3 optional notes
         '(?:,? (.+))?' +
@@ -387,6 +394,9 @@ function parseHeader (header: string): ResourceMetadata {
 
     if ('catalog' in config && typeof config.catalog === 'object' && config.catalog !== null) {
         const catalog: Record<string, string> = {}
+        if ('id' in config.catalog) {
+            throw new SyntaxError('"catalog" should not contain id')
+        }
         for (const key in config.catalog) {
             const value = config.catalog[key as keyof object]
             if (typeof value === 'number') {
@@ -397,7 +407,7 @@ function parseHeader (header: string): ResourceMetadata {
                 throw new SyntaxError(`"catalog" should contain only strings ("${key}")`)
             }
         }
-        const work = new Work(catalog)
+        const work = new WorkResource(catalog)
         const errors = work.validate().filter(({ error }) => error !== 'Value(s) required but missing')
         if (errors.length > 0) {
             throw new SyntaxError(`"catalog" contains errors: ${errors.map(({ field, error }) => `[${field}] ${error}`).join('; ')}`)
@@ -573,6 +583,8 @@ export function parseFile (file: string, id: WorkId, old?: ResourceHistory): Res
         let diff
         if (oldResources[index]) {
             diff = createDiff(content, parseResource(oldResources[index])[1])
+            // Ignore empty lines
+            diff = diff.filter(line => line.text !== '')
         } else {
             diff = createDiff(content, content)
         }

package/src/resources/resource.ts

@@ -0,0 +1,10 @@
+import { Work } from '../catalog/tables/work'
+
+export class WorkResource extends Work {
+    constructor (values: Record<string, string>) {
+        super(values)
+
+        this.schema.version_of.format = /^B[1-9]\d*:[1-9]\d*$/
+        this.schema.duplicate_of.format = /^B[1-9]\d*:[1-9]\d*$/
+    }
+}