@larsgw/formica 0.8.3 → 0.8.4

package/CHANGELOG.md

@@ -1,3 +1,18 @@
+## [0.8.4](https://github.com/identification-resources/formica/compare/v0.8.3...v0.8.4) (2025-09-19)
+
+
+### Bug Fixes
+
+* **catalog:** clearer error message when validating ([b1c34f0](https://github.com/identification-resources/formica/commit/b1c34f00ed9a262251d2d24b3e6c46fd17730405))
+* **resources:** optimize diffing algorithm ([0c86c49](https://github.com/identification-resources/formica/commit/0c86c49474754dced74c8423f3e6b7ed2fd2a78f)), closes [#6](https://github.com/identification-resources/formica/issues/6)
+
+
+### Features
+
+* **catalog:** map additional scope value ([80c6d26](https://github.com/identification-resources/formica/commit/80c6d269a7d5b03600991fb353280e81afcefb0e))
+
+
+
 ## [0.8.3](https://github.com/identification-resources/formica/compare/v0.8.2...v0.8.3) (2025-07-15)
 
 

package/lib/bin/generate-linked-data.js

@@ -115,6 +115,7 @@ var SCOPES = {
     'nymphs': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
     'nypmhs': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
     'nymphs (instar V)': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
+    'nymphs (instar IV)': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
     'eggs': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/embryo'],
     // plant life stage
     'flowering plants': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/adult'],

package/lib/bin/validate-catalog.js

@@ -84,17 +84,14 @@ function validateFile(arg) {
                 case 1:
                     file = _a.sent();
                     sheet = path.basename(filePath, '.csv');
-                    return [2 /*return*/, {
-                            filePath: filePath,
-                            errors: index_1.catalog.loadData(file, sheet).validate()
-                        }];
+                    return [2 /*return*/, index_1.catalog.loadData(file, sheet).validate()];
             }
         });
     });
 }
 function main(args) {
     return __awaiter(this, void 0, void 0, function () {
-        var exitStatus, results, _i, results_1, result;
+        var exitStatus, results, i, result;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -102,16 +99,17 @@ function main(args) {
                     return [4 /*yield*/, Promise.allSettled(args.map(validateFile))];
                 case 1:
                     results = _a.sent();
-                    for (_i = 0, results_1 = results; _i < results_1.length; _i++) {
-                        result = results_1[_i];
+                    for (i = 0; i < results.length; i++) {
+                        result = results[i];
                         if (result.status === 'rejected') {
+                            console.error("".concat(args[i], ":"));
                             console.error(result.reason);
                             console.error();
                             exitStatus = 1;
                         }
-                        else if (result.value.errors.length > 0) {
-                            console.error("".concat(result.value.filePath, ":"));
-                            console.table(result.value.errors);
+                        else if (result.value.length > 0) {
+                            console.error("".concat(args[i], ":"));
+                            console.table(result.value);
                             console.error();
                             exitStatus = 1;
                         }

package/lib/resources/diff-resource.d.ts

@@ -4,4 +4,4 @@ export declare enum ResourceDiffType {
     Modified = "~",
     Unchanged = "="
 }
-export declare function createDiff(a: string, b: string, tokenize?: ResourceDiffTokenizer): ResourceDiff;
+export declare function createDiff(a: string, b: string): ResourceDiff;

package/lib/resources/diff-resource.js

@@ -18,18 +18,32 @@ var ResourceDiffType;
     ResourceDiffType["Modified"] = "~";
     ResourceDiffType["Unchanged"] = "=";
 })(ResourceDiffType || (exports.ResourceDiffType = ResourceDiffType = {}));
+var Matrix = /** @class */ (function () {
+    function Matrix(m, n) {
+        this.values = Array(m * n).fill(0);
+        this.m = m;
+        this.n = n;
+    }
+    Matrix.prototype.getValue = function (i, j) {
+        return this.values[(i * this.n) + j];
+    };
+    Matrix.prototype.setValue = function (i, j, value) {
+        this.values[(i * this.n) + j] = value;
+    };
+    return Matrix;
+}());
 function LCS(X, Y) {
     var m = X.length;
     var n = Y.length;
     // Build matrix
-    var C = Array(m + 1).fill(0).map(function () { return Array(n + 1).fill(0); });
+    var C = new Matrix(m + 1, n + 1);
     for (var i_1 = 0; i_1 < m; i_1++) {
         for (var j_1 = 0; j_1 < n; j_1++) {
             if (X[i_1] === Y[j_1]) {
-                C[i_1 + 1][j_1 + 1] = C[i_1][j_1] + 1;
+                C.setValue(i_1 + 1, j_1 + 1, C.getValue(i_1, j_1) + 1);
             }
             else {
-                C[i_1 + 1][j_1 + 1] = Math.max(C[i_1][j_1 + 1], C[i_1 + 1][j_1]);
+                C.setValue(i_1 + 1, j_1 + 1, Math.max(C.getValue(i_1, j_1 + 1), C.getValue(i_1 + 1, j_1)));
             }
         }
     }
@@ -46,7 +60,7 @@ function LCS(X, Y) {
             i--;
             j--;
         }
-        else if (i !== 0 && (j === 0 || C[i - 1][j] > C[i][j - 1])) {
+        else if (i !== 0 && (j === 0 || C.getValue(i - 1, j) > C.getValue(i, j - 1))) {
             diff.unshift({
                 text: X[i - 1],
                 type: ResourceDiffType.Added
@@ -63,17 +77,16 @@ function LCS(X, Y) {
     }
     return diff;
 }
-function gitTokenize(text) {
+function tokenizeWords(text) {
     if (text.length === 0) {
         return [];
     }
     return text.match(/\S+|\n|[\r\t\f\v \u00a0\u1680\u2000-\u200a\u2028\u2029\u202f\u205f\u3000\ufeff]+/g);
 }
-function createDiff(a, b, tokenize) {
-    var _a, _b;
-    if (tokenize === void 0) { tokenize = gitTokenize; }
-    var X = tokenize(a.trimEnd());
-    var Y = tokenize(b.trimEnd());
+function tokenizeLines(text) {
+    return text.split('\n');
+}
+function diffTokens(X, Y) {
     // Remove common prefix
     var prefix = [];
     while (X.length && X[0] === Y[0]) {
@@ -94,12 +107,11 @@ function createDiff(a, b, tokenize) {
         X.pop();
         Y.pop();
     }
-    // Generate word from remains, combine with prefix and suffix, add trailing
-    // newline
-    var changes = __spreadArray(__spreadArray(__spreadArray(__spreadArray([], prefix, true), LCS(X, Y), true), suffix, true), [
-        { text: '\n', type: ResourceDiffType.Unchanged }
-    ], false);
-    // Convert word diff to line diff
+    // Generate diff from remains, combine with prefix and suffix
+    return __spreadArray(__spreadArray(__spreadArray([], prefix, true), LCS(X, Y), true), suffix, true);
+}
+function convertWordDiff(changes) {
+    var _a, _b;
     var lines = [];
     var line = null;
     var deletedNewlines = 0;
@@ -156,3 +168,36 @@ function createDiff(a, b, tokenize) {
     }
     return lines;
 }
+function getWordTokensFromLines(lines) {
+    return lines.flatMap(function (change) { return tokenizeWords(change.text).concat('\n'); });
+}
+function createDiff(a, b) {
+    var lines = diffTokens(tokenizeLines(a.trimEnd()), tokenizeLines(b.trimEnd()));
+    var changes = [];
+    var diffPart = { added: [], deleted: [] };
+    for (var i = 0; i < lines.length; i++) {
+        if (lines[i].type === ResourceDiffType.Added) {
+            diffPart.added.push(lines[i]);
+            continue;
+        }
+        else if (lines[i].type === ResourceDiffType.Deleted) {
+            diffPart.deleted.push(lines[i]);
+            continue;
+        }
+        if (diffPart.added.length && diffPart.deleted.length) {
+            changes.push.apply(changes, convertWordDiff(diffTokens(getWordTokensFromLines(diffPart.added), getWordTokensFromLines(diffPart.deleted))));
+            diffPart.added.length = 0;
+            diffPart.deleted.length = 0;
+        }
+        else if (diffPart.added.length) {
+            changes.push.apply(changes, diffPart.added);
+            diffPart.added.length = 0;
+        }
+        else if (diffPart.deleted.length) {
+            changes.push.apply(changes, diffPart.deleted.map(function (change) { return ({ text: undefined, original: change.text, type: change.type }); }));
+            diffPart.deleted.length = 0;
+        }
+        changes.push(lines[i]);
+    }
+    return changes;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@larsgw/formica",
-  "version": "0.8.3",
+  "version": "0.8.4",
   "description": "SDK and tools for data from the Library of Identification Resources",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",

package/src/bin/generate-linked-data.ts

@@ -45,6 +45,7 @@ const SCOPES: Record<string, [string, string]> = {
     'nymphs': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
     'nypmhs': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
     'nymphs (instar V)': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
+    'nymphs (instar IV)': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
     'eggs': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/embryo'],
 
     // plant life stage

package/src/bin/validate-catalog.ts

@@ -4,28 +4,28 @@ import { promises as fs } from 'fs'
 import * as path from 'path'
 import { catalog } from '../index'
 
-async function validateFile (arg: string): Promise<{ filePath: string, errors: WorkError[]}> {
+async function validateFile (arg: string): Promise<WorkError[]> {
     const filePath = path.resolve(arg)
     const file = await fs.readFile(filePath, 'utf8')
     const sheet = path.basename(filePath, '.csv')
-    return {
-        filePath,
-        errors: catalog.loadData(file, sheet).validate()
-    }
+    return catalog.loadData(file, sheet).validate()
 }
 
 async function main (args: string[]): Promise<void> {
     let exitStatus = 0
 
     const results = await Promise.allSettled(args.map(validateFile))
-    for (const result of results) {
+    for (let i = 0; i < results.length; i++) {
+        const result = results[i]
+
         if (result.status === 'rejected') {
+            console.error(`${args[i]}:`)
             console.error(result.reason)
             console.error()
             exitStatus = 1
-        } else if (result.value.errors.length > 0) {
-            console.error(`${result.value.filePath}:`)
-            console.table(result.value.errors)
+        } else if (result.value.length > 0) {
+            console.error(`${args[i]}:`)
+            console.table(result.value)
             console.error()
             exitStatus = 1
         }

package/src/module.d.ts

@@ -100,8 +100,6 @@ interface ResourceDiffPart {
     type: ResourceDiffType
 }
 
-type ResourceDiffTokenizer = (text: string) => string[]
-
 declare enum ResourceDiffType {
     Added = '+',
     Deleted = '-',

package/src/resources/diff-resource.ts

@@ -10,18 +10,38 @@ interface DiffPart {
     type: ResourceDiffType
 }
 
+class Matrix {
+    values: Array<number>
+    m: number
+    n: number
+
+    constructor (m: number, n: number) {
+        this.values = Array(m * n).fill(0)
+        this.m = m
+        this.n = n
+    }
+
+    getValue (i: number, j: number) {
+        return this.values[(i * this.n) + j]
+    }
+
+    setValue (i: number, j: number, value: number) {
+        this.values[(i * this.n) + j] = value
+    }
+}
+
 function LCS (X: string[], Y: string[]): DiffPart[] {
     const m = X.length
     const n = Y.length
 
     // Build matrix
-    const C = Array(m + 1).fill(0).map(() => Array(n + 1).fill(0))
+    const C = new Matrix(m + 1, n + 1)
     for (let i = 0; i < m; i++) {
         for (let j = 0; j < n; j++) {
             if (X[i] === Y[j]) {
-                C[i + 1][j + 1] = C[i][j] + 1
+                C.setValue(i + 1, j + 1, C.getValue(i, j) + 1)
             } else {
-                C[i + 1][j + 1] = Math.max(C[i][j + 1], C[i + 1][j])
+                C.setValue(i + 1, j + 1, Math.max(C.getValue(i, j + 1), C.getValue(i + 1, j)))
             }
         }
     }
@@ -38,7 +58,7 @@ function LCS (X: string[], Y: string[]): DiffPart[] {
             })
             i--
             j--
-        } else if (i !== 0 && (j === 0 || C[i - 1][j] > C[i][j - 1])) {
+        } else if (i !== 0 && (j === 0 || C.getValue(i - 1, j) > C.getValue(i, j - 1))) {
             diff.unshift({
                 text: X[i - 1],
                 type: ResourceDiffType.Added
@@ -56,17 +76,18 @@ function LCS (X: string[], Y: string[]): DiffPart[] {
     return diff
 }
 
-function gitTokenize (text: string): string[] {
+function tokenizeWords (text: string): string[] {
     if (text.length === 0) {
         return []
     }
     return text.match(/\S+|\n|[\r\t\f\v \u00a0\u1680\u2000-\u200a\u2028\u2029\u202f\u205f\u3000\ufeff]+/g) as string[]
 }
 
-export function createDiff (a: string, b: string, tokenize: ResourceDiffTokenizer = gitTokenize): ResourceDiff {
-    const X = tokenize(a.trimEnd())
-    const Y = tokenize(b.trimEnd())
+function tokenizeLines (text: string): string[] {
+    return text.split('\n')
+}
 
+function diffTokens (X: string[], Y: string[]): ResourceDiff {
     // Remove common prefix
     const prefix = []
     while (X.length && X[0] === Y[0]) {
@@ -89,16 +110,15 @@ export function createDiff (a: string, b: string, tokenize: ResourceDiffTokenize
         Y.pop()
     }
 
-    // Generate word from remains, combine with prefix and suffix, add trailing
-    // newline
-    const changes = [
+    // Generate diff from remains, combine with prefix and suffix
+    return [
         ...prefix,
         ...LCS(X, Y),
-        ...suffix,
-        { text: '\n', type: ResourceDiffType.Unchanged }
+        ...suffix
     ]
+}
 
-    // Convert word diff to line diff
+function convertWordDiff (changes: ResourceDiff): ResourceDiff {
     const lines: ResourceDiff = []
     let line: ResourceDiffPart|null = null
     let deletedNewlines = 0
@@ -164,3 +184,39 @@ export function createDiff (a: string, b: string, tokenize: ResourceDiffTokenize
 
     return lines
 }
+
+function getWordTokensFromLines (lines: ResourceDiff): string[] {
+    return lines.flatMap(change => tokenizeWords(change.text as string).concat('\n'))
+}
+
+export function createDiff (a: string, b: string): ResourceDiff {
+    const lines: ResourceDiff = diffTokens(tokenizeLines(a.trimEnd()), tokenizeLines(b.trimEnd()))
+
+    const changes: ResourceDiff = []
+    const diffPart: Record<string, ResourceDiff> = { added: [], deleted: [] }
+    for (let i = 0; i < lines.length; i++) {
+        if (lines[i].type === ResourceDiffType.Added) {
+            diffPart.added.push(lines[i])
+            continue
+        } else if (lines[i].type === ResourceDiffType.Deleted) {
+            diffPart.deleted.push(lines[i])
+            continue
+        }
+
+        if (diffPart.added.length && diffPart.deleted.length) {
+            changes.push(...convertWordDiff(diffTokens(getWordTokensFromLines(diffPart.added), getWordTokensFromLines(diffPart.deleted))))
+            diffPart.added.length = 0
+            diffPart.deleted.length = 0
+        } else if (diffPart.added.length) {
+            changes.push(...diffPart.added)
+            diffPart.added.length = 0
+        } else if (diffPart.deleted.length) {
+            changes.push(...diffPart.deleted.map(change => ({ text: undefined, original: change.text, type: change.type })))
+            diffPart.deleted.length = 0
+        }
+
+        changes.push(lines[i])
+    }
+
+    return changes
+}