@larsgw/formica 0.6.2 → 0.6.4

package/CHANGELOG.md

@@ -1,3 +1,21 @@
+## [0.6.4](https://github.com/identification-resources/formica/compare/v0.6.3...v0.6.4) (2024-12-16)
+
+
+### Bug Fixes
+
+* **resources:** fix matching of some ICBN names ([3c18458](https://github.com/identification-resources/formica/commit/3c184586b64e2a31f1eb7298bcd7c80c1d119069))
+
+
+
+## [0.6.3](https://github.com/identification-resources/formica/compare/v0.6.2...v0.6.3) (2024-04-12)
+
+
+### Bug Fixes
+
+* **resources:** allow 'phylum' rank ([ff9be66](https://github.com/identification-resources/formica/commit/ff9be66abab79a86263764b54d6a2709833b14d4))
+
+
+
 ## [0.6.2](https://github.com/identification-resources/formica/compare/v0.6.1...v0.6.2) (2024-04-08)
 
 

package/lib/bin/process-resources.js

@@ -398,9 +398,9 @@ var ResourceProcessor = /** @class */ (function () {
     };
     ResourceProcessor.prototype.processResourceDwc = function (resource, config) {
         return __awaiter(this, void 0, void 0, function () {
-            var file, _a, header_1, rows, _b, _c, _i, rows_1, row, oldTaxon, taxon, filteredResults, taxonNames, names, id, name_1, result, _d, _e, results, _f, name_2, matches, _g, matches_1, match, source, currentRank, _h, _j, loirId, taxon, _k, amendResource, groupNameMatches, groupedNameMatches, amendedResource, _l, _m, _o, _p, source, matches;
-            return __generator(this, function (_q) {
-                switch (_q.label) {
+            var file, _a, header_1, rows, _b, _c, _i, rows_1, row, oldTaxon, taxon, filteredResults, taxonNames, names, id, name_1, result, _loop_2, _d, _e, results, _f, amendResource, groupNameMatches, groupedNameMatches, amendedResource, _g, _h, _j, _k, source, matches;
+            return __generator(this, function (_l) {
+                switch (_l.label) {
                     case 0:
                         console.log("".concat(resource.workId, ": matching ").concat(resource.id));
                         if (!!config.updateMappings) return [3 /*break*/, 3];
@@ -409,7 +409,7 @@ var ResourceProcessor = /** @class */ (function () {
                         _c = (_b = index_1.csv).parseCsv;
                         return [4 /*yield*/, fs_1.promises.readFile(file, 'utf-8')];
                     case 1:
-                        _a = _c.apply(_b, [_q.sent()]), header_1 = _a[0], rows = _a.slice(1);
+                        _a = _c.apply(_b, [_l.sent()]), header_1 = _a[0], rows = _a.slice(1);
                         for (_i = 0, rows_1 = rows; _i < rows_1.length; _i++) {
                             row = rows_1[_i];
                             oldTaxon = row.reduce(function (taxon, value, index) {
@@ -424,7 +424,7 @@ var ResourceProcessor = /** @class */ (function () {
                                 taxon.gbifAcceptedTaxonID = oldTaxon.gbifAcceptedTaxonID;
                             }
                         }
-                        _q.label = 2;
+                        _l.label = 2;
                     case 2: return [2 /*return*/, resource];
                     case 3:
                         filteredResults = {};
@@ -441,17 +441,23 @@ var ResourceProcessor = /** @class */ (function () {
                         }
                         return [4 /*yield*/, runGnverifier(Array.from(names).join('\n'))];
                     case 4:
-                        result = _q.sent();
-                        for (_d = 0, _e = result.trim().split('\n'); _d < _e.length; _d++) {
-                            results = _e[_d];
-                            _f = JSON.parse(results), name_2 = _f.name, matches = _f.results;
+                        result = _l.sent();
+                        _loop_2 = function (results) {
+                            var _m = JSON.parse(results), name_2 = _m.name, matches = _m.results;
                             if (!matches) {
-                                continue;
+                                return "continue";
                             }
-                            for (_g = 0, matches_1 = matches; _g < matches_1.length; _g++) {
-                                match = matches_1[_g];
-                                source = match.dataSourceId;
-                                currentRank = match.classificationRanks.split('|').pop();
+                            // Fix author scoring for some species, see https://github.com/gnames/gnverifier/issues/129
+                            matches.sort(function (a, b) {
+                                if (a.sortScore !== b.sortScore) {
+                                    return b.sortScore - a.sortScore;
+                                }
+                                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];
+                                var source = match.dataSourceId;
+                                var currentRank = match.classificationRanks.split('|').pop();
                                 if (match.scoreDetails.cardinalityScore === 0) {
                                     // Rank mismatch
                                     continue;
@@ -460,9 +466,9 @@ var ResourceProcessor = /** @class */ (function () {
                                     // GBIF species like "Nomada spec"
                                     continue;
                                 }
-                                for (_h = 0, _j = taxonNames[name_2]; _h < _j.length; _h++) {
-                                    loirId = _j[_h];
-                                    taxon = resource.taxa[loirId];
+                                for (var _p = 0, _q = taxonNames[name_2]; _p < _q.length; _p++) {
+                                    var loirId = _q[_p];
+                                    var taxon = resource.taxa[loirId];
                                     if (source === 11 && !GBIF_RANKS.includes(taxon.taxonRank)) {
                                         // Exclude GBIF matches for ranks that are not in GBIF
                                         continue;
@@ -483,30 +489,34 @@ var ResourceProcessor = /** @class */ (function () {
                                     });
                                 }
                             }
+                        };
+                        for (_d = 0, _e = result.trim().split('\n'); _d < _e.length; _d++) {
+                            results = _e[_d];
+                            _loop_2(results);
                         }
                         return [4 /*yield*/, Promise.resolve().then(function () { return require('../index'); })];
                     case 5:
-                        _k = (_q.sent()).taxonNames, amendResource = _k.amendResource, groupNameMatches = _k.groupNameMatches;
+                        _f = (_l.sent()).taxonNames, amendResource = _f.amendResource, groupNameMatches = _f.groupNameMatches;
                         groupedNameMatches = groupNameMatches(filteredResults);
                         amendedResource = __assign(__assign({}, resource), { taxa: __assign({}, resource.taxa) });
-                        _l = groupedNameMatches;
-                        _m = [];
-                        for (_o in _l)
-                            _m.push(_o);
-                        _p = 0;
-                        _q.label = 6;
+                        _g = groupedNameMatches;
+                        _h = [];
+                        for (_j in _g)
+                            _h.push(_j);
+                        _k = 0;
+                        _l.label = 6;
                     case 6:
-                        if (!(_p < _m.length)) return [3 /*break*/, 9];
-                        _o = _m[_p];
-                        if (!(_o in _l)) return [3 /*break*/, 8];
-                        source = _o;
+                        if (!(_k < _h.length)) return [3 /*break*/, 9];
+                        _j = _h[_k];
+                        if (!(_j in _g)) return [3 /*break*/, 8];
+                        source = _j;
                         return [4 /*yield*/, this.selectPrefixes(resource, groupedNameMatches, source)];
                     case 7:
-                        matches = _q.sent();
+                        matches = _l.sent();
                         amendResource(amendedResource, source, matches);
-                        _q.label = 8;
+                        _l.label = 8;
                     case 8:
-                        _p++;
+                        _k++;
                         return [3 /*break*/, 6];
                     case 9: return [2 /*return*/, amendedResource];
                 }

package/lib/resources/parse-text.js

@@ -16,6 +16,7 @@ var yaml = require("js-yaml");
 var work_1 = require("../catalog/tables/work");
 var diff_resource_1 = require("./diff-resource");
 var RANKS = [
+    'phylum',
     'class',
     'infraclass',
     'superorder',

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@larsgw/formica",
-  "version": "0.6.2",
+  "version": "0.6.4",
   "description": "SDK and tools for data from the Library of Identification Resources",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",

package/src/bin/process-resources.ts

@@ -293,6 +293,15 @@ class ResourceProcessor {
                 continue
             }
 
+            // Fix author scoring for some species, see https://github.com/gnames/gnverifier/issues/129
+            matches.sort((a: Record<string, any>, b: Record<string, any>) => {
+                if (a.sortScore !== b.sortScore) {
+                    return b.sortScore - a.sortScore
+                }
+
+                return name === a.matchedName ? -1 : name === b.matchedName ? 1 : 0
+            })
+
             for (const match of matches) {
                 const source = match.dataSourceId
                 const currentRank = match.classificationRanks.split('|').pop()

package/src/resources/parse-text.ts

@@ -3,6 +3,7 @@ import { Work } from '../catalog/tables/work'
 import { createDiff, ResourceDiffType } from './diff-resource'
 
 const RANKS: Rank[] = [
+    'phylum',
     'class',
     'infraclass',
     'superorder',