@larsgw/formica 0.10.5 → 0.11.0

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

@@ -397,7 +397,7 @@ function makeLinkedDataForScientificName(name) {
     return node;
 }
 function makeLinkedDataForResource(work, files, resourceId) {
-    var _a, _b, _c, _d, _e, _f, _g, _h;
+    var _a, _b, _c, _d, _e, _f, _g, _h, _j;
     const resource = new resource_1.WorkResource({});
     if (!resourceId) {
         resourceId = `${work.get('id')}:0`;
@@ -479,7 +479,7 @@ function makeLinkedDataForResource(work, files, resourceId) {
     if (tags.length) {
         node['ac:tag'] = tags;
     }
-    if (files.resources[resourceId].taxa) {
+    if ((_j = files.resources[resourceId]) === null || _j === void 0 ? void 0 : _j.taxa) {
         const leafs = new Set(files.resources[resourceId].taxa.map(taxon => taxon.scientificNameID));
         const taxa = [];
         for (const taxon of files.resources[resourceId].taxa) {
@@ -679,9 +679,16 @@ function* makeLinkedDataForWorks(files) {
     for (const work of works.entities) {
         const id = work.get('id');
         const node = makeLinkedDataForWork(work, files);
+        const resources = [];
         let resourceIndex = 1;
         let resourceId;
         while ((resourceId = `${id}:${resourceIndex++}`) in files.resources) {
+            resources.push(resourceId);
+        }
+        if (!resources.length) {
+            resources.push(undefined);
+        }
+        for (const resourceId of resources) {
             const resource = makeLinkedDataForResource(work, files, resourceId);
             if (!Array.isArray(node['dcterms:hasPart'])) {
                 node['dcterms:hasPart'] = [];

package/lib/resources/parse-text.js

@@ -66,6 +66,13 @@ const FLAGS = [
 ];
 const RESOURCE_DELIMITER = '\n\n===\n\n';
 const INDENT = 2;
+function isStructuralLine(line) {
+    return line.startsWith('[indet]') || line.startsWith('[incertae sedis]');
+}
+function isNameLine(line) {
+    line = line.trim();
+    return !line.startsWith('> ') && !isStructuralLine(line);
+}
 function makeParseError(message, line, column = 1) {
     return new SyntaxError(`[${line}:${column}] ${message}`);
 }
@@ -190,7 +197,7 @@ function parseResourceContent(content, resource, oldIds, offsetLine) {
     const parents = [];
     const previous = { id: '', indent: 0, group: { isLeaf: false, indent: 0 }, errors: [] };
     for (const line of content) {
-        const hasOriginalId = line.type !== diff_resource_1.ResourceDiffType.Added && !/^\s*(\[indet\]|> )/.test((_a = line.original) !== null && _a !== void 0 ? _a : line.text);
+        const hasOriginalId = line.type !== diff_resource_1.ResourceDiffType.Added && isNameLine((_a = line.original) !== null && _a !== void 0 ? _a : line.text);
         if (hasOriginalId) {
             id++;
         }
@@ -217,7 +224,7 @@ function parseResourceContent(content, resource, oldIds, offsetLine) {
         // Update parentage
         if (lineIndent > previous.indent) {
             // Do not count synonyms as parents (unless this is correcting a typo in the synonym)
-            if (data[previous.id] && data[previous.id].taxonomicStatus === 'accepted' || name.startsWith('> ')) {
+            if (data[previous.id] && (data[previous.id].taxonomicStatus === 'accepted' || name.startsWith('> '))) {
                 parents.push(previous.id);
             }
             else {
@@ -235,9 +242,13 @@ function parseResourceContent(content, resource, oldIds, offsetLine) {
             parents.splice(lineIndent / INDENT);
         }
         previous.indent = lineIndent;
-        // Do not process "indet" lines further, as they only serve to indicate
-        // that subtaxa are explicitely omitted
-        if (name.startsWith('[indet]')) {
+        if (name.startsWith('[incertae sedis]')) {
+            previous.id = '';
+            previous.group.indent = previous.indent;
+        }
+        // Do not process "indet" or "incertae sedis" lines further, as they only
+        // serve as structural indicators.
+        if (isStructuralLine(name)) {
             errors.push(...previous.errors);
             previous.errors.length = 0;
             previous.group.isLeaf = lineIndent / INDENT >= leafTaxonIndex;
@@ -281,10 +292,6 @@ 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;
@@ -293,6 +300,14 @@ function parseResourceContent(content, resource, oldIds, offsetLine) {
                 errors.push(makeParseError('Cannot apply a correction to nothing', lineNumber));
                 continue;
             }
+            else if (parents.indexOf(parentId) !== parents.length - 1) {
+                errors.push(makeParseError('Cannot apply a correction after skipping a rank', lineNumber));
+                continue;
+            }
+            if (parent.taxonomicStatus !== 'accepted') {
+                // Remove corrected synonym from parentage
+                parents[parents.length - 1] = null;
+            }
             parent.incorrect = Object.assign({}, parent);
             for (const key in item) {
                 if (key !== 'taxonomicStatus' && key !== 'verbatimIdentification') {
@@ -305,8 +320,17 @@ function parseResourceContent(content, resource, oldIds, offsetLine) {
             errors.push(...itemErrors);
             continue;
         }
-        // Add more classification info
+        // Validate synonyms
         const isSynonym = item.taxonomicStatus !== 'accepted';
+        if (isSynonym) {
+            if (parentId === null) {
+                errors.push(makeParseError('Cannot define a synonym of nothing', lineNumber));
+            }
+            else if (parents.indexOf(parentId) !== parents.length - 1) {
+                errors.push(makeParseError('Cannot define a synonym after skipping a rank', lineNumber));
+            }
+        }
+        // Add more classification info
         if (isSynonym) {
             item.higherClassification = parent.higherClassification;
         }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@larsgw/formica",
-  "version": "0.10.5",
+  "version": "0.11.0",
   "description": "SDK and tools for data from the Library of Identification Resources",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",
@@ -39,7 +39,7 @@
   "dependencies": {
     "ietf-language-tag-regex": "^0.0.5",
     "js-yaml": "^5.2.1",
-    "jsonld": "^9.0.0",
+    "jsonld": "larsgw/jsonld.js#larsgw-patch-1",
     "n3": "^2.1.1",
     "shex": "^1.0.0-alpha.30",
     "spdx-license-list": "^6.6.0"