feat(data): Add organism group processing

- Implemented logic to process organism_groups.csv.
- Organisms can now be assigned to multiple groups via a semicolon-separated list in organisms.csv.
- The system now resolves synonyms for organism groups, mapping them to all associated organism IDs.

Author: Uli-Z

src/data/index.ts

@@ -79,6 +79,7 @@ export function getSharedData(
     sources: string;
     abxClasses: string;
     orgClasses: string;
+    orgGroups: string;
   },
 ) {
   if (!sharedDataPromise) {
@@ -88,7 +89,8 @@ export function getSharedData(
       loadCsv(dir, files.sources),
       loadCsv(dir, files.abxClasses),
       loadCsv(dir, files.orgClasses),
-    ]).then(([abx, org, rawSources, abxClasses, orgClasses]) => {
+      loadCsv(dir, files.orgGroups),
+    ]).then(([abx, org, rawSources, abxClasses, orgClasses, orgGroups]) => {
       const sources = rawSources.map((s: any) => ({
         ...s,
         url: s.source_url,
@@ -182,6 +184,34 @@ export function getSharedData(
       }
       // --- End Organism Class Synonym Integration ---
 
+      // --- Organism Group Synonym Integration ---
+      const groupIdToOrgIds = new Map<string, string[]>();
+      for (const organism of org) {
+        const groupIdsStr = organism.groups;
+        if (groupIdsStr) {
+          const groupIds = groupIdsStr.split(';').map(id => id.trim()).filter(Boolean);
+          for (const groupId of groupIds) {
+            if (!groupIdToOrgIds.has(groupId)) {
+              groupIdToOrgIds.set(groupId, []);
+            }
+            groupIdToOrgIds.get(groupId)!.push(organism.amr_code);
+          }
+        }
+      }
+
+      for (const group of orgGroups) {
+        const members = groupIdToOrgIds.get(group.id);
+        if (members && members.length > 0) {
+          const synonyms = collectSynonyms(group);
+          for (const syn of synonyms) {
+            const existingIds = orgSyn2Id.has(syn) ? orgSyn2Id.get(syn)!.split(',') : [];
+            const allIds = [...new Set([...existingIds, ...members])];
+            orgSyn2Id.set(syn, allIds.join(','));
+          }
+        }
+      }
+      // --- End Organism Group Synonym Integration ---
+
       const allAbxIds = abx
         .filter((r: any) => r.class)
         .map((r: any) => r.amr_code);

src/index.ts

@@ -28,6 +28,7 @@ export default function docusaurusPluginResistogram(
     sources: opts.files?.sources ?? "data_sources.csv",
     abxClasses: opts.files?.abxClasses ?? "antibiotic_classes.csv",
     orgClasses: opts.files?.orgClasses ?? "organism_classes.csv",
+    orgGroups: opts.files?.orgGroups ?? "organism_groups.csv",
   };
   const dataPath = join(siteDir, dataDir);
   const pluginId = opts.id ?? "default";

src/remark/index.ts

@@ -92,6 +92,7 @@ export default function remarkResistogram(options: { dataDir?: string, files?: a
         sources: files.sources ?? "data_sources.csv",
         abxClasses: files.abxClasses ?? "antibiotic_classes.csv",
         orgClasses: files.orgClasses ?? "organism_classes.csv",
+        orgGroups: files.orgGroups ?? "organism_groups.csv",
     });
 
     let importAdded = false;