feat: Add organism group data and fix directive defaults

- Adds organism_groups.csv to the data preparation script.
- The resistogram directive now correctly defaults to abx=auto and org=auto when no parameters are provided.
- Updates dependencies and removes an obsolete test asset.

Author: Uli-Z

dist/remark/index.mjs

@@ -126,8 +126,10 @@ function remarkResistogram(options) {
       const afterText = text.slice(match.index + match[0].length).trim();
       const paramsStr = match[1];
       const params = parseParams(paramsStr);
-      const { resolved: antibioticIds, unresolved: unresolvedAbx } = resolveIds(params.abx, sharedData.allAbxIds, sharedData.abxSyn2Id, pageText);
-      const { resolved: organismIds, unresolved: unresolvedOrg } = resolveIds(params.org, sharedData.allOrgIds, sharedData.orgSyn2Id, pageText);
+      const abxParam = params.abx ?? "auto";
+      const orgParam = params.org ?? "auto";
+      const { resolved: antibioticIds, unresolved: unresolvedAbx } = resolveIds(abxParam, sharedData.allAbxIds, sharedData.abxSyn2Id, pageText);
+      const { resolved: organismIds, unresolved: unresolvedOrg } = resolveIds(orgParam, sharedData.allOrgIds, sharedData.orgSyn2Id, pageText);
       const selectedSource = selectDataSource(params.source, sharedData.sources);
       const resistogramNode = {
         type: "mdxJsxFlowElement",

example/data/organism_groups.csv

@@ -0,0 +1,9 @@
+id,name_en,name_de,synonyms_en,synonyms_de
+enterococci,Enterococci,Enterokokken,enterococcus spp.; enterococcus species,Enterococcus spp.; Enterococcus-Arten
+staphylococci,Staphylococci,Staphylokokken,staphylococcus spp.; staphylococcus species,Staphylococcus spp.; Staphylococcus-Arten
+cons,Coagulase-negative staphylococci,Koagulase-negative Staphylokokken,coagulase negative staphylococci; CoNS,koagulase negative Staphylokokken; CoNS
+staphylococcus-aureus,Staphylococcus aureus,Staphylococcus aureus,S. aureus; Staph aureus; coagulase-positive staphylococcus,S. aureus; koagulase-positiver Staphylococcus
+streptococci,Streptococci,Streptokokken,streptococcus spp.; streptococcus species,Streptococcus spp.; Streptococcus-Arten
+fermenters,Glucose-fermenting Gram-negative bacilli,Glukose-fermentierende gramnegative Stäbchen,fermenters; enterobacterales,Fermenter; Enterobakterien
+nonfermenters,Non-fermenting Gram-negative bacilli,Nicht-fermentierende gramnegative Stäbchen,nonfermenters; non-fermenters; NFGNB,Nicht-Fermenter; NFGNB
+enterobakteriaceae,Enterobakteriaceae,Enterobakteriaceae,,

example/package-lock.json

@@ -12,6 +12,7 @@ const STATIC_FILES = [
   'organisms.csv',
   'antibiotic_classes.csv',
   'organism_classes.csv',
+  'organism_groups.csv',
 ];
 
 async function downloadFile(url, dest) {