@ca-plant-list/ca-plant-list 0.4.21 → 0.4.22

package/lib/tools/jepsoneflora.js

@@ -102,8 +102,25 @@ export class JepsonEFlora {
                 idsToUpdate.set(name, jepsInfo.id);
             }
 
-            const efStatus = this.#getStatusCode(jepsInfo);
+            let efStatus = this.#getStatusCode(jepsInfo);
             const taxonStatus = taxon.getStatus();
+            // Override if exception is specified.
+            const nativeException = exceptions.getValue(
+                name,
+                "jepson",
+                "native",
+            );
+            if (typeof nativeException === "boolean") {
+                const overrideStatus = nativeException ? "N" : "X";
+                if (overrideStatus === efStatus) {
+                    this.#errorLog.log(
+                        name,
+                        "has unnecessary Jepson native override",
+                    );
+                }
+                efStatus = overrideStatus;
+            }
+
             if (
                 efStatus !== taxonStatus &&
                 !(taxonStatus === "NC" && efStatus === "N")
@@ -154,6 +171,8 @@ export class JepsonEFlora {
             for (const [k] of Object.entries(exceptions)) {
                 const jepsonData = this.#nameInfo.get(name);
                 switch (k) {
+                    case "native":
+                        break;
                     case "notineflora":
                         // Make sure it is really not in eFlora.
                         if (jepsonData) {

package/lib/tools/rpi.js

@@ -80,8 +80,8 @@ class RPI {
             const rank = row["CRPR"];
             const rawCESA = row["CESA"];
             const rawFESA = row["FESA"];
-            const cesa = rawCESA === "None" ? undefined : rawCESA;
-            const fesa = rawFESA === "None" ? undefined : rawFESA;
+            const cesa = rawCESA === "None" ? "" : rawCESA;
+            const fesa = rawFESA === "None" ? "" : rawFESA;
             const cnddb = row["SRank"];
             const globalRank = row["GRank"];
             const taxon = taxa.getTaxon(name);

package/lib/tools/taxacsv.js

@@ -1,9 +1,30 @@
 import path from "path";
 import { CSV } from "../csv.js";
 
+const HEADERS = [
+    "taxon_name",
+    "common name",
+    "status",
+    "jepson id",
+    "calrecnum",
+    "inat id",
+    "cch2_id",
+    "fna",
+    "calscape_cn",
+    "life_cycle",
+    "flower_color",
+    "bloom_start",
+    "bloom_end",
+    "RPI ID",
+    "CRPR",
+    "CESA",
+    "FESA",
+    "SRank",
+    "GRank",
+];
+
 export class TaxaCSV {
     #filePath;
-    #headers;
     /** @type {import("../index.js").TaxonData[]} */
     #taxa;
 
@@ -13,9 +34,7 @@ export class TaxaCSV {
     constructor(dataDir) {
         this.#filePath = path.join(dataDir, "taxa.csv");
         const csv = CSV.readFileAndHeaders(this.#filePath);
-        // @ts-ignore
         this.#taxa = csv.data;
-        this.#headers = csv.headers;
     }
 
     /**
@@ -26,6 +45,6 @@ export class TaxaCSV {
     }
 
     write() {
-        CSV.writeFileObject(this.#filePath, this.#taxa, this.#headers);
+        CSV.writeFileObject(this.#filePath, this.#taxa, HEADERS);
     }
 }

package/lib/web/pagetaxon.js

@@ -34,19 +34,13 @@ export class PageTaxon extends GenericPage {
         if (iNatLink) {
             links.push(iNatLink);
         }
-        const calscapeLink = HTMLTaxon.getCalscapeLink(this.#taxon);
-        if (calscapeLink) {
-            links.push(calscapeLink);
-        }
         const rpiLink = this.#taxon.getRPITaxonLink();
         if (rpiLink) {
             links.push(rpiLink);
         }
-        HTMLTaxon.addLink(
-            links,
-            ExternalSites.getCCH2RefLink(this.#taxon),
-            "CCH2",
-        );
+        HTMLTaxon.addRefLink(links, this.#taxon, "fna");
+        HTMLTaxon.addRefLink(links, this.#taxon, "cch");
+        HTMLTaxon.addRefLink(links, this.#taxon, "calscape");
         return links;
     }
 

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.4.21",
+    "version": "0.4.22",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {
@@ -58,6 +58,7 @@
         "eslint": "^9.18.0",
         "jest": "^29.7.0",
         "prettier": "^3.4.2",
+        "puppeteer": "^24.1.1",
         "typescript": "^5.7.3"
     }
 }

package/scripts/cpl-tools.js

@@ -14,11 +14,13 @@ import { Taxa } from "../lib/taxa.js";
 import { SupplementalText } from "../lib/tools/supplementaltext.js";
 import { JepsonFamilies } from "../lib/tools/jepsonfamilies.js";
 import { CCH2 } from "../lib/tools/cch2.js";
+import { FNA } from "../lib/tools/fna.js";
 
 const TOOLS = {
     CALFLORA: "calflora",
     CALSCAPE: "calscape",
     CCH2: "cch",
+    FNA: "fna",
     INAT: "inat",
     JEPSON_EFLORA: "jepson-eflora",
     JEPSON_FAM: "jepson-families",
@@ -30,6 +32,7 @@ const ALL_TOOLS = [
     TOOLS.CALFLORA,
     TOOLS.CALSCAPE,
     TOOLS.CCH2,
+    TOOLS.FNA,
     TOOLS.INAT,
     TOOLS.JEPSON_EFLORA,
     TOOLS.RPI,
@@ -84,11 +87,22 @@ async function build(program, options) {
                 await CCH2.analyze(
                     TOOLS_DATA_DIR,
                     options.datadir,
+                    exceptions,
                     taxa,
                     errorLog,
                     !!options.update,
                 );
                 break;
+            case TOOLS.FNA:
+                await FNA.analyze(
+                    TOOLS_DATA_DIR,
+                    options.datadir,
+                    taxa,
+                    errorLog,
+                    !!options.update,
+                );
+                break;
+
             case TOOLS.INAT:
                 await INat.analyze(
                     TOOLS_DATA_DIR,
@@ -150,9 +164,11 @@ program.addHelpText(
     "after",
     `
 Tools:
-    'all' runs the 'calflora', '${TOOLS.CALSCAPE}', 'inat', 'jepson-eflora', 'rpi', and 'text' tools.
+    'all' runs the 'calflora', '${TOOLS.CALSCAPE}', '${TOOLS.CCH2}, '${TOOLS.FNA}, 'inat', 'jepson-eflora', 'rpi', and 'text' tools.
     '${TOOLS.CALFLORA}' retrieves data from Calflora and compares with local data.
     '${TOOLS.CALSCAPE}' retrieves data from Calscape and compares with local data.
+    '${TOOLS.CCH2}' retrieves data from CCH2 and compares with local data.
+    '${TOOLS.FNA}' retrieves data from Flora of North America and compares with local data.
     '${TOOLS.INAT}' retrieves data from iNaturalist and compares with local data.
     '${TOOLS.JEPSON_EFLORA}' retrieves data from Jepson eFlora indexes and compares with local data.
     '${TOOLS.JEPSON_FAM}' retrieves section, family and genus data from Jepson eFlora and creates data files for use by ca-plant-list.