@ca-plant-list/ca-plant-list 0.4.20 → 0.4.21

package/lib/config.js

@@ -2,9 +2,15 @@ import * as path from "node:path";
 import * as url from "node:url";
 import { Files } from "./files.js";
 
+/** @type {Object<string,string>} */
+const COUNTY_NAMES = {
+    ALA: "Alameda",
+    CCA: "Contra Costa",
+};
+
 class Config {
     static #packageDir = path.dirname(
-        path.dirname(url.fileURLToPath(import.meta.url))
+        path.dirname(url.fileURLToPath(import.meta.url)),
     );
 
     /** @type {Object<string,Object<string,Object<string,{}>>>} */
@@ -55,6 +61,14 @@ class Config {
         return [];
     }
 
+    /**
+     * @returns {string[]}
+     */
+    getCountyNames() {
+        const counties = this.getCountyCodes();
+        return counties.map((c) => COUNTY_NAMES[c]);
+    }
+
     /**
      * @param {string} name
      * @param {string} dflt

package/lib/csv.js

@@ -13,7 +13,7 @@ class CSV {
      */
     static #getOptions(fileName, columns, delimiter) {
         /** @type {import("csv-parse").Options} */
-        const options = { relax_column_count_less: true };
+        const options = { relax_column_count_less: true, bom: true };
         options.columns = columns;
         if (path.extname(fileName) === ".tsv") {
             options.delimiter = "\t";
@@ -44,6 +44,7 @@ class CSV {
      * @param {boolean|import("csv-parse").ColumnOption[]} columns
      * @param {string|undefined} delimiter
      * @param {function (any):void} callback
+     * @deprecated Use parseFileStream
      */
     static async parseStream(
         dir,
@@ -72,6 +73,27 @@ class CSV {
         await processFile();
     }
 
+    /**
+     * @template T
+     * @param {string} fileName
+     * @param {function (T):void} callback
+     */
+    static async parseFileStream(fileName, callback) {
+        const options = this.#getOptions(fileName, true, undefined);
+        const processFile = async () => {
+            const parser = fs.createReadStream(fileName).pipe(parse(options));
+            parser.on("readable", function () {
+                let record;
+                while ((record = parser.read()) !== null) {
+                    callback(record);
+                }
+            });
+            await finished(parser);
+        };
+        // Parse the CSV content
+        await processFile();
+    }
+
     /**
      * @param {string} fileName
      * @param {boolean|import("csv-parse").ColumnOption[]|function (string[]):string[]} [columns]

package/lib/externalsites.js

@@ -5,7 +5,35 @@
     taxon_id?: string;
 }} InatObsOptions */
 
-class ExternalSites {
+export class ExternalSites {
+    /**
+     * @param {import("./taxon.js").Taxon} taxon
+     * @param {import("./config.js").Config} config
+     * @returns {URL|undefined}
+     */
+    static getCCH2ObsLink(taxon, config) {
+        const url = new URL(
+            "https://www.cch2.org/portal/collections/listtabledisplay.php?usethes=1&taxontype=2&sortfield1=o.eventDate&sortorder=desc",
+        );
+        url.searchParams.set("county", config.getCountyNames().join(";"));
+        url.searchParams.set("taxa", taxon.getName());
+        return url;
+    }
+
+    /**
+     * @param {import("./taxon.js").Taxon} taxon
+     * @returns {URL|undefined}
+     */
+    static getCCH2RefLink(taxon) {
+        const id = taxon.getCCH2ID();
+        if (!id) {
+            return;
+        }
+        const url = new URL("https://www.cch2.org/portal/taxa/index.php");
+        url.searchParams.set("taxon", id);
+        return url;
+    }
+
     /**
      * @param {InatObsOptions} options
      */
@@ -44,5 +72,3 @@ class ExternalSites {
         return url.toString();
     }
 }
-
-export { ExternalSites };

package/lib/files.js

@@ -140,7 +140,7 @@ class Files {
             if (entry.path === fileNameToUnzip) {
                 await this.#createFileFromStream(
                     targetFilePath,
-                    entry.stream()
+                    entry.stream(),
                 );
                 break;
             }

package/lib/genera.js

@@ -56,6 +56,9 @@ class Genus {
         return this.#data.familyObj;
     }
 
+    /**
+     * @returns {import("./taxon.js").Taxon[]}
+     */
     getTaxa() {
         return this.#data.taxa.sort((a, b) =>
             a.getName().localeCompare(b.getName()),

package/lib/htmltaxon.js

@@ -54,6 +54,19 @@ const DEFAULT_TAXA_COLUMNS = [
 ];
 
 class HTMLTaxon {
+    /**
+     * @param {string[]} links
+     * @param {URL|string|undefined} href
+     * @param {string} label
+     */
+    static addLink(links, href, label) {
+        if (href === undefined) {
+            return;
+        }
+        const link = HTML.getLink(href.toString(), label, {}, true);
+        links.push(link);
+    }
+
     /**
      * @param {import("./taxon.js").Taxon} taxon
      * @returns {string|undefined}

package/lib/index.d.ts

@@ -2,11 +2,14 @@ import { Command } from "commander";
 
 // Types
 
+export type NativeStatusCode = "N" | "NC" | "U" | "X";
+
 export type TaxonData = {
     bloom_end: string;
     bloom_start: string;
     calrecnum: string;
     calscape_cn?: string;
+    cch2_id: string;
     CESA: string;
     "common name": string;
     CRPR: string;
@@ -18,7 +21,7 @@ export type TaxonData = {
     life_cycle: string;
     "RPI ID": string;
     SRank: string;
-    status: "N" | "NC" | "U" | "X";
+    status: NativeStatusCode;
     taxon_name: string;
 };
 
@@ -58,6 +61,15 @@ export class Exceptions {
     hasException(name: string, cat: string, subcat: string): boolean;
 }
 
+export class ExternalSites {
+    static getCCH2ObsLink(taxon: Taxon, config: Config): URL | undefined;
+    static getCCH2RefLink(taxon: Taxon): URL | undefined;
+}
+
+export class Family {
+    getName(): string;
+}
+
 export class Files {
     static exists(fileName: string): boolean;
     static fetch(
@@ -69,6 +81,12 @@ export class Files {
     static write(fileName: string, data: string, overwrite: boolean): void;
 }
 
+export class Genera {}
+
+export class Genus {
+    getTaxa(): Taxon[];
+}
+
 export class HTML {
     static arrayToLI(items: string[]): string;
     static getLink(
@@ -90,6 +108,11 @@ export class HTML {
 }
 
 export class HTMLTaxon {
+    static addLink(
+        links: string[],
+        href: URL | string | undefined,
+        label: string,
+    ): void;
     static getFooterHTML(taxon: Taxon): string;
     static getListSectionHTML(
         list: string[],
@@ -118,12 +141,6 @@ export class Program {
     static getProgram(): Command;
 }
 
-export class Family {}
-
-export class Genera {}
-
-export class Genus {}
-
 export class Taxa {
     constructor(
         inclusionList: Record<string, TaxonData> | true,
@@ -145,6 +162,7 @@ export class Taxon {
     getCNDDBRank(): string | undefined;
     getCommonNames(): string[];
     getFamily(): Family;
+    getFileName(): string;
     getFESA(): string | undefined;
     getGenus(): Genus;
     getGenusName(): string;

package/lib/index.js

@@ -3,6 +3,7 @@ import { Config } from "./config.js";
 import { CSV } from "./csv.js";
 import { ErrorLog } from "./errorlog.js";
 import { Exceptions } from "./exceptions.js";
+import { ExternalSites } from "./externalsites.js";
 import { Families } from "./families.js";
 import { Files } from "./files.js";
 import { HTML } from "./html.js";
@@ -11,7 +12,7 @@ import { Jekyll } from "./jekyll.js";
 import { PlantBook } from "./ebook/plantbook.js";
 import { Program } from "./program.js";
 import { Taxa } from "./taxa.js";
-import { Taxon, TAXA_COLNAMES } from "./taxon.js";
+import { Taxon } from "./taxon.js";
 
 export {
     BasePageRenderer,
@@ -19,6 +20,7 @@ export {
     CSV,
     ErrorLog,
     Exceptions,
+    ExternalSites,
     Families,
     Files,
     HTML,
@@ -27,6 +29,5 @@ export {
     PlantBook,
     Program,
     Taxa,
-    TAXA_COLNAMES,
     Taxon,
 };

package/lib/taxa.js

@@ -255,7 +255,7 @@ class Taxa {
         for (const row of taxaCSV) {
             const name = row["taxon_name"];
 
-            /** @type {import("./index.js").TaxonData|{status?:import("./taxon.js").StatusCode}} */
+            /** @type {import("./index.js").TaxonData|{status?:import("./index.js").NativeStatusCode}} */
             let taxon_overrides = {};
             if (inclusionList !== true) {
                 taxon_overrides = inclusionList[name];

package/lib/taxon.js

@@ -1,17 +1,6 @@
 import { HTML } from "./html.js";
 import { RarePlants } from "./rareplants.js";
 
-/**
- * @typedef {"N" | "NC" | "U" | "X"} StatusCode
- */
-
-const TAXA_COLNAMES = {
-    BLOOM_START: "bloom_start",
-    BLOOM_END: "bloom_end",
-    COMMON_NAME: "common name",
-    FLOWER_COLOR: "flower_color",
-};
-
 class Taxon {
     #genera;
     #name;
@@ -25,6 +14,7 @@ class Taxon {
     #iNatID;
     /**@type {string|undefined} */
     #iNatSyn;
+    #cch2id;
     #calscapeCN;
     #lifeCycle;
     #flowerColors;
@@ -62,6 +52,7 @@ class Taxon {
         this.#jepsonID = data["jepson id"];
         this.#calRecNum = data["calrecnum"];
         this.#iNatID = data["inat id"];
+        this.#cch2id = data.cch2_id;
         this.#calscapeCN =
             data.calscape_cn === "" ? undefined : data.calscape_cn;
         this.#lifeCycle = data.life_cycle;
@@ -173,6 +164,13 @@ class Taxon {
         return name.replace(" subsp.", " ssp.");
     }
 
+    /**
+     * @returns {string}
+     */
+    getCCH2ID() {
+        return this.#cch2id;
+    }
+
     getCESA() {
         return this.#cesa;
     }
@@ -303,12 +301,18 @@ class Taxon {
         return this.#rankRPI;
     }
 
+    /**
+     * @deprecated
+     */
     getRPIRankAndThreatTooltip() {
         return RarePlants.getRPIRankAndThreatDescriptions(
             this.getRPIRankAndThreat(),
         ).join("<br>");
     }
 
+    /**
+     * @deprecated
+     */
     getRPITaxonLink() {
         const rpiID = this.getRPIID();
         if (!rpiID) {
@@ -323,9 +327,6 @@ class Taxon {
         return link;
     }
 
-    /**
-     * @returns {StatusCode}
-     */
     getStatus() {
         return this.#status;
     }
@@ -385,4 +386,4 @@ class Taxon {
     }
 }
 
-export { TAXA_COLNAMES, Taxon };
+export { Taxon };

package/lib/tools/calflora.js

@@ -23,7 +23,6 @@ export class Calflora {
     static #taxa = {};
 
     /**
-     *
      * @param {string} toolsDataDir
      * @param {string} dataDir
      * @param {import("../taxa.js").Taxa} taxa

package/lib/tools/cch2.js

@@ -0,0 +1,95 @@
+import path from "node:path";
+import { CSV } from "../csv.js";
+import { TaxaCSV } from "./taxacsv.js";
+
+/**
+ * @typedef {{id:string}} CCHTaxon
+ * @typedef {Map<string,CCHTaxon>} CCHTaxa
+ */
+
+export class CCH2 {
+    /**
+     * @param {string} toolsDataDir
+     * @param {string} dataDir
+     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../errorlog.js").ErrorLog} errorLog
+     * @param {boolean} update
+     */
+    static async analyze(toolsDataDir, dataDir, taxa, errorLog, update) {
+        const toolsDataPath = path.join(toolsDataDir, "cch2");
+
+        const cchTaxa = await getCCHTaxa(toolsDataPath, taxa);
+
+        const idsToUpdate = new Map();
+        for (const taxon of taxa.getTaxonList()) {
+            const cchTaxon = cchTaxa.get(taxon.getName());
+            if (!cchTaxon) {
+                errorLog.log(taxon.getName(), "not found in CCH data");
+                continue;
+            }
+            if (cchTaxon.id !== taxon.getCCH2ID()) {
+                errorLog.log(
+                    taxon.getName(),
+                    "id in CCH data does not match id in taxa.csv",
+                    cchTaxon.id,
+                    taxon.getCCH2ID(),
+                );
+                idsToUpdate.set(taxon.getName(), cchTaxon.id);
+            }
+        }
+
+        if (update) {
+            updateTaxaCSV(dataDir, idsToUpdate);
+        }
+    }
+}
+
+/**
+ * @param {string} toolsDataPath
+ * @param {import("../taxa.js").Taxa} taxa
+ * @returns {Promise<CCHTaxa>}
+ */
+async function getCCHTaxa(toolsDataPath, taxa) {
+    /**
+     * @param {{taxonID:string,scientificName:string,rankID:string,acceptance:"0"|"1",acceptedTaxonID:string}} record
+     */
+    function callback(record) {
+        if (parseInt(record.rankID) < 220) {
+            // Ignore ranks above species.
+            return;
+        }
+        if (record.acceptance !== "1") {
+            return;
+        }
+        if (!taxa.getTaxon(record.scientificName)) {
+            // If we're not tracking the taxon, ignore it.
+            return;
+        }
+        data.set(record.scientificName, { id: record.acceptedTaxonID });
+    }
+
+    const fileName = path.join(toolsDataPath, "taxa.csv");
+    const data = new Map();
+
+    await CSV.parseFileStream(fileName, callback);
+
+    return data;
+}
+
+/**
+ * @param {string} dataDir
+ * @param {Map<string,string>} idsToUpdate
+ */
+function updateTaxaCSV(dataDir, idsToUpdate) {
+    const taxa = new TaxaCSV(dataDir);
+
+    for (const taxonData of taxa.getTaxa()) {
+        const id = idsToUpdate.get(taxonData.taxon_name);
+        if (!id) {
+            continue;
+        }
+        taxonData.cch2_id = id;
+    }
+
+    taxa.write();
+}

package/lib/tools/jepsoneflora.js

@@ -228,7 +228,7 @@ export class JepsonEFlora {
 
     /**
      * @param {JepsonTaxon} jepsInfo
-     * @returns {import("../taxon.js").StatusCode|undefined}
+     * @returns {import("../index.js").NativeStatusCode|undefined}
      */
     #getStatusCode(jepsInfo) {
         switch (jepsInfo.type) {

package/lib/web/pagetaxon.js

@@ -5,7 +5,7 @@ import { ExternalSites } from "../externalsites.js";
 import { HTML } from "../html.js";
 import { HTMLTaxon } from "../htmltaxon.js";
 
-class PageTaxon extends GenericPage {
+export class PageTaxon extends GenericPage {
     #config;
     #taxon;
 
@@ -42,6 +42,11 @@ class PageTaxon extends GenericPage {
         if (rpiLink) {
             links.push(rpiLink);
         }
+        HTMLTaxon.addLink(
+            links,
+            ExternalSites.getCCH2RefLink(this.#taxon),
+            "CCH2",
+        );
         return links;
     }
 
@@ -76,6 +81,11 @@ class PageTaxon extends GenericPage {
                 ),
             );
         }
+        HTMLTaxon.addLink(
+            links,
+            ExternalSites.getCCH2ObsLink(this.#taxon, this.#config),
+            "CCH2",
+        );
 
         return links;
     }
@@ -218,5 +228,3 @@ class PageTaxon extends GenericPage {
         this.writeFile(html);
     }
 }
-
-export { PageTaxon };

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.4.20",
+    "version": "0.4.21",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {

package/scripts/cpl-tools.js

@@ -13,10 +13,12 @@ import { Config } from "../lib/config.js";
 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";
 
 const TOOLS = {
     CALFLORA: "calflora",
     CALSCAPE: "calscape",
+    CCH2: "cch",
     INAT: "inat",
     JEPSON_EFLORA: "jepson-eflora",
     JEPSON_FAM: "jepson-families",
@@ -27,6 +29,7 @@ const TOOLS = {
 const ALL_TOOLS = [
     TOOLS.CALFLORA,
     TOOLS.CALSCAPE,
+    TOOLS.CCH2,
     TOOLS.INAT,
     TOOLS.JEPSON_EFLORA,
     TOOLS.RPI,
@@ -77,6 +80,15 @@ async function build(program, options) {
                     !!options.update,
                 );
                 break;
+            case TOOLS.CCH2:
+                await CCH2.analyze(
+                    TOOLS_DATA_DIR,
+                    options.datadir,
+                    taxa,
+                    errorLog,
+                    !!options.update,
+                );
+                break;
             case TOOLS.INAT:
                 await INat.analyze(
                     TOOLS_DATA_DIR,