@ca-plant-list/ca-plant-list 0.4.20 → 0.4.22

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/errorlog.js

@@ -17,7 +17,7 @@ class ErrorLog {
     }
 
     /**
-     * @param  {...string} args
+     * @param  {...any} args
      */
     log(...args) {
         if (this.#echo) {

package/lib/externalsites.js

@@ -5,7 +5,64 @@
     taxon_id?: string;
 }} InatObsOptions */
 
-class ExternalSites {
+export class ExternalSites {
+    /**
+     * @param {import("./taxon.js").Taxon} taxon
+     * @returns {URL|undefined}
+     */
+    static getCalscapeLink(taxon) {
+        const calscapeCN = taxon.getCalscapeCommonName();
+        if (!calscapeCN) {
+            return;
+        }
+        return new URL(
+            `https://www.calscape.org/${taxon.getCalscapeName().replaceAll(" ", "-")}-()`,
+        );
+    }
+
+    /**
+     * @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 {import("./taxon.js").Taxon} taxon
+     * @returns {URL|undefined}
+     */
+    static getFNARefLink(taxon) {
+        const name = taxon.getFNAName();
+        if (!name) {
+            return;
+        }
+        const url = new URL(
+            "http://floranorthamerica.org/" + name.replaceAll(" ", "_"),
+        );
+        return url;
+    }
+
     /**
      * @param {InatObsOptions} options
      */
@@ -44,5 +101,3 @@ class ExternalSites {
         return url.toString();
     }
 }
-
-export { ExternalSites };

package/lib/files.js

@@ -13,15 +13,13 @@ class Files {
 
     /**
      * @param {string} fileName
-     * @param {*} inStream
-     * @access private
+     * @param {import("node:stream").Stream} inStream
      */
     static #createFileFromStream(fileName, inStream) {
         /**
-         *
          * @param {string} fileName
-         * @param {*} inStream
-         * @param {*} resolve
+         * @param {import("node:stream").Stream} inStream
+         * @param {function(boolean):void} resolve
          */
         function implementation(fileName, inStream, resolve) {
             const outStream = fs.createWriteStream(fileName);
@@ -140,7 +138,7 @@ 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

@@ -1,5 +1,6 @@
 import { Config } from "./config.js";
 import { DateUtils } from "./dateutils.js";
+import { ExternalSites } from "./externalsites.js";
 import { HTML } from "./html.js";
 import { Markdown } from "./markdown.js";
 import { RarePlants } from "./rareplants.js";
@@ -53,22 +54,44 @@ const DEFAULT_TAXA_COLUMNS = [
     TAXA_LIST_COLS.COMMON_NAME,
 ];
 
+/** @type {Object<string,{label:string,href:function(import("./taxon.js").Taxon):URL|undefined}>} */
+const REFLINKS = {
+    calscape: {
+        label: "Calscape",
+        href: (taxon) => ExternalSites.getCalscapeLink(taxon),
+    },
+    fna: {
+        label: "Flora of North America",
+        href: (taxon) => ExternalSites.getFNARefLink(taxon),
+    },
+    cch: {
+        label: "CCH2",
+        href: (taxon) => ExternalSites.getCCH2RefLink(taxon),
+    },
+};
+
 class HTMLTaxon {
     /**
-     * @param {import("./taxon.js").Taxon} taxon
-     * @returns {string|undefined}
+     * @param {string[]} links
+     * @param {URL|string|undefined} href
+     * @param {string} label
      */
-    static getCalscapeLink(taxon) {
-        const calscapeCN = taxon.getCalscapeCommonName();
-        if (!calscapeCN) {
+    static addLink(links, href, label) {
+        if (href === undefined) {
             return;
         }
-        return HTML.getLink(
-            `https://www.calscape.org/${taxon.getCalscapeName().replaceAll(" ", "-")}-()`,
-            "Calscape",
-            {},
-            true,
-        );
+        const link = HTML.getLink(href.toString(), label, {}, true);
+        links.push(link);
+    }
+
+    /**
+     * @param {string[]} links
+     * @param {import("./taxon.js").Taxon} taxon
+     * @param {import("./index.js").RefSourceCode} sourceCode
+     */
+    static addRefLink(links, taxon, sourceCode) {
+        const source = REFLINKS[sourceCode];
+        this.addLink(links, source.href(taxon), source.label);
     }
 
     /**

package/lib/index.d.ts

@@ -2,15 +2,23 @@ import { Command } from "commander";
 
 // Types
 
+export type NativeStatusCode = "N" | "NC" | "U" | "X";
+
+type PhotoRights = "CC0" | "CC BY" | "CC BY-NC" | "C" | null;
+
+type RefSourceCode = "calscape" | "cch" | "fna";
+
 export type TaxonData = {
     bloom_end: string;
     bloom_start: string;
     calrecnum: string;
     calscape_cn?: string;
+    cch2_id: string;
     CESA: string;
     "common name": string;
     CRPR: string;
     FESA: string;
+    fna: string;
     flower_color: string;
     GRank: string;
     "inat id": string;
@@ -18,7 +26,7 @@ export type TaxonData = {
     life_cycle: string;
     "RPI ID": string;
     SRank: string;
-    status: "N" | "NC" | "U" | "X";
+    status: NativeStatusCode;
     taxon_name: string;
 };
 
@@ -58,6 +66,14 @@ export class Exceptions {
     hasException(name: string, cat: string, subcat: string): boolean;
 }
 
+export class ExternalSites {
+    static getCCH2ObsLink(taxon: Taxon, config: Config): URL | undefined;
+}
+
+export class Family {
+    getName(): string;
+}
+
 export class Files {
     static exists(fileName: string): boolean;
     static fetch(
@@ -66,11 +82,18 @@ export class Files {
     ): Promise<Headers>;
     static mkdir(dir: string): void;
     static rmDir(dir: string): void;
-    static write(fileName: string, data: string, overwrite: boolean): void;
+    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 escapeText(text: string): string;
     static getLink(
         href: string | undefined,
         linkText: string,
@@ -90,6 +113,16 @@ export class HTML {
 }
 
 export class HTMLTaxon {
+    static addLink(
+        links: string[],
+        href: URL | string | undefined,
+        label: string,
+    ): void;
+    static addRefLink(
+        links: string[],
+        taxon: Taxon,
+        sourceCode: RefSourceCode,
+    ): void;
     static getFooterHTML(taxon: Taxon): string;
     static getListSectionHTML(
         list: string[],
@@ -100,11 +133,10 @@ export class HTMLTaxon {
 }
 
 export class Jekyll {
+    static hasInclude(baseDir: string, path: string): boolean;
     static include(fileName: string): string;
 }
 
-type PhotoRights = "CC0" | "CC BY" | "CC BY-NC" | "C" | null;
-
 export class Photo {
     getAttribution(): string;
     getExt(): string;
@@ -118,37 +150,33 @@ export class Program {
     static getProgram(): Command;
 }
 
-export class Family {}
-
-export class Genera {}
-
-export class Genus {}
-
-export class Taxa {
+export class Taxa<T> {
     constructor(
         inclusionList: Record<string, TaxonData> | true,
         errorLog: ErrorLog,
         showFlowerErrors: boolean,
-        taxonFactory?: (td: TaxonData, g: Genera) => Taxon,
+        taxonFactory?: (td: TaxonData, g: Genera) => T,
         extraTaxa?: TaxonData[],
         extraSynonyms?: Record<string, string>[],
     );
-    getTaxon(name: string): Taxon;
-    getTaxonList(): Taxon[];
+    getTaxon(name: string): T;
+    getTaxonList(): T[];
 }
 
 export class Taxon {
+    constructor(data: TaxonData, genera: Genera);
     getBaseFileName(): string;
     getCalfloraID(): string;
     getCalfloraTaxonLink(): string;
-    getCESA(): string | undefined;
-    getCNDDBRank(): string | undefined;
+    getCESA(): string;
+    getCNDDBRank(): string;
     getCommonNames(): string[];
     getFamily(): Family;
-    getFESA(): string | undefined;
+    getFileName(): string;
+    getFESA(): string;
     getGenus(): Genus;
     getGenusName(): string;
-    getGlobalRank(): string | undefined;
+    getGlobalRank(): string;
     getINatID(): string;
     getINatTaxonLink(): string;
     getJepsonID(): 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 +14,8 @@ class Taxon {
     #iNatID;
     /**@type {string|undefined} */
     #iNatSyn;
+    #cch2id;
+    #fnaName;
     #calscapeCN;
     #lifeCycle;
     #flowerColors;
@@ -62,6 +53,8 @@ class Taxon {
         this.#jepsonID = data["jepson id"];
         this.#calRecNum = data["calrecnum"];
         this.#iNatID = data["inat id"];
+        this.#cch2id = data.cch2_id;
+        this.#fnaName = data.fna ?? "";
         this.#calscapeCN =
             data.calscape_cn === "" ? undefined : data.calscape_cn;
         this.#lifeCycle = data.life_cycle;
@@ -173,12 +166,25 @@ class Taxon {
         return name.replace(" subsp.", " ssp.");
     }
 
+    /**
+     * @returns {string}
+     */
+    getCCH2ID() {
+        return this.#cch2id;
+    }
+
+    /**
+     * @returns {string}
+     */
     getCESA() {
-        return this.#cesa;
+        return this.#cesa ?? "";
     }
 
+    /**
+     * @returns {string}
+     */
     getCNDDBRank() {
-        return this.#rankCNDDB;
+        return this.#rankCNDDB ?? "";
     }
 
     getCommonNames() {
@@ -189,14 +195,27 @@ class Taxon {
         return this.getGenus().getFamily();
     }
 
+    /**
+     * @returns {string}
+     */
     getFESA() {
-        return this.#fesa;
+        return this.#fesa ?? "";
     }
 
     getFileName(ext = "html") {
         return this.getBaseFileName() + "." + ext;
     }
 
+    /**
+     * @returns {string}
+     */
+    getFNAName() {
+        if (this.#fnaName === "true") {
+            return this.getName();
+        }
+        return this.#fnaName;
+    }
+
     getFlowerColors() {
         return this.#flowerColors;
     }
@@ -209,8 +228,11 @@ class Taxon {
         return this.#genus;
     }
 
+    /**
+     * @returns {string}
+     */
     getGlobalRank() {
-        return this.#rankGlobal;
+        return this.#rankGlobal ?? "";
     }
 
     /**
@@ -289,6 +311,9 @@ class Taxon {
         return this.#rpiID;
     }
 
+    /**
+     * @returns {string}
+     */
     getRPIRank() {
         if (!this.#rankRPI) {
             return this.#rankRPI;
@@ -303,12 +328,18 @@ class Taxon {
         return this.#rankRPI;
     }
 
+    /**
+     * @deprecated
+     */
     getRPIRankAndThreatTooltip() {
         return RarePlants.getRPIRankAndThreatDescriptions(
             this.getRPIRankAndThreat(),
         ).join("<br>");
     }
 
+    /**
+     * @deprecated
+     */
     getRPITaxonLink() {
         const rpiID = this.getRPIID();
         if (!rpiID) {
@@ -323,9 +354,6 @@ class Taxon {
         return link;
     }
 
-    /**
-     * @returns {StatusCode}
-     */
     getStatus() {
         return this.#status;
     }
@@ -340,6 +368,8 @@ class Taxon {
                 return "Native";
             case "NC":
                 return config.getLabel("status-NC", "Introduced");
+            case "U":
+                return "Nativity Uncertain";
             case "X":
                 return "Introduced";
         }
@@ -385,4 +415,4 @@ 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