@ca-plant-list/ca-plant-list 0.4.22 → 0.4.23

package/lib/index.d.ts

@@ -6,9 +6,26 @@ export type NativeStatusCode = "N" | "NC" | "U" | "X";
 
 type PhotoRights = "CC0" | "CC BY" | "CC BY-NC" | "C" | null;
 
-type RefSourceCode = "calscape" | "cch" | "fna";
+type RefSourceCode =
+    | "calflora"
+    | "calscape"
+    | "cch"
+    | "fna"
+    | "inat"
+    | "jepson"
+    | "rpi";
+
+type TaxaColDef<T> = {
+    title: string;
+    class?: string;
+    data: (taxon: T) => string | number;
+};
 
-export type TaxonData = {
+type TaxonomyData = {
+    "jepson id": string;
+};
+
+export type TaxonData = TaxonomyData & {
     bloom_end: string;
     bloom_start: string;
     calrecnum: string;
@@ -22,7 +39,6 @@ export type TaxonData = {
     flower_color: string;
     GRank: string;
     "inat id": string;
-    "jepson id": string;
     life_cycle: string;
     "RPI ID": string;
     SRank: string;
@@ -32,6 +48,14 @@ export type TaxonData = {
 
 // Classes
 
+export class BasePageRenderer {
+    static renderBasePages<T extends Taxon>(
+        outputDir: string,
+        taxa: Taxa<T>,
+        familyCols?: TaxaColDef<T>[],
+    ): void;
+}
+
 export class Config {
     constructor(dataDir: string);
     getConfigValue(
@@ -45,7 +69,10 @@ export class Config {
 }
 
 export class CSV {
-    static parseFile(dir: string, fileName: string): Record<string, string>[];
+    static readFile(
+        fileName: string,
+        delimeter?: string,
+    ): Record<string, string>[];
 }
 
 export class ErrorLog {
@@ -66,10 +93,6 @@ 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;
 }
@@ -87,8 +110,8 @@ export class Files {
 
 export class Genera {}
 
-export class Genus {
-    getTaxa(): Taxon[];
+export class Genus<T extends Taxon> {
+    getTaxa(): T[];
 }
 
 export class HTML {
@@ -100,14 +123,19 @@ export class HTML {
         attrs?: Record<string, string> | string,
         openInNewWindow?: boolean,
     ): string;
+    static getToolTip(
+        text: string,
+        tooltip: string,
+        options?: { icon: boolean },
+    ): string;
     static textElement(
         elName: string,
-        text: string,
+        text: string | number,
         attrs?: Record<string, string>,
     ): string;
     static wrap(
         elName: string,
-        text: string,
+        text: string | number,
         attrs?: string | Record<string, string> | undefined,
     ): string;
 }
@@ -118,6 +146,13 @@ export class HTMLTaxon {
         href: URL | string | undefined,
         label: string,
     ): void;
+    static addObsLink(
+        links: string[],
+        taxon: Taxon,
+        config: Config,
+        sourceCode: RefSourceCode,
+        label?: string,
+    ): void;
     static addRefLink(
         links: string[],
         taxon: Taxon,
@@ -167,22 +202,22 @@ export class Taxon {
     constructor(data: TaxonData, genera: Genera);
     getBaseFileName(): string;
     getCalfloraID(): string;
-    getCalfloraTaxonLink(): string;
+    getCalfloraName(): string;
     getCESA(): string;
     getCNDDBRank(): string;
     getCommonNames(): string[];
     getFamily(): Family;
     getFileName(): string;
     getFESA(): string;
-    getGenus(): Genus;
+    getGenus<T extends Taxon>(): Genus<T>;
     getGenusName(): string;
     getGlobalRank(): string;
     getINatID(): string;
-    getINatTaxonLink(): string;
+    getINatName(): string;
     getJepsonID(): string;
     getName(): string;
     getPhotos(): Photo[];
+    getRPIRank(): string;
     getRPIRankAndThreat(): string;
-    getRPITaxonLink(): string;
     getSynonyms(): string[];
 }

package/lib/index.js

@@ -4,15 +4,15 @@ 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 { Families } from "./taxonomy/families.js";
 import { Files } from "./files.js";
 import { HTML } from "./html.js";
 import { HTMLTaxon } from "./htmltaxon.js";
 import { Jekyll } from "./jekyll.js";
 import { PlantBook } from "./ebook/plantbook.js";
 import { Program } from "./program.js";
-import { Taxa } from "./taxa.js";
-import { Taxon } from "./taxon.js";
+import { Taxa } from "./taxonomy/taxa.js";
+import { Taxon } from "./taxonomy/taxon.js";
 
 export {
     BasePageRenderer,

package/lib/pagerenderer.js

@@ -22,7 +22,7 @@ class PageRenderer extends BasePageRenderer {
     /**
      * @param {string} outputDir
      * @param {import('./config.js').Config} config
-     * @param {import("./taxa.js").Taxa} taxa
+     * @param {import("./types.js").Taxa} taxa
      */
     static render(outputDir, config, taxa) {
         super.renderBasePages(outputDir, taxa);
@@ -38,13 +38,13 @@ class PageRenderer extends BasePageRenderer {
     /**
      * @param {string} outputDir
      * @param {import('./config.js').Config} config
-     * @param {import("./taxa.js").Taxa} taxa
+     * @param {import("./types.js").Taxa} taxa
      */
     static renderLists(outputDir, config, taxa) {
         /**
          * @param {ListInfo[]} listInfo
          * @param {Object<string,string>} attributes
-         * @param {import("./htmltaxon.js").TaxaColDef[]} [columns]
+         * @param {import("./types.js").TaxaColDef[]} [columns]
          * @returns {string}
          */
         function getListArray(listInfo, attributes = {}, columns) {
@@ -117,7 +117,7 @@ class PageRenderer extends BasePageRenderer {
             return html;
         }
 
-        /** @typedef {{name:string,filename:string,include:function(import("./taxon.js").Taxon):boolean,columns?:import("./htmltaxon.js").TaxaColDef[],listInfo?:ListInfo[]}} ListInfo */
+        /** @typedef {{name:string,filename:string,include:function(import("./types.js").Taxon):boolean,columns?:import("./types.js").TaxaColDef[],listInfo?:ListInfo[]}} ListInfo */
         /** @type {{title:string,listInfo:ListInfo[]}[]} */
         const sections = [
             {
@@ -227,8 +227,8 @@ class PageTaxonList extends GenericPage {
 
     /**
      *
-     * @param {import("./taxon.js").Taxon[]} taxa
-     * @param {import("./htmltaxon.js").TaxaColDef[]|undefined} columns
+     * @param {import("./types.js").Taxon[]} taxa
+     * @param {import("./types.js").TaxaColDef[]|undefined} columns
      */
     render(taxa, columns) {
         let html = this.getDefaultIntro();

package/lib/taxonomy/families.js

@@ -0,0 +1,104 @@
+import { Files } from "../files.js";
+import { Config } from "../config.js";
+import { Taxonomy } from "./taxonomy.js";
+
+/**
+ * @typedef {{id:string,section:string,taxa?:import("../types.js").Taxon[]}} FamilyData
+ */
+
+export class Family extends Taxonomy {
+    #name;
+    #data;
+
+    /**
+     * @param {string} name
+     * @param {FamilyData} data
+     */
+    constructor(name, data) {
+        super({ "jepson id": data.id });
+        this.#name = name;
+        this.#data = data;
+    }
+
+    /**
+     * @param {import("../types.js").Taxon} taxon
+     */
+    addTaxon(taxon) {
+        if (!this.#data.taxa) {
+            this.#data.taxa = [];
+        }
+        this.#data.taxa.push(taxon);
+        Sections.addTaxon(this.getSectionName(), taxon);
+    }
+
+    getBaseFileName() {
+        return this.getName();
+    }
+
+    getFileName(ext = "html") {
+        return this.getBaseFileName() + "." + ext;
+    }
+
+    getName() {
+        return this.#name;
+    }
+
+    getSectionName() {
+        return this.#data.section;
+    }
+
+    getTaxa() {
+        return this.#data.taxa;
+    }
+}
+
+export class Families {
+    #families;
+
+    constructor() {
+        const dataDir = Config.getPackageDir() + "/data";
+
+        this.#families = JSON.parse(Files.read(dataDir + "/families.json"));
+        for (const [k, v] of Object.entries(this.#families)) {
+            this.#families[k] = new Family(k, v);
+        }
+    }
+
+    /**
+     * @returns {Family[]}
+     */
+    getFamilies() {
+        return Object.values(this.#families).sort((a, b) =>
+            a.getName().localeCompare(b.getName()),
+        );
+    }
+
+    /**
+     * @param {string} familyName
+     */
+    getFamily(familyName) {
+        return this.#families[familyName];
+    }
+}
+
+export class Sections {
+    /** @type {Object<string,import("../types.js").Taxon[]>} */
+    static #sections = {};
+
+    /**
+     * @param {string} name
+     * @param {import("../types.js").Taxon} taxon
+     */
+    static addTaxon(name, taxon) {
+        let section = this.#sections[name];
+        if (!section) {
+            section = [];
+            this.#sections[name] = section;
+        }
+        section.push(taxon);
+    }
+
+    static getSections() {
+        return this.#sections;
+    }
+}

package/lib/{taxa.js → taxonomy/taxa.js}

@@ -1,16 +1,16 @@
 import * as fs from "node:fs";
 import path from "node:path";
 
-import { Config } from "./config.js";
-import { CSV } from "./csv.js";
-import { Genera } from "./genera.js";
+import { Config } from "../config.js";
+import { CSV } from "../csv.js";
+import { Genera } from "../genera.js";
 import { Taxon } from "./taxon.js";
 import { Families } from "./families.js";
-import { FlowerColor } from "./flowercolor.js";
-import { TaxaCSV } from "./tools/taxacsv.js";
-import { ErrorLog } from "./errorlog.js";
-import { Program } from "./program.js";
-import { Photo } from "./photo.js";
+import { FlowerColor } from "../flowercolor.js";
+import { TaxaCSV } from "../tools/taxacsv.js";
+import { ErrorLog } from "../errorlog.js";
+import { Program } from "../program.js";
+import { Photo } from "../photo.js";
 
 /**
  * @typedef {{Current: string;Former: string;Type: string;}} SynonymData
@@ -40,11 +40,11 @@ class Taxa {
     #isSubset;
 
     /**
-     * @param {Object<string,import("./index.js").TaxonData>|true} inclusionList
+     * @param {Object<string,import("../index.js").TaxonData>|true} inclusionList
      * @param {ErrorLog} errorLog
      * @param {boolean} showFlowerErrors
-     * @param {function(import("./index.js").TaxonData,Genera):Taxon} taxonFactory
-     * @param {import("./index.js").TaxonData[]} [extraTaxa=[]]
+     * @param {function(import("../index.js").TaxonData,Genera):Taxon} taxonFactory
+     * @param {import("../index.js").TaxonData[]} [extraTaxa=[]]
      * @param {SynonymData[]} [extraSynonyms=[]]
      * @param {boolean} includePhotos
      */
@@ -114,9 +114,9 @@ class Taxa {
      */
     #loadPhotosFromFile(dataDir, filename) {
         if (!fs.existsSync(path.join(dataDir, filename))) return;
-        /** @type {import("./utils/inat-tools.js").InatCsvPhoto[]} */
+        /** @type {import("../utils/inat-tools.js").InatCsvPhoto[]} */
         const csvPhotos = CSV.parseFile(dataDir, filename).map((row) => {
-            /** @type {import("./utils/inat-tools.js").InatLicenseCode} */
+            /** @type {import("../utils/inat-tools.js").InatLicenseCode} */
             let licenseCode = "cc-by";
             if (row.licenseCode === "cc-by-nc-sa") licenseCode = "cc-by-nc-sa";
             else if (row.licenseCode === "cc-by-nc") licenseCode = "cc-by-nc";
@@ -224,7 +224,7 @@ class Taxa {
 
     /**
      * @param {SynonymData[]} synCSV
-     * @param {Object<string,import("./index.js").TaxonData>|boolean} inclusionList
+     * @param {Object<string,import("../index.js").TaxonData>|boolean} inclusionList
      */
     #loadSyns(synCSV, inclusionList) {
         for (const syn of synCSV) {
@@ -245,9 +245,9 @@ class Taxa {
     }
 
     /**
-     * @param {import("./index.js").TaxonData[]} taxaCSV
-     * @param {Object<string,import("./index.js").TaxonData>|true} inclusionList
-     * @param {function(import("./index.js").TaxonData,Genera):Taxon} taxonFactory
+     * @param {import("../index.js").TaxonData[]} taxaCSV
+     * @param {Object<string,import("../index.js").TaxonData>|true} inclusionList
+     * @param {function(import("../index.js").TaxonData,Genera):Taxon} taxonFactory
      * @param {Genera} genera
      * @param {boolean} showFlowerErrors
      */
@@ -255,7 +255,7 @@ class Taxa {
         for (const row of taxaCSV) {
             const name = row["taxon_name"];
 
-            /** @type {import("./index.js").TaxonData|{status?:import("./index.js").NativeStatusCode}} */
+            /** @type {import("../index.js").TaxonData|{status?:import("../index.js").NativeStatusCode}} */
             let taxon_overrides = {};
             if (inclusionList !== true) {
                 taxon_overrides = inclusionList[name];

package/lib/{taxon.js → taxonomy/taxon.js}

@@ -1,16 +1,12 @@
-import { HTML } from "./html.js";
-import { RarePlants } from "./rareplants.js";
+import { Taxonomy } from "./taxonomy.js";
 
-class Taxon {
+class Taxon extends Taxonomy {
     #genera;
     #name;
     #genus;
     #commonNames;
     #status;
-    #jepsonID;
     #calRecNum;
-    /**@type {string|undefined} */
-    #cfSyn;
     #iNatID;
     /**@type {string|undefined} */
     #iNatSyn;
@@ -29,14 +25,15 @@ class Taxon {
     #rankGlobal;
     /** @type {string[]} */
     #synonyms = [];
-    /** @type {import("./photo.js").Photo[]}*/
+    /** @type {import("../photo.js").Photo[]}*/
     #photos = [];
 
     /**
-     * @param {import("./index.js").TaxonData} data
-     * @param {import("./genera.js").Genera} genera
+     * @param {import("../index.js").TaxonData} data
+     * @param {import("../genera.js").Genera} genera
      */
     constructor(data, genera) {
+        super(data);
         this.#genera = genera;
         const name = data["taxon_name"];
         const commonNames = data["common name"];
@@ -50,7 +47,6 @@ class Taxon {
             ? commonNames.split(",").map((t) => t.trim())
             : [];
         this.#status = data["status"];
-        this.#jepsonID = data["jepson id"];
         this.#calRecNum = data["calrecnum"];
         this.#iNatID = data["inat id"];
         this.#cch2id = data.cch2_id;
@@ -82,10 +78,6 @@ class Taxon {
     addSynonym(syn, type) {
         this.#synonyms.push(syn);
         switch (type) {
-            case "CF":
-                // Synonym is in Calflora format.
-                this.#cfSyn = syn;
-                break;
             case "INAT":
                 // Synonyms should be in Jepson format, but store iNatName in iNat format (no var or subsp, space after x).
                 this.#iNatSyn = syn;
@@ -94,14 +86,14 @@ class Taxon {
     }
 
     /**
-     * @param {import("./photo.js").Photo} photo
+     * @param {import("../photo.js").Photo} photo
      */
     addPhoto(photo) {
         this.#photos = this.#photos.concat([photo]);
     }
 
     /**
-     * @returns {import("./photo.js").Photo[]}
+     * @returns {import("../photo.js").Photo[]}
      */
     getPhotos() {
         return this.#photos;
@@ -127,9 +119,6 @@ class Taxon {
     }
 
     getCalfloraName() {
-        if (this.#cfSyn) {
-            return this.#cfSyn;
-        }
         return this.getName().replace(" subsp.", " ssp.").replace("×", "X");
     }
 
@@ -137,20 +126,6 @@ class Taxon {
         return this.#calRecNum;
     }
 
-    getCalfloraTaxonLink() {
-        const calfloraID = this.getCalfloraID();
-        if (!calfloraID) {
-            return;
-        }
-        const link = HTML.getLink(
-            "https://www.calflora.org/app/taxon?crn=" + calfloraID,
-            "Calflora",
-            {},
-            true,
-        );
-        return this.#cfSyn ? link + " (" + this.#cfSyn + ")" : link;
-    }
-
     getCalscapeCommonName() {
         return this.#calscapeCN;
     }
@@ -235,33 +210,6 @@ class Taxon {
         return this.#rankGlobal ?? "";
     }
 
-    /**
-     *
-     * @param {boolean|string|undefined} href
-     * @param {boolean} includeRPI
-     */
-    getHTMLLink(href = true, includeRPI = true) {
-        href = href ? "./" + this.getFileName() : undefined;
-        let className = this.isNative() ? "native" : "non-native";
-        let isRare = false;
-        if (includeRPI && this.isRare()) {
-            isRare = true;
-            className += " rare";
-        }
-        const attributes = { class: className };
-        const link = HTML.wrap(
-            "span",
-            HTML.getLink(href, this.getName()),
-            attributes,
-        );
-        if (isRare) {
-            return HTML.getToolTip(link, this.getRPIRankAndThreatTooltip(), {
-                icon: false,
-            });
-        }
-        return link;
-    }
-
     getINatID() {
         return this.#iNatID;
     }
@@ -278,27 +226,6 @@ class Taxon {
         return this.#iNatSyn;
     }
 
-    getINatTaxonLink() {
-        const iNatID = this.getINatID();
-        if (!iNatID) {
-            return "";
-        }
-        const link = HTML.getLink(
-            "https://www.inaturalist.org/taxa/" + iNatID,
-            "iNaturalist",
-            {},
-            true,
-        );
-        return this.#iNatSyn ? link + " (" + this.#iNatSyn + ")" : link;
-    }
-
-    /**
-     * @returns {string}
-     */
-    getJepsonID() {
-        return this.#jepsonID;
-    }
-
     getLifeCycle() {
         return this.#lifeCycle;
     }
@@ -328,38 +255,12 @@ class Taxon {
         return this.#rankRPI;
     }
 
-    /**
-     * @deprecated
-     */
-    getRPIRankAndThreatTooltip() {
-        return RarePlants.getRPIRankAndThreatDescriptions(
-            this.getRPIRankAndThreat(),
-        ).join("<br>");
-    }
-
-    /**
-     * @deprecated
-     */
-    getRPITaxonLink() {
-        const rpiID = this.getRPIID();
-        if (!rpiID) {
-            return "";
-        }
-        const link = HTML.getLink(
-            "https://rareplants.cnps.org/Plants/Details/" + rpiID,
-            "CNPS Rare Plant Inventory",
-            {},
-            true,
-        );
-        return link;
-    }
-
     getStatus() {
         return this.#status;
     }
 
     /**
-     * @param {import("./config.js").Config} config
+     * @param {import("../config.js").Config} config
      * @returns {string}
      */
     getStatusDescription(config) {

package/lib/taxonomy/taxonomy.js

@@ -0,0 +1,17 @@
+export class Taxonomy {
+    #data;
+
+    /**
+     * @param {import("../index.js").TaxonomyData} data
+     */
+    constructor(data) {
+        this.#data = data;
+    }
+
+    /**
+     * @returns {string}
+     */
+    getJepsonID() {
+        return this.#data["jepson id"];
+    }
+}

package/lib/tools/calflora.js

@@ -25,7 +25,7 @@ export class Calflora {
     /**
      * @param {string} toolsDataDir
      * @param {string} dataDir
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../exceptions.js").Exceptions} exceptions
      * @param {import("../errorlog.js").ErrorLog} errorLog
      * @param {boolean} update
@@ -175,7 +175,7 @@ export class Calflora {
     }
 
     /**
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../exceptions.js").Exceptions} exceptions
      * @param {import("../errorlog.js").ErrorLog} errorLog
      */

package/lib/tools/calscape.js

@@ -2,13 +2,13 @@ import path from "node:path";
 import xlsx from "exceljs";
 import { Files } from "../files.js";
 import { TaxaCSV } from "./taxacsv.js";
-import { Taxon } from "../taxon.js";
+import { Taxon } from "../taxonomy/taxon.js";
 
 export class Calscape {
     /**
      * @param {string} toolsDataDir
      * @param {string} dataDir
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../exceptions.js").Exceptions} exceptions
      * @param {import("../errorlog.js").ErrorLog} errorLog
      * @param {boolean} update
@@ -58,7 +58,7 @@ export class Calscape {
 }
 
 /**
- * @param {import("../taxa.js").Taxa} taxa
+ * @param {import("../types.js").Taxa} taxa
  * @param {import("../exceptions.js").Exceptions} exceptions
  * @param {import("../errorlog.js").ErrorLog} errorLog
  */

package/lib/tools/cch2.js

@@ -15,7 +15,7 @@ export class CCH2 {
      * @param {string} toolsDataDir
      * @param {string} dataDir
      * @param {import("../exceptions.js").Exceptions} exceptions
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../errorlog.js").ErrorLog} errorLog
      * @param {boolean} update
      */
@@ -61,7 +61,7 @@ export class CCH2 {
 
     /**
      * @param {import("../exceptions.js").Exceptions} exceptions
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../errorlog.js").ErrorLog} errorLog
      * @param {CCHTaxa} cchTaxa
      */
@@ -106,7 +106,7 @@ export class CCH2 {
 
 /**
  * @param {string} toolsDataPath
- * @param {import("../taxa.js").Taxa} taxa
+ * @param {import("../types.js").Taxa} taxa
  * @returns {Promise<CCHTaxa>}
  */
 async function getCCHTaxa(toolsDataPath, taxa) {