@ca-plant-list/ca-plant-list 0.3.7 → 0.4.0

package/lib/genera.js

@@ -6,7 +6,6 @@ class Genera {
     #genera;
 
     /**
-     *
      * @param {Families} families
      */
     constructor(families) {
@@ -22,21 +21,17 @@ class Genera {
         const genusName = taxon.getGenusName();
         const genusData = this.#genera[genusName];
         if (!genusData) {
-            console.log(taxon.getName() + " genus not found");
-            return;
+            throw new Error(taxon.getName() + " genus not found");
         }
 
-        if (genusData.taxa === undefined) {
+        if (genusData.familyObj === undefined) {
+            // Initialize genus data.
+            genusData.familyObj = this.#families.getFamily(genusData.family);
             genusData.taxa = [];
         }
-        genusData.taxa.push(taxon);
+        genusData.familyObj.addTaxon(taxon);
 
-        const family = this.getFamily(genusName);
-        if (!family) {
-            console.log(taxon.getName() + " family not found");
-            return;
-        }
-        family.addTaxon(taxon);
+        genusData.taxa.push(taxon);
     }
 
     /**
@@ -45,25 +40,22 @@ class Genera {
     getGenus(genusName) {
         return new Genus(this.#genera[genusName]);
     }
-
-    /**
-     * @param {string} genusName
-     */
-    getFamily(genusName) {
-        const genus = this.#genera[genusName];
-        if (genus) {
-            return this.#families.getFamily(genus.family);
-        }
-    }
 }
 
 class Genus {
     #data;
 
+    /**
+     * @param {{family:string,familyObj:Family,taxa:Taxon[]}} data
+     */
     constructor(data) {
         this.#data = data;
     }
 
+    getFamily() {
+        return this.#data.familyObj;
+    }
+
     getTaxa() {
         return this.#data.taxa.sort((a, b) =>
             a.getName().localeCompare(b.getName())

package/lib/genericpage.js

@@ -10,6 +10,12 @@ class GenericPage {
     #baseFileName;
     #js;
 
+    /**
+     * @param {string} outputDir
+     * @param {string} title
+     * @param {string} baseFileName
+     * @param {string} [js]
+     */
     constructor(outputDir, title, baseFileName, js) {
         this.#outputDir = outputDir;
         this.#title = title;
@@ -53,6 +59,9 @@ class GenericPage {
         return html;
     }
 
+    /**
+     * @param {string} path
+     */
     #getMarkdown(path) {
         const textPath = path + "/" + this.#baseFileName + ".md";
         if (!Jekyll.hasInclude(this.#outputDir, textPath)) {
@@ -69,6 +78,9 @@ class GenericPage {
         return this.#title;
     }
 
+    /**
+     * @param {string} html
+     */
     writeFile(html) {
         Files.write(this.#outputDir + "/" + this.#baseFileName + ".html", html);
     }

package/lib/html.js

@@ -1,11 +1,3 @@
-/**
- * @deprecated
- */
-export const HTML_OPTIONS = {
-    OPEN_NEW: 1,
-    NO_ESCAPE: 2,
-};
-
 /** HTML utility functions. */
 export class HTML {
     /**
@@ -35,19 +27,6 @@ export class HTML {
             .replaceAll(">", ">");
     }
 
-    /**
-     * @deprecated
-     */
-    static getElement(elName, text, attributes = {}, options = 0) {
-        let html = "<" + elName;
-        html += this.renderAttributes(attributes);
-        if (!(options & HTML_OPTIONS.NO_ESCAPE)) {
-            text = this.escapeText(text);
-        }
-        html += ">" + text + "</" + elName + ">";
-        return html;
-    }
-
     /**
      * @param {string} elName
      * @param {string} text
@@ -71,7 +50,7 @@ export class HTML {
      * Generate HTML for an &lt;a> element.
      * @param {string|undefined} href
      * @param {string} linkText
-     * @param {Object} [attributes]
+     * @param {string|Object<string,string>} [attributes]
      * @param {boolean} [openInNewWindow] true if the link should open in a new window.
      * @returns {string} an HTML &lt;a> element.
      */
@@ -92,7 +71,7 @@ export class HTML {
      * @param {string} text - The text or HTML that should trigger the tooltip on hover.
      * @param {string} tooltip - The tooltip text or HTML.
      * @param {Object} options
-     * @param {boolean} options.icon [true] display an icon after the text
+     * @param {boolean} [options.icon] [true] display an icon after the text
      * @returns {string} A &lt;span> element to be used as a Bootstrap tooltip.
      */
     static getToolTip(text, tooltip, options = {}) {
@@ -103,6 +82,10 @@ export class HTML {
         return func("span", text, { "data-bs-html": "true", title: tooltip });
     }
 
+    /**
+     * @param {string} n
+     * @param {string} v
+     */
     static renderAttribute(n, v) {
         return " " + n + '="' + this.escapeAttribute(v) + '"';
     }
@@ -121,6 +104,11 @@ export class HTML {
         return html;
     }
 
+    /**
+     * @param {string} elName
+     * @param {string} text
+     * @param {Object<string,string>} attributes
+     */
     static textElement(elName, text, attributes = {}) {
         return HTML.#getElement(elName, text, attributes, true);
     }

package/lib/htmltaxon.js

@@ -1,21 +1,68 @@
 import { DateUtils } from "./dateutils.js";
 import { HTML } from "./html.js";
+import { RarePlants } from "./rareplants.js";
 import { TextUtils } from "./textutils.js";
 
+/**
+ * @type {Object<string,{title:string,data:function (Taxon):string}>}
+ */
+const TAXA_LIST_COLS = {
+    CESA: {
+        title: "California",
+        data: (t) => RarePlants.getCESADescription(t.getCESA()),
+    },
+    COMMON_NAME: {
+        title: "Common Name",
+        data: (t) => t.getCommonNames().join(", "),
+    },
+    CNPS_RANK: {
+        title: "CNPS Rank",
+        data: (t) =>
+            HTML.getToolTip(
+                HTML.textElement("span", t.getRPIRankAndThreat()),
+                t.getRPIRankAndThreatTooltip()
+            ),
+    },
+    FESA: {
+        title: "Federal",
+        data: (t) => RarePlants.getFESADescription(t.getFESA()),
+    },
+    SPECIES: {
+        title: "Species",
+        data: (t) => t.getHTMLLink(true, true),
+    },
+    SPECIES_BARE: {
+        title: "Species",
+        data: (t) => t.getHTMLLink(true, false),
+    },
+};
+
+const DEFAULT_TAXA_COLUMNS = [
+    TAXA_LIST_COLS.SPECIES,
+    TAXA_LIST_COLS.COMMON_NAME,
+];
+
 class HTMLTaxon {
     /**
-     * @param {string[]} colors
+     * @param {string[]|undefined} colors
      */
-    static getFlowerColors(colors) {
+    static getFlowerColors(colors, includeColorLink = true) {
         let html = "";
         if (colors) {
             for (const color of colors) {
-                html += HTML.textElement("img", "", {
+                const img = HTML.textElement("img", "", {
                     src: "./i/f-" + color + ".svg",
                     alt: color + " flowers",
                     title: color,
                     class: "flr-color",
                 });
+                if (includeColorLink) {
+                    html += HTML.wrap("a", img, {
+                        href: "./list_fc_" + color + ".html",
+                    });
+                } else {
+                    html += img;
+                }
             }
         }
         return html;
@@ -24,8 +71,13 @@ class HTMLTaxon {
     /**
      * @param {Taxon} taxon
      * @param {string} classNames
+     * @param {boolean} [includeColorLink=true]
      */
-    static getFlowerInfo(taxon, classNames = "section") {
+    static getFlowerInfo(
+        taxon,
+        classNames = "section",
+        includeColorLink = true
+    ) {
         const lifeCycle = taxon.getLifeCycle();
         const colors = taxon.getFlowerColors();
         const monthStart = taxon.getBloomStart();
@@ -40,7 +92,7 @@ class HTMLTaxon {
 
         if (colors || monthStart) {
             let html = "Flowers: ";
-            html += this.getFlowerColors(colors);
+            html += this.getFlowerColors(colors, includeColorLink);
             if (monthStart && monthEnd) {
                 html += HTML.wrap(
                     "span",
@@ -64,6 +116,37 @@ class HTMLTaxon {
             this.getFlowerColors(taxon.getFlowerColors())
         );
     }
+
+    /**
+     * @param {Taxon[]} taxa
+     * @param {TaxaCol[]} [columns]
+     */
+    static getTaxaTable(taxa, columns = DEFAULT_TAXA_COLUMNS) {
+        let html = "<table><thead>";
+        for (const col of columns) {
+            const className = col.class;
+            const atts = className !== undefined ? className : {};
+            html += HTML.textElement("th", col.title, atts);
+        }
+        html += "</thead>";
+        html += "<tbody>";
+
+        for (const taxon of taxa) {
+            html += "<tr>";
+            for (const col of columns) {
+                const data = col.data(taxon);
+                const className = col.class;
+                const atts = className !== undefined ? className : {};
+                html += HTML.wrap("td", data, atts);
+            }
+            html += "</tr>";
+        }
+
+        html += "</tbody>";
+        html += "</table>";
+
+        return html;
+    }
 }
 
-export { HTMLTaxon };
+export { HTMLTaxon, TAXA_LIST_COLS };

package/lib/index.d.ts

@@ -0,0 +1,54 @@
+import { Command } from "commander";
+
+export class Config {
+    constructor(dataDir: string);
+    getConfigValue(
+        prefix: string,
+        name: string,
+        subcategory?: string,
+        defaultValue?: string
+    ): string;
+    getCountyCodes(): string[];
+    getLabel(name: string, dflt: string): string;
+}
+
+export class CSV {
+    static parseFile(dir: string, fileName: string);
+}
+
+export class ErrorLog {
+    constructor(fileName: string, echo?: boolean);
+    log(...msg: string[]);
+    write(): void;
+}
+
+export class Exceptions {
+    constructor(dataDir: string);
+    hasException(name: string, cat: string, subcat: string);
+}
+
+export class Files {
+    static exists(fileName: string): boolean;
+    static async fetch(url: string | URL, targetFileName: string | undefined);
+    static mkdir(dir: string);
+    static rmDir(dir: string);
+    static write(fileName: string, data: string, overwrite: boolean);
+}
+
+export class Program {
+    static getIncludeList(dataDir: string): string[];
+    static getProgram(): Command;
+}
+
+export class Taxa {
+    constructor(
+        inclusionList: Object<string, TaxonData> | true,
+        errorLog: ErrorLog,
+        showFlowerErrors: boolean,
+        taxonFactory?: (td: TaxonData, g: Genera) => Taxon,
+        extraTaxa?: TaxonData[],
+        extraSynonyms?: SynonymData[]
+    );
+    getTaxon(string): Taxon;
+    getTaxonList(): Taxon[];
+}

package/lib/index.js

@@ -1,58 +1,30 @@
-/**
- * @typedef {{
- * bloom_end:string;
- * bloom_start:string;
- * calrecnum:string;
- * CESA:string;
- * CRPR:string;
- * "common name":string;
- * FESA:string;
- * flower_color:string;
- * GRank:string;
- * "inat id":string;
- * "jepson id":string;
- * life_cycle:"annual"|"perennial"|undefined
- * SRank:string;
- * status:string;
- * "RPI ID":string;
- * taxon_name:string}} TaxonData
- */
-
 import { BasePageRenderer } from "./basepagerenderer.js";
-import { CommandProcessor } from "./commandprocessor.js";
-import { CommandAndTaxaProcessor } from "./commandandtaxaprocessor.js";
 import { Config } from "./config.js";
 import { CSV } from "./csv.js";
 import { ErrorLog } from "./errorlog.js";
 import { Exceptions } from "./exceptions.js";
 import { Families } from "./families.js";
 import { Files } from "./files.js";
-import { GenericTaxaLoader } from "./generictaxaloader.js";
 import { HTML } from "./html.js";
 import { Jekyll } from "./jekyll.js";
 import { PlantBook } from "./ebook/plantbook.js";
+import { Program } from "./program.js";
 import { Taxa } from "./taxa.js";
-import { TaxaLoader } from "./taxaloader.js";
-import { TaxaProcessor } from "./taxaprocessor.js";
 import { Taxon, TAXA_COLNAMES } from "./taxon.js";
 
 export {
     BasePageRenderer,
-    CommandProcessor,
-    CommandAndTaxaProcessor,
     Config,
     CSV,
     ErrorLog,
     Exceptions,
     Families,
     Files,
-    GenericTaxaLoader,
     HTML,
     Jekyll,
     PlantBook,
+    Program,
     Taxa,
-    TaxaLoader,
-    TaxaProcessor,
     TAXA_COLNAMES,
     Taxon,
 };

package/lib/jekyll.js

@@ -4,40 +4,68 @@ import { SiteGenerator } from "./sitegenerator.js";
 const FRONT_DELIM = "---";
 
 class Jekyll extends SiteGenerator {
-
-    constructor( baseDir ) {
-        super( baseDir );
+    /**
+     * @param {string} baseDir
+     */
+    constructor(baseDir) {
+        super(baseDir);
     }
 
-    static getFrontMatter( atts ) {
-        const lines = [ FRONT_DELIM ];
-        for ( const [ k, v ] of Object.entries( atts ) ) {
-            lines.push( k + ": \"" + v + "\"" );
+    /**
+     * @param {Object<string,string>} atts
+     */
+    static getFrontMatter(atts) {
+        const lines = [FRONT_DELIM];
+        for (const [k, v] of Object.entries(atts)) {
+            lines.push(k + ': "' + v + '"');
         }
-        if ( !atts.layout ) {
-            lines.push( "layout: default" );
+        if (!atts.layout) {
+            lines.push("layout: default");
         }
-        lines.push( FRONT_DELIM );
-        return lines.join( "\n" ) + "\n";
+        lines.push(FRONT_DELIM);
+        return lines.join("\n") + "\n";
     }
 
-    static hasInclude( baseDir, path ) {
-        return Files.exists( baseDir + "/_includes/" + path );
+    /**
+     * @param {string} baseDir
+     * @param {string} path
+     */
+    static hasInclude(baseDir, path) {
+        return Files.exists(baseDir + "/_includes/" + path);
     }
 
-    static include( path ) {
+    /**
+     * @param {string} path
+     */
+    static include(path) {
         // This works for .md includes; should have conditional logic to detect other types.
-        return "{% capture my_include %}{% include " + path + " %}{% endcapture %}{{ my_include | markdownify }}";
+        return (
+            "{% capture my_include %}{% include " +
+            path +
+            " %}{% endcapture %}{{ my_include | markdownify }}"
+        );
     }
 
-    static writeInclude( baseDir, path, data ) {
-        Files.write( baseDir + "/_includes/" + path, data );
+    /**
+     * @param {string} baseDir
+     * @param {string} path
+     * @param {string} data
+     */
+    static writeInclude(baseDir, path, data) {
+        Files.write(baseDir + "/_includes/" + path, data);
     }
 
-    writeTemplate( content, attributes, filename ) {
-        Files.write( Files.join( this.getBaseDir(), filename ), Jekyll.getFrontMatter( attributes ) + content );
+    /**
+     * @param {string} content
+     * @param {Object<string,string>} attributes
+     * @param {string} filename
+     */
+    writeTemplate(content, attributes, filename) {
+        Files.write(
+            Files.join(this.getBaseDir(), filename),
+            Jekyll.getFrontMatter(attributes) + content
+        );
     }
-
 }
 
-export { Jekyll };
+export { Jekyll };

package/lib/jepson.js

@@ -1,18 +1,17 @@
-import { HTML, HTML_OPTIONS } from "./html.js";
+import { HTML } from "./html.js";
 
 class Jepson {
-
-    static getEFloraLink( id ) {
-
+    /**
+     * @param {string} id
+     */
+    static getEFloraLink(id) {
         return HTML.getLink(
             "https://ucjeps.berkeley.edu/eflora/eflora_display.php?tid=" + id,
             "Jepson eFlora",
             {},
-            HTML_OPTIONS.OPEN_NEW
+            true
         );
-
     }
-
 }
 
-export { Jepson };
+export { Jepson };

package/lib/markdown.js

@@ -4,10 +4,16 @@ import { Files } from "./files.js";
 class Markdown {
     static #md = new markdownIt({ xhtmlOut: true });
 
+    /**
+     * @param {string} filePath
+     */
     static fileToHTML(filePath) {
         return this.strToHTML(Files.read(filePath));
     }
 
+    /**
+     * @param {string} str
+     */
     static strToHTML(str) {
         return this.#md.render(str);
     }

package/lib/pagerenderer.js

@@ -1,10 +1,10 @@
-import { Taxa, TAXA_LIST_COLS } from "./taxa.js";
 import { PageTaxon } from "./web/pagetaxon.js";
 import { RarePlants } from "./rareplants.js";
 import { BasePageRenderer } from "./basepagerenderer.js";
 import { GenericPage } from "./genericpage.js";
 import { Files } from "./files.js";
 import { HTML } from "./html.js";
+import { HTMLTaxon, TAXA_LIST_COLS } from "./htmltaxon.js";
 
 const ENDANGERED_COLS = [
     TAXA_LIST_COLS.SPECIES,
@@ -19,8 +19,13 @@ const RPI_COLUMNS = [
 ];
 
 class PageRenderer extends BasePageRenderer {
+    /**
+     * @param {string} outputDir
+     * @param {Config} config
+     * @param {Taxa} taxa
+     */
     static render(outputDir, config, taxa) {
-        super.render(outputDir, taxa);
+        super.renderBasePages(outputDir, taxa);
 
         this.renderLists(outputDir, config, taxa);
 
@@ -30,7 +35,18 @@ class PageRenderer extends BasePageRenderer {
         }
     }
 
+    /**
+     * @param {string} outputDir
+     * @param {Config} config
+     * @param {Taxa} taxa
+     */
     static renderLists(outputDir, config, taxa) {
+        /**
+         * @param {ListInfo[]} listInfo
+         * @param {Object<string,string>} attributes
+         * @param {TaxaCol[]} [columns]
+         * @returns {string}
+         */
         function getListArray(listInfo, attributes = {}, columns) {
             const listArray = [];
             for (const list of listInfo) {
@@ -81,10 +97,18 @@ class PageRenderer extends BasePageRenderer {
             return renderList(listArray, attributes);
         }
 
+        /**
+         * @param {string[]} listsHTML
+         * @param {Object<string,string>} attributes
+         */
         function renderList(listsHTML, attributes = {}) {
             return HTML.wrap("ul", HTML.arrayToLI(listsHTML), attributes);
         }
 
+        /**
+         * @param {string} title
+         * @param {string} listsHTML
+         */
         function renderSection(title, listsHTML) {
             let html = '<div class="section">';
             html += HTML.textElement("h2", title);
@@ -93,6 +117,8 @@ class PageRenderer extends BasePageRenderer {
             return html;
         }
 
+        /** @typedef {{name:string,filename:string,include:function(Taxon):boolean,columns?:TaxaCol[],listInfo?:ListInfo[]}} ListInfo */
+        /** @type {{title:string,listInfo:ListInfo[]}[]} */
         const sections = [
             {
                 title: "All Species",
@@ -158,7 +184,9 @@ class PageRenderer extends BasePageRenderer {
                     {
                         name: "Endangered Species",
                         filename: "list_endangered",
-                        include: (t) => t.getCESA() || t.getFESA(),
+                        include: (t) =>
+                            t.getCESA() !== undefined ||
+                            t.getFESA() !== undefined,
                         columns: ENDANGERED_COLS,
                     },
                 ],
@@ -167,10 +195,7 @@ class PageRenderer extends BasePageRenderer {
 
         let html = '<div class="wrapper">';
         for (const section of sections) {
-            const listHTML = getListArray(
-                section.listInfo,
-                section.listInfo.columns
-            );
+            const listHTML = getListArray(section.listInfo);
 
             if (listHTML.length > 0) {
                 html += renderSection(section.title, listHTML);
@@ -189,17 +214,27 @@ class PageRenderer extends BasePageRenderer {
 }
 
 class PageTaxonList extends GenericPage {
+    /**
+     * @param {string} outputDir
+     * @param {string} title
+     * @param {string} baseName
+     */
     constructor(outputDir, title, baseName) {
         super(outputDir, title, baseName);
     }
 
+    /**
+     *
+     * @param {Taxon[]} taxa
+     * @param {TaxaCol[]|undefined} columns
+     */
     render(taxa, columns) {
         let html = this.getDefaultIntro();
 
         html += '<div class="wrapper">';
 
         html += '<div class="section">';
-        html += Taxa.getHTMLTable(taxa, columns);
+        html += HTMLTaxon.getTaxaTable(taxa, columns);
         html += "</div>";
 
         html += '<div class="section">';