@ca-plant-list/ca-plant-list 0.3.7 → 0.4.1

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">';

package/lib/plants/glossary.js

@@ -3,6 +3,7 @@ import { Files } from "../files.js";
 
 class Glossary {
     #srcPath;
+    /** @type {GlossaryEntry[]} */
     #srcEntries = [];
 
     constructor() {
@@ -25,6 +26,10 @@ class GlossaryEntry {
     #fileName;
     #term;
 
+    /**
+     * @param {string} srcPath
+     * @param {string} fileName
+     */
     constructor(srcPath, fileName) {
         this.#srcPath = srcPath;
         this.#fileName = fileName;

package/lib/program.js

@@ -0,0 +1,47 @@
+import { Command } from "commander";
+import { Files } from "./files.js";
+import { CSV } from "./csv.js";
+
+class Program {
+    /**
+     * @param {string} dataDir
+     */
+    static getIncludeList(dataDir) {
+        // Read inclusion list.
+        const includeFileName = "taxa_include.csv";
+        const includeFilePath = dataDir + "/" + includeFileName;
+        if (!Files.exists(includeFilePath)) {
+            console.log(includeFilePath + " not found; loading all taxa");
+            return true;
+        }
+        const includeCSV = CSV.parseFile(dataDir, includeFileName);
+        /** @type {Object<string,TaxonData>} */
+        const include = {};
+        for (const row of includeCSV) {
+            include[row["taxon_name"]] = row;
+        }
+        return include;
+    }
+
+    static getProgram() {
+        const program = new Command();
+        program
+            .option(
+                "-d, --datadir <dir>",
+                "The directory containing plant data.",
+                "./data"
+            )
+            .option(
+                "-f, --show-flower-errors",
+                "Include missing flower color/flowering time in the error log when loading taxa."
+            )
+            .option(
+                "-o, --outputdir <dir>",
+                "The directory to which output should be written.",
+                "./output"
+            );
+        return program;
+    }
+}
+
+export { Program };

package/lib/rareplants.js

@@ -1,60 +1,74 @@
+/** @type {Object<string,string>} */
 const RANK_DESCRIPS = {
     "1A": "Presumed Extirpated or Extinct",
     "1B": "Rare or Endangered",
     "2A": "Extirpated in California",
     "2B": "Rare or Endangered in California",
-    "3": "Needs Review",
-    "4": "Uncommon in California",
+    3: "Needs Review",
+    4: "Uncommon in California",
 };
 
+/** @type {Object<string,string>} */
 const THREAT_DESCRIPS = {
-    "1": "Seriously threatened in California",
-    "2": "Moderately threatened in California",
-    "3": "Not very threatened in California",
+    1: "Seriously threatened in California",
+    2: "Moderately threatened in California",
+    3: "Not very threatened in California",
 };
 
+/** @type {Object<string,string>} */
 const CESA_DESCRIPS = {
-    "CC": "Candidate",
-    "CE": "Endangered",
-    "CR": "Rare",
-    "CT": "Threatened",
+    CC: "Candidate",
+    CE: "Endangered",
+    CR: "Rare",
+    CT: "Threatened",
 };
 
+/** @type {Object<string,string>} */
 const FESA_DESCRIPS = {
-    "FE": "Endangered",
-    "FT": "Threatened",
-    "PE": "Proposed Endangered",
-    "PT": "Proposed Threatened",
-    "FC": "Candidate",
-    "FD": "Delisted",
+    FE: "Endangered",
+    FT: "Threatened",
+    PE: "Proposed Endangered",
+    PT: "Proposed Threatened",
+    FC: "Candidate",
+    FD: "Delisted",
 };
 
 class RarePlants {
-
-    static getCESADescription( cesa ) {
-        if ( !cesa ) {
+    /**
+     * @param {string|undefined} cesa
+     */
+    static getCESADescription(cesa) {
+        if (!cesa) {
             return "";
         }
-        return CESA_DESCRIPS[ cesa ];
+        return CESA_DESCRIPS[cesa];
     }
 
-    static getFESADescription( fesa ) {
-        if ( !fesa ) {
+    /**
+     * @param {string|undefined} fesa
+     */
+    static getFESADescription(fesa) {
+        if (!fesa) {
             return "";
         }
-        return FESA_DESCRIPS[ fesa ];
+        return FESA_DESCRIPS[fesa];
     }
 
-    static getRPIRankDescription( rank ) {
-        const pieces = rank.split( "." );
-        return RANK_DESCRIPS[ pieces[ 0 ] ];
+    /**
+     * @param {string} rank
+     */
+    static getRPIRankDescription(rank) {
+        const pieces = rank.split(".");
+        return RANK_DESCRIPS[pieces[0]];
     }
 
-    static getRPIRankAndThreatDescriptions( rank ) {
-        const pieces = rank.split( "." );
-        return [ RANK_DESCRIPS[ pieces[ 0 ] ], THREAT_DESCRIPS[ pieces[ 1 ] ] ];
+    /**
+     * @param {string} rank
+     */
+    static getRPIRankAndThreatDescriptions(rank) {
+        const pieces = rank.split(".");
+        return [RANK_DESCRIPS[pieces[0]], THREAT_DESCRIPS[pieces[1]]];
     }
-
 }
 
-export { RarePlants };
+export { RarePlants };

package/lib/sitegenerator.js

@@ -6,32 +6,46 @@ import { Files } from "./files.js";
 class SiteGenerator {
     #baseDir;
 
-    constructor( baseDir ) {
+    /**
+     * @param {string} baseDir
+     */
+    constructor(baseDir) {
         this.#baseDir = baseDir;
     }
 
-    copyIllustrations( flowerColors ) {
-        function createFlowerColorIcons( outputDir, flowerColors ) {
+    /**
+     * @param {FlowerColor[]} flowerColors
+     */
+    copyIllustrations(flowerColors) {
+        /**
+         * @param {string} outputDir
+         * @param {FlowerColor[]} flowerColors
+         */
+        function createFlowerColorIcons(outputDir, flowerColors) {
             // Read generic input.
-            const inputFileName = Files.join( outputDir, "flower.svg" );
-            const srcSVG = Files.read( inputFileName );
-            for ( const color of flowerColors ) {
+            const inputFileName = Files.join(outputDir, "flower.svg");
+            const srcSVG = Files.read(inputFileName);
+            for (const color of flowerColors) {
                 Files.write(
-                    Files.join( outputDir, "f-" + color.name + ".svg" ),
-                    srcSVG.replace( "#ff0", color.color )
+                    Files.join(outputDir, "f-" + color.getColorName() + ".svg"),
+                    srcSVG.replace("#ff0", color.getColorCode())
                 );
             }
             // Delete input file.
-            Files.rmDir( inputFileName );
+            Files.rmDir(inputFileName);
         }
 
-        function optimizeSVG( outputDir ) {
-            const srcDir = Config.getPackageDir() + "/data/illustrations/inkscape";
-            const entries = Files.getDirEntries( srcDir );
-            for ( const entry of entries ) {
-                const srcFile = Files.join( srcDir, entry );
-                const srcSVG = Files.read( srcFile );
-                const result = optimize( srcSVG, {
+        /**
+         * @param {string} outputDir
+         */
+        function optimizeSVG(outputDir) {
+            const srcDir =
+                Config.getPackageDir() + "/data/illustrations/inkscape";
+            const entries = Files.getDirEntries(srcDir);
+            for (const entry of entries) {
+                const srcFile = Files.join(srcDir, entry);
+                const srcSVG = Files.read(srcFile);
+                const result = optimize(srcSVG, {
                     plugins: [
                         {
                             name: "preset-default",
@@ -55,24 +69,27 @@ class SiteGenerator {
                         "minifyStyles",
                     ],
                     multipass: true,
-                } );
-                Files.write( Files.join( outputDir, entry ), result.data );
+                });
+                Files.write(Files.join(outputDir, entry), result.data);
             }
         }
 
-        const outputDir = Files.join( this.#baseDir, "i" );
-        Files.mkdir( outputDir );
+        const outputDir = Files.join(this.#baseDir, "i");
+        Files.mkdir(outputDir);
 
-        optimizeSVG( outputDir );
-        createFlowerColorIcons( outputDir, flowerColors );
+        optimizeSVG(outputDir);
+        createFlowerColorIcons(outputDir, flowerColors);
     }
 
     getBaseDir() {
         return this.#baseDir;
     }
 
-    mkdir( path ) {
-        Files.mkdir( Files.join( this.#baseDir, path ) );
+    /**
+     * @param {string} path
+     */
+    mkdir(path) {
+        Files.mkdir(Files.join(this.#baseDir, path));
     }
 }
 

package/lib/taxa.js

@@ -1,11 +1,9 @@
 import { Config } from "./config.js";
-import { HTML } from "./html.js";
 import { CSV } from "./csv.js";
-import { RarePlants } from "./rareplants.js";
 import { Genera } from "./genera.js";
-import { TextUtils } from "./textutils.js";
 import { Taxon } from "./taxon.js";
 import { Families } from "./families.js";
+import { FlowerColor } from "./flowercolor.js";
 
 const FLOWER_COLORS = [
     { name: "white", color: "white" },
@@ -19,74 +17,6 @@ const FLOWER_COLORS = [
     { name: "brown", color: "brown" },
 ];
 
-/**
- * @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_COLUMNS = [TAXA_LIST_COLS.SPECIES, TAXA_LIST_COLS.COMMON_NAME];
-
-class FlowerColor {
-    #color;
-    /** @type {Taxon[]} */
-    #taxa = [];
-
-    /**
-     * @param {string} color
-     */
-    constructor(color) {
-        this.#color = color;
-    }
-
-    /**
-     * @param {Taxon} taxon
-     */
-    addTaxon(taxon) {
-        this.#taxa.push(taxon);
-    }
-
-    getColorName(uc = false) {
-        return uc ? TextUtils.ucFirst(this.#color) : this.#color;
-    }
-
-    getFileName() {
-        return "list_fc_" + this.#color + ".html";
-    }
-
-    getTaxa() {
-        return this.#taxa;
-    }
-}
-
 class Taxa {
     #families;
     #errorLog;
@@ -99,17 +29,18 @@ class Taxa {
     #isSubset;
 
     /**
-     * @param {string[]|boolean} inclusionList
+     * @param {Object<string,TaxonData>|true} inclusionList
      * @param {ErrorLog} errorLog
      * @param {boolean} showFlowerErrors
-     * @param {Taxon} taxonClass
+     * @param {function(TaxonData,Genera):Taxon} taxonFactory
+     * @param {TaxonData[]} [extraTaxa=[]]
+     * @param {SynonymData[]} [extraSynonyms=[]]
      */
     constructor(
         inclusionList,
         errorLog,
         showFlowerErrors,
-        taxaMeta = {},
-        taxonClass = Taxon,
+        taxonFactory = (td, g) => new Taxon(td, g),
         extraTaxa = [],
         extraSynonyms = []
     ) {
@@ -126,18 +57,11 @@ class Taxa {
         this.#families = new Families();
 
         const taxaCSV = CSV.parseFile(dataDir, "taxa.csv");
-        this.#loadTaxa(
-            taxaCSV,
-            inclusionList,
-            taxaMeta,
-            taxonClass,
-            showFlowerErrors
-        );
+        this.#loadTaxa(taxaCSV, inclusionList, taxonFactory, showFlowerErrors);
         this.#loadTaxa(
             extraTaxa,
             inclusionList,
-            taxaMeta,
-            taxonClass,
+            taxonFactory,
             showFlowerErrors
         );
 
@@ -157,54 +81,14 @@ class Taxa {
         this.#loadSyns(extraSynonyms, inclusionList);
     }
 
-    /**
-     * @param {Taxon[]} taxa
-     * @param {TaxaCol} columns
-     */
-    static getHTMLTable(taxa, columns = DEFAULT_COLUMNS) {
-        let html = "<table><thead>";
-        for (const col of columns) {
-            const className = col.class;
-            const atts = className ? { class: 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 ? { class: className } : {};
-                html += HTML.wrap("td", data, atts);
-            }
-            html += "</tr>";
-        }
-
-        html += "</tbody>";
-        html += "</table>";
-
-        return html;
-    }
-
     getFamilies() {
         return this.#families;
     }
 
-    /**
-     * @param {string} name
-     */
-    getFlowerColor(name) {
-        return this.#flower_colors[name];
-    }
-
-    static getFlowerColorNames() {
-        return FLOWER_COLORS.map((o) => o.name);
-    }
-
-    static getFlowerColors() {
-        return FLOWER_COLORS;
+    getFlowerColors() {
+        return Object.values(this.#flower_colors).filter(
+            (fc) => fc.getTaxa().length > 0
+        );
     }
 
     /**
@@ -234,8 +118,8 @@ class Taxa {
     }
 
     /**
-     * @param {*} synCSV
-     * @param {*} inclusionList
+     * @param {SynonymData[]} synCSV
+     * @param {Object<string,TaxonData>|boolean} inclusionList
      */
     #loadSyns(synCSV, inclusionList) {
         for (const syn of synCSV) {
@@ -257,14 +141,16 @@ class Taxa {
 
     /**
      * @param {TaxonData[]} taxaCSV
-     * @param {Taxon} taxonClass
+     * @param {Object<string,TaxonData>|true} inclusionList
+     * @param {function(TaxonData,Genera):Taxon} taxonFactory
      * @param {boolean} showFlowerErrors
      */
-    #loadTaxa(taxaCSV, inclusionList, taxaMeta, taxonClass, showFlowerErrors) {
+    #loadTaxa(taxaCSV, inclusionList, taxonFactory, showFlowerErrors) {
         const genera = new Genera(this.#families);
         for (const row of taxaCSV) {
             const name = row["taxon_name"];
 
+            /** @type {TaxonData|{status?:string}} */
             let taxon_overrides = {};
             if (inclusionList !== true) {
                 taxon_overrides = inclusionList[name];
@@ -281,7 +167,7 @@ class Taxa {
             if (status !== undefined) {
                 row["status"] = status;
             }
-            const taxon = new taxonClass(row, genera, taxaMeta[name]);
+            const taxon = taxonFactory(row, genera);
             this.#taxa[name] = taxon;
             const colors = taxon.getFlowerColors();
             if (colors) {
@@ -326,4 +212,4 @@ class Taxa {
     }
 }
 
-export { Taxa, TAXA_LIST_COLS };
+export { Taxa };

package/lib/taxon.js

@@ -149,7 +149,7 @@ class Taxon {
     }
 
     getFamily() {
-        return this.#genera.getFamily(this.#genus);
+        return this.getGenus().getFamily();
     }
 
     getFESA() {

package/lib/web/glossarypages.js

@@ -9,11 +9,17 @@ class GlossaryPages {
     #siteGenerator;
     #glossary;
 
+    /**
+     * @param {SiteGenerator} siteGenerator
+     */
     constructor(siteGenerator) {
         this.#siteGenerator = siteGenerator;
         this.#glossary = new Glossary();
     }
 
+    /**
+     * @param {GlossaryEntry} entry
+     */
     #generateEntryPage(entry) {
         const title = entry.getTermName();
         let html = HTML.textElement("h1", title);

package/lib/web/pagetaxon.js

@@ -3,10 +3,6 @@ import { RarePlants } from "../rareplants.js";
 import { GenericPage } from "../genericpage.js";
 import { ExternalSites } from "../externalsites.js";
 import { HTML } from "../html.js";
-// eslint-disable-next-line no-unused-vars
-import { Config } from "../config.js";
-// eslint-disable-next-line no-unused-vars
-import { Taxon } from "../taxon.js";
 import { HTMLTaxon } from "../htmltaxon.js";
 
 class PageTaxon extends GenericPage {
@@ -178,7 +174,7 @@ class PageTaxon extends GenericPage {
 
         html += "</div>";
 
-        html += HTMLTaxon.getFlowerInfo(this.#taxon);
+        html += HTMLTaxon.getFlowerInfo(this.#taxon, undefined, false);
 
         html += this.getMarkdown();