@ca-plant-list/ca-plant-list 0.2.15 → 0.2.17

package/data/glossary/peduncle.md

@@ -1 +1,3 @@
-A stalk supporting an inflorescence (one or more flowers).
+A stalk supporting an inflorescence (one or more flowers).
+
+![peduncle](../i/peduncle.svg)

package/data/illustrations/inkscape/peduncle.svg

@@ -0,0 +1,170 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
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+   height="60"
+   viewBox="0 0 102.55142 60"
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+   sodipodi:docname="peduncle.svg"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:xlink="http://www.w3.org/1999/xlink"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg">
+  <sodipodi:namedview
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+     pagecolor="#ffffff"
+     bordercolor="#000000"
+     borderopacity="0.25"
+     inkscape:showpageshadow="2"
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+       id="path3" />
+    <text
+       xml:space="preserve"
+       style="font-size:8px;font-family:Arial;-inkscape-font-specification:Arial;letter-spacing:0.5px;opacity:0.558428;fill:#14140c;fill-opacity:1;stroke:#160707;stroke-width:0.1;stroke-dasharray:none;stroke-opacity:1"
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+       y="47.068359"
+       id="text3"><tspan
+         sodipodi:role="line"
+         id="tspan3"
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+    <path
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+  </g>
+</svg>

package/data/illustrations/optimized/peduncle.svg

@@ -0,0 +1,21 @@
+<svg version="1.1" viewBox="0 0 102.55 60" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<defs>
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+<path transform="scale(.5)" d="m5.77 0-8.65 5v-10z" fill="context-stroke" fill-rule="evenodd" stroke="context-stroke" stroke-width="1pt"/>
+</marker>
+</defs>
+<path d="m15 60v-45" fill="#14140c" stroke="#160707"/>
+<use xlink:href="#a"/>
+<use transform="rotate(30,15,15)" xlink:href="#a"/>
+<use transform="rotate(60,15,15)" xlink:href="#a"/>
+<use transform="rotate(90,15,15)" xlink:href="#a"/>
+<use transform="rotate(120,15,15)" xlink:href="#a"/>
+<use transform="rotate(150,15,15)" xlink:href="#a"/>
+<ellipse id="a" cx="15" cy="15" rx="2.5" ry="15" fill="#ff0" stroke-width="0"/>
+<g fill="#14140c" stroke="#160707">
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+<path d="m35 15h10" marker-start="url(#b)" stroke-width=".5"/>
+<text x="49.696735" y="17.068359" font-family="Arial" font-size="8px" letter-spacing=".5px" opacity=".55843" stroke-width=".1" xml:space="preserve"><tspan x="49.696735" y="17.068359" font-family="Arial" font-size="8px" letter-spacing=".5px" stroke-width=".1" style="font-variant-caps:normal;font-variant-east-asian:normal;font-variant-ligatures:normal;font-variant-numeric:normal">inflorescence</tspan></text>
+</g>
+</svg>

package/data/synonyms.csv

@@ -811,7 +811,6 @@ Helianthemum scoparium var. vulgare,Crocanthemum scoparium var. vulgare
 Helianthus annuus subsp. jaegeri,Helianthus annuus
 Helianthus annuus subsp. lenticularis,Helianthus annuus
 Helianthus annuus var. macrocarpus,Helianthus annuus
-Helichrysum luteoalbum,Pseudognaphalium luteoalbum,INAT
 Heliotropium oculatum,Heliotropium curassavicum var. oculatum
 Heliotropium spathulatum subsp. oculatum,Heliotropium curassavicum var. oculatum
 Helxine soleirolii,Soleirolia soleirolii
@@ -979,7 +978,6 @@ Lessingia filaginifolia var. filaginifolia,Corethrogyne filaginifolia
 Lessingia germanorum var. parvula,Lessingia tenuis
 Lessingia germanorum var. tenuis,Lessingia tenuis
 Lessingia nemaclada var. albiflora,Lessingia nemaclada
-Leuzea repens,Rhaponticum repens,INAT
 Lewisia alba,Lewisia rediviva var. rediviva
 Leymus ×multiflorus,Elymus ×gouldii,INAT
 Leymus mollis subsp. mollis,Elymus mollis subsp. mollis,INAT
@@ -1538,6 +1536,7 @@ Prunella vulgaris var. atropurpurea,Prunella vulgaris var. lanceolata
 Prunella vulgaris var. parviflora,Prunella vulgaris var. vulgaris
 Prunus amygdalus,Prunus dulcis,INAT
 Pseudognaphalium canescens subsp. beneolens,Pseudognaphalium beneolens
+Pseudognaphalium luteoalbum,Pseudognaphalium luteoalbum,INAT
 Pseudognaphalium microcephalum var. thermale,Pseudognaphalium thermale
 Psilocarphus tenellus var. globiferus,Psilocarphus chilensis
 Psilocarphus tenellus var. tenellus,Psilocarphus tenellus
@@ -1590,6 +1589,7 @@ Rhamnus tomentella subsp. tomentella,Frangula californica subsp. tomentella
 Rhamnus tomentella,Frangula californica subsp. tomentella
 Rhamphospermum arvense,Sinapis arvensis,INAT
 Rhamphospermum nigrum,Brassica nigra,INAT
+Rhaponticum repens,Rhaponticum repens,INAT
 Rhus aromatica subsp. trilobata,Rhus aromatica
 Rhus aromatica var. simplicifolia,Rhus aromatica
 Rhus aromatica var. trilobata,Rhus aromatica

package/data/taxa.csv

@@ -248,7 +248,7 @@ Bromus sitchensis var. maritimus,maritime brome,N,108591,13625,71142
 Bromus sterilis,poverty brome,X,16288,1216,57163
 Bromus tectorum,cheat grass,X,16290,1218,58369
 Buddleja davidii,butterfly bush,X,16349,1222,75916
-Cabomba caroliniana,fanwort,X,16450,8513,75921
+Cabomba caroliniana,fanwort,X,16450,8513,75921,white,5,9
 Cakile edentula,sea rocket,X,16523,1232,52162
 Cakile maritima,sea rocket,X,16531,1233,60982
 Calamagrostis koelerioides,,N,16557,1240,75927
@@ -267,7 +267,7 @@ Calochortus albus,white globe lily,N,16710,1264,51315,white
 Calochortus argillosus,clay mariposa lily,N,76542,1268,64330,"white,pink"
 Calochortus clavatus var. pallidus,,N,55455,1275,58360
 Calochortus invenustus,,N,16733,1284,64432
-Calochortus leichtlinii
+Calochortus leichtlinii,,N,16735,1288,52542
 Calochortus luteus,yellow mariposa lily,N,16737,1290,51077,yellow
 Calochortus pulchellus,Mt. Diablo fairy lantern,N,16755,1303,47326,,,,50,1B.2,,,S2,G2
 Calochortus splendens,,N,16759,1306,58361
@@ -362,7 +362,7 @@ Centromadia pungens subsp. pungens,common spikeweed,N,80173,9544,64196
 Cephalanthus occidentalis,button bush,N,18612,9794,52763
 Cerastium fontanum subsp. vulgare,,X,49818,1872,1005385
 Cerastium glomeratum,mouse-ear chickweed,X,18675,1873,52973
-Ceratophyllum demersum,hornwort,N,18711,1874,60997
+Ceratophyllum demersum,hornwort,N,18711,1874,60997,,6,8
 Cercis occidentalis,western redbud,N,18736,1877,59556
 Cercocarpus betuloides var. betuloides,mountain-mahogany,N,71734,1879,59001
 Cestrum parqui,Chilean jessamine,X,18790,8746,76226
@@ -907,7 +907,7 @@ Impatiens balfourii,touch-me-not,X,28954,4320,77490
 Iris douglasiana,Douglas' iris,N,29188,4346,50854
 Iris foetidissima,stinking iris,X,29193,8604,64331
 Iris longipetala,central coast iris,N,29293,4354,67703,,,,3169,4.2,,,S3,G3
-Iris macrosiphon,,N,29289
+Iris macrosiphon,,N,29289,4355,54057
 Iris pseudacorus,yellow flag,X,29301,4358,47779
 Isocoma arguta,Carquinez goldenbush,N,3633,4369,77510,,,,1264,1B.1,,,S1,G1
 Isoetes howellii,Howell's quillwort,N,29392,4379,63823
@@ -1216,7 +1216,7 @@ Navarretia squarrosa,skunkweed,N,34475,5807,53157
 Navarretia tagetina,,N,34477,5809,60226
 Navarretia viscidula,sticky navarretia,N,34478,5810,78195
 Nemophila heterophylla,,N,34539,5834,53158
-Nemophila menziesii var. atomaria,,N,62279,,,white,2,6
+Nemophila menziesii var. atomaria,,N,62279,5837,50647,white,2,6
 Nemophila menziesii var. menziesii,baby blue-eyes,N,62285,5839,50650
 Nemophila parviflora var. parviflora,,N,62288,5842,58921
 Nemophila pedunculata,,N,34544,5844,55461
@@ -1425,7 +1425,7 @@ Prunus virginiana var. demissa,western choke-cherry,N,64546,6898,63900
 Pseudognaphalium beneolens,,N,81674,11047,64303
 Pseudognaphalium biolettii,,N,81666,11955,58829
 Pseudognaphalium californicum,,N,80569,11956,53077
-Pseudognaphalium luteoalbum,cudweed,X,101867,11957,209711
+Pseudognaphalium luteoalbum,cudweed,X,101867,11957,53083
 Pseudognaphalium microcephalum,,N,81265,11048,78763
 Pseudognaphalium ramosissimum,,N,80579,11959,53088
 Pseudognaphalium stramineum,,N,40045,11960,53089
@@ -1480,7 +1480,7 @@ Raphanus sativus,wild radish,X,40992,7064,55410
 Rhamnus alaternus,Italian buckthorn,X,81104,9447,82856
 Rhamnus crocea,spiny redberry,N,41069,7075,57243
 Rhamnus ilicifolia,holly-leaf redberry,N,41070,7076,58308
-Rhaponticum repens,Russian knapweed,X,103802,13621,1061170
+Rhaponticum repens,Russian knapweed,X,103802,13621,339502
 Rhinotropis californica,California milkwort,N,107535,14636,876453
 Rhus aromatica,skunkbrush,N,41175,11056,58738
 Ribes amarum,bitter gooseberry,N,41372,7099,53433

package/jekyll/name_search.html

@@ -4,14 +4,14 @@ js: name_search.js
 ---
 
 <script>
-    const NAMES = {% include names.json%};
+    const NAMES = {% include names.json %};
 </script>
 
 <form id="search_form">
-    <input type="text" id="name"><label for="name">Search for scientific name, common name, or synonym</label>
+    <input type="text" id="name">
+    <label for="name">Search for scientific name, common name, or synonym.</label>
 </form>
 
 <div class="section" id="message"></div>
 
-<table id="results">
-</table>
+<table id="results"></table>

package/lib/basepagerenderer.js

@@ -27,7 +27,7 @@ class BasePageRenderer {
     static renderTools( outputDir, taxa ) {
 
         const names = [];
-        for ( const taxon of taxa.getTaxa() ) {
+        for ( const taxon of taxa.getTaxonList() ) {
             const row = [];
             row.push( taxon.getName() );
             const cn = taxon.getCommonNames().join( ", " );

package/lib/commandandtaxaprocessor.js

@@ -0,0 +1,37 @@
+import { CommandProcessor } from "./commandprocessor.js";
+import { TaxaProcessor } from "./taxaprocessor.js";
+
+class GenericTaxaProcessor extends TaxaProcessor {
+
+    #fnCustomProcess;
+
+    constructor( fnCustomProcess, options, taxaLoaderClass ) {
+        super( options, taxaLoaderClass );
+        this.#fnCustomProcess = fnCustomProcess;
+    }
+
+    async customProcess() {
+        await this.#fnCustomProcess( this );
+    }
+
+}
+
+class CommandAndTaxaProcessor extends CommandProcessor {
+
+    #taxaProcessor;
+
+    constructor( commandName, commandDesc, fnCustomProcess, optionDefs = [], optionHelp = [], commandHelp = [], taxaLoaderClass ) {
+        super( commandName, commandDesc, optionDefs, optionHelp, commandHelp );
+        this.#taxaProcessor = new GenericTaxaProcessor( fnCustomProcess, this.getOptions(), taxaLoaderClass );
+    }
+
+    async process() {
+        if ( this.helpShown() ) {
+            return;
+        }
+        await this.#taxaProcessor.process();
+    }
+
+}
+
+export { CommandAndTaxaProcessor };

package/lib/commandprocessor.js

@@ -0,0 +1,108 @@
+import commandLineArgs from "command-line-args";
+import commandLineUsage from "command-line-usage";
+
+const OPTION_DEFS = [
+    { name: "datadir", type: String, defaultValue: "./data" },
+    { name: "help", type: Boolean },
+    { name: "outputdir", type: String, defaultValue: "./output" },
+    { name: "show-flower-errors", type: Boolean },
+];
+
+const OPTION_HELP = [
+    {
+        name: "datadir",
+        type: String,
+        typeLabel: "{underline path}",
+        description: "The directory in which the data files for the local plant list are located. Defaults to {bold ./data}."
+
+    },
+    {
+        name: "outputdir",
+        type: String,
+        typeLabel: "{underline path}",
+        description: "The directory in which the output files should be written. Any files or subdirectories originally" +
+            " in this directory will be deleted. Defaults to {bold ./output}."
+
+    },
+    {
+        name: "show-flower-errors",
+        type: Boolean,
+        description: "Include flower color and flowering time errors in errors.tsv."
+    },
+    {
+        name: "help",
+        type: Boolean,
+        description: "Print this usage guide."
+    },
+];
+
+class CommandProcessor {
+
+    #commandName;
+    #commandDesc;
+
+    #optionHelp;
+    #commandHelp;
+
+    #options;
+
+    #helpShown = false;
+
+    /**
+     * @param {String} commandName 
+     * @param {String} commandDesc 
+     * @param {*} optionDefs An array of command line options to be added to the standard options.
+     * @param {*} optionHelp An array of help descriptions to be added to the standard options in the first section.
+     * @param {*} commandHelp An array of help sections to be appended to the first option section in the help display.
+     */
+    constructor( commandName, commandDesc, optionDefs = [], optionHelp = [], commandHelp = [] ) {
+
+        this.#commandName = commandName;
+        this.#commandDesc = commandDesc;
+
+        this.#optionHelp = optionHelp;
+        this.#commandHelp = commandHelp;
+
+        this.#options = commandLineArgs( OPTION_DEFS.concat( optionDefs ) );
+
+        if ( this.#options.help ) {
+            this.showHelp();
+        }
+
+    }
+
+    getOptions() {
+        return this.#options;
+    }
+
+    helpShown() {
+        return this.#helpShown;
+    }
+
+    showHelp() {
+
+        if ( this.#helpShown ) {
+            return;
+        }
+
+        this.#helpShown = true;
+
+        const mainOptions = OPTION_HELP.concat( this.#optionHelp );
+        mainOptions.sort( ( a, b ) => a.name.localeCompare( b.name ) );
+
+        const help = [
+            {
+                header: this.#commandName,
+                content: this.#commandDesc
+            },
+            {
+                header: "Options",
+                optionList: mainOptions
+            }
+        ];
+        console.log( commandLineUsage( help.concat( this.#commandHelp ) ) );
+    }
+
+}
+
+export { CommandProcessor };

package/lib/dataloader.js

@@ -1,10 +1,17 @@
 import { CSV } from "./csv.js";
 import { Taxa } from "./taxa.js";
 import { Files } from "./files.js";
+import { ErrorLog } from "./errorlog.js";
 
 class DataLoader {
 
-    static load( dataDir ) {
+    static #errorLog = new ErrorLog();
+
+    static getErrorLog() {
+        return DataLoader.#errorLog;
+    }
+
+    static load( options ) {
 
         function getIncludeList( dataDir ) {
             // Read inclusion list.
@@ -22,10 +29,16 @@ class DataLoader {
             return include;
         }
 
+        const showFlowerErrors = options[ "show-flower-errors" ];
+
         console.log( "loading data" );
 
-        return new Taxa( getIncludeList( dataDir ) );
+        return new Taxa( getIncludeList( options.datadir ), this.getErrorLog(), showFlowerErrors );
+
+    }
 
+    static writeErrorLog() {
+        DataLoader.#errorLog.write();
     }
 
 }

package/lib/ebook/pages/page_list_flowers.js

@@ -93,7 +93,7 @@ class PageListFlowerTime extends EBookPage {
 
         const range = [ this.#m1, this.#m2 ];
         const links = [];
-        for ( const taxon of this.#taxa.getTaxa() ) {
+        for ( const taxon of this.#taxa.getTaxonList() ) {
             const m1 = taxon.getBloomStart();
             const m2 = taxon.getBloomEnd();
             if ( m1 && DateUtils.monthRangesOverlap( range, [ m1, m2 ] ) ) {

package/lib/ebook/pages/taxonpage.js

@@ -28,8 +28,10 @@ class TaxonPage extends EBookPage {
                 return "";
             }
             let html = "";
-            for ( const color of colors ) {
-                html += XHTML.textElement( "img", "", { src: "./i/f-" + color + ".svg", class: "flr" } );
+            if ( colors ) {
+                for ( const color of colors ) {
+                    html += XHTML.textElement( "img", "", { src: "./i/f-" + color + ".svg", class: "flr" } );
+                }
             }
             if ( monthStart ) {
                 html += XHTML.textElement( "div", DateUtils.getMonthName( monthStart ) + "-" + DateUtils.getMonthName( monthEnd ) );

package/lib/ebook/plantbook.js

@@ -36,7 +36,7 @@ class PlantBook extends EBook {
         const contentDir = this.getContentDir();
 
         console.log( "creating taxon pages" );
-        const taxonList = this.#taxa.getTaxa();
+        const taxonList = this.#taxa.getTaxonList();
         for ( const taxon of taxonList ) {
             const name = taxon.getName();
             new TaxonPage( contentDir, taxon, this.#images[ name ] ).create();
@@ -124,7 +124,7 @@ class PlantBook extends EBook {
         }
 
         // Add taxa.
-        for ( let index = 0; index < this.#taxa.getTaxa().length; index++ ) {
+        for ( let index = 0; index < this.#taxa.getTaxonList().length; index++ ) {
             xml += "<itemref idref=\"t" + index + "\"/>";
         }
 

package/lib/errorlog.js

@@ -2,14 +2,24 @@ import * as fs from "node:fs";
 
 class ErrorLog {
 
-    static #errors = [];
+    #fileName;
+    #echo;
+    #errors = [];
 
-    static log( ...args ) {
+    constructor( fileName, echo = false ) {
+        this.#fileName = fileName;
+        this.#echo = echo;
+    }
+
+    log( ...args ) {
+        if ( this.#echo ) {
+            console.log( args.join() );
+        }
         this.#errors.push( args.join( "\t" ) );
     }
 
-    static write( fileName ) {
-        fs.writeFileSync( fileName, this.#errors.join( "\n" ) );
+    write() {
+        fs.writeFileSync( this.#fileName, this.#errors.join( "\n" ) );
     }
 
 }

package/lib/generictaxaloader.js

@@ -0,0 +1,40 @@
+import { ErrorLog } from "./errorlog.js";
+
+class GenericTaxaLoader {
+
+    #options;
+    #errorLog;
+    #taxa;
+
+    constructor( options ) {
+        this.#options = options;
+        this.#errorLog = new ErrorLog( options.outputdir + "/errors.tsv" );
+    }
+
+    getErrorLog() {
+        return this.#errorLog;
+    }
+
+    getOptions() {
+        return this.#options;
+    }
+
+    getTaxa() {
+        return this.#taxa;
+    }
+
+    async load() {
+        this.#taxa = await this.loadTaxa();
+    }
+
+    async loadTaxa() {
+        throw new Error( "must be implemented by subclass" );
+    }
+
+    writeErrorLog() {
+        this.#errorLog.write();
+    }
+
+}
+
+export { GenericTaxaLoader };

package/lib/index.d.ts

@@ -2,9 +2,23 @@ export class BasePageRenderer {
     static render(outputDir: any, taxa: any, familyCols: any): void;
     static renderTools(outputDir: any, taxa: any): void;
 }
-export class CommandRunner {
-    constructor(commandName: any, commandDesc: any, optionDefs: any, optionHelp: any, additionalHelp: any[], commandFunc: any);
-    processCommandLine(): Promise<void>;
+export class CommandAndTaxaProcessor extends CommandProcessor {
+    constructor(commandName: any, commandDesc: any, fnCustomProcess: any, optionDefs: any[], optionHelp: any[], commandHelp: any[], taxaLoaderClass: any);
+    process(): Promise<void>;
+    #private;
+}
+import { CommandProcessor } from "./commandprocessor.js";
+export class CommandProcessor {
+    /**
+     * @param {String} commandName
+     * @param {String} commandDesc
+     * @param {*} optionDefs An array of command line options to be added to the standard options.
+     * @param {*} optionHelp An array of help descriptions to be added to the standard options in the first section.
+     * @param {*} commandHelp An array of help sections to be appended to the first option section in the help display.
+     */
+    constructor(commandName: string, commandDesc: string, optionDefs?: any, optionHelp?: any, commandHelp?: any);
+    getOptions(): any;
+    helpShown(): boolean;
     showHelp(): void;
     #private;
 }
@@ -19,24 +33,21 @@ export class Config {
 }
 export class CSV {
     static getMap(dir: any, fileName: any): {};
-    static "__#9@#getOptions"(fileName: any, columns: any, delimiter: any): {
+    static "__#8@#getOptions"(fileName: any, columns: any, delimiter: any): {
         relax_column_count_less: boolean;
     };
     static parseFile(dir: any, fileName: any, columns: boolean, delimiter: any): any;
     static parseStream(dir: any, fileName: any, columns: boolean, delimiter: any, callback: any): Promise<void>;
 }
-export class DataLoader {
-    static load(dataDir: any): Taxa;
-}
-import { Taxa } from "./taxa.js";
 export class DateUtils {
     static getMonthName(monthNum: any): string;
     static monthRangesOverlap(r1: any, r2: any): any;
 }
 export class ErrorLog {
-    static "__#8@#errors": any[];
-    static log(...args: any[]): void;
-    static write(fileName: any): void;
+    constructor(fileName: any, echo?: boolean);
+    log(...args: any[]): void;
+    write(): void;
+    #private;
 }
 export class Exceptions {
     constructor(dir: any);
@@ -46,7 +57,7 @@ export class Exceptions {
     #private;
 }
 export class Families {
-    static "__#13@#families": any;
+    static "__#12@#families": any;
     static getFamilies(): any[];
     static getFamily(familyName: any): any;
     static renderPages(outputDir: any, taxaColumns: any): void;
@@ -94,6 +105,17 @@ export class GenericPage {
     writeFile(html: any): void;
     #private;
 }
+export class GenericTaxaLoader {
+    constructor(options: any);
+    getErrorLog(): ErrorLog;
+    getOptions(): any;
+    getTaxa(): any;
+    load(): Promise<void>;
+    loadTaxa(): Promise<void>;
+    writeErrorLog(): void;
+    #private;
+}
+import { ErrorLog } from "./errorlog.js";
 export namespace HTML_OPTIONS {
     const OPEN_NEW: number;
     const NO_ESCAPE: number;
@@ -134,21 +156,21 @@ export class HTML {
     static wrap(elName: any, text: any, attributes?: {}): string;
 }
 import { BasePageRenderer } from "./basepagerenderer.js";
-import { CommandRunner } from "./commandrunner.js";
+import { CommandAndTaxaProcessor } from "./commandandtaxaprocessor.js";
 import { Config } from "./config.js";
 import { CSV } from "./csv.js";
-import { DataLoader } from "./dataloader.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 { Taxa } from "./taxa.js";
 import { TAXA_COLNAMES } from "./taxon.js";
 import { Taxon } from "./taxon.js";
-export { BasePageRenderer, CommandRunner, Config, CSV, DataLoader, ErrorLog, Exceptions, Families, Files, HTML, Jekyll, PlantBook, Taxa, TAXA_COLNAMES, Taxon };
+export { BasePageRenderer, CommandAndTaxaProcessor, Config, CSV, ErrorLog, Exceptions, Families, Files, GenericTaxaLoader, HTML, Jekyll, PlantBook, Taxa, TAXA_COLNAMES, Taxon };
 export class Jekyll {
     static getFrontMatter(atts: any): string;
     static hasInclude(baseDir: any, path: any): boolean;
@@ -175,13 +197,8 @@ export class Taxa {
         title: string;
         data: (t: any) => any;
     }[]): string;
-    constructor(inclusionList: any, taxaMeta?: {}, taxonClass?: typeof Taxon, extraTaxa?: any[], extraSynonyms?: any[]);
+    constructor(inclusionList: any, errorLog: any, showFlowerErrors: any, taxaMeta?: {}, taxonClass?: typeof Taxon, extraTaxa?: any[], extraSynonyms?: any[]);
     getFlowerColor(name: any): any;
-    /**
-     *
-     * @deprecated
-     */
-    getTaxa(): any[];
     getTaxon(name: any): any;
     getTaxonList(): any[];
     #private;
@@ -223,6 +240,21 @@ export namespace TAXA_LIST_COLS {
     }
 }
 import { Taxon } from "./taxon.js";
+export class TaxaLoader extends GenericTaxaLoader {
+    loadTaxa(): Promise<Taxa>;
+}
+import { GenericTaxaLoader } from "./generictaxaloader.js";
+import { Taxa } from "./taxa.js";
+export class TaxaProcessor {
+    constructor(options: any, taxaLoaderClass?: typeof TaxaLoader);
+    customProcess(): Promise<void>;
+    getErrorLog(): any;
+    getOptions(): any;
+    getTaxa(): any;
+    process(): Promise<void>;
+    #private;
+}
+import { TaxaLoader } from "./taxaloader.js";
 export namespace TAXA_COLNAMES {
     const BLOOM_START: string;
     const BLOOM_END: string;
@@ -273,5 +305,6 @@ export class Taxon {
      */
     isNative(): boolean;
     isRare(): boolean;
+    shouldHaveFlowers(): boolean;
     #private;
 }

package/lib/index.js

@@ -1,16 +1,16 @@
 import { BasePageRenderer } from "./basepagerenderer.js";
-import { CommandRunner } from "./commandrunner.js";
+import { CommandAndTaxaProcessor } from "./commandandtaxaprocessor.js";
 import { Config } from "./config.js";
 import { CSV } from "./csv.js";
-import { DataLoader } from "./dataloader.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 { Taxa } from "./taxa.js";
 import { Taxon, TAXA_COLNAMES } from "./taxon.js";
 
-export { BasePageRenderer, CommandRunner, Config, CSV, DataLoader, ErrorLog, Exceptions, Families, Files, HTML, Jekyll, PlantBook, Taxa, TAXA_COLNAMES, Taxon };
+export { BasePageRenderer, CommandAndTaxaProcessor, Config, CSV, ErrorLog, Exceptions, Families, Files, GenericTaxaLoader, HTML, Jekyll, PlantBook, Taxa, TAXA_COLNAMES, Taxon };

package/lib/pagerenderer.js

@@ -32,7 +32,7 @@ class PageRenderer extends BasePageRenderer {
                 const listTaxa = [];
                 const calfloraTaxa = [];
                 const iNatTaxa = [];
-                for ( const taxon of taxa.getTaxa() ) {
+                for ( const taxon of taxa.getTaxonList() ) {
                     if ( list.include( taxon ) ) {
                         listTaxa.push( taxon );
                         calfloraTaxa.push( taxon.getCalfloraName() );

package/lib/taxa.js

@@ -1,6 +1,5 @@
 import { Config } from "./config.js";
 import { Taxon } from "./taxon.js";
-import { ErrorLog } from "./errorlog.js";
 import { HTML } from "./html.js";
 import { CSV } from "./csv.js";
 import { RarePlants } from "./rareplants.js";
@@ -65,11 +64,15 @@ class FlowerColor {
 
 class Taxa {
 
+    #errorLog;
     #taxa = {};
     #flower_colors = {};
     #sortedTaxa;
 
-    constructor( inclusionList, taxaMeta = {}, taxonClass = Taxon, extraTaxa = [], extraSynonyms = [] ) {
+    constructor( inclusionList, errorLog, showFlowerErrors, taxaMeta = {}, taxonClass = Taxon, extraTaxa = [], extraSynonyms = [] ) {
+
+        this.#errorLog = errorLog;
+
         for ( const color of FLOWER_COLOR_NAMES ) {
             this.#flower_colors[ color ] = new FlowerColor( color );
         }
@@ -77,13 +80,13 @@ class Taxa {
         const dataDir = Config.getPackageDir() + "/data";
 
         const taxaCSV = CSV.parseFile( dataDir, "taxa.csv" );
-        this.#loadTaxa( taxaCSV, inclusionList, taxaMeta, taxonClass );
-        this.#loadTaxa( extraTaxa, inclusionList, taxaMeta, taxonClass );
+        this.#loadTaxa( taxaCSV, inclusionList, taxaMeta, taxonClass, showFlowerErrors );
+        this.#loadTaxa( extraTaxa, inclusionList, taxaMeta, taxonClass, showFlowerErrors );
 
         // Make sure everything in the inclusionList has been loaded.
         for ( const name of Object.keys( inclusionList ) ) {
             if ( !this.getTaxon( name ) ) {
-                ErrorLog.log( name, "not found in taxon list" );
+                this.#errorLog.log( name, "not found in taxon list" );
             }
         }
 
@@ -127,14 +130,6 @@ class Taxa {
         return this.#flower_colors[ name ];
     }
 
-    /**
-     * 
-     * @deprecated
-     */
-    getTaxa() {
-        return this.#sortedTaxa;
-    }
-
     getTaxon( name ) {
         return this.#taxa[ name ];
     }
@@ -158,7 +153,7 @@ class Taxa {
         }
     }
 
-    #loadTaxa( taxaCSV, inclusionList, taxaMeta, taxonClass ) {
+    #loadTaxa( taxaCSV, inclusionList, taxaMeta, taxonClass, showFlowerErrors ) {
         for ( const row of taxaCSV ) {
 
             const name = row[ "taxon_name" ];
@@ -172,7 +167,7 @@ class Taxa {
             }
 
             if ( this.#taxa[ name ] ) {
-                ErrorLog.log( name, "has multiple entries" );
+                this.#errorLog.log( name, "has multiple entries" );
             }
 
             const status = taxon_overrides[ "status" ];
@@ -192,6 +187,18 @@ class Taxa {
                 }
             }
 
+            if ( showFlowerErrors ) {
+                // Make sure flower colors/bloom times are present or not depending on taxon.
+                if ( taxon.shouldHaveFlowers() ) {
+                    if ( !colors || !taxon.getBloomStart() || !taxon.getBloomEnd() ) {
+                        this.#errorLog.log( name, "does not have all flower info" );
+                    }
+                } else {
+                    if ( colors || taxon.getBloomStart() || taxon.getBloomEnd() ) {
+                        this.#errorLog.log( name, "should not have flower info" );
+                    }
+                }
+            }
         }
 
     }

package/lib/taxaloader.js

@@ -0,0 +1,35 @@
+import { CSV } from "./csv.js";
+import { Files } from "./files.js";
+import { GenericTaxaLoader } from "./generictaxaloader.js";
+import { Taxa } from "./taxa.js";
+
+class TaxaLoader extends GenericTaxaLoader {
+
+    constructor( options ) {
+        super( options );
+    }
+
+    async loadTaxa() {
+        function 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 );
+            const include = {};
+            for ( const row of includeCSV ) {
+                include[ row[ "taxon_name" ] ] = row;
+            }
+            return include;
+        }
+
+        const options = this.getOptions();
+        return new Taxa( getIncludeList( options.datadir ), this.getErrorLog(), options[ "show-flower-errors" ] );
+    }
+
+}
+
+export { TaxaLoader };

package/lib/taxaprocessor.js

@@ -0,0 +1,40 @@
+import { TaxaLoader } from "./taxaloader.js";
+
+class TaxaProcessor {
+
+    #options;
+    #taxaLoaderClass;
+    #taxaLoader;
+
+    constructor( options, taxaLoaderClass = TaxaLoader ) {
+        this.#options = options;
+        this.#taxaLoaderClass = taxaLoaderClass;
+    }
+
+    async customProcess() {
+        throw new Error( "must be implemented by subclass" );
+    }
+
+    getErrorLog() {
+        return this.#taxaLoader.getErrorLog();
+    }
+
+    getOptions() {
+        return this.#options;
+    }
+
+    getTaxa() {
+        return this.#taxaLoader.getTaxa();
+    }
+
+    async process() {
+        console.log( "loading data" );
+        this.#taxaLoader = new this.#taxaLoaderClass( this.#options );
+        await this.#taxaLoader.load();
+        await this.customProcess();
+        this.#taxaLoader.writeErrorLog();
+    }
+
+}
+
+export { TaxaProcessor };

package/lib/taxon.js

@@ -255,6 +255,23 @@ class Taxon {
         return this.getRPIRank() !== undefined;
     }
 
+    shouldHaveFlowers() {
+        const sectionName = this.getFamily().getSectionName();
+        switch ( sectionName ) {
+            case "Ceratophyllales":
+            case "Eudicots":
+            case "Magnoliids":
+            case "Monocots":
+            case "Nymphaeales":
+                return true;
+            case "Ferns":
+            case "Gymnosperms":
+            case "Lycophytes":
+                return false;
+            default:
+                throw new Error( sectionName );
+        }
+    }
 }
 
 export { TAXA_COLNAMES, Taxon };

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.2.15",
+    "version": "0.2.17",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {

package/scripts/build-ebook.js

@@ -1,74 +1,73 @@
 #!/usr/bin/env node
 
-import { CommandRunner, PlantBook } from "@ca-plant-list/ca-plant-list";
-import { DataLoader } from "../lib/dataloader.js";
+import { PlantBook } from "@ca-plant-list/ca-plant-list";
 import { Config } from "../lib/config.js";
 import { Files } from "../lib/files.js";
-import { ErrorLog } from "../lib/errorlog.js";
-
-const OUTPUT_DIR = "./output";
-const LOC_DIR = "./locations";
+import { TaxaProcessor } from "../lib/taxaprocessor.js";
+import { CommandProcessor } from "../lib/commandprocessor.js";
 
 const OPTION_DEFS = [
-    { name: "datadir", type: String },
+    { name: "locationsdir", type: String },
 ];
 
 const OPTION_HELP = [
     {
-        name: "datadir",
+        name: "locationsdir",
         type: String,
         typeLabel: "{underline path}",
-        description: "The directory in which the data files for the local plant list are located. If no directory is specified:\n"
-            + "- if there is a {bold locations} subdirectory in the current directory, each subdirectory of the {bold locations} subdirectory"
-            + " will be used as the data directory from which to generate an ebook (multiple ebooks will be generated)\n"
-            + "- otherwise {bold ./data} will be used as the {bold datadir}"
+        description: "If this option is specified, multiple ebooks will be generated. {bold locationsdir} must be a subdirectory"
+            + " of the current directory, and each subdirectory of {bold locationsdir} is processed in turn to generate an ebook."
+            + " Each ebook is placed in a subdirectory of {bold outputdir}."
     },
 ];
 
-const cr = new CommandRunner(
-    "ca-plant-book",
-    "A tool to generate an ebook with local plant data.",
-    OPTION_DEFS,
-    OPTION_HELP,
-    undefined,
-    generateEBooks,
-);
-await cr.processCommandLine();
+class BookCommand extends CommandProcessor {
 
-async function generateEBooks( options ) {
+    constructor() {
+        super( "ca-plant-book", "A tool to generate an ebook with local plant data.", OPTION_DEFS, OPTION_HELP );
+    }
 
-    const dataDir = options.datadir;
+}
 
-    // If a data directory was specified, use it.
-    if ( dataDir ) {
-        await generateEBook( dataDir );
-        return;
+class BookGenerator extends TaxaProcessor {
+
+    async customProcess() {
+        const options = this.getOptions();
+        const ebook = new PlantBook( options.outputdir, new Config( options.datadir ), this.getTaxa() );
+        await ebook.create();
     }
 
+}
+
+async function generateEBooks( options ) {
+    const locationsDir = options.locationsdir;
+
     // If there is a "locations" directory, generate a book for all subdirectories.
-    const hasLocations = Files.isDir( LOC_DIR );
-    if ( hasLocations ) {
+    if ( locationsDir ) {
         // Generate ebook for each location.
-        const subdirs = Files.getDirEntries( LOC_DIR );
+        const outputBase = options.outputdir;
+        const subdirs = Files.getDirEntries( locationsDir );
         for ( const subdir of subdirs ) {
+            console.log( "Generating " + subdir );
             const suffix = "/" + subdir;
-            const path = LOC_DIR + suffix;
+            const path = locationsDir + suffix;
             if ( Files.isDir( path ) ) {
-                await generateEBook( path, suffix );
+                options.datadir = path;
+                options.outputdir = outputBase + suffix;
+                const gen = new BookGenerator( options );
+                await gen.process( options );
             }
         }
-        return;
+    } else {
+        // Otherwise use the default directory.
+        const gen = new BookGenerator( options );
+        await gen.process( options );
     }
 
-    // Otherwise use the default directory.
-    await generateEBook( "./data" );
-
-    ErrorLog.write( OUTPUT_DIR + "/errors.tsv" );
-
-}
-
-async function generateEBook( dataDir, outputSuffix = "" ) {
-    const ebook = new PlantBook( OUTPUT_DIR + outputSuffix, new Config( dataDir ), DataLoader.load( dataDir ) );
-    await ebook.create();
 }
 
+const cmd = new BookCommand();
+const options = cmd.getOptions();
+if ( !options.help ) {
+    generateEBooks( options );
+}

package/scripts/build-site.js

@@ -4,26 +4,8 @@ import * as child_process from "node:child_process";
 import * as path from "node:path";
 import { Files } from "@ca-plant-list/ca-plant-list";
 import { Config } from "../lib/config.js";
-import { DataLoader } from "../lib/dataloader.js";
 import { PageRenderer } from "../lib/pagerenderer.js";
-import { CommandRunner } from "../lib/commandrunner.js";
-import { ErrorLog } from "../lib/errorlog.js";
-
-const OUTPUT_DIR = "./output";
-
-const OPTION_DEFS = [
-    { name: "datadir", type: String, defaultValue: "./data" },
-];
-
-const OPTION_HELP = [
-    {
-        name: "datadir",
-        type: String,
-        typeLabel: "{underline path}",
-        description: "The directory in which the data files for the local plant list are located. Defaults to {bold ./data}."
-
-    },
-];
+import { CommandAndTaxaProcessor } from "../lib/commandandtaxaprocessor.js";
 
 class JekyllRenderer {
 
@@ -57,22 +39,17 @@ class JekyllRenderer {
 
 }
 
-const cr = new CommandRunner(
-    "ca-plant-list",
-    "A tool to generate a website with local plant data.",
-    OPTION_DEFS,
-    OPTION_HELP,
-    undefined,
-    generateSite,
-);
-await cr.processCommandLine();
-
-async function generateSite( options ) {
-    const dataDir = options.datadir;
-    PageRenderer.render( OUTPUT_DIR, new Config( dataDir ), DataLoader.load( dataDir ) );
-    ErrorLog.write( OUTPUT_DIR + "/errors.tsv" );
+async function generateSite( taxaProcessor ) {
 
+    const options = taxaProcessor.getOptions();
+
+    PageRenderer.render( options.outputdir, new Config( options.datadir ), taxaProcessor.getTaxa() );
+
+    console.log( "generating site" );
     const r = new JekyllRenderer();
     await r.renderPages();
+
 }
 
+const gen = new CommandAndTaxaProcessor( "ca-plant-list", "A tool to generate a website with local plant data.", generateSite );
+await gen.process();

package/lib/commandrunner.js

@@ -1,63 +0,0 @@
-import commandLineArgs from "command-line-args";
-import commandLineUsage from "command-line-usage";
-
-const OPTION_DEFS = [
-    { name: "help", type: Boolean },
-];
-
-class CommandRunner {
-
-    #commandName;
-    #commandDesc;
-    #optionDefs;
-    #optionHelp;
-    #additionalHelp;
-    #commandFunc;
-
-    constructor( commandName, commandDesc, optionDefs, optionHelp, additionalHelp = [], commandFunc ) {
-        this.#commandName = commandName;
-        this.#commandDesc = commandDesc;
-        this.#optionDefs = optionDefs;
-        this.#optionHelp = optionHelp;
-        this.#additionalHelp = additionalHelp;
-        this.#commandFunc = commandFunc;
-    }
-
-    async processCommandLine() {
-
-        const options = commandLineArgs( this.#optionDefs.concat( OPTION_DEFS ) );
-
-        if ( options.help ) {
-            this.showHelp();
-            return;
-        }
-
-        console.log( "Use --help to see all options" );
-        await this.#commandFunc( options );
-
-    }
-
-    showHelp() {
-        const help = [
-            {
-                header: this.#commandName,
-                content: this.#commandDesc
-            },
-            {
-                header: "Options",
-                optionList: [
-                    {
-                        name: "help",
-                        type: Boolean,
-                        description: "Print this usage guide."
-                    },
-                ]
-            }
-        ];
-        help[ 1 ].optionList = help[ 1 ].optionList.concat( this.#optionHelp );
-        console.log( commandLineUsage( help.concat( this.#additionalHelp ) ) );
-    }
-
-}
-
-export { CommandRunner };