@ca-plant-list/ca-plant-list 0.2.16 → 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/) -->
+
+<svg
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+   height="60"
+   viewBox="0 0 102.55142 60"
+   version="1.1"
+   id="svg1"
+   inkscape:version="1.3 (0e150ed6c4, 2023-07-21)"
+   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
+     id="namedview1"
+     pagecolor="#ffffff"
+     bordercolor="#000000"
+     borderopacity="0.25"
+     inkscape:showpageshadow="2"
+     inkscape:pageopacity="0.0"
+     inkscape:pagecheckerboard="0"
+     inkscape:deskcolor="#d1d1d1"
+     inkscape:document-units="px"
+     showgrid="true"
+     inkscape:zoom="4"
+     inkscape:cx="50.625"
+     inkscape:cy="59.875"
+     inkscape:window-width="1920"
+     inkscape:window-height="991"
+     inkscape:window-x="-9"
+     inkscape:window-y="-9"
+     inkscape:window-maximized="1"
+     inkscape:current-layer="layer1">
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+       originx="0"
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+       spacingy="1"
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+       empopacity="0.30196078"
+       color="#0099e5"
+       opacity="0.14901961"
+       empspacing="5"
+       dotted="false"
+       gridanglex="30"
+       gridanglez="30"
+       visible="true" />
+  </sodipodi:namedview>
+  <defs
+     id="defs1">
+    <marker
+       style="overflow:visible"
+       id="Triangle"
+       refX="0"
+       refY="0"
+       orient="auto-start-reverse"
+       inkscape:stockid="Triangle arrow"
+       markerWidth="1"
+       markerHeight="1"
+       viewBox="0 0 1 1"
+       inkscape:isstock="true"
+       inkscape:collect="always"
+       preserveAspectRatio="xMidYMid">
+      <path
+         transform="scale(0.5)"
+         style="fill:context-stroke;fill-rule:evenodd;stroke:context-stroke;stroke-width:1pt"
+         d="M 5.77,0 -2.88,5 V -5 Z"
+         id="path135" />
+    </marker>
+  </defs>
+  <g
+     inkscape:label="Layer 1"
+     inkscape:groupmode="layer"
+     id="layer1">
+    <path
+       style="fill:#14140c;fill-opacity:1;stroke:#160707;stroke-width:1;stroke-dasharray:none;stroke-opacity:1"
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+    <use
+       x="0"
+       y="0"
+       inkscape:tiled-clone-of="#path1"
+       xlink:href="#path1"
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+       x="0"
+       y="0"
+       inkscape:tiled-clone-of="#path1"
+       xlink:href="#path1"
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+       x="0"
+       y="0"
+       inkscape:tiled-clone-of="#path1"
+       xlink:href="#path1"
+       transform="rotate(60,15,15)"
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+    <use
+       x="0"
+       y="0"
+       inkscape:tiled-clone-of="#path1"
+       xlink:href="#path1"
+       transform="rotate(90,15,15)"
+       id="use4" />
+    <use
+       x="0"
+       y="0"
+       inkscape:tiled-clone-of="#path1"
+       xlink:href="#path1"
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+    <use
+       x="0"
+       y="0"
+       inkscape:tiled-clone-of="#path1"
+       xlink:href="#path1"
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+    <ellipse
+       style="fill:#ffff00;stroke-width:0"
+       id="path1"
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+       cy="15"
+       rx="2.5"
+       ry="15"
+       inkscape:tile-cx="15"
+       inkscape:tile-cy="15"
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+       inkscape:tile-h="30"
+       inkscape:tile-x0="12.5"
+       inkscape:tile-y0="0" />
+    <path
+       style="fill:#14140c;fill-opacity:1;stroke:#160707;stroke-width:0.5;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#Triangle)"
+       d="M 20,45 H 45"
+       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"
+       x="50"
+       y="47.068359"
+       id="text3"><tspan
+         sodipodi:role="line"
+         id="tspan3"
+         x="50"
+         y="47.068359"
+         style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:8px;font-family:Arial;-inkscape-font-specification:'Arial, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-east-asian:normal;letter-spacing:0.5px;stroke-width:0.1;stroke-dasharray:none">peduncle</tspan></text>
+    <path
+       style="fill:#14140c;fill-opacity:1;stroke:#160707;stroke-width:0.5;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#Triangle)"
+       d="M 35,15 H 45"
+       id="path4"
+       sodipodi:nodetypes="cc" />
+    <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="17.068359"
+       id="text4"><tspan
+         sodipodi:role="line"
+         id="tspan4"
+         x="49.696735"
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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>
+<marker id="b" overflow="visible" markerHeight="1" markerWidth="1" orient="auto-start-reverse" preserveAspectRatio="xMidYMid" viewBox="0 0 1 1">
+<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">
+<path d="m20 45h25" marker-start="url(#b)" stroke-width=".5"/>
+<text x="50" y="47.068359" font-family="Arial" font-size="8px" letter-spacing=".5px" opacity=".55843" stroke-width=".1" xml:space="preserve"><tspan x="50" y="47.068359" 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">peduncle</tspan></text>
+<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/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/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

@@ -1,9 +1,16 @@
 import { CSV } from "./csv.js";
 import { Taxa } from "./taxa.js";
 import { Files } from "./files.js";
+import { ErrorLog } from "./errorlog.js";
 
 class DataLoader {
 
+    static #errorLog = new ErrorLog();
+
+    static getErrorLog() {
+        return DataLoader.#errorLog;
+    }
+
     static load( options ) {
 
         function getIncludeList( dataDir ) {
@@ -26,8 +33,12 @@ class DataLoader {
 
         console.log( "loading data" );
 
-        return new Taxa( getIncludeList( options.datadir ), showFlowerErrors );
+        return new Taxa( getIncludeList( options.datadir ), this.getErrorLog(), showFlowerErrors );
+
+    }
 
+    static writeErrorLog() {
+        DataLoader.#errorLog.write();
     }
 
 }

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(options: 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;
@@ -175,7 +197,7 @@ export class Taxa {
         title: string;
         data: (t: any) => any;
     }[]): string;
-    constructor(inclusionList: any, showFlowerErrors: 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;
     getTaxon(name: any): any;
     getTaxonList(): any[];
@@ -218,6 +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;

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/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, showFlowerErrors, 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 );
         }
@@ -83,7 +86,7 @@ class Taxa {
         // 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" );
             }
         }
 
@@ -164,7 +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" ];
@@ -188,11 +191,11 @@ class Taxa {
                 // Make sure flower colors/bloom times are present or not depending on taxon.
                 if ( taxon.shouldHaveFlowers() ) {
                     if ( !colors || !taxon.getBloomStart() || !taxon.getBloomEnd() ) {
-                        ErrorLog.log( name, "does not have all flower info" );
+                        this.#errorLog.log( name, "does not have all flower info" );
                     }
                 } else {
                     if ( colors || taxon.getBloomStart() || taxon.getBloomEnd() ) {
-                        ErrorLog.log( name, "should not have flower info" );
+                        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/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.2.16",
+    "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

@@ -1,76 +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( options );
-        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 ) ) {
                 options.datadir = path;
-                await generateEBook( options, suffix );
+                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.
-    options.datadir = "./data";
-    await generateEBook( options );
-
-    ErrorLog.write( OUTPUT_DIR + "/errors.tsv" );
-
-}
-
-async function generateEBook( options, outputSuffix = "" ) {
-    const ebook = new PlantBook( OUTPUT_DIR + outputSuffix, new Config( options.datadir ), DataLoader.load( options ) );
-    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 {
 
@@ -57,23 +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( options ) );
-    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

@@ -1,71 +0,0 @@
-import commandLineArgs from "command-line-args";
-import commandLineUsage from "command-line-usage";
-
-const OPTION_DEFS = [
-    { name: "help", type: Boolean },
-    { name: "show-flower-errors", type: Boolean },
-];
-
-const OPTION_HELP = [
-    {
-        name: "help",
-        type: Boolean,
-        description: "Print this usage guide."
-    },
-    {
-        name: "show-flower-errors",
-        type: Boolean,
-        description: "Include flower color and flowering time errors in errors.tsv."
-    },
-];
-
-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: OPTION_HELP
-            }
-        ];
-        help[ 1 ].optionList = help[ 1 ].optionList.concat( this.#optionHelp );
-        console.log( commandLineUsage( help.concat( this.#additionalHelp ) ) );
-    }
-
-}
-
-export { CommandRunner };