@ca-plant-list/ca-plant-list 0.1.13 → 0.1.15

package/build-site.js

@@ -1,6 +1,5 @@
 #!/usr/bin/env node
 
-import { Config } from "./lib/config.js";
 import { DataLoader } from "./lib/dataloader.js";
 import { ErrorLog } from "./lib/errorlog.js";
 import { PageRenderer } from "./lib/pagerenderer.js";
@@ -8,11 +7,9 @@ import commandLineArgs from "command-line-args";
 
 const options = commandLineArgs( DataLoader.getOptionDefs() );
 
-const CONFIG_DATA_DIR = "./data";
 const OUTPUT_DIR = "./output";
 
-Config.init( CONFIG_DATA_DIR );
 DataLoader.load( options );
 PageRenderer.render( OUTPUT_DIR );
 
-ErrorLog.write( OUTPUT_DIR + "/errors.txt" );
+ErrorLog.write( OUTPUT_DIR + "/errors.tsv" );

package/data/genera.json

@@ -11,6 +11,10 @@
         "family": "Lycopodiaceae",
         "id": "9179"
     },
+    "Rhinotropis": {
+        "family": "Polygalaceae",
+        "id": 99965
+    },
     "Selaginella": {
         "family": "Selaginellaceae",
         "id": "8877"

package/jekyll/assets/css/main.css

@@ -1,7 +1,10 @@
 /* Defaults */
 
 :root {
-    --bs-body-bg: #ECF87F;
+    /* See https://visme.co/blog/website-color-schemes/ theme 4 */
+    --bs-body-bg: #5cdb95;
+    --bs-link-color: #05386b;
+    --pl-navbar-bg: #379683;
 }
 
 .navbar-nav {
@@ -14,7 +17,7 @@
     --bs-navbar-brand-hover-color: rgba(255, 255, 255, .5);
     --bs-navbar-brand-color: white;
     --bs-navbar-nav-link-padding-x: 1rem;
-    background-color: #3D550C;
+    background-color: var(--pl-navbar-bg);
 }
 
 span.label {

package/lib/config.js

@@ -1,12 +1,20 @@
 import * as path from "node:path";
 import * as url from "node:url";
-import * as fs from "node:fs";
+import { Files } from "./files.js";
 
 class Config {
 
     static #config = {};
     static #packageDir = path.dirname( path.dirname( url.fileURLToPath( import.meta.url ) ) );
 
+    static {
+        try {
+            this.#config = JSON.parse( Files.read( "./data/config.json" ) );
+        } catch ( e ) {
+            console.log( e );
+        }
+    }
+
     static getConfigValue( prefix, name, subcat, dflt ) {
         const obj = this.#config[ prefix ];
         if ( obj ) {
@@ -26,6 +34,10 @@ class Config {
         return dflt;
     }
 
+    static getCountyCodes() {
+        return this.#config[ "counties" ];
+    }
+
     static getLabel( name, dflt ) {
         return this.getConfigValue( "labels", name, undefined, dflt );
     }
@@ -34,14 +46,6 @@ class Config {
         return this.#packageDir;
     }
 
-    static init( dir ) {
-        try {
-            this.#config = JSON.parse( fs.readFileSync( dir + "/config.json" ) );
-        } catch ( e ) {
-            console.log( e );
-        }
-    }
-
 }
 
 export { Config };

package/lib/dataloader.js

@@ -1,7 +1,5 @@
 import { Taxa } from "./taxa.js";
-import { Genera } from "./genera.js";
 import { Families } from "./families.js";
-import { Config } from "./config.js";
 import { Exceptions } from "./exceptions.js";
 
 const OPTION_DEFS = [
@@ -15,12 +13,8 @@ class DataLoader {
     }
 
     static init( taxaDir ) {
-
-        const defaultDataDir = Config.getPackageDir() + "/data";
-
         Exceptions.init( taxaDir );
-        Families.init( defaultDataDir );
-        Genera.init( defaultDataDir );
+        Families.init();
     }
 
     static load( options ) {

package/lib/exceptions.js

@@ -1,35 +1,39 @@
-import * as fs from "node:fs";
+import { Files } from "./files.js";
 
 class Exceptions {
 
     static #exceptions = {};
 
-    static hasException( name, cat, subcat ) {
+    static getExceptions() {
+        return Object.entries( this.#exceptions );
+    }
+
+    static getValue( name, cat, subcat, defaultValue ) {
         const taxonData = this.#exceptions[ name ];
         if ( taxonData ) {
             const catData = taxonData[ cat ];
             if ( catData ) {
-                return catData[ subcat ] !== undefined;
+                const val = catData[ subcat ];
+                return ( val === undefined ) ? defaultValue : val;
             }
         }
-        return false;
+        return defaultValue;
     }
 
-    static getValue( name, cat, subcat, defaultValue ) {
+    static hasException( name, cat, subcat ) {
         const taxonData = this.#exceptions[ name ];
         if ( taxonData ) {
             const catData = taxonData[ cat ];
             if ( catData ) {
-                const val = catData[ subcat ];
-                return ( val === undefined ) ? defaultValue : val;
+                return catData[ subcat ] !== undefined;
             }
         }
-        return defaultValue;
+        return false;
     }
 
     static init( dir ) {
         try {
-            this.#exceptions = JSON.parse( fs.readFileSync( dir + "/exceptions.json" ) );
+            this.#exceptions = JSON.parse( Files.read( dir + "/exceptions.json" ) );
         } catch ( e ) {
             console.log( e );
         }

package/lib/families.js

@@ -3,6 +3,8 @@ import { HTML } from "./html.js";
 import { Jepson } from "./jepson.js";
 import { Taxa } from "./taxa.js";
 import { Files } from "./files.js";
+import { Config } from "./config.js";
+import { Genera } from "./genera.js";
 
 class Families {
 
@@ -12,11 +14,17 @@ class Families {
         return this.#families[ familyName ];
     }
 
-    static init( dataDir ) {
+    static init() {
+
+        const dataDir = Config.getPackageDir() + "/data";
+
         this.#families = JSON.parse( Files.read( dataDir + "/families.json" ) );
         for ( const [ k, v ] of Object.entries( this.#families ) ) {
             this.#families[ k ] = new Family( k, { id: v } );
         }
+
+        Genera.init( dataDir );
+
     }
 
     static renderPages( outputDir, columns ) {

package/lib/files.js

@@ -22,11 +22,25 @@ class Files {
         return fs.existsSync( path );
     }
 
-    static async fetch( url, targetFileName ) {
-        const response = await fetch( url );
+    /**
+     * Retrieve data from a URL and write it to a file. If the response status is anything other than 200, an Error is thrown.
+     * @param {string|URL} url 
+     * @param {string|undefined} targetFileName If targetFileName is undefined, the data will be retrieved but not written to a file.
+     * @param {Object} [headers={}] Request Headers.
+     * @returns {Headers} The Response headers.
+     */
+    static async fetch( url, targetFileName, headers = {} ) {
+        const response = await fetch( url, headers );
+        if ( response.status !== 200 ) {
+            throw new Error( response.status + " retrieving " + url );
+        }
         const data = await response.blob();
-        const buffer = await data.arrayBuffer();
-        fs.writeFileSync( targetFileName, Buffer.from( buffer ) );
+        const arrayBuffer = await data.arrayBuffer();
+        const buffer = Buffer.from( arrayBuffer );
+        if ( targetFileName ) {
+            fs.writeFileSync( targetFileName, buffer );
+        }
+        return response.headers;
     }
 
     static mkdir( path ) {
@@ -41,8 +55,8 @@ class Files {
         fs.rmSync( dir, { force: true, recursive: true, maxRetries: 2, retryDelay: 1000 } );
     }
 
-    static write( path, data ) {
-        if ( this.exists( path ) ) {
+    static write( path, data, overwrite = false ) {
+        if ( !overwrite && this.exists( path ) ) {
             throw new Error( path + " already exists" );
         }
         fs.writeFileSync( path, data );

package/lib/genera.js

@@ -1,5 +1,5 @@
-import * as fs from "node:fs";
 import { Families } from "./families.js";
+import { Files } from "./files.js";
 
 class Genera {
 
@@ -39,7 +39,7 @@ class Genera {
     }
 
     static init( dataDir ) {
-        this.#genera = JSON.parse( fs.readFileSync( dataDir + "/genera.json" ) );
+        this.#genera = JSON.parse( Files.read( dataDir + "/genera.json" ) );
     }
 
 }

package/lib/genericpage.js

@@ -14,6 +14,10 @@ class GenericPage {
         this.#js = js;
     }
 
+    getBaseFileName() {
+        return this.#baseFileName;
+    }
+
     getDefaultIntro() {
         let html = this.#getFrontMatter();
         html += HTML.textElement( "h1", this.#title );

package/lib/index.d.ts

@@ -2,11 +2,18 @@ export class Files {
     static copyDir(srcDir: any, targetDir: any): void;
     static createFileFromStream(fileName: any, inStream: any): Promise<any>;
     static exists(path: any): boolean;
-    static fetch(url: any, targetFileName: any): Promise<void>;
+    /**
+     * Retrieve data from a URL and write it to a file. If the response status is anything other than 200, an Error is thrown.
+     * @param {string|URL} url
+     * @param {string|undefined} targetFileName If targetFileName is undefined, the data will be retrieved but not written to a file.
+     * @param {Object} [headers={}] Request Headers.
+     * @returns {Headers} The Response headers.
+     */
+    static fetch(url: string | URL, targetFileName: string | undefined, headers?: any): Headers;
     static mkdir(path: any): void;
     static read(path: any): string;
     static rmDir(dir: any): void;
-    static write(path: any, data: any): void;
+    static write(path: any, data: any, overwrite?: boolean): void;
     static zipFileExtract(zipFilePath: any, fileNameToUnzip: any, targetFilePath: any): Promise<void>;
 }
 export namespace HTML_OPTIONS {

package/lib/pagerenderer.js

@@ -1,11 +1,11 @@
 import { HTML } from "./html.js";
 import { Taxa, TAXA_LIST_COLS } from "./taxa.js";
-import { HTMLPage } from "./htmlpage.js";
 import { PageTaxon } from "./pagetaxon.js";
 import { Config } from "./config.js";
 import { RarePlants } from "./rareplants.js";
 import { BasePageRenderer } from "./basepagerenderer.js";
 import { Files } from "./files.js";
+import { GenericPage } from "./genericpage.js";
 
 const RPI_CESA = [ TAXA_LIST_COLS.SPECIES, TAXA_LIST_COLS.COMMON_NAME, TAXA_LIST_COLS.CESA ];
 const RPI_COLUMNS = [ TAXA_LIST_COLS.SPECIES_BARE, TAXA_LIST_COLS.COMMON_NAME, TAXA_LIST_COLS.CNPS_RANK ];
@@ -50,7 +50,7 @@ class PageRenderer extends BasePageRenderer {
                 Files.write( outputDir + "/inat_" + list.filename + ".txt", iNatTaxa.join( "\n" ) );
 
                 const cols = columns ? columns : list.columns;
-                new PageTaxonList().render( outputDir, taxa, list.filename, list.name, cols );
+                new PageTaxonList( outputDir, list.name, list.filename ).render( taxa, cols );
 
                 // Check for sublists.
                 const subListHTML = list.listInfo ? getListArray( list.listInfo, { class: "indent" }, cols ) : "";
@@ -128,28 +128,6 @@ class PageRenderer extends BasePageRenderer {
                         filename: "list_cesa",
                         include: ( t ) => t.getCESA() !== undefined,
                         columns: RPI_CESA,
-                        listInfo: [
-                            {
-                                name: RarePlants.getCESADescription( "CE" ),
-                                filename: "list_rpi_ce",
-                                include: ( t ) => t.getCESA() === "CE",
-                            },
-                            {
-                                name: RarePlants.getCESADescription( "CT" ),
-                                filename: "list_rpi_ct",
-                                include: ( t ) => t.getCESA() === "CT",
-                            },
-                            {
-                                name: RarePlants.getCESADescription( "CR" ),
-                                filename: "list_rpi_cr",
-                                include: ( t ) => t.getCESA() === "CR",
-                            },
-                            {
-                                name: RarePlants.getCESADescription( "CC" ),
-                                filename: "list_rpi_cc",
-                                include: ( t ) => t.getCESA() === "CC",
-                            },
-                        ]
                     },
                 ]
             },
@@ -176,13 +154,15 @@ class PageRenderer extends BasePageRenderer {
 
 }
 
-class PageTaxonList extends HTMLPage {
+class PageTaxonList extends GenericPage {
 
-    render( outputDir, taxa, baseName, title, columns ) {
+    constructor( outputDir, title, baseName ) {
+        super( outputDir, title, baseName );
+    }
 
-        let html = this.getFrontMatter( title );
+    render( taxa, columns ) {
 
-        html += HTML.textElement( "h1", title );
+        let html = this.getDefaultIntro();
 
         html += "<div class=\"wrapper\">";
 
@@ -193,14 +173,14 @@ class PageTaxonList extends HTMLPage {
         html += "<div class=\"section\">";
         html += HTML.textElement( "h2", "Download" );
         html += "<ul>";
-        html += "<li>" + HTML.getLink( "./calflora_" + baseName + ".txt", "Calflora List" ) + "</li>";
-        html += "<li>" + HTML.getLink( "./inat_" + baseName + ".txt", "iNaturalist List" ) + "</li>";
+        html += "<li>" + HTML.getLink( "./calflora_" + this.getBaseFileName() + ".txt", "Calflora List" ) + "</li>";
+        html += "<li>" + HTML.getLink( "./inat_" + this.getBaseFileName() + ".txt", "iNaturalist List" ) + "</li>";
         html += "</ul>";
         html += "</div>";
 
         html += "</div>";
 
-        this.writeFile( outputDir, baseName + ".html", html );
+        this.writeFile( html );
 
     }
 }

package/lib/pagetaxon.js

@@ -40,7 +40,7 @@ class PageTaxon extends GenericPage {
         links.push(
             HTML.getLink(
                 "https://www.calflora.org/entry/observ.html?track=m#srch=t&grezc=5&cols=b&lpcli=t&cc="
-                + Config.getConfigValue( "calflora", "counties" ).join( "!" ) + "&incobs=f&taxon="
+                + Config.getCountyCodes().join( "!" ) + "&incobs=f&taxon="
                 + this.#taxon.getCalfloraName().replaceAll( " ", "+" ),
                 "Calflora",
                 {},

package/lib/taxa.js

@@ -3,6 +3,7 @@ import { ErrorLog } from "./errorlog.js";
 import { HTML } from "./html.js";
 import { CSV } from "./csv.js";
 import { RarePlants } from "./rareplants.js";
+import { Exceptions } from "./exceptions.js";
 
 const TAXA_LIST_COLS = {
     CESA: {
@@ -95,7 +96,7 @@ class Taxa {
                         row[ "CRPR" ],
                         row[ "CESA" ]
                     );
-                    if ( !jepsonID ) {
+                    if ( !jepsonID && !Exceptions.hasException( name, "jepson", "badjepsonid" ) ) {
                         ErrorLog.log( name, "has no Jepson ID" );
                     }
                     break;

package/lib/taxon.js

@@ -192,6 +192,10 @@ class Taxon {
         return this.#status === "N" || this.#status === "NC";
     }
 
+    /**
+     * Determine whether a species is a local native.
+     * @returns {boolean} true if taxon is a local native; false if not a CA native, or native elsewhere in CA.
+     */
     isNative() {
         return this.#status === "N";
     }

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.1.13",
+    "version": "0.1.15",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {
@@ -11,6 +11,7 @@
     "type": "module",
     "exports": {
         ".": "./lib/index.js",
+        "./Families": "./lib/families.js",
         "./Files": "./lib/files.js",
         "./HTML": "./lib/html.js",
         "./Jekyll": "./lib/jekyll.js"
@@ -21,6 +22,7 @@
     },
     "dependencies": {
         "command-line-args": "^5.2.1",
+        "command-line-usage": "^6.1.3",
         "csv-parse": "^5.3.1",
         "unzipper": "^0.10.11"
     },