@ca-plant-list/ca-plant-list 0.0.1 → 0.1.0

package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 ca-plant-list
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

@@ -1 +1 @@
-This module contains tools for producing Jekyll files to create a set of static HTML pages with information about plants growing in the will in areas of California.
+This module contains tools for producing Jekyll files to create a set of static HTML pages with information about plants growing in the wild in areas of California.

package/build-site.js

@@ -1,19 +1,23 @@
 #!/usr/bin/env node
 
-import * as path from "node:path";
-import * as url from "node:url";
 import { Config } from "./lib/config.js";
 import { DataLoader } from "./lib/dataloader.js";
 import { ErrorLog } from "./lib/errorlog.js";
 import { PageRenderer } from "./lib/pagerenderer.js";
+import commandLineArgs from "command-line-args";
 
-const DATA_DIR = "./data";
-const PACKAGE_DIR = path.dirname( url.fileURLToPath( import.meta.url ) );
-const DEFAULT_DATA_DIR = PACKAGE_DIR + "/data";
+const OPTION_DEFS = [
+    { name: "data", type: String, defaultValue: "./data" },
+];
+
+const options = commandLineArgs( OPTION_DEFS );
+
+const TAXA_DATA_DIR = options.data;
+const CONFIG_DATA_DIR = "./data";
 const OUTPUT_DIR = "./output";
 
-Config.init( DATA_DIR );
-DataLoader.load( DATA_DIR, DEFAULT_DATA_DIR );
-PageRenderer.render( PACKAGE_DIR, OUTPUT_DIR );
+Config.init( CONFIG_DATA_DIR );
+DataLoader.load( TAXA_DATA_DIR );
+PageRenderer.render( OUTPUT_DIR );
 
 ErrorLog.write( OUTPUT_DIR + "/errors.txt" );

package/jekyll/_layouts/html.html

@@ -28,6 +28,7 @@
                     <li class="nav-item">
                         <a class="nav-link" href="{{site.baseurl}}/common_name_search.html">Common Name Search</a>
                     </li>
+                    {%include menu_extra.html %}
                 </ul>
             </div>
         </div>

package/jekyll/assets/css/main.css

@@ -13,9 +13,19 @@
     --bs-navbar-color: white;
     --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;
 }
 
+span[title] {
+    text-decoration: underline dotted;
+}
+
+span.label {
+    font-weight: 600;
+    padding-right: .5rem;
+}
+
 td {
     border: solid 1px;
     vertical-align: top;
@@ -27,9 +37,16 @@ th {
 
 /* Lists */
 
-a.native {
+span.native {
     font-weight: bold;
-    font-style: italic;
+}
+
+span.rare {
+    font-weight: bold;
+}
+
+span.rare::before {
+    content: "\2606";
 }
 
 /* Taxon Page */
@@ -61,4 +78,8 @@ div.section ul {
 
 div.section li {
     display: block;
+}
+
+div.section ul.indent {
+    padding-left: 1rem;
 }

package/lib/config.js

@@ -1,8 +1,11 @@
+import * as path from "node:path";
+import * as url from "node:url";
 import * as fs from "node:fs";
 
 class Config {
 
     static #config = {};
+    static #packageDir = path.dirname( path.dirname( url.fileURLToPath( import.meta.url ) ) );
 
     static getConfigValue( prefix, name, dflt ) {
         const obj = this.#config[ prefix ];
@@ -18,6 +21,10 @@ class Config {
         return this.getConfigValue( "labels", name, dflt );
     }
 
+    static getPackageDir() {
+        return this.#packageDir;
+    }
+
     static init( dir ) {
         try {
             this.#config = JSON.parse( fs.readFileSync( dir + "/config.json" ) );

package/lib/dataloader.js

@@ -1,15 +1,21 @@
 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";
+
 
 class DataLoader {
 
-    static load( taxaDir, dataDir ) {
+    static load( taxaDir ) {
+
+        const defaultDataDir = Config.getPackageDir() + "/data";
 
         console.log( "loading data" );
 
-        Families.init( dataDir );
-        Genera.init( dataDir );
+        Exceptions.init( taxaDir );
+        Families.init( defaultDataDir );
+        Genera.init( defaultDataDir );
         Taxa.init( taxaDir );
 
     }

package/lib/exceptions.js

@@ -0,0 +1,28 @@
+import * as fs from "node:fs";
+
+class Exceptions {
+
+    static #exceptions = {};
+
+    static hasException( name, cat, subcat ) {
+        const taxonData = this.#exceptions[ name ];
+        if ( taxonData ) {
+            const catData = taxonData[ cat ];
+            if ( catData ) {
+                return catData[ subcat ] !== undefined;
+            }
+        }
+        return false;
+    }
+
+    static init( dir ) {
+        try {
+            this.#exceptions = JSON.parse( fs.readFileSync( dir + "/exceptions.json" ) );
+        } catch ( e ) {
+            console.log( e );
+        }
+    }
+
+}
+
+export { Exceptions };

package/lib/html.js

@@ -29,7 +29,10 @@ class HTML {
     }
 
     static getLink( href, linkText, attributes = {}, options = 0 ) {
-        let html = "<a href=\"" + this.escapeAttribute( href ) + "\"";
+        let html = "<a";
+        if ( href !== undefined ) {
+            html += this.renderAttribute( "href", href );
+        }
         html += this.renderAttributes( attributes );
         if ( options & HTML_OPTIONS.OPEN_NEW ) {
             html += this.renderAttribute( "target", "_blank" );

package/lib/pagerenderer.js

@@ -1,19 +1,20 @@
 import * as fs from "node:fs";
 import { Families } from "./families.js";
-import { HTML } from "./html.js";
+import { HTML, HTML_OPTIONS } from "./html.js";
 import { Taxa } from "./taxa.js";
 import { HTMLPage } from "./htmlpage.js";
 import { PageTaxon } from "./pagetaxon.js";
 import { Config } from "./config.js";
+import { RPI } from "./rpi.js";
 
 class PageRenderer {
 
-    static render( packageDir, outputDir ) {
+    static render( outputDir ) {
 
         // Copy static files
         fs.rmSync( outputDir, { force: true, recursive: true } );
         // First copy default Jekyll files from package.
-        fs.cpSync( packageDir + "/jekyll", outputDir, { recursive: true } );
+        fs.cpSync( Config.getPackageDir() + "/jekyll", outputDir, { recursive: true } );
         // Then copy Jekyll files from current dir (which may override default files).
         fs.cpSync( "jekyll", outputDir, { recursive: true } );
 
@@ -31,34 +32,118 @@ class PageRenderer {
 
     static renderLists( outputDir ) {
 
-        const listInfo = [
-            { name: Config.getLabel( "native", "Native" ), filename: "list_native", include: ( t ) => t.isNative() },
-            { name: Config.getLabel( "introduced", "Introduced" ), filename: "list_introduced", include: ( t ) => !t.isNative() },
-            { name: "All Plants", filename: "list_all", include: () => true },
-        ];
+        function getListArray( listInfo, attributes = {} ) {
+            const listArray = [];
+            for ( const list of listInfo ) {
+                const taxa = [];
+                const calfloraTaxa = [];
+                const iNatTaxa = [];
+                for ( const taxon of Taxa.getTaxa() ) {
+                    if ( list.include( taxon ) ) {
+                        taxa.push( taxon );
+                        calfloraTaxa.push( taxon.getCalfloraName() );
+                        iNatTaxa.push( taxon.getINatName() );
+                    }
+                }
 
-        const listsHTML = [];
-        for ( const list of listInfo ) {
-            const taxa = [];
-            const calfloraTaxa = [];
-            const iNatTaxa = [];
-            for ( const taxon of Taxa.getTaxa() ) {
-                if ( list.include( taxon ) ) {
-                    taxa.push( taxon );
-                    calfloraTaxa.push( taxon.getCalfloraName() );
-                    iNatTaxa.push( taxon.getINatName() );
+                if ( taxa.length === 0 ) {
+                    continue;
                 }
+
+                fs.writeFileSync( outputDir + "/calflora_" + list.filename + ".txt", calfloraTaxa.join( "\n" ) );
+                fs.writeFileSync( outputDir + "/inat_" + list.filename + ".txt", iNatTaxa.join( "\n" ) );
+
+                new PageTaxonList().render( outputDir, taxa, list.filename, list.name );
+
+                // Check for sublists.
+                const subListHTML = list.listInfo ? getListArray( list.listInfo, { class: "indent" } ) : "";
+
+                listArray.push( HTML.getLink( "./" + list.filename + ".html", list.name ) + " (" + taxa.length + ")" + subListHTML );
             }
+            return renderList( listArray, attributes );
+        }
+
+        function renderList( listsHTML, attributes = {} ) {
+            return HTML.getElement( "ul", HTML.arrayToLI( listsHTML ), attributes, HTML_OPTIONS.NO_ESCAPE );
+        }
 
-            fs.writeFileSync( outputDir + "/calflora_" + list.filename + ".txt", calfloraTaxa.join( "\n" ) );
-            fs.writeFileSync( outputDir + "/inat_" + list.filename + ".txt", iNatTaxa.join( "\n" ) );
+        function renderSection( title, listsHTML ) {
+            let html = "<div class=\"section\">";
+            html += HTML.getElement( "h2", title );
+            html += listsHTML;
+            html += "</div>";
+            return html;
+        }
+
+        const sections = [
+            {
+                title: "All Species",
+                listInfo: [
+                    { name: Config.getLabel( "native", "Native" ), filename: "list_native", include: ( t ) => t.isNative() },
+                    { name: Config.getLabel( "introduced", "Introduced" ), filename: "list_introduced", include: ( t ) => !t.isNative() },
+                    { name: "All Plants", filename: "list_all", include: () => true },
+                ]
+            },
+            {
+                title: "Rare Plants",
+                listInfo: [
+                    {
+                        name: "CNPS Ranked Plants",
+                        filename: "list_rpi",
+                        include: ( t ) => t.getRPIRank() !== undefined,
+                        listInfo: [
+                            {
+                                name: RPI.getRankDescription( "1A" ),
+                                filename: "list_rpi_1a",
+                                include: ( t ) => t.getRPIRank() === "1A",
+                            },
+                            {
+                                name: RPI.getRankDescription( "1B" ),
+                                filename: "list_rpi_1b",
+                                include: ( t ) => t.getRPIRank() === "1B",
+                            },
+                            {
+                                name: RPI.getRankDescription( "2A" ),
+                                filename: "list_rpi_2a",
+                                include: ( t ) => t.getRPIRank() === "2A",
+                            },
+                            {
+                                name: RPI.getRankDescription( "2B" ),
+                                filename: "list_rpi_2b",
+                                include: ( t ) => t.getRPIRank() === "2B",
+                            },
+                            {
+                                name: RPI.getRankDescription( "3" ),
+                                filename: "list_rpi_3",
+                                include: ( t ) => t.getRPIRank() === "3",
+                            },
+                            {
+                                name: RPI.getRankDescription( "4" ),
+                                filename: "list_rpi_4",
+                                include: ( t ) => t.getRPIRank() === "4",
+                            },
+                        ]
+                    },
+                ]
+            },
+        ];
+
+        let html = "<div class=\"wrapper\">";
+        for ( const section of sections ) {
+
+            const listHTML = getListArray( section.listInfo );
+
+            if ( listHTML.length > 0 ) {
+                html += renderSection( section.title, listHTML );
+            }
 
-            new PageTaxonList().render( outputDir, taxa, list.filename, list.name );
-            listsHTML.push( HTML.getLink( "./" + list.filename + ".html", list.name ) + " (" + taxa.length + ")" );
         }
+        html += renderSection( "Taxonomy", renderList( [ HTML.getLink( "./list_families.html", "Plant Families" ) ] ) );
+
+        html += "</div>";
 
         // Write lists to includes directory so it can be inserted into pages.
-        fs.writeFileSync( outputDir + "/_includes/plantlists.html", "<ul>" + HTML.arrayToLI( listsHTML ) + "</ul>" );
+        fs.writeFileSync( outputDir + "/_includes/plantlists.html", html );
 
     }
 

package/lib/pagetaxon.js

@@ -3,6 +3,7 @@ import { HTML, HTML_OPTIONS } from "./html.js";
 import { Jepson } from "./jepson.js";
 import { HTMLPage } from "./htmlpage.js";
 import { Config } from "./config.js";
+import { RPI } from "./rpi.js";
 
 class PageTaxon extends HTMLPage {
 
@@ -91,15 +92,7 @@ class PageTaxon extends HTMLPage {
         if ( genus ) {
             const taxa = genus.getTaxa();
             for ( const taxon of taxa ) {
-                if ( taxon.getName() !== this.#taxon.getName() ) {
-                    links.push(
-                        HTML.getLink(
-                            "./" + taxon.getFileName(),
-                            taxon.getName(),
-                            { class: taxon.getHTMLClassName() }
-                        )
-                    );
-                }
+                links.push( taxon.getHTMLLink( taxon.getName() !== this.#taxon.getName() ) );
             }
         }
         return links;
@@ -126,11 +119,22 @@ class PageTaxon extends HTMLPage {
         const family = this.#taxon.getFamily();
         html += HTML.getElement(
             "div",
-            "Family: " + HTML.getLink( "./" + family.getFileName(), family.getName() ),
+            HTML.getElement( "span", "Family:", { class: "label" } ) + HTML.getLink( "./" + family.getFileName(), family.getName() ),
             { class: "section" },
             HTML_OPTIONS.NO_ESCAPE
         );
 
+        const cnpsRank = this.#taxon.getRPIRankAndThreat();
+        if ( cnpsRank ) {
+            html += HTML.getElement(
+                "div",
+                HTML.getElement( "span", "CNPS Rare Plant Rank:", { class: "label" } )
+                + HTML.getElement( "span", cnpsRank, { title: RPI.getRankAndThreatDescriptions( cnpsRank ).join( "\n" ) } ),
+                { class: "section" },
+                HTML_OPTIONS.NO_ESCAPE
+            );
+        }
+
         html += "</div>";
 
         const introName = "intros/" + this.#taxon.getFileName( "md" );

package/lib/rpi.js

@@ -0,0 +1,30 @@
+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",
+};
+
+const THREAT_DESCRIPS = {
+    "1": "Seriously threatened in California",
+    "2": "Moderately threatened in California",
+    "3": "Not very threatened in California",
+};
+
+class RPI {
+
+    static getRankDescription( rank ) {
+        const pieces = rank.split( "." );
+        return RANK_DESCRIPS[ pieces[ 0 ] ];
+    }
+
+    static getRankAndThreatDescriptions( rank ) {
+        const pieces = rank.split( "." );
+        return [ RANK_DESCRIPS[ pieces[ 0 ] ], THREAT_DESCRIPS[ pieces[ 1 ] ] ];
+    }
+
+}
+
+export { RPI };

package/lib/taxa.js

@@ -19,7 +19,7 @@ class Taxa {
             html += "<tr>";
             html += HTML.getElement(
                 "td",
-                HTML.getLink( "./" + taxon.getFileName(), taxon.getName(), { class: taxon.getHTMLClassName() } ),
+                taxon.getHTMLLink(),
                 undefined,
                 HTML_OPTIONS.NO_ESCAPE
             );
@@ -55,7 +55,15 @@ class Taxa {
                         ErrorLog.log( name, "has multiple entries" );
                     }
                     const commonName = row[ "common name" ];
-                    this.#taxa[ name ] = new Taxon( name, commonName, status, jepsonID, row[ "calrecnum" ], row[ "inat id" ] );
+                    this.#taxa[ name ] = new Taxon(
+                        name,
+                        commonName,
+                        status,
+                        jepsonID,
+                        row[ "calrecnum" ],
+                        row[ "inat id" ],
+                        row[ "CRPR" ]
+                    );
                     if ( !jepsonID ) {
                         ErrorLog.log( name, "has no Jepson ID" );
                     }

package/lib/taxon.js

@@ -1,6 +1,8 @@
 import { Config } from "./config.js";
 import { ErrorLog } from "./errorlog.js";
 import { Genera } from "./genera.js";
+import { RPI } from "./rpi.js";
+import { HTML, HTML_OPTIONS } from "./html.js";
 
 class Taxon {
 
@@ -12,9 +14,10 @@ class Taxon {
     #calRecNum;
     #iNatID;
     #iNatName;
+    #rankRPI;
     #synonyms = [];
 
-    constructor( name, commonNames, status, jepsonID, calRecNum, iNatID ) {
+    constructor( name, commonNames, status, jepsonID, calRecNum, iNatID, rankRPI ) {
         this.#name = name;
         this.#genus = name.split( " " )[ 0 ];
         this.#commonNames = commonNames ? commonNames.split( "," ).map( t => t.trim() ) : [];
@@ -22,6 +25,7 @@ class Taxon {
         this.#jepsonID = jepsonID;
         this.#calRecNum = calRecNum;
         this.#iNatID = iNatID;
+        this.#rankRPI = rankRPI;
         Genera.addTaxon( this );
         if ( !calRecNum ) {
             ErrorLog.log( this.getName(), "has no Calflora ID" );
@@ -63,14 +67,20 @@ class Taxon {
         return Genera.getGenus( this.#genus );
     }
 
-    getHTMLClassName() {
-        return this.isNative() ? "native" : "non-native";
-    }
-
     getGenusName() {
         return this.#genus;
     }
 
+    getHTMLLink( href = true ) {
+        href = href ? ( "./" + this.getFileName() ) : undefined;
+        const className = this.isNative() ? ( this.isRare() ? "rare" : "native" ) : "non-native";
+        const attributes = { class: className };
+        if ( className === "rare" ) {
+            attributes[ "title" ] = RPI.getRankAndThreatDescriptions( this.getRPIRankAndThreat() ).join( "\n" );
+        }
+        return HTML.getElement( "span", HTML.getLink( href, this.getName() ), attributes, HTML_OPTIONS.NO_ESCAPE );
+    }
+
     getINatID() {
         return this.#iNatID;
     }
@@ -88,6 +98,17 @@ class Taxon {
         return this.#name;
     }
 
+    getRPIRank() {
+        if ( !this.#rankRPI ) {
+            return this.#rankRPI;
+        }
+        return this.#rankRPI.split( "." )[ 0 ];
+    }
+
+    getRPIRankAndThreat() {
+        return this.#rankRPI;
+    }
+
     getStatus() {
         return this.#status;
     }
@@ -103,6 +124,7 @@ class Taxon {
         }
         throw new Error( this.#status );
     }
+
     getSynonyms() {
         return this.#synonyms;
     }
@@ -111,6 +133,10 @@ class Taxon {
         return this.#status === "N";
     }
 
+    isRare() {
+        return this.getRPIRank() !== undefined;
+    }
+
 }
 
 export { Taxon };

package/package.json

@@ -1,13 +1,33 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.0.1",
+    "version": "0.1.0",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
+    "repository": {
+        "type": "git",
+        "url": "https://github.com/ca-plants/ca-plant-list.git"
+    },
+    "homepage": "https://github.com/ca-plants/ca-plant-list",
     "type": "module",
+    "exports": {
+        "./CSV": {
+            "import": "./lib/csv.js"
+        },
+        "./DataLoader": {
+            "import": "./lib/dataloader.js"
+        },
+        "./Exceptions": {
+            "import": "./lib/exceptions.js"
+        },
+        "./Taxa": {
+            "import": "./lib/taxa.js"
+        }
+    },
     "bin": {
         "ca-plant-list": "build-site.js"
     },
     "dependencies": {
+        "command-line-args": "^5.2.1",
         "csv-parse": "^5.3.1"
     },
     "devDependencies": {