@ca-plant-list/ca-plant-list 0.1.0 → 0.1.1

package/build-site.js

@@ -6,18 +6,13 @@ import { ErrorLog } from "./lib/errorlog.js";
 import { PageRenderer } from "./lib/pagerenderer.js";
 import commandLineArgs from "command-line-args";
 
-const OPTION_DEFS = [
-    { name: "data", type: String, defaultValue: "./data" },
-];
+const options = commandLineArgs( DataLoader.getOptionDefs() );
 
-const options = commandLineArgs( OPTION_DEFS );
-
-const TAXA_DATA_DIR = options.data;
 const CONFIG_DATA_DIR = "./data";
 const OUTPUT_DIR = "./output";
 
 Config.init( CONFIG_DATA_DIR );
-DataLoader.load( TAXA_DATA_DIR );
+DataLoader.load( options );
 PageRenderer.render( OUTPUT_DIR );
 
 ErrorLog.write( OUTPUT_DIR + "/errors.txt" );

package/jekyll/_layouts/html.html

@@ -25,6 +25,9 @@
                     <li class="nav-item">
                         <a class="nav-link" href="{{site.baseurl}}/index_lists.html">Plant Lists</a>
                     </li>
+                    <li class="nav-item">
+                        <a class="nav-link" href="{{site.baseurl}}/rare_plants.html">Rare Plants</a>
+                    </li>
                     <li class="nav-item">
                         <a class="nav-link" href="{{site.baseurl}}/common_name_search.html">Common Name Search</a>
                     </li>

package/jekyll/assets/css/main.css

@@ -56,6 +56,10 @@ span.rare::before {
     font-weight: bold;
 }
 
+.native-status {
+    font-weight: 600;
+}
+
 div.wrapper {
     display: flex;
     flex-wrap: wrap;
@@ -64,7 +68,6 @@ div.wrapper {
 
 div.section {
     margin-bottom: .5rem;
-    ;
 }
 
 div.section h2 {

package/lib/csv.js

@@ -1,6 +1,8 @@
 import * as fs from "node:fs";
-import { parse } from "csv-parse/sync";
 import path from "node:path";
+import { finished } from "stream/promises";
+import { parse as parseSync } from "csv-parse/sync";
+import { parse } from "csv-parse";
 
 class CSV {
 
@@ -22,9 +24,7 @@ class CSV {
         return map;
     }
 
-    static parseFile( dir, fileName, columns = true, delimiter ) {
-        const content = fs.readFileSync( dir + "/" + fileName );
-
+    static #getOptions( fileName, columns, delimiter ) {
         const options = { relax_column_count_less: true };
         options.columns = columns;
         if ( path.extname( fileName ) === ".tsv" ) {
@@ -33,7 +33,35 @@ class CSV {
         } else {
             options.delimiter = delimiter ? delimiter : ",";
         }
-        return parse( content, options );
+        return options;
+    }
+
+    static parseFile( dir, fileName, columns = true, delimiter ) {
+        const content = fs.readFileSync( dir + "/" + fileName );
+
+        const options = this.#getOptions( fileName, columns, delimiter );
+        return parseSync( content, options );
+    }
+
+    static async parseStream( dir, fileName, columns = true, delimiter, callback ) {
+        const options = this.#getOptions( fileName, columns, delimiter );
+        const processFile = async () => {
+            const records = [];
+            const parser = fs
+                .createReadStream( dir + "/" + fileName )
+                .pipe( parse( options ) );
+            parser.on( "readable", function () {
+                let record;
+                while ( ( record = parser.read() ) !== null ) {
+                    callback( record );
+                }
+            } );
+            await finished( parser );
+            return records;
+        };
+        // Parse the CSV content
+        await processFile();
+
     }
 
 }

package/lib/dataloader.js

@@ -4,12 +4,20 @@ import { Families } from "./families.js";
 import { Config } from "./config.js";
 import { Exceptions } from "./exceptions.js";
 
+const OPTION_DEFS = [
+    { name: "datadir", type: String, defaultValue: "./data" },
+];
 
 class DataLoader {
 
-    static load( taxaDir ) {
+    static getOptionDefs() {
+        return OPTION_DEFS;
+    }
+
+    static load( options ) {
 
         const defaultDataDir = Config.getPackageDir() + "/data";
+        const taxaDir = options.datadir;
 
         console.log( "loading data" );
 

package/lib/exceptions.js

@@ -15,6 +15,16 @@ class Exceptions {
         return false;
     }
 
+    static getValue( name, cat, subcat ) {
+        const taxonData = this.#exceptions[ name ];
+        if ( taxonData ) {
+            const catData = taxonData[ cat ];
+            if ( catData ) {
+                return catData[ subcat ];
+            }
+        }
+    }
+
     static init( dir ) {
         try {
             this.#exceptions = JSON.parse( fs.readFileSync( dir + "/exceptions.json" ) );

package/lib/pagerenderer.js

@@ -5,7 +5,7 @@ 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";
+import { RarePlants } from "./rareplants.js";
 
 class PageRenderer {
 
@@ -93,37 +93,64 @@ class PageRenderer {
                         include: ( t ) => t.getRPIRank() !== undefined,
                         listInfo: [
                             {
-                                name: RPI.getRankDescription( "1A" ),
+                                name: RarePlants.getRPIRankDescription( "1A" ),
                                 filename: "list_rpi_1a",
                                 include: ( t ) => t.getRPIRank() === "1A",
                             },
                             {
-                                name: RPI.getRankDescription( "1B" ),
+                                name: RarePlants.getRPIRankDescription( "1B" ),
                                 filename: "list_rpi_1b",
                                 include: ( t ) => t.getRPIRank() === "1B",
                             },
                             {
-                                name: RPI.getRankDescription( "2A" ),
+                                name: RarePlants.getRPIRankDescription( "2A" ),
                                 filename: "list_rpi_2a",
                                 include: ( t ) => t.getRPIRank() === "2A",
                             },
                             {
-                                name: RPI.getRankDescription( "2B" ),
+                                name: RarePlants.getRPIRankDescription( "2B" ),
                                 filename: "list_rpi_2b",
                                 include: ( t ) => t.getRPIRank() === "2B",
                             },
                             {
-                                name: RPI.getRankDescription( "3" ),
+                                name: RarePlants.getRPIRankDescription( "3" ),
                                 filename: "list_rpi_3",
                                 include: ( t ) => t.getRPIRank() === "3",
                             },
                             {
-                                name: RPI.getRankDescription( "4" ),
+                                name: RarePlants.getRPIRankDescription( "4" ),
                                 filename: "list_rpi_4",
                                 include: ( t ) => t.getRPIRank() === "4",
                             },
                         ]
                     },
+                    {
+                        name: "California Endangered Species Act",
+                        filename: "list_cesa",
+                        include: ( t ) => t.getCESA() !== undefined,
+                        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",
+                            },
+                        ]
+                    },
                 ]
             },
         ];

package/lib/pagetaxon.js

@@ -3,7 +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";
+import { RarePlants } from "./rareplants.js";
 
 class PageTaxon extends HTMLPage {
 
@@ -20,7 +20,7 @@ class PageTaxon extends HTMLPage {
         if ( jepsonID ) {
             links.push( Jepson.getEFloraLink( jepsonID ) );
         }
-        const calRecNum = this.#taxon.getCalRecNum();
+        const calRecNum = this.#taxon.getCalfloraID();
         if ( calRecNum ) {
             links.push(
                 HTML.getLink(
@@ -86,13 +86,36 @@ class PageTaxon extends HTMLPage {
         return html;
     }
 
+    #getRarityInfo() {
+        const cnpsRank = this.#taxon.getRPIRankAndThreat();
+        if ( !cnpsRank ) {
+            return "";
+        }
+        const ranks = [];
+
+        ranks.push( HTML.getElement( "span", "CNPS Rare Plant Rank:", { class: "label" } )
+            + HTML.getElement( "span", cnpsRank, { title: RarePlants.getRPIRankAndThreatDescriptions( cnpsRank ).join( "\n" ) } ) );
+        if ( this.#taxon.getCESA() ) {
+            ranks.push( HTML.getElement( "span", "CESA:", { class: "label" } ) + RarePlants.getCESADescription( this.#taxon.getCESA() ) );
+        }
+
+        return HTML.getElement(
+            "div",
+            "<ul>" + HTML.arrayToLI( ranks ) + "</ul>",
+            { class: "section" },
+            HTML_OPTIONS.NO_ESCAPE
+        );
+    }
+
     #getRelatedTaxaLinks() {
         const links = [];
         const genus = this.#taxon.getGenus();
         if ( genus ) {
             const taxa = genus.getTaxa();
-            for ( const taxon of taxa ) {
-                links.push( taxon.getHTMLLink( taxon.getName() !== this.#taxon.getName() ) );
+            if ( taxa.length > 1 ) {
+                for ( const taxon of taxa ) {
+                    links.push( taxon.getHTMLLink( taxon.getName() !== this.#taxon.getName() ) );
+                }
             }
         }
         return links;
@@ -114,7 +137,8 @@ class PageTaxon extends HTMLPage {
         if ( cn.length > 0 ) {
             html += HTML.getElement( "div", cn.join( ", " ), { class: "section common-names" } );
         }
-        html += HTML.getElement( "div", this.#taxon.getStatusDescription(), { class: "section" } );
+
+        html += HTML.getElement( "div", this.#taxon.getStatusDescription(), { class: "section native-status" } );
 
         const family = this.#taxon.getFamily();
         html += HTML.getElement(
@@ -124,22 +148,17 @@ class PageTaxon extends HTMLPage {
             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 += this.#getRarityInfo();
 
         html += "</div>";
 
         const introName = "intros/" + this.#taxon.getFileName( "md" );
         if ( fs.existsSync( "./jekyll/_includes/" + introName ) ) {
-            html += HTML.getElement( "div", "{% capture my_include %}{% include " + introName + "%}{% endcapture %}{{ my_include | markdownify }}" );
+            html += HTML.getElement(
+                "div",
+                "{% capture my_include %}{% include " + introName + "%}{% endcapture %}{{ my_include | markdownify }}",
+                { class: "section" }
+            );
         }
 
         html += "<div class=\"wrapper\">";

package/lib/{rpi.js → rareplants.js}

@@ -13,18 +13,29 @@ const THREAT_DESCRIPS = {
     "3": "Not very threatened in California",
 };
 
-class RPI {
+const CESA_DESCRIPS = {
+    "CC": "Candidate",
+    "CE": "Endangered",
+    "CR": "Rare",
+    "CT": "Threatened",
+};
+
+class RarePlants {
+
+    static getCESADescription( cesa ) {
+        return CESA_DESCRIPS[ cesa ];
+    }
 
-    static getRankDescription( rank ) {
+    static getRPIRankDescription( rank ) {
         const pieces = rank.split( "." );
         return RANK_DESCRIPS[ pieces[ 0 ] ];
     }
 
-    static getRankAndThreatDescriptions( rank ) {
+    static getRPIRankAndThreatDescriptions( rank ) {
         const pieces = rank.split( "." );
         return [ RANK_DESCRIPS[ pieces[ 0 ] ], THREAT_DESCRIPS[ pieces[ 1 ] ] ];
     }
 
 }
 
-export { RPI };
+export { RarePlants };

package/lib/taxa.js

@@ -62,7 +62,8 @@ class Taxa {
                         jepsonID,
                         row[ "calrecnum" ],
                         row[ "inat id" ],
-                        row[ "CRPR" ]
+                        row[ "CRPR" ],
+                        row[ "CESA" ]
                     );
                     if ( !jepsonID ) {
                         ErrorLog.log( name, "has no Jepson ID" );

package/lib/taxon.js

@@ -1,8 +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";
+import { RarePlants } from "./rareplants.js";
 
 class Taxon {
 
@@ -13,11 +13,12 @@ class Taxon {
     #jepsonID;
     #calRecNum;
     #iNatID;
-    #iNatName;
+    #iNatSyn;
     #rankRPI;
+    #cesa;
     #synonyms = [];
 
-    constructor( name, commonNames, status, jepsonID, calRecNum, iNatID, rankRPI ) {
+    constructor( name, commonNames, status, jepsonID, calRecNum, iNatID, rankRPI, cesa ) {
         this.#name = name;
         this.#genus = name.split( " " )[ 0 ];
         this.#commonNames = commonNames ? commonNames.split( "," ).map( t => t.trim() ) : [];
@@ -26,6 +27,7 @@ class Taxon {
         this.#calRecNum = calRecNum;
         this.#iNatID = iNatID;
         this.#rankRPI = rankRPI;
+        this.#cesa = cesa;
         Genera.addTaxon( this );
         if ( !calRecNum ) {
             ErrorLog.log( this.getName(), "has no Calflora ID" );
@@ -38,7 +40,8 @@ class Taxon {
     addSynonym( syn, type ) {
         this.#synonyms.push( syn );
         if ( type === "INAT" ) {
-            this.#iNatName = syn;
+            // Synonyms should be in Jepson format, but store iNatName in iNat format (no var or subsp, space after x).
+            this.#iNatSyn = syn;
         }
     }
 
@@ -46,10 +49,14 @@ class Taxon {
         return this.#name.replace( " subsp.", " ssp." ).replace( "×", "X" );
     }
 
-    getCalRecNum() {
+    getCalfloraID() {
         return this.#calRecNum;
     }
 
+    getCESA() {
+        return this.#cesa;
+    }
+
     getCommonNames() {
         return this.#commonNames;
     }
@@ -76,7 +83,7 @@ class Taxon {
         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" );
+            attributes[ "title" ] = RarePlants.getRPIRankAndThreatDescriptions( this.getRPIRankAndThreat() ).join( "\n" );
         }
         return HTML.getElement( "span", HTML.getLink( href, this.getName() ), attributes, HTML_OPTIONS.NO_ESCAPE );
     }
@@ -86,7 +93,7 @@ class Taxon {
     }
 
     getINatName() {
-        const name = this.#iNatName ? this.#iNatName : this.#name;
+        const name = this.#iNatSyn ? this.#iNatSyn : this.getName();
         return name.replace( / (subsp|var)\./, "" ).replace( "×", "× " );
     }
 

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.1.0",
+    "version": "0.1.1",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {