@ca-plant-list/ca-plant-list 0.1.2 → 0.1.4

package/jekyll/_layouts/html.html

@@ -29,7 +29,7 @@
                         <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>
+                        <a class="nav-link" href="{{site.baseurl}}/name_search.html">Name Search</a>
                     </li>
                     {%include menu_extra.html %}
                 </ul>

package/jekyll/assets/css/main.css

@@ -28,6 +28,7 @@ span.label {
 
 td {
     border: solid 1px;
+    padding: 0 .5rem;
     vertical-align: top;
 }
 
@@ -85,4 +86,9 @@ div.section li {
 
 div.section ul.indent {
     padding-left: 1rem;
+}
+
+/* Forms */
+input {
+    margin-right: .5em;
 }

package/jekyll/assets/js/name_search.js

@@ -0,0 +1,156 @@
+const MIN_LEN = 2;
+const MAX_RESULTS = 50;
+
+class Search {
+
+    static #debounceTimer;
+    static #searchData;
+
+    static #debounce( func ) {
+        clearTimeout( this.#debounceTimer );
+        this.#debounceTimer = setTimeout( func, 500 );
+    }
+
+    static #doSearch() {
+
+        function matchTaxon( taxon, value ) {
+
+            function matchSynonyms( syns, value ) {
+                const matchedIndexes = [];
+                if ( syns ) {
+                    for ( let index = 0; index < syns.length; index++ ) {
+                        if ( syns[ index ].includes( value ) ) {
+                            matchedIndexes.push( index );
+                        }
+                    }
+                }
+                return matchedIndexes;
+            }
+
+            const rawData = taxon[ 0 ];
+            const name = taxon[ 1 ];
+            const cn = taxon[ 2 ];
+            const syns = matchSynonyms( taxon[ 3 ], value );
+            if ( syns.length > 0 ) {
+                // Include any matching synonyms.
+                for ( const index of syns ) {
+                    matches.push( [ rawData[ 0 ], rawData[ 1 ], rawData[ 2 ][ index ] ] );
+                }
+            } else {
+                // No synonyms match; see if the scientific or common names match.
+                const namesMatch = name.includes( value ) || ( cn && cn.includes( value ) );
+                if ( namesMatch ) {
+                    matches.push( [ rawData[ 0 ], rawData[ 1 ] ] );
+                }
+            }
+
+        }
+
+        Search.#debounceTimer = undefined;
+
+        const value = document.getElementById( "name" ).value.toLowerCase();
+
+        const matches = [];
+        const shouldSearch = ( value.length >= MIN_LEN );
+
+        if ( shouldSearch ) {
+
+            // If the search data is not done generating, try again later.
+            if ( !Search.#searchData ) {
+                this.#debounce( Search.#doSearch );
+            }
+
+            for ( const taxon of Search.#searchData ) {
+                matchTaxon( taxon, value );
+            }
+        }
+
+        const eBody = document.createElement( "tbody" );
+        if ( matches.length <= MAX_RESULTS ) {
+            for ( const match of matches ) {
+
+                const tr = document.createElement( "tr" );
+
+                // Scientific name.
+                const name = match[ 0 ];
+                const syn = match[ 2 ];
+                const td1 = document.createElement( "td" );
+                const link = document.createElement( "a" );
+                link.setAttribute( "href", "./" + name.replaceAll( ".", "" ).replaceAll( " ", "-" ) + ".html" );
+                link.textContent = name;
+                td1.appendChild( link );
+                if ( syn ) {
+                    td1.appendChild( document.createTextNode( " (" + syn + ")" ) );
+                }
+                tr.appendChild( td1 );
+
+                const cn = match[ 1 ];
+                const td2 = document.createElement( "td" );
+                if ( cn ) {
+                    td2.textContent = cn;
+                }
+                tr.appendChild( td2 );
+
+                eBody.appendChild( tr );
+
+            }
+        }
+
+        // Delete current message
+        const eMessage = document.getElementById( "message" );
+        if ( eMessage.firstChild ) {
+            eMessage.removeChild( eMessage.firstChild );
+        }
+        if ( shouldSearch ) {
+            if ( matches.length === 0 ) {
+                eMessage.textContent = "Nothing found.";
+            }
+            if ( matches.length > MAX_RESULTS ) {
+                eMessage.textContent = "Too many results.";
+            }
+        }
+
+        // Delete current results
+        const eTable = document.getElementById( "results" );
+        if ( eTable.firstChild ) {
+            eTable.removeChild( eTable.firstChild );
+        }
+
+        eTable.appendChild( eBody );
+    }
+
+    static async generateSearchData() {
+        const searchData = [];
+        // eslint-disable-next-line no-undef
+        for ( const taxon of NAMES ) {
+            const taxonData = [ taxon ];
+            taxonData.push( taxon[ 0 ].toLowerCase().replace( / (subsp|var)\./, "" ) );
+            if ( taxon[ 1 ] ) {
+                taxonData.push( taxon[ 1 ].toLowerCase() );
+            }
+            if ( taxon[ 2 ] ) {
+                const syns = [];
+                for ( const syn of taxon[ 2 ] ) {
+                    syns.push( syn.toLowerCase().replace( / (subsp|var)\./, "" ) );
+                }
+                taxonData[ 3 ] = syns;
+            }
+            searchData.push( taxonData );
+        }
+        this.#searchData = searchData;
+    }
+
+    static #handleChange() {
+        this.#debounce( Search.#doSearch );
+    }
+
+    static init() {
+        this.generateSearchData();
+        const eName = document.getElementById( "name" );
+        eName.focus();
+        eName.oninput = ( ev ) => { return this.#handleChange( ev ); };
+    }
+
+}
+
+Search.init();

package/jekyll/name_search.html

@@ -0,0 +1,18 @@
+---
+title: Name Search
+js: name_search.js
+---
+<h1>Search</h1>
+
+<script>
+    const NAMES = {% include names.json%};
+</script>
+
+<form>
+    <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>

package/lib/basepagerenderer.js

@@ -0,0 +1,46 @@
+import * as fs from "node:fs";
+import { Config } from "./config.js";
+
+class BasePageRenderer {
+
+    static render( outputDir, Taxa ) {
+
+        // Copy static files
+        fs.rmSync( outputDir, { force: true, recursive: true, maxRetries: 2, retryDelay: 200 } );
+        // First copy default Jekyll files from package.
+        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 } );
+
+        this.renderTools( outputDir, Taxa );
+
+    }
+
+    static renderTools( outputDir, Taxa ) {
+
+        const names = [];
+        for ( const taxon of Taxa.getTaxa() ) {
+            const row = [];
+            row.push( taxon.getName() );
+            const cn = taxon.getCommonNames().join( "," );
+            if ( cn ) {
+                row.push( cn );
+            }
+            const synonyms = [];
+            for ( const syn of taxon.getSynonyms() ) {
+                synonyms.push( syn );
+            }
+            if ( synonyms.length > 0 ) {
+                row[ 2 ] = synonyms;
+            }
+            names.push( row );
+        }
+
+        fs.writeFileSync( outputDir + "/_includes/names.json", JSON.stringify( names ) );
+
+    }
+
+
+}
+
+export { BasePageRenderer };

package/lib/dataloader.js

@@ -14,16 +14,22 @@ class DataLoader {
         return OPTION_DEFS;
     }
 
-    static load( options ) {
+    static init( taxaDir ) {
 
         const defaultDataDir = Config.getPackageDir() + "/data";
-        const taxaDir = options.datadir;
-
-        console.log( "loading data" );
 
         Exceptions.init( taxaDir );
         Families.init( defaultDataDir );
         Genera.init( defaultDataDir );
+    }
+
+    static load( options ) {
+
+        const taxaDir = options.datadir;
+
+        console.log( "loading data" );
+
+        this.init( taxaDir );
         Taxa.init( taxaDir );
 
     }

package/lib/exceptions.js

@@ -15,14 +15,16 @@ class Exceptions {
         return false;
     }
 
-    static getValue( name, cat, subcat ) {
+    static getValue( name, cat, subcat, defaultValue ) {
         const taxonData = this.#exceptions[ name ];
         if ( taxonData ) {
             const catData = taxonData[ cat ];
             if ( catData ) {
-                return catData[ subcat ];
+                const val = catData[ subcat ];
+                return ( val === undefined ) ? defaultValue : val;
             }
         }
+        return defaultValue;
     }
 
     static init( dir ) {

package/lib/files.js

@@ -0,0 +1,17 @@
+import * as fs from "node:fs";
+
+class Files {
+
+    static async fetch( url, targetFileName ) {
+        const response = await fetch( url );
+        const data = await response.text();
+        fs.writeFileSync( targetFileName, data );
+    }
+
+    static read( path ) {
+        return fs.readFileSync( path, "utf8" );
+    }
+
+}
+
+export { Files };

package/lib/genera.js

@@ -9,6 +9,11 @@ class Genera {
 
         const genusName = taxon.getGenusName();
         const genusData = this.#genera[ genusName ];
+        if ( !genusData ) {
+            console.log( taxon.getName() + " genus not found" );
+            return;
+        }
+
         if ( genusData.taxa === undefined ) {
             genusData.taxa = [];
         }
@@ -16,7 +21,7 @@ class Genera {
 
         const family = this.getFamily( genusName );
         if ( !family ) {
-            console.log( taxon.getName() + " genus/family not found" );
+            console.log( taxon.getName() + " family not found" );
             return;
         }
         family.addTaxon( taxon );

package/lib/index.js

@@ -0,0 +1,10 @@
+import { BasePageRenderer } from "./basepagerenderer.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 { HTML, HTML_OPTIONS } from "./html.js";
+import { Taxon } from "./taxon.js";
+
+export { BasePageRenderer, Config, CSV, DataLoader, ErrorLog, Exceptions, HTML, HTML_OPTIONS, Taxon };

package/lib/pagerenderer.js

@@ -6,20 +6,15 @@ 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";
 
-class PageRenderer {
+class PageRenderer extends BasePageRenderer {
 
     static render( outputDir ) {
 
-        // Copy static files
-        fs.rmSync( outputDir, { force: true, recursive: true } );
-        // First copy default Jekyll files from package.
-        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 } );
+        super.render( outputDir, Taxa );
 
         this.renderLists( outputDir );
-        this.renderTools( outputDir );
 
         Families.renderPages( outputDir );
 
@@ -174,30 +169,6 @@ class PageRenderer {
 
     }
 
-    static renderTools( outputDir ) {
-
-        const commonNames = [];
-        for ( const taxon of Taxa.getTaxa() ) {
-            for ( const commonName of taxon.getCommonNames() ) {
-                commonNames.push( [ commonName, taxon.getName() ] );
-            }
-        }
-
-        const cnObj = {};
-        for ( const commonName of commonNames.sort( ( a, b ) => a[ 0 ].localeCompare( b[ 0 ] ) ) ) {
-            const normalizedName = commonName[ 0 ].toLowerCase().replaceAll( "-", " " ).replaceAll( "'", "" );
-            let data = cnObj[ normalizedName ];
-            if ( !data ) {
-                data = { cn: commonName[ 0 ], names: [] };
-                cnObj[ normalizedName ] = data;
-            }
-            data.names.push( commonName[ 1 ] );
-        }
-        fs.writeFileSync( outputDir + "/_includes/common_names.json", JSON.stringify( cnObj ) );
-
-
-    }
-
 }
 
 class PageTaxonList extends HTMLPage {

package/lib/pagetaxon.js

@@ -31,16 +31,9 @@ class PageTaxon extends HTMLPage {
                 )
             );
         }
-        const iNatID = this.#taxon.getINatID();
-        if ( iNatID ) {
-            links.push(
-                HTML.getLink(
-                    "https://www.inaturalist.org/taxa/" + iNatID,
-                    "iNaturalist",
-                    {},
-                    HTML_OPTIONS.OPEN_NEW
-                )
-            );
+        const iNatLink = this.#taxon.getINatTaxonLink();
+        if ( iNatLink ) {
+            links.push( iNatLink );
         }
         return links;
     }

package/lib/taxa.js

@@ -62,6 +62,7 @@ class Taxa {
                         jepsonID,
                         row[ "calrecnum" ],
                         row[ "inat id" ],
+                        row[ "RPI ID" ],
                         row[ "CRPR" ],
                         row[ "CESA" ]
                     );

package/lib/taxon.js

@@ -12,13 +12,15 @@ class Taxon {
     #status;
     #jepsonID;
     #calRecNum;
+    #cfSyn;
     #iNatID;
     #iNatSyn;
+    #rpiID;
     #rankRPI;
     #cesa;
     #synonyms = [];
 
-    constructor( name, commonNames, status, jepsonID, calRecNum, iNatID, rankRPI, cesa ) {
+    constructor( name, commonNames, status, jepsonID, calRecNum, iNatID, rpiID, rankRPI, cesa ) {
         this.#name = name;
         this.#genus = name.split( " " )[ 0 ];
         this.#commonNames = commonNames ? commonNames.split( "," ).map( t => t.trim() ) : [];
@@ -26,6 +28,7 @@ class Taxon {
         this.#jepsonID = jepsonID;
         this.#calRecNum = calRecNum;
         this.#iNatID = iNatID;
+        this.#rpiID = rpiID;
         this.#rankRPI = rankRPI;
         this.#cesa = cesa;
         Genera.addTaxon( this );
@@ -39,14 +42,23 @@ class Taxon {
 
     addSynonym( syn, type ) {
         this.#synonyms.push( syn );
-        if ( type === "INAT" ) {
-            // Synonyms should be in Jepson format, but store iNatName in iNat format (no var or subsp, space after x).
-            this.#iNatSyn = syn;
+        switch ( type ) {
+            case "CF":
+                // Synonym is in Calflora format.
+                this.#cfSyn = syn;
+                break;
+            case "INAT":
+                // Synonyms should be in Jepson format, but store iNatName in iNat format (no var or subsp, space after x).
+                this.#iNatSyn = syn;
+                break;
         }
     }
 
     getCalfloraName() {
-        return this.#name.replace( " subsp.", " ssp." ).replace( "×", "X" );
+        if ( this.#cfSyn ) {
+            return this.#cfSyn;
+        }
+        return this.getName().replace( " subsp.", " ssp." ).replace( "×", "X" );
     }
 
     getCalfloraID() {
@@ -65,9 +77,13 @@ class Taxon {
         return Genera.getFamily( this.#genus );
     }
 
-    getFileName( ext = "html" ) {
+    getFileName( ext ) {
+        return Taxon.getFileName( this.getName(), ext );
+    }
+
+    static getFileName( name, ext = "html" ) {
         // Convert spaces to "-" and remove ".".
-        return this.getName().replaceAll( " ", "-" ).replaceAll( ".", "" ) + "." + ext;
+        return name.replaceAll( " ", "-" ).replaceAll( ".", "" ) + "." + ext;
     }
 
     getGenus() {
@@ -97,6 +113,15 @@ class Taxon {
         return name.replace( / (subsp|var)\./, "" ).replace( "×", "× " );
     }
 
+    getINatTaxonLink() {
+        const iNatID = this.getINatID();
+        if ( !iNatID ) {
+            return "";
+        }
+        const link = HTML.getLink( "https://www.inaturalist.org/taxa/" + iNatID, "iNaturalist", {}, HTML_OPTIONS.OPEN_NEW );
+        return this.#iNatSyn ? ( link + " (" + this.#iNatSyn + ")" ) : link;
+    }
+
     getJepsonID() {
         return this.#jepsonID;
     }
@@ -105,6 +130,10 @@ class Taxon {
         return this.#name;
     }
 
+    getRPIID() {
+        return this.#rpiID;
+    }
+
     getRPIRank() {
         if ( !this.#rankRPI ) {
             return this.#rankRPI;
@@ -144,6 +173,18 @@ class Taxon {
         return this.getRPIRank() !== undefined;
     }
 
+    setCalfloraID( id ) {
+        this.#calRecNum = id;
+    }
+
+    setINatID( id ) {
+        this.#iNatID = id;
+    }
+
+    setJepsonID( id ) {
+        this.#jepsonID = id;
+    }
+
 }
 
 export { Taxon };

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.1.2",
+    "version": "0.1.4",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {
@@ -10,21 +10,7 @@
     "homepage": "https://github.com/ca-plants/ca-plant-list",
     "type": "module",
     "exports": {
-        "./Config": {
-            "import": "./lib/config.js"
-        },
-        "./CSV": {
-            "import": "./lib/csv.js"
-        },
-        "./DataLoader": {
-            "import": "./lib/dataloader.js"
-        },
-        "./Exceptions": {
-            "import": "./lib/exceptions.js"
-        },
-        "./Taxa": {
-            "import": "./lib/taxa.js"
-        }
+        ".": "./lib/index.js"
     },
     "bin": {
         "ca-plant-list": "build-site.js"

package/jekyll/assets/js/common_name_search.js

@@ -1,87 +0,0 @@
-const MIN_LEN = 2;
-const MAX_RESULTS = 50;
-
-class Search {
-
-    static #debounceTimer;
-
-    static #debounce( func ) {
-        clearTimeout( this.#debounceTimer );
-        this.#debounceTimer = setTimeout( func, 500 );
-    }
-
-    static #doSearch() {
-
-        Search.#debounceTimer = undefined;
-
-        const value = document.getElementById( "common-name" ).value.toLowerCase();
-
-        const matches = [];
-        const shouldSearch = ( value.length >= MIN_LEN );
-
-        if ( shouldSearch ) {
-            // eslint-disable-next-line no-undef
-            for ( const key of Object.keys( COMMON_NAMES ) ) {
-                if ( key.includes( value ) ) {
-                    matches.push( key );
-                }
-            }
-        }
-
-        const eBody = document.createElement( "tbody" );
-        if ( matches.length <= MAX_RESULTS ) {
-            for ( const match of matches ) {
-                // eslint-disable-next-line no-undef
-                const data = COMMON_NAMES[ match ];
-                for ( const name of data.names ) {
-                    const tr = document.createElement( "tr" );
-                    const td1 = document.createElement( "td" );
-                    const td2 = document.createElement( "td" );
-                    const link = document.createElement( "a" );
-                    td1.textContent = data.cn;
-                    link.setAttribute( "href", "./" + name.replaceAll( ".", "" ).replaceAll( " ", "-" ) + ".html" );
-                    link.textContent = name;
-                    td2.appendChild( link );
-                    tr.appendChild( td1 );
-                    tr.appendChild( td2 );
-                    eBody.appendChild( tr );
-                }
-            }
-        }
-
-        // Delete current message
-        const eMessage = document.getElementById( "message" );
-        if ( eMessage.firstChild ) {
-            eMessage.removeChild( eMessage.firstChild );
-        }
-        if ( shouldSearch ) {
-            if ( matches.length === 0 ) {
-                eMessage.textContent = "Nothing found.";
-            }
-            if ( matches.length > MAX_RESULTS ) {
-                eMessage.textContent = "Too many results.";
-            }
-        }
-
-        // Delete current results
-        const eTable = document.getElementById( "results" );
-        if ( eTable.firstChild ) {
-            eTable.removeChild( eTable.firstChild );
-        }
-
-        eTable.appendChild( eBody );
-    }
-
-    static #handleChange() {
-        this.#debounce( Search.#doSearch );
-    }
-
-    static init() {
-        const eName = document.getElementById( "common-name" );
-        eName.focus();
-        eName.oninput = ( ev ) => { return this.#handleChange( ev ); };
-    }
-
-}
-
-Search.init();

package/jekyll/common_name_search.html

@@ -1,18 +0,0 @@
----
-title: Common Name Search
-js: common_name_search.js
----
-<h1>Search for Common Name</h1>
-
-<script>
-    const COMMON_NAMES = {% include common_names.json%};
-</script>
-
-<form>
-    <input type="text" id="common-name">
-</form>
-
-<div class="section" id="message"></div>
-
-<table id="results">
-</table>