@ca-plant-list/ca-plant-list 0.1.3 → 0.1.5

package/lib/basepagerenderer.js

@@ -6,7 +6,7 @@ class BasePageRenderer {
     static render( outputDir, Taxa ) {
 
         // Copy static files
-        fs.rmSync( outputDir, { force: true, recursive: true, maxRetries: 2, retryDelay: 200 } );
+        fs.rmSync( outputDir, { force: true, recursive: true, maxRetries: 2, retryDelay: 300 } );
         // 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).

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/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

@@ -1,5 +1,12 @@
 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 { Files } from "./files.js";
 import { HTML, HTML_OPTIONS } from "./html.js";
+import { Taxa } from "./taxa.js";
+import { Taxon } from "./taxon.js";
 
-export { BasePageRenderer, Config, HTML, HTML_OPTIONS };
+export { BasePageRenderer, Config, CSV, DataLoader, ErrorLog, Exceptions, Files, HTML, HTML_OPTIONS, Taxa, Taxon };

package/lib/pagetaxon.js

@@ -20,27 +20,17 @@ class PageTaxon extends HTMLPage {
         if ( jepsonID ) {
             links.push( Jepson.getEFloraLink( jepsonID ) );
         }
-        const calRecNum = this.#taxon.getCalfloraID();
-        if ( calRecNum ) {
-            links.push(
-                HTML.getLink(
-                    "https://www.calflora.org/app/taxon?crn=" + calRecNum,
-                    "Calflora",
-                    {},
-                    HTML_OPTIONS.OPEN_NEW
-                )
-            );
+        const cfLink = this.#taxon.getCalfloraTaxonLink();
+        if ( cfLink ) {
+            links.push( cfLink );
         }
-        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 );
+        }
+        const rpiLink = this.#taxon.getRPITaxonLink();
+        if ( rpiLink ) {
+            links.push( rpiLink );
         }
         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

@@ -1,5 +1,4 @@
 import { Config } from "./config.js";
-import { ErrorLog } from "./errorlog.js";
 import { Genera } from "./genera.js";
 import { HTML, HTML_OPTIONS } from "./html.js";
 import { RarePlants } from "./rareplants.js";
@@ -12,13 +11,15 @@ 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() ) : [];
@@ -26,33 +27,50 @@ class Taxon {
         this.#jepsonID = jepsonID;
         this.#calRecNum = calRecNum;
         this.#iNatID = iNatID;
+        this.#rpiID = rpiID;
         this.#rankRPI = rankRPI;
         this.#cesa = cesa;
         Genera.addTaxon( this );
-        if ( !calRecNum ) {
-            ErrorLog.log( this.getName(), "has no Calflora ID" );
-        }
-        if ( !iNatID ) {
-            ErrorLog.log( this.getName(), "has no iNat ID" );
-        }
     }
 
     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() {
         return this.#calRecNum;
     }
 
+    getCalfloraTaxonLink() {
+        const calfloraID = this.getCalfloraID();
+        if ( !calfloraID ) {
+            return;
+        }
+        return HTML.getLink(
+            "https://www.calflora.org/app/taxon?crn=" + calfloraID,
+            "Calflora",
+            {},
+            HTML_OPTIONS.OPEN_NEW
+        );
+    }
+
     getCESA() {
         return this.#cesa;
     }
@@ -65,9 +83,13 @@ 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 +119,15 @@ 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 +136,10 @@ class Taxon {
         return this.#name;
     }
 
+    getRPIID() {
+        return this.#rpiID;
+    }
+
     getRPIRank() {
         if ( !this.#rankRPI ) {
             return this.#rankRPI;
@@ -116,6 +151,15 @@ class Taxon {
         return this.#rankRPI;
     }
 
+    getRPITaxonLink() {
+        const rpiID = this.getRPIID();
+        if ( !rpiID ) {
+            return "";
+        }
+        const link = HTML.getLink( "https://rareplants.cnps.org/Plants/Details/" + rpiID, "CNPS Rare Plant Inventory", {}, HTML_OPTIONS.OPEN_NEW );
+        return link;
+    }
+
     getStatus() {
         return this.#status;
     }
@@ -136,6 +180,10 @@ class Taxon {
         return this.#synonyms;
     }
 
+    isCANative() {
+        return this.#status === "N" || this.#status === "NC";
+    }
+
     isNative() {
         return this.#status === "N";
     }

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.1.3",
+    "version": "0.1.5",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {
@@ -10,22 +10,7 @@
     "homepage": "https://github.com/ca-plants/ca-plant-list",
     "type": "module",
     "exports": {
-        ".": "./lib/index.js",
-        "./CSV": {
-            "import": "./lib/csv.js"
-        },
-        "./DataLoader": {
-            "import": "./lib/dataloader.js"
-        },
-        "./Exceptions": {
-            "import": "./lib/exceptions.js"
-        },
-        "./Files": {
-            "import": "./lib/files.js"
-        },
-        "./Taxa": {
-            "import": "./lib/taxa.js"
-        }
+        ".": "./lib/index.js"
     },
     "bin": {
         "ca-plant-list": "build-site.js"