@ca-plant-list/ca-plant-list 0.1.22 → 0.2.0

package/lib/dataloader.js

@@ -1,6 +1,8 @@
+import { CSV } from "./csv.js";
 import { Taxa } from "./taxa.js";
 import { Families } from "./families.js";
 import { Exceptions } from "./exceptions.js";
+import { Files } from "./files.js";
 
 const OPTION_DEFS = [
     { name: "datadir", type: String, defaultValue: "./data" },
@@ -19,12 +21,28 @@ class DataLoader {
 
     static load( options ) {
 
+        function getIncludeList() {
+            // Read inclusion list.
+            const includeFileName = "taxa_include.csv";
+            if ( !Files.exists( taxaDir + "/" + includeFileName ) ) {
+                console.log( includeFileName + " not found; loading all taxa" );
+                return true;
+            }
+            const includeCSV = CSV.parseFile( taxaDir, includeFileName );
+            const include = {};
+            for ( const row of includeCSV ) {
+                include[ row[ "taxon_name" ] ] = row;
+            }
+            return include;
+        }
+
         const taxaDir = options.datadir;
 
         console.log( "loading data" );
 
         this.init( taxaDir );
-        Taxa.init( taxaDir );
+
+        Taxa.init( getIncludeList() );
 
     }
 

package/lib/files.js

@@ -43,6 +43,10 @@ class Files {
         return response.headers;
     }
 
+    static getDirEntries( path ) {
+        return fs.readdirSync( path );
+    }
+
     static mkdir( path ) {
         fs.mkdirSync( path, { recursive: true } );
     }

package/lib/genera.js

@@ -53,7 +53,7 @@ class Genus {
     }
 
     getTaxa() {
-        return this.#data.taxa;
+        return this.#data.taxa.sort( ( a, b ) => a.getName().localeCompare( b.getName() ) );
     }
 }
 

package/lib/html.js

@@ -41,8 +41,11 @@ export class HTML {
         if ( escape && ( typeof text === "string" ) ) {
             text = this.escapeText( text );
         }
-        html += ">" + text + "</" + elName + ">";
-        return html;
+        // If tag is empty, make it self-closing so it is XHTML (epub) compatible.
+        if ( text === "" ) {
+            return html + "/>";
+        }
+        return html + ">" + text + "</" + elName + ">";
     }
 
     /**

package/lib/index.d.ts

@@ -1,3 +1,50 @@
+export class BasePageRenderer {
+    static render(outputDir: any, Taxa: any, familyCols: any): void;
+    static renderTools(outputDir: any, Taxa: any): void;
+}
+export class Config {
+    static "__#1@#config": {};
+    static "__#1@#packageDir": string;
+    static getConfigValue(prefix: any, name: any, subcat: any, dflt: any): any;
+    static getCountyCodes(): any;
+    static getLabel(name: any, dflt: any): any;
+    static getPackageDir(): string;
+}
+export class CSV {
+    static getMap(dir: any, fileName: any): {};
+    static "__#8@#getOptions"(fileName: any, columns: any, delimiter: any): {
+        relax_column_count_less: boolean;
+    };
+    static parseFile(dir: any, fileName: any, columns: boolean, delimiter: any): any;
+    static parseStream(dir: any, fileName: any, columns: boolean, delimiter: any, callback: any): Promise<void>;
+}
+export class DataLoader {
+    static getOptionDefs(): {
+        name: string;
+        type: StringConstructor;
+        defaultValue: string;
+    }[];
+    static init(taxaDir: any): void;
+    static load(options: any): void;
+}
+export class ErrorLog {
+    static "__#7@#errors": any[];
+    static log(...args: any[]): void;
+    static write(fileName: any): void;
+}
+export class Exceptions {
+    static "__#16@#exceptions": {};
+    static getExceptions(): [string, any][];
+    static getValue(name: any, cat: any, subcat: any, defaultValue: any): any;
+    static hasException(name: any, cat: any, subcat: any): boolean;
+    static init(dir: any): void;
+}
+export class Families {
+    static "__#10@#families": any;
+    static getFamily(familyName: any): any;
+    static init(): void;
+    static renderPages(outputDir: any, taxaColumns: any): void;
+}
 export class Files {
     static copyDir(srcDir: any, targetDir: any): void;
     static createFileFromStream(fileName: any, inStream: any): Promise<any>;
@@ -10,12 +57,35 @@ export class Files {
      * @returns {Promise<Headers>} The Response headers.
      */
     static fetch(url: string | URL, targetFileName: string | undefined, headers?: any): Promise<Headers>;
+    static getDirEntries(path: any): string[];
     static mkdir(path: any): void;
     static read(path: any): string;
     static rmDir(dir: any): void;
     static write(path: any, data: any, overwrite?: boolean): void;
     static zipFileExtract(zipFilePath: any, fileNameToUnzip: any, targetFilePath: any): Promise<void>;
 }
+export class Genera {
+    static "__#4@#genera": any;
+    static addTaxon(taxon: any): void;
+    static getGenus(genusName: any): Genus;
+    static getFamily(genusName: any): any;
+    static init(dataDir: any): void;
+}
+declare class Genus {
+    constructor(data: any);
+    getTaxa(): any;
+    #private;
+}
+export {};
+export class GenericPage {
+    constructor(outputDir: any, title: any, baseFileName: any, js: any);
+    getBaseFileName(): any;
+    getDefaultIntro(): string;
+    getOutputDir(): any;
+    getTitle(): any;
+    writeFile(html: any): void;
+    #private;
+}
 export namespace HTML_OPTIONS {
     const OPEN_NEW: number;
     const NO_ESCAPE: number;
@@ -55,8 +125,127 @@ export class HTML {
     static textElement(elName: any, text: any, attributes?: {}): string;
     static wrap(elName: any, text: any, attributes?: {}): string;
 }
+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 { Families } from "./families.js";
+import { Files } from "./files.js";
+import { HTML } from "./html.js";
+import { Jekyll } from "./jekyll.js";
+import { Taxa } from "./taxa.js";
+import { TAXA_COLNAMES } from "./taxon.js";
+import { Taxon } from "./taxon.js";
+export { BasePageRenderer, Config, CSV, DataLoader, ErrorLog, Exceptions, Families, Files, HTML, Jekyll, Taxa, TAXA_COLNAMES, Taxon };
 export class Jekyll {
     static hasInclude(baseDir: any, path: any): boolean;
     static include(path: any): string;
     static writeInclude(baseDir: any, path: any, data: any): void;
 }
+export class Jepson {
+    static getEFloraLink(id: any): string;
+}
+export class RarePlants {
+    static getCESADescription(cesa: any): any;
+    static getFESADescription(fesa: any): any;
+    static getRPIRankDescription(rank: any): any;
+    static getRPIRankAndThreatDescriptions(rank: any): any[];
+}
+export class Taxa {
+    static "__#9@#taxa": {};
+    static "__#9@#sortedTaxa": any;
+    static getHTMLTable(taxa: any, columns?: {
+        title: string;
+        data: (t: any) => any;
+    }[]): string;
+    static getTaxa(): any;
+    static getTaxon(name: any): any;
+    static init(inclusionList: any, taxaMeta?: {}, taxonClass?: typeof Taxon, extraTaxa?: any[], extraSynonyms?: any[]): void;
+    static "__#9@#loadSyns"(synCSV: any, inclusionList: any): void;
+    static "__#9@#loadTaxa"(taxaCSV: any, inclusionList: any, taxaMeta: any, taxonClass: any): void;
+}
+export namespace TAXA_LIST_COLS {
+    namespace CESA {
+        const title: string;
+        function data(t: any): any;
+    }
+    namespace COMMON_NAME {
+        const title_1: string;
+        export { title_1 as title };
+        export function data_1(t: any): any;
+        export { data_1 as data };
+    }
+    namespace CNPS_RANK {
+        const title_2: string;
+        export { title_2 as title };
+        export function data_2(t: any): string;
+        export { data_2 as data };
+    }
+    namespace FESA {
+        const title_3: string;
+        export { title_3 as title };
+        export function data_3(t: any): any;
+        export { data_3 as data };
+    }
+    namespace SPECIES {
+        const title_4: string;
+        export { title_4 as title };
+        export function data_4(t: any): any;
+        export { data_4 as data };
+    }
+    namespace SPECIES_BARE {
+        const title_5: string;
+        export { title_5 as title };
+        export function data_5(t: any): any;
+        export { data_5 as data };
+    }
+}
+import { Taxon } from "./taxon.js";
+export namespace TAXA_COLNAMES {
+    const COMMON_NAME: string;
+}
+export class Taxon {
+    constructor(data: any);
+    addSynonym(syn: any, type: any): void;
+    getBaseFileName(): any;
+    getCalfloraName(): any;
+    getCalfloraID(): any;
+    getCalfloraTaxonLink(): string;
+    getCESA(): any;
+    getCNDDBRank(): any;
+    getCommonNames(): any;
+    getFamily(): any;
+    getFESA(): any;
+    getFileName(ext?: string): string;
+    getGenus(): {
+        "__#5@#data": any;
+        getTaxa(): any;
+    };
+    getGenusName(): any;
+    getGlobalRank(): any;
+    getHTMLLink(href?: boolean, includeRPI?: boolean): string;
+    getINatID(): any;
+    getINatName(): any;
+    getINatSyn(): any;
+    getINatTaxonLink(): string;
+    getJepsonID(): any;
+    getName(): any;
+    getRPIID(): any;
+    getRPIRank(): any;
+    getRPIRankAndThreat(): any;
+    getRPIRankAndThreatTooltip(): string;
+    getRPITaxonLink(): string;
+    getStatus(): any;
+    getStatusDescription(): any;
+    getSynonyms(): any[];
+    isCANative(): boolean;
+    /**
+     * 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(): boolean;
+    isRare(): boolean;
+    #private;
+}

package/lib/index.js

@@ -6,9 +6,9 @@ import { ErrorLog } from "./errorlog.js";
 import { Exceptions } from "./exceptions.js";
 import { Families } from "./families.js";
 import { Files } from "./files.js";
-import { HTML, HTML_OPTIONS } from "./html.js";
+import { HTML } from "./html.js";
 import { Jekyll } from "./jekyll.js";
 import { Taxa } from "./taxa.js";
-import { Taxon } from "./taxon.js";
+import { Taxon, TAXA_COLNAMES } from "./taxon.js";
 
-export { BasePageRenderer, Config, CSV, DataLoader, ErrorLog, Exceptions, Families, Files, HTML, HTML_OPTIONS, Jekyll, Taxa, Taxon };
+export { BasePageRenderer, Config, CSV, DataLoader, ErrorLog, Exceptions, Families, Files, HTML, Jekyll, Taxa, TAXA_COLNAMES, Taxon };

package/lib/taxa.js

@@ -1,9 +1,9 @@
+import { Config } from "./config.js";
 import { Taxon } from "./taxon.js";
 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: {
@@ -75,57 +75,72 @@ class Taxa {
         return this.#taxa[ name ];
     }
 
-    static init( dataDir ) {
+    static init( inclusionList, taxaMeta = {}, taxonClass = Taxon, extraTaxa = [], extraSynonyms = [] ) {
+
+        const dataDir = Config.getPackageDir() + "/data";
+
         const taxaCSV = CSV.parseFile( dataDir, "taxa.csv" );
-        for ( const row of taxaCSV ) {
-            const name = row[ "taxon" ];
-            const status = row[ "status" ];
-            const jepsonID = row[ "jepson id" ];
-            switch ( status ) {
-                case "N":
-                case "NC":
-                case "X": {
-                    if ( this.#taxa[ name ] ) {
-                        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" ],
-                        row[ "RPI ID" ],
-                        row[ "CRPR" ],
-                        row[ "CESA" ],
-                        row[ "FESA" ]
-                    );
-                    if ( !jepsonID && !Exceptions.hasException( name, "jepson", "badjepsonid" ) ) {
-                        ErrorLog.log( name, "has no Jepson ID" );
-                    }
-                    break;
-                }
-                default:
-                    ErrorLog.log( name, "has unrecognized status", status );
+        this.#loadTaxa( taxaCSV, inclusionList, taxaMeta, taxonClass );
+        this.#loadTaxa( extraTaxa, inclusionList, taxaMeta, taxonClass );
+
+        // Make sure everything in the inclusionList has been loaded.
+        for ( const name of Object.keys( inclusionList ) ) {
+            if ( !this.getTaxon( name ) ) {
+                ErrorLog.log( name, "not found in taxon list" );
             }
         }
 
         this.#sortedTaxa = Object.values( this.#taxa ).sort( ( a, b ) => a.getName().localeCompare( b.getName() ) );
 
         const synCSV = CSV.parseFile( dataDir, "synonyms.csv" );
+        this.#loadSyns( synCSV, inclusionList );
+        this.#loadSyns( extraSynonyms, inclusionList );
+
+    }
+
+    static #loadSyns( synCSV, inclusionList ) {
         for ( const syn of synCSV ) {
             const currName = syn[ "Current" ];
             const taxon = this.getTaxon( currName );
             if ( !taxon ) {
-                ErrorLog.log( currName, "has synonym but not in taxa.csv" );
+                if ( inclusionList === true ) {
+                    // If including all taxa, note the error.
+                    console.log( "synonym target not found: " + currName );
+                }
                 continue;
             }
             taxon.addSynonym( syn[ "Former" ], syn[ "Type" ] );
         }
+    }
+
+    static #loadTaxa( taxaCSV, inclusionList, taxaMeta, taxonClass ) {
+        for ( const row of taxaCSV ) {
+
+            const name = row[ "taxon_name" ];
+
+            let taxon_overrides = {};
+            if ( inclusionList !== true ) {
+                taxon_overrides = inclusionList[ name ];
+                if ( !taxon_overrides ) {
+                    continue;
+                }
+            }
+
+            if ( this.#taxa[ name ] ) {
+                ErrorLog.log( name, "has multiple entries" );
+            }
+
+            const status = taxon_overrides[ "status" ];
+            if ( status !== undefined ) {
+                row[ "status" ] = status;
+            }
+            this.#taxa[ name ] = new taxonClass( row, taxaMeta[ name ] );
+
+        }
 
     }
 
+
 }
 
 export { Taxa, TAXA_LIST_COLS };

package/lib/taxon.js

@@ -3,6 +3,10 @@ import { Genera } from "./genera.js";
 import { HTML } from "./html.js";
 import { RarePlants } from "./rareplants.js";
 
+const TAXA_COLNAMES = {
+    COMMON_NAME: "common name"
+};
+
 class Taxon {
 
     #name;
@@ -22,16 +26,22 @@ class Taxon {
     #rankGlobal;
     #synonyms = [];
 
-    constructor( name, commonNames, status, jepsonID, calRecNum, iNatID, rpiID, rankRPI, cesa, fesa, rankCNDDB, rankGlobal ) {
+    constructor( data ) {
+        const name = data[ "taxon_name" ];
+        const commonNames = data[ TAXA_COLNAMES.COMMON_NAME ];
+        const cesa = data[ "CESA" ];
+        const fesa = data[ "FESA" ];
+        const rankGlobal = data[ "GRank" ];
+        const rankCNDDB = data[ "SRank" ];
         this.#name = name;
         this.#genus = name.split( " " )[ 0 ];
         this.#commonNames = commonNames ? commonNames.split( "," ).map( t => t.trim() ) : [];
-        this.#status = status;
-        this.#jepsonID = jepsonID;
-        this.#calRecNum = calRecNum;
-        this.#iNatID = iNatID;
-        this.#rpiID = rpiID;
-        this.#rankRPI = rankRPI;
+        this.#status = data[ "status" ];
+        this.#jepsonID = data[ "jepson id" ];
+        this.#calRecNum = data[ "calrecnum" ];
+        this.#iNatID = data[ "inat id" ];
+        this.#rpiID = data[ "RPI ID" ];
+        this.#rankRPI = data[ "CRPR" ];
         this.#cesa = cesa ? cesa : undefined;
         this.#fesa = fesa ? fesa : undefined;
         this.#rankCNDDB = rankCNDDB ? rankCNDDB : undefined;
@@ -224,4 +234,4 @@ class Taxon {
 
 }
 
-export { Taxon };
+export { TAXA_COLNAMES, Taxon };

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.1.22",
+    "version": "0.2.0",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {
@@ -18,9 +18,10 @@
     },
     "types": "./lib/index.d.ts",
     "bin": {
-        "ca-plant-list": "build-site.js"
+        "ca-plant-list": "scripts/build-site.js"
     },
     "dependencies": {
+        "@ca-plant-list/tools": "file:../ca-tools",
         "command-line-args": "^5.2.1",
         "command-line-usage": "^6.1.3",
         "csv-parse": "^5.3.1",

package/{build-site.js → scripts/build-site.js}

@@ -1,8 +1,8 @@
 #!/usr/bin/env node
 
-import { DataLoader } from "./lib/dataloader.js";
-import { ErrorLog } from "./lib/errorlog.js";
-import { PageRenderer } from "./lib/pagerenderer.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 options = commandLineArgs( DataLoader.getOptionDefs() );

package/tsconfig.json

@@ -1,14 +0,0 @@
-{
-    // Change this to match your project
-    "files": [
-        "lib/index.js",
-    ],
-    "compilerOptions": {
-        "allowJs": true,
-        "declaration": true,
-        "emitDeclarationOnly": true,
-        "outDir": "output",
-        "module": "es6",
-        "newLine": "lf"
-    }
-}