@ca-plant-list/ca-plant-list 0.4.23 → 0.4.26

package/data/taxa.csv

@@ -720,11 +720,11 @@ Eriophyllum confertiflorum var. confertiflorum,golden-yarrow,N,69866,3423,53397,
 Eriophyllum jepsonii,Jepson's woolly-sunflower,N,2816,3426,77048,203742,true,Jepson's Woolly Sunflower,,,,,776,4.3,,,S3,G3
 Eriophyllum lanatum var. achilleoides,,N,7369,10587,80880,260847,true,Common Woollysunflower
 Eriophyllum staechadifolium,seaside woolly-sunflower,N,2825,3444,60963,203755,true,Seaside Woolly Sunflower
-Erodium botrys,long-beaked filaree,X,25037,3446,57090,17986,,,,pink,3,7
-Erodium brachycarpum,,X,25038,3447,58171,17987
-Erodium cicutarium,red-stemmed filaree,X,25041,3448,47687,17989
+Erodium botrys,long-beaked filaree,X,25037,3446,57090,17986,,,annual,pink,3,7
+Erodium brachycarpum,,X,25038,3447,58171,17987,,,annual,pink,3,7
+Erodium cicutarium,red-stemmed filaree,X,25041,3448,47687,17989,,,annual,pink,3,9
 Erodium malacoides,,X,76818,3451,77056,17994
-Erodium moschatum,white-stem filaree,X,25048,3452,57092,17995
+Erodium moschatum,white-stem filaree,X,25048,3452,57092,17995,,,"annual,biennial",pink,2,9
 Eryngium aristulatum var. aristulatum,coyote-thistle,N,58845,3458,64189,211707,,California Eryngo
 Eryngium aristulatum var. hooveri,,N,58846,3459,57904,203761,,Hoover's Button-celery,,,,,783,1B.1,,,S1,G5T1
 Eryngium aristulatum,Jepson's button celery,N,25070,3457,57901,203759,,Jepson's Button Celery
@@ -1599,7 +1599,7 @@ Salix exigua var. hindsiana,Hind's willow,N,81242,11063,64195,51553,true,Sandbar
 Salix gooddingii,Goodding's black willow,N,42825,7272,60240,31274,true,Goodding's Black Willow
 Salix laevigata,red willow,N,42850,7276,58319,31302,true,Red Willow
 Salix lasiandra var. lasiandra,Pacific willow,N,76043,11065,81358,51640,true,Yellow Willow
-Salix lasiolepis,arroyo willow,N,42855,7277,53452,31307,true,Arroyo Willow
+Salix lasiolepis,arroyo willow,N,42855,7277,53452,31307,true,Arroyo Willow,perennial,,1,6
 Salix melanopsis,dusky willow,N,42881,7284,78947,31332,true,Dusky Willow
 Salix scouleriana,Scouler's willow,N,42973,7289,71076,31425,true,Scouler's Willow
 Salix sitchensis,Sitka willow,N,42994,7291,61100,31435,true,Sitka Willow
@@ -1676,7 +1676,7 @@ Silene lemmonii,Lemmon's catchfly,N,44533,7603,60523,119295,true,Lemmon's Catchf
 Silene sargentii,Sargent's catchfly,N,44566,7614,62697,119340,true,Sargent's Catchfly,perennial,white,7,8
 Silene verecunda,,N,44589,7617,60581,119364,true,San Francisco Campion
 Silybum marianum,milk-thistle,X,4918,7622,52586,205950,true
-Sinapis arvensis,charlock,X,44609,7625,1562069,32232,true
+Sinapis arvensis,charlock,X,44609,7625,1562069,32232,true,,annual,yellow,3,10
 Sisymbrium irio,London rocket,X,44651,7628,58085,32256,true
 Sisymbrium officinale,hedge mustard,X,44653,7630,53266,32267,true
 Sisymbrium orientale,,X,44654,7631,58086,32268,true

package/data/text/Erodium-botrys.footer.md

@@ -0,0 +1,3 @@
+## Resources
+
+- [How to identify Erodium botrys](https://www.inaturalist.org/projects/erodium-botrys-mediterranean-stork-s-bill/journal/61038-how-to-identify-erodium-botrys-mediterranean-stork-s-bill) iNaturalist journal post

package/data/text/Erodium-botrys.md

@@ -0,0 +1 @@
+Petals with purple streaks.

package/data/text/Erodium-brachycarpum.footer.md

@@ -0,0 +1,3 @@
+## Resources
+
+- [How to identify Erodium brachycarpum](https://www.inaturalist.org/projects/erodium-brachycarpum-hairy-pitted-stork-s-bill/journal/61042-how-to-identify-erodium-brachycarpum-hairy-pitted-stork-s-bill) iNaturalist journal post

package/data/text/Erodium-brachycarpum.md

@@ -0,0 +1 @@
+Petals with purple streaks.

package/data/text/Erodium-cicutarium.md

@@ -0,0 +1 @@
+Petals not streaked. Leaf compound, fern-like. Bristles on sepals.

package/data/text/Erodium-moschatum.footer.md

@@ -0,0 +1,3 @@
+## Resources
+
+- [How to identify Erodium moschatum](https://www.inaturalist.org/projects/erodium-moschatum-musk-stork-s-bill/journal/61039-how-to-identify-erodium-moschatum-musk-stork-s-bill) iNaturalist journal post

package/data/text/Erodium-moschatum.md

@@ -0,0 +1 @@
+Petals not streaked, except near base. Leaves compound but not fern-like. No bristles on sepals.

package/jekyll/assets/js/name_search.js

@@ -1,141 +1,173 @@
 import { Utils } from "./utils.js";
 
+/**
+ * @typedef {[string]|[string,string]|[string,string|undefined,string[]]} RawSearchData
+ * @typedef {{raw:RawSearchData,searchSci:string,searchCommon?:string,synonyms?:string[]}} SearchData
+ */
+
 const MIN_LEN = 2;
 const MAX_RESULTS = 50;
 
 class Search {
-
+    /** @type {number|undefined} */
     static #debounceTimer;
+    /** @type {SearchData[]} */
     static #searchData;
 
-    static #debounce( timeout = 500 ) {
-        clearTimeout( this.#debounceTimer );
-        this.#debounceTimer = setTimeout( Search.#doSearch, timeout );
+    /**
+     * @param {number} [timeout]
+     */
+    static #debounce(timeout = 500) {
+        clearTimeout(this.#debounceTimer);
+        this.#debounceTimer = window.setTimeout(Search.#doSearch, timeout);
     }
 
     static #doSearch() {
-
-        function matchTaxon( taxon, value ) {
-
-            function matchSynonyms( syns, value ) {
+        /**
+         * @param {SearchData} taxon
+         * @param {string} value
+         */
+        function matchTaxon(taxon, value) {
+            /**
+             * @param {string[]|undefined} syns
+             * @param {string} value
+             * @returns {number[]}
+             */
+            function matchSynonyms(syns, value) {
                 const matchedIndexes = [];
-                if ( syns ) {
-                    for ( let index = 0; index < syns.length; index++ ) {
-                        if ( syns[ index ].includes( value ) ) {
-                            matchedIndexes.push( index );
+                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 ) {
+            const name = taxon.searchSci;
+            const cn = taxon.searchCommon;
+            const syns = matchSynonyms(taxon.synonyms, value);
+            if (syns.length > 0) {
                 // Include any matching synonyms.
-                for ( const index of syns ) {
-                    matches.push( [ rawData[ 0 ], rawData[ 1 ], rawData[ 2 ][ index ] ] );
+                for (const index of syns) {
+                    matches.push([
+                        taxon.raw[0],
+                        taxon.raw[1],
+                        taxon.raw[2] ? taxon.raw[2][index] : undefined,
+                    ]);
                 }
             } 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 ] ] );
+                const namesMatch =
+                    name.includes(value) || (cn && cn.includes(value));
+                if (namesMatch) {
+                    matches.push([taxon.raw[0], taxon.raw[1]]);
                 }
             }
-
         }
 
         Search.#debounceTimer = undefined;
 
-        const value = Search.#normalizeName( document.getElementById( "name" ).value );
+        const input = Utils.getElement("name");
+        if (!(input instanceof HTMLInputElement)) {
+            throw new Error();
+        }
+        const value = Search.#normalizeName(input.value);
 
+        /**
+         * @type {([string,string|undefined]|[string,string|undefined,string|undefined])[]}
+         */
         const matches = [];
-        const shouldSearch = ( value.length >= MIN_LEN );
-
-        if ( shouldSearch ) {
+        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 );
+            if (!Search.#searchData) {
+                this.#debounce();
             }
 
-            for ( const taxon of Search.#searchData ) {
-                matchTaxon( taxon, value );
+            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" );
+        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 = Utils.domTaxonLink( name );
-                td1.appendChild( link );
-                if ( syn ) {
-                    td1.appendChild( document.createTextNode( " (" + syn + ")" ) );
+                const name = match[0];
+                const syn = match[2];
+                const td1 = document.createElement("td");
+                const link = Utils.domTaxonLink(name);
+                td1.appendChild(link);
+                if (syn) {
+                    td1.appendChild(document.createTextNode(" (" + syn + ")"));
                 }
-                tr.appendChild( td1 );
+                tr.appendChild(td1);
 
-                const cn = match[ 1 ];
-                const td2 = document.createElement( "td" );
-                if ( cn ) {
+                const cn = match[1];
+                const td2 = document.createElement("td");
+                if (cn) {
                     td2.textContent = cn;
                 }
-                tr.appendChild( td2 );
-
-                eBody.appendChild( tr );
+                tr.appendChild(td2);
 
+                eBody.appendChild(tr);
             }
         }
 
         // Delete current message
-        const eMessage = document.getElementById( "message" );
-        if ( eMessage.firstChild ) {
-            eMessage.removeChild( eMessage.firstChild );
+        const eMessage = Utils.getElement("message");
+        if (eMessage.firstChild) {
+            eMessage.removeChild(eMessage.firstChild);
         }
-        if ( shouldSearch ) {
-            if ( matches.length === 0 ) {
+        if (shouldSearch) {
+            if (matches.length === 0) {
                 eMessage.textContent = "Nothing found.";
             }
-            if ( matches.length > MAX_RESULTS ) {
+            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 );
+        const eTable = Utils.getElement("results");
+        if (eTable.firstChild) {
+            eTable.removeChild(eTable.firstChild);
         }
 
-        eTable.appendChild( eBody );
+        eTable.appendChild(eBody);
     }
 
     static async generateSearchData() {
+        /** @type {SearchData[]} */
         const searchData = [];
+
+        /** @type {RawSearchData[]} */
+        // @ts-ignore
         // eslint-disable-next-line no-undef
-        for ( const taxon of NAMES ) {
-            const taxonData = [ taxon ];
-            taxonData.push( this.#normalizeName( taxon[ 0 ] ) );
-            if ( taxon[ 1 ] ) {
-                taxonData.push( taxon[ 1 ].toLowerCase() );
+        const names = NAMES;
+
+        for (const taxon of names) {
+            /** @type {SearchData} */
+            const taxonData = {
+                raw: taxon,
+                searchSci: this.#normalizeName(taxon[0]),
+            };
+            if (taxon[1]) {
+                taxonData.searchCommon = taxon[1].toLowerCase();
             }
-            if ( taxon[ 2 ] ) {
+            if (taxon[2]) {
                 const syns = [];
-                for ( const syn of taxon[ 2 ] ) {
-                    syns.push( this.#normalizeName( syn ) );
+                for (const syn of taxon[2]) {
+                    syns.push(this.#normalizeName(syn));
                 }
-                taxonData[ 3 ] = syns;
+                taxonData.synonyms = syns;
             }
-            searchData.push( taxonData );
+            searchData.push(taxonData);
         }
         this.#searchData = searchData;
     }
@@ -145,21 +177,29 @@ class Search {
     }
 
     static #handleSubmit() {
-        this.#debounce( 0 );
+        this.#debounce(0);
     }
 
     static init() {
         this.generateSearchData();
-        const eName = document.getElementById( "name" );
+        const eName = Utils.getElement("name");
         eName.focus();
-        eName.oninput = ( ev ) => { return this.#handleChange( ev ); };
-        document.getElementById( "search_form" ).onsubmit = () => { this.#handleSubmit(); return false; };
+        eName.oninput = () => {
+            return this.#handleChange();
+        };
+        Utils.getElement("search_form").onsubmit = () => {
+            this.#handleSubmit();
+            return false;
+        };
     }
 
-    static #normalizeName( name ) {
-        return name.toLowerCase().replace( / (subsp|var)\./, "" );
+    /**
+     * @param {string} name
+     * @returns {string}
+     */
+    static #normalizeName(name) {
+        return name.toLowerCase().replace(/ (subsp|var)\./, "");
     }
-
 }
 
-Search.init();
+Search.init();

package/jekyll/assets/js/ui.js

@@ -1,10 +1,11 @@
 class UI {
-
     static init() {
-        const tooltips = document.querySelectorAll( "span[title]" );
-        [ ...tooltips ].map( tooltipTriggerEl => new bootstrap.Tooltip( tooltipTriggerEl ) );
+        const tooltips = document.querySelectorAll("span[title]");
+        [...tooltips].map(
+            // @ts-ignore
+            (tooltipTriggerEl) => new bootstrap.Tooltip(tooltipTriggerEl),
+        );
     }
-
 }
 
 UI.init();

package/jekyll/assets/js/utils.js

@@ -1,26 +1,56 @@
-class Utils {
-
-    static domElement( name, attributes = {}, content ) {
-        const e = document.createElement( name );
-        for ( const [ k, v ] of Object.entries( attributes ) ) {
-            e.setAttribute( k, v );
+export class Utils {
+    /**
+     * @param {string} name
+     * @param {Object<string,string>} attributes
+     * @param {string} [content]
+     * @returns {Element}
+     */
+    static domElement(name, attributes = {}, content) {
+        const e = document.createElement(name);
+        for (const [k, v] of Object.entries(attributes)) {
+            e.setAttribute(k, v);
         }
-        if ( content ) {
+        if (content) {
             e.textContent = content;
         }
         return e;
     }
 
-    static domLink( href, text, attributes = {} ) {
-        const e = this.domElement( "a", Object.assign( { href: href }, attributes ) );
+    /**
+     * @param {string} href
+     * @param {string} text
+     * @param {Object<string,string>} attributes
+     * @returns {Element}
+     */
+    static domLink(href, text, attributes = {}) {
+        const e = this.domElement(
+            "a",
+            Object.assign({ href: href }, attributes),
+        );
         e.textContent = text;
         return e;
     }
 
-    static domTaxonLink( name ) {
-        return this.domLink( "./" + name.replaceAll( ".", "" ).replaceAll( " ", "-" ) + ".html", name );
+    /**
+     * @param {string} name
+     * @returns {Element}
+     */
+    static domTaxonLink(name) {
+        return this.domLink(
+            "./" + name.replaceAll(".", "").replaceAll(" ", "-") + ".html",
+            name,
+        );
     }
 
+    /**
+     * @param {string} id
+     * @returns {HTMLElement}
+     */
+    static getElement(id) {
+        const e = document.getElementById(id);
+        if (e === null) {
+            throw new Error();
+        }
+        return e;
+    }
 }
-
-export { Utils };

package/lib/basepagerenderer.js

@@ -4,7 +4,7 @@ import { Jekyll } from "./jekyll.js";
 import { GlossaryPages } from "./web/glossarypages.js";
 import { PageFamilyList } from "./web/pageFamily.js";
 
-class BasePageRenderer {
+export class BasePageRenderer {
     /**
      * @param {string} outputDir
      * @param {import("./types.js").Taxa} taxa
@@ -60,5 +60,3 @@ class BasePageRenderer {
         Files.write(outputDir + "/_includes/names.json", JSON.stringify(names));
     }
 }
-
-export { BasePageRenderer };

package/lib/index.d.ts

@@ -46,6 +46,10 @@ export type TaxonData = TaxonomyData & {
     taxon_name: string;
 };
 
+export type TaxonOverrides = {
+    status?: NativeStatusCode;
+};
+
 // Classes
 
 export class BasePageRenderer {
@@ -73,6 +77,11 @@ export class CSV {
         fileName: string,
         delimeter?: string,
     ): Record<string, string>[];
+    static writeFileObject(
+        fileName: string,
+        data: Record<string, any>[],
+        headerData: string[],
+    ): void;
 }
 
 export class ErrorLog {
@@ -104,6 +113,7 @@ export class Files {
         targetFileName: string | undefined,
     ): Promise<Headers>;
     static mkdir(dir: string): void;
+    static read(path: string): string;
     static rmDir(dir: string): void;
     static write(fileName: string, data: string, overwrite?: boolean): void;
 }
@@ -170,6 +180,7 @@ export class HTMLTaxon {
 export class Jekyll {
     static hasInclude(baseDir: string, path: string): boolean;
     static include(fileName: string): string;
+    static writeInclude(baseDir: string, path: string, data: string): void;
 }
 
 export class Photo {
@@ -187,11 +198,11 @@ export class Program {
 
 export class Taxa<T> {
     constructor(
-        inclusionList: Record<string, TaxonData> | true,
+        inclusionList: Record<string, TaxonOverrides> | true,
         errorLog: ErrorLog,
         showFlowerErrors: boolean,
         taxonFactory?: (td: TaxonData, g: Genera) => T,
-        extraTaxa?: TaxonData[],
+        extraTaxa?: TaxonOverrides[],
         extraSynonyms?: Record<string, string>[],
     );
     getTaxon(name: string): T;

package/lib/pagerenderer.js

@@ -184,9 +184,7 @@ class PageRenderer extends BasePageRenderer {
                     {
                         name: "Endangered Species",
                         filename: "list_endangered",
-                        include: (t) =>
-                            t.getCESA() !== undefined ||
-                            t.getFESA() !== undefined,
+                        include: (t) => !!t.getCESA() || !!t.getFESA(),
                         columns: ENDANGERED_COLS,
                     },
                 ],

package/lib/taxonomy/taxa.js

@@ -40,7 +40,7 @@ class Taxa {
     #isSubset;
 
     /**
-     * @param {Object<string,import("../index.js").TaxonData>|true} inclusionList
+     * @param {Object<string,import("../index.js").TaxonOverrides>|true} inclusionList
      * @param {ErrorLog} errorLog
      * @param {boolean} showFlowerErrors
      * @param {function(import("../index.js").TaxonData,Genera):Taxon} taxonFactory
@@ -224,7 +224,7 @@ class Taxa {
 
     /**
      * @param {SynonymData[]} synCSV
-     * @param {Object<string,import("../index.js").TaxonData>|boolean} inclusionList
+     * @param {Object<string,import("../index.js").TaxonOverrides>|boolean} inclusionList
      */
     #loadSyns(synCSV, inclusionList) {
         for (const syn of synCSV) {
@@ -246,7 +246,7 @@ class Taxa {
 
     /**
      * @param {import("../index.js").TaxonData[]} taxaCSV
-     * @param {Object<string,import("../index.js").TaxonData>|true} inclusionList
+     * @param {Object<string,import("../index.js").TaxonOverrides>|true} inclusionList
      * @param {function(import("../index.js").TaxonData,Genera):Taxon} taxonFactory
      * @param {Genera} genera
      * @param {boolean} showFlowerErrors
@@ -255,7 +255,7 @@ class Taxa {
         for (const row of taxaCSV) {
             const name = row["taxon_name"];
 
-            /** @type {import("../index.js").TaxonData|{status?:import("../index.js").NativeStatusCode}} */
+            /** @type {import("../index.js").TaxonOverrides} */
             let taxon_overrides = {};
             if (inclusionList !== true) {
                 taxon_overrides = inclusionList[name];

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.4.23",
+    "version": "0.4.26",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {