@ca-plant-list/ca-plant-list 0.4.22 → 0.4.24

package/lib/basepagerenderer.js

@@ -2,12 +2,13 @@ import { Config } from "./config.js";
 import { Files } from "./files.js";
 import { Jekyll } from "./jekyll.js";
 import { GlossaryPages } from "./web/glossarypages.js";
+import { PageFamilyList } from "./web/pageFamily.js";
 
 class BasePageRenderer {
     /**
      * @param {string} outputDir
-     * @param {import("./taxa.js").Taxa} taxa
-     * @param {import("./htmltaxon.js").TaxaColDef[]} [familyCols]
+     * @param {import("./types.js").Taxa} taxa
+     * @param {import("./types.js").TaxaColDef[]} [familyCols]
      */
     static renderBasePages(outputDir, taxa, familyCols) {
         const siteGenerator = new Jekyll(outputDir);
@@ -21,7 +22,12 @@ class BasePageRenderer {
         // Copy illustrations.
         siteGenerator.copyIllustrations(taxa.getFlowerColors());
 
-        taxa.getFamilies().renderPages(outputDir, familyCols);
+        const fl = new PageFamilyList(
+            outputDir,
+            taxa.getFamilies().getFamilies(),
+        );
+        fl.render(familyCols);
+        fl.renderPages(outputDir, familyCols);
 
         new GlossaryPages(siteGenerator).renderPages();
 
@@ -30,7 +36,7 @@ class BasePageRenderer {
 
     /**
      * @param {string} outputDir
-     * @param {import("./taxa.js").Taxa} taxa
+     * @param {import("./types.js").Taxa} taxa
      */
     static renderTools(outputDir, taxa) {
         const names = [];

package/lib/ebook/images.js

@@ -14,7 +14,7 @@ class Images {
     /**
      * @param {import("../sitegenerator.js").SiteGenerator} siteGenerator
      * @param {string} contentDir
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      */
     constructor(siteGenerator, contentDir, taxa) {
         this.#siteGenerator = siteGenerator;
@@ -23,7 +23,7 @@ class Images {
     }
 
     /**
-     * @param {import("../taxon.js").Taxon[]} taxa
+     * @param {import("../taxonomy/taxon.js").Taxon[]} taxa
      */
     async createImages(taxa) {
         const meter = new ProgressMeter("processing photos", taxa.length);
@@ -118,7 +118,7 @@ class Images {
     }
 
     /**
-     * @param {import("../taxon.js").Taxon} taxon
+     * @param {import("../taxonomy/taxon.js").Taxon} taxon
      * @returns {import("../photo.js").Photo[]}
      */
     static getTaxonPhotos(taxon) {

package/lib/ebook/pages/{page_list_families.js → pageListFamilies.js}

@@ -6,7 +6,7 @@ class PageListFamilies extends EBookPage {
 
     /**
      * @param {string} outputDir
-     * @param {import("../../families.js").Families} families
+     * @param {import("../../types.js").Families} families
      */
     constructor(outputDir, families) {
         super(outputDir + "/list_families.html", "All Families");

package/lib/ebook/pages/{page_list_flowers.js → pageListFlowers.js}

@@ -8,7 +8,7 @@ const FN_FLOWER_TIME_INDEX = "fm.html";
 class PageListFlowers {
     /**
      * @param {string} contentDir
-     * @param {import("../../taxa.js").Taxa} taxa
+     * @param {import("../../types.js").Taxa} taxa
      */
     static createPages(contentDir, taxa) {
         new PageListFlowerTimeIndex(contentDir).create();
@@ -83,7 +83,7 @@ class PageListFlowerTime extends EBookPage {
 
     /**
      * @param {string} outputDir
-     * @param {import("../../taxa.js").Taxa} taxa
+     * @param {import("../../types.js").Taxa} taxa
      * @param {number} month
      */
     constructor(outputDir, taxa, month) {

package/lib/ebook/pages/page_list_species.js

@@ -8,7 +8,7 @@ class PageListSpecies extends EBookPage {
     /**
      *
      * @param {string} outputDir
-     * @param {import("../../taxon.js").Taxon[]} taxa
+     * @param {import("../../taxonomy/taxon.js").Taxon[]} taxa
      * @param {string} filename
      * @param {string} title
      */

package/lib/ebook/pages/taxonpage.js

@@ -13,7 +13,7 @@ class TaxonPage extends EBookPage {
 
     /**
      * @param {string} outputDir
-     * @param {import("../../taxon.js").Taxon} taxon
+     * @param {import("../../taxonomy/taxon.js").Taxon} taxon
      * @param {Images} images
      */
     constructor(outputDir, taxon, images) {

package/lib/ebook/pages/tocpage.js

@@ -1,13 +1,13 @@
 import { EBookPage } from "../ebookpage.js";
 import { XHTML } from "../xhtml.js";
-import { PageListFlowers } from "./page_list_flowers.js";
+import { PageListFlowers } from "./pageListFlowers.js";
 
 class TOCPage extends EBookPage {
     #taxa;
 
     /**
      * @param {string} outputDir
-     * @param {import("../../taxa.js").Taxa} taxa
+     * @param {import("../../taxonomy/taxa.js").Taxa} taxa
      */
     constructor(outputDir, taxa) {
         super(outputDir + "/toc.xhtml", "Table of Contents");

package/lib/ebook/plantbook.js

@@ -3,9 +3,9 @@ import { EBook } from "./ebook.js";
 import { EBookSiteGenerator } from "./ebooksitegenerator.js";
 import { GlossaryPages } from "./glossarypages.js";
 import { Images } from "./images.js";
-import { PageListFamilies } from "./pages/page_list_families.js";
+import { PageListFamilies } from "./pages/pageListFamilies.js";
 import { PageListFlowerColor } from "./pages/page_list_flower_color.js";
-import { PageListFlowers } from "./pages/page_list_flowers.js";
+import { PageListFlowers } from "./pages/pageListFlowers.js";
 import { PageListSpecies } from "./pages/page_list_species.js";
 import { TaxonPage } from "./pages/taxonpage.js";
 import { TOCPage } from "./pages/tocpage.js";
@@ -18,7 +18,7 @@ class PlantBook extends EBook {
     /**
      * @param {string} outputDir
      * @param {import("../config.js").Config} config
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      */
     constructor(outputDir, config, taxa) {
         super(

package/lib/externalsites.js

@@ -1,13 +1,37 @@
-/** @typedef {{
-    coords?: [number, number];
-    project_id?: string;
-    subview?: "grid" | "list" | "map";
-    taxon_id?: string;
-}} InatObsOptions */
-
 export class ExternalSites {
     /**
-     * @param {import("./taxon.js").Taxon} taxon
+     * @param {import("./types.js").Taxon} taxon
+     * @param {import("./types.js").Config} config
+     * @returns {URL|undefined}
+     */
+    static getCalfloraObsLink(taxon, config) {
+        const name = taxon.getCalfloraName();
+        if (!name) {
+            return;
+        }
+        const url = new URL(
+            "https://www.calflora.org/entry/observ.html?track=m#srch=t&grezc=5&cols=b&lpcli=t&cc=" +
+                config.getCountyCodes().join("!") +
+                "&incobs=f&taxon=" +
+                name,
+        );
+        return url;
+    }
+
+    /**
+     * @param {import("./types.js").Taxon} taxon
+     * @returns {URL|undefined}
+     */
+    static getCalfloraRefLink(taxon) {
+        const calfloraID = taxon.getCalfloraID();
+        if (!calfloraID) {
+            return;
+        }
+        return new URL("https://www.calflora.org/app/taxon?crn=" + calfloraID);
+    }
+
+    /**
+     * @param {import("./types.js").Taxon} taxon
      * @returns {URL|undefined}
      */
     static getCalscapeLink(taxon) {
@@ -21,7 +45,7 @@ export class ExternalSites {
     }
 
     /**
-     * @param {import("./taxon.js").Taxon} taxon
+     * @param {import("./types.js").Taxon} taxon
      * @param {import("./config.js").Config} config
      * @returns {URL|undefined}
      */
@@ -35,7 +59,7 @@ export class ExternalSites {
     }
 
     /**
-     * @param {import("./taxon.js").Taxon} taxon
+     * @param {import("./types.js").Taxon} taxon
      * @returns {URL|undefined}
      */
     static getCCH2RefLink(taxon) {
@@ -49,7 +73,7 @@ export class ExternalSites {
     }
 
     /**
-     * @param {import("./taxon.js").Taxon} taxon
+     * @param {import("./types.js").Taxon} taxon
      * @returns {URL|undefined}
      */
     static getFNARefLink(taxon) {
@@ -64,40 +88,65 @@ export class ExternalSites {
     }
 
     /**
-     * @param {InatObsOptions} options
+     * @param {import("./types.js").Taxon} taxon
+     * @param {import("./config.js").Config} config
+     * @returns {URL|undefined}
      */
-    static getInatObsLink(options) {
+    static getInatObsLink(taxon, config) {
+        const iNatID = taxon.getINatID();
+        if (!iNatID) {
+            return;
+        }
+
         const url = new URL(
             "https://www.inaturalist.org/observations?subview=map",
         );
+        url.searchParams.set("taxon_id", iNatID);
+        for (const p of ["place_id", "project_id"]) {
+            const v = config.getConfigValue("inat", p);
+            if (v) {
+                url.searchParams.set(p, v);
+            }
+        }
+
+        return url;
+    }
 
-        if (options.coords) {
-            const delta = 0.1;
-            const params = url.searchParams;
-            const lat = options.coords[1];
-            const lng = options.coords[0];
-            params.set("nelat", (lat + delta).toString());
-            params.set("swlat", (lat - delta).toString());
-            params.set("nelng", (lng + delta).toString());
-            params.set("swlng", (lng - delta).toString());
+    /**
+     * @param {import("./types.js").Taxon} taxon
+     * @returns {URL|undefined}
+     */
+    static getINatRefLink(taxon) {
+        const iNatID = taxon.getINatID();
+        if (!iNatID) {
+            return;
         }
+        return new URL("https://www.inaturalist.org/taxa/" + iNatID);
+    }
 
-        for (const [k, v] of Object.entries(options)) {
-            switch (k) {
-                case "created_d1":
-                case "list_id":
-                case "place_id":
-                case "project_id":
-                case "subview":
-                case "taxon_id":
-                case "taxon_name":
-                    if (typeof v === "string") {
-                        url.searchParams.set(k, v);
-                    }
-                    break;
-            }
+    /**
+     * @param {import("./types.js").Taxonomy} taxon
+     * @returns {URL|undefined}
+     */
+    static getJepsonRefLink(taxon) {
+        const id = taxon.getJepsonID();
+        if (!id) {
+            return;
         }
+        return new URL(
+            "https://ucjeps.berkeley.edu/eflora/eflora_display.php?tid=" + id,
+        );
+    }
 
-        return url.toString();
+    /**
+     * @param {import("./types.js").Taxon} taxon
+     * @returns {URL|undefined}
+     */
+    static getRPIRefLink(taxon) {
+        const rpiID = taxon.getRPIID();
+        if (!rpiID) {
+            return;
+        }
+        return new URL("https://rareplants.cnps.org/Plants/Details/" + rpiID);
     }
 }

package/lib/flowercolor.js

@@ -3,7 +3,7 @@ import { TextUtils } from "./textutils.js";
 class FlowerColor {
     #colorName;
     #colorCode;
-    /** @type {import("./taxon.js").Taxon[]} */
+    /** @type {import("./types.js").Taxon[]} */
     #taxa = [];
 
     /**
@@ -16,7 +16,7 @@ class FlowerColor {
     }
 
     /**
-     * @param {import("./taxon.js").Taxon} taxon
+     * @param {import("./types.js").Taxon} taxon
      */
     addTaxon(taxon) {
         this.#taxa.push(taxon);

package/lib/genera.js

@@ -6,7 +6,7 @@ class Genera {
     #genera;
 
     /**
-     * @param {import("./families.js").Families} families
+     * @param {import("./types.js").Families} families
      */
     constructor(families) {
         const dataDir = Config.getPackageDir() + "/data";
@@ -15,7 +15,7 @@ class Genera {
     }
 
     /**
-     * @param {import("./taxon.js").Taxon} taxon
+     * @param {import("./types.js").Taxon} taxon
      */
     addTaxon(taxon) {
         const genusName = taxon.getGenusName();
@@ -46,7 +46,7 @@ class Genus {
     #data;
 
     /**
-     * @param {{family:string,familyObj:import("./families.js").Family,taxa:import("./taxon.js").Taxon[]}} data
+     * @param {{family:string,familyObj:import("./types.js").Family,taxa:import("./types.js").Taxon[]}} data
      */
     constructor(data) {
         this.#data = data;
@@ -57,7 +57,7 @@ class Genus {
     }
 
     /**
-     * @returns {import("./taxon.js").Taxon[]}
+     * @returns {import("./types.js").Taxon[]}
      */
     getTaxa() {
         return this.#data.taxa.sort((a, b) =>

package/lib/html.js

@@ -48,7 +48,7 @@ export class HTML {
 
     /**
      * Generate HTML for an <a> element.
-     * @param {string|undefined} href
+     * @param {URL|string|undefined} href
      * @param {string} linkText
      * @param {string|Object<string,string>} [attributes]
      * @param {boolean} [openInNewWindow] true if the link should open in a new window.
@@ -57,7 +57,7 @@ export class HTML {
     static getLink(href, linkText, attributes = {}, openInNewWindow) {
         let html = "<a";
         if (href !== undefined) {
-            html += this.renderAttribute("href", href);
+            html += this.renderAttribute("href", href.toString());
         }
         html += this.renderAttributes(attributes);
         if (openInNewWindow) {
@@ -70,8 +70,7 @@ export class HTML {
      * Get a Bootstrap formatted tooltip element.
      * @param {string} text - The text or HTML that should trigger the tooltip on hover.
      * @param {string} tooltip - The tooltip text or HTML.
-     * @param {Object} options
-     * @param {boolean} [options.icon] [true] display an icon after the text
+     * @param {{icon?:boolean}} options
      * @returns {string} A &lt;span> element to be used as a Bootstrap tooltip.
      */
     static getToolTip(text, tooltip, options = {}) {
@@ -106,19 +105,19 @@ export class HTML {
 
     /**
      * @param {string} elName
-     * @param {string} text
+     * @param {string|number} text
      * @param {Object<string,string>} [attributes]
      */
     static textElement(elName, text, attributes = {}) {
-        return HTML.#getElement(elName, text, attributes, true);
+        return HTML.#getElement(elName, text.toString(), attributes, true);
     }
 
     /**
      * @param {string} elName
-     * @param {string} text
+     * @param {string|number} text
      * @param {string|Object<string,string>|undefined} [attributes]
      */
     static wrap(elName, text, attributes) {
-        return HTML.#getElement(elName, text, attributes, false);
+        return HTML.#getElement(elName, text.toString(), attributes, false);
     }
 }

package/lib/htmltaxon.js

@@ -7,15 +7,7 @@ import { RarePlants } from "./rareplants.js";
 import { TextUtils } from "./textutils.js";
 
 /**
- * @typedef {{
-    class?: string;
-    data: (taxon: import("./taxon.js").Taxon) => string;
-    title: string;
-     }} TaxaColDef
- */
-
-/**
- * @type {Record<string,TaxaColDef>}
+ * @type {Record<string,import("./types.js").TaxaColDef>}
  */
 const TAXA_LIST_COLS = {
     CESA: {
@@ -31,7 +23,7 @@ const TAXA_LIST_COLS = {
         data: (t) =>
             HTML.getToolTip(
                 HTML.textElement("span", t.getRPIRankAndThreat()),
-                t.getRPIRankAndThreatTooltip(),
+                HTMLTaxon.getRPIRankAndThreatTooltip(t),
             ),
     },
     FESA: {
@@ -40,33 +32,66 @@ const TAXA_LIST_COLS = {
     },
     SPECIES: {
         title: "Species",
-        data: (t) => t.getHTMLLink(true, true),
+        data: (t) => HTMLTaxon.getHTMLLink(t, true, true),
     },
     SPECIES_BARE: {
         title: "Species",
-        data: (t) => t.getHTMLLink(true, false),
+        data: (t) => HTMLTaxon.getHTMLLink(t, true, false),
     },
 };
 
-/** @type {TaxaColDef[]} */
+/** @type {import("./types.js").TaxaColDef[]} */
 const DEFAULT_TAXA_COLUMNS = [
     TAXA_LIST_COLS.SPECIES,
     TAXA_LIST_COLS.COMMON_NAME,
 ];
 
-/** @type {Object<string,{label:string,href:function(import("./taxon.js").Taxon):URL|undefined}>} */
+/** @type {Object<string,{label:string,href:function(import("./types.js").Taxon,import("./types.js").Config):URL|undefined}>} */
+const OBSLINKS = {
+    calflora: {
+        label: "Calflora",
+        href: (taxon, config) =>
+            ExternalSites.getCalfloraObsLink(taxon, config),
+    },
+    cch: {
+        label: "CCH2",
+        href: (taxon, config) => ExternalSites.getCCH2ObsLink(taxon, config),
+    },
+    inat: {
+        label: "iNaturalist",
+        href: (taxon, config) => ExternalSites.getInatObsLink(taxon, config),
+    },
+};
+
+/** @type {Object<string,{label:string,href:function(import("./types.js").Taxon):URL|undefined}>} */
 const REFLINKS = {
+    calflora: {
+        label: "Calflora",
+        href: (taxon) => ExternalSites.getCalfloraRefLink(taxon),
+    },
     calscape: {
         label: "Calscape",
         href: (taxon) => ExternalSites.getCalscapeLink(taxon),
     },
+    cch: {
+        label: "CCH2",
+        href: (taxon) => ExternalSites.getCCH2RefLink(taxon),
+    },
     fna: {
         label: "Flora of North America",
         href: (taxon) => ExternalSites.getFNARefLink(taxon),
     },
-    cch: {
-        label: "CCH2",
-        href: (taxon) => ExternalSites.getCCH2RefLink(taxon),
+    inat: {
+        label: "iNaturalist",
+        href: (taxon) => ExternalSites.getINatRefLink(taxon),
+    },
+    jepson: {
+        label: "Jepson eFlora",
+        href: (taxon) => ExternalSites.getJepsonRefLink(taxon),
+    },
+    rpi: {
+        label: "CNPS Rare Plant Inventory",
+        href: (taxon) => ExternalSites.getRPIRefLink(taxon),
     },
 };
 
@@ -75,23 +100,37 @@ class HTMLTaxon {
      * @param {string[]} links
      * @param {URL|string|undefined} href
      * @param {string} label
+     * @param {string} [suffix=""]
      */
-    static addLink(links, href, label) {
+    static addLink(links, href, label, suffix = "") {
         if (href === undefined) {
             return;
         }
         const link = HTML.getLink(href.toString(), label, {}, true);
-        links.push(link);
+        links.push(link + suffix);
     }
 
     /**
      * @param {string[]} links
-     * @param {import("./taxon.js").Taxon} taxon
+     * @param {import("./types.js").Taxon} taxon
+     * @param {import("./types.js").Config} config
      * @param {import("./index.js").RefSourceCode} sourceCode
+     * @param {string} [label]
      */
-    static addRefLink(links, taxon, sourceCode) {
+    static addObsLink(links, taxon, config, sourceCode, label) {
+        const source = OBSLINKS[sourceCode];
+        this.addLink(links, source.href(taxon, config), label ?? source.label);
+    }
+
+    /**
+     * @param {string[]} links
+     * @param {import("./types.js").Taxon} taxon
+     * @param {import("./index.js").RefSourceCode} sourceCode
+     * @param {string} [suffix=""]
+     */
+    static addRefLink(links, taxon, sourceCode, suffix = "") {
         const source = REFLINKS[sourceCode];
-        this.addLink(links, source.href(taxon), source.label);
+        this.addLink(links, source.href(taxon), source.label, suffix);
     }
 
     /**
@@ -120,7 +159,7 @@ class HTMLTaxon {
     }
 
     /**
-     * @param {import("./taxon.js").Taxon} taxon
+     * @param {import("./types.js").Taxon} taxon
      * @param {string} classNames
      * @param {boolean} [includeColorLink=true]
      */
@@ -161,7 +200,7 @@ class HTMLTaxon {
     }
 
     /**
-     * @param {import("./taxon.js").Taxon} taxon
+     * @param {import("./types.js").Taxon} taxon
      * @returns {string}
      */
     static getFooterHTML(taxon) {
@@ -174,7 +213,38 @@ class HTMLTaxon {
     }
 
     /**
-     * @param {import("./taxon.js").Taxon} taxon
+     * @param {import("./types.js").Taxon} taxon
+     * @param {boolean|string|undefined} href
+     * @param {boolean} includeRPI
+     */
+    static getHTMLLink(taxon, href = true, includeRPI = true) {
+        href = href ? "./" + taxon.getFileName() : undefined;
+        let className = taxon.isNative() ? "native" : "non-native";
+        let isRare = false;
+        if (includeRPI && taxon.isRare()) {
+            isRare = true;
+            className += " rare";
+        }
+        const attributes = { class: className };
+        const link = HTML.wrap(
+            "span",
+            HTML.getLink(href, taxon.getName()),
+            attributes,
+        );
+        if (isRare) {
+            return HTML.getToolTip(
+                link,
+                this.getRPIRankAndThreatTooltip(taxon),
+                {
+                    icon: false,
+                },
+            );
+        }
+        return link;
+    }
+
+    /**
+     * @param {import("./types.js").Taxon} taxon
      */
     static getLink(taxon) {
         return (
@@ -214,8 +284,17 @@ class HTMLTaxon {
     }
 
     /**
-     * @param {import("./taxon.js").Taxon[]} taxa
-     * @param {TaxaColDef[]} [columns]
+     * @param {import("./types.js").Taxon} taxon
+     */
+    static getRPIRankAndThreatTooltip(taxon) {
+        return RarePlants.getRPIRankAndThreatDescriptions(
+            taxon.getRPIRankAndThreat(),
+        ).join("<br>");
+    }
+
+    /**
+     * @param {import("./types.js").Taxon[]} taxa
+     * @param {import("./types.js").TaxaColDef[]} [columns]
      */
     static getTaxaTable(taxa, columns = DEFAULT_TAXA_COLUMNS) {
         let html = "<table><thead>";