@ca-plant-list/ca-plant-list 0.4.22 → 0.4.23

package/lib/tools/fna.js

@@ -12,7 +12,7 @@ export class FNA {
     /**
      * @param {string} toolsDataDir
      * @param {string} dataDir
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../errorlog.js").ErrorLog} errorLog
      * @param {boolean} update
      */
@@ -44,7 +44,7 @@ export class FNA {
 }
 
 /**
- * @param {import("../taxon.js").Taxon} taxon
+ * @param {import("../types.js").Taxon} taxon
  * @param {FNATaxa} fnaTaxa
  * @returns {string|undefined}
  */

package/lib/tools/inat.js

@@ -21,7 +21,7 @@ export class INat {
     /**
      * @param {string} toolsDataDir
      * @param {string} dataDir
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../exceptions.js").Exceptions} exceptions
      * @param {import("../errorlog.js").ErrorLog} errorLog
      * @param {string} csvFileName
@@ -115,7 +115,7 @@ export class INat {
 
     /**
      *
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../exceptions.js").Exceptions} exceptions
      * @param {import("../errorlog.js").ErrorLog} errorLog
      */
@@ -168,7 +168,7 @@ export class INat {
 
     /**
      *
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../exceptions.js").Exceptions} exceptions
      * @param {import("../errorlog.js").ErrorLog} errorLog
      * @param {string} name

package/lib/tools/jepsoneflora.js

@@ -54,7 +54,7 @@ export class JepsonEFlora {
 
     /**
      * @param {string} toolsDataDir
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../taxonomy/taxa.js").Taxa} taxa
      * @param {import("../errorlog.js").ErrorLog} errorLog
      */
     constructor(toolsDataDir, taxa, errorLog) {

package/lib/tools/rpi.js

@@ -12,7 +12,7 @@ class RPI {
 
     /**
      * @param {string} toolsDataDir
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../config.js").Config} config
      * @param {import("../exceptions.js").Exceptions} exceptions
      * @param {import("../errorlog.js").ErrorLog} errorLog
@@ -202,7 +202,7 @@ class RPI {
     }
 
     /**
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../config.js").Config} config
      * @param {import("../exceptions.js").Exceptions} exceptions
      * @param {import("../errorlog.js").ErrorLog} errorLog
@@ -366,7 +366,7 @@ class RPI {
 
     /**
      * @param {string} toolsDataDir
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../exceptions.js").Exceptions} exceptions
      * @param {import("../errorlog.js").ErrorLog} errorLog
      */

package/lib/tools/supplementaltext.js

@@ -5,7 +5,7 @@ const VALID_EXTENSIONS = new Set(["md", "footer.md"]);
 export class SupplementalText {
     /**
      *
-     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../types.js").Taxa} taxa
      * @param {import("../errorlog.js").ErrorLog} errorLog
      */
     static analyze(taxa, errorLog) {

package/lib/types.js

@@ -0,0 +1,10 @@
+/**
+ * Classes
+ * @typedef {import("./config.js").Config} Config
+ * @typedef {import("./taxonomy/families.js").Families} Families
+ * @typedef {import("./taxonomy/families.js").Family} Family
+ * @typedef {import("./taxonomy/taxa.js").Taxa} Taxa
+ * @typedef {import("./index.js").TaxaColDef<import("./types.js").Taxon>} TaxaColDef
+ * @typedef {import("./taxonomy/taxon.js").Taxon} Taxon
+ * @typedef {import("./taxonomy/taxonomy.js").Taxonomy} Taxonomy
+ */

package/lib/utils/inat-tools.js

@@ -41,7 +41,7 @@ import { chunk, sleep } from "../util.js";
 const ALLOWED_LICENSE_CODES = ["cc0", "cc-by", "cc-by-nc"];
 
 /**
- * @param {import("../taxon.js").Taxon[]} taxa
+ * @param {import("../types.js").Taxon[]} taxa
  * @return {Promise<InatApiTaxon[]>}
  */
 async function fetchInatTaxa(taxa) {
@@ -57,7 +57,7 @@ async function fetchInatTaxa(taxa) {
 }
 
 /**
- * @param {import("../taxon.js").Taxon[]} taxaToUpdate
+ * @param {import("../types.js").Taxon[]} taxaToUpdate
  * @returns {Promise<Map<string,InatPhotoInfo[]>>}
  */
 export async function getTaxonPhotos(taxaToUpdate) {

package/lib/web/pageFamily.js

@@ -0,0 +1,146 @@
+import { ExternalSites } from "../externalsites.js";
+import { GenericPage } from "../genericpage.js";
+import { HTML } from "../html.js";
+import { HTMLTaxon } from "../htmltaxon.js";
+import { Sections } from "../taxonomy/families.js";
+
+export class PageFamilyList extends GenericPage {
+    #families;
+
+    /**
+     * @param {string} outputDir
+     * @param {import("../types.js").Family[]} families
+     */
+    constructor(outputDir, families) {
+        super(outputDir, "Families", "list_families");
+        this.#families = families;
+    }
+
+    /**
+     * @param {import("../types.js").TaxaColDef[]} [taxaColumns]
+     */
+    render(taxaColumns) {
+        let html = this.getDefaultIntro();
+
+        const sections = Sections.getSections();
+        const sectionLinks = [];
+        for (const name of Object.keys(sections).sort()) {
+            const taxa = sections[name];
+
+            // Render the section page.
+            new PageSection(this.getOutputDir(), name, taxa).render(
+                taxaColumns,
+            );
+
+            // Render the link.
+            const href = "./" + name + ".html";
+            sectionLinks.push(
+                HTML.getLink(href, name) + " (" + taxa.length + ")",
+            );
+        }
+        html += HTML.wrap("ul", HTML.arrayToLI(sectionLinks), {
+            class: "listmenu",
+        });
+
+        html += "<table>";
+        html += "<thead>";
+        html += HTML.textElement("th", "Family");
+        html += HTML.textElement("th", "Number of Species", { class: "right" });
+        html += "</thead>";
+
+        html += "<tbody>";
+        for (const family of this.#families) {
+            const taxa = family.getTaxa();
+            if (!taxa) {
+                continue;
+            }
+            let cols = HTML.wrap(
+                "td",
+                HTML.getLink("./" + family.getFileName(), family.getName()),
+            );
+            cols += HTML.wrap("td", taxa.length, { class: "right" });
+            html += HTML.wrap("tr", cols);
+        }
+        html += "</tbody>";
+
+        html += "</table>";
+
+        this.writeFile(html);
+    }
+
+    /**
+     * @param {string} outputDir
+     * @param {import("../types.js").TaxaColDef[]} [taxaColumns]
+     */
+    renderPages(outputDir, taxaColumns) {
+        for (const family of this.#families) {
+            if (family.getTaxa()) {
+                new PageFamily(outputDir, family).render(taxaColumns);
+            }
+        }
+    }
+}
+
+class PageFamily extends GenericPage {
+    #family;
+
+    /**
+     * @param {string} outputDir
+     * @param {import("../types.js").Family} family
+     */
+    constructor(outputDir, family) {
+        super(outputDir, family.getName(), family.getBaseFileName());
+        this.#family = family;
+    }
+
+    /**
+     * @param {import("../types.js").TaxaColDef[]} [columns]
+     */
+    render(columns) {
+        let html = this.getDefaultIntro();
+
+        const jepsonLink = ExternalSites.getJepsonRefLink(this.#family);
+        if (jepsonLink) {
+            html += HTML.wrap(
+                "div",
+                HTML.getLink(jepsonLink, "Jepson eFlora", {}, true),
+                {
+                    class: "section",
+                },
+            );
+        }
+
+        const taxa = this.#family.getTaxa();
+        if (!taxa) {
+            throw new Error();
+        }
+        html += HTMLTaxon.getTaxaTable(taxa, columns);
+
+        this.writeFile(html);
+    }
+}
+
+class PageSection extends GenericPage {
+    #taxa;
+
+    /**
+     * @param {string} outputDir
+     * @param {string} name
+     * @param {import("../types.js").Taxon[]} taxa
+     */
+    constructor(outputDir, name, taxa) {
+        super(outputDir, name, name);
+        this.#taxa = taxa;
+    }
+
+    /**
+     * @param {import("../types.js").TaxaColDef[]} [columns]
+     */
+    render(columns) {
+        let html = this.getDefaultIntro();
+
+        html += HTMLTaxon.getTaxaTable(this.#taxa, columns);
+
+        this.writeFile(html);
+    }
+}

package/lib/web/pagetaxon.js

@@ -1,7 +1,5 @@
-import { Jepson } from "../jepson.js";
 import { RarePlants } from "../rareplants.js";
 import { GenericPage } from "../genericpage.js";
-import { ExternalSites } from "../externalsites.js";
 import { HTML } from "../html.js";
 import { HTMLTaxon } from "../htmltaxon.js";
 
@@ -12,7 +10,7 @@ export class PageTaxon extends GenericPage {
     /**
      * @param {string} outputDir
      * @param {import("../config.js").Config} config
-     * @param {import("../taxon.js").Taxon} taxon
+     * @param {import("../types.js").Taxon} taxon
      */
     constructor(outputDir, config, taxon) {
         super(outputDir, taxon.getName(), taxon.getBaseFileName());
@@ -21,23 +19,19 @@ export class PageTaxon extends GenericPage {
     }
 
     #getInfoLinks() {
+        /** @type {string[]} */
         const links = [];
-        const jepsonID = this.#taxon.getJepsonID();
-        if (jepsonID) {
-            links.push(Jepson.getEFloraLink(jepsonID));
-        }
-        const cfLink = this.#taxon.getCalfloraTaxonLink();
-        if (cfLink) {
-            links.push(cfLink);
-        }
-        const iNatLink = this.#taxon.getINatTaxonLink();
-        if (iNatLink) {
-            links.push(iNatLink);
-        }
-        const rpiLink = this.#taxon.getRPITaxonLink();
-        if (rpiLink) {
-            links.push(rpiLink);
-        }
+        HTMLTaxon.addRefLink(links, this.#taxon, "jepson");
+        HTMLTaxon.addRefLink(links, this.#taxon, "calflora");
+        HTMLTaxon.addRefLink(
+            links,
+            this.#taxon,
+            "inat",
+            this.#taxon.getINatSyn()
+                ? " (" + this.#taxon.getINatSyn() + ")"
+                : "",
+        );
+        HTMLTaxon.addRefLink(links, this.#taxon, "rpi");
         HTMLTaxon.addRefLink(links, this.#taxon, "fna");
         HTMLTaxon.addRefLink(links, this.#taxon, "cch");
         HTMLTaxon.addRefLink(links, this.#taxon, "calscape");
@@ -45,42 +39,11 @@ export class PageTaxon extends GenericPage {
     }
 
     #getObsLinks() {
+        /** @type {string[]} */
         const links = [];
-        links.push(
-            HTML.getLink(
-                "https://www.calflora.org/entry/observ.html?track=m#srch=t&grezc=5&cols=b&lpcli=t&cc=" +
-                    this.#config.getCountyCodes().join("!") +
-                    "&incobs=f&taxon=" +
-                    this.#taxon.getCalfloraName().replaceAll(" ", "+"),
-                "Calflora",
-                {},
-                true,
-            ),
-        );
-        const iNatID = this.#taxon.getINatID();
-        if (iNatID) {
-            links.push(
-                HTML.getLink(
-                    ExternalSites.getInatObsLink({
-                        project_id: this.#config.getConfigValue(
-                            "inat",
-                            "project_id",
-                        ),
-                        subview: "map",
-                        taxon_id: iNatID,
-                    }),
-                    "iNaturalist",
-                    {},
-                    true,
-                ),
-            );
-        }
-        HTMLTaxon.addLink(
-            links,
-            ExternalSites.getCCH2ObsLink(this.#taxon, this.#config),
-            "CCH2",
-        );
-
+        HTMLTaxon.addObsLink(links, this.#taxon, this.#config, "inat");
+        HTMLTaxon.addObsLink(links, this.#taxon, this.#config, "calflora");
+        HTMLTaxon.addObsLink(links, this.#taxon, this.#config, "cch");
         return links;
     }
 
@@ -97,7 +60,7 @@ export class PageTaxon extends GenericPage {
             }) +
                 HTML.getToolTip(
                     cnpsRank,
-                    this.#taxon.getRPIRankAndThreatTooltip(),
+                    HTMLTaxon.getRPIRankAndThreatTooltip(this.#taxon),
                 ),
         );
         if (this.#taxon.getCESA()) {
@@ -120,7 +83,8 @@ export class PageTaxon extends GenericPage {
             if (taxa.length > 1) {
                 for (const taxon of taxa) {
                     links.push(
-                        taxon.getHTMLLink(
+                        HTMLTaxon.getHTMLLink(
+                            taxon,
                             taxon.getName() !== this.#taxon.getName(),
                         ),
                     );

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.4.22",
+    "version": "0.4.23",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {

package/scripts/build-ebook.js

@@ -5,7 +5,7 @@ import { ErrorLog } from "../lib/errorlog.js";
 import { Files } from "../lib/files.js";
 import { PlantBook } from "../lib/ebook/plantbook.js";
 import { Program } from "../lib/program.js";
-import { Taxa } from "../lib/taxa.js";
+import { Taxa } from "../lib/taxonomy/taxa.js";
 
 const program = Program.getProgram();
 program
@@ -33,7 +33,7 @@ async function build(options) {
                 await buildBook(
                     outputBase + suffix,
                     path,
-                    options.showFlowerErrors
+                    options.showFlowerErrors,
                 );
             }
         }
@@ -42,7 +42,7 @@ async function build(options) {
         await buildBook(
             options.outputdir,
             options.datadir,
-            options.showFlowerErrors
+            options.showFlowerErrors,
         );
     }
 }
@@ -58,7 +58,7 @@ async function buildBook(outputDir, dataDir, showFlowerErrors) {
     const taxa = new Taxa(
         Program.getIncludeList(dataDir),
         errorLog,
-        showFlowerErrors
+        showFlowerErrors,
     );
 
     const config = new Config(dataDir);

package/scripts/build-site.js

@@ -6,7 +6,7 @@ import { Config } from "../lib/config.js";
 import { PageRenderer } from "../lib/pagerenderer.js";
 import { Files } from "../lib/files.js";
 import { Program } from "../lib/program.js";
-import { Taxa } from "../lib/taxa.js";
+import { Taxa } from "../lib/taxonomy/taxa.js";
 import { ErrorLog } from "../lib/errorlog.js";
 
 class JekyllRenderer {
@@ -45,7 +45,7 @@ class JekyllRenderer {
         options.push("--config", `"${configFiles.join()}"`);
 
         const result = child_process.execSync(
-            "bundle exec jekyll build " + options.join(" ")
+            "bundle exec jekyll build " + options.join(" "),
         );
         console.log(result.toString());
     }
@@ -60,7 +60,7 @@ async function build(options) {
     const taxa = new Taxa(
         Program.getIncludeList(options.datadir),
         errorLog,
-        options.showFlowerErrors
+        options.showFlowerErrors,
     );
     PageRenderer.render(options.outputdir, new Config(options.datadir), taxa);
     errorLog.write();

package/scripts/cpl-photos.js

@@ -3,7 +3,7 @@
 import path from "path";
 import { ErrorLog } from "../lib/errorlog.js";
 import { Program } from "../lib/program.js";
-import { Taxa } from "../lib/taxa.js";
+import { Taxa } from "../lib/taxonomy/taxa.js";
 import { getTaxonPhotos } from "../lib/utils/inat-tools.js";
 import { existsSync } from "fs";
 import { CSV } from "../lib/csv.js";

package/scripts/cpl-tools.js

@@ -10,7 +10,7 @@ import { INat } from "../lib/tools/inat.js";
 import { JepsonEFlora } from "../lib/tools/jepsoneflora.js";
 import { RPI } from "../lib/tools/rpi.js";
 import { Config } from "../lib/config.js";
-import { Taxa } from "../lib/taxa.js";
+import { Taxa } from "../lib/taxonomy/taxa.js";
 import { SupplementalText } from "../lib/tools/supplementaltext.js";
 import { JepsonFamilies } from "../lib/tools/jepsonfamilies.js";
 import { CCH2 } from "../lib/tools/cch2.js";

package/scripts/inatobsphotos.js

@@ -6,7 +6,7 @@ import { stringify } from "csv-stringify";
 import path from "path";
 
 import { Program } from "../lib/program.js";
-import { Taxa } from "../lib/taxa.js";
+import { Taxa } from "../lib/taxonomy/taxa.js";
 import { sleep } from "../lib/util.js";
 
 /**
@@ -27,7 +27,7 @@ const ALLOWED_LICENSE_CODES = ["cc0", "cc-by", "cc-by-nc"];
 const DEFAULT_FILENAME = "inatobsphotos.csv";
 
 /**
- * @param {import("../lib/taxon.js").Taxon} taxon
+ * @param {import("../lib/types.js").Taxon} taxon
  * @param {InatObsPhotosCommandLineOptions} options
  * @return {Promise<InatApiObservation[]>}
  */

package/scripts/inattaxonphotos.js

@@ -7,7 +7,7 @@ import path from "path";
 
 import { ErrorLog } from "../lib/errorlog.js";
 import { Program } from "../lib/program.js";
-import { Taxa } from "../lib/taxa.js";
+import { Taxa } from "../lib/taxonomy/taxa.js";
 import { chunk, sleep } from "../lib/util.js";
 
 /**
@@ -23,7 +23,7 @@ const ALLOWED_LICENSE_CODES = ["cc0", "cc-by", "cc-by-nc"];
 const DEFAULT_FILENAME = "inattaxonphotos.csv";
 
 /**
- * @param {import("../lib/taxon.js").Taxon[]} taxa
+ * @param {import("../lib/types.js").Taxon[]} taxa
  * @return {Promise<import("../lib/utils/inat-tools.js").InatApiTaxon[]>}
  */
 async function fetchInatTaxa(taxa) {