@ca-plant-list/ca-plant-list 0.4.21 → 0.4.23

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

@@ -10,15 +10,17 @@ 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";
+import { FNA } from "../lib/tools/fna.js";
 
 const TOOLS = {
     CALFLORA: "calflora",
     CALSCAPE: "calscape",
     CCH2: "cch",
+    FNA: "fna",
     INAT: "inat",
     JEPSON_EFLORA: "jepson-eflora",
     JEPSON_FAM: "jepson-families",
@@ -30,6 +32,7 @@ const ALL_TOOLS = [
     TOOLS.CALFLORA,
     TOOLS.CALSCAPE,
     TOOLS.CCH2,
+    TOOLS.FNA,
     TOOLS.INAT,
     TOOLS.JEPSON_EFLORA,
     TOOLS.RPI,
@@ -84,11 +87,22 @@ async function build(program, options) {
                 await CCH2.analyze(
                     TOOLS_DATA_DIR,
                     options.datadir,
+                    exceptions,
                     taxa,
                     errorLog,
                     !!options.update,
                 );
                 break;
+            case TOOLS.FNA:
+                await FNA.analyze(
+                    TOOLS_DATA_DIR,
+                    options.datadir,
+                    taxa,
+                    errorLog,
+                    !!options.update,
+                );
+                break;
+
             case TOOLS.INAT:
                 await INat.analyze(
                     TOOLS_DATA_DIR,
@@ -150,9 +164,11 @@ program.addHelpText(
     "after",
     `
 Tools:
-    'all' runs the 'calflora', '${TOOLS.CALSCAPE}', 'inat', 'jepson-eflora', 'rpi', and 'text' tools.
+    'all' runs the 'calflora', '${TOOLS.CALSCAPE}', '${TOOLS.CCH2}, '${TOOLS.FNA}, 'inat', 'jepson-eflora', 'rpi', and 'text' tools.
     '${TOOLS.CALFLORA}' retrieves data from Calflora and compares with local data.
     '${TOOLS.CALSCAPE}' retrieves data from Calscape and compares with local data.
+    '${TOOLS.CCH2}' retrieves data from CCH2 and compares with local data.
+    '${TOOLS.FNA}' retrieves data from Flora of North America and compares with local data.
     '${TOOLS.INAT}' retrieves data from iNaturalist and compares with local data.
     '${TOOLS.JEPSON_EFLORA}' retrieves data from Jepson eFlora indexes and compares with local data.
     '${TOOLS.JEPSON_FAM}' retrieves section, family and genus data from Jepson eFlora and creates data files for use by ca-plant-list.

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) {

package/lib/families.js

@@ -1,243 +0,0 @@
-import { GenericPage } from "./genericpage.js";
-import { HTML } from "./html.js";
-import { Jepson } from "./jepson.js";
-import { Files } from "./files.js";
-import { Config } from "./config.js";
-import { HTMLTaxon } from "./htmltaxon.js";
-
-export class Family {
-    #name;
-    #data;
-
-    /**
-     * @param {string} name
-     * @param {*} data
-     */
-    constructor(name, data) {
-        this.#name = name;
-        this.#data = data;
-    }
-
-    /**
-     * @param {import("./taxon.js").Taxon} taxon
-     */
-    addTaxon(taxon) {
-        if (!this.#data.taxa) {
-            this.#data.taxa = [];
-        }
-        this.#data.taxa.push(taxon);
-        Sections.addTaxon(this.getSectionName(), taxon);
-    }
-
-    getBaseFileName() {
-        return this.getName();
-    }
-
-    getFileName(ext = "html") {
-        return this.getBaseFileName() + "." + ext;
-    }
-
-    getJepsonID() {
-        return this.#data.id;
-    }
-
-    getName() {
-        return this.#name;
-    }
-
-    getSectionName() {
-        return this.#data.section;
-    }
-
-    getTaxa() {
-        return this.#data.taxa;
-    }
-}
-
-class Families {
-    #families;
-
-    constructor() {
-        const dataDir = Config.getPackageDir() + "/data";
-
-        this.#families = JSON.parse(Files.read(dataDir + "/families.json"));
-        for (const [k, v] of Object.entries(this.#families)) {
-            this.#families[k] = new Family(k, v);
-        }
-    }
-
-    getFamilies() {
-        return Object.values(this.#families).sort((a, b) =>
-            a.getName().localeCompare(b.getName()),
-        );
-    }
-
-    /**
-     * @param {string} familyName
-     */
-    getFamily(familyName) {
-        return this.#families[familyName];
-    }
-
-    /**
-     * @param {string} outputDir
-     * @param {import("./htmltaxon.js").TaxaColDef[]} [taxaColumns]
-     */
-    renderPages(outputDir, taxaColumns) {
-        new PageFamilyList(outputDir, this.#families).render(taxaColumns);
-
-        const names = Object.keys(this.#families);
-        for (const name of names.sort()) {
-            const family = this.#families[name];
-            if (family.getTaxa()) {
-                new PageFamily(outputDir, family).render(taxaColumns);
-            }
-        }
-    }
-}
-
-class PageFamilyList extends GenericPage {
-    #families;
-
-    /**
-     * @param {string} outputDir
-     * @param {Object<string,Family>} families
-     */
-    constructor(outputDir, families) {
-        super(outputDir, "Families", "list_families");
-        this.#families = families;
-    }
-
-    /**
-     * @param {import("./htmltaxon.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>";
-        const names = Object.keys(this.#families).sort();
-        for (const name of names) {
-            const family = this.#families[name];
-            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);
-    }
-}
-
-class PageFamily extends GenericPage {
-    #family;
-
-    /**
-     * @param {string} outputDir
-     * @param {Family} family
-     */
-    constructor(outputDir, family) {
-        super(outputDir, family.getName(), family.getBaseFileName());
-        this.#family = family;
-    }
-
-    /**
-     * @param {import("./htmltaxon.js").TaxaColDef[]} [columns]
-     */
-    render(columns) {
-        let html = this.getDefaultIntro();
-
-        html += HTML.wrap(
-            "div",
-            Jepson.getEFloraLink(this.#family.getJepsonID()),
-            { class: "section" },
-        );
-
-        html += HTMLTaxon.getTaxaTable(this.#family.getTaxa(), columns);
-
-        this.writeFile(html);
-    }
-}
-
-class PageSection extends GenericPage {
-    #taxa;
-
-    /**
-     * @param {string} outputDir
-     * @param {string} name
-     * @param {import("./taxon.js").Taxon[]} taxa
-     */
-    constructor(outputDir, name, taxa) {
-        super(outputDir, name, name);
-        this.#taxa = taxa;
-    }
-
-    /**
-     * @param {import("./htmltaxon.js").TaxaColDef[]} [columns]
-     */
-    render(columns) {
-        let html = this.getDefaultIntro();
-
-        html += HTMLTaxon.getTaxaTable(this.#taxa, columns);
-
-        this.writeFile(html);
-    }
-}
-
-class Sections {
-    /** @type {Object<string,import("./taxon.js").Taxon[]>} */
-    static #sections = {};
-
-    /**
-     * @param {string} name
-     * @param {import("./taxon.js").Taxon} taxon
-     */
-    static addTaxon(name, taxon) {
-        let section = this.#sections[name];
-        if (!section) {
-            section = [];
-            this.#sections[name] = section;
-        }
-        section.push(taxon);
-    }
-
-    static getSections() {
-        return this.#sections;
-    }
-}
-
-export { Families };

package/lib/jepson.js

@@ -1,17 +0,0 @@
-import { HTML } from "./html.js";
-
-class Jepson {
-    /**
-     * @param {string} id
-     */
-    static getEFloraLink(id) {
-        return HTML.getLink(
-            "https://ucjeps.berkeley.edu/eflora/eflora_display.php?tid=" + id,
-            "Jepson eFlora",
-            {},
-            true
-        );
-    }
-}
-
-export { Jepson };