@ca-plant-list/ca-plant-list 0.4.8 → 0.4.10

package/lib/web/pagetaxon.js

@@ -8,197 +8,206 @@ import { Markdown } from "../markdown.js";
 import { Config } from "../config.js";
 
 class PageTaxon extends GenericPage {
-  #config;
-  #taxon;
-
-  /**
-   * @param {string} outputDir
-   * @param {Config} config
-   * @param {Taxon} taxon
-   */
-  constructor(outputDir, config, taxon) {
-    super(outputDir, taxon.getName(), taxon.getBaseFileName());
-    this.#config = config;
-    this.#taxon = taxon;
-  }
-
-  #getInfoLinks() {
-    const links = [];
-    const jepsonID = this.#taxon.getJepsonID();
-    if (jepsonID) {
-      links.push(Jepson.getEFloraLink(jepsonID));
+    #config;
+    #taxon;
+
+    /**
+     * @param {string} outputDir
+     * @param {Config} config
+     * @param {Taxon} taxon
+     */
+    constructor(outputDir, config, taxon) {
+        super(outputDir, taxon.getName(), taxon.getBaseFileName());
+        this.#config = config;
+        this.#taxon = taxon;
     }
-    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);
-    }
-    return links;
-  }
-
-  #getObsLinks() {
-    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) {
-      const projectId = links.push(
-        HTML.getLink(
-          ExternalSites.getInatObsLink({
-            project_id: this.#config.getConfigValue("inat", "project_id"),
-            subview: "map",
-            taxon_id: iNatID,
-          }),
-          "iNaturalist",
-          {},
-          true
-        )
-      );
+
+    #getInfoLinks() {
+        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);
+        }
+        return links;
     }
 
-    return links;
-  }
-
-  /**
-   * @param {string[]} list
-   * @param {string} header
-   * @param {string} className
-   */
-  #getListSectionHTML(list, header, className) {
-    let html = "";
-    if (list.length > 0) {
-      html += '<div class="section nobullet ' + className + '">';
-      html += HTML.textElement("h2", header);
-      html += "<ul>";
-      html += HTML.arrayToLI(list);
-      html += "</ul>";
-      html += "</div>";
+    #getObsLinks() {
+        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,
+                ),
+            );
+        }
+
+        return links;
     }
-    return html;
-  }
 
-  #getRarityInfo() {
-    const cnpsRank = this.#taxon.getRPIRankAndThreat();
-    if (!cnpsRank) {
-      return "";
+    /**
+     * @param {string[]} list
+     * @param {string} header
+     * @param {string} className
+     */
+    #getListSectionHTML(list, header, className) {
+        let html = "";
+        if (list.length > 0) {
+            html += '<div class="section nobullet ' + className + '">';
+            html += HTML.textElement("h2", header);
+            html += "<ul>";
+            html += HTML.arrayToLI(list);
+            html += "</ul>";
+            html += "</div>";
+        }
+        return html;
     }
-    const ranks = [];
-
-    ranks.push(
-      HTML.textElement("span", "CNPS Rare Plant Rank:", {
-        class: "label",
-      }) + HTML.getToolTip(cnpsRank, this.#taxon.getRPIRankAndThreatTooltip())
-    );
-    if (this.#taxon.getCESA()) {
-      ranks.push(
-        HTML.textElement("span", "CESA:", { class: "label" }) +
-          RarePlants.getCESADescription(this.#taxon.getCESA())
-      );
+
+    #getRarityInfo() {
+        const cnpsRank = this.#taxon.getRPIRankAndThreat();
+        if (!cnpsRank) {
+            return "";
+        }
+        const ranks = [];
+
+        ranks.push(
+            HTML.textElement("span", "CNPS Rare Plant Rank:", {
+                class: "label",
+            }) +
+                HTML.getToolTip(
+                    cnpsRank,
+                    this.#taxon.getRPIRankAndThreatTooltip(),
+                ),
+        );
+        if (this.#taxon.getCESA()) {
+            ranks.push(
+                HTML.textElement("span", "CESA:", { class: "label" }) +
+                    RarePlants.getCESADescription(this.#taxon.getCESA()),
+            );
+        }
+
+        return HTML.wrap("div", "<ul>" + HTML.arrayToLI(ranks) + "</ul>", {
+            class: "section",
+        });
     }
 
-    return HTML.wrap("div", "<ul>" + HTML.arrayToLI(ranks) + "</ul>", {
-      class: "section",
-    });
-  }
-
-  #getRelatedTaxaLinks() {
-    const links = [];
-    const genus = this.#taxon.getGenus();
-    if (genus) {
-      const taxa = genus.getTaxa();
-      if (taxa.length > 1) {
-        for (const taxon of taxa) {
-          links.push(
-            taxon.getHTMLLink(taxon.getName() !== this.#taxon.getName())
-          );
+    #getRelatedTaxaLinks() {
+        const links = [];
+        const genus = this.#taxon.getGenus();
+        if (genus) {
+            const taxa = genus.getTaxa();
+            if (taxa.length > 1) {
+                for (const taxon of taxa) {
+                    links.push(
+                        taxon.getHTMLLink(
+                            taxon.getName() !== this.#taxon.getName(),
+                        ),
+                    );
+                }
+            }
         }
-      }
+        return links;
     }
-    return links;
-  }
 
-  #getSynonyms() {
-    return this.#taxon.getSynonyms();
-  }
+    #getSynonyms() {
+        return this.#taxon.getSynonyms();
+    }
 
-  render() {
-    let html = this.getFrontMatter();
+    render() {
+        let html = this.getFrontMatter();
 
-    html += '<div class="wrapper">';
+        html += '<div class="wrapper">';
 
-    const cn = this.#taxon.getCommonNames();
-    if (cn.length > 0) {
-      html += HTML.textElement("div", cn.join(", "), {
-        class: "section common-names",
-      });
-    }
+        const cn = this.#taxon.getCommonNames();
+        if (cn.length > 0) {
+            html += HTML.textElement("div", cn.join(", "), {
+                class: "section common-names",
+            });
+        }
 
-    html += HTML.textElement(
-      "div",
-      this.#taxon.getStatusDescription(this.#config),
-      { class: "section native-status" }
-    );
-
-    const family = this.#taxon.getFamily();
-    html += HTML.wrap(
-      "div",
-      HTML.textElement("span", "Family:", { class: "label" }) +
-        HTML.getLink("./" + family.getFileName(), family.getName()),
-      { class: "section" }
-    );
-
-    html += this.#getRarityInfo();
-
-    html += "</div>";
-
-    html += HTMLTaxon.getFlowerInfo(this.#taxon, undefined, false);
-
-    html += this.getMarkdown();
-
-    html += '<div class="grid borders">';
-    html += this.#getListSectionHTML(
-      this.#getInfoLinks(),
-      "References",
-      "info"
-    );
-    html += this.#getListSectionHTML(
-      this.#getObsLinks(),
-      "Observations",
-      "obs"
-    );
-    html += this.#getListSectionHTML(
-      this.#getRelatedTaxaLinks(),
-      "Related Species",
-      "rel-taxa"
-    );
-    html += this.#getListSectionHTML(
-      this.#getSynonyms(),
-      "Synonyms",
-      "synonyms"
-    );
-    html += "</div>";
-
-    const photos = this.#taxon.getPhotos( );
-    if ( photos.length > 0 ) {
-      let photosHtml = "";
-      for ( const photo of photos ) {
-        photosHtml += `
+        html += HTML.textElement(
+            "div",
+            this.#taxon.getStatusDescription(this.#config),
+            { class: "section native-status" },
+        );
+
+        const family = this.#taxon.getFamily();
+        html += HTML.wrap(
+            "div",
+            HTML.textElement("span", "Family:", { class: "label" }) +
+                HTML.getLink("./" + family.getFileName(), family.getName()),
+            { class: "section" },
+        );
+
+        html += this.#getRarityInfo();
+
+        html += "</div>";
+
+        html += HTMLTaxon.getFlowerInfo(this.#taxon, undefined, false);
+
+        html += this.getMarkdown();
+
+        html += '<div class="grid borders">';
+        html += this.#getListSectionHTML(
+            this.#getInfoLinks(),
+            "References",
+            "info",
+        );
+        html += this.#getListSectionHTML(
+            this.#getObsLinks(),
+            "Observations",
+            "obs",
+        );
+        html += this.#getListSectionHTML(
+            this.#getRelatedTaxaLinks(),
+            "Related Species",
+            "rel-taxa",
+        );
+        html += this.#getListSectionHTML(
+            this.#getSynonyms(),
+            "Synonyms",
+            "synonyms",
+        );
+        html += "</div>";
+
+        const photos = this.#taxon.getPhotos();
+        if (photos.length > 0) {
+            let photosHtml = "";
+            for (const photo of photos) {
+                photosHtml += `
           <figure class="col">
             <a href="${photo.getSourceUrl()}">
               <img
@@ -213,27 +222,27 @@ class PageTaxon extends GenericPage {
             </figcaption>
           </figure>
         `;
-      }
-      html += `
+            }
+            html += `
         <h2>Photos</h2>
         <div class="row">
           ${photosHtml}
         </div>
       `;
-    }
+        }
 
-    const footerTextPath =
-      Config.getPackageDir() +
-      "/data/text/" +
-      this.getBaseFileName() +
-      ".footer.md";
-    const footerMarkdown = Markdown.fileToHTML(footerTextPath);
-    if (footerMarkdown) {
-      html += HTML.wrap("div", footerMarkdown, "section");
-    }
+        const footerTextPath =
+            Config.getPackageDir() +
+            "/data/text/" +
+            this.getBaseFileName() +
+            ".footer.md";
+        const footerMarkdown = Markdown.fileToHTML(footerTextPath);
+        if (footerMarkdown) {
+            html += HTML.wrap("div", footerMarkdown, "section");
+        }
 
-    this.writeFile(html);
-  }
+        this.writeFile(html);
+    }
 }
 
 export { PageTaxon };

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.4.8",
+    "version": "0.4.10",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {
@@ -15,7 +15,8 @@
     "types": "./lib/index.d.ts",
     "bin": {
         "ca-plant-list": "scripts/build-site.js",
-        "ca-plant-book": "scripts/build-ebook.js"
+        "ca-plant-book": "scripts/build-ebook.js",
+        "cpl-photos": "scripts/cpl-photos.js"
     },
     "dependencies": {
         "archiver": "^5.3.1",
@@ -25,7 +26,7 @@
         "csv-stringify": "^6.5.1",
         "image-size": "^1.1.1",
         "markdown-it": "^14.1.0",
-        "sharp": "^0.32.1",
+        "sharp": "^0.33.5",
         "svgo-ll": "^5.6.0",
         "unzipper": "^0.10.11"
     },

package/scripts/cpl-photos.js

@@ -0,0 +1,179 @@
+#!/usr/bin/env node
+
+import path from "path";
+import { ErrorLog } from "../lib/errorlog.js";
+import { Program } from "../lib/program.js";
+import { Taxa } from "../lib/taxa.js";
+import { getTaxonPhotos } from "../lib/utils/inat-tools.js";
+import { existsSync } from "fs";
+import { CSV } from "../lib/csv.js";
+
+const PHOTO_FILE_NAME = "inattaxonphotos.csv";
+
+const OPT_LOADER = "loader";
+
+const MAX_PHOTOS = 5;
+
+/**
+ * @param {import("commander").OptionValues} options
+ */
+async function addMissingPhotos(options) {
+    const taxaMissingPhotos = [];
+
+    const taxa = await getTaxa(options);
+    const errorLog = new ErrorLog(options.outputdir + "/log.tsv", true);
+
+    for (const taxon of taxa.getTaxonList()) {
+        const photos = taxon.getPhotos();
+        if (photos.length < MAX_PHOTOS) {
+            taxaMissingPhotos.push(taxon);
+        }
+    }
+
+    const newPhotos = await getTaxonPhotos(taxaMissingPhotos);
+    const currentTaxaPhotos = readPhotos();
+
+    for (const [taxonName, photos] of newPhotos) {
+        let currentPhotos = currentTaxaPhotos.get(taxonName);
+        if (!currentPhotos) {
+            currentPhotos = [];
+            currentTaxaPhotos.set(taxonName, currentPhotos);
+        }
+        for (const photo of photos) {
+            if (currentPhotos.length === MAX_PHOTOS) {
+                break;
+            }
+            if (
+                currentPhotos.some(
+                    (currentPhoto) => currentPhoto.id === photo.id,
+                )
+            ) {
+                continue;
+            }
+            currentPhotos.push(photo);
+            errorLog.log("adding photo", taxonName, photo.id);
+        }
+    }
+
+    errorLog.write();
+
+    // Write updated photo file.
+    const headers = ["name", "id", "ext", "licenseCode", "attrName"];
+    /** @type {string[][]} */
+    const data = [];
+    for (const taxonName of [...currentTaxaPhotos.keys()].sort()) {
+        // @ts-ignore
+        for (const photo of currentTaxaPhotos.get(taxonName)) {
+            data.push([
+                taxonName,
+                photo.id,
+                photo.ext,
+                photo.licenseCode,
+                photo.attrName ?? "",
+            ]);
+        }
+    }
+
+    CSV.writeFile(`${options.outputdir}/${PHOTO_FILE_NAME}`, data, headers);
+}
+
+/**
+ * @param {import("commander").OptionValues} options
+ * @param {import("commander").OptionValues} commandOptions
+ */
+async function checkmissing(options, commandOptions) {
+    const taxa = await getTaxa(options);
+    const errorLog = new ErrorLog(options.outputdir + "/log.tsv", true);
+
+    const minPhotos = commandOptions.minphotos;
+    for (const taxon of taxa.getTaxonList()) {
+        const photos = taxon.getPhotos();
+        if (
+            minPhotos === undefined
+                ? photos.length !== MAX_PHOTOS
+                : photos.length < minPhotos
+        ) {
+            errorLog.log(taxon.getName(), photos.length.toString());
+        }
+    }
+
+    errorLog.write();
+}
+
+/**
+ * @param {import("commander").OptionValues} options
+ * @return {Promise<Taxa>}
+ */
+async function getTaxa(options) {
+    const errorLog = new ErrorLog(options.outputdir + "/errors.tsv", true);
+
+    const loader = options[OPT_LOADER];
+    let taxa;
+    if (loader) {
+        const taxaLoaderClass = await import("file:" + path.resolve(loader));
+        taxa = await taxaLoaderClass.TaxaLoader.loadTaxa(options, errorLog);
+    } else {
+        taxa = new Taxa(
+            Program.getIncludeList(options.datadir),
+            errorLog,
+            options.showFlowerErrors,
+        );
+    }
+
+    errorLog.write();
+    return taxa;
+}
+
+/**
+ * @returns {Map<string,InatPhotoInfo[]>}
+ */
+function readPhotos() {
+    const photosFileName = `./data/${PHOTO_FILE_NAME}`;
+    if (!existsSync(photosFileName)) {
+        return new Map();
+    }
+
+    /** @type {Map<string,{id:string,ext:string,licenseCode:string,attrName:string}[]>} */
+    const taxonPhotos = new Map();
+
+    /** @type {InatCsvPhoto[]} */
+    const csvPhotos = CSV.readFile(photosFileName);
+    for (const csvPhoto of csvPhotos) {
+        const taxonName = csvPhoto.name;
+        let photos = taxonPhotos.get(taxonName);
+        if (!photos) {
+            photos = [];
+            taxonPhotos.set(taxonName, photos);
+        }
+        photos.push({
+            id: csvPhoto.id.toString(),
+            ext: csvPhoto.ext,
+            licenseCode: csvPhoto.licenseCode,
+            attrName: csvPhoto.attrName,
+        });
+    }
+
+    return taxonPhotos;
+}
+
+const program = Program.getProgram();
+program
+    .command("checkmissing")
+    .description("List taxa with less than the maximum number of photos")
+    .option(
+        "--minphotos <number>",
+        "Minimum number of photos. Taxa with fewer than this number will be listed.",
+    )
+    .action((options) => checkmissing(program.opts(), options));
+if (process.env.npm_package_name === "@ca-plant-list/ca-plant-list") {
+    // Only allow updates in ca-plant-list.
+    program
+        .command("addmissing")
+        .description("Add photos to taxa with fewer than the maximum")
+        .action(() => addMissingPhotos(program.opts()));
+}
+program.option(
+    "--loader <path>",
+    "The path (relative to the current directory) of the JavaScript file containing the TaxaLoader class. If not provided, the default TaxaLoader will be used.",
+);
+await program.parseAsync();

package/tmp/config.json

@@ -0,0 +1,21 @@
+{
+    "calflora": {
+        "counties": [
+            "ALA",
+            "CCA"
+        ]
+    },
+    "inat": {
+        "project": "ebcnps"
+    },
+    "labels": {
+        "introduced": "Introduced to the East Bay",
+        "native": "Native to the East Bay",
+        "status-NC": "California native introduced to the East Bay"
+    },
+    "ebook": {
+        "filename": "ebplants",
+        "pub_id": "ebplants",
+        "title": "East Bay Plants"
+    }
+}