@ca-plant-list/ca-plant-list 0.4.3 → 0.4.6

package/lib/taxon.js

@@ -34,6 +34,8 @@ class Taxon {
     #rankGlobal;
     /** @type {string[]} */
     #synonyms = [];
+    /** @type {Photo[]} */
+    #photos = [];
 
     /**
      * @param {TaxonData} data
@@ -92,6 +94,17 @@ class Taxon {
         }
     }
 
+    /**
+     * @param {InatPhoto} photo
+     */
+    addPhoto(photo) {
+        this.#photos = this.#photos.concat( [photo] );
+    }
+
+    getPhotos() {
+        return this.#photos;
+    }
+
     getBaseFileName() {
         // Convert spaces to "-" and remove ".".
         return this.#name.replaceAll(" ", "-").replaceAll(".", "");

package/lib/util.js

@@ -0,0 +1,20 @@
+/**
+ * Break an array into chunks of a desired size
+ * https://github.com/you-dont-need/You-Dont-Need-Lodash-Underscore?tab=readme-ov-file#_chunk
+ * @param {any[]} input
+ * @param {number} size
+ */
+export function chunk( input, size ) {
+    return input.reduce((arr, item, idx) => {
+        return idx % size === 0
+            ? [...arr, [item]]
+            : [...arr.slice(0, -1), [...arr.slice(-1)[0], item]];
+    }, []);
+}
+
+/**
+ * @param {number} time
+ */
+export async function sleep( time ) {
+    return new Promise( resolve => setTimeout( resolve, time ) );
+}

package/lib/web/pagetaxon.js

@@ -4,205 +4,236 @@ import { GenericPage } from "../genericpage.js";
 import { ExternalSites } from "../externalsites.js";
 import { HTML } from "../html.js";
 import { HTMLTaxon } from "../htmltaxon.js";
+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;
+  #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));
     }
-
-    #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;
+    const cfLink = this.#taxon.getCalfloraTaxonLink();
+    if (cfLink) {
+      links.push(cfLink);
     }
-
-    #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;
+    const iNatLink = this.#taxon.getINatTaxonLink();
+    if (iNatLink) {
+      links.push(iNatLink);
     }
-
-    /**
-     * @param {string[]} list
-     * @param {string} header
-     * @param {string} className
-     */
-    #getListSectionHTML(list, header, className) {
-        let html = "";
-        if (list.length > 0) {
-            html += '<div class="section ' + className + '">';
-            html += HTML.textElement("h2", header);
-            html += "<ul>";
-            html += HTML.arrayToLI(list);
-            html += "</ul>";
-            html += "</div>";
-        }
-        return html;
+    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
+        )
+      );
     }
 
-    #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 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>";
+    }
+    return html;
+  }
 
-        return HTML.wrap("div", "<ul>" + HTML.arrayToLI(ranks) + "</ul>", {
-            class: "section",
-        });
+  #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())
+      );
     }
 
-    #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 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())
+          );
         }
-        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>";
-
-        this.writeFile(html);
+    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="${photo.getSourceUrl()}">
+              <img
+                class="img-fluid"
+                src="${photo.getUrl()}"
+              />
+            </a>
+            <figcaption>
+              ${photo.rights === "CC0" ? "By" : "(c)"}
+              ${photo.rightsHolder}
+              ${photo.rights && `(${photo.rights})`}
+            </figcaption>
+          </figure>
+        `;
+      }
+      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");
+    }
+
+    this.writeFile(html);
+  }
 }
 
 export { PageTaxon };

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.4.3",
+    "version": "0.4.6",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {
@@ -19,21 +19,24 @@
     },
     "dependencies": {
         "archiver": "^5.3.1",
+        "cli-progress": "^3.12.0",
         "commander": "^12.1.0",
         "csv-parse": "^5.3.1",
+        "csv-stringify": "^6.5.1",
         "image-size": "^1.1.1",
-        "markdown-it": "^13.0.1",
+        "markdown-it": "^14.1.0",
         "sharp": "^0.32.1",
-        "svgo-ll": "^5.4.0",
+        "svgo-ll": "^5.6.0",
         "unzipper": "^0.10.11"
     },
     "devDependencies": {
         "@types/archiver": "^6.0.2",
+        "@types/cli-progress": "^3.11.6",
         "@types/markdown-it": "^14.1.2",
-        "@types/node": "^22.5.5",
+        "@types/node": "^22.7.8",
         "@types/unzipper": "^0.10.9",
         "ajv-cli": "^5.0.0",
-        "eslint": "^8.26.0",
-        "typescript": "^5.3.3"
+        "eslint": "^9.13.0",
+        "typescript": "^5.6.3"
     }
 }

package/scripts/build-site.js

@@ -42,7 +42,7 @@ class JekyllRenderer {
         addConfigFile(configFiles, this.#srcDir, "_config.yml");
         addConfigFile(configFiles, this.#srcDir, "_config-local.yml");
         addConfigFile(configFiles, ".", "_config-dev.yml");
-        options.push("--config", '"' + configFiles.join() + '"');
+        options.push("--config", `"${configFiles.join()}"`);
 
         const result = child_process.execSync(
             "bundle exec jekyll build " + options.join(" ")

package/scripts/inattaxonphotos.js

@@ -0,0 +1,106 @@
+#!/usr/bin/env node
+
+import fs from "fs";
+import cliProgress from "cli-progress";
+import { stringify } from "csv-stringify";
+import path from "path";
+
+import { ErrorLog } from "../lib/errorlog.js";
+import { Program } from "../lib/program.js";
+import { Taxa } from "../lib/taxa.js";
+import { chunk, sleep } from "../lib/util.js";
+
+// While I'm guessing the products of this data will be non-commercial, it's
+// not clear how they'll be licensed so the ShareAlike clause is out, and
+// they'll probably be derivative works so the "No Derivatives" clause should
+// be respected.
+const ALLOWED_LICENSE_CODES = [
+    "cc0", "cc-by", "cc-by-nc"
+];
+
+/**
+ * @param {Taxon[]} taxa
+ * @return {Promise<InatApiTaxon[]>}
+ */
+async function fetchInatTaxa( taxa ) {
+    const inatTaxonIDs = taxa.map( taxon => taxon.getINatID( ) ).filter( Boolean );
+    const url = `https://api.inaturalist.org/v2/taxa/${inatTaxonIDs.join( "," )}?fields=(taxon_photos:(photo:(medium_url:!t,attribution:!t,license_code:!t)))`;
+    const resp = await fetch( url );
+    if (!resp.ok) {
+        const error = await resp.text();
+        throw new Error(`Failed to fetch taxa from iNat: ${error}`);
+    }
+    const json = await resp.json();
+    return json.results;
+}
+
+/**
+ * @param {CommandLineOptions} options
+ */
+async function getTaxonPhotos( options ) {
+    const errorLog = new ErrorLog(options.outputdir + "/errors.tsv");
+    const taxa = new Taxa(
+        Program.getIncludeList(options.datadir),
+        errorLog,
+        false
+    );
+    const targetTaxa = taxa.getTaxonList( );
+
+    const filename = path.join( "data", "inattaxonphotos.csv" );
+    const writableStream = fs.createWriteStream( filename );
+    const columns = [
+        "name",
+        "id",
+        "ext",
+        "licenseCode",
+        "attrName",
+    ];
+    const stringifier = stringify( { header: true, columns: columns } );
+    stringifier.pipe(writableStream);
+    const prog = new cliProgress.SingleBar({
+        format: "Downloading [{bar}] {percentage}% | ETA: {eta}s | {value}/{total}",
+        etaBuffer: targetTaxa.length
+    });
+    prog.setMaxListeners( 100 );
+    prog.start( targetTaxa.length, 0 );
+
+    // Fetch endpoint can load multiple taxa, but it will created some long URLs so best to keep this smallish
+    for ( const batch of chunk( targetTaxa, 30 ) ) {
+        const inatTaxa = await fetchInatTaxa( batch );
+        for ( const taxon of batch ) {
+            prog.increment( );
+            const iNatTaxon = inatTaxa.find( it => it.id === Number( taxon.getINatID() ) );
+            if ( !iNatTaxon ) continue;
+            // Just get the CC-licensed ones, 5 per taxon should be fine (max is 20 on iNat). Whether or not 
+            const taxonPhotos = iNatTaxon.taxon_photos
+                .filter( tp => ALLOWED_LICENSE_CODES.includes( tp.photo.license_code ) )
+                .slice( 0, 5 );
+
+            for ( const taxonPhoto of taxonPhotos ) {
+                const row = [
+                    taxon.getName(),
+                    taxonPhoto.photo.id,
+                    taxonPhoto.photo.medium_url.split( "." ).at( -1 ),
+                    // Need the license code to do attribution properly
+                    taxonPhoto.photo.license_code,
+                    // Photographers retain copyright for most CC licenses,
+                    // except CC0, so attribution is a bit different
+                    (
+                        taxonPhoto.photo.attribution.match( /\(c\) (.*?),/ )?.[1]
+                        || taxonPhoto.photo.attribution.match( /uploaded by (.*)/ )?.[1]
+                    )
+                ];
+                stringifier.write( row );
+            }
+        }
+        // iNat will throttle you if you make more than 1 request a second.
+        // See https://www.inaturalist.org/pages/api+recommended+practices
+        await sleep( 1_100 );
+    }
+    prog.stop();
+}
+
+const program = Program.getProgram();
+program.action(getTaxonPhotos).description( "Write a CSV to datadir with iNaturalist taxon photos" );
+
+await program.parseAsync();