@ca-plant-list/ca-plant-list 0.4.4 → 0.4.6

package/data/taxa.csv

@@ -114,6 +114,7 @@ Antirrhinum kelloggii,,N,13568,401,165675
 Antirrhinum majus,snapdragon,X,13557,404,48969
 Antirrhinum thompsonii,Sierra snapdragon,N,108978,14286,168306,,pink,4,8
 Antirrhinum vexillocalyculatum subsp. vexillocalyculatum,,N,88873,10499,840919,annual,purple,6,8
+Aphanes occidentalis,western lady's mantle,N,13608,,1452907,annual,,3,5
 Aphyllon californicum subsp. jepsonii,,N,103325,13438,802459
 Aphyllon epigalium subsp. epigalium,,N,103327,13527,809377
 Aphyllon fasciculatum,clustered broom-rape,N,100018,13441,802543

package/eslint.config.mjs

@@ -0,0 +1,13 @@
+export default [
+    {
+        rules: {
+            indent: ["error", 4, {
+                SwitchCase: 1,
+            }],
+
+            "linebreak-style": ["error", "unix"],
+            quotes: ["error", "double"],
+            semi: ["error", "always"],
+        },
+    }
+];

package/jekyll/index.md

@@ -1,3 +1,6 @@
 ---
+layout: html
 title: HOME PAGE
 ---
+
+This is the home page.

package/lib/ebook/plantbook.js

@@ -167,7 +167,7 @@ class PlantBook extends EBook {
 function getRequiredConfigValue(config, name) {
   const value = config.getConfigValue("ebook", name);
   if (value === undefined) {
-    throw new Error();
+    throw new Error(`Failed to find ebook config for ${name}`);
   }
   return value;
 }

package/lib/inat_photo.js

@@ -0,0 +1,43 @@
+import {
+    CC0,
+    CC_BY,
+    CC_BY_NC,
+    COPYRIGHT,
+    Photo,
+} from "./photo.js";
+
+class InatPhoto extends Photo {
+    /** @type {number} */
+    inatPhotoId;
+    /** @type {string} */
+    ext;
+
+    /**
+     * @param {number} id
+     * @param {string} ext
+     * @param {InatLicenseCode} licenseCode
+     * @param {string} attrName
+     */
+    constructor( id, ext, licenseCode, attrName ) {
+        /** @type {typeof COPYRIGHT | typeof CC_BY | typeof CC_BY_NC | typeof CC0} */
+        let rights = COPYRIGHT;
+        if ( licenseCode === "cc0" ) rights = CC0;
+        else if ( licenseCode === "cc-by" ) rights = CC_BY;
+        else if ( licenseCode === "cc-by-nc" ) rights = CC_BY_NC;
+        super( null, attrName, rights );
+        this.inatPhotoId = id;
+        this.ext = ext;
+    }
+
+    getUrl() {
+        return `https://inaturalist-open-data.s3.amazonaws.com/photos/${this.inatPhotoId}/medium.${this.ext}`;
+    }
+
+    getSourceUrl() {
+        return `https://www.inaturalist.org/photos/${this.inatPhotoId}`;
+    }
+}
+
+export {
+    InatPhoto
+};

package/lib/photo.js

@@ -0,0 +1,44 @@
+const CC0 = "CC0";
+const CC_BY = "CC BY";
+const CC_BY_NC = "CC BY-NC";
+const COPYRIGHT = "C";
+
+class Photo {
+    /** @type {string?} */
+    #url;
+    /** @type {string?} */
+    rightsHolder;
+    /** @type {null | typeof COPYRIGHT | typeof CC_BY | typeof CC_BY_NC | typeof CC0} */
+    rights;
+
+    /**
+     * @param {string?} url
+     * @param {string?} rightsHolder
+     * @param {null | typeof COPYRIGHT | typeof CC_BY | typeof CC_BY_NC | typeof CC0} rights
+     */
+    constructor( url, rightsHolder, rights ) {
+        this.#url = url;
+        this.rightsHolder = rightsHolder;
+        this.rights = rights;
+    }
+
+    getUrl() {
+        return this.#url;
+    }
+
+    /**
+     * Return URL of page from whence this photo came
+     * @return {string?}
+     */
+    getSourceUrl() {
+        return null;
+    }
+}
+
+export {
+    CC0,
+    CC_BY,
+    CC_BY_NC,
+    COPYRIGHT,
+    Photo
+};

package/lib/taxa.js

@@ -1,9 +1,13 @@
+import * as fs from "node:fs";
+import path from "node:path";
+
 import { Config } from "./config.js";
 import { CSV } from "./csv.js";
 import { Genera } from "./genera.js";
 import { Taxon } from "./taxon.js";
 import { Families } from "./families.js";
 import { FlowerColor } from "./flowercolor.js";
+import { InatPhoto } from "./inat_photo.js";
 
 const FLOWER_COLORS = [
     { name: "white", color: "white" },
@@ -35,6 +39,7 @@ class Taxa {
      * @param {function(TaxonData,Genera):Taxon} taxonFactory
      * @param {TaxonData[]} [extraTaxa=[]]
      * @param {SynonymData[]} [extraSynonyms=[]]
+     * @param {boolean} includePhotos
      */
     constructor(
         inclusionList,
@@ -42,7 +47,8 @@ class Taxa {
         showFlowerErrors,
         taxonFactory = (td, g) => new Taxon(td, g),
         extraTaxa = [],
-        extraSynonyms = []
+        extraSynonyms = [],
+        includePhotos = true
     ) {
         this.#isSubset = inclusionList !== true;
 
@@ -76,11 +82,39 @@ class Taxa {
             a.getName().localeCompare(b.getName())
         );
 
+
+        if ( includePhotos ) {
+            this.#loadInatPhotos( dataDir );
+        }
+
         const synCSV = CSV.parseFile(dataDir, "synonyms.csv");
         this.#loadSyns(synCSV, inclusionList);
         this.#loadSyns(extraSynonyms, inclusionList);
     }
 
+    /**
+     * @param {string} dataDir
+     */
+    #loadInatPhotos( dataDir ) {
+        const photosFileName = "inattaxonphotos.csv";
+        if ( fs.existsSync( path.join( dataDir, photosFileName ) ) ) {
+            /** @type {InatCsvPhoto[]} */
+            const csvPhotos = CSV.parseFile( dataDir, photosFileName );
+            for ( const csvPhoto of csvPhotos ) {
+                const taxon = this.getTaxon(csvPhoto.name);
+                if(!taxon) {
+                    continue;
+                }
+                taxon.addPhoto(new InatPhoto(
+                    csvPhoto.id,
+                    csvPhoto.ext,
+                    csvPhoto.licenseCode,
+                    csvPhoto.attrName
+                ) );
+            }
+        }
+    }
+
     getFamilies() {
         return this.#families;
     }
@@ -175,9 +209,9 @@ class Taxa {
                     const color = this.#flower_colors[colorName];
                     if (!color) {
                         throw new Error(
-                            'flower color "' +
+                            "flower color \"" +
                                 colorName +
-                                '" not found for ' +
+                                "\" not found for " +
                                 name
                         );
                     }

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

@@ -194,6 +194,34 @@ class PageTaxon extends GenericPage {
     );
     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/" +

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.4.4",
+    "version": "0.4.6",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {
@@ -19,16 +19,19 @@
     },
     "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": "^14.1.0",
         "sharp": "^0.32.1",
-        "svgo-ll": "^5.5.0",
+        "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": "^22.7.8",
         "@types/unzipper": "^0.10.9",

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();

package/types/classes.d.ts

@@ -91,7 +91,7 @@ declare class Taxa {
 
 declare class TaxaCol {
     class?: string;
-    data: function (Taxon):string;
+    data:  (taxon:Taxon)=>string
     title: string;
 }
 
@@ -120,6 +120,7 @@ declare class Taxon {
     getJepsonID(): string;
     getLifeCycle(): string;
     getName(): string;
+    getPhotos(): Photo[];
     getRPIRank(): string;
     getRPIRankAndThreat(): string;
     getRPIRankAndThreatTooltip(): string;
@@ -152,3 +153,48 @@ declare class TaxonImage {
     getCaption(): string | undefined;
     getSrc(): string;
 }
+
+type PhotoRights = "CC0"| "CC BY"| "CC BY-NC"| "C"|null;
+
+declare class Photo {
+    url?: string;
+    rightsHolder: null | string;
+    rights?: PhotoRights;
+    getUrl: ( ) => string;
+    getSourceUrl: ( ) => string;
+}
+
+declare class InatPhoto extends Photo {
+    inatPhotoId: number;
+    ext: string;
+}
+
+type InatLicenseCode = "cc-by-nc-sa"
+    | "cc-by-nc"
+    | "cc-by-nc-nd"
+    | "cc-by"
+    | "cc-by-sa"
+    | "cc-by-nd"
+    | "pd"
+    | "gdfl"
+    | "cc0";
+
+declare class InatCsvPhoto {
+    name: string;
+    id: number;
+    ext: string;
+    licenseCode: InatLicenseCode;
+    attrName: string;
+}
+
+declare class InatApiTaxon {
+    id: number;
+    taxon_photos: {
+        photo: {
+            id: number;
+            attribution: string;
+            license_code: InatLicenseCode
+            medium_url: string;
+        }
+    }[]
+}

package/.vscode/settings.json

@@ -1,12 +0,0 @@
-{
-    "editor.formatOnSave": true,
-    "editor.defaultFormatter": "esbenp.prettier-vscode",
-    "prettier.tabWidth": 4,
-    "json.schemas": [
-        {
-            "fileMatch": ["**/exceptions.json"],
-            "url": "./schemas/exceptions.schema.json"
-        }
-    ],
-    "editor.tabSize": 2
-}