@ca-plant-list/ca-plant-list 0.4.29 → 0.4.31

package/data/taxa.csv

@@ -94,7 +94,8 @@ Amsinckia grandiflora,large-flowered fiddleneck,N,13130,323,75424,202030,,Large-
 Amsinckia intermedia,fiddleneck,N,13131,11324,49141,202031,,Common Fiddleneck
 Amsinckia lunaris,bent-flower fiddleneck,N,13139,324,75425,202032,,Bent Flowered Fiddleneck,,,,,5,1B.2,,,S3,G3
 Amsinckia lycopsoides,,N,13140,325,58048,202033,,Bugloss-flowered Fiddleneck
-Amsinckia menziesii,rancher's fireweed,N,13145,326,55436,202034,,Menzies' Fiddleneck,,orange
+Amsinckia menziesii,rancher's fireweed,N,13145,326,55436,202034,,Menzies' Fiddleneck,annual,orange
+Amsinckia retrorsa,rigid fiddleneck,N,13147,11325,58049,202037,,Rigid Fiddleneck,annual,yellow,2,5
 Amsinckia tessellata var. gloriosa,,N,77019,333,80365,202042,,Carrizo Fiddleneck
 Amsinckia tessellata var. tessellata,devil's lettuce,N,77020,334,58852,202043,,Desert Fiddleneck
 Amsinckia vernicosa,,N,13155,335,58051,202027,,Green Fiddleneck
@@ -207,7 +208,8 @@ Balsamorhiza deltoidea,,N,1634,1047,70383,202414,true,Balsam Deltoid
 Balsamorhiza macrolepis,,N,1639,1051,69665,211633,true,California Balsamroot,,,,,350,1B.2,,,S2,G2
 Barbarea orthoceras,winter cress,N,15481,1057,52976,11356,true,American Wintercress,,yellow,3,7
 Bassia hyssopifolia,,X,15511,1060,58125,109432,true
-Bellardia trixago var. trixago,,X,8635,14706,1115038,416937,Bellardia trixago
+Bellardia trixago var. trixago,Mediterranean lineseed,X,8635,14706,1115038,416937,Bellardia trixago,,annual,"white,pink",4,8
+Bellardia viscosa,yellow glandweed,X,103729,14707,537967,206574,true,,annual,yellow,4,10
 Bellis perennis,English daisy,X,1652,1065,55563,202429,true
 Berberis aquifolium var. aquifolium,,N,71483,1068,126887,45198,Berberis aquifolium,Piper's Barberry
 Berberis aquifolium var. dictyota,,N,76967,1069,775436,45199,Berberis dictyota,Shining Netvein Barberry
@@ -636,7 +638,7 @@ Elymus condensatus,giant wild-rye,N,24165,11636,164673,140055,Leymus condensatus
 Elymus elymoides var. elymoides,squirreltail,N,72180,11639,58377,211223,Elymus elymoides subsp. elymoides,Squirreltail
 Elymus glaucus subsp. glaucus,blue wildrye,N,50264,2937,57171,167143,true,Western Rye Grass
 Elymus glaucus subsp. virescens,,N,50266,2939,61203,206754,true,Blue Wildrye
-Elymus hispidus,wheatgrass,X,24153,11640,155848,140096,Thinopyrum intermedium subsp. barbulatum
+Elymus hispidus,wheatgrass,X,24153,11640,155848,140096,Thinopyrum intermedium
 Elymus mollis subsp. mollis,,N,70142,11641,118426,206755,Leymus mollis subsp. mollis,Dune Wild Rye
 Elymus multisetus,big squirreltail,N,24122,2941,57167,140134,true,Big Squirreltail
 Elymus ponticus,tall wheatgrass,X,91896,11643,1301269,206756,Thinopyrum ponticum
@@ -783,7 +785,7 @@ Festuca elmeri,Elmer fescue,N,25798,3580,64333,141011,true,Elmer Fescue
 Festuca idahoensis,Idaho fescue,N,25808,3581,61200,141076,true,Idaho Fescue
 Festuca microstachys,,N,25865,11688,77138,141123,Vulpia microstachys var. ciliata,Pacific Fescue
 Festuca myuros,zorro grass,X,25869,11689,77140,141133,Vulpia myuros
-Festuca octoflora,six-week's fescue,N,25872,11690,77141,141148,Vulpia octoflora var. hirtella,Six Weeks Fescue
+Festuca octoflora,six-week's fescue,N,25872,11690,77141,141148,Vulpia octoflora,Six Weeks Fescue
 Festuca perennis,Italian ryegrass,X,91964,11691,52801,203852,Lolium multiflorum
 Festuca rubra,red fescue,N,25825,3586,61061,141223,true,Red Fescue
 Festuca temulenta,darnel,X,93753,11692,164712,203853,Lolium temulentum
@@ -1557,7 +1559,7 @@ Romulea rosea var. australis,,X,65230,7162,68895,207249
 Rorippa curvisiliqua,yellow cress,N,41580,7168,58866,30089,true,Curvepod Yellowcress
 Rorippa palustris subsp. palustris,,N,52673,11988,64157,43562,true,Bog Yellowcress
 Rosa californica,California rose,N,41631,7179,53437,30158,true,California Wildrose,,pink
-Rosa gymnocarpa,wood rose,N,41652,7182,53441,30212,true,Baldhip Rose,,pink
+Rosa gymnocarpa,wood rose,N,41652,7182,53441,30212,true,Wood Rose,,pink
 Rosa rubiginosa,sweet-brier,X,41648,11057,78886,30313,true
 Rosa spithamea,ground rose,N,41696,7187,53442,30338,true,Ground Rose
 Rubus armeniacus,Himalayan blackberry,X,87465,10319,61317,30459
@@ -1737,7 +1739,7 @@ Stephanomeria virgata subsp. pleurocarpa,,N,6227,7806,58849,206092,true,Wand Wir
 Stipa cernua,nodding needlegrass,N,45640,12042,165654,149288,Nassella cernua,Nodding Needle Grass
 Stipa lemmonii var. lemmonii,Lemmon's needlegrass,N,73899,12053,1220756,173006,Achnatherum lemmonii subsp. lemmonii
 Stipa lepida,foothill needlegrass,N,45641,12054,165656,149399,Nassella lepida,Foothill Needlegrass
-Stipa miliacea var. miliacea,smilo grass,X,91920,12058,524183,206097,Piptatherum miliaceum subsp. miliaceum
+Stipa miliacea var. miliacea,smilo grass,X,91920,12058,524183,206097,Piptatherum miliaceum
 Stipa pulchra,purple needlegrass,N,45644,12067,165659,149498,Nassella pulchra,Purple Needlegrass
 Streptanthus albidus subsp. peramoenus,most beautiful jewelflower,N,53142,7814,58783,258754,Streptanthus glandulosus subsp. glandulosus,,,,,,1490,1B.2,,,S2,G2T2
 Streptanthus breweri,,N,45725,7822,79258,32606,true,Brewer's Jewelflower

package/lib/csv.js

@@ -5,7 +5,7 @@ import { parse as parseSync } from "csv-parse/sync";
 import { parse } from "csv-parse";
 import { stringify } from "csv-stringify/sync";
 
-class CSV {
+export class CSV {
     /**
      * @param {string} fileName
      * @param {import("csv-parse").ColumnOption[]|boolean|function (string[]):string[]} columns
@@ -95,10 +95,11 @@ class CSV {
     }
 
     /**
+     * @template T
      * @param {string} fileName
      * @param {boolean|import("csv-parse").ColumnOption[]|function (string[]):string[]} [columns]
      * @param {string} [delimiter]
-     * @returns {Object<string,string>[]}
+     * @returns {T[]}
      */
     static readFile(fileName, columns = true, delimiter) {
         const content = fs.readFileSync(fileName);
@@ -155,5 +156,3 @@ class CSV {
         fs.writeFileSync(fileName, content.replaceAll(/,+\n/g, "\n"));
     }
 }
-
-export { CSV };

package/lib/externalsites.js

@@ -88,20 +88,26 @@ export class ExternalSites {
     }
 
     /**
-     * @param {import("./types.js").Taxon} taxon
+     * @param {{taxon_id?:string,taxon_name?:string,subview?:"map"|"table",view?:"species"}} params
      * @param {import("./config.js").Config} config
      * @returns {URL|undefined}
      */
-    static getInatObsLink(taxon, config) {
-        const iNatID = taxon.getINatID();
-        if (!iNatID) {
-            return;
-        }
-
+    static getInatObsLink(params, config) {
         const url = new URL(
-            "https://www.inaturalist.org/observations?subview=map",
+            "https://www.inaturalist.org/observations?subview=map&iconic_taxa=Plantae",
         );
-        url.searchParams.set("taxon_id", iNatID);
+        if (params.subview) {
+            url.searchParams.set("subview", params.subview);
+        }
+        if (params.taxon_id) {
+            url.searchParams.set("taxon_id", params.taxon_id);
+        }
+        if (params.taxon_name) {
+            url.searchParams.set("taxon_name", params.taxon_name);
+        }
+        if (params.view) {
+            url.searchParams.set("view", params.view);
+        }
         for (const p of ["place_id", "project_id"]) {
             const v = config.getConfigValue("inat", p);
             if (v) {

package/lib/htmltaxon.js

@@ -60,7 +60,11 @@ const OBSLINKS = {
     },
     inat: {
         label: "iNaturalist",
-        href: (taxon, config) => ExternalSites.getInatObsLink(taxon, config),
+        href: (taxon, config) =>
+            ExternalSites.getInatObsLink(
+                { taxon_id: taxon.getINatID() },
+                config,
+            ),
     },
 };
 
@@ -120,6 +124,45 @@ class HTMLTaxon {
      */
     static addObsLink(links, taxon, config, sourceCode, label) {
         const source = OBSLINKS[sourceCode];
+        if (sourceCode === "inat") {
+            const iNatName = taxon.getINatName().split(" ");
+            /** @type {string[]} */
+            const iNatLinks = [];
+            iNatLinks.push(
+                HTML.getLink(
+                    ExternalSites.getInatObsLink(
+                        { taxon_name: iNatName[0], view: "species" },
+                        config,
+                    ),
+                    `Genus ${iNatName[0]}`,
+                    undefined,
+                    true,
+                ),
+            );
+            if (iNatName.length > 2) {
+                const species = `${iNatName[0]} ${iNatName[1]}`;
+                iNatLinks.push(
+                    HTML.getLink(
+                        ExternalSites.getInatObsLink(
+                            { taxon_name: species },
+                            config,
+                        ),
+                        species,
+                        undefined,
+                        true,
+                    ),
+                );
+            }
+            this.addLink(
+                iNatLinks,
+                source.href(taxon, config),
+                taxon.getINatSyn() ?? taxon.getName(),
+            );
+
+            const html = HTML.textElement("span", label ?? source.label);
+            links.push(html + HTML.wrap("ul", HTML.arrayToLI(iNatLinks)));
+            return;
+        }
         this.addLink(links, source.href(taxon, config), label ?? source.label);
     }
 

package/lib/index.d.ts

@@ -82,10 +82,7 @@ export class Config {
 }
 
 export class CSV {
-    static readFile(
-        fileName: string,
-        delimeter?: string,
-    ): Record<string, string>[];
+    static readFile<T>(fileName: string, delimeter?: string): T[];
     static writeFileObject(
         fileName: string,
         data: Record<string, any>[],
@@ -129,6 +126,21 @@ export class Files {
 
 export class Genera {}
 
+export class GenericPage {
+    constructor(
+        siteGenerator: SiteGenerator,
+        title: string,
+        baseFileName: string,
+        js?: string,
+    );
+    getBaseFileName(): string;
+    getFrontMatter(): string;
+    getOutputDir(): string;
+    getSiteGenerator(): SiteGenerator;
+    getTitle(): string;
+    writeFile(content: string): void;
+}
+
 export class Genus<T extends Taxon> {
     getTaxa(): T[];
 }

package/lib/index.js

@@ -6,6 +6,7 @@ import { Exceptions } from "./exceptions.js";
 import { ExternalSites } from "./externalsites.js";
 import { Families } from "./taxonomy/families.js";
 import { Files } from "./files.js";
+import { GenericPage } from "./web/pageGeneric.js";
 import { HTML } from "./html.js";
 import { HTMLFragments } from "./utils/htmlFragments.js";
 import { HTMLTaxon } from "./htmltaxon.js";
@@ -24,6 +25,7 @@ export {
     ExternalSites,
     Families,
     Files,
+    GenericPage,
     HTML,
     HTMLFragments,
     HTMLTaxon,

package/lib/photo.js

@@ -60,6 +60,15 @@ export class Photo {
      * @returns {string} The URL to retrieve the image file.
      */
     getUrl() {
-        return `https://inaturalist-open-data.s3.amazonaws.com/photos/${this.#id}/medium.${this.#ext}`;
+        return Photo.getUrl(this.#id, this.#ext);
+    }
+
+    /**
+     * @param {number|string} id
+     * @param {string} ext
+     * @returns {string} The URL to retrieve the image file.
+     */
+    static getUrl(id, ext) {
+        return `https://inaturalist-open-data.s3.amazonaws.com/photos/${id}/medium.${ext}`;
     }
 }

package/lib/tools/inat.js

@@ -3,6 +3,7 @@ import { Files } from "../files.js";
 import { CSV } from "../csv.js";
 import { sleep } from "../util.js";
 import { TaxaCSV } from "./taxacsv.js";
+import { SynCSV } from "./syncsv.js";
 
 /**
  * @typedef {{id:string,
@@ -65,8 +66,10 @@ export class INat {
 
         const missingTaxa = [];
 
-        /**@type {Map<string,string>} */
+        /** @type {Map<string,string>} */
         const idsToUpdate = new Map();
+        /** @type {import("./syncsv.js").SynData[]} */
+        const synonymsToAdd = [];
 
         for (const taxon of taxa.getTaxonList()) {
             const name = taxon.getName();
@@ -103,12 +106,14 @@ export class INat {
                 errorLog,
                 data.name,
                 data.iNatName,
+                synonymsToAdd,
             );
         }
 
         this.#checkExceptions(taxa, exceptions, errorLog);
 
         if (update) {
+            updateSynCSV(dataDir, synonymsToAdd);
             updateTaxaCSV(dataDir, idsToUpdate);
         }
     }
@@ -167,14 +172,21 @@ export class INat {
     }
 
     /**
-     *
      * @param {import("../types.js").Taxa} taxa
      * @param {import("../exceptions.js").Exceptions} exceptions
      * @param {import("../errorlog.js").ErrorLog} errorLog
      * @param {string} name
      * @param {string} iNatName
+     * @param {import("./syncsv.js").SynData[]} synonymsToAdd
      */
-    static async #findCurrentName(taxa, exceptions, errorLog, name, iNatName) {
+    static async #findCurrentName(
+        taxa,
+        exceptions,
+        errorLog,
+        name,
+        iNatName,
+        synonymsToAdd,
+    ) {
         /**
          * @param {{matched_term:string,name:string,rank:string}[]} results
          * @param {string} iNatName
@@ -242,11 +254,17 @@ export class INat {
                 }
             }
         } else {
+            const formerName = this.makeSynonymName(result, errorLog);
             errorLog.log(
                 name,
                 "found iNat synonym",
-                this.makeSynonymName(result, errorLog) + "," + name + ",INAT",
+                formerName + "," + name + ",INAT",
             );
+            synonymsToAdd.push({
+                Former: formerName,
+                Current: name,
+                Type: "INAT",
+            });
         }
 
         // Delay to throttle queries to iNat API.
@@ -297,6 +315,17 @@ class InatTaxon {
     }
 }
 
+/**
+ * @param {string} dataDir
+ * @param {import("./syncsv.js").SynData[]} synonymsToAdd
+ */
+function updateSynCSV(dataDir, synonymsToAdd) {
+    const csv = new SynCSV(dataDir);
+    const data = csv.getData();
+    data.push(...synonymsToAdd);
+    csv.write();
+}
+
 /**
  * @param {string} dataDir
  * @param {Map<string,string>} idsToUpdate

package/lib/util.js

@@ -1,16 +1,19 @@
 /**
  * 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
+ * @template T
+ * @param {T[]} input
  * @param {number} size
- * @returns {any[][]}
+ * @returns {T[][]}
  */
 export function chunk(input, size) {
+    /** @type {T[][]} */
+    const result = [];
     return input.reduce((arr, item, idx) => {
         return idx % size === 0
             ? [...arr, [item]]
             : [...arr.slice(0, -1), [...arr.slice(-1)[0], item]];
-    }, []);
+    }, result);
 }
 
 /**

package/lib/utils/httpUtils.js

@@ -0,0 +1,10 @@
+export class HttpUtils {
+    /**
+     * @param {URL|string} url
+     * @returns {Promise<boolean>}
+     */
+    static async UrlExists(url) {
+        const response = await fetch(url, { method: "HEAD" });
+        return response.status === 200;
+    }
+}

package/lib/utils/inat-tools.js

@@ -41,11 +41,10 @@ import { chunk, sleep } from "../util.js";
 const ALLOWED_LICENSE_CODES = ["cc0", "cc-by", "cc-by-nc"];
 
 /**
- * @param {import("../types.js").Taxon[]} taxa
+ * @param {string[]} inatTaxonIDs
  * @return {Promise<InatApiTaxon[]>}
  */
-async function fetchInatTaxa(taxa) {
-    const inatTaxonIDs = taxa.map((taxon) => taxon.getINatID()).filter(Boolean);
+async function fetchInatTaxa(inatTaxonIDs) {
     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) {
@@ -77,13 +76,11 @@ export async function getTaxonPhotos(taxaToUpdate) {
     let taxaRetrieved = 0;
 
     for (const batch of chunk(taxaToUpdate, 30)) {
-        const inatTaxa = await fetchInatTaxa(batch);
+        const inatTaxa = await fetchInatTaxa(batch.map((t) => t.getINatID()));
         for (const iNatTaxon of inatTaxa) {
-            const iNatTaxonPhotos = iNatTaxon.taxon_photos
-                .filter((tp) =>
-                    ALLOWED_LICENSE_CODES.includes(tp.photo.license_code),
-                )
-                .slice(0, 5);
+            const iNatTaxonPhotos = iNatTaxon.taxon_photos.filter((tp) =>
+                ALLOWED_LICENSE_CODES.includes(tp.photo.license_code),
+            );
 
             const taxonName = idMap.get(iNatTaxon.id.toString());
             if (!taxonName) {

package/lib/web/pageGeneric.js

@@ -27,8 +27,7 @@ export class GenericPage {
     }
 
     getDefaultIntro() {
-        let html = this.getFrontMatter();
-        return html + this.getMarkdown();
+        return this.getFrontMatter() + this.getMarkdown();
     }
 
     getFrontMatter() {

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.4.29",
+    "version": "0.4.31",
     "description": "Tools to create files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {