@ca-plant-list/ca-plant-list 0.4.13 → 0.4.14

package/data/glossary/awn.md

@@ -0,0 +1 @@
+A bristle-like structure projecting from a [lemma](./lemma.html) or [glume](./glume.html).

package/data/glossary/floret.md

@@ -0,0 +1,4 @@
+A floret is a small flower on a grass [spikelet](./spikelet.html). The floret is composed of:
+
+-   A [lemma](./lemma.html) at the base of the floret.
+-   A [palea](./palea.html), usually smaller than and partially enclosed by the lemma.

package/data/glossary/glume.md

@@ -0,0 +1 @@
+In a grass [spikelet](./spikelet.html), the glume is a bract below all the individual flowers. Each spikelet generally has 2 glumes, one slightly below the other; the lower glume is usually shorter than the upper.

package/data/glossary/lemma.md

@@ -0,0 +1,5 @@
+A bract at the base of a [grass flower](./floret.html) (floret). The lemma is often visually similar to the [glumes](./glume.html), and often has striped veins running along its length.
+
+The lemma may contain an [awn](./awn.html) (a bristle-like structure projecting beyond the lemma).
+
+The lemma is fertile if there is a flower above it (attached to the [rachilla](./rachilla.html) at the same point as the lemma), otherwise it is sterile.

package/data/glossary/palea.md

@@ -0,0 +1 @@
+A bract at the base of a [grass flower](./floret.html) (floret).

package/data/glossary/rachilla.md

@@ -0,0 +1 @@
+In a grass [spikelet](./spikelet.html), the central stem to which other structures are attached.

package/data/glossary/spikelet.md

@@ -0,0 +1,5 @@
+In grasses, a structure holding one or more flowers. The spikelet contains:
+
+-   A [rachilla](./rachilla.html) (central stem) to which the flowers and other structures are attached.
+-   2 [glumes](./glume.html) below all the flowers.
+-   One or more [flowers](./floret.html) (florets) above the glumes.

package/data/synonyms.csv

@@ -1515,7 +1515,7 @@ Phlox gracilis,Microsteris gracilis
 Phoradendron macrophyllum,Phoradendron leucarpum subsp. macrophyllum,INAT
 Phoradendron serotinum subsp. macrophyllum,Phoradendron leucarpum subsp. macrophyllum
 Phoradendron serotinum subsp. tomentosum,Phoradendron leucarpum subsp. tomentosum
-Phoradendron villosum,Phoradendron leucarpum subsp. tomentosum
+Phoradendron villosum,Phoradendron leucarpum subsp. tomentosum,INAT
 Phragmites australis var. berlandieri,Phragmites australis
 Phragmites berlandieri,Phragmites australis
 Phragmites communis var. berlandieri,Phragmites australis

package/data/taxa.csv

@@ -971,7 +971,7 @@ Juncus phaeocephalus var. phaeocephalus,brown-headed rush,N,60393,4491,61036,Bro
 Juncus tenuis,poverty rush,N,29725,4496,69930,Poverty Rush
 Juncus xiphioides,iris-leaved rush,N,29743,4502,57110,Irisleaf Rush
 Juniperus californica,California juniper,N,29749,4503,57889,California Juniper
-Juniperus communis var. saxatilis,mountain juniper,N,60424,10933,,Common Juniper
+Juniperus communis var. saxatilis,mountain juniper,N,60424,10933,81001,Common Juniper
 Keckiella breviflora var. breviflora,,N,75718,4520,59015,Gaping Keckiella
 Keckiella corymbosa,,N,29883,4523,62043,Keckiella
 Kickxia elatine,fluellin,X,29898,4532,64332
@@ -1347,8 +1347,8 @@ Phacelia ramosissima,branching phacelia,N,37557,6389,50617,Branching Phacelia
 Phacelia rattanii,,N,37563,6396,58925,Rattan's Phacelia,,"white,blue",5,7
 Phacelia suaveolens,sweet scented phacelia,N,37577,6402,68816,Sweetscented Phacelia
 Phacelia tanacetifolia,tansy-leaf phacelia,N,37579,6405,58185,Lacy Phacelia
-Phalaris angusta,timothy canary grass,N,37600,6415,78534,Timothy Canary Grass
-Phalaris aquatica,Harding grass,X,37601,6416,57188
+Phalaris angusta,timothy canary grass,N,37600,6415,78534,Timothy Canary Grass,annual,,5,6
+Phalaris aquatica,Harding grass,X,37601,6416,57188,,annual,,4,8
 Phalaris arundinacea,reed canary grass,N,37604,6417,63337,Reed Canarygrass
 Phalaris brachystachys,short-spiked canary grass,X,37605,6418,78535
 Phalaris californica,California canary grass,N,37606,6419,57192,California Canarygrass
@@ -1360,7 +1360,7 @@ Phoenix canariensis,Canary Island date palm,X,37878,6449,78554
 Pholistoma auritum var. auritum,fiesta flower,N,63599,6455,58926,Fiesta Flower
 Pholistoma membranaceum,white fiesta flower,N,37886,6456,57352,White Fiesta Flower
 Phoradendron leucarpum subsp. macrophyllum,big leaf mistletoe,N,98417,13230,166732,Colorado Desert Mistletoe
-Phoradendron leucarpum subsp. tomentosum,oak mistletoe,N,98416,13231,545020,Pacific Mistletoe
+Phoradendron leucarpum subsp. tomentosum,oak mistletoe,N,98416,13231,343310,Pacific Mistletoe
 Phragmites australis,common reed,N,37931,6465,64237,Common Reed
 Phyla lanceolata,,N,37942,6466,59042,Lanceleaf Fogfruit
 Phyla nodiflora,,N,37943,6467,59040,Common Lippia,perennial,white,5,11
@@ -1526,7 +1526,7 @@ Ranunculus orthorhynchus var. bloomeri,,N,64956,7051,81337,Bloomer's Buttercup
 Ranunculus orthorhynchus var. orthorhynchus,,N,64957,7052,81338,Straightbeak Buttercup
 Ranunculus repens,,X,40965,7056,48229
 Ranunculus sceleratus,cursed crowsfoot,N,40971,7059,59301,Cursed Buttercup
-Ranunculus sceleratus var. sceleratus,,X,64987,11983,,,annual,yellow,4,6
+Ranunculus sceleratus var. sceleratus,,X,64987,11983,81341,,annual,yellow,4,6
 Raphanus raphanistrum,jointed charlock,X,40991,7063,55411
 Raphanus sativus,wild radish,X,40992,7064,995125
 Rhamnus alaternus,Italian buckthorn,X,81104,9447,82856

package/jekyll/assets/css/main.css

@@ -1,152 +1,152 @@
 /* Defaults */
 
 :root {
-  /* See https://visme.co/blog/website-color-schemes/ theme 4 */
-  --bs-body-bg: #5cdb95;
-  --bs-link-color: #05386b;
-  --pl-navbar-bg: #379683;
+    /* See https://visme.co/blog/website-color-schemes/ theme 4 */
+    --bs-body-bg: #5cdb95;
+    --bs-link-color: #05386b;
+    --pl-navbar-bg: #379683;
 }
 
 .navbar-nav {
-  --bs-nav-link-hover-color: rgba(255, 255, 255, .5);
+    --bs-nav-link-hover-color: rgba(255, 255, 255, .5);
 }
 
 .navbar {
-  --bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='white' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");
-  --bs-navbar-color: white;
-  --bs-navbar-brand-hover-color: rgba(255, 255, 255, .5);
-  --bs-navbar-brand-color: white;
-  --bs-navbar-nav-link-padding-x: 1rem;
-  background-color: var(--pl-navbar-bg);
+    --bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='white' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");
+    --bs-navbar-color: white;
+    --bs-navbar-brand-hover-color: rgba(255, 255, 255, .5);
+    --bs-navbar-brand-color: white;
+    --bs-navbar-nav-link-padding-x: 1rem;
+    background-color: var(--pl-navbar-bg);
 }
 
 p {
-  margin-bottom: .5rem;
+    margin-bottom: .5rem;
 }
 
 span.label {
-  font-weight: 600;
-  padding-right: .5rem;
+    font-weight: 600;
+    padding-right: .5rem;
 }
 
 td {
-  border: solid 1px;
-  padding: 0 .5rem;
-  vertical-align: top;
+    border: solid 1px;
+    padding: 0 .5rem;
+    vertical-align: top;
 }
 
 th {
-  vertical-align: bottom;
+    vertical-align: bottom;
 }
 
 ul.listmenu {
-  display: flex;
-  padding: 0;
+    display: flex;
+    padding: 0;
 }
 
 ul.listmenu li {
-  display: inline-block;
-  padding: 0;
-  padding-right: .25em;
+    display: inline-block;
+    padding: 0;
+    padding-right: .25em;
 }
 
 ul.listmenu li::after {
-  content: "  |";
+    content: "  |";
 }
 
 ul.listmenu li:last-child:after {
-  content: "";
+    content: "";
 }
 
 /* Utilities */
 .right {
-  text-align: right;
+    text-align: right;
 }
 
 /* Lists */
 
 span.native {
-  font-weight: bold;
+    font-weight: bold;
 }
 
 span.rare::before {
-  content: "\2606";
+    content: "\2606";
 }
 
 /* Glossary */
 div.glossary img {
-  max-height: 300px;
+    max-height: 300px;
 }
 
 /* Taxon Page */
 
 .common-names {
-  font-size: larger;
-  font-weight: bold;
+    font-size: larger;
+    font-weight: bold;
 }
 
 .native-status {
-  font-weight: 600;
+    font-weight: 600;
 }
 
 div.grid {
-  display: grid;
-  grid-auto-flow: row;
-  grid-template-columns: repeat(auto-fit, minmax(15rem, 1fr));
-  column-gap: 2rem;
+    display: grid;
+    grid-auto-flow: row;
+    grid-template-columns: repeat(auto-fit, minmax(15rem, 1fr));
+    column-gap: 2rem;
 }
 
 div.grid.borders>div.section {
-  border: solid 1px;
-  border-radius: 3%;
-  padding: .5rem;
+    border: solid 1px;
+    border-radius: 3%;
+    padding: .5rem;
 }
 
 div.wrapper {
-  display: flex;
-  flex-wrap: wrap;
-  column-gap: 4rem;
+    display: flex;
+    flex-wrap: wrap;
+    column-gap: 4rem;
 }
 
 div.section {
-  margin-bottom: .5rem;
+    margin-bottom: .5rem;
 }
 
 div.section h2 {
-  font-size: 1.25rem;
+    font-size: 1.25rem;
 }
 
 div.section.nobullet ul {
-  margin: 0;
-  padding: 0;
+    margin: 0;
+    padding: 0;
 }
 
 div.section.nobullet li {
-  display: block;
-  margin-left: 1rem;
-  text-indent: -1rem;
+    display: block;
+    padding-left: .5rem;
+    text-indent: -.5rem;
 }
 
 div.section ul.indent {
-  padding-left: 1rem;
+    padding-left: 1rem;
 }
 
 img.flr-color {
-  margin-bottom: .2rem;
-  margin-right: .5rem;
-  width: 1rem;
+    margin-bottom: .2rem;
+    margin-right: .5rem;
+    width: 1rem;
 }
 
 span.flr-time,
 span.lc {
-  font-weight: bold;
+    font-weight: bold;
 }
 
 span.lcs {
-  margin-right: 1rem;
+    margin-right: 1rem;
 }
 
 /* Forms */
 input {
-  margin-right: .5em;
+    margin-right: .5em;
 }

package/lib/html.js

@@ -6,7 +6,7 @@ export class HTML {
     static arrayToLI(items) {
         return items.reduce(
             (itemHTML, currVal) => itemHTML + "<li>" + currVal + "</li>",
-            ""
+            "",
         );
     }
 
@@ -107,7 +107,7 @@ export class HTML {
     /**
      * @param {string} elName
      * @param {string} text
-     * @param {Object<string,string>} attributes
+     * @param {Object<string,string>} [attributes]
      */
     static textElement(elName, text, attributes = {}) {
         return HTML.#getElement(elName, text, attributes, true);

package/lib/htmltaxon.js

@@ -1,5 +1,6 @@
 import { DateUtils } from "./dateutils.js";
 import { HTML } from "./html.js";
+import { Markdown } from "./markdown.js";
 import { RarePlants } from "./rareplants.js";
 import { TextUtils } from "./textutils.js";
 
@@ -136,6 +137,36 @@ class HTMLTaxon {
         );
     }
 
+    /**
+     * @param {string[]} list
+     * @param {string} header
+     * @param {string} [className]
+     */
+    static getListSectionHTML(list, header, className) {
+        let html = "";
+        if (list.length > 0) {
+            html += `<div class="section nobullet${className ? " " + className : ""}">`;
+            html += HTML.textElement("h2", header);
+            html += "<ul>";
+            html += HTML.arrayToLI(list);
+            html += "</ul>";
+            html += "</div>";
+        }
+        return html;
+    }
+
+    /**
+     * @param {string} filePath
+     * @returns {string}
+     */
+    static getMarkdownSection(filePath) {
+        const footerMarkdown = Markdown.fileToHTML(filePath);
+        if (footerMarkdown) {
+            return HTML.wrap("div", footerMarkdown, "section");
+        }
+        return "";
+    }
+
     /**
      * @param {Taxon[]} taxa
      * @param {TaxaCol[]} [columns]

package/lib/index.d.ts

@@ -38,6 +38,39 @@ export class Files {
     static write(fileName: string, data: string, overwrite: boolean): void;
 }
 
+export class HTML {
+    static arrayToLI(items: string[]): string;
+    static getLink(
+        href: string | undefined,
+        linkText: string,
+        attrs?: Record<string, string> | string,
+        openInNewWindow?: boolean,
+    ): string;
+    static textElement(
+        elName: string,
+        text: string,
+        attrs?: Record<string, string>,
+    ): string;
+    static wrap(
+        elName: string,
+        text: string,
+        attrs?: string | Record<string, string> | undefined,
+    ): string;
+}
+
+export class HTMLTaxon {
+    static getListSectionHTML(
+        list: string[],
+        header: string,
+        className?: string,
+    ): string;
+    static getMarkdownSection(filePath: string): string;
+}
+
+export class Jekyll {
+    static include(fileName: string): string;
+}
+
 export class Program {
     static getIncludeList(dataDir: string): string[];
     static getProgram(): Command;
@@ -55,3 +88,18 @@ export class Taxa {
     getTaxon(name: string): Taxon;
     getTaxonList(): Taxon[];
 }
+
+export class Taxon {
+    getBaseFileName(): string;
+    getCalfloraID(): string;
+    getCalfloraTaxonLink(): string;
+    getCommonNames(): string[];
+    getFamily(): Family;
+    getGenus(): Genus;
+    getGenusName(): string;
+    getINatID(): string;
+    getINatTaxonLink(): string;
+    getName(): string;
+    getRPITaxonLink(): string;
+    getSynonyms(): string[];
+}

package/lib/index.js

@@ -6,6 +6,7 @@ import { Exceptions } from "./exceptions.js";
 import { Families } from "./families.js";
 import { Files } from "./files.js";
 import { HTML } from "./html.js";
+import { HTMLTaxon } from "./htmltaxon.js";
 import { Jekyll } from "./jekyll.js";
 import { PlantBook } from "./ebook/plantbook.js";
 import { Program } from "./program.js";
@@ -21,6 +22,7 @@ export {
     Families,
     Files,
     HTML,
+    HTMLTaxon,
     Jekyll,
     PlantBook,
     Program,

package/lib/tools/inat.js

@@ -0,0 +1,316 @@
+import path from "node:path";
+import { Files } from "../files.js";
+import { CSV } from "../csv.js";
+import { sleep } from "../util.js";
+import { TaxaCSV } from "./taxacsv.js";
+
+/**
+ * @typedef {{id:string,
+ * name:string,
+ * phylum:string,
+ * rank:string,
+ * scientificName:string,
+ * specificEpithet:string
+ * }} INatCSVData
+ */
+
+export class INat {
+    /** @type {Object<string,InatTaxon>} */
+    static #taxa = {};
+
+    /**
+     * @param {string} toolsDataDir
+     * @param {string} dataDir
+     * @param {Taxa} taxa
+     * @param {import("../exceptions.js").Exceptions} exceptions
+     * @param {ErrorLog} errorLog
+     * @param {string} csvFileName
+     * @param {boolean} update
+     */
+    static async analyze(
+        toolsDataDir,
+        dataDir,
+        taxa,
+        exceptions,
+        errorLog,
+        csvFileName,
+        update,
+    ) {
+        const inatDataDir = toolsDataDir + "/inat";
+        const csvFilePath = inatDataDir + "/" + csvFileName;
+
+        // Create data directory if it's not there.
+        Files.mkdir(inatDataDir);
+
+        // Download the data file if it doesn't exist.
+        if (!Files.exists(csvFilePath)) {
+            const url =
+                "https://www.inaturalist.org/taxa/inaturalist-taxonomy.dwca.zip";
+            const zipFileName = path.basename(url);
+            const zipFilePath = inatDataDir + "/" + zipFileName;
+            console.log("retrieving iNaturalist species");
+            await Files.fetch(url, zipFilePath);
+            await Files.zipFileExtract(zipFilePath, "taxa.csv", csvFilePath);
+        }
+
+        console.log("loading iNaturalist species");
+        await CSV.parseStream(
+            inatDataDir,
+            csvFileName,
+            undefined,
+            undefined,
+            this.#checkTaxon,
+        );
+        console.log("iNat: " + Object.keys(this.#taxa).length + " taxa loaded");
+
+        const missingTaxa = [];
+
+        /**@type {Map<string,string>} */
+        const idsToUpdate = new Map();
+
+        for (const taxon of taxa.getTaxonList()) {
+            const name = taxon.getName();
+            if (name.includes(" unknown")) {
+                continue;
+            }
+            const iNatName = taxon.getINatName();
+            const iNatTaxon = this.#taxa[iNatName];
+            if (!iNatTaxon) {
+                if (!exceptions.hasException(name, "inat", "notintaxondata")) {
+                    errorLog.log(name, "not found in " + csvFileName, iNatName);
+                }
+                missingTaxa.push({ name: name, iNatName: iNatName });
+                continue;
+            }
+            if (iNatTaxon.getID() !== taxon.getINatID()) {
+                errorLog.log(
+                    name,
+                    "iNat ID in " +
+                        csvFileName +
+                        " does not match ID in taxa.csv",
+                    iNatTaxon.getID(),
+                    taxon.getINatID(),
+                );
+                idsToUpdate.set(name, iNatTaxon.getID());
+            }
+        }
+
+        console.log("iNat: looking up missing names");
+        for (const data of missingTaxa) {
+            await this.#findCurrentName(
+                taxa,
+                exceptions,
+                errorLog,
+                data.name,
+                data.iNatName,
+            );
+        }
+
+        this.#checkExceptions(taxa, exceptions, errorLog);
+
+        if (update) {
+            updateTaxaCSV(dataDir, idsToUpdate);
+        }
+    }
+
+    /**
+     *
+     * @param {Taxa} taxa
+     * @param {import("../exceptions.js").Exceptions} exceptions
+     * @param {ErrorLog} errorLog
+     */
+    static #checkExceptions(taxa, exceptions, errorLog) {
+        // Check the iNat exceptions and make sure they still apply.
+        for (const [name, v] of exceptions.getExceptions()) {
+            const exceptions = v.inat;
+            if (!exceptions) {
+                continue;
+            }
+
+            // Make sure the taxon is still in our list.
+            const taxon = taxa.getTaxon(name);
+            if (!taxon) {
+                // Don't process global exceptions if taxon is not in local list.
+                if (taxa.isSubset() && !v.local) {
+                    continue;
+                }
+                errorLog.log(name, "has iNat exceptions but not in taxa.tsv");
+                continue;
+            }
+
+            for (const [k] of Object.entries(exceptions)) {
+                const iNatData = INat.#taxa[name];
+                switch (k) {
+                    case "notintaxondata":
+                        if (iNatData) {
+                            errorLog.log(
+                                name,
+                                "found in iNat data but has notintaxondata exception",
+                            );
+                        }
+                        break;
+                    default:
+                        errorLog.log(name, "unrecognized iNat exception", k);
+                }
+            }
+        }
+    }
+
+    /**
+     * @param {INatCSVData} record
+     */
+    static #checkTaxon(record) {
+        if (record["phylum"] === "Tracheophyta" && record["specificEpithet"]) {
+            const name = record["scientificName"];
+            INat.#taxa[name] = new InatTaxon(record["id"]);
+        }
+    }
+
+    /**
+     *
+     * @param {Taxa} taxa
+     * @param {import("../exceptions.js").Exceptions} exceptions
+     * @param {ErrorLog} errorLog
+     * @param {string} name
+     * @param {string} iNatName
+     */
+    static async #findCurrentName(taxa, exceptions, errorLog, name, iNatName) {
+        /**
+         * @param {{matched_term:string,name:string,rank:string}[]} results
+         * @param {string} iNatName
+         */
+        function findMatchingResult(results, iNatName) {
+            if (results.length === 1) {
+                return results[0];
+            }
+            let match;
+            for (const result of results) {
+                if (result.matched_term === iNatName) {
+                    if (match) {
+                        errorLog.log(
+                            iNatName,
+                            "found more than one matched_term",
+                            match.matched_term,
+                            result.matched_term,
+                        );
+                        return;
+                    }
+                    match = result;
+                }
+            }
+            return match;
+        }
+
+        const url = new URL("https://api.inaturalist.org/v1/taxa");
+        url.searchParams.set("q", iNatName);
+
+        const response = await fetch(url);
+        const data = await response.json();
+
+        /** @type {{name:string,rank:string}|undefined} */
+        let result = findMatchingResult(data.results, iNatName);
+        if (result === undefined) {
+            const parts = iNatName.split(" ");
+            switch (parts.length) {
+                case 2:
+                    // If it's "genus species", try "genus species species".
+                    parts.push(parts[1]);
+                    iNatName = parts.join(" ");
+                    result = findMatchingResult(data.results, iNatName);
+                    break;
+                case 3:
+                    // If it's "genus species species", try "genus species".
+                    if (parts[1] === parts[2]) {
+                        iNatName = parts[0] + " " + parts[1];
+                        result = findMatchingResult(data.results, iNatName);
+                    }
+                    break;
+            }
+        }
+
+        if (result === undefined) {
+            if (!exceptions.hasException(name, "inat", "notintaxondata")) {
+                errorLog.log(name, "iNat lookup found no results");
+                // Make sure this doesn't have an iNat ID.
+                const iNatID = taxa.getTaxon(name).getINatID();
+                if (iNatID) {
+                    errorLog.log(
+                        name,
+                        "iNat lookup failed but has iNat ID",
+                        iNatID,
+                    );
+                }
+            }
+        } else {
+            errorLog.log(
+                name,
+                "found iNat synonym",
+                this.makeSynonymName(result, errorLog) + "," + name + ",INAT",
+            );
+        }
+
+        // Delay to throttle queries to iNat API.
+        await sleep(800);
+    }
+
+    /**
+     * @param {{name:string,rank:string}} iNatResult
+     * @param {ErrorLog} errorLog
+     */
+    static makeSynonymName(iNatResult, errorLog) {
+        const synParts = iNatResult.name.split(" ");
+        if (synParts.length === 3) {
+            switch (iNatResult.rank) {
+                case "subspecies":
+                case "variety":
+                    synParts[3] = synParts[2];
+                    synParts[2] =
+                        iNatResult.rank === "variety" ? "var." : "subsp.";
+                    break;
+                case "hybrid":
+                    // Leave as is.
+                    break;
+                default:
+                    errorLog.log(
+                        iNatResult.name,
+                        "unrecognized iNat rank",
+                        iNatResult.rank,
+                    );
+            }
+        }
+        return synParts.join(" ");
+    }
+}
+
+class InatTaxon {
+    #id;
+
+    /**
+     * @param {string} id
+     */
+    constructor(id) {
+        this.#id = id;
+    }
+
+    getID() {
+        return this.#id;
+    }
+}
+
+/**
+ * @param {string} dataDir
+ * @param {Map<string,string>} idsToUpdate
+ */
+function updateTaxaCSV(dataDir, idsToUpdate) {
+    const taxa = new TaxaCSV(dataDir);
+
+    for (const taxonData of taxa.getTaxa()) {
+        const id = idsToUpdate.get(taxonData.taxon_name);
+        if (!id) {
+            continue;
+        }
+        taxonData["inat id"] = id;
+    }
+
+    taxa.write();
+}

package/lib/web/pagetaxon.js

@@ -4,7 +4,6 @@ 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 {
@@ -82,24 +81,6 @@ class PageTaxon extends GenericPage {
         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;
-    }
-
     #getRarityInfo() {
         const cnpsRank = this.#taxon.getRPIRankAndThreat();
         if (!cnpsRank) {
@@ -185,28 +166,35 @@ class PageTaxon extends GenericPage {
         html += this.getMarkdown();
 
         html += '<div class="grid borders">';
-        html += this.#getListSectionHTML(
+        html += HTMLTaxon.getListSectionHTML(
             this.#getInfoLinks(),
             "References",
             "info",
         );
-        html += this.#getListSectionHTML(
+        html += HTMLTaxon.getListSectionHTML(
             this.#getObsLinks(),
             "Observations",
             "obs",
         );
-        html += this.#getListSectionHTML(
+        html += HTMLTaxon.getListSectionHTML(
             this.#getRelatedTaxaLinks(),
             "Related Species",
             "rel-taxa",
         );
-        html += this.#getListSectionHTML(
+        html += HTMLTaxon.getListSectionHTML(
             this.#getSynonyms(),
             "Synonyms",
             "synonyms",
         );
         html += "</div>";
 
+        const footerTextPath =
+            Config.getPackageDir() +
+            "/data/text/" +
+            this.getBaseFileName() +
+            ".footer.md";
+        html += HTMLTaxon.getMarkdownSection(footerTextPath);
+
         const photos = this.#taxon.getPhotos();
         if (photos.length > 0) {
             let photosHtml = "";
@@ -235,16 +223,6 @@ class PageTaxon extends GenericPage {
       `;
         }
 
-        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);
     }
 }

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.4.13",
+    "version": "0.4.14",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {

package/scripts/cpl-tools.js

@@ -8,6 +8,7 @@ import { Calflora } from "../lib/tools/calflora.js";
 import { Exceptions } from "../lib/exceptions.js";
 import { ErrorLog } from "../lib/errorlog.js";
 import { Calscape } from "../lib/tools/calscape.js";
+import { INat } from "../lib/tools/inat.js";
 
 const TOOLS = {
     CALFLORA: "calflora",
@@ -72,13 +73,15 @@ async function build(program, options) {
                 );
                 break;
             case TOOLS.INAT:
-                // await INat.analyze(
-                //     TOOLS_DATA_DIR,
-                //     taxa,
-                //     exceptions,
-                //     errorLog,
-                //     options.inTaxafile,
-                // );
+                await INat.analyze(
+                    TOOLS_DATA_DIR,
+                    options.datadir,
+                    taxa,
+                    exceptions,
+                    errorLog,
+                    options.inTaxafile,
+                    !!options.update,
+                );
                 break;
             case TOOLS.JEPSON_EFLORA: {
                 // const eflora = new JepsonEFlora(