@ca-plant-list/ca-plant-list 0.4.26 → 0.4.28

package/scripts/cpl-photos.js

@@ -9,6 +9,7 @@ import { existsSync } from "fs";
 import { CSV } from "../lib/csv.js";
 
 const PHOTO_FILE_NAME = "inattaxonphotos.csv";
+const PHOTO_FILE_PATH = `./data/${PHOTO_FILE_NAME}`;
 
 const OPT_LOADER = "loader";
 
@@ -58,27 +59,7 @@ async function addMissingPhotos(options) {
     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.writeFileArray(
-        `${options.outputdir}/${PHOTO_FILE_NAME}`,
-        data,
-        headers,
-    );
+    writePhotos(currentTaxaPhotos);
 }
 
 /**
@@ -128,12 +109,39 @@ async function getTaxa(options) {
     return taxa;
 }
 
+/**
+ * @param {{outputdir:string,update:boolean}} options
+ */
+async function prune(options) {
+    const taxa = await getTaxa(options);
+    const errorLog = new ErrorLog(options.outputdir + "/log.tsv", true);
+    const currentTaxaPhotos = readPhotos();
+
+    const invalidNames = new Set();
+
+    for (const name of currentTaxaPhotos.keys()) {
+        const taxon = taxa.getTaxon(name);
+        if (!taxon) {
+            errorLog.log(name, `is in ${PHOTO_FILE_NAME} but not in taxa list`);
+            invalidNames.add(name);
+        }
+    }
+
+    if (options.update) {
+        for (const name of invalidNames) {
+            currentTaxaPhotos.delete(name);
+        }
+        writePhotos(currentTaxaPhotos);
+    }
+
+    errorLog.write();
+}
+
 /**
  * @returns {Map<string,import("../lib/utils/inat-tools.js").InatPhotoInfo[]>}
  */
 function readPhotos() {
-    const photosFileName = `./data/${PHOTO_FILE_NAME}`;
-    if (!existsSync(photosFileName)) {
+    if (!existsSync(PHOTO_FILE_PATH)) {
         return new Map();
     }
 
@@ -142,7 +150,7 @@ function readPhotos() {
 
     /** @type {import("../lib/utils/inat-tools.js").InatCsvPhoto[]} */
     // @ts-ignore
-    const csvPhotos = CSV.readFile(photosFileName);
+    const csvPhotos = CSV.readFile(PHOTO_FILE_PATH);
     for (const csvPhoto of csvPhotos) {
         const taxonName = csvPhoto.name;
         let photos = taxonPhotos.get(taxonName);
@@ -161,6 +169,30 @@ function readPhotos() {
     return taxonPhotos;
 }
 
+/**
+ * @param {Map<string,import("../lib/utils/inat-tools.js").InatPhotoInfo[]>} currentTaxaPhotos
+ */
+function writePhotos(currentTaxaPhotos) {
+    // Write updated photo file.
+    const headers = ["name", "id", "ext", "licenseCode", "attrName"];
+    /** @type {string[][]} */
+    const data = [];
+    for (const taxonName of [...currentTaxaPhotos.keys()].sort()) {
+        // @ts-ignore - should always be defined at this point
+        for (const photo of currentTaxaPhotos.get(taxonName)) {
+            data.push([
+                taxonName,
+                photo.id,
+                photo.ext,
+                photo.licenseCode,
+                photo.attrName ?? "",
+            ]);
+        }
+    }
+
+    CSV.writeFileArray(PHOTO_FILE_PATH, data, headers);
+}
+
 const program = Program.getProgram();
 program
     .command("checkmissing")
@@ -176,9 +208,14 @@ if (process.env.npm_package_name === "@ca-plant-list/ca-plant-list") {
         .command("addmissing")
         .description("Add photos to taxa with fewer than the maximum")
         .action(() => addMissingPhotos(program.opts()));
+    program
+        .command("prune")
+        .description("Remove photos without valid taxon names")
+        .action(() => prune(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.",
 );
+program.option("--update", "Update the file if possible.");
 await program.parseAsync();

package/scripts/cpl-tools.js

@@ -58,10 +58,13 @@ async function build(program, options) {
 
     const exceptions = new Exceptions(options.datadir);
     const config = new Config(options.datadir);
-    const taxa = await Taxa.loadTaxa(options);
 
     const errorLog = new ErrorLog(options.outputdir + "/log.tsv", true);
     for (const tool of tools) {
+        const taxa =
+            tool === TOOLS.JEPSON_FAM
+                ? undefined
+                : await Taxa.loadTaxa(options);
         switch (tool) {
             case TOOLS.CALFLORA:
                 await Calflora.analyze(

package/static/assets/js/nameSearchData.js

@@ -0,0 +1,2 @@
+/** @type {import("../../../lib/types.js").NameSearchData[]} */
+export const NAMES = [];

package/{jekyll → static}/assets/js/name_search.js

@@ -1,8 +1,8 @@
+import { NAMES } from "./nameSearchData.js";
 import { Utils } from "./utils.js";
 
 /**
- * @typedef {[string]|[string,string]|[string,string|undefined,string[]]} RawSearchData
- * @typedef {{raw:RawSearchData,searchSci:string,searchCommon?:string,synonyms?:string[]}} SearchData
+ * @typedef {{raw:import("../../../lib/types.js").NameSearchData,searchSci:string,searchCommon?:string,synonyms?:string[]}} SearchData
  */
 
 const MIN_LEN = 2;
@@ -52,9 +52,9 @@ class Search {
                 // Include any matching synonyms.
                 for (const index of syns) {
                     matches.push([
-                        taxon.raw[0],
-                        taxon.raw[1],
-                        taxon.raw[2] ? taxon.raw[2][index] : undefined,
+                        taxon.raw.t,
+                        taxon.raw.c,
+                        taxon.raw.s ? taxon.raw.s[index] : undefined,
                     ]);
                 }
             } else {
@@ -62,7 +62,7 @@ class Search {
                 const namesMatch =
                     name.includes(value) || (cn && cn.includes(value));
                 if (namesMatch) {
-                    matches.push([taxon.raw[0], taxon.raw[1]]);
+                    matches.push([taxon.raw.t, taxon.raw.c]);
                 }
             }
         }
@@ -146,23 +146,21 @@ class Search {
         /** @type {SearchData[]} */
         const searchData = [];
 
-        /** @type {RawSearchData[]} */
-        // @ts-ignore
-        // eslint-disable-next-line no-undef
+        /** @type {import("../../../lib/types.js").NameSearchData[]} */
         const names = NAMES;
 
         for (const taxon of names) {
             /** @type {SearchData} */
             const taxonData = {
                 raw: taxon,
-                searchSci: this.#normalizeName(taxon[0]),
+                searchSci: this.#normalizeName(taxon.t),
             };
-            if (taxon[1]) {
-                taxonData.searchCommon = taxon[1].toLowerCase();
+            if (taxon.c) {
+                taxonData.searchCommon = taxon.c.toLowerCase();
             }
-            if (taxon[2]) {
+            if (taxon.s) {
                 const syns = [];
-                for (const syn of taxon[2]) {
+                for (const syn of taxon.s) {
                     syns.push(this.#normalizeName(syn));
                 }
                 taxonData.synonyms = syns;

package/static/name_search.html

@@ -0,0 +1,15 @@
+---
+title: Name Search
+js: name_search.js
+---
+
+<form id="search_form">
+    <input type="text" id="name" />
+    <label for="name"
+        >Search for scientific name, common name, or synonym.</label
+    >
+</form>
+
+<div class="section" id="message"></div>
+
+<table id="results"></table>

package/jekyll/name_search.html

@@ -1,17 +0,0 @@
----
-title: Name Search
-js: name_search.js
----
-
-<script>
-    const NAMES = {% include names.json %};
-</script>
-
-<form id="search_form">
-    <input type="text" id="name">
-    <label for="name">Search for scientific name, common name, or synonym.</label>
-</form>
-
-<div class="section" id="message"></div>
-
-<table id="results"></table>

package/lib/genericpage.js

@@ -1,88 +0,0 @@
-import { Config } from "./config.js";
-import { Files } from "./files.js";
-import { HTML } from "./html.js";
-import { Jekyll } from "./jekyll.js";
-import { Markdown } from "./markdown.js";
-
-class GenericPage {
-    #outputDir;
-    #title;
-    #baseFileName;
-    #js;
-
-    /**
-     * @param {string} outputDir
-     * @param {string} title
-     * @param {string} baseFileName
-     * @param {string} [js]
-     */
-    constructor(outputDir, title, baseFileName, js) {
-        this.#outputDir = outputDir;
-        this.#title = title;
-        this.#baseFileName = baseFileName;
-        this.#js = js;
-    }
-
-    getBaseFileName() {
-        return this.#baseFileName;
-    }
-
-    getDefaultIntro() {
-        let html = this.getFrontMatter();
-        return html + this.getMarkdown();
-    }
-
-    getFrontMatter() {
-        return (
-            "---\n" +
-            'title: "' +
-            this.#title +
-            '"\n' +
-            (this.#js ? "js: " + this.#js + "\n" : "") +
-            "---\n"
-        );
-    }
-
-    getMarkdown() {
-        // Include site-specific markdown.
-        let html = this.#getMarkdown("intros");
-
-        // Include package markdown.
-        const mdPath =
-            Config.getPackageDir() + "/data/text/" + this.#baseFileName + ".md";
-        const markdownHTML = Markdown.fileToHTML(mdPath);
-        if (markdownHTML) {
-            html += HTML.wrap("div", markdownHTML, { class: "section" });
-        }
-
-        return html;
-    }
-
-    /**
-     * @param {string} path
-     */
-    #getMarkdown(path) {
-        const textPath = path + "/" + this.#baseFileName + ".md";
-        if (!Jekyll.hasInclude(this.#outputDir, textPath)) {
-            return "";
-        }
-        return HTML.wrap("div", Jekyll.include(textPath), { class: "section" });
-    }
-
-    getOutputDir() {
-        return this.#outputDir;
-    }
-
-    getTitle() {
-        return this.#title;
-    }
-
-    /**
-     * @param {string} html
-     */
-    writeFile(html) {
-        Files.write(this.#outputDir + "/" + this.#baseFileName + ".html", html);
-    }
-}
-
-export { GenericPage };