@ca-plant-list/ca-plant-list 0.2.5 → 0.2.7

package/data/text/Clematis-ligusticifolia.md

@@ -0,0 +1 @@
+Found along streams and in wet places.

package/data/text/Galium-californicum-subsp-californicum.md

@@ -0,0 +1 @@
+Not woody (except sometimes at base). Leaves in whorls of 4. Fruit and plant hairy.

package/data/text/Galium-porrigens-var-porrigens.md

@@ -0,0 +1 @@
+Woody. Leaves in whorls of 4. Fruit not hairy. Leaves about twice as long as wide.

package/data/text/Galium-porrigens-var-tenue.md

@@ -0,0 +1 @@
+Woody. Leaves in whorls of 4. Fruit not hairy. Leaves at least 3 times as long as wide.

package/data/text/Grindelia-camporum.md

@@ -1 +1 @@
-Phyllaries flattened only at bases (rounded in cross section distally), phyllary tips often reflexed, or coiled; plants generally not hairy.
+[Phyllaries](g/phyllary.html) flattened only at bases (rounded in cross section distally), phyllary tips often reflexed, or coiled; plants generally not hairy.

package/data/text/Grindelia-hirsutula.md

@@ -1 +1 @@
-Phyllaries flattened, plants generally hairy.
+[Phyllaries](g/phyllary.html) flattened, plants generally hairy.

package/data/text/Hordeum-marinum-subsp-gussoneanum.md

@@ -0,0 +1 @@
+Auricles generally not present.

package/data/text/Hordeum-murinum-subsp-glaucum.md

@@ -0,0 +1 @@
+Auricles of upper leaves well developed, 1–4mm.

package/data/text/Hordeum-murinum-subsp-leporinum.md

@@ -0,0 +1 @@
+Auricles of upper leaves well developed, 1–4mm.

package/data/text/Hordeum-murinum-subsp-murinum.md

@@ -0,0 +1 @@
+Auricles of upper leaves well developed, 1–4mm.

package/data/text/Horkelia-californica-var-californica.md

@@ -0,0 +1 @@
+Sepal red-mottled inside.

package/data/text/Horkelia-californica-var-elata.md

@@ -0,0 +1 @@
+Sepal not red-mottled.

package/data/text/Horkelia-californica-var-frondosa.md

@@ -0,0 +1 @@
+Sepal not red-mottled.

package/data/text/Lonicera-interrupta.md

@@ -0,0 +1 @@
+Upper leaf pairs fused around stem. No [stipules](g/stipule.html), corolla not hairy.

package/data/text/Lonicera-subspicata-var-denudata.md

@@ -0,0 +1 @@
+Upper leaf pairs not fused around stem.

package/data/text/Navarretia-mellita.md

@@ -0,0 +1 @@
+Corolla 5-7mm, same length as calyx. Odor not skunk-like. Petals light blue.

package/data/text/Navarretia-squarrosa.md

@@ -0,0 +1 @@
+Corolla 9-12mm, longer than calyx. Odor skunk-like. Petals dark or light blue, pinkish or whitish.

package/data/text/Piperia-elegans-subsp-elegans.md

@@ -0,0 +1 @@
+Sepals white with dark green midvein.

package/data/text/Piperia-elongata.md

@@ -0,0 +1 @@
+Perianth green to yellow-green.

package/data/text/Piperia-michaelii.md

@@ -0,0 +1 @@
+Perianth green to yellow-green.

package/data/text/Piperia-transversa.md

@@ -0,0 +1 @@
+Spur mostly straight and perpendicular to inflorescence axis.

package/data/text/Piperia-unalascensis.md

@@ -0,0 +1 @@
+Perianth green.

package/data/text/Taraxacum-officinale.md

@@ -1 +1 @@
-Leaves basal. Stem not branched. Outer phyllaries much smaller than inner.
+Leaves basal. Stem not branched. Outer [phyllaries](g/phyllary.html) much smaller than inner.

package/data/text/Wyethia-angustifolia.md

@@ -1 +1 @@
-Outer phyllaries narrow and roughly the same width as inner.
+Outer [phyllaries](g/phyllary.html) narrow and roughly the same width as inner.

package/data/text/Wyethia-glabra.md

@@ -1 +1 @@
-Outer phyllaries wide, leaf-like, and usually much larger than inner phyllaries. Generally not hairy or with some glandular hairs.
+Outer [phyllaries](g/phyllary.html) wide, leaf-like, and usually much larger than inner phyllaries. Generally not hairy or with some glandular hairs.

package/data/text/Wyethia-helenioides.md

@@ -1 +1 @@
-Outer phyllaries wide, leaf-like, and usually much larger than inner phyllaries. Plant densely tomentose.
+Outer [phyllaries](g/phyllary.html) wide, leaf-like, and usually much larger than inner phyllaries. Plant densely tomentose.

package/jekyll/_layouts/html.html

@@ -31,6 +31,9 @@
                     <li class="nav-item">
                         <a class="nav-link" href="{{site.baseurl}}/name_search.html">Name Search</a>
                     </li>
+                    <li class="nav-item">
+                        <a class="nav-link" href="{{site.baseurl}}/glossary.html">Glossary</a>
+                    </li>
                     {%include menu_extra.html %}
                 </ul>
             </div>

package/jekyll/glossary.md

@@ -0,0 +1,5 @@
+---
+title: Glossary
+---
+
+{%include glossary.html %}

package/lib/basepagerenderer.js

@@ -1,6 +1,7 @@
 import { Config } from "./config.js";
 import { Families } from "./families.js";
 import { Files } from "./files.js";
+import { GlossaryPages } from "./web/glossarypages.js";
 
 class BasePageRenderer {
 
@@ -12,9 +13,13 @@ class BasePageRenderer {
         Files.copyDir( Config.getPackageDir() + "/jekyll", outputDir );
         // Then copy Jekyll files from current dir (which may override default files).
         Files.copyDir( "jekyll", outputDir );
+        // Copy illustrations.
+        Files.copyDir( Config.getPackageDir() + "/data/illustrations/optimized", outputDir + "/i" );
 
         Families.renderPages( outputDir, familyCols );
 
+        new GlossaryPages( outputDir ).renderPages();
+
         this.renderTools( outputDir, Taxa );
 
     }

package/lib/ebook/ebook.js

@@ -3,6 +3,18 @@ import { default as archiver } from "archiver";
 import { XHTML } from "./xhtml.js";
 import { Config } from "../config.js";
 
+const MEDIA_TYPES = {
+    SVG: "image/svg+xml",
+    JPG: "image/jpeg",
+    XHTML: "application/xhtml+xml",
+};
+
+const EXT_MEDIA_MAP = {
+    "jpeg": MEDIA_TYPES.JPG,
+    "jpg": MEDIA_TYPES.JPG,
+    "svg": MEDIA_TYPES.SVG,
+};
+
 class EBook {
 
     #outputDir;
@@ -103,6 +115,18 @@ class EBook {
         return this.#outputDir + "/epub";
     }
 
+    static getManifestEntry( id, href, mediaType = MEDIA_TYPES.XHTML ) {
+        return "<item id=\"" + id + "\" href=\"" + href + "\" media-type=\"" + mediaType + "\" />";
+    }
+
+    static getMediaTypeForExt( ext ) {
+        return EXT_MEDIA_MAP[ ext ];
+    }
+
+    static getSpineEntry( id ) {
+        return "<itemref idref=\"" + id + "\"/>";
+    }
+
     #getMetaDir() {
         return this.#outputDir + "/META-INF";
     }

package/lib/ebook/ebookpage.js

@@ -4,10 +4,12 @@ class EBookPage {
 
     #fileName;
     #title;
+    #rootPrefix;
 
-    constructor( fileName, title ) {
+    constructor( fileName, title, rootPrefix = "" ) {
         this.#fileName = fileName;
         this.#title = title;
+        this.#rootPrefix = rootPrefix;
     }
 
     create() {
@@ -37,7 +39,7 @@ class EBookPage {
         let html = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n";
         html += "<html xmlns=\"http://www.w3.org/1999/xhtml\" xmlns:epub=\"http://www.idpf.org/2007/ops\">";
         html += "<head><title>" + title + "</title>";
-        html += "<link href=\"./css/main.css\" rel=\"stylesheet\" />";
+        html += "<link href=\"" + this.#rootPrefix + "css/main.css\" rel=\"stylesheet\" />";
         html += "</head>" + this.#renderBodyStart();
         return html;
     }

package/lib/ebook/glossarypages.js

@@ -0,0 +1,101 @@
+import * as fs from "node:fs";
+
+import { EBookPage } from "./ebookpage.js";
+import { XHTML } from "./xhtml.js";
+
+import { HTML } from "../html.js";
+import { Markdown } from "../markdown.js";
+import { EBook } from "./ebook.js";
+
+import { Glossary } from "../plants/glossary.js";
+
+class GlossaryPages {
+
+    #glossary;
+
+    constructor() {
+        this.#glossary = new Glossary();
+    }
+
+    createPages( contentDir ) {
+
+        const termList = [];
+
+        // Create target directory.
+        const dirTarget = contentDir + "/g";
+        fs.mkdirSync( dirTarget, { recursive: true } );
+
+        for ( const entry of this.#glossary.getEntries() ) {
+
+            new PageGlossaryEntry( contentDir, entry ).create();
+
+            // Add term to index page list.
+            termList.push( HTML.getLink( "g/" + entry.getHTMLFileName(), entry.getTermName() ) );
+
+        }
+
+        // Write glossary index page.
+        new PageGlossary( contentDir, termList ).create();
+    }
+
+    getManifestEntries() {
+
+        const glossaryEntries = this.#glossary.getEntries();
+        const manifestEntries = [];
+
+        manifestEntries.push( EBook.getManifestEntry( "g", "glossary.html" ) );
+        for ( let index = 0; index < glossaryEntries.length; index++ ) {
+            const entry = glossaryEntries[ index ];
+            manifestEntries.push( EBook.getManifestEntry( "g" + index, "g/" + entry.getHTMLFileName() ) );
+        }
+
+        return manifestEntries.join( "" );
+    }
+
+    getSpineEntries() {
+
+        const glossaryEntries = this.#glossary.getEntries();
+        const spineEntries = [];
+
+        spineEntries.push( EBook.getSpineEntry( "g", "glossary.html" ) );
+        for ( let index = 0; index < glossaryEntries.length; index++ ) {
+            spineEntries.push( EBook.getSpineEntry( "g" + index ) );
+        }
+
+        return spineEntries.join( "" );
+
+    }
+
+}
+
+class PageGlossary extends EBookPage {
+
+    #entries;
+
+    constructor( outputDir, entries ) {
+        super( outputDir + "/glossary.html", "Glossary" );
+        this.#entries = entries;
+    }
+
+    renderPageBody() {
+        const html = XHTML.textElement( "h1", this.getTitle() );
+        return html + XHTML.wrap( "ol", XHTML.arrayToLI( this.#entries ) );
+    }
+}
+
+class PageGlossaryEntry extends EBookPage {
+
+    #entry;
+
+    constructor( outputDir, entry ) {
+        super( outputDir + "/g/" + entry.getHTMLFileName(), entry.getTermName(), "../" );
+        this.#entry = entry;
+    }
+
+    renderPageBody() {
+        const html = XHTML.textElement( "h1", this.getTitle() );
+        return html + Markdown.strToHTML( this.#entry.getMarkdown() );
+    }
+}
+
+export { GlossaryPages };

package/lib/ebook/images.js

@@ -0,0 +1,86 @@
+import * as fs from "node:fs";
+import path from "node:path";
+
+import sharp from "sharp";
+
+import { Config, CSV, Files, Taxa } from "@ca-plant-list/ca-plant-list";
+
+import { Image } from "./image.js";
+import { EBook } from "./ebook.js";
+
+class Images {
+
+    #contentDir;
+    #images = {};
+
+    constructor( contentDir ) {
+        this.#contentDir = contentDir;
+    }
+
+    async createImages() {
+
+        const photoDirSrc = "external_data/photos";
+        const imagePrefix = "i";
+        const photoDirTarget = this.#contentDir + "/" + imagePrefix;
+        fs.mkdirSync( photoDirSrc, { recursive: true } );
+        fs.mkdirSync( photoDirTarget, { recursive: true } );
+
+        const rows = CSV.parseFile( Config.getPackageDir() + "/data", "photos.csv" );
+        for ( const row of rows ) {
+
+            const name = row[ "taxon_name" ];
+            const taxon = Taxa.getTaxon( name );
+            if ( !taxon ) {
+                continue;
+            }
+
+            let imageList = this.#images[ name ];
+            if ( !imageList ) {
+                imageList = [];
+                this.#images[ name ] = imageList;
+            }
+
+            const src = new URL( row[ "source" ] );
+            const parts = path.parse( src.pathname ).dir.split( "/" );
+            const prefix = src.host.includes( "calflora" ) ? "cf-" : "inat-";
+            const filename = prefix + parts.slice( -1 )[ 0 ] + ".jpg";
+            const srcFileName = photoDirSrc + "/" + filename;
+            const targetFileName = photoDirTarget + "/" + filename;
+
+            if ( !fs.existsSync( srcFileName ) ) {
+                // File is not there; retrieve it.
+                console.log( "retrieving " + srcFileName );
+                await Files.fetch( src, srcFileName );
+            }
+
+            await new sharp( srcFileName ).resize( { width: 400 } ).jpeg( { quality: 40 } ).toFile( targetFileName );
+
+            imageList.push( new Image( imagePrefix + "/" + filename, row[ "credit" ] ) );
+
+        }
+
+        this.#getIllustrations( this.#contentDir );
+
+    }
+
+    #getIllustrations() {
+        Files.copyDir( Config.getPackageDir() + "/data/illustrations/optimized", this.#contentDir + "/i" );
+    }
+
+    getManifestEntries() {
+
+        const entries = [];
+        const images = Files.getDirEntries( this.#contentDir + "/i" ).sort();
+
+        for ( let index = 0; index < images.length; index++ ) {
+            const fileName = images[ index ];
+            const ext = fileName.split( "." )[ 1 ];
+            entries.push( EBook.getManifestEntry( "i" + index, "i/" + fileName, EBook.getMediaTypeForExt( ext ) ) );
+        }
+
+        return entries.join( "" );
+    }
+
+}
+
+export { Images };

package/lib/ebook/pages/taxonpage.js

@@ -1,8 +1,8 @@
 import sizeOf from "image-size";
-import markdownIt from "markdown-it";
 import { Config, Files } from "@ca-plant-list/ca-plant-list";
 import { EBookPage } from "../ebookpage.js";
 import { XHTML } from "../xhtml.js";
+import { Markdown } from "../../markdown.js";
 
 class TaxonPage extends EBookPage {
 
@@ -39,8 +39,7 @@ class TaxonPage extends EBookPage {
                 return "";
             }
             const text = Files.read( fileName );
-            const md = new markdownIt();
-            return md.render( text );
+            return Markdown.strToHTML( text );
         }
 
         const name = this.#taxon.getName();

package/lib/ebook/pages/tocpage.js

@@ -17,6 +17,7 @@ class TOCPage extends EBookPage {
         mainLinks.push( this.#getFlowerColorLinks() );
         mainLinks.push( XHTML.getLink( "./list_families.html", "All Families" ) );
         mainLinks.push( XHTML.getLink( "./list_species.html", "All Species" ) );
+        mainLinks.push( XHTML.getLink( "./glossary.html", "Glossary" ) );
         html += XHTML.wrap( "ol", XHTML.arrayToLI( mainLinks ) );
 
         html += "</nav>";

package/lib/ebook/plantbook.js

@@ -1,9 +1,7 @@
-import * as fs from "node:fs";
-import path from "node:path";
-import sharp from "sharp";
-import { CSV, Families, Files, Taxa } from "@ca-plant-list/ca-plant-list";
+import { Families, Taxa } from "@ca-plant-list/ca-plant-list";
 import { EBook } from "./ebook.js";
-import { Image } from "./image.js";
+import { GlossaryPages } from "./glossarypages.js";
+import { Images } from "./images.js";
 import { PageListFamilies } from "./pages/page_list_families.js";
 import { PageListFlowerColor } from "./pages/page_list_flower_color.js";
 import { PageListSpecies } from "./pages/page_list_species.js";
@@ -14,7 +12,8 @@ import { FLOWER_COLOR_NAMES } from "../taxa.js";
 
 class PlantBook extends EBook {
 
-    #images = {};
+    #glossary;
+    #images;
 
     constructor() {
 
@@ -25,13 +24,13 @@ class PlantBook extends EBook {
             Config.getConfigValue( "ebook", "title" )
         );
 
+        this.#glossary = new GlossaryPages();
+        this.#images = new Images( this.getContentDir() );
+
     }
 
     async createPages() {
 
-        console.log( "checking images" );
-        await this.#importImages();
-
         const contentDir = this.getContentDir();
 
         console.log( "creating taxon pages" );
@@ -56,63 +55,16 @@ class PlantBook extends EBook {
         }
         new PageListSpecies( contentDir, taxa, "list_species.html", "All Species" ).create();
 
-        new TOCPage( contentDir ).create();
-    }
-
-    async #importImages() {
-
-        const photoDirSrc = "external_data/photos";
-        const imagePrefix = "i";
-        const photoDirTarget = this.getContentDir() + "/" + imagePrefix;
-        fs.mkdirSync( photoDirSrc, { recursive: true } );
-        fs.mkdirSync( photoDirTarget, { recursive: true } );
-
-        const rows = CSV.parseFile( Config.getPackageDir() + "/data", "photos.csv" );
-        for ( const row of rows ) {
-
-            const name = row[ "taxon_name" ];
-            const taxon = Taxa.getTaxon( name );
-            if ( !taxon ) {
-                continue;
-            }
-
-            let imageList = this.#images[ name ];
-            if ( !imageList ) {
-                imageList = [];
-                this.#images[ name ] = imageList;
-            }
-
-            const src = new URL( row[ "source" ] );
-            const parts = path.parse( src.pathname ).dir.split( "/" );
-            const prefix = src.host.includes( "calflora" ) ? "cf-" : "inat-";
-            const filename = prefix + parts.slice( -1 )[ 0 ] + ".jpg";
-            const srcFileName = photoDirSrc + "/" + filename;
-            const targetFileName = photoDirTarget + "/" + filename;
-
-            if ( !fs.existsSync( srcFileName ) ) {
-                // File is not there; retrieve it.
-                console.log( "retrieving " + srcFileName );
-                await Files.fetch( src, srcFileName );
-            }
-
-            await new sharp( srcFileName ).resize( { width: 400 } ).jpeg( { quality: 40 } ).toFile( targetFileName );
+        await this.#images.createImages( contentDir );
+        this.#glossary.createPages( contentDir );
 
-            imageList.push( new Image( imagePrefix + "/" + filename, row[ "credit" ] ) );
-
-        }
+        new TOCPage( contentDir ).create();
     }
 
     renderManifestEntries() {
 
         let xml = "";
 
-        xml += "<item id=\"f0\" href=\"i/f-blue.svg\" media-type=\"image/svg+xml\" />";
-        xml += "<item id=\"f1\" href=\"i/f-orange.svg\" media-type=\"image/svg+xml\" />";
-        xml += "<item id=\"f2\" href=\"i/f-pink.svg\" media-type=\"image/svg+xml\" />";
-        xml += "<item id=\"f3\" href=\"i/f-red.svg\" media-type=\"image/svg+xml\" />";
-        xml += "<item id=\"f4\" href=\"i/f-white.svg\" media-type=\"image/svg+xml\" />";
-        xml += "<item id=\"f5\" href=\"i/f-yellow.svg\" media-type=\"image/svg+xml\" />";
-
         // Add lists.
         xml += "<item id=\"lspecies\" href=\"list_species.html\" media-type=\"application/xhtml+xml\" />";
         xml += "<item id=\"lfamilies\" href=\"list_families.html\" media-type=\"application/xhtml+xml\" />";
@@ -137,14 +89,9 @@ class PlantBook extends EBook {
             xml += "<item id=\"t" + index + "\" href=\"" + taxon.getFileName() + "\" media-type=\"application/xhtml+xml\" />";
         }
 
-        // Add images.
-        let index = 0;
-        for ( const imageList of Object.values( this.#images ) ) {
-            for ( const image of imageList ) {
-                xml += "<item id=\"i" + index + "\" href=\"" + image.getSrc() + "\" media-type=\"image/jpeg\" />";
-                index++;
-            }
-        }
+        xml += this.#glossary.getManifestEntries();
+        xml += this.#images.getManifestEntries();
+
         return xml;
     }
 
@@ -172,6 +119,9 @@ class PlantBook extends EBook {
         for ( let index = 0; index < Taxa.getTaxa().length; index++ ) {
             xml += "<itemref idref=\"t" + index + "\"/>";
         }
+
+        xml += this.#glossary.getSpineEntries();
+
         return xml;
     }
 }

package/lib/genericpage.js

@@ -1,4 +1,5 @@
-import { Files, HTML, Jekyll } from "@ca-plant-list/ca-plant-list";
+import { Config, Files, HTML, Jekyll } from "@ca-plant-list/ca-plant-list";
+import { Markdown } from "./markdown.js";
 
 class GenericPage {
 
@@ -19,11 +20,18 @@ class GenericPage {
     }
 
     getDefaultIntro() {
+
         let html = this.#getFrontMatter();
-        const introPath = "intros/" + this.#baseFileName + ".md";
-        if ( Jekyll.hasInclude( this.#outputDir, introPath ) ) {
-            html += HTML.wrap( "div", Jekyll.include( introPath ), { class: "section" } );
+
+        // Include site-specific markdown.
+        html += this.#getMarkdown( "intros" );
+
+        // Include package markdown.
+        const mdPath = Config.getPackageDir() + "/data/text/" + this.#baseFileName + ".md";
+        if ( Files.exists( mdPath ) ) {
+            html += HTML.wrap( "div", Markdown.fileToHTML( mdPath ), { class: "section" } );
         }
+
         return html;
     }
 
@@ -34,6 +42,14 @@ class GenericPage {
             + "---\n";
     }
 
+    #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;
     }

package/lib/html.js

@@ -65,7 +65,7 @@ export class HTML {
         if ( openInNewWindow ) {
             html += this.renderAttribute( "target", "_blank" );
         }
-        return html + ">" + this.escapeText( linkText ) + "</a >";
+        return html + ">" + this.escapeText( linkText ) + "</a>";
     }
 
     /**