@ca-plant-list/ca-plant-list 0.4.17 → 0.4.19

package/data/taxa.csv

@@ -227,10 +227,10 @@ Bolboschoenus maritimus subsp. paludosus,saltmarsh bulrush,N,49436,10796,79646,P
 Bolboschoenus robustus,seacoast bulrush,N,77450,10798,75840,Big Bulrush
 Bowlesia incana,,N,15999,1133,56822,Hoary Bowlesia
 Brachypodium distachyon,false-brome,X,16042,1137,57158
-Brassica juncea,India mustard,X,16072,1142,64241
-Brassica nigra,black mustard,X,16079,1144,1555489,,,yellow
-Brassica oleracea,cabbage,X,16080,9040,54516
-Brassica rapa,field mustard,X,16081,1145,53271,,,yellow
+Brassica juncea,India mustard,X,16072,1142,64241,,"annual,perennial",yellow,5,9
+Brassica nigra,black mustard,X,16079,1144,1555489,,annual,yellow,4,9
+Brassica oleracea,cabbage,X,16080,9040,54516,,"biennial,perennial",yellow,5,8
+Brassica rapa,field mustard,X,16081,1145,53271,,"annual,biennial",yellow,1,5
 Brickellia californica,California brickelbush,N,1794,1152,58803,Brickell Bush
 Briza maxima,quaking grass,X,16135,1165,57157
 Briza minor,little quaking grass,X,16137,1166,57162
@@ -1075,11 +1075,11 @@ Linanthus dichotomus subsp. meridianus,,N,51287,10625,80001
 Linanthus pungens subsp. pulchriflorus,granite prickly phlox,N,98684,14586,861790,,perennial,"white,pink",5,8
 Linum bienne,,X,31144,4906,55679
 Linum lewisii var. lewisii,blue flax,N,60912,4910,60495,Prairie Flax
-Lithophragma affine,woodland star,N,31236,4922,50803,San Francisco Woodland Star,,white,3,4
-Lithophragma bolanderi,,N,31238,4923,77787,Bolander's Woodland Star
-Lithophragma cymbalaria,,N,31241,4925,58323,Mission Woodland Star
-Lithophragma heterophyllum,hill starflower,N,31244,4927,53124,Hillside Woodland Star,,white
-Lithophragma parviflorum var. parviflorum,,N,60952,4930,81027,Smallflower Woodland-star,,"white,pink",3,7
+Lithophragma affine,woodland star,N,31236,4922,50803,San Francisco Woodland Star,perennial,white,3,4
+Lithophragma bolanderi,,N,31238,4923,77787,Bolander's Woodland Star,perennial,white,2,7
+Lithophragma cymbalaria,,N,31241,4925,58323,Mission Woodland Star,perennial,white,3,5
+Lithophragma heterophyllum,hill starflower,N,31244,4927,53124,Hillside Woodland Star,perennial,white,2,6
+Lithophragma parviflorum var. parviflorum,,N,60952,4930,81027,Smallflower Woodland-star,perennial,"white,pink",3,7
 Lobularia maritima,sweet alyssum,X,31347,4939,56992
 Logfia filaginoides,herba impia,N,81847,10960,64254,California Cottonrose,annual,red,2,5
 Logfia gallica,,X,31363,9521,56949,,annual,"brown,yellow",3,7
@@ -1285,9 +1285,10 @@ Osmorhiza berteroi,wood cicely,N,35560,10164,53166,Sweet Cicely
 Osmorhiza brachypoda,California cicely,N,35564,6000,58793,California Sweetcicely
 Oxalis corniculata,creeping wood sorrel,X,35609,6010,53168,,,yellow,1,12
 Oxalis incarnata,crimson wood sorrel,X,35636,6012,61776,,,"white,pink",3,6
-Oxalis oregana,redwood sorrel,N,35641,6015,47757,Redwood Sorrel,,"white,pink",2,8
+Oxalis oregana,Oregon wood sorrel,N,35641,6015,47757,Redwood Sorrel,perennial,white,2,10
 Oxalis pes-caprae,Bermuda-buttercup,X,35642,6016,53169,,,yellow,1,5
 Oxalis pilosa,hairy wood sorrel,N,35601,11895,78300,Radishroot Woodsorrel,,yellow,2,9
+Oxalis smalliana,redwood sorrel,N,8615,14752,1464017,,perennial,"white,pink,blue",1,8
 Packera breweri,Brewer groundsel,N,77383,9613,56983,Groundsel
 Panicum acuminatum,Pacific panic grass,N,35923,6044,128949,Western Panicgrass
 Panicum capillare,witchgrass,N,36094,6048,78337,Witch Grass
@@ -1563,17 +1564,17 @@ Rubus pensilvanicus,,X,42114,7202,78894
 Rubus spectabilis,,N,42231,7203,47543,Salmon Berry
 Rubus ulmifolius var. anoplothyrsus,,X,91783,11997,81352
 Rubus ursinus,California blackberry,N,42267,7206,53445,California Blackberry
-Rumex acetosella,sheep sorrel,X,42362,7213,53195
-Rumex californicus,,N,42423,11058,78901,California Dock
-Rumex conglomeratus,green dock,X,42385,7214,57215
-Rumex crassus,,N,42422,11059,61087,Willow Dock
-Rumex crispus,curly dock,X,42386,7215,53197
-Rumex fueginus,golden dock,N,42405,10679,78903,Golden Dock
-Rumex obtusifolius,bitter dock,X,42409,7220,63371
-Rumex occidentalis,western dock,N,42376,7221,61086,Western Dock
-Rumex pulcher,fiddle dock,X,42419,7224,60232
-Rumex salicifolius,willow dock,N,42421,7225,60233,Willow Dock
-Rumex transitorius,,N,42429,11999,78910
+Rumex acetosella,sheep sorrel,X,42362,7213,53195,,perennial,,4,7
+Rumex californicus,,N,42423,11058,78901,California Dock,perennial,,5,9
+Rumex conglomeratus,green dock,X,42385,7214,57215,,perennial,,5,8
+Rumex crassus,,N,42422,11059,61087,Willow Dock,perennial,,2,7
+Rumex crispus,curly dock,X,42386,7215,53197,,perennial,,1,12
+Rumex fueginus,golden dock,N,42405,10679,78903,Golden Dock,annual,,5,8
+Rumex obtusifolius,bitter dock,X,42409,7220,63371,,perennial,,5,9
+Rumex occidentalis,western dock,N,42376,7221,61086,Western Dock,perennial,,5,8
+Rumex pulcher,fiddle dock,X,42419,7224,60232,,perennial,,5,9
+Rumex salicifolius,willow dock,N,42421,7225,60233,Willow Dock,perennial,,5,7
+Rumex transitorius,,N,42429,11999,78910,,perennial,,4,6
 Rupertia physodes,California tea,N,42446,7236,53198,Common Rupertia
 Ruppia cirrhosa,ditch-grass,N,42449,7238,61089,Spiral Ditchgrass
 Ruppia maritima,ditch-grass,N,42451,7239,61090,Beaked Tasselweed

package/data/text/Brassica-nigra.md

@@ -0,0 +1 @@
+Upper leaves not clasping stem. Usually hairy.

package/data/text/Brassica-rapa.md

@@ -0,0 +1 @@
+Upper leaves clasping stem. Usually not hairy.

package/data/text/Oxalis-oregana.footer.md

@@ -0,0 +1,3 @@
+## Resources
+
+- Brinegar, Chris. (2023). [THE TRUE REDWOOD SORREL: REINSTATEMENT OF OXALIS SMALLIANA (OXALIDACEAE) AS A SPECIES SEPARATE FROM OXALIS OREGANA](https://www.researchgate.net/publication/369602947_THE_TRUE_REDWOOD_SORREL_REINSTATEMENT_OF_OXALIS_SMALLIANA_OXALIDACEAE_AS_A_SPECIES_SEPARATE_FROM_OXALIS_OREGANA). Madroño. 69. 10.3120/0024-9637-69.4.304.

package/data/text/Oxalis-smalliana.footer.md

@@ -0,0 +1,3 @@
+## Resources
+
+- Brinegar, Chris. (2023). [THE TRUE REDWOOD SORREL: REINSTATEMENT OF OXALIS SMALLIANA (OXALIDACEAE) AS A SPECIES SEPARATE FROM OXALIS OREGANA](https://www.researchgate.net/publication/369602947_THE_TRUE_REDWOOD_SORREL_REINSTATEMENT_OF_OXALIS_SMALLIANA_OXALIDACEAE_AS_A_SPECIES_SEPARATE_FROM_OXALIS_OREGANA). Madroño. 69. 10.3120/0024-9637-69.4.304.

package/data/text/Polypodium-calirhiza.md

@@ -0,0 +1 @@
+Frond narrows at base (not triangle shaped). Sori not sunken.

package/data/text/Polypodium-scouleri.md

@@ -0,0 +1 @@
+Frond not hairy on center rib. Frond brittle.

package/data/text/Rumex-acetosella.md

@@ -0,0 +1 @@
+Leaves with lobes at base. Plants unisexual.

package/lib/basepagerenderer.js

@@ -6,8 +6,8 @@ import { GlossaryPages } from "./web/glossarypages.js";
 class BasePageRenderer {
     /**
      * @param {string} outputDir
-     * @param {Taxa} taxa
-     * @param {TaxaCol[]} [familyCols]
+     * @param {import("./taxa.js").Taxa} taxa
+     * @param {import("./htmltaxon.js").TaxaColDef[]} [familyCols]
      */
     static renderBasePages(outputDir, taxa, familyCols) {
         const siteGenerator = new Jekyll(outputDir);
@@ -30,7 +30,7 @@ class BasePageRenderer {
 
     /**
      * @param {string} outputDir
-     * @param {Taxa} taxa
+     * @param {import("./taxa.js").Taxa} taxa
      */
     static renderTools(outputDir, taxa) {
         const names = [];

package/lib/csv.js

@@ -85,9 +85,10 @@ class CSV {
     }
 
     /**
+     * @template T
      * @param {string} fileName
      * @param {string} [delimiter]
-     * @returns {{headers:string[],data:Object<string,any>[]}}
+     * @returns {{headers:string[],data:T[]}}
      */
     static readFileAndHeaders(fileName, delimiter) {
         let headers;

package/lib/ebook/images.js

@@ -23,7 +23,7 @@ class Images {
     }
 
     /**
-     * @param {Taxon[]} taxa
+     * @param {import("../taxon.js").Taxon[]} taxa
      */
     async createImages(taxa) {
         const meter = new ProgressMeter("processing photos", taxa.length);
@@ -102,7 +102,7 @@ class Images {
     }
 
     /**
-     * @param {Photo} photo
+     * @param {import("../photo.js").Photo} photo
      * @returns {string}
      */
     getCompressedFilePath(photo) {
@@ -110,7 +110,7 @@ class Images {
     }
 
     /**
-     * @param {Photo} photo
+     * @param {import("../photo.js").Photo} photo
      * @returns {string}
      */
     getCompressedImageName(photo) {
@@ -118,8 +118,8 @@ class Images {
     }
 
     /**
-     * @param {Taxon} taxon
-     * @returns {Photo[]}
+     * @param {import("../taxon.js").Taxon} taxon
+     * @returns {import("../photo.js").Photo[]}
      */
     static getTaxonPhotos(taxon) {
         const photos = taxon

package/lib/ebook/pages/page_list_species.js

@@ -8,7 +8,7 @@ class PageListSpecies extends EBookPage {
     /**
      *
      * @param {string} outputDir
-     * @param {Taxon[]} taxa
+     * @param {import("../../taxon.js").Taxon[]} taxa
      * @param {string} filename
      * @param {string} title
      */

package/lib/ebook/pages/taxonpage.js

@@ -13,7 +13,7 @@ class TaxonPage extends EBookPage {
 
     /**
      * @param {string} outputDir
-     * @param {Taxon} taxon
+     * @param {import("../../taxon.js").Taxon} taxon
      * @param {Images} images
      */
     constructor(outputDir, taxon, images) {
@@ -69,7 +69,7 @@ class TaxonPage extends EBookPage {
                 src: `i/${this.#images.getCompressedImageName(photo)}`,
                 style: "max-width:" + dimensions.width + "px",
             });
-            const caption = `${photo.rights === "CC0" ? "By" : "(c)"} ${photo.rightsHolder} ${photo.rights && `(${photo.rights})`}`;
+            const caption = photo.getAttribution();
             if (caption) {
                 img += XHTML.textElement("figcaption", caption);
             }

package/lib/ebook/plantbook.js

@@ -18,7 +18,7 @@ class PlantBook extends EBook {
     /**
      * @param {string} outputDir
      * @param {Config} config
-     * @param {Taxa} taxa
+     * @param {import("../taxa.js").Taxa} taxa
      */
     constructor(outputDir, config, taxa) {
         super(

package/lib/exceptions.js

@@ -30,6 +30,9 @@ class Exceptions {
         }
     }
 
+    /**
+     * @returns {[string,Object<string,Object<string,string>>][]}
+     */
     getExceptions() {
         return Object.entries(this.#exceptions);
     }

package/lib/families.js

@@ -19,7 +19,7 @@ class Family {
     }
 
     /**
-     * @param {Taxon} taxon
+     * @param {import("./taxon.js").Taxon} taxon
      */
     addTaxon(taxon) {
         if (!this.#data.taxa) {
@@ -68,7 +68,7 @@ class Families {
 
     getFamilies() {
         return Object.values(this.#families).sort((a, b) =>
-            a.getName().localeCompare(b.getName())
+            a.getName().localeCompare(b.getName()),
         );
     }
 
@@ -81,7 +81,7 @@ class Families {
 
     /**
      * @param {string} outputDir
-     * @param {TaxaCol[]} taxaColumns
+     * @param {import("./htmltaxon.js").TaxaColDef[]} [taxaColumns]
      */
     renderPages(outputDir, taxaColumns) {
         new PageFamilyList(outputDir, this.#families).render(taxaColumns);
@@ -109,7 +109,7 @@ class PageFamilyList extends GenericPage {
     }
 
     /**
-     * @param {TaxaCol[]} taxaColumns
+     * @param {import("./htmltaxon.js").TaxaColDef[]} [taxaColumns]
      */
     render(taxaColumns) {
         let html = this.getDefaultIntro();
@@ -121,13 +121,13 @@ class PageFamilyList extends GenericPage {
 
             // Render the section page.
             new PageSection(this.getOutputDir(), name, taxa).render(
-                taxaColumns
+                taxaColumns,
             );
 
             // Render the link.
             const href = "./" + name + ".html";
             sectionLinks.push(
-                HTML.getLink(href, name) + " (" + taxa.length + ")"
+                HTML.getLink(href, name) + " (" + taxa.length + ")",
             );
         }
         html += HTML.wrap("ul", HTML.arrayToLI(sectionLinks), {
@@ -150,7 +150,7 @@ class PageFamilyList extends GenericPage {
             }
             let cols = HTML.wrap(
                 "td",
-                HTML.getLink("./" + family.getFileName(), family.getName())
+                HTML.getLink("./" + family.getFileName(), family.getName()),
             );
             cols += HTML.wrap("td", taxa.length, { class: "right" });
             html += HTML.wrap("tr", cols);
@@ -176,7 +176,7 @@ class PageFamily extends GenericPage {
     }
 
     /**
-     * @param {TaxaCol[]} columns
+     * @param {import("./htmltaxon.js").TaxaColDef[]} [columns]
      */
     render(columns) {
         let html = this.getDefaultIntro();
@@ -184,7 +184,7 @@ class PageFamily extends GenericPage {
         html += HTML.wrap(
             "div",
             Jepson.getEFloraLink(this.#family.getJepsonID()),
-            { class: "section" }
+            { class: "section" },
         );
 
         html += HTMLTaxon.getTaxaTable(this.#family.getTaxa(), columns);
@@ -199,7 +199,7 @@ class PageSection extends GenericPage {
     /**
      * @param {string} outputDir
      * @param {string} name
-     * @param {Taxon[]} taxa
+     * @param {import("./taxon.js").Taxon[]} taxa
      */
     constructor(outputDir, name, taxa) {
         super(outputDir, name, name);
@@ -207,7 +207,7 @@ class PageSection extends GenericPage {
     }
 
     /**
-     * @param {TaxaCol[]} [columns]
+     * @param {import("./htmltaxon.js").TaxaColDef[]} [columns]
      */
     render(columns) {
         let html = this.getDefaultIntro();
@@ -219,12 +219,12 @@ class PageSection extends GenericPage {
 }
 
 class Sections {
-    /** @type {Object<string,Taxon[]>} */
+    /** @type {Object<string,import("./taxon.js").Taxon[]>} */
     static #sections = {};
 
     /**
      * @param {string} name
-     * @param {Taxon} taxon
+     * @param {import("./taxon.js").Taxon} taxon
      */
     static addTaxon(name, taxon) {
         let section = this.#sections[name];

package/lib/genera.js

@@ -15,7 +15,7 @@ class Genera {
     }
 
     /**
-     * @param {Taxon} taxon
+     * @param {import("./taxon.js").Taxon} taxon
      */
     addTaxon(taxon) {
         const genusName = taxon.getGenusName();

package/lib/htmltaxon.js

@@ -6,7 +6,15 @@ import { RarePlants } from "./rareplants.js";
 import { TextUtils } from "./textutils.js";
 
 /**
- * @type {Record<string,{title:string,data:function (Taxon):string}>}
+ * @typedef {{
+    class?: string;
+    data: (taxon: import("./taxon.js").Taxon) => string;
+    title: string;
+     }} TaxaColDef
+ */
+
+/**
+ * @type {Record<string,TaxaColDef>}
  */
 const TAXA_LIST_COLS = {
     CESA: {
@@ -39,6 +47,7 @@ const TAXA_LIST_COLS = {
     },
 };
 
+/** @type {TaxaColDef[]} */
 const DEFAULT_TAXA_COLUMNS = [
     TAXA_LIST_COLS.SPECIES,
     TAXA_LIST_COLS.COMMON_NAME,
@@ -46,7 +55,7 @@ const DEFAULT_TAXA_COLUMNS = [
 
 class HTMLTaxon {
     /**
-     * @param {Taxon} taxon
+     * @param {import("./taxon.js").Taxon} taxon
      * @returns {string|undefined}
      */
     static getCalscapeLink(taxon) {
@@ -88,7 +97,7 @@ class HTMLTaxon {
     }
 
     /**
-     * @param {Taxon} taxon
+     * @param {import("./taxon.js").Taxon} taxon
      * @param {string} classNames
      * @param {boolean} [includeColorLink=true]
      */
@@ -129,7 +138,7 @@ class HTMLTaxon {
     }
 
     /**
-     * @param {Taxon} taxon
+     * @param {import("./taxon.js").Taxon} taxon
      * @returns {string}
      */
     static getFooterHTML(taxon) {
@@ -142,7 +151,7 @@ class HTMLTaxon {
     }
 
     /**
-     * @param {Taxon} taxon
+     * @param {import("./taxon.js").Taxon} taxon
      */
     static getLink(taxon) {
         return (
@@ -182,8 +191,8 @@ class HTMLTaxon {
     }
 
     /**
-     * @param {Taxon[]} taxa
-     * @param {TaxaCol[]} [columns]
+     * @param {import("./taxon.js").Taxon[]} taxa
+     * @param {TaxaColDef[]} [columns]
      */
     static getTaxaTable(taxa, columns = DEFAULT_TAXA_COLUMNS) {
         let html = "<table><thead>";

package/lib/index.d.ts

@@ -24,6 +24,13 @@ export class ErrorLog {
 
 export class Exceptions {
     constructor(dataDir: string);
+    getExceptions(): [string, Record<string, Record<string, string>>][];
+    getValue(
+        name: string,
+        cat: string,
+        subcat: string,
+        defaultValue?: string | undefined,
+    ): string | undefined;
     hasException(name: string, cat: string, subcat: string): boolean;
 }
 
@@ -72,6 +79,16 @@ export class Jekyll {
     static include(fileName: string): string;
 }
 
+type PhotoRights = "CC0" | "CC BY" | "CC BY-NC" | "C" | null;
+
+export class Photo {
+    getAttribution(): string;
+    getExt(): string;
+    getId(): number;
+    getSourceUrl(): string;
+    getUrl(): string;
+}
+
 export class Program {
     static getIncludeList(dataDir: string): string[];
     static getProgram(): Command;
@@ -94,13 +111,20 @@ export class Taxon {
     getBaseFileName(): string;
     getCalfloraID(): string;
     getCalfloraTaxonLink(): string;
+    getCESA(): string | undefined;
+    getCNDDBRank(): string | undefined;
     getCommonNames(): string[];
     getFamily(): Family;
+    getFESA(): string | undefined;
     getGenus(): Genus;
     getGenusName(): string;
+    getGlobalRank(): string | undefined;
     getINatID(): string;
     getINatTaxonLink(): string;
+    getJepsonID(): string;
     getName(): string;
+    getPhotos(): Photo[];
+    getRPIRankAndThreat(): string;
     getRPITaxonLink(): string;
     getSynonyms(): string[];
 }