chore: update tools to use local taxaloader when present (#24)

* chore: update Phacelia

* chore: update taxa photos

* chore: update tools to use local taxaloader when present

README.md

@@ -37,15 +37,15 @@ npm i --save @ca-plant-list/ca-plant-list
 ca-plant-list loads photos of plants from iNat and maintains lists of photos of all the plants it knows about from both licensed iNat taxon photos and licensed iNat observation photos. If you want to customize the photos that appear on your site, you can add a file of iNat photo data to your local setup. This package provides some tools for doing so. For example, if you wanted to use photos from observations from Alameda and Contra Costa Counties, you could do this:
 
 ```zsh
-npx node ./node_modules/@ca-plant-list/ca-plant-list/scripts/inatobsphotos.js -fn inatphotos.csv -q "place_id=845,1527"
+npx inatobsphotos -q "place_id=845,1527"
 ```
 
 That will create `data/inatphotos.csv` in your repo, populated by photos from verifiable observations of the taxa in data/taxa.csv from the place IDs identified in the `-q` param. It chooses from the most-faved observations with the "CC BY" or "CC BY-NC" licenses, or the CC0 declaration.
 
 If you want to load from iNat taxon photos instead, you can do
 
 ```zsh
-npx node ./node_modules/@ca-plant-list/ca-plant-list/scripts/inattaxonphotos.js -fn inatphotos.csv
+npx inattaxonphotos
 ```
 
 The only reason to do that would be to get more recently-updated iNat taxon photos than ca-plant-list knows about.

data/inattaxonphotos.csv

@@ -736,6 +736,9 @@ Blepharizonia plumosa,89389624,jpg,cc-by-nc,Chloe Novak
 Boechera breweri subsp. breweri,854971,jpg,cc-by-nc,Robert
 Bolboschoenus fluviatilis,5421230,jpg,cc-by-nc,sarahaj
 Bolboschoenus maritimus subsp. paludosus,132800260,jpeg,cc-by-nc,Peter Zika
+Bolboschoenus maritimus subsp. paludosus,132800264,jpeg,cc-by-nc,Peter Zika
+Bolboschoenus maritimus subsp. paludosus,448262257,jpg,cc-by-nc,Fred Melgert / Carla Hoegen
+Bolboschoenus maritimus subsp. paludosus,448262847,jpg,cc-by-nc,Fred Melgert / Carla Hoegen
 Bolboschoenus robustus,79020136,jpeg,cc-by-nc,Sarah Towne
 Bowlesia incana,1678991,JPG,cc-by-nc,Carolyn Gritzmaker
 Bowlesia incana,128744293,jpg,cc-by,Zihao Wang
@@ -964,6 +967,8 @@ Calystegia sepium subsp. limnophila,5091992,jpg,cc-by,Ken-ichi Ueda
 Calystegia sepium subsp. limnophila,38875324,jpeg,cc-by,Lauren McLaurin
 Calystegia silvatica subsp. disjuncta,2839177,jpg,cc0,Peter de Lange
 Calystegia silvatica subsp. disjuncta,2839178,jpg,cc0,Peter de Lange
+Calystegia silvatica subsp. disjuncta,132744682,jpeg,cc-by-nc,lflovesnature
+Calystegia silvatica subsp. disjuncta,132744715,jpeg,cc-by-nc,lflovesnature
 Calystegia soldanella,106263751,jpg,cc-by-nc,Dani Montijo
 Calystegia soldanella,16180949,jpeg,cc-by,Arnim Littek
 Calystegia soldanella,62295020,jpeg,cc0,葉子
@@ -1036,6 +1041,7 @@ Carex barbarae,16259864,jpeg,cc-by,Millie Basden
 Carex barbarae,76197561,jpg,cc-by-nc,jrmorris
 Carex barbarae,9536063,jpeg,cc-by-nc,James Bailey
 Carex brevicaulis,13079255,jpeg,cc-by-nc,Robert Pergl
+Carex brevicaulis,336177289,jpeg,cc-by,Flavien Saboureau
 Carex comosa,2097792,jpg,cc-by-nc,Susan Elliott
 Carex comosa,2097794,jpg,cc-by-nc,Susan Elliott
 Carex densa,70367090,jpeg,cc-by-nc,James Miskelly
@@ -1598,6 +1604,7 @@ Cryptantha corollata,6694854,jpg,cc-by-nc,Steve Jones
 Cryptantha corollata,6694853,jpg,cc-by-nc,Steve Jones
 Cryptantha flaccida,103049,jpg,cc-by,dloarie
 Cryptantha intermedia var. intermedia,17323919,jpg,cc-by-nc,BJ Stacey
+Cryptantha intermedia var. intermedia,5699495,jpg,cc-by-nc,Chris Evers
 Cryptantha juniperensis,378730932,jpg,cc-by-nc,madge
 Cryptantha juniperensis,378730814,jpg,cc-by-nc,madge
 Cryptantha juniperensis,38799107,jpeg,cc-by-nc,Conor and Alexandra
@@ -1680,6 +1687,9 @@ Cyperus involucratus,175703429,jpeg,cc-by,Licheng Shih
 Cyperus involucratus,181908056,jpeg,cc-by-nc,Chris Close
 Cyperus involucratus,7928186,jpg,cc-by-nc,LSchare (she/her)
 Cyperus involucratus,55787221,jpeg,cc-by,agujaceratops
+Cyperus niger,89856671,jpg,cc-by-nc,jrebman
+Cyperus niger,161421212,jpeg,cc-by,Ken-ichi Ueda
+Cyperus niger,237485592,jpeg,cc-by,Ken-ichi Ueda
 Cyperus odoratus,24788159,jpeg,cc-by,Zihao Wang
 Cyperus odoratus,25385210,jpg,cc-by-nc,Dan Johnson
 Cyperus strigosus,321391275,jpeg,cc-by,Michael J. Papay
@@ -1752,6 +1762,7 @@ Delphinium californicum subsp. californicum,42625517,jpeg,cc-by-nc,kalibardo
 Delphinium californicum subsp. californicum,42625528,jpeg,cc-by-nc,kalibardo
 Delphinium californicum subsp. californicum,745389,jpg,cc-by-nc,Eric Wrubel
 Delphinium californicum subsp. interius,4087,jpg,cc-by,Ken-ichi Ueda
+Delphinium californicum subsp. interius,129448412,jpg,cc-by-nc,kevinsherrill
 Delphinium glaucum,37397608,jpg,cc-by-nc,Guy Lemelin
 Delphinium glaucum,3738355,jpg,cc-by,Andrey Zharkikh
 Delphinium gypsophilum,15118,jpg,cc-by,marlin harms
@@ -2247,6 +2258,8 @@ Eriophyllum confertiflorum var. confertiflorum,17035891,jpg,cc-by-nc,Fred Melger
 Eriophyllum confertiflorum var. confertiflorum,42156614,jpg,cc-by-nc,docprt
 Eriophyllum jepsonii,35246132,jpg,cc-by-nc,Christian Schwarz
 Eriophyllum jepsonii,64529857,jpg,cc-by-nc,Chloe and Trevor Van Loon
+Eriophyllum lanatum var. achilleoides,375544135,jpg,cc-by-nc,Karlyn H. Lewis
+Eriophyllum lanatum var. achilleoides,62642791,png,cc-by-nc,James Gonsman
 Eriophyllum staechadifolium,171909656,jpg,cc-by,DeeF
 Eriophyllum staechadifolium,2266969,JPG,cc-by,Don Loarie
 Eriophyllum staechadifolium,8009436,jpg,cc-by-nc,Bill Miller
@@ -2350,6 +2363,7 @@ Erythranthe microphylla,121654136,jpg,cc-by-nc,alivea009
 Erythranthe microphylla,127754761,jpeg,cc-by-nc,Dan Tucker
 Erythranthe microphylla,6708076,jpeg,cc-by-nc,Andrew Simon
 Erythranthe microphylla,268075917,jpg,cc-by-nc,Dean Lyons
+Erythranthe microphylla,373764496,jpg,cc-by-nc,Ocean Fleskes
 Erythranthe moschata,301068789,jpg,cc-by-nc,nathantay
 Erythranthe moschata,305753498,jpg,cc-by-nc,Ocean Fleskes
 Erythranthe moschata,948210,jpg,cc-by-nc,Susan
@@ -3070,6 +3084,9 @@ Juncus xiphioides,9806786,jpg,cc-by-nc,Sarah Wilson
 Juniperus californica,185052,jpg,cc-by,Ken-ichi Ueda
 Juniperus californica,20654,jpg,cc-by,Ken-ichi Ueda
 Juniperus californica,528925,jpg,cc-by-nc,Tom Scott
+Juniperus communis var. saxatilis,62016689,jpg,cc-by-nc,Boris Bolshakov
+Juniperus communis var. saxatilis,142708159,jpeg,cc-by-nc,Alexander Rumpel
+Juniperus communis var. saxatilis,108219672,jpg,cc-by-nc,Felipe Castilla Lattke
 Keckiella breviflora var. breviflora,160934765,jpg,cc-by,Steve Matson
 Keckiella breviflora var. breviflora,160934761,jpg,cc-by,Steve Matson
 Keckiella corymbosa,149319402,jpeg,cc-by-nc,Jason Cantley
@@ -3242,6 +3259,7 @@ Lepidium dictyotum,272680,jpg,cc-by-nc,2009 Zoya Akulova
 Lepidium didymum,175706599,jpeg,cc-by-nc,Aleksandr_Levon
 Lepidium didymum,8011861,jpg,cc0,Jesse Rorabaugh
 Lepidium didymum,114049269,jpeg,cc-by-nc,博甫
+Lepidium didymum,207927754,jpg,cc-by-nc,Chuangzao
 Lepidium draba,17017121,jpg,cc-by,Conrad Altmann
 Lepidium draba,127389190,jpg,cc-by-nc,africaspotter
 Lepidium draba,34927501,jpg,cc-by-nc,Kayla Echols
@@ -4286,6 +4304,10 @@ Phoradendron leucarpum subsp. macrophyllum,248523345,jpeg,cc-by-nc,James Bailey
 Phoradendron leucarpum subsp. macrophyllum,34637175,jpg,cc-by-nc,jimpark67
 Phoradendron leucarpum subsp. macrophyllum,51724554,jpg,cc-by-nc,ellen hildebrandt
 Phoradendron leucarpum subsp. tomentosum,37764,jpg,cc-by,Franco Folini
+Phoradendron leucarpum subsp. tomentosum,274597968,jpg,cc-by-nc,Ryan Brooks
+Phoradendron leucarpum subsp. tomentosum,175973152,jpeg,cc-by-nc,Anne Parsons
+Phoradendron leucarpum subsp. tomentosum,106352640,jpeg,cc-by-nc,Patricia
+Phoradendron leucarpum subsp. tomentosum,275717813,jpeg,cc-by,Cricket Raspet
 Phragmites australis,51566082,jpg,cc-by-nc,mimzee
 Phragmites australis,53131602,jpg,cc-by-nc,Sergey Mayorov
 Phragmites australis,57666377,jpeg,cc-by-nc,Roger Debenham
@@ -4760,6 +4782,8 @@ Quercus durata var. durata,22844206,jpg,cc-by,John Rusk
 Quercus garryana var. garryana,1765723,jpg,cc-by-nc,Di
 Quercus garryana var. garryana,132101933,jpg,cc-by,Biodiversity Heritage Library
 Quercus garryana var. garryana,132101934,jpg,cc-by,The Marmot
+Quercus garryana var. garryana,294381780,jpg,cc-by-nc,JoeJoe Clark
+Quercus garryana var. garryana,428986606,jpeg,cc-by-nc,Mart Hughes
 Quercus ilex,52702145,jpg,cc-by-nc,Muriel Bendel
 Quercus ilex,165811504,jpeg,cc-by-nc,juristi
 Quercus ilex,243199963,jpeg,cc-by-nc,Platon Kleanthidis
@@ -4834,6 +4858,7 @@ Ranunculus sceleratus,146317741,jpg,cc-by-nc,Vladimir Bryukhov
 Ranunculus sceleratus,31618021,jpg,cc-by-nc,Марина Горбунова-Ëлкина
 Ranunculus sceleratus,17360630,jpeg,cc-by-nc,Nathan Taylor
 Ranunculus sceleratus,74753531,jpeg,cc-by,Nina Filippova
+Ranunculus sceleratus var. sceleratus,3155996,JPG,cc-by-nc,Bob O'Kennon
 Raphanus raphanistrum,381509992,jpg,cc-by-nc,califorag3r
 Raphanus raphanistrum,79344995,jpeg,cc-by-nc,Nadezhda Nayanova
 Raphanus raphanistrum,284199344,jpg,cc-by-nc,chedar
@@ -5483,6 +5508,8 @@ Spergula arvensis,5060236,jpg,cc-by-nc,Simon Nicholas
 Spergularia bocconi,24556284,jpeg,cc-by-nc,James Bailey
 Spergularia bocconi,112060330,jpeg,cc-by-nc,James Bailey
 Spergularia bocconi,34753827,jpg,cc-by-nc,sue_meiman
+Spergularia macrotheca var. leucantha,270639696,jpg,cc-by-nc,Bonnie Nickel
+Spergularia macrotheca var. leucantha,270639736,jpg,cc-by-nc,Bonnie Nickel
 Spergularia macrotheca var. longistyla,183054472,jpg,cc-by-nc,jpgalvan
 Spergularia macrotheca var. longistyla,187421118,jpg,cc-by-nc,chrisdan
 Spergularia macrotheca var. longistyla,186674278,jpg,cc0,Scott Yarger

data/taxa.csv

@@ -1331,10 +1331,10 @@ Persicaria punctata,,N,37303,11014,78456,Water Smartweed
 Petasites frigidus var. palmatus,coltsfoot,N,8060,6269,55778,Arctic Sweet Coltsfoot
 Petrorhagia dubia,pink grass,X,37370,6275,60602
 Petunia parviflora,wild petunia,N,37378,6279,159650,Seaside Petunia
-Phacelia breweri,,N,37425,6292,68813,Brewer's Phacelia,,blue,3,6
-Phacelia californica,rock phacelia,N,37426,6293,53170,Rock Phacelia
-Phacelia ciliata,great valley phacelia,N,37432,6302,58180,Great Valley Phacelia
-Phacelia distans,"sordid phacelia,distant phacelia",N,37450,6318,56631,Wild Heliotrope,,"white,blue",3,5
+Phacelia breweri,Brewer's phacelia,N,37425,6292,68813,Brewer's Phacelia,annual,blue,3,6
+Phacelia californica,rock phacelia,N,37426,6293,53170,Rock Phacelia,perennial,blue,3,9
+Phacelia ciliata,great valley phacelia,N,37432,6302,58180,Great Valley Phacelia,annual,blue,3,6
+Phacelia distans,"sordid phacelia,distant phacelia",N,37450,6318,56631,Wild Heliotrope,annual,"white,blue",3,5
 Phacelia divaricata,,N,37451,6319,51093,Divaricate Phacelia
 Phacelia douglasii,,N,37452,6320,58182,Douglas' Phacelia
 Phacelia egena,,N,37455,6322,58183,Kaweah River Phacelia

lib/taxa.js

@@ -9,6 +9,8 @@ import { Families } from "./families.js";
 import { FlowerColor } from "./flowercolor.js";
 import { InatPhoto } from "./inat_photo.js";
 import { TaxaCSV } from "./tools/taxacsv.js";
+import { ErrorLog } from "./errorlog.js";
+import { Program } from "./program.js";
 
 const FLOWER_COLORS = [
     { name: "white", color: "white" },
@@ -109,12 +111,13 @@ class Taxa {
     #loadPhotosFromFile(dataDir, filename) {
         if (!fs.existsSync(path.join(dataDir, filename))) return;
         /** @type {InatCsvPhoto[]} */
-        const csvPhotos = CSV.parseFile(dataDir, filename).map( row => {
+        const csvPhotos = CSV.parseFile(dataDir, filename).map((row) => {
             /** @type {InatLicenseCode} */
             let licenseCode = "cc-by";
             if (row.licenseCode === "cc-by-nc-sa") licenseCode = "cc-by-nc-sa";
             else if (row.licenseCode === "cc-by-nc") licenseCode = "cc-by-nc";
-            else if (row.licenseCode === "cc-by-nc-nd") licenseCode = "cc-by-nc-nd";
+            else if (row.licenseCode === "cc-by-nc-nd")
+                licenseCode = "cc-by-nc-nd";
             else if (row.licenseCode === "cc-by") licenseCode = "cc-by";
             else if (row.licenseCode === "cc-by-sa") licenseCode = "cc-by-sa";
             else if (row.licenseCode === "cc-by-nd") licenseCode = "cc-by-nd";
@@ -124,11 +127,11 @@ class Taxa {
             return {
                 attrName: row.attrName,
                 ext: row.ext,
-                id: Number( row.id ),
+                id: Number(row.id),
                 licenseCode,
-                name: row.name
+                name: row.name,
             };
-        } );
+        });
         for (const csvPhoto of csvPhotos) {
             const taxon = this.getTaxon(csvPhoto.name);
             if (!taxon) {
@@ -149,9 +152,9 @@ class Taxa {
      * @param {string} dataDir
      */
     #loadInatPhotos(dataDir) {
-        this.#loadPhotosFromFile( "./data", "inatphotos.csv" );
-        this.#loadPhotosFromFile( dataDir, "inattaxonphotos.csv" );
-        this.#loadPhotosFromFile( dataDir, "inatobsphotos.csv" );
+        this.#loadPhotosFromFile("./data", "inatphotos.csv");
+        this.#loadPhotosFromFile(dataDir, "inattaxonphotos.csv");
+        this.#loadPhotosFromFile(dataDir, "inatobsphotos.csv");
     }
 
     getFamilies() {
@@ -190,6 +193,31 @@ class Taxa {
         return this.#isSubset;
     }
 
+    /**
+     * @param {import("commander").OptionValues} options
+     */
+    static async loadTaxa(options) {
+        const errorLog = new ErrorLog(options.outputdir + "/errors.tsv", false);
+
+        const loaderPath = "./js/taxaloader.js";
+        let taxa;
+        if (fs.existsSync(loaderPath)) {
+            const taxaLoaderClass = await import(
+                "file:" + path.resolve(loaderPath)
+            );
+            taxa = await taxaLoaderClass.TaxaLoader.loadTaxa(options, errorLog);
+        } else {
+            taxa = new Taxa(
+                Program.getIncludeList(options.datadir),
+                errorLog,
+                options.showFlowerErrors,
+            );
+        }
+
+        errorLog.write();
+        return taxa;
+    }
+
     /**
      * @param {SynonymData[]} synCSV
      * @param {Object<string,TaxonData>|boolean} inclusionList

package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.4.14",
+    "version": "0.4.16",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {
@@ -31,7 +31,8 @@
         "ca-plant-list": "scripts/build-site.js",
         "ca-plant-book": "scripts/build-ebook.js",
         "cpl-photos": "scripts/cpl-photos.js",
-        "cpl-tools": "scripts/cpl-tools.js"
+        "cpl-tools": "scripts/cpl-tools.js",
+        "inatobsphotos": "scripts/inatobsphotos.js"
     },
     "dependencies": {
         "archiver": "^5.3.1",

scripts/cpl-tools.js

@@ -1,8 +1,6 @@
 #!/usr/bin/env node
 
-import * as path from "node:path";
 import { Option } from "commander";
-import { Taxa } from "../lib/taxa.js";
 import { Program } from "../lib/program.js";
 import { Calflora } from "../lib/tools/calflora.js";
 import { Exceptions } from "../lib/exceptions.js";
@@ -12,6 +10,7 @@ import { INat } from "../lib/tools/inat.js";
 import { JepsonEFlora } from "../lib/tools/jepsoneflora.js";
 import { RPI } from "../lib/tools/rpi.js";
 import { Config } from "../lib/config.js";
+import { Taxa } from "../lib/taxa.js";
 
 const TOOLS = {
     CALFLORA: "calflora",
@@ -32,7 +31,6 @@ const ALL_TOOLS = [
     TOOLS.TEXT,
 ];
 
-const OPT_LOADER = "loader";
 const OPT_TOOL = "tool";
 
 const TOOLS_DATA_DIR = "./external_data";
@@ -52,7 +50,7 @@ async function build(program, options) {
 
     const exceptions = new Exceptions(options.datadir);
     const config = new Config(options.datadir);
-    const taxa = await getTaxa(options);
+    const taxa = await Taxa.loadTaxa(options);
 
     const errorLog = new ErrorLog(options.outputdir + "/log.tsv", true);
     for (const tool of tools) {
@@ -120,29 +118,6 @@ async function build(program, options) {
     errorLog.write();
 }
 
-/**
- * @param {import("commander").OptionValues} options
- */
-async function getTaxa(options) {
-    const errorLog = new ErrorLog(options.outputdir + "/errors.tsv", true);
-
-    const loader = options[OPT_LOADER];
-    let taxa;
-    if (loader) {
-        const taxaLoaderClass = await import("file:" + path.resolve(loader));
-        taxa = await taxaLoaderClass.TaxaLoader.loadTaxa(options, errorLog);
-    } else {
-        taxa = new Taxa(
-            Program.getIncludeList(options.datadir),
-            errorLog,
-            options.showFlowerErrors,
-        );
-    }
-
-    errorLog.write();
-    return taxa;
-}
-
 const program = Program.getProgram();
 program.addOption(
     new Option(
@@ -159,10 +134,6 @@ program.option(
     "--ef-lognotes",
     "When running the jepson-eflora tool, include eFlora notes, invalid names, etc. in the log file.",
 );
-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 taxa.csv to remove errors if possible.");
 program.addHelpText(
     "after",