@ca-plant-list/ca-plant-list 0.4.9 → 0.4.10

package/scripts/cpl-photos.js

@@ -0,0 +1,179 @@
+#!/usr/bin/env node
+
+import path from "path";
+import { ErrorLog } from "../lib/errorlog.js";
+import { Program } from "../lib/program.js";
+import { Taxa } from "../lib/taxa.js";
+import { getTaxonPhotos } from "../lib/utils/inat-tools.js";
+import { existsSync } from "fs";
+import { CSV } from "../lib/csv.js";
+
+const PHOTO_FILE_NAME = "inattaxonphotos.csv";
+
+const OPT_LOADER = "loader";
+
+const MAX_PHOTOS = 5;
+
+/**
+ * @param {import("commander").OptionValues} options
+ */
+async function addMissingPhotos(options) {
+    const taxaMissingPhotos = [];
+
+    const taxa = await getTaxa(options);
+    const errorLog = new ErrorLog(options.outputdir + "/log.tsv", true);
+
+    for (const taxon of taxa.getTaxonList()) {
+        const photos = taxon.getPhotos();
+        if (photos.length < MAX_PHOTOS) {
+            taxaMissingPhotos.push(taxon);
+        }
+    }
+
+    const newPhotos = await getTaxonPhotos(taxaMissingPhotos);
+    const currentTaxaPhotos = readPhotos();
+
+    for (const [taxonName, photos] of newPhotos) {
+        let currentPhotos = currentTaxaPhotos.get(taxonName);
+        if (!currentPhotos) {
+            currentPhotos = [];
+            currentTaxaPhotos.set(taxonName, currentPhotos);
+        }
+        for (const photo of photos) {
+            if (currentPhotos.length === MAX_PHOTOS) {
+                break;
+            }
+            if (
+                currentPhotos.some(
+                    (currentPhoto) => currentPhoto.id === photo.id,
+                )
+            ) {
+                continue;
+            }
+            currentPhotos.push(photo);
+            errorLog.log("adding photo", taxonName, photo.id);
+        }
+    }
+
+    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.writeFile(`${options.outputdir}/${PHOTO_FILE_NAME}`, data, headers);
+}
+
+/**
+ * @param {import("commander").OptionValues} options
+ * @param {import("commander").OptionValues} commandOptions
+ */
+async function checkmissing(options, commandOptions) {
+    const taxa = await getTaxa(options);
+    const errorLog = new ErrorLog(options.outputdir + "/log.tsv", true);
+
+    const minPhotos = commandOptions.minphotos;
+    for (const taxon of taxa.getTaxonList()) {
+        const photos = taxon.getPhotos();
+        if (
+            minPhotos === undefined
+                ? photos.length !== MAX_PHOTOS
+                : photos.length < minPhotos
+        ) {
+            errorLog.log(taxon.getName(), photos.length.toString());
+        }
+    }
+
+    errorLog.write();
+}
+
+/**
+ * @param {import("commander").OptionValues} options
+ * @return {Promise<Taxa>}
+ */
+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;
+}
+
+/**
+ * @returns {Map<string,InatPhotoInfo[]>}
+ */
+function readPhotos() {
+    const photosFileName = `./data/${PHOTO_FILE_NAME}`;
+    if (!existsSync(photosFileName)) {
+        return new Map();
+    }
+
+    /** @type {Map<string,{id:string,ext:string,licenseCode:string,attrName:string}[]>} */
+    const taxonPhotos = new Map();
+
+    /** @type {InatCsvPhoto[]} */
+    const csvPhotos = CSV.readFile(photosFileName);
+    for (const csvPhoto of csvPhotos) {
+        const taxonName = csvPhoto.name;
+        let photos = taxonPhotos.get(taxonName);
+        if (!photos) {
+            photos = [];
+            taxonPhotos.set(taxonName, photos);
+        }
+        photos.push({
+            id: csvPhoto.id.toString(),
+            ext: csvPhoto.ext,
+            licenseCode: csvPhoto.licenseCode,
+            attrName: csvPhoto.attrName,
+        });
+    }
+
+    return taxonPhotos;
+}
+
+const program = Program.getProgram();
+program
+    .command("checkmissing")
+    .description("List taxa with less than the maximum number of photos")
+    .option(
+        "--minphotos <number>",
+        "Minimum number of photos. Taxa with fewer than this number will be listed.",
+    )
+    .action((options) => checkmissing(program.opts(), options));
+if (process.env.npm_package_name === "@ca-plant-list/ca-plant-list") {
+    // Only allow updates in ca-plant-list.
+    program
+        .command("addmissing")
+        .description("Add photos to taxa with fewer than the maximum")
+        .action(() => addMissingPhotos(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.",
+);
+await program.parseAsync();

package/tmp/config.json

@@ -0,0 +1,21 @@
+{
+    "calflora": {
+        "counties": [
+            "ALA",
+            "CCA"
+        ]
+    },
+    "inat": {
+        "project": "ebcnps"
+    },
+    "labels": {
+        "introduced": "Introduced to the East Bay",
+        "native": "Native to the East Bay",
+        "status-NC": "California native introduced to the East Bay"
+    },
+    "ebook": {
+        "filename": "ebplants",
+        "pub_id": "ebplants",
+        "title": "East Bay Plants"
+    }
+}

package/tmp/exceptions.json

@@ -0,0 +1,93 @@
+{
+    "Campanula exigua": {
+        "rpi": {
+            "translation-to-rpi": "Ravenella exigua"
+        }
+    },
+    "Campanula sharsmithiae": {
+        "rpi": {
+            "translation-to-rpi": "Ravenella sharsmithiae"
+        }
+    },
+    "Castilleja ambigua subsp. ambigua": {
+        "rpi": {
+            "translation-to-rpi": "Castilleja ambigua var. ambigua"
+        }
+    },
+    "Castilleja ambigua var. ambigua": {
+        "rpi": {
+            "translation": "Castilleja ambigua subsp. ambigua"
+        }
+    },
+    "Downingia ornatissima var. mirabilis": {
+        "inat": {
+            "notintaxondata": true
+        }
+    },
+    "Erysimum capitatum var. angustatum": {
+        "calflora": {
+            "badjepsonid": true
+        },
+        "jepson": {
+            "allowsynonym": true
+        }
+    },
+    "Heterotheca oregona var. rudis": {
+        "inat": {
+            "notintaxondata": true
+        }
+    },
+    "Horkelia californica var. frondosa": {
+        "inat": {
+            "notintaxondata": true
+        }
+    },
+    "Lupinus littoralis var. variicolor": {
+        "inat": {
+            "notintaxondata": true
+        }
+    },
+    "Malacothamnus hallii": {
+        "comment": "in CNPS Rare Plant Inventory",
+        "calflora": {
+            "notintaxondata": true
+        },
+        "jepson": {
+            "allowsynonym": true
+        },
+        "rpi": {
+            "translation": "Malacothamnus arcuatus var. elmeri"
+        }
+    },
+    "Malacothamnus arcuatus var. elmeri": {
+        "comment": "in CNPS Rare Plant Inventory as Malacothamnus hallii",
+        "rpi": {
+            "translation-to-rpi": "Malacothamnus hallii"
+        }
+    },
+    "Myosurus minimus subsp. apus": {
+        "comment": "in CNPS Rare Plant Inventory",
+        "jepson": {
+            "notineflora": true
+        }
+    },
+    "Ravenella exigua": {
+        "comment": "in CNPS Rare Plant Inventory as Ravenella",
+        "rpi": {
+            "translation": "Campanula exigua"
+        }
+    },
+    "Ravenella sharsmithiae": {
+        "rpi": {
+            "translation": "Campanula sharsmithiae"
+        }
+    },
+    "Streptanthus albidus subsp. peramoenus": {
+        "calflora": {
+            "notintaxondata": true
+        },
+        "jepson": {
+            "allowsynonym": true
+        }
+    }
+}