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migrate Calflora tools from ca-plant-tools (#15)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,220 @@ | ||
| import * as path from "path"; | ||
| import { CSV } from "../csv.js"; | ||
| import { Files } from "../files.js"; | ||
|
|
||
| const CALFLORA_URL_ALL = | ||
| "https://www.calflora.org/app/downtext?xun=117493&table=species&format=Tab&cols=0,1,4,5,8,38,41,43&psp=lifeform::grass,Tree,Herb,Fern,Shrub,Vine!!&par=f&active="; | ||
| const CALFLORA_URL_COUNTY = | ||
| "https://www.calflora.org/app/downtext?xun=117493&table=species&format=Tab&cols=0,1,4,5,8,38,41,43&psp=countylist::ALA,CCA!!&active=1"; | ||
|
|
||
| /** | ||
| * @typedef {{ | ||
| * "Native Status":string, | ||
| * TJMTID:string | ||
| * "Active in Calflora?":string | ||
| * Calrecnum:string | ||
| * }} CalfloraData | ||
| */ | ||
|
|
||
| class Calflora { | ||
| /** @type {Object<string,CalfloraData>} */ | ||
| static #taxa = {}; | ||
|
|
||
| /** | ||
| * | ||
| * @param {string} toolsDataDir | ||
| * @param {Taxa} taxa | ||
| * @param {import("../exceptions.js").Exceptions} exceptions | ||
| * @param {ErrorLog} errorLog | ||
| */ | ||
| static async analyze(toolsDataDir, taxa, exceptions, errorLog) { | ||
| /** | ||
| * @param {string} url | ||
| * @param {string} targetFile | ||
| */ | ||
| async function retrieveCalfloraFile(url, targetFile) { | ||
| // Retrieve file if it's not there. | ||
| targetFile = toolsDataPath + "/" + targetFile; | ||
| if (Files.exists(targetFile)) { | ||
| return; | ||
| } | ||
| console.log("retrieving " + targetFile); | ||
| await Files.fetch(url, targetFile); | ||
| } | ||
|
|
||
| const toolsDataPath = toolsDataDir + "/calflora"; | ||
| // Create data directory if it's not there. | ||
| Files.mkdir(toolsDataPath); | ||
|
|
||
| const calfloraDataFileNameActive = "calflora_taxa_active.tsv"; | ||
| const calfloraDataFileNameCounties = "calflora_taxa_counties.tsv"; | ||
|
|
||
| await retrieveCalfloraFile( | ||
| CALFLORA_URL_ALL + "1", | ||
| calfloraDataFileNameActive, | ||
| ); | ||
| // County list and "all" lists are both incomplete; load everything to get as much as possible. | ||
| await retrieveCalfloraFile( | ||
| CALFLORA_URL_COUNTY, | ||
| calfloraDataFileNameCounties, | ||
| ); | ||
|
|
||
| const csvActive = CSV.readFile( | ||
| path.join(toolsDataPath, calfloraDataFileNameActive), | ||
| ); | ||
| const csvCounties = CSV.readFile( | ||
| path.join(toolsDataPath, calfloraDataFileNameCounties), | ||
| ); | ||
|
|
||
| for (const row of csvActive) { | ||
| this.#taxa[row["Taxon"]] = row; | ||
| } | ||
| for (const row of csvCounties) { | ||
| this.#taxa[row["Taxon"]] = row; | ||
| } | ||
|
|
||
| for (const taxon of taxa.getTaxonList()) { | ||
| const name = taxon.getName(); | ||
| if (name.includes(" unknown")) { | ||
| continue; | ||
| } | ||
| const cfName = taxon.getCalfloraName(); | ||
| const cfData = Calflora.#taxa[cfName]; | ||
| if (!cfData) { | ||
| if ( | ||
| !exceptions.hasException(name, "calflora", "notintaxondata") | ||
| ) { | ||
| errorLog.log(name, "not found in Calflora files"); | ||
| } | ||
| continue; | ||
| } | ||
|
|
||
| // Check native status. | ||
| const cfNative = cfData["Native Status"]; | ||
| let cfIsNative = cfNative === "rare" || cfNative === "native"; | ||
| // Override if exception is specified. | ||
| const nativeException = exceptions.getValue( | ||
| name, | ||
| "calflora", | ||
| "native", | ||
| undefined, | ||
| ); | ||
| if (typeof nativeException === "boolean") { | ||
| if (nativeException === cfIsNative) { | ||
| errorLog.log( | ||
| name, | ||
| "has unnecessary Calflora native override", | ||
| ); | ||
| } | ||
| cfIsNative = nativeException; | ||
| } | ||
| if (cfIsNative !== taxon.isCANative()) { | ||
| errorLog.log( | ||
| name, | ||
| "has different nativity status in Calflora", | ||
| cfIsNative.toString(), | ||
| ); | ||
| } | ||
|
|
||
| // Check if it is active in Calflora. | ||
| const isActive = cfData["Active in Calflora?"]; | ||
| if (isActive !== "YES") { | ||
| errorLog.log(name, "is not active in Calflora", isActive); | ||
| } | ||
|
|
||
| // Check Jepson IDs. | ||
| const cfJepsonID = cfData.TJMTID; | ||
| if (cfJepsonID !== taxon.getJepsonID()) { | ||
| if ( | ||
| !exceptions.hasException(name, "calflora", "badjepsonid") && | ||
| !exceptions.hasException(name, "calflora", "notintaxondata") | ||
| ) { | ||
| errorLog.log( | ||
| name, | ||
| "Jepson ID in Calflora is different than taxa.csv", | ||
| cfJepsonID, | ||
| taxon.getJepsonID(), | ||
| ); | ||
| } | ||
| } | ||
|
|
||
| // Check Calflora ID. | ||
| const cfID = cfData["Calrecnum"]; | ||
| if (cfID !== taxon.getCalfloraID()) { | ||
| errorLog.log( | ||
| name, | ||
| "Calflora ID in Calflora is different than taxa.csv", | ||
| cfID, | ||
| taxon.getCalfloraID(), | ||
| ); | ||
| } | ||
| } | ||
|
|
||
| this.#checkExceptions(taxa, exceptions, errorLog); | ||
| } | ||
|
|
||
| /** | ||
| * @param {Taxa} taxa | ||
| * @param {import("../exceptions.js").Exceptions} exceptions | ||
| * @param {ErrorLog} errorLog | ||
| */ | ||
| static #checkExceptions(taxa, exceptions, errorLog) { | ||
| // Check the Calflora exceptions and make sure they still apply. | ||
| for (const [name, v] of exceptions.getExceptions()) { | ||
| const exceptions = v.calflora; | ||
| if (!exceptions) { | ||
| continue; | ||
| } | ||
|
|
||
| // Make sure the taxon is still in our list. | ||
| const taxon = taxa.getTaxon(name); | ||
| if (!taxon) { | ||
| // Don't process global exceptions if taxon is not in local list. | ||
| if (taxa.isSubset() && !v.local) { | ||
| continue; | ||
| } | ||
| errorLog.log( | ||
| name, | ||
| "has Calflora exceptions but not in Taxa collection", | ||
| ); | ||
| continue; | ||
| } | ||
|
|
||
| for (const [k] of Object.entries(exceptions)) { | ||
| const cfData = Calflora.#taxa[name]; | ||
| switch (k) { | ||
| case "badjepsonid": { | ||
| // Make sure Jepson ID is still wrong. | ||
| const cfID = cfData.TJMTID; | ||
| const jepsID = taxon.getJepsonID(); | ||
| if (cfID === jepsID) { | ||
| errorLog.log( | ||
| name, | ||
| "has Calflora badjepsonid exception but IDs are the same", | ||
| ); | ||
| } | ||
| break; | ||
| } | ||
| case "native": | ||
| break; | ||
| case "notintaxondata": | ||
| if (cfData) { | ||
| errorLog.log( | ||
| name, | ||
| "found in Calflora data but has notintaxondata exception", | ||
| ); | ||
| } | ||
| break; | ||
| default: | ||
| errorLog.log( | ||
| name, | ||
| "unrecognized Calflora exception", | ||
| k, | ||
| ); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| export { Calflora }; |
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