chore: taxa updates (ca-plants#37)

data/exceptions.json

@@ -19,6 +19,8 @@
             "translation": "Castilleja ambigua subsp. ambigua"
         }
     },
+    "Chenopodium rubrum var. humile": { "calflora": { "native": true } },
+    "Chenopodium rubrum var. rubrum": { "calflora": { "native": false } },
     "Delphinium gypsophilum": {
         "calflora": { "notintaxondata": true }
     },
@@ -46,6 +48,22 @@
             "notintaxondata": true
         }
     },
+    "Juncus ambiguus": {
+        "comment": "Jepson: Presumed introduced. Taxonomy, relationship to Eurasian Juncus bufonius complex needs study.",
+        "calflora": { "native": false }
+    },
+    "Juncus elliottii": {
+        "calflora": { "native": false }
+    },
+    "Juncus gerardi subsp. gerardi": {
+        "comment": "Jepson: Possibly native, needs study",
+        "calflora": { "native": false }
+    },
+    "Lepidium strictum": {
+        "calflora": { "native": false },
+        "calscape": { "notnative": true }
+    },
+    "Limosella australis": { "jepson": { "native": true } },
     "Lupinus littoralis var. variicolor": {
         "inat": {
             "notintaxondata": true
@@ -75,10 +93,12 @@
     },
     "Myosurus minimus subsp. apus": {
         "comment": "in CNPS Rare Plant Inventory",
+        "cch": { "notincch": true },
         "jepson": {
             "notineflora": true
         }
     },
+    "Polypogon interruptus": { "calflora": { "native": true } },
     "Ranunculus sceleratus var. sceleratus": {
         "calflora": { "native": false }
     },
@@ -106,5 +126,6 @@
     },
     "Typha angustifolia": {
         "calscape": { "notnative": true }
-    }
+    },
+    "Veronica catenata": { "calflora": { "native": true } }
 }

data/synonyms.csv

@@ -1051,6 +1051,7 @@ Lessingia nemaclada var. albiflora,Lessingia nemaclada
 Lewisia alba,Lewisia rediviva var. rediviva
 Lewisia eastwoodiana,Lewisia leeana
 Leymus ×multiflorus,Elymus ×gouldii,INAT
+Leymus condensatus,Elymus condensatus,INAT
 Leymus mollis subsp. mollis,Elymus mollis subsp. mollis,INAT
 Leymus triticoides,Elymus triticoides,INAT
 Lilaea scilloides,Triglochin scilloides
@@ -1962,6 +1963,7 @@ Sorghum virgatum,Sorghum bicolor
 Sparganium erectum subsp. stoloniferum,Sparganium eurycarpum var. greenei
 Sparganium eurycarpum subsp. eurycarpum,Sparganium eurycarpum var. eurycarpum
 Sparganium greenei,Sparganium eurycarpum var. greenei
+Sparganium stoloniferum subsp. stoloniferum,Sparganium eurycarpum var. greenei,INAT
 Spergularia bocconei,Spergularia bocconi,INAT
 Spergularia marina var. tenuis,Spergularia marina
 Spergularia maritima,Spergularia media var. media

data/taxa.csv

@@ -390,7 +390,7 @@ Chenopodium macrospermum,coast goosefoot,X,19179,9069,76280,112467
 Chenopodium murale,sowbane,X,19182,1983,514012,112470
 Chenopodium pratericola,,N,19195,1986,76284,112486,Desert Goosefoot
 Chenopodium rubrum var. humile,,N,56454,10813,931680,129567
-Chenopodium rubrum var. rubrum,,N,71774,10531,931836,129568
+Chenopodium rubrum var. rubrum,,X,71774,10531,931836,129568
 Chenopodium rubrum,red goosefoot,N,19200,1988,931679,112490,Red Goosefoot
 Chenopodium vulvaria,stinking goosefoot,X,19212,1991,76288,112502
 Chlorogalum pomeridianum var. minus,dwarf soaproot,N,56470,2005,80562,202860,,,,,,1618,1B.2,,,S3,G5T3
@@ -438,13 +438,13 @@ Clarkia rhomboidea,,N,19595,2210,61870,13686,Diamond Clarkia,annual
 Clarkia rubicunda,farewell-to-spring,N,19597,2212,57148,13688,Ruby Chalice Clarkia,annual,pink,5,8
 Clarkia tembloriensis subsp. tembloriensis,temblor range clarkia,N,49915,2223,79746,42016,Temblor Range Clarkia,annual
 Clarkia unguiculata,elegant clarkia,N,19605,2224,51735,13696,Elegant Clarkia,annual,pink,4,9
-Claytonia exigua subsp. exigua,little spring beauty,N,76950,2232,57234,127854,Serpentine Springbeauty
-Claytonia exigua subsp. glauca,,N,76949,2233,57229,127855,Serpentine Springbeauty
-Claytonia gypsophiloides,candy stripers,N,19620,2234,55344,112597,Gypsum Springbeauty,,pink
-Claytonia parviflora subsp. parviflora,,N,74695,2242,58296,127861,Utah Miner's Lettuce
-Claytonia perfoliata subsp. mexicana,,N,76956,2245,53004,127866,Southern Miner's Lettuce
-Claytonia perfoliata subsp. perfoliata,Miner's lettuce,N,49921,2246,53002,127867,Miner's Lettuce,,white
-Claytonia rubra subsp. depressa,red stem spring beauty,N,76957,2248,79751,127869,Miner's Lettuce
+Claytonia exigua subsp. exigua,little spring beauty,N,76950,2232,57234,127854,Serpentine Springbeauty,annual,white,4,7
+Claytonia exigua subsp. glauca,,N,76949,2233,57229,127855,Serpentine Springbeauty,annual,white,4,7
+Claytonia gypsophiloides,candy stripers,N,19620,2234,55344,112597,Gypsum Springbeauty,annual,pink,3,5
+Claytonia parviflora subsp. parviflora,,N,74695,2242,58296,127861,Utah Miner's Lettuce,"annual,perennial",white,3,6
+Claytonia perfoliata subsp. mexicana,,N,76956,2245,53004,127866,Southern Miner's Lettuce,annual,white,2,4
+Claytonia perfoliata subsp. perfoliata,Miner's lettuce,N,49921,2246,53002,127867,Miner's Lettuce,annual,white,1,5
+Claytonia rubra subsp. depressa,red stem spring beauty,N,76957,2248,79751,127869,Miner's Lettuce,annual,white,2,4
 Clematis lasiantha,pipestems,N,19682,2254,49876,13749,Chaparral Clematis,,white,1,6
 Clematis ligusticifolia,virgin's bower,N,19683,2255,58996,13750,Virgin's Bower,,white,6,9
 Clinopodium douglasii,yerba buena,N,80483,11541,53203,65180,Yerba Buena
@@ -634,6 +634,7 @@ Elodea canadensis,common waterweed,N,24052,2926,76793,203519,Elodea
 Elodea nuttallii,,N,24057,2927,57623,206753,Nuttall's Waterweed
 Elymus ×gouldii,,N,93810,11632,170838,389951
 Elymus caput-medusae,medusa-head rye,X,24187,11634,169522,140047
+Elymus condensatus,giant wild-rye,N,24165,11636,164673,140055,Giant Wildrye
 Elymus elymoides var. elymoides,squirreltail,N,72180,11639,58377,211223,Squirreltail
 Elymus glaucus subsp. glaucus,blue wildrye,N,50264,2937,57171,167143,Western Rye Grass
 Elymus glaucus subsp. virescens,,N,50266,2939,61203,206754,Blue Wildrye
@@ -734,7 +735,7 @@ Eryngium jepsonii,,N,78144,11674,77062,264168,Jepson's Eryngo,,,,,3927,1B.2,,,S2
 Eryngium racemosum,Delta button-celery,N,25097,3467,77066,206800,Delta Button-celery,,,,,787,1B.1,CE,,S1,G1
 Eryngium spinosepalum,,N,25099,3468,57894,203769,Spiny-sepaled Button-celery,,,,,788,1B.2,,,S2,G2
 Eryngium vaseyi var. vallicola,,N,58851,11675,80888,211709
-Erysimum capitatum var. angustatum,Contra Costa wallflower,N,58866,9942,119564,,,,,,,790,1B.1,CE,FE,S1,G5T1
+Erysimum capitatum var. angustatum,Contra Costa wallflower,N,58866,9942,119564,47096,,,,,,790,1B.1,CE,FE,S1,G5T1
 Erysimum capitatum var. capitatum,western wallflower,N,58866,9943,50627,47096,Sanddune Wallflower,,"orange,yellow",3,9
 Erythranthe androsacea,,N,99088,13487,771845,203774
 Erythranthe arvensis,"villous-bracted monkeyflower,field monkeyflower",N,99091,13552,771848,206807,,,yellow,4,7
@@ -1027,11 +1028,11 @@ Lepidium didymum,wart cress,X,30511,10940,60987,24162
 Lepidium draba,hoary cress,X,30510,10943,63352,24164
 Lepidium latifolium,perennial pepperweed,X,30544,4691,60153,24179
 Lepidium latipes,dwarf peppergrass,N,30545,4692,60154,24180,San Diego Pepperweed
-Lepidium nitidum,shining peppergrass,N,30549,4699,47202,24187,Peppergrass
+Lepidium nitidum,shining peppergrass,N,30549,4699,47202,24187,Peppergrass,annual,white,2,3
 Lepidium oblongum,,N,30550,4703,77671,24188,Veiny Pepperweed
 Lepidium oxycarpum,,N,30553,4706,60155,24192,Forked Pepperweed
 Lepidium pinnatifidum,,X,30556,4708,77673,24196
-Lepidium strictum,,N,30566,4710,58865,24211,Upright Pepperweed
+Lepidium strictum,,X,30566,4710,58865,24211
 Lepidospartum squamatum,California broomsage,N,3776,4718,58010,204598,Scale Broom
 Leptochloa fusca subsp. fascicularis,bearded sprangletop,N,80525,11795,1377298,167408,Bearded Sprangletop
 Leptochloa fusca subsp. uninervia,Mexican sprangletop,N,80527,11796,1377299,167410,Mexican Sprangletop
@@ -1070,7 +1071,7 @@ Limonium californicum,sea-lavender,N,31014,4839,63364,115150,Western Marsh Rosem
 Limonium ramosissimum,Algerian sea-lavender,X,80703,9147,77757,115163
 Limosella acaulis,,N,31027,4843,61107,71439,Owyhee Mudwort
 Limosella aquatica,,N,31028,4844,59016,71440,Water Mudwort
-Limosella australis,delta mudwort,X,31029,10069,60248,71441,,,,,,1715,2B.1,,,S2,G5
+Limosella australis,delta mudwort,N,31029,10069,60248,71441,,,,,,1715,2B.1,,,S2,G5
 Linanthus dichotomus subsp. dichotomus,evening snow,N,51286,10624,80000,95800,Evening Snow
 Linanthus dichotomus subsp. meridianus,,N,51287,10625,80001,95801
 Linanthus pungens subsp. pulchriflorus,granite prickly phlox,N,98684,14586,861790,204699,,perennial,"white,pink",5,8
@@ -1145,7 +1146,7 @@ Maianthemum racemosum,false Solomon's seal,N,32495,10096,51062,204837,Large Fals
 Maianthemum stellatum,,N,32497,9629,53268,204838,False Solomon Seal
 Malacothamnus arcuatus var. elmeri,,N,108345,14681,1497404,412621,Eastern Bewildering Bushmallow,perennial,pink,4,5,1065,1B.2,,,S2,G2
 Malacothamnus fremontii var. fremontii,long-haired unfurled bushmallow,N,108341,14689,70398,400947,,perennial,pink,5,6
-Malacothamnus hallii,Hall's bushmallow,N,108345,14681,1497404,,,perennial,pink,4,5,1065,1B.2,,,S2,G2
+Malacothamnus hallii,Hall's bushmallow,N,108345,14681,1497404,412621,,perennial,pink,4,5,1065,1B.2,,,S2,G2
 Malacothrix californica,,N,4059,5325,58026,204841,California Desertdandelion
 Malacothrix clevelandii,Cleveland's malacothrix,N,4060,5326,58841,204842,Cleveland's Desertdandelion
 Malacothrix coulteri,snake's-head,N,4061,5327,58027,204843,Snake's Head
@@ -1411,7 +1412,7 @@ Plantago subnuda,naked plantain,N,38605,6626,60223,74567,Naked Plantain
 Platanthera dilatata var. leucostachys,white-flowered bog orchid,N,63974,9593,81271,205521,White Bog Orchid
 Platanus racemosa,western sycamore,N,38655,6633,58231,28255,Western Sycamore,perennial,red,2,4
 Platystemon californicus,cream cups,N,38664,6635,51288,28269,Creamcups
-Plectritis ciliosa,,N,38677,6639,57284,,Longspur Seablush,,pink,3,6
+Plectritis ciliosa,,N,38677,6639,57284,205525,Longspur Seablush,,pink,3,6
 Plectritis congesta subsp. brachystemon,,N,52336,11937,57787,205537,Small-flowered Plectritis
 Plectritis congesta subsp. congesta,,N,52337,11938,59253,205535,Sea Blush
 Plectritis macrocera,,N,38684,6643,57287,205540,Longhorn Seablush,,white,3,6
@@ -1440,7 +1441,7 @@ Polygonum ramosissimum subsp. ramosissimum,bushy knotweed,N,82468,11037,80161,12
 Polypodium calirhiza,polypody,N,39352,6776,52678,199631,Nested Polypody
 Polypodium scouleri,leather-leaf fern,N,39364,6779,64288,199683,Leathery Polypody
 Polypogon imberbis,beard grass,X,89096,8696,78695,147782
-Polypogon interruptus,ditch beard grass,X,39375,6782,59099,147785
+Polypogon interruptus,ditch beard grass,N,39375,6782,59099,147785
 Polypogon monspeliensis,rabbitfoot grass,X,39378,6784,57197,147792
 Polypogon viridis,water bentgrass,X,39379,11945,64144,147805
 Polystichum californicum,sword fern,N,39407,6785,63867,199711,California Sword Fern
@@ -1700,7 +1701,7 @@ Sonchus tenerrimus,,X,5119,7683,79157,206034
 Sorghum bicolor,sorghum,X,45003,7690,58389,148856
 Sorghum halepense,Johnson-grass,X,45017,7691,58387,148887
 Sparganium eurycarpum var. eurycarpum,bur-reed,N,73845,12031,63347,207940,Bur Reed
-Sparganium eurycarpum var. greenei,,N,66594,12032,63349,174978,Simplestem Bur Reed
+Sparganium eurycarpum var. greenei,,N,66594,12032,842663,174978,Simplestem Bur Reed
 Spartina alterniflora,saltwater cordgrass,X,45038,7699,772903,148951
 Spartina densiflora,dense-flowered cordgrass,X,45043,7700,772990,148961
 Spartina foliosa,California cordgrass,N,45044,7701,772992,148963,California Cord Grass
@@ -1738,7 +1739,7 @@ Stipa lemmonii var. lemmonii,Lemmon's needlegrass,N,73899,12053,1220756,173006
 Stipa lepida,foothill needlegrass,N,45641,12054,165656,149399,Foothill Needlegrass
 Stipa miliacea var. miliacea,smilo grass,X,91920,12058,524183,206097
 Stipa pulchra,purple needlegrass,N,45644,12067,165659,149498,Purple Needlegrass
-Streptanthus albidus subsp. peramoenus,most beautiful jewelflower,N,53142,7814,58783,,,,,,,1490,1B.2,,,S2,G2T2
+Streptanthus albidus subsp. peramoenus,most beautiful jewelflower,N,53142,7814,58783,43881,,,,,,1490,1B.2,,,S2,G2T2
 Streptanthus breweri,,N,45725,7822,79258,32606,Brewer's Jewelflower
 Streptanthus glandulosus subsp. glandulosus,jewelflower,N,53142,7837,58783,43881,Most Beautiful Jewel Flower
 Streptanthus hispidus,Mt. Diablo jewelflower,N,45741,7842,50620,32624,Mount Diablo Jewelflower,,,,,1502,1B.3,,,S2,G2
@@ -1837,7 +1838,7 @@ Tropaeolum majus,garden nasturtium,X,47408,8167,54329,34321
 Tropidocarpum capparideum,caper-fruited tropidocarpum,N,47411,8168,79456,34327,Caper-fruited Tropidocarpum,annual,yellow,3,4,1255,1B.1,,,S1,G1
 Tropidocarpum gracile,dobie pod,N,47412,8169,58091,34328,Dobie Pod,annual,yellow,3,5
 Turritis glabra,tower mustard,N,47457,12119,79460,34347,Tower Mustard
-Typha angustifolia,narrow-leaved cattail,X,47462,8176,60316,174863
+Typha angustifolia,narrow-leaved cattail,U,47462,8176,60316,174863
 Typha domingensis,southern cattail,N,47463,8177,58392,174864,Southern Cattail
 Typha latifolia,cattail,N,47466,8178,48685,174865,Broadleaf Cattail
 Ulmus minor,English elm,X,47478,8180,79461,34372
@@ -1859,7 +1860,7 @@ Verbesina encelioides subsp. exauriculata,golden crownbeard,X,6252,8241,79495,20
 Veronica americana,American brooklime,N,47941,8242,57277,78627,Brooklime
 Veronica anagallis-aquatica,water speedwell,X,47942,8243,57858,78628
 Veronica arvensis,,X,47950,8244,55748,78630
-Veronica catenata,chain speedwell,X,47944,8246,79496,78637
+Veronica catenata,chain speedwell,N,47944,8246,79496,78637
 Veronica peregrina subsp. xalapensis,purslane speedwell,N,53337,8252,491173,206335,Purslane Speedwell
 Veronica persica,Persian speedwell,X,47976,8253,55666,78667
 Viburnum ellipticum,western viburnum,N,48020,8259,79500,211467,Common Viburnum,,,,,2056,2B.3,,,S3,G4G5

lib/tools/cch2.js

@@ -14,37 +14,94 @@ export class CCH2 {
     /**
      * @param {string} toolsDataDir
      * @param {string} dataDir
+     * @param {import("../exceptions.js").Exceptions} exceptions
      * @param {import("../taxa.js").Taxa} taxa
      * @param {import("../errorlog.js").ErrorLog} errorLog
      * @param {boolean} update
      */
-    static async analyze(toolsDataDir, dataDir, taxa, errorLog, update) {
+    static async analyze(
+        toolsDataDir,
+        dataDir,
+        exceptions,
+        taxa,
+        errorLog,
+        update,
+    ) {
         const toolsDataPath = path.join(toolsDataDir, "cch2");
 
         const cchTaxa = await getCCHTaxa(toolsDataPath, taxa);
 
         const idsToUpdate = new Map();
         for (const taxon of taxa.getTaxonList()) {
-            const cchTaxon = cchTaxa.get(taxon.getName());
+            const name = taxon.getName();
+            const cchTaxon = cchTaxa.get(name);
             if (!cchTaxon) {
-                errorLog.log(taxon.getName(), "not found in CCH data");
+                if (!exceptions.hasException(name, "cch", "notincch")) {
+                    errorLog.log(name, "not found in CCH data");
+                }
                 continue;
             }
             if (cchTaxon.id !== taxon.getCCH2ID()) {
                 errorLog.log(
-                    taxon.getName(),
+                    name,
                     "id in CCH data does not match id in taxa.csv",
                     cchTaxon.id,
                     taxon.getCCH2ID(),
                 );
-                idsToUpdate.set(taxon.getName(), cchTaxon.id);
+                idsToUpdate.set(name, cchTaxon.id);
             }
         }
 
+        this.#checkExceptions(exceptions, taxa, errorLog, cchTaxa);
+
         if (update) {
             updateTaxaCSV(dataDir, idsToUpdate);
         }
     }
+
+    /**
+     * @param {import("../exceptions.js").Exceptions} exceptions
+     * @param {import("../taxa.js").Taxa} taxa
+     * @param {import("../errorlog.js").ErrorLog} errorLog
+     * @param {CCHTaxa} cchTaxa
+     */
+    static #checkExceptions(exceptions, taxa, errorLog, cchTaxa) {
+        // Check the CCH exceptions and make sure they still apply.
+        for (const [name, v] of exceptions.getExceptions()) {
+            const exceptions = v.cch;
+            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 CCH exceptions but is not in taxa.tsv");
+                continue;
+            }
+
+            for (const [k] of Object.entries(exceptions)) {
+                const jepsonData = cchTaxa.get(name);
+                switch (k) {
+                    case "notincch":
+                        // Make sure it is really not in CCH data.
+                        if (jepsonData) {
+                            errorLog.log(
+                                name,
+                                "has CCH notincch exception but is in CCH data",
+                            );
+                        }
+                        break;
+                    default:
+                        errorLog.log(name, "unrecognized CCH exception", k);
+                }
+            }
+        }
+    }
 }
 
 /**
@@ -61,13 +118,14 @@ async function getCCHTaxa(toolsDataPath, taxa) {
             // Ignore ranks above species.
             return;
         }
-        if (record.acceptance !== "1") {
-            return;
-        }
         if (!taxa.getTaxon(record.scientificName)) {
             // If we're not tracking the taxon, ignore it.
             return;
         }
+        if (record.acceptance !== "1" && data.has(record.scientificName)) {
+            // Only add the synonym if there is no main entry.
+            return;
+        }
         data.set(record.scientificName, { id: record.acceptedTaxonID });
     }
 

lib/tools/jepsoneflora.js

@@ -102,8 +102,25 @@ export class JepsonEFlora {
                 idsToUpdate.set(name, jepsInfo.id);
             }
 
-            const efStatus = this.#getStatusCode(jepsInfo);
+            let efStatus = this.#getStatusCode(jepsInfo);
             const taxonStatus = taxon.getStatus();
+            // Override if exception is specified.
+            const nativeException = exceptions.getValue(
+                name,
+                "jepson",
+                "native",
+            );
+            if (typeof nativeException === "boolean") {
+                const overrideStatus = nativeException ? "N" : "X";
+                if (overrideStatus === efStatus) {
+                    this.#errorLog.log(
+                        name,
+                        "has unnecessary Jepson native override",
+                    );
+                }
+                efStatus = overrideStatus;
+            }
+
             if (
                 efStatus !== taxonStatus &&
                 !(taxonStatus === "NC" && efStatus === "N")
@@ -154,6 +171,8 @@ export class JepsonEFlora {
             for (const [k] of Object.entries(exceptions)) {
                 const jepsonData = this.#nameInfo.get(name);
                 switch (k) {
+                    case "native":
+                        break;
                     case "notineflora":
                         // Make sure it is really not in eFlora.
                         if (jepsonData) {

lib/tools/rpi.js

@@ -80,8 +80,8 @@ class RPI {
             const rank = row["CRPR"];
             const rawCESA = row["CESA"];
             const rawFESA = row["FESA"];
-            const cesa = rawCESA === "None" ? undefined : rawCESA;
-            const fesa = rawFESA === "None" ? undefined : rawFESA;
+            const cesa = rawCESA === "None" ? "" : rawCESA;
+            const fesa = rawFESA === "None" ? "" : rawFESA;
             const cnddb = row["SRank"];
             const globalRank = row["GRank"];
             const taxon = taxa.getTaxon(name);