<commit_before>/*
 * Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
 * Copyright [2016-2018] EMBL-European Bioinformatics Institute
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *      http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.ensembl.healthcheck;

import java.util.EnumMap;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.logging.Logger;
import org.ensembl.healthcheck.DatabaseType;

public enum Species {
	// defined new Species and properties: taxonomy_id, assemblyprefix, stableIDprefix, alias
	
	ASTATOTILAPIA_CALLIPTERA(8154, "fAstCal", "ENSACL", ""),
	SCOPHTHALMUS_MAXIMUS(52904, "ASM318616", "ENSSMA", ""),
	AMPHILOPHUS_CITRINELLUS(61819, "Midas", "ENSACI", ""),
	AMPHIPRION_PERCULA(161767, "Nemo", "ENSAPE", ""),
	ANABAS_TESTUDINEUS(64144, "fAnaTes", "ENSATE", ""),
	ASTYANAX_MEXICANUS(7994, "Astyanax_mexicanus", "ENSAMX", ""),
	GAMBUSIA_AFFINIS(33528, "ASM309773", "ENSGAF", ""),
	KRYPTOLEBIAS_MARMORATUS(37003, "ASM164957", "ENSKMA", ""),
	MASTACEMBELUS_ARMATUS(205130, "fMasArm", "ENSMAM", ""),
	MAYLANDIA_ZEBRA(106582, "M_zebra_UMD", "ENSMZE", ""),
	MOLA_MOLA(94237, "ASM169857", "ENSMMO", ""),
	NEOLAMPROLOGUS_BRICHARDI(32507, "NeoBri", "ENSNBR", ""),
	PERIOPHTHALMUS_MAGNUSPINNATUS(409849, "PM", "ENSPMG", ""),
	PUNDAMILIA_NYEREREI(303518, "PunNye", "ENSPNY", ""),
	XIPHOPHORUS_COUCHIANUS(32473, "Xiphophorus_couchianus", "ENSXCO", ""),
	XIPHOPHORUS_MACULATUS(8083, "X_maculatus", "ENSXMA", ""),
	TAKIFUGU_RUBRIPES(31033, "FUGU", "ENSTRU", ""),
	ORYZIAS_LATIPES(8090,"ASM223467","ENSORL",""),
	ORYZIAS_LATIPES_HNI(8090, "ASM223471", "ENSORL", ""),
	ORYZIAS_LATIPES_HSOK(8090, "ASM223469", "ENSORL", ""),
	POECILIA_LATIPINNA(48699, "P_latipinna", "ENSPLA", ""),
	POECILIA_MEXICANA(48701, "P_mexicana", "ENSPME", ""),
	HAPLOCHROMIS_BURTONI(8153, "AstBur", "ENSHBU", ""),
	CYPRINODON_VARIEGATUS(28743, "C_variegatus", "ENSCVA", ""),
	ESOX_LUCIUS(8010, "Eluc", "ENSELU", ""),
	FUNDULUS_HETEROCLITUS(8078, "Fundulus_heteroclitus", "ENSFHE", ""),
	ACANTHOCHROMIS_POLYACANTHUS(80966, "ASM210954", "ENSAPO", ""),
	AMPHIPRION_OCELLARIS(80972, "AmpOce", "ENSAOC", ""),
	ORYZIAS_MELASTIGMA(30732, "Om", "ENSOME", ""),
	SIMOCHROMIS_DIAGRAMMA(43689, "fSimDia", "ENSSDI", ""), 
	LABRUS_BERGYLTA(56723, "BallGen", "ENSLBE", ""), 
	PYGOCENTRUS_NATTERERI(42514, "Pygocentrus_nattereri", "ENSPNA", ""), 
	TRACHINOTUS_OVATUS(173339, "golden_pompano", "ENSTOV", ""), 
	SCLEROPAGES_FORMOSUS(113540, "ASM162426", "ENSSFO", ""), 
	STEGASTES_PARTITUS(144197, "Stegastes_partitus", "ENSSPA", ""), 
	SERIOLA_DUMERILI(41447, "Sdu", "ENSSDU", ""), 
	SERIOLA_QUINQUERADIATA(8161, "Squ", "ENSSQU", ""), 
	SERIOLA_RIVOLIANA(173321, "ASM299450", "ENSSRI", ""), 
	CYNOGLOSSUS_SEMILAEVIS(244447, "Cse", "ENSCSE", ""), 
	DICENTRARCHUS_LABRAX(13489, "seabass", "ENSDLA", ""), 
	ICTALURUS_PUNCTATUS(7998, "IpCoco", "ENSIPU", ""), 
	MIICHTHYS_MIIUY(240162, "ASM159371", "ENSMMI", ""), 
	MORONE_SAXATILIS(34816, "SB", "ENSMSA", ""), 
	NOTOTHENIA_CORIICEPS(8208, "NC", "ENSNCO", ""), 
	PERIOPHTHALMODON_SCHLOSSERI(1365757, "PS", "ENSPSC", ""), 
	POECILIA_RETICULATA(8081, "Guppy_female", "ENSPRE", ""), 
	MACCULLOCHELLA_PEELII(135761, "mcod", "ENSMPE", ""), 
	MONOPTERUS_ALBUS(43700, "M_albus", "ENSMAL", ""), 
	PARAMORMYROPS_KINGSLEYAE(1676925, "PKINGS", "ENSPKI", ""), 
	
	
	OCTODON_DEGUS(10160, "OctDeg", "ENSODE", "degu,brush_tailed_rat,10160"),
	CHINCHILLA_LANIGERA(34839, "ChiLan", "ENSCLA", "long_tailed_chinchilla,Chinchilla_lanigera,chinchilla,chinchilla_lanigera"),
	CAVIA_APEREA(37548, "CavAp", "ENSCAP",""),
	FUKOMYS_DAMARENSIS(885580,"DMR_v","ENSFDA",""), 
	JACULUS_JACULUS(51337,"JacJac","ENSJJA",""),
	MESOCRICETUS_AURATUS(10036,"MesAur","ENSMAU",""),
	MUS_CAROLI(10089,"CAROLI_EIJ","MGP_CAROLIEiJ_",""),
	MUS_PAHARI(10093,"PAHARI_EIJ","MGP_PahariEiJ_",""),
	NANNOSPALAX_GALILI(1026970,"S.galili","ENSNGA",""),
	PEROMYSCUS_MANICULATUS_BAIRDII(230844,"Pman","ENSPEM",""),
	MICROTUS_OCHROGASTER(79684,"MicOch","ENSMOC",""), 
	HETEROCEPHALUS_GLABER_FEMALE(10181,"HetGla_female","ENSHGL",""),<commit_msg>Update species.java<commit_after>/*
 * Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
 * Copyright [2016-2018] EMBL-European Bioinformatics Institute
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *      http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.ensembl.healthcheck;

import java.util.EnumMap;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.logging.Logger;
import org.ensembl.healthcheck.DatabaseType;

public enum Species {
	// defined new Species and properties: taxonomy_id, assemblyprefix, stableIDprefix, alias
	
	ASTATOTILAPIA_CALLIPTERA(8154, "fAstCal", "ENSACL", ""),
	SCOPHTHALMUS_MAXIMUS(52904, "ASM318616", "ENSSMA", ""),
	AMPHILOPHUS_CITRINELLUS(61819, "Midas", "ENSACI", ""),
	AMPHIPRION_PERCULA(161767, "Nemo", "ENSAPE", ""),
	ANABAS_TESTUDINEUS(64144, "fAnaTes", "ENSATE", ""),
	ASTYANAX_MEXICANUS(7994, "Astyanax_mexicanus", "ENSAMX", ""),
	GAMBUSIA_AFFINIS(33528, "ASM309773", "ENSGAF", ""),
	KRYPTOLEBIAS_MARMORATUS(37003, "ASM164957", "ENSKMA", ""),
	MASTACEMBELUS_ARMATUS(205130, "fMasArm", "ENSMAM", ""),
	MAYLANDIA_ZEBRA(106582, "M_zebra_UMD", "ENSMZE", ""),
	MOLA_MOLA(94237, "ASM169857", "ENSMMO", ""),
	NEOLAMPROLOGUS_BRICHARDI(32507, "NeoBri", "ENSNBR", ""),
	PERIOPHTHALMUS_MAGNUSPINNATUS(409849, "PM", "ENSPMG", ""),
	PUNDAMILIA_NYEREREI(303518, "PunNye", "ENSPNY", ""),
	XIPHOPHORUS_COUCHIANUS(32473, "Xiphophorus_couchianus", "ENSXCO", ""),
	XIPHOPHORUS_MACULATUS(8083, "X_maculatus", "ENSXMA", ""),
	TAKIFUGU_RUBRIPES(31033, "FUGU", "ENSTRU", ""),
	ORYZIAS_LATIPES(8090,"ASM223467","ENSORL",""),
	ORYZIAS_LATIPES_HNI(8090, "ASM223471", "ENSORL", ""),
	ORYZIAS_LATIPES_HSOK(8090, "ASM223469", "ENSORL", ""),
	POECILIA_LATIPINNA(48699, "P_latipinna", "ENSPLA", ""),
	POECILIA_MEXICANA(48701, "P_mexicana", "ENSPME", ""),
	HAPLOCHROMIS_BURTONI(8153, "AstBur", "ENSHBU", ""),
	CYPRINODON_VARIEGATUS(28743, "C_variegatus", "ENSCVA", ""),
	ESOX_LUCIUS(8010, "Eluc", "ENSELU", ""),
	FUNDULUS_HETEROCLITUS(8078, "Fundulus_heteroclitus", "ENSFHE", ""),
	ACANTHOCHROMIS_POLYACANTHUS(80966, "ASM210954", "ENSAPO", ""),
	AMPHIPRION_OCELLARIS(80972, "AmpOce", "ENSAOC", ""),
	ORYZIAS_MELASTIGMA(30732, "Om", "ENSOME", ""),
	SIMOCHROMIS_DIAGRAMMA(43689, "fSimDia", "ENSSDI", ""), 
	LABRUS_BERGYLTA(56723, "BallGen", "ENSLBE", ""), 
	PYGOCENTRUS_NATTERERI(42514, "Pygocentrus_nattereri", "ENSPNA", ""), 
	TRACHINOTUS_OVATUS(173339, "golden_pompano", "ENSTOV", ""), 
	SCLEROPAGES_FORMOSUS(113540, "ASM162426", "ENSSFO", ""), 
	STEGASTES_PARTITUS(144197, "Stegastes_partitus", "ENSSPA", ""), 
	SERIOLA_DUMERILI(41447, "Sdu", "ENSSDU", ""), 
	SERIOLA_QUINQUERADIATA(8161, "Squ", "ENSSQU", ""), 
	SERIOLA_RIVOLIANA(173321, "ASM299450", "ENSSRI", ""), 
	CYNOGLOSSUS_SEMILAEVIS(244447, "Cse", "ENSCSE", ""), 
	DICENTRARCHUS_LABRAX(13489, "seabass", "ENSDLA", ""), 
	ICTALURUS_PUNCTATUS(7998, "IpCoco", "ENSIPU", ""), 
	MIICHTHYS_MIIUY(240162, "ASM159371", "ENSMMI", ""), 
	MORONE_SAXATILIS(34816, "SB", "ENSMSA", ""), 
	NOTOTHENIA_CORIICEPS(8208, "NC", "ENSNCO", ""), 
	PERIOPHTHALMODON_SCHLOSSERI(1365757, "PS", "ENSPSC", ""), 
	POECILIA_RETICULATA(8081, "Guppy_female", "ENSPRE", ""), 
	MACCULLOCHELLA_PEELII(135761, "mcod", "ENSMPE", ""), 
	MONOPTERUS_ALBUS(43700, "M_albus", "ENSMAL", ""), 
	PARAMORMYROPS_KINGSLEYAE(1676925, "PKINGS", "ENSPKI", ""), 
	SERIOLA_LALANDI_DORSALIS(1841481, "Sedor1", "ENSSLD", ""),
	
	
	OCTODON_DEGUS(10160, "OctDeg", "ENSODE", "degu,brush_tailed_rat,10160"),
	CHINCHILLA_LANIGERA(34839, "ChiLan", "ENSCLA", "long_tailed_chinchilla,Chinchilla_lanigera,chinchilla,chinchilla_lanigera"),
	CAVIA_APEREA(37548, "CavAp", "ENSCAP",""),
	FUKOMYS_DAMARENSIS(885580,"DMR_v","ENSFDA",""), 
	JACULUS_JACULUS(51337,"JacJac","ENSJJA",""),
	MESOCRICETUS_AURATUS(10036,"MesAur","ENSMAU",""),
	MUS_CAROLI(10089,"CAROLI_EIJ","MGP_CAROLIEiJ_",""),
	MUS_PAHARI(10093,"PAHARI_EIJ","MGP_PahariEiJ_",""),
	NANNOSPALAX_GALILI(1026970,"S.galili","ENSNGA",""),
	PEROMYSCUS_MANICULATUS_BAIRDII(230844,"Pman","ENSPEM",""),
	MICROTUS_OCHROGASTER(79684,"MicOch","ENSMOC",""), 
	HETEROCEPHALUS_GLABER_FEMALE(10181,"HetGla_female","ENSHGL",""),
{'fraction_non_alphanumeric': 0.17948995029176573, 'fraction_numerical': 0.08796196239464016, 'mean_word_length': 8.055772994129159, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3857018', 'n_tokens_mistral': 4910, 'n_tokens_neox': 4196, 'n_words': 579}