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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.iapt;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport;
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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
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import eu.etaxonomy.cdm.model.agent.Institution;
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import eu.etaxonomy.cdm.model.common.*;
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import eu.etaxonomy.cdm.model.name.*;
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import eu.etaxonomy.cdm.model.occurrence.*;
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import eu.etaxonomy.cdm.model.occurrence.Collection;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.*;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import org.apache.commons.lang.ArrayUtils;
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import org.apache.commons.lang.StringEscapeUtils;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Level;
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import org.apache.log4j.Logger;
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import org.joda.time.DateTimeFieldType;
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import org.joda.time.Partial;
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import org.joda.time.format.DateTimeFormat;
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import org.joda.time.format.DateTimeFormatter;
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import org.springframework.stereotype.Component;
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import java.util.*;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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/**
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* @author a.mueller
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* @created 05.01.2016
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*/
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@Component("iAPTExcelImport")
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public class IAPTExcelImport<CONFIG extends IAPTImportConfigurator> extends SimpleExcelTaxonImport<CONFIG> {
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private static final long serialVersionUID = -747486709409732371L;
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private static final Logger logger = Logger.getLogger(IAPTExcelImport.class);
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public static final String ANNOTATION_MARKER_STRING = "[*]";
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private static UUID ROOT_UUID = UUID.fromString("4137fd2a-20f6-4e70-80b9-f296daf51d82");
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private static NonViralNameParserImpl nameParser = NonViralNameParserImpl.NewInstance();
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private final static String REGISTRATIONNO_PK= "RegistrationNo_Pk";
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private final static String HIGHERTAXON= "HigherTaxon";
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private final static String FULLNAME= "FullName";
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private final static String AUTHORSSPELLING= "AuthorsSpelling";
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private final static String LITSTRING= "LitString";
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private final static String REGISTRATION= "Registration";
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private final static String TYPE= "Type";
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private final static String CAVEATS= "Caveats";
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private final static String FULLBASIONYM= "FullBasionym";
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private final static String FULLSYNSUBST= "FullSynSubst";
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private final static String NOTESTXT= "NotesTxt";
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private final static String REGDATE= "RegDate";
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private final static String NAMESTRING= "NameString";
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private final static String BASIONYMSTRING= "BasionymString";
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private final static String SYNSUBSTSTR= "SynSubstStr";
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private final static String AUTHORSTRING= "AuthorString";
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private static List<String> expectedKeys= Arrays.asList(new String[]{
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REGISTRATIONNO_PK, HIGHERTAXON, FULLNAME, AUTHORSSPELLING, LITSTRING, REGISTRATION, TYPE, CAVEATS, FULLBASIONYM, FULLSYNSUBST, NOTESTXT, REGDATE, NAMESTRING, BASIONYMSTRING, SYNSUBSTSTR, AUTHORSTRING});
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private static final Pattern nomRefTokenizeP = Pattern.compile("^(.*):\\s([^\\.:]+)\\.(.*?)\\.?$");
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private static final Pattern[] nomRefPubDatePs = new Pattern[]{
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// NOTE:
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// The order of the patterns is extremely important!!!
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//
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// all patterns cover the years 1700 - 1999
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Pattern.compile("^(?<year>1[7,8,9][0-9]{2})$"), // only year, like '1969'
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Pattern.compile("^(?<monthName>\\p{L}+\\.?)\\s(?<day>[0-9]{1,2})(?:st|rd|th)?\\.?,?\\s(?<year>(?:1[7,8,9])?[0-9]{2})$"), // full date like April 12, 1969 or april 12th 1999
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Pattern.compile("^(?<monthName>\\p{L}+\\.?),?\\s(?<year>(?:1[7,8,9])?[0-9]{2})$"), // April 99 or April, 1999 or Apr. 12
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Pattern.compile("^(?<day>[0-9]{1,2})([\\.\\-/])(?<month>[0-1]?[0-9])\\2(?<year>(?:1[7,8,9])?[0-9]{2})$"), // full date like 12.04.1969 or 12/04/1969 or 12-04-1969
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Pattern.compile("^(?<day>[0-9]{1,2})([\\.\\-/])(?<month>[IVX]{1,2})\\2(?<year>(?:1[7,8,9])?[0-9]{2})$"), // full date like 12-VI-1969
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Pattern.compile("^(?:(?<day>[0-9]{1,2})\\sde\\s)(?<monthName>\\p{L}+)\\sde\\s(?<year>(?:1[7,8,9])?[0-9]{2})$"), // full and partial date like 12 de Enero de 1999 or Enero de 1999
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Pattern.compile("^(?<month>[0-1]?[0-9])([\\.\\-/])(?<year>(?:1[7,8,9])?[0-9]{2})$"), // partial date like 04.1969 or 04/1969 or 04-1969
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Pattern.compile("^(?<year>(?:1[7,8,9])?[0-9]{2})([\\.\\-/])(?<month>[0-1]?[0-9])$"),// partial date like 1999-04
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Pattern.compile("^(?<day>[0-9]{1,2})(?:[\\./]|th|rd)?\\s(?<monthName>\\p{L}+\\.?),?\\s(?<year>(?:1[7,8,9])?[0-9]{2})$"), // full date like 12. April 1969 or april 1999 or 22 Dec.1999
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};
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private static final Pattern typeSplitPattern = Pattern.compile("^(?:\"*[Tt]ype: (?<type>.*?))(?:[Hh]olotype:(?<holotype>.*?)\\.?)?(?:[Ii]sotype[^:]*:(?<isotype>.*)\\.?)?\\.?$");
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// AccessionNumbers: , #.*, n°:?, 96/3293, No..*, -?\w{1,3}-[0-9\-/]*
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private static final Pattern accessionNumberOnlyPattern = Pattern.compile("^(?<accNumber>(?:n°\\:?\\s?|#|No\\.?\\s?)?[\\d\\w\\-/]*)$");
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private static final Pattern[] specimenTypePatterns = new Pattern[]{
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Pattern.compile("^(?<colCode>[A-Z]+|CPC Micropaleontology Lab\\.?)\\s+(?:\\((?<institute>.*[^\\)])\\))(?<accNumber>.*)?$"), // like: GAUF (Gansu Agricultural University) No. 1207-1222
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Pattern.compile("^(?<colCode>[A-Z]+|CPC Micropaleontology Lab\\.?)\\s+(?:Coll\\.\\s(?<subCollection>[^\\.,;]*)(.))(?<accNumber>.*)?$"), // like KASSEL Coll. Krasske, Praep. DII 78
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Pattern.compile("^(?:Coll\\.\\s(?<subCollection>[^\\.,;]*)(.))(?<institute>.*)\\2(?<accNumber>.*)?$"), // like Coll. Lange-Bertalot, Bot. Inst., Univ. Frankfurt/Main, Germany Praep. Neukaledonien OTL 62
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Pattern.compile("^(?<colCode>[A-Z]+)(?:\\s+(?<accNumber>.*))?$"), // identifies the Collection code and takes the rest as accessionNumber if any
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};
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private static Map<String, Integer> monthFromNameMap = new HashMap<>();
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static {
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String[] ck = new String[]{"leden", "únor", "březen", "duben", "květen", "červen", "červenec ", "srpen", "září", "říjen", "listopad", "prosinec"};
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String[] fr = new String[]{"janvier", "février", "mars", "avril", "mai", "juin", "juillet", "août", "septembre", "octobre", "novembre", "décembre"};
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String[] de = new String[]{"januar", "februar", "märz", "april", "mai", "juni", "juli", "august", "september", "oktober", "november", "dezember"};
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String[] en = new String[]{"january", "february", "march", "april", "may", "june", "july", "august", "september", "october", "november", "december"};
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String[] it = new String[]{"gennaio", "febbraio", "marzo", "aprile", "maggio", "giugno", "luglio", "agosto", "settembre", "ottobre", "novembre", "dicembre"};
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String[] sp = new String[]{"enero", "febrero", "marzo", "abril", "mayo", "junio", "julio", "agosto", "septiembre", "octubre", "noviembre", "diciembre"};
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String[] de_abbrev = new String[]{"jan.", "feb.", "märz", "apr.", "mai", "jun.", "jul.", "aug.", "sept.", "okt.", "nov.", "dez."};
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String[] en_abbrev = new String[]{"jan.", "feb.", "mar.", "apr.", "may", "jun.", "jul.", "aug.", "sep.", "oct.", "nov.", "dec."};
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String[] port = new String[]{"Janeiro", "Fevereiro", "Março", "Abril", "Maio", "Junho", "Julho", "Agosto", "Setembro", "Outubro", "Novembro", "Dezembro"};
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String[] rom_num = new String[]{"i", "ii", "iii", "iv", "v", "vi", "vii", "viii", "ix", "x", "xi", "xii"};
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String[][] perLang = new String[][]{ck, de, fr, en, it, sp, port, de_abbrev, en_abbrev, rom_num};
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for (String[] months: perLang) {
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for(int m = 1; m < 13; m++){
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monthFromNameMap.put(months[m - 1].toLowerCase(), m);
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}
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}
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// special cases
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monthFromNameMap.put("mar", 3);
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monthFromNameMap.put("dec", 12);
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monthFromNameMap.put("Februari", 2);
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}
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DateTimeFormatter formatterYear = DateTimeFormat.forPattern("yyyy");
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private Map<String, Collection> collectionMap = new HashMap<>();
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enum TypesName {
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type, holotype, isotype;
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public SpecimenTypeDesignationStatus status(){
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switch (this) {
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case holotype:
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return SpecimenTypeDesignationStatus.HOLOTYPE();
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case isotype:
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return SpecimenTypeDesignationStatus.ISOTYPE();
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default:
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return null;
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}
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}
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}
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private MarkerType markerTypeFossil = null;
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private Rank rankUnrankedSupraGeneric = null;
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private Rank familyIncertisSedis = null;
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private AnnotationType annotationTypeCaveats = null;
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private Taxon makeTaxon(HashMap<String, String> record, SimpleExcelTaxonImportState<CONFIG> state,
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TaxonNode higherTaxonNode, boolean isFossil) {
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String line = state.getCurrentLine() + ": ";
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String regNumber = getValue(record, REGISTRATIONNO_PK, false);
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String regStr = getValue(record, REGISTRATION, true);
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String titleCacheStr = getValue(record, FULLNAME, true);
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String nameStr = getValue(record, NAMESTRING, true);
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String authorStr = getValue(record, AUTHORSTRING, true);
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String nomRefStr = getValue(record, LITSTRING, true);
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String authorsSpelling = getValue(record, AUTHORSSPELLING, true);
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String notesTxt = getValue(record, NOTESTXT, true);
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String caveats = getValue(record, CAVEATS, true);
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String fullSynSubstStr = getValue(record, FULLSYNSUBST, true);
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String synSubstStr = getValue(record, SYNSUBSTSTR, true);
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String typeStr = getValue(record, TYPE, true);
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String nomRefTitle = null;
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String nomRefDetail;
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String nomRefPupDate = null;
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Partial pupDate = null;
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// preprocess nomRef: separate citation, reference detail, publishing date
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if(!StringUtils.isEmpty(nomRefStr)){
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nomRefStr = nomRefStr.trim();
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Matcher m = nomRefTokenizeP.matcher(nomRefStr);
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if(m.matches()){
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nomRefTitle = m.group(1);
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nomRefDetail = m.group(2);
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nomRefPupDate = m.group(3).trim();
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pupDate = parsePubDate(regNumber, nomRefStr, nomRefPupDate);
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if (pupDate != null) {
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nomRefTitle = nomRefTitle + ": " + nomRefDetail + ". " + pupDate.toString(formatterYear) + ".";
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}
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} else {
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nomRefTitle = nomRefStr;
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}
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}
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BotanicalName taxonName = makeBotanicalName(state, regNumber, titleCacheStr, nameStr, authorStr, nomRefTitle);
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// always add the original strings of parsed data as annotation
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taxonName.addAnnotation(Annotation.NewInstance("imported and parsed data strings:" +
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"\n - '" + LITSTRING + "': "+ nomRefStr +
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"\n - '" + TYPE + "': " + typeStr +
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"\n - '" + REGISTRATION + "': " + regStr
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, AnnotationType.TECHNICAL(), Language.DEFAULT()));
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if(pupDate != null) {
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taxonName.getNomenclaturalReference().setDatePublished(TimePeriod.NewInstance(pupDate));
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}
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if(!StringUtils.isEmpty(notesTxt)){
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notesTxt = notesTxt.replace("Notes: ", "").trim();
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taxonName.addAnnotation(Annotation.NewInstance(notesTxt, AnnotationType.EDITORIAL(), Language.DEFAULT()));
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}
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if(!StringUtils.isEmpty(caveats)){
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caveats = caveats.replace("Caveats: ", "").trim();
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taxonName.addAnnotation(Annotation.NewInstance(caveats, annotationTypeCaveats(), Language.DEFAULT()));
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}
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//
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// Namerelations
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if(!StringUtils.isEmpty(authorsSpelling)){
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authorsSpelling = authorsSpelling.replaceFirst("Author's spelling:", "").replaceAll("\"", "").trim();
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String[] authorSpellingTokens = StringUtils.split(authorsSpelling, " ");
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String[] nameStrTokens = StringUtils.split(nameStr, " ");
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ArrayUtils.reverse(authorSpellingTokens);
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ArrayUtils.reverse(nameStrTokens);
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for (int i = 0; i < nameStrTokens.length; i++){
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if(i < authorSpellingTokens.length){
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nameStrTokens[i] = authorSpellingTokens[i];
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}
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}
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ArrayUtils.reverse(nameStrTokens);
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String misspelledNameStr = StringUtils.join (nameStrTokens, ' ');
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// build the fullnameString of the misspelled name
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misspelledNameStr = taxonName.getTitleCache().replace(nameStr, misspelledNameStr);
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TaxonNameBase misspelledName = (BotanicalName) nameParser.parseReferencedName(misspelledNameStr, NomenclaturalCode.ICNAFP, null);
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misspelledName.addRelationshipToName(taxonName, NameRelationshipType.MISSPELLING(), null);
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getNameService().save(misspelledName);
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}
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// Replaced Synonyms
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if(!StringUtils.isEmpty(fullSynSubstStr)){
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fullSynSubstStr = fullSynSubstStr.replace("Syn. subst.: ", "");
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BotanicalName replacedSynonymName = makeBotanicalName(state, regNumber, fullSynSubstStr, synSubstStr, null, null);
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replacedSynonymName.addReplacedSynonym(taxonName, null, null, null);
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getNameService().save(replacedSynonymName);
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}
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Reference sec = state.getConfig().getSecReference();
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Taxon taxon = Taxon.NewInstance(taxonName, sec);
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// Markers
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if(isFossil){
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taxon.addMarker(Marker.NewInstance(markerTypeFossil(), true));
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}
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// Types
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if(!StringUtils.isEmpty(typeStr)){
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makeTypeData(typeStr, taxonName, regNumber);
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}
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getTaxonService().save(taxon);
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if(higherTaxonNode != null){
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higherTaxonNode.addChildTaxon(taxon, null, null);
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getTaxonNodeService().save(higherTaxonNode);
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}
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return taxon;
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}
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private void makeTypeData(String typeStr, BotanicalName taxonName, String regNumber) {
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Matcher m = typeSplitPattern.matcher(typeStr);
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if(m.matches()){
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String typeString = m.group(TypesName.type.name());
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boolean isFieldUnit = typeStr.matches(".*([°']|\\d+\\s?m\\s|\\d+\\s?km\\s).*"); // check for location or unit m, km
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if(isFieldUnit) {
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// type as fieldUnit
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FieldUnit fu = FieldUnit.NewInstance();
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fu.setTitleCache(typeString, true);
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getOccurrenceService().save(fu);
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// all others ..
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addSpecimenTypes(taxonName, fu, m.group(TypesName.holotype.name()), TypesName.holotype, false, regNumber);
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addSpecimenTypes(taxonName, fu, m.group(TypesName.isotype.name()), TypesName.isotype, true, regNumber);
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} else {
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TaxonNameBase typeName = nameParser.parseFullName(typeString);
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taxonName.addNameTypeDesignation(typeName, null, null, null, NameTypeDesignationStatus.AUTOMATIC(), true, true, true, true);
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}
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}
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getNameService().save(taxonName);
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}
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private Partial parsePubDate(String regNumber, String nomRefStr, String nomRefPupDate) {
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Partial pupDate = null;
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boolean parseError = false;
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String nomRefPupDay = null;
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String nomRefPupMonth = null;
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String nomRefPupMonthName = null;
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String nomRefPupYear = null;
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// nomRefDetail.replaceAll("[\\:\\.\\s]", ""); // TODO integrate into nomRefTokenizeP
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for(Pattern p : nomRefPubDatePs){
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Matcher m2 = p.matcher(nomRefPupDate);
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if(m2.matches()){
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try {
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nomRefPupYear = m2.group("year");
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} catch (IllegalArgumentException e){
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// named capture group not found
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}
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try {
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nomRefPupMonth = m2.group("month");
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} catch (IllegalArgumentException e){
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// named capture group not found
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}
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try {
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nomRefPupMonthName = m2.group("monthName");
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nomRefPupMonth = monthFromName(nomRefPupMonthName, regNumber);
|
331
|
if(nomRefPupMonth == null){
|
332
|
parseError = true;
|
333
|
}
|
334
|
} catch (IllegalArgumentException e){
|
335
|
// named capture group not found
|
336
|
}
|
337
|
try {
|
338
|
nomRefPupDay = m2.group("day");
|
339
|
} catch (IllegalArgumentException e){
|
340
|
// named capture group not found
|
341
|
}
|
342
|
|
343
|
if(nomRefPupYear == null){
|
344
|
logger.error("nomRefPupYear in " + nomRefStr + " is NULL" );
|
345
|
parseError = true;
|
346
|
}
|
347
|
if(nomRefPupYear.length() == 2 ){
|
348
|
// it is an abbreviated year from the 19** years
|
349
|
nomRefPupYear = "19" + nomRefPupYear;
|
350
|
}
|
351
|
|
352
|
break;
|
353
|
}
|
354
|
}
|
355
|
if(nomRefPupYear == null){
|
356
|
logger.warn(csvReportLine(regNumber, "Pub date", nomRefPupDate, "in", nomRefStr, "not parsable"));
|
357
|
parseError = true;
|
358
|
}
|
359
|
List<DateTimeFieldType> types = new ArrayList<>();
|
360
|
List<Integer> values = new ArrayList<>();
|
361
|
if(!parseError) {
|
362
|
types.add(DateTimeFieldType.year());
|
363
|
values.add(Integer.parseInt(nomRefPupYear));
|
364
|
if (nomRefPupMonth != null) {
|
365
|
types.add(DateTimeFieldType.monthOfYear());
|
366
|
values.add(Integer.parseInt(nomRefPupMonth));
|
367
|
}
|
368
|
if (nomRefPupDay != null) {
|
369
|
types.add(DateTimeFieldType.dayOfMonth());
|
370
|
values.add(Integer.parseInt(nomRefPupDay));
|
371
|
}
|
372
|
pupDate = new Partial(types.toArray(new DateTimeFieldType[types.size()]), ArrayUtils.toPrimitive(values.toArray(new Integer[values.size()])));
|
373
|
}
|
374
|
return pupDate;
|
375
|
}
|
376
|
|
377
|
private String monthFromName(String monthName, String regNumber) {
|
378
|
|
379
|
Integer month = monthFromNameMap.get(monthName.toLowerCase());
|
380
|
if(month == null){
|
381
|
logger.warn(csvReportLine(regNumber, "Unknown month name", monthName));
|
382
|
return null;
|
383
|
} else {
|
384
|
return month.toString();
|
385
|
}
|
386
|
}
|
387
|
|
388
|
|
389
|
private void addSpecimenTypes(BotanicalName taxonName, FieldUnit fieldUnit, String typeStr, TypesName typeName, boolean multiple, String regNumber){
|
390
|
|
391
|
if(StringUtils.isEmpty(typeStr)){
|
392
|
return;
|
393
|
}
|
394
|
typeStr = typeStr.trim().replaceAll("\\.$", "");
|
395
|
|
396
|
Collection collection = null;
|
397
|
DerivedUnit specimen = null;
|
398
|
|
399
|
List<DerivedUnit> specimens = new ArrayList<>();
|
400
|
if(multiple){
|
401
|
String[] tokens = typeStr.split("\\s?,\\s?");
|
402
|
for (String t : tokens) {
|
403
|
// command to list all complex parsabel types:
|
404
|
// csvcut -t -c RegistrationNo_Pk,Type iapt.csv | csvgrep -c Type -m "Holotype" | egrep -o 'Holotype:\s([A-Z]*\s)[^.]*?'
|
405
|
// csvcut -t -c RegistrationNo_Pk,Type iapt.csv | csvgrep -c Type -m "Holotype" | egrep -o 'Isotype[^:]*:\s([A-Z]*\s)[^.]*?'
|
406
|
|
407
|
if(!t.isEmpty()){
|
408
|
// trying to parse the string
|
409
|
specimen = parseSpecimenType(fieldUnit, typeName, collection, t, regNumber);
|
410
|
if(specimen != null){
|
411
|
specimens.add(specimen);
|
412
|
} else {
|
413
|
// parsing was not successful make simple specimen
|
414
|
specimens.add(makeSpecimenType(fieldUnit, t));
|
415
|
}
|
416
|
}
|
417
|
}
|
418
|
} else {
|
419
|
specimen = parseSpecimenType(fieldUnit, typeName, collection, typeStr, regNumber);
|
420
|
if(specimen != null) {
|
421
|
specimens.add(specimen);
|
422
|
// remember current collection
|
423
|
collection = specimen.getCollection();
|
424
|
} else {
|
425
|
// parsing was not successful make simple specimen
|
426
|
specimens.add(makeSpecimenType(fieldUnit, typeStr));
|
427
|
}
|
428
|
}
|
429
|
|
430
|
for(DerivedUnit s : specimens){
|
431
|
taxonName.addSpecimenTypeDesignation(s, typeName.status(), null, null, null, false, true);
|
432
|
}
|
433
|
}
|
434
|
|
435
|
private DerivedUnit makeSpecimenType(FieldUnit fieldUnit, String titleCache) {
|
436
|
DerivedUnit specimen;DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen, fieldUnit);
|
437
|
facade.setTitleCache(titleCache.trim(), true);
|
438
|
specimen = facade.innerDerivedUnit();
|
439
|
return specimen;
|
440
|
}
|
441
|
|
442
|
/**
|
443
|
*
|
444
|
* @param fieldUnit
|
445
|
* @param typeName
|
446
|
* @param collection
|
447
|
* @param text
|
448
|
* @param regNumber
|
449
|
* @return
|
450
|
*/
|
451
|
private DerivedUnit parseSpecimenType(FieldUnit fieldUnit, TypesName typeName, Collection collection, String text, String regNumber) {
|
452
|
|
453
|
DerivedUnit specimen = null;
|
454
|
|
455
|
String collectionCode = null;
|
456
|
String subCollectionStr = null;
|
457
|
String instituteStr = null;
|
458
|
String accessionNumber = null;
|
459
|
|
460
|
boolean unusualAccessionNumber = false;
|
461
|
|
462
|
text = text.trim();
|
463
|
|
464
|
// 1. For Isotypes often the accession number is noted alone if the
|
465
|
// preceeding entry has a collection code.
|
466
|
if(typeName .equals(TypesName.isotype) && collection != null){
|
467
|
Matcher m = accessionNumberOnlyPattern.matcher(text);
|
468
|
if(m.matches()){
|
469
|
try {
|
470
|
accessionNumber = m.group("accNumber");
|
471
|
specimen = makeSpecimenType(fieldUnit, collection, accessionNumber);
|
472
|
} catch (IllegalArgumentException e){
|
473
|
// match group acc_number not found
|
474
|
}
|
475
|
}
|
476
|
}
|
477
|
|
478
|
//2. try it the 'normal' way
|
479
|
if(specimen == null) {
|
480
|
for (Pattern p : specimenTypePatterns) {
|
481
|
Matcher m = p.matcher(text);
|
482
|
if (m.matches()) {
|
483
|
// collection code is mandatory
|
484
|
try {
|
485
|
collectionCode = m.group("colCode");
|
486
|
} catch (IllegalArgumentException e){
|
487
|
logger.warn(csvReportLine(regNumber, "match group colCode not found"));
|
488
|
continue;
|
489
|
}
|
490
|
try {
|
491
|
subCollectionStr = m.group("subCollection");
|
492
|
} catch (IllegalArgumentException e){
|
493
|
// match group subCollection not found
|
494
|
}
|
495
|
try {
|
496
|
instituteStr = m.group("institute");
|
497
|
} catch (IllegalArgumentException e){
|
498
|
// match group col_name not found
|
499
|
}
|
500
|
try {
|
501
|
accessionNumber = m.group("accNumber");
|
502
|
|
503
|
// try to improve the accessionNumber
|
504
|
if(accessionNumber!= null) {
|
505
|
accessionNumber = accessionNumber.trim();
|
506
|
Matcher m2 = accessionNumberOnlyPattern.matcher(accessionNumber);
|
507
|
String betterAccessionNumber = null;
|
508
|
if (m2.matches()) {
|
509
|
try {
|
510
|
betterAccessionNumber = m.group("accNumber");
|
511
|
} catch (IllegalArgumentException e) {
|
512
|
// match group acc_number not found
|
513
|
}
|
514
|
}
|
515
|
if (betterAccessionNumber != null) {
|
516
|
accessionNumber = betterAccessionNumber;
|
517
|
} else {
|
518
|
unusualAccessionNumber = true;
|
519
|
}
|
520
|
}
|
521
|
|
522
|
} catch (IllegalArgumentException e){
|
523
|
// match group acc_number not found
|
524
|
}
|
525
|
|
526
|
collection = getCollection(collectionCode, instituteStr, subCollectionStr);
|
527
|
specimen = makeSpecimenType(fieldUnit, collection, accessionNumber);
|
528
|
break;
|
529
|
}
|
530
|
}
|
531
|
}
|
532
|
if(specimen == null) {
|
533
|
logger.warn(csvReportLine(regNumber, "Could not parse specimen type", typeName.name().toString(), text));
|
534
|
}
|
535
|
if(unusualAccessionNumber){
|
536
|
logger.warn(csvReportLine(regNumber, "Unusual accession number", typeName.name().toString(), text, accessionNumber));
|
537
|
}
|
538
|
return specimen;
|
539
|
}
|
540
|
|
541
|
private DerivedUnit makeSpecimenType(FieldUnit fieldUnit, Collection collection, String accessionNumber) {
|
542
|
|
543
|
DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen, fieldUnit);
|
544
|
facade.setCollection(collection);
|
545
|
facade.setAccessionNumber(accessionNumber);
|
546
|
return facade.innerDerivedUnit();
|
547
|
}
|
548
|
|
549
|
private BotanicalName makeBotanicalName(SimpleExcelTaxonImportState<CONFIG> state, String regNumber, String titleCacheStr, String nameStr,
|
550
|
String authorStr, String nomRefTitle) {
|
551
|
|
552
|
BotanicalName taxonName;// cache field for the taxonName.titleCache
|
553
|
String taxonNameTitleCache = null;
|
554
|
Map<String, AnnotationType> nameAnnotations = new HashMap<>();
|
555
|
|
556
|
// TitleCache preprocessing
|
557
|
if(titleCacheStr.endsWith(ANNOTATION_MARKER_STRING) || (authorStr != null && authorStr.endsWith(ANNOTATION_MARKER_STRING))){
|
558
|
nameAnnotations.put("Author abbreviation not checked.", AnnotationType.EDITORIAL());
|
559
|
titleCacheStr = titleCacheStr.replace(ANNOTATION_MARKER_STRING, "").trim();
|
560
|
authorStr = authorStr.replace(ANNOTATION_MARKER_STRING, "").trim();
|
561
|
}
|
562
|
|
563
|
// parse the full taxon name
|
564
|
if(!StringUtils.isEmpty(nomRefTitle)){
|
565
|
String referenceSeparator = nomRefTitle.startsWith("in ") ? " " : ", ";
|
566
|
String taxonFullNameStr = titleCacheStr + referenceSeparator + nomRefTitle;
|
567
|
logger.debug(":::::" + taxonFullNameStr);
|
568
|
taxonName = (BotanicalName) nameParser.parseReferencedName(taxonFullNameStr, NomenclaturalCode.ICNAFP, null);
|
569
|
} else {
|
570
|
taxonName = (BotanicalName) nameParser.parseFullName(titleCacheStr, NomenclaturalCode.ICNAFP, null);
|
571
|
}
|
572
|
|
573
|
taxonNameTitleCache = taxonName.getTitleCache().trim();
|
574
|
if (taxonName.isProtectedTitleCache()) {
|
575
|
logger.warn(csvReportLine(regNumber, "Name could not be parsed", titleCacheStr));
|
576
|
} else {
|
577
|
|
578
|
boolean doRestoreTitleCacheStr = false;
|
579
|
|
580
|
// Check if titleCache and nameCache are plausible
|
581
|
String titleCacheCompareStr = titleCacheStr;
|
582
|
String nameCache = taxonName.getNameCache();
|
583
|
String nameCompareStr = nameStr;
|
584
|
if(taxonName.isBinomHybrid()){
|
585
|
titleCacheCompareStr = titleCacheCompareStr.replace(" x ", " ×");
|
586
|
nameCompareStr = nameCompareStr.replace(" x ", " ×");
|
587
|
}
|
588
|
if(taxonName.isMonomHybrid()){
|
589
|
titleCacheCompareStr = titleCacheCompareStr.replaceAll("^X ", "× ");
|
590
|
nameCompareStr = nameCompareStr.replace("^X ", "× ");
|
591
|
}
|
592
|
if(authorStr != null && authorStr.contains(" et ")){
|
593
|
titleCacheCompareStr = titleCacheCompareStr.replaceAll(" et ", " & ");
|
594
|
}
|
595
|
if (!taxonNameTitleCache.equals(titleCacheCompareStr)) {
|
596
|
logger.warn(csvReportLine(regNumber, "The generated titleCache differs from the imported string", taxonNameTitleCache, " != ", titleCacheStr, " ==> original titleCacheStr has been restored"));
|
597
|
doRestoreTitleCacheStr = true;
|
598
|
}
|
599
|
if (!nameCache.trim().equals(nameCompareStr)) {
|
600
|
logger.warn(csvReportLine(regNumber, "The parsed nameCache differs from field '" + NAMESTRING + "'", nameCache, " != ", nameCompareStr));
|
601
|
}
|
602
|
|
603
|
// Author
|
604
|
//nameParser.handleAuthors(taxonName, titleCacheStr, authorStr);
|
605
|
//if (!titleCacheStr.equals(taxonName.getTitleCache())) {
|
606
|
// logger.warn(regNumber + ": titleCache has changed after setting authors, will restore original titleCacheStr");
|
607
|
// doRestoreTitleCacheStr = true;
|
608
|
//}
|
609
|
|
610
|
if(doRestoreTitleCacheStr){
|
611
|
taxonName.setTitleCache(titleCacheStr, true);
|
612
|
}
|
613
|
|
614
|
// deduplicate
|
615
|
replaceAuthorNamesAndNomRef(state, taxonName);
|
616
|
}
|
617
|
|
618
|
// Annotations
|
619
|
if(!nameAnnotations.isEmpty()){
|
620
|
for(String text : nameAnnotations.keySet()){
|
621
|
taxonName.addAnnotation(Annotation.NewInstance(text, nameAnnotations.get(text), Language.DEFAULT()));
|
622
|
}
|
623
|
getNameService().save(taxonName);
|
624
|
}
|
625
|
return taxonName;
|
626
|
}
|
627
|
|
628
|
/**
|
629
|
* @param state
|
630
|
* @return
|
631
|
*/
|
632
|
private TaxonNode getClassificationRootNode(IAPTImportState state) {
|
633
|
|
634
|
// Classification classification = state.getClassification();
|
635
|
// if (classification == null){
|
636
|
// IAPTImportConfigurator config = state.getConfig();
|
637
|
// classification = Classification.NewInstance(state.getConfig().getClassificationName());
|
638
|
// classification.setUuid(config.getClassificationUuid());
|
639
|
// classification.setReference(config.getSecReference());
|
640
|
// classification = getClassificationService().find(state.getConfig().getClassificationUuid());
|
641
|
// }
|
642
|
TaxonNode rootNode = state.getRootNode();
|
643
|
if (rootNode == null){
|
644
|
rootNode = getTaxonNodeService().find(ROOT_UUID);
|
645
|
}
|
646
|
if (rootNode == null){
|
647
|
Classification classification = state.getClassification();
|
648
|
if (classification == null){
|
649
|
Reference sec = state.getSecReference();
|
650
|
String classificationName = state.getConfig().getClassificationName();
|
651
|
Language language = Language.DEFAULT();
|
652
|
classification = Classification.NewInstance(classificationName, sec, language);
|
653
|
state.setClassification(classification);
|
654
|
classification.setUuid(state.getConfig().getClassificationUuid());
|
655
|
classification.getRootNode().setUuid(ROOT_UUID);
|
656
|
getClassificationService().save(classification);
|
657
|
}
|
658
|
rootNode = classification.getRootNode();
|
659
|
state.setRootNode(rootNode);
|
660
|
}
|
661
|
return rootNode;
|
662
|
}
|
663
|
|
664
|
private Collection getCollection(String collectionCode, String instituteStr, String subCollectionStr){
|
665
|
|
666
|
Collection superCollection = null;
|
667
|
if(subCollectionStr != null){
|
668
|
superCollection = getCollection(collectionCode, instituteStr, null);
|
669
|
collectionCode = subCollectionStr;
|
670
|
instituteStr = null;
|
671
|
}
|
672
|
|
673
|
final String key = collectionCode + "-#i:" + StringUtils.defaultString(instituteStr);
|
674
|
|
675
|
Collection collection = collectionMap.get(key);
|
676
|
|
677
|
if(collection == null) {
|
678
|
collection = Collection.NewInstance();
|
679
|
collection.setCode(collectionCode);
|
680
|
if(instituteStr != null){
|
681
|
collection.setInstitute(Institution.NewNamedInstance(instituteStr));
|
682
|
}
|
683
|
if(superCollection != null){
|
684
|
collection.setSuperCollection(superCollection);
|
685
|
}
|
686
|
collectionMap.put(key, collection);
|
687
|
getCollectionService().save(collection);
|
688
|
}
|
689
|
|
690
|
return collection;
|
691
|
}
|
692
|
|
693
|
|
694
|
/**
|
695
|
* @param record
|
696
|
* @param originalKey
|
697
|
* @param doUnescapeHtmlEntities
|
698
|
* @return
|
699
|
*/
|
700
|
private String getValue(HashMap<String, String> record, String originalKey, boolean doUnescapeHtmlEntities) {
|
701
|
String value = record.get(originalKey);
|
702
|
|
703
|
value = fixCharacters(value);
|
704
|
|
705
|
if (! StringUtils.isBlank(value)) {
|
706
|
if (logger.isDebugEnabled()) {
|
707
|
logger.debug(originalKey + ": " + value);
|
708
|
}
|
709
|
value = CdmUtils.removeDuplicateWhitespace(value.trim()).toString();
|
710
|
if(doUnescapeHtmlEntities){
|
711
|
value = StringEscapeUtils.unescapeHtml(value);
|
712
|
}
|
713
|
return value.trim();
|
714
|
}else{
|
715
|
return null;
|
716
|
}
|
717
|
}
|
718
|
|
719
|
/**
|
720
|
* Fixes broken characters.
|
721
|
* For details see
|
722
|
* http://dev.e-taxonomy.eu/redmine/issues/6035
|
723
|
*
|
724
|
* @param value
|
725
|
* @return
|
726
|
*/
|
727
|
private String fixCharacters(String value) {
|
728
|
|
729
|
value = StringUtils.replace(value, "s$K", "š");
|
730
|
value = StringUtils.replace(value, "n$K", "ň");
|
731
|
value = StringUtils.replace(value, "e$K", "ě");
|
732
|
value = StringUtils.replace(value, "r$K", "ř");
|
733
|
value = StringUtils.replace(value, "c$K", "č");
|
734
|
value = StringUtils.replace(value, "z$K", "ž");
|
735
|
value = StringUtils.replace(value, "S>U$K", "Š");
|
736
|
value = StringUtils.replace(value, "C>U$K", "Č");
|
737
|
value = StringUtils.replace(value, "R>U$K", "Ř");
|
738
|
value = StringUtils.replace(value, "Z>U$K", "Ž");
|
739
|
value = StringUtils.replace(value, "g$K", "ǧ");
|
740
|
value = StringUtils.replace(value, "s$A", "ś");
|
741
|
value = StringUtils.replace(value, "n$A", "ń");
|
742
|
value = StringUtils.replace(value, "c$A", "ć");
|
743
|
value = StringUtils.replace(value, "e$E", "ę");
|
744
|
value = StringUtils.replace(value, "o$H", "õ");
|
745
|
value = StringUtils.replace(value, "s$C", "ş");
|
746
|
value = StringUtils.replace(value, "t$C", "ț");
|
747
|
value = StringUtils.replace(value, "S>U$C", "Ş");
|
748
|
value = StringUtils.replace(value, "a$O", "å");
|
749
|
value = StringUtils.replace(value, "A>U$O", "Å");
|
750
|
value = StringUtils.replace(value, "u$O", "ů");
|
751
|
value = StringUtils.replace(value, "g$B", "ğ");
|
752
|
value = StringUtils.replace(value, "g$B", "ĕ");
|
753
|
value = StringUtils.replace(value, "a$B", "ă");
|
754
|
value = StringUtils.replace(value, "l$/", "ł");
|
755
|
value = StringUtils.replace(value, ">i", "ı");
|
756
|
value = StringUtils.replace(value, "i$U", "ï");
|
757
|
// Special-cases
|
758
|
value = StringUtils.replace(value, "ý", "ý");
|
759
|
value = StringUtils.replace(value, ">L", "Ł"); // corrected rule
|
760
|
value = StringUtils.replace(value, "E>U$D", "З");
|
761
|
value = StringUtils.replace(value, "S>U$E", "Ş");
|
762
|
value = StringUtils.replace(value, "s$E", "ş");
|
763
|
|
764
|
value = StringUtils.replace(value, "c$k", "č");
|
765
|
value = StringUtils.replace(value, " U$K", " Š");
|
766
|
|
767
|
return value;
|
768
|
}
|
769
|
|
770
|
|
771
|
/**
|
772
|
* Stores taxa records in DB
|
773
|
*/
|
774
|
@Override
|
775
|
protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {
|
776
|
|
777
|
String lineNumber = "L#" + state.getCurrentLine() + ": ";
|
778
|
logger.setLevel(Level.DEBUG);
|
779
|
HashMap<String, String> record = state.getOriginalRecord();
|
780
|
logger.debug(lineNumber + record.toString());
|
781
|
|
782
|
Set<String> keys = record.keySet();
|
783
|
for (String key: keys) {
|
784
|
if (! expectedKeys.contains(key)){
|
785
|
logger.warn(lineNumber + "Unexpected Key: " + key);
|
786
|
}
|
787
|
}
|
788
|
|
789
|
String reg_id = record.get(REGISTRATIONNO_PK);
|
790
|
|
791
|
//higherTaxon
|
792
|
String higherTaxaString = record.get(HIGHERTAXON);
|
793
|
boolean isFossil = false;
|
794
|
if(higherTaxaString.startsWith("FOSSIL ")){
|
795
|
higherTaxaString = higherTaxaString.replace("FOSSIL ", "");
|
796
|
isFossil = true;
|
797
|
}
|
798
|
TaxonNode higherTaxon = getHigherTaxon(higherTaxaString, (IAPTImportState)state);
|
799
|
|
800
|
//Taxon
|
801
|
Taxon taxon = makeTaxon(record, state, higherTaxon, isFossil);
|
802
|
if (taxon == null){
|
803
|
logger.warn(lineNumber + "taxon could not be created and is null");
|
804
|
return;
|
805
|
}
|
806
|
((IAPTImportState)state).setCurrentTaxon(taxon);
|
807
|
|
808
|
|
809
|
return;
|
810
|
}
|
811
|
|
812
|
private TaxonNode getHigherTaxon(String higherTaxaString, IAPTImportState state) {
|
813
|
String[] higherTaxaNames = higherTaxaString.toLowerCase().replaceAll("[\\[\\]]", "").split(":");
|
814
|
TaxonNode higherTaxonNode = null;
|
815
|
|
816
|
ITaxonTreeNode rootNode = getClassificationRootNode(state);
|
817
|
for (String htn : higherTaxaNames) {
|
818
|
htn = StringUtils.capitalize(htn.trim());
|
819
|
Taxon higherTaxon = state.getHigherTaxon(htn);
|
820
|
if (higherTaxon != null){
|
821
|
higherTaxonNode = higherTaxon.getTaxonNodes().iterator().next();
|
822
|
}else{
|
823
|
BotanicalName name = makeHigherTaxonName(state, htn);
|
824
|
Reference sec = state.getSecReference();
|
825
|
higherTaxon = Taxon.NewInstance(name, sec);
|
826
|
getTaxonService().save(higherTaxon);
|
827
|
higherTaxonNode = rootNode.addChildTaxon(higherTaxon, sec, null);
|
828
|
state.putHigherTaxon(htn, higherTaxon);
|
829
|
getClassificationService().saveTreeNode(higherTaxonNode);
|
830
|
}
|
831
|
rootNode = higherTaxonNode;
|
832
|
}
|
833
|
return higherTaxonNode;
|
834
|
}
|
835
|
|
836
|
private BotanicalName makeHigherTaxonName(IAPTImportState state, String name) {
|
837
|
|
838
|
Rank rank = guessRank(name);
|
839
|
|
840
|
BotanicalName taxonName = BotanicalName.NewInstance(rank);
|
841
|
taxonName.addSource(makeOriginalSource(state));
|
842
|
taxonName.setGenusOrUninomial(StringUtils.capitalize(name));
|
843
|
return taxonName;
|
844
|
}
|
845
|
|
846
|
private Rank guessRank(String name) {
|
847
|
|
848
|
// normalize
|
849
|
name = name.replaceAll("\\(.*\\)", "").trim();
|
850
|
|
851
|
if(name.matches("^Plantae$|^Fungi$")){
|
852
|
return Rank.KINGDOM();
|
853
|
} else if(name.matches("^Incertae sedis$|^No group assigned$")){
|
854
|
return rankFamilyIncertisSedis();
|
855
|
} else if(name.matches(".*phyta$|.*mycota$")){
|
856
|
return Rank.SECTION_BOTANY();
|
857
|
} else if(name.matches(".*phytina$|.*mycotina$")){
|
858
|
return Rank.SUBSECTION_BOTANY();
|
859
|
} else if(name.matches("Gymnospermae$|.*ones$")){ // Monocotyledones, Dicotyledones
|
860
|
return rankUnrankedSupraGeneric();
|
861
|
} else if(name.matches(".*opsida$|.*phyceae$|.*mycetes$|.*ones$|^Musci$|^Hepaticae$")){
|
862
|
return Rank.CLASS();
|
863
|
} else if(name.matches(".*idae$|.*phycidae$|.*mycetidae$")){
|
864
|
return Rank.SUBCLASS();
|
865
|
} else if(name.matches(".*ales$")){
|
866
|
return Rank.ORDER();
|
867
|
} else if(name.matches(".*ineae$")){
|
868
|
return Rank.SUBORDER();
|
869
|
} else if(name.matches(".*aceae$")){
|
870
|
return Rank.FAMILY();
|
871
|
} else if(name.matches(".*oideae$")){
|
872
|
return Rank.SUBFAMILY();
|
873
|
} else
|
874
|
// if(name.matches(".*eae$")){
|
875
|
// return Rank.TRIBE();
|
876
|
// } else
|
877
|
if(name.matches(".*inae$")){
|
878
|
return Rank.SUBTRIBE();
|
879
|
} else if(name.matches(".*ae$")){
|
880
|
return Rank.FAMILY();
|
881
|
}
|
882
|
return Rank.UNKNOWN_RANK();
|
883
|
}
|
884
|
|
885
|
private Rank rankUnrankedSupraGeneric() {
|
886
|
|
887
|
if(rankUnrankedSupraGeneric == null){
|
888
|
rankUnrankedSupraGeneric = Rank.NewInstance(RankClass.Suprageneric, "Unranked supra generic", " ", " ");
|
889
|
getTermService().save(rankUnrankedSupraGeneric);
|
890
|
}
|
891
|
return rankUnrankedSupraGeneric;
|
892
|
}
|
893
|
|
894
|
private Rank rankFamilyIncertisSedis() {
|
895
|
|
896
|
if(familyIncertisSedis == null){
|
897
|
familyIncertisSedis = Rank.NewInstance(RankClass.Suprageneric, "Family incertis sedis", " ", " ");
|
898
|
getTermService().save(familyIncertisSedis);
|
899
|
}
|
900
|
return familyIncertisSedis;
|
901
|
}
|
902
|
|
903
|
private AnnotationType annotationTypeCaveats(){
|
904
|
if(annotationTypeCaveats == null){
|
905
|
annotationTypeCaveats = AnnotationType.NewInstance("Caveats", "Caveats", "");
|
906
|
getTermService().save(annotationTypeCaveats);
|
907
|
}
|
908
|
return annotationTypeCaveats;
|
909
|
}
|
910
|
|
911
|
|
912
|
/**
|
913
|
* @param state
|
914
|
* @return
|
915
|
*/
|
916
|
private IdentifiableSource makeOriginalSource(IAPTImportState state) {
|
917
|
return IdentifiableSource.NewDataImportInstance("line: " + state.getCurrentLine(), null, state.getConfig().getSourceReference());
|
918
|
}
|
919
|
|
920
|
|
921
|
private Reference makeReference(IAPTImportState state, UUID uuidRef) {
|
922
|
Reference ref = state.getReference(uuidRef);
|
923
|
if (ref == null){
|
924
|
ref = getReferenceService().find(uuidRef);
|
925
|
state.putReference(uuidRef, ref);
|
926
|
}
|
927
|
return ref;
|
928
|
}
|
929
|
|
930
|
private MarkerType markerTypeFossil(){
|
931
|
if(this.markerTypeFossil == null){
|
932
|
markerTypeFossil = MarkerType.NewInstance("isFossilTaxon", "isFossil", null);
|
933
|
getTermService().save(this.markerTypeFossil);
|
934
|
}
|
935
|
return markerTypeFossil;
|
936
|
}
|
937
|
|
938
|
private String csvReportLine(String regId, String message, String ... fields){
|
939
|
StringBuilder out = new StringBuilder("regID#");
|
940
|
out.append(regId).append(",\"").append(message).append('"');
|
941
|
|
942
|
for(String f : fields){
|
943
|
out.append(",\"").append(f).append('"');
|
944
|
}
|
945
|
return out.toString();
|
946
|
}
|
947
|
|
948
|
|
949
|
}
|