Revision 4fe9a46d
Added by Patrick Plitzner about 8 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportAuthor.java | ||
|---|---|---|
| 63 | 63 |
|
| 64 | 64 |
@Override |
| 65 | 65 |
protected void doInvoke(RedListGefaesspflanzenImportState state) {
|
| 66 |
makeAuthors(state, "AUTOR_KOMB");
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|
| 67 |
makeAuthors(state, "AUTOR_BASI");
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|
| 66 |
makeAuthors(state, RedListUtil.AUTOR_KOMB);
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|
| 67 |
makeAuthors(state, RedListUtil.AUTOR_BASI);
|
|
| 68 | 68 |
} |
| 69 | 69 |
|
| 70 | 70 |
|
| ... | ... | |
| 100 | 100 |
} |
| 101 | 101 |
TeamOrPersonBase teamOrPerson; |
| 102 | 102 |
//check if there are ex authors |
| 103 |
if(authorName.contains(" ex ")){
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|
| 104 |
String[] split = authorName.split(" ex ");
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|
| 103 |
if(authorName.contains(RedListUtil.EX)){
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|
| 104 |
String[] split = authorName.split(RedListUtil.EX);
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|
| 105 | 105 |
for (int i = 0; i < split.length; i++) {
|
| 106 | 106 |
makePerson(state, split[i].trim()); |
| 107 | 107 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportClassification.java | ||
|---|---|---|
| 93 | 93 |
|
| 94 | 94 |
private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs, Classification classification) |
| 95 | 95 |
throws SQLException {
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| 96 |
String id = String.valueOf(rs.getLong("NAMNR"));
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|
| 97 |
String parentId = String.valueOf(rs.getLong("LOWER"));
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|
| 98 |
String gueltString = rs.getString("GUELT");
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|
| 96 |
String id = String.valueOf(rs.getLong(RedListUtil.NAMNR));
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|
| 97 |
String parentId = String.valueOf(rs.getLong(RedListUtil.LOWER));
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|
| 98 |
String gueltString = rs.getString(RedListUtil.GUELT);
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|
| 99 | 99 |
|
| 100 | 100 |
TaxonBase taxonBase = state.getRelatedObject(RedListUtil.TAXON_NAMESPACE, id, TaxonBase.class); |
| 101 | 101 |
Taxon parent = (Taxon) state.getRelatedObject(RedListUtil.TAXON_NAMESPACE, parentId, TaxonBase.class); |
| ... | ... | |
| 113 | 113 |
} |
| 114 | 114 |
else if(taxonBase.isInstanceOf(Synonym.class)){
|
| 115 | 115 |
//basionym |
| 116 |
if(gueltString.equals("b")){
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|
| 116 |
if(gueltString.equals(RedListUtil.GUELT_BASIONYM)){
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|
| 117 | 117 |
parent.addHomotypicSynonym((Synonym) taxonBase, null, null); |
| 118 | 118 |
parent.getName().addBasionym(taxonBase.getName()); |
| 119 | 119 |
} |
| ... | ... | |
| 134 | 134 |
Set<String> idSet = new HashSet<String>(); |
| 135 | 135 |
try {
|
| 136 | 136 |
while (rs.next()){
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idSet.add(String.valueOf(rs.getLong("NAMNR")));
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| 138 |
idSet.add(String.valueOf(rs.getLong("LOWER")));
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| 137 |
idSet.add(String.valueOf(rs.getLong(RedListUtil.NAMNR)));
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| 138 |
idSet.add(String.valueOf(rs.getLong(RedListUtil.LOWER)));
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|
| 139 | 139 |
} |
| 140 | 140 |
} catch (SQLException e) {
|
| 141 | 141 |
e.printStackTrace(); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java | ||
|---|---|---|
| 46 | 46 |
@SuppressWarnings("serial")
|
| 47 | 47 |
public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
|
| 48 | 48 |
|
| 49 |
private static final String EX = " ex "; |
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| 50 |
|
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| 51 | 49 |
private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportNames.class); |
| 52 | 50 |
|
| 53 | 51 |
private static final String tableName = "Rote Liste Gefäßpflanzen"; |
| ... | ... | |
| 101 | 99 |
|
| 102 | 100 |
private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave, Set<TaxonBase> taxaToSave) |
| 103 | 101 |
throws SQLException {
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long id = rs.getLong("NAMNR");
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| 105 |
String taxNameString = rs.getString("TAXNAME");
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| 106 |
String gueltString = rs.getString("GUELT");
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| 107 |
String rangString = rs.getString("RANG");
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| 108 |
String ep1String = rs.getString("EPI1");
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| 109 |
String ep2String = rs.getString("EPI2");
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| 110 |
String ep3String = rs.getString("EPI3");
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| 111 |
String nomZusatzString = rs.getString("NOM_ZUSATZ");
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| 112 |
String zusatzString = rs.getString("ZUSATZ");
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| 113 |
String authorKombString = rs.getString("AUTOR_KOMB");
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| 114 |
String authorBasiString = rs.getString("AUTOR_BASI");
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| 102 |
long id = rs.getLong(RedListUtil.NAMNR);
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| 103 |
String taxNameString = rs.getString(RedListUtil.TAXNAME);
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| 104 |
String gueltString = rs.getString(RedListUtil.GUELT);
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String rangString = rs.getString(RedListUtil.RANG);
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| 106 |
String ep1String = rs.getString(RedListUtil.EPI1);
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| 107 |
String ep2String = rs.getString(RedListUtil.EPI2);
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| 108 |
String ep3String = rs.getString(RedListUtil.EPI3);
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String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);
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| 110 |
String zusatzString = rs.getString(RedListUtil.ZUSATZ);
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| 111 |
String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
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| 112 |
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
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| 115 | 113 |
|
| 116 | 114 |
if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
|
| 117 | 115 |
RedListUtil.logMessage(id, "No name found!", logger); |
| ... | ... | |
| 125 | 123 |
|
| 126 | 124 |
//ep1 should always be present |
| 127 | 125 |
if(CdmUtils.isBlank(ep1String)){
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| 128 |
RedListUtil.logMessage(id, "EPI1 is empty!", logger);
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| 126 |
RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);
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|
| 129 | 127 |
} |
| 130 | 128 |
name.setGenusOrUninomial(ep1String); |
| 131 | 129 |
if(!CdmUtils.isBlank(ep2String)){
|
| ... | ... | |
| 140 | 138 |
|
| 141 | 139 |
//--- AUTHORS --- |
| 142 | 140 |
//combination author |
| 143 |
if(authorKombString.contains(EX)){
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|
| 141 |
if(authorKombString.contains(RedListUtil.EX)){
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|
| 144 | 142 |
//TODO: what happens with multiple ex authors?? |
| 145 |
String[] kombSplit = authorKombString.split(EX); |
|
| 143 |
String[] kombSplit = authorKombString.split(RedListUtil.EX);
|
|
| 146 | 144 |
if(kombSplit.length!=2){
|
| 147 | 145 |
RedListUtil.logMessage(id, "Multiple ex combination authors found", logger); |
| 148 | 146 |
} |
| ... | ... | |
| 159 | 157 |
} |
| 160 | 158 |
} |
| 161 | 159 |
else if(authorKombString.trim().equals(RedListUtil.AUCT)){
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| 162 |
RedListUtil.logMessage(id, "AUCT information in AUTOR_KOMB column", logger);
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|
| 160 |
RedListUtil.logMessage(id, "AUCT information in "+RedListUtil.AUTOR_KOMB+" column", logger);
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|
| 163 | 161 |
} |
| 164 | 162 |
else if(!CdmUtils.isBlank(authorKombString)){
|
| 165 | 163 |
TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorKombString); |
| 166 | 164 |
name.setCombinationAuthorship(authorKomb); |
| 167 | 165 |
} |
| 168 | 166 |
//basionym author |
| 169 |
if(authorBasiString.contains(EX)){
|
|
| 170 |
String[] basiSplit = authorBasiString.split(EX); |
|
| 167 |
if(authorBasiString.contains(RedListUtil.EX)){
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|
| 168 |
String[] basiSplit = authorBasiString.split(RedListUtil.EX);
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|
| 171 | 169 |
for (int i = 0; i < basiSplit.length; i++) {
|
| 172 | 170 |
if(basiSplit.length!=2){
|
| 173 | 171 |
RedListUtil.logMessage(id, "Multiple ex basionymn authors found", logger); |
| ... | ... | |
| 207 | 205 |
} |
| 208 | 206 |
|
| 209 | 207 |
//check authorship consistency |
| 210 |
String authorString = rs.getString("AUTOR");
|
|
| 208 |
String authorString = rs.getString(RedListUtil.AUTOR);
|
|
| 211 | 209 |
String authorshipCache = name.getAuthorshipCache(); |
| 212 | 210 |
|
| 213 | 211 |
if(!CdmUtils.isBlank(zusatzString)){
|
| ... | ... | |
| 220 | 218 |
authorString = ""; |
| 221 | 219 |
} |
| 222 | 220 |
if(!authorString.equals(authorshipCache)){
|
| 223 |
RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column AUTOR: "+authorshipCache+" <-> "+authorString, logger);
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|
| 221 |
RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
|
|
| 224 | 222 |
} |
| 225 | 223 |
|
| 226 | 224 |
//id |
| ... | ... | |
| 231 | 229 |
|
| 232 | 230 |
//---TAXON--- |
| 233 | 231 |
TaxonBase taxonBase = null; |
| 234 |
if(gueltString.equals("1") || (name.getAppendedPhrase()!=null && name.getAppendedPhrase().equals(RedListUtil.AUCT))){
|
|
| 232 |
if(gueltString.equals(RedListUtil.GUELT_ACCEPTED_TAXON) || (name.getAppendedPhrase()!=null && name.getAppendedPhrase().equals(RedListUtil.AUCT))){
|
|
| 235 | 233 |
taxonBase = Taxon.NewInstance(name, null); |
| 236 | 234 |
} |
| 237 |
else if(gueltString.equals("x") || gueltString.equals("b")){
|
|
| 235 |
else if(gueltString.equals(RedListUtil.GUELT_SYNONYM) || gueltString.equals(RedListUtil.GUELT_BASIONYM)){
|
|
| 238 | 236 |
taxonBase = Synonym.NewInstance(name, null); |
| 239 | 237 |
} |
| 240 | 238 |
if(taxonBase==null){
|
| ... | ... | |
| 272 | 270 |
|
| 273 | 271 |
try {
|
| 274 | 272 |
while (rs.next()){
|
| 275 |
String authorKombString = rs.getString("AUTOR_KOMB");
|
|
| 273 |
String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
|
|
| 276 | 274 |
|
| 277 |
if(authorKombString.contains(EX)){
|
|
| 278 |
String[] kombSplit = authorKombString.split(EX); |
|
| 275 |
if(authorKombString.contains(RedListUtil.EX)){
|
|
| 276 |
String[] kombSplit = authorKombString.split(RedListUtil.EX);
|
|
| 279 | 277 |
for (int i = 0; i < kombSplit.length; i++) {
|
| 280 | 278 |
if(!authorMap.containsKey(kombSplit[i])){
|
| 281 | 279 |
authorMap.put(kombSplit[i], getAgentService().load(state.getAuthorMap().get(kombSplit[i]))); |
| ... | ... | |
| 286 | 284 |
authorMap.put(authorKombString, getAgentService().load(state.getAuthorMap().get(authorKombString))); |
| 287 | 285 |
} |
| 288 | 286 |
|
| 289 |
String authorBasiString = rs.getString("AUTOR_BASI");
|
|
| 287 |
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
|
|
| 290 | 288 |
//basionym author |
| 291 |
if(authorBasiString.contains(EX)){
|
|
| 292 |
String[] basiSplit = authorBasiString.split(EX); |
|
| 289 |
if(authorBasiString.contains(RedListUtil.EX)){
|
|
| 290 |
String[] basiSplit = authorBasiString.split(RedListUtil.EX);
|
|
| 293 | 291 |
for (int i = 0; i < basiSplit.length; i++) {
|
| 294 | 292 |
if(!authorMap.containsKey(basiSplit[i])){
|
| 295 | 293 |
authorMap.put(basiSplit[i], getAgentService().load(state.getAuthorMap().get(basiSplit[i]))); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListUtil.java | ||
|---|---|---|
| 21 | 21 |
public static final String NAME_NAMESPACE = "name"; |
| 22 | 22 |
public static final String TAXON_NAMESPACE = "taxon"; |
| 23 | 23 |
public static final String AUTHOR_NAMESPACE = "author"; |
| 24 |
|
|
| 24 | 25 |
public static final String AUCT = "auct."; |
| 26 |
public static final String EX = " ex "; |
|
| 27 |
public static final String GUELT_BASIONYM = "b"; |
|
| 28 |
public static final String GUELT_SYNONYM = "x"; |
|
| 29 |
public static final String GUELT_ACCEPTED_TAXON = "1"; |
|
| 30 |
|
|
| 31 |
|
|
| 32 |
public static final String GUELT = "GUELT"; |
|
| 33 |
public static final String LOWER = "LOWER"; |
|
| 34 |
public static final String NAMNR = "NAMNR"; |
|
| 35 |
public static final String AUTOR_BASI = "AUTOR_BASI"; |
|
| 36 |
public static final String AUTOR_KOMB = "AUTOR_KOMB"; |
|
| 37 |
public static final String ZUSATZ = "ZUSATZ"; |
|
| 38 |
public static final String NOM_ZUSATZ = "NOM_ZUSATZ"; |
|
| 39 |
public static final String EPI3 = "EPI3"; |
|
| 40 |
public static final String EPI2 = "EPI2"; |
|
| 41 |
public static final String EPI1 = "EPI1"; |
|
| 42 |
public static final String RANG = "RANG"; |
|
| 43 |
public static final String TAXNAME = "TAXNAME"; |
|
| 44 |
public static final String AUTOR = "AUTOR"; |
|
| 25 | 45 |
|
| 26 | 46 |
public static void logMessage(long id, String message, Logger logger){
|
| 27 |
logger.error("NAMNR: "+id+" "+message);
|
|
| 47 |
logger.error(NAMNR+": "+id+" "+message);
|
|
| 28 | 48 |
} |
| 49 |
|
|
| 29 | 50 |
} |
Also available in: Unified diff
Refactor string constants