Revision d9f92b40
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java | ||
|---|---|---|
| 26 | 26 |
|
| 27 | 27 |
import org.apache.commons.lang.StringUtils; |
| 28 | 28 |
import org.apache.log4j.Logger; |
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import org.joda.time.DateTime; |
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| 30 |
import org.joda.time.format.DateTimeFormat; |
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import org.joda.time.format.DateTimeFormatter; |
|
| 32 | 29 |
import org.springframework.stereotype.Component; |
| 33 | 30 |
import org.springframework.transaction.TransactionStatus; |
| 34 | 31 |
|
| ... | ... | |
| 37 | 34 |
import eu.etaxonomy.cdm.io.common.Source; |
| 38 | 35 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| 39 | 36 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbConstantMapper; |
| 40 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbExtensionMapper; |
|
| 41 | 37 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbLastActionMapper; |
| 42 | 38 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbObjectMapper; |
| 43 | 39 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbStringMapper; |
| ... | ... | |
| 172 | 168 |
success &= doPhase01(state, mapping, additionalSourceMapping); |
| 173 | 169 |
|
| 174 | 170 |
//"PHASE 1b: Handle names without taxa ... |
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success &= doNames(state, additionalSourceMapping); |
|
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success &= doPhase01b_Names(state, additionalSourceMapping);
|
|
| 176 | 172 |
|
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// 2nd Round: Add ParentTaxonFk to each taxon |
| 178 | 174 |
success &= doPhase02(state); |
| ... | ... | |
| 881 | 877 |
return inferredSynonymsDataToBeSaved; |
| 882 | 878 |
} |
| 883 | 879 |
|
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|
|
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/** |
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* Handles names that do not appear in taxa |
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* @param state |
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* @param mapping |
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*/ |
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private boolean doNames(PesiExportState state, PesiExportMapping additionalSourceMapping) throws SQLException {
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|
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private boolean doPhase01b_Names(PesiExportState state, PesiExportMapping additionalSourceMapping) {
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|
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|
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boolean success = true; |
| 893 | 888 |
if (! state.getConfig().isDoPureNames()){
|
| ... | ... | |
| 1399 | 1394 |
//TODO define for FE + IF and for multiple sources |
| 1400 | 1395 |
result = cacheStrategy.getFullTitleCache(taxonName, tagRules); |
| 1401 | 1396 |
} |
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return result.replaceAll(",?\\<@status@\\>.*\\</@status@\\>", "");
|
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return result.replaceAll("(, ?)?\\<@status@\\>.*\\</@status@\\>", "").trim();
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|
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} |
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} |
| 1405 | 1400 |
|
| ... | ... | |
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Integer result = null; |
| 1600 | 1595 |
|
| 1601 | 1596 |
try {
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if (isMisappliedName(taxon)) {
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Synonym synonym = Synonym.NewInstance(null, null); |
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|
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// This works as long as only the instance is important to differentiate between TaxonStatus. |
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result = PesiTransformer.taxonBase2statusFk(synonym); // Auct References are treated as Synonyms in Datawarehouse now. |
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} else {
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// if (isMisappliedName(taxon)) {
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// Synonym synonym = Synonym.NewInstance(null, null); |
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// |
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// // This works as long as only the instance is important to differentiate between TaxonStatus. |
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// result = PesiTransformer.taxonBase2statusFk(synonym); // Auct References are treated as Synonyms in datawarehouse now. |
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// } else {
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//this should work now, the method itself distinguishes MAN etc. |
|
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result = PesiTransformer.taxonBase2statusFk(taxon); |
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} |
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// }
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|
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} catch (Exception e) {
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e.printStackTrace(); |
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} |
| ... | ... | |
| 2019 | 2015 |
* @return The <code>OriginalDB</code> attribute. |
| 2020 | 2016 |
* @see MethodMapper |
| 2021 | 2017 |
*/ |
| 2022 |
@SuppressWarnings("unused")
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|
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// @SuppressWarnings("unused")
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|
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private static String getOriginalDB(IdentifiableEntity<?> identifiableEntity) {
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| 2024 | 2020 |
EnumSet<PesiSource> sources = getSources(identifiableEntity); |
| 2025 | 2021 |
return PesiTransformer.getOriginalDbBySources(sources); |
| 2026 | 2022 |
} |
| 2027 | 2023 |
|
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/** |
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* Returns the <code>LastAction</code> attribute. |
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* @param taxonName The {@link TaxonNameBase TaxonName}.
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* @return The <code>LastAction</code> attribute. |
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* @see MethodMapper |
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*/ |
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//TODO still in use? |
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private static String getLastAction(IdentifiableEntity<?> identEntity) {
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String result = null; |
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try {
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Set<Extension> extensions = identEntity.getExtensions(); |
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for (Extension extension : extensions) {
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if (extension.getType().equals(lastActionExtensionType)) {
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result = extension.getValue(); |
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} |
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} |
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} catch (Exception e) {
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e.printStackTrace(); |
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} |
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return result; |
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} |
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|
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/** |
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* Returns the <code>LastActionDate</code> attribute. |
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* @param taxonName The {@link TaxonNameBase TaxonName}.
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* @return The <code>LastActionDate</code> attribute. |
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* @see MethodMapper |
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*/ |
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//TODO still in use? |
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private static DateTime getLastActionDate(IdentifiableEntity<?> identEntity) {
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DateTime result = null; |
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try {
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Set<Extension> extensions = identEntity.getExtensions(); |
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for (Extension extension : extensions) {
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if (extension.getType().equals(lastActionDateExtensionType)) {
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String dateTime = extension.getValue(); |
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if (dateTime != null) {
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DateTimeFormatter formatter = DateTimeFormat.forPattern("yyyy-MM-dd HH:mm:ss.S");
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result = formatter.parseDateTime(dateTime); |
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} |
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} |
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} |
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} catch (Exception e) {
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e.printStackTrace(); |
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} |
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return result; |
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} |
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|
|
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/** |
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* Returns the <code>ExpertName</code> attribute. |
| 2078 | 2026 |
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
| ... | ... | |
| 2080 | 2028 |
* @see MethodMapper |
| 2081 | 2029 |
*/ |
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@SuppressWarnings("unused") //for some reason it is also called by getCacheCitation
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private static String getExpertName(TaxonBase<?> taxonName) {
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String result = null; |
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private static String getExpertName(TaxonBase<?> taxon) {
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|
| 2085 | 2032 |
try {
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String result = null; |
|
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if(expertNameExtensionType!=null){ //some databases do not have this extension type
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Set<Extension> extensions = taxonName.getExtensions();
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Set<Extension> extensions = taxon.getExtensions(); |
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for (Extension extension : extensions) {
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if (extension.getType().equals(expertNameExtensionType)) {
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result = extension.getValue(); |
| 2091 | 2039 |
} |
| 2092 | 2040 |
} |
| 2093 | 2041 |
} |
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if (getPesiSources(taxon).contains(PesiSource.EM)){
|
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| 2043 |
return taxon.getSec().getTitleCache(); |
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} |
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| 2045 |
return null; |
|
| 2094 | 2046 |
} catch (Exception e) {
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| 2095 | 2047 |
e.printStackTrace(); |
| 2048 |
return null; |
|
| 2096 | 2049 |
} |
| 2097 |
return result; |
|
| 2098 | 2050 |
} |
| 2099 | 2051 |
|
| 2100 |
/** |
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* Returns the <code>ExpertFk</code> attribute. |
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* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
| 2103 |
* @param state The {@link PesiExportState PesiExportState}.
|
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| 2104 |
* @return The <code>ExpertFk</code> attribute. |
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| 2105 |
* @see MethodMapper |
|
| 2106 |
*/ |
|
| 2052 |
//TODO change to ExpertGUID |
|
| 2107 | 2053 |
private static Integer getExpertFk(Reference reference, PesiExportState state) {
|
| 2108 | 2054 |
Integer result = state.getDbId(reference); |
| 2109 | 2055 |
return result; |
| ... | ... | |
| 2115 | 2061 |
* @return The <code>SpeciesExpertName</code> attribute. |
| 2116 | 2062 |
* @see MethodMapper |
| 2117 | 2063 |
*/ |
| 2118 |
//TODO still in use? |
|
| 2119 |
private static String getSpeciesExpertName(TaxonBase<?> taxonName) {
|
|
| 2120 |
String result = null; |
|
| 2064 |
@SuppressWarnings("unused")
|
|
| 2065 |
private static String getSpeciesExpertName(TaxonBase<?> taxon) {
|
|
| 2121 | 2066 |
try {
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| 2122 |
Set<Extension> extensions = taxonName.getExtensions(); |
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| 2123 |
for (Extension extension : extensions) {
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| 2124 |
if (extension.getType().equals(speciesExpertNameExtensionType)) {
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| 2125 |
result = extension.getValue(); |
|
| 2126 |
} |
|
| 2067 |
Set<Extension> extensions = taxon.getExtensions(); |
|
| 2068 |
if(speciesExpertNameExtensionType!=null){ //some databases do not have this extension type
|
|
| 2069 |
for (Extension extension : extensions) {
|
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| 2070 |
if (extension.getType().equals(speciesExpertNameExtensionType)) {
|
|
| 2071 |
return extension.getValue(); |
|
| 2072 |
} |
|
| 2073 |
} |
|
| 2127 | 2074 |
} |
| 2075 |
if (getPesiSources(taxon).contains(PesiSource.EM)){
|
|
| 2076 |
return taxon.getSec().getTitleCache(); |
|
| 2077 |
} |
|
| 2078 |
return null; |
|
| 2128 | 2079 |
} catch (Exception e) {
|
| 2129 | 2080 |
e.printStackTrace(); |
| 2081 |
return null; |
|
| 2130 | 2082 |
} |
| 2131 |
return result; |
|
| 2132 | 2083 |
} |
| 2133 | 2084 |
|
| 2134 | 2085 |
/** |
| ... | ... | |
| 2138 | 2089 |
* @return The <code>SpeciesExpertFk</code> attribute. |
| 2139 | 2090 |
* @see MethodMapper |
| 2140 | 2091 |
*/ |
| 2092 |
//TODO should be changed to SpeciesExpertGUID |
|
| 2141 | 2093 |
private static Integer getSpeciesExpertFk(Reference reference, PesiExportState state) {
|
| 2142 | 2094 |
Integer result = state.getDbId(reference); |
| 2143 | 2095 |
return result; |
| ... | ... | |
| 2219 | 2171 |
mapping.addMapper(DbLastActionMapper.NewInstance("LastAction", true));
|
| 2220 | 2172 |
|
| 2221 | 2173 |
//experts |
| 2222 |
ExtensionType extensionTypeSpeciesExpertName = (ExtensionType)getTermService().find(PesiTransformer.uuidExtSpeciesExpertName); |
|
| 2223 |
mapping.addMapper(DbExtensionMapper.NewInstance(extensionTypeSpeciesExpertName, "SpeciesExpertName")); |
|
| 2224 |
ExtensionType extensionTypeExpertName = (ExtensionType)getTermService().find(PesiTransformer.uuidExtExpertName); |
|
| 2225 |
mapping.addMapper(DbExtensionMapper.NewInstance(extensionTypeExpertName, "ExpertName")); |
|
| 2174 |
// mapping.addMapper(DbExtensionMapper.NewInstance(extensionTypeSpeciesExpertName, "SpeciesExpertName")); |
|
| 2175 |
mapping.addMapper(MethodMapper.NewInstance("SpeciesExpertName", this, TaxonBase.class));
|
|
| 2176 |
// ExtensionType extensionTypeExpertName = (ExtensionType)getTermService().find(PesiTransformer.uuidExtExpertName); |
|
| 2177 |
// mapping.addMapper(DbExtensionMapper.NewInstance(extensionTypeExpertName, "ExpertName")); |
|
| 2178 |
mapping.addMapper(MethodMapper.NewInstance("ExpertName", this, TaxonBase.class));
|
|
| 2226 | 2179 |
|
| 2227 | 2180 |
//ParentTaxonFk handled in Phase02 now |
| 2228 | 2181 |
mapping.addMapper(ObjectChangeMapper.NewInstance(TaxonBase.class, TaxonName.class, "Name")); |
| ... | ... | |
| 2259 | 2212 |
mapping.addMapper(DbLastActionMapper.NewInstance("LastAction", true));
|
| 2260 | 2213 |
|
| 2261 | 2214 |
addNameMappers(mapping); |
| 2262 |
//TODO add author mapper |
|
| 2263 |
|
|
| 2264 | 2215 |
return mapping; |
| 2265 | 2216 |
} |
| 2266 | 2217 |
|
Also available in: Unified diff
ref #8509, ref #8508 some fixes to E+M PESI export and validation