Revision 51171c9d
Added by Andreas Müller over 12 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelAuthorTeamImport.java | ||
|---|---|---|
| 53 | 53 |
} |
| 54 | 54 |
|
| 55 | 55 |
|
| 56 |
protected boolean doInvoke(BerlinModelImportState state){
|
|
| 56 |
protected void doInvoke(BerlinModelImportState state){
|
|
| 57 | 57 |
BerlinModelImportConfigurator config = state.getConfig(); |
| 58 | 58 |
source = config.getSource(); |
| 59 | 59 |
|
| 60 | 60 |
logger.info("start make " + pluralString + " ...");
|
| 61 |
boolean success = true ; |
|
| 62 |
|
|
| 63 |
|
|
| 61 |
|
|
| 64 | 62 |
//queryStrings |
| 65 | 63 |
String strIdQuery = getIdQuery(); |
| 66 | 64 |
|
| ... | ... | |
| 79 | 77 |
} |
| 80 | 78 |
} catch (SQLException e) {
|
| 81 | 79 |
logger.error("SQLException:" + e);
|
| 82 |
return false; |
|
| 80 |
state.setUnsuccessfull(); |
|
| 81 |
return; |
|
| 83 | 82 |
} |
| 84 | 83 |
|
| 85 | 84 |
|
| 86 |
logger.info("end make " + pluralString + " ... " + getSuccessString(success));
|
|
| 87 |
return success;
|
|
| 85 |
logger.info("end make " + pluralString + " ... " + getSuccessString(true));
|
|
| 86 |
return; |
|
| 88 | 87 |
} |
| 89 | 88 |
|
| 90 | 89 |
protected String getIdQuery(){
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelCommonNamesImport.java | ||
|---|---|---|
| 118 | 118 |
|
| 119 | 119 |
|
| 120 | 120 |
@Override |
| 121 |
protected boolean doInvoke(BerlinModelImportState state) {
|
|
| 122 |
boolean result = true; |
|
| 121 |
protected void doInvoke(BerlinModelImportState state) {
|
|
| 123 | 122 |
try {
|
| 124 |
result &= makeRegions(state);
|
|
| 123 |
makeRegions(state); |
|
| 125 | 124 |
} catch (Exception e) {
|
| 126 | 125 |
logger.error("Error when creating common name regions:" + e.getMessage());
|
| 127 |
result = false;
|
|
| 126 |
state.setUnsuccessfull();
|
|
| 128 | 127 |
} |
| 129 |
result &= super.doInvoke(state);
|
|
| 130 |
return result;
|
|
| 128 |
super.doInvoke(state); |
|
| 129 |
return; |
|
| 131 | 130 |
} |
| 132 | 131 |
|
| 133 | 132 |
/** |
| 134 | 133 |
* @param state |
| 135 | 134 |
* |
| 136 | 135 |
*/ |
| 137 |
private boolean makeRegions(BerlinModelImportState state) {
|
|
| 138 |
boolean result = true; |
|
| 136 |
private void makeRegions(BerlinModelImportState state) {
|
|
| 139 | 137 |
try {
|
| 140 | 138 |
SortedSet<Integer> regionFks = new TreeSet<Integer>(); |
| 141 | 139 |
Source source = state.getConfig().getSource(); |
| 142 | 140 |
|
| 143 |
result = getRegionFks(result, regionFks, source);
|
|
| 141 |
getRegionFks(state, regionFks, source);
|
|
| 144 | 142 |
//concat filter string |
| 145 | 143 |
String sqlWhere = getSqlWhere(regionFks); |
| 146 | 144 |
|
| ... | ... | |
| 149 | 147 |
//fill regionMap |
| 150 | 148 |
fillRegionMap(source, sqlWhere, emTdwgMap); |
| 151 | 149 |
|
| 152 |
return result;
|
|
| 150 |
return; |
|
| 153 | 151 |
} catch (NumberFormatException e) {
|
| 154 | 152 |
e.printStackTrace(); |
| 155 |
return false; |
|
| 153 |
state.setUnsuccessfull(); |
|
| 154 |
return; |
|
| 156 | 155 |
} catch (SQLException e) {
|
| 157 | 156 |
e.printStackTrace(); |
| 158 |
return false; |
|
| 157 |
state.setUnsuccessfull(); |
|
| 158 |
return; |
|
| 159 | 159 |
} |
| 160 | 160 |
} |
| 161 | 161 |
|
| ... | ... | |
| 462 | 462 |
|
| 463 | 463 |
|
| 464 | 464 |
/** |
| 465 |
* @param result
|
|
| 465 |
* @param state
|
|
| 466 | 466 |
* @param regionFks |
| 467 | 467 |
* @param source |
| 468 | 468 |
* @return |
| 469 | 469 |
* @throws SQLException |
| 470 | 470 |
*/ |
| 471 |
private boolean getRegionFks(boolean result, SortedSet<Integer> regionFks,
|
|
| 471 |
private void getRegionFks(BerlinModelImportState state, SortedSet<Integer> regionFks,
|
|
| 472 | 472 |
Source source) throws SQLException {
|
| 473 | 473 |
String sql = " SELECT DISTINCT RegionFks FROM emCommonName"; |
| 474 | 474 |
ResultSet rs = source.getResultSet(sql); |
| ... | ... | |
| 478 | 478 |
for (String regionFk: regionFkArray){
|
| 479 | 479 |
regionFk = regionFk.trim(); |
| 480 | 480 |
if (! StringUtils.isNumeric(regionFk) || "".equals(regionFk) ){
|
| 481 |
result = false;
|
|
| 481 |
state.setUnsuccessfull();
|
|
| 482 | 482 |
logger.warn("RegionFk is not numeric: " + regionFk);
|
| 483 | 483 |
}else{
|
| 484 | 484 |
regionFks.add(Integer.valueOf(regionFk)); |
| 485 | 485 |
} |
| 486 | 486 |
} |
| 487 | 487 |
} |
| 488 |
return result;
|
|
| 488 |
return; |
|
| 489 | 489 |
} |
| 490 | 490 |
|
| 491 | 491 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelFactsImport.java | ||
|---|---|---|
| 144 | 144 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#doInvoke(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState) |
| 145 | 145 |
*/ |
| 146 | 146 |
@Override |
| 147 |
protected boolean doInvoke(BerlinModelImportState state) {
|
|
| 147 |
protected void doInvoke(BerlinModelImportState state) {
|
|
| 148 | 148 |
featureMap = invokeFactCategories(state.getConfig()); |
| 149 |
return super.doInvoke(state); |
|
| 149 |
super.doInvoke(state); |
|
| 150 |
return; |
|
| 150 | 151 |
} |
| 151 | 152 |
|
| 152 | 153 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelImportBase.java | ||
|---|---|---|
| 53 | 53 |
super(); |
| 54 | 54 |
} |
| 55 | 55 |
|
| 56 |
protected boolean doInvoke(BerlinModelImportState state){
|
|
| 56 |
protected void doInvoke(BerlinModelImportState state){
|
|
| 57 | 57 |
// String strTeamStore = ICdmIO.TEAM_STORE; |
| 58 | 58 |
BerlinModelImportConfigurator config = state.getConfig(); |
| 59 | 59 |
Source source = config.getSource(); |
| ... | ... | |
| 77 | 77 |
} |
| 78 | 78 |
} catch (SQLException e) {
|
| 79 | 79 |
logger.error("SQLException:" + e);
|
| 80 |
return false;
|
|
| 80 |
state.setUnsuccessfull();
|
|
| 81 | 81 |
} |
| 82 | 82 |
|
| 83 | 83 |
logger.info("end make " + getPluralString() + " ... " + getSuccessString(success));
|
| 84 |
return success; |
|
| 84 |
if (success == false){
|
|
| 85 |
state.setUnsuccessfull(); |
|
| 86 |
} |
|
| 87 |
return; |
|
| 85 | 88 |
} |
| 86 | 89 |
|
| 87 | 90 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelOccurrenceSourceImport.java | ||
|---|---|---|
| 22 | 22 |
import org.springframework.stereotype.Component; |
| 23 | 23 |
|
| 24 | 24 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 25 |
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
|
| 26 |
import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer; |
|
| 27 |
import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelOccurrenceImportValidator; |
|
| 28 | 25 |
import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelOccurrenceSourceImportValidator; |
| 29 |
import eu.etaxonomy.cdm.io.common.ICdmIO; |
|
| 30 | 26 |
import eu.etaxonomy.cdm.io.common.IOValidator; |
| 31 |
import eu.etaxonomy.cdm.io.common.MapWrapper; |
|
| 32 | 27 |
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
| 33 | 28 |
import eu.etaxonomy.cdm.io.common.Source; |
| 34 | 29 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 35 | 30 |
import eu.etaxonomy.cdm.model.common.DescriptionElementSource; |
| 36 | 31 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| 37 | 32 |
import eu.etaxonomy.cdm.model.description.Distribution; |
| 38 |
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase; |
|
| 39 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
|
| 40 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
|
| 41 |
import eu.etaxonomy.cdm.model.location.TdwgArea; |
|
| 42 | 33 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| 43 | 34 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 44 | 35 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 45 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
| 46 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 47 |
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
|
| 48 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
|
| 49 | 36 |
|
| 50 | 37 |
|
| 51 | 38 |
/** |
| ... | ... | |
| 92 | 79 |
|
| 93 | 80 |
|
| 94 | 81 |
@Override |
| 95 |
protected boolean doInvoke(BerlinModelImportState state) {
|
|
| 82 |
protected void doInvoke(BerlinModelImportState state) {
|
|
| 96 | 83 |
try {
|
| 97 | 84 |
sourceNumberRefIdMap = makeSourceNameReferenceIdMap(state); |
| 98 | 85 |
} catch (SQLException e) {
|
| 99 | 86 |
e.printStackTrace(); |
| 100 | 87 |
throw new RuntimeException(e); |
| 101 | 88 |
} |
| 102 |
boolean result = super.doInvoke(state);
|
|
| 89 |
super.doInvoke(state); |
|
| 103 | 90 |
sourceNumberRefIdMap = null; |
| 104 |
return result;
|
|
| 91 |
return; |
|
| 105 | 92 |
} |
| 106 | 93 |
|
| 107 | 94 |
/* (non-Javadoc) |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelReferenceImport.java | ||
|---|---|---|
| 96 | 96 |
super(); |
| 97 | 97 |
} |
| 98 | 98 |
|
| 99 |
protected boolean initializeMappers(BerlinModelImportState state){
|
|
| 99 |
protected void initializeMappers(BerlinModelImportState state){
|
|
| 100 | 100 |
for (CdmAttributeMapperBase mapper: classMappers){
|
| 101 | 101 |
if (mapper instanceof DbImportExtensionMapper){
|
| 102 | 102 |
((DbImportExtensionMapper)mapper).initialize(state, Reference.class); |
| 103 | 103 |
} |
| 104 | 104 |
} |
| 105 |
return true;
|
|
| 105 |
return; |
|
| 106 | 106 |
} |
| 107 | 107 |
|
| 108 | 108 |
protected static CdmAttributeMapperBase[] classMappers = new CdmAttributeMapperBase[]{
|
| ... | ... | |
| 161 | 161 |
|
| 162 | 162 |
|
| 163 | 163 |
@Override |
| 164 |
protected boolean doInvoke(BerlinModelImportState state){
|
|
| 165 |
boolean success = true; |
|
| 164 |
protected void doInvoke(BerlinModelImportState state){
|
|
| 166 | 165 |
logger.info("start make " + getPluralString() + " ...");
|
| 167 | 166 |
|
| 168 |
success &= initializeMappers(state); |
|
| 167 |
boolean success = true; |
|
| 168 |
initializeMappers(state); |
|
| 169 | 169 |
BerlinModelImportConfigurator config = state.getConfig(); |
| 170 | 170 |
Source source = config.getSource(); |
| 171 | 171 |
|
| ... | ... | |
| 188 | 188 |
try {
|
| 189 | 189 |
if (testMaxRecursionResultSet.next() == true){
|
| 190 | 190 |
logger.error("Maximum allowed InReference recursions exceeded in Berlin Model. Maximum recursion level is 2.");
|
| 191 |
return false; |
|
| 191 |
state.setUnsuccessfull(); |
|
| 192 |
return; |
|
| 192 | 193 |
} |
| 193 | 194 |
} catch (SQLException e1) {
|
| 194 | 195 |
e1.printStackTrace(); |
| ... | ... | |
| 239 | 240 |
|
| 240 | 241 |
} catch (SQLException e) {
|
| 241 | 242 |
logger.error("SQLException:" + e);
|
| 242 |
return false; |
|
| 243 |
state.setUnsuccessfull(); |
|
| 244 |
return; |
|
| 243 | 245 |
} |
| 244 | 246 |
logger.info("end make " + getPluralString() + " ... " + getSuccessString(success));
|
| 245 |
return success; |
|
| 247 |
if (! success){
|
|
| 248 |
state.setUnsuccessfull(); |
|
| 249 |
} |
|
| 250 |
return; |
|
| 246 | 251 |
} |
| 247 | 252 |
|
| 248 | 253 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonRelationImport.java | ||
|---|---|---|
| 80 | 80 |
* @return |
| 81 | 81 |
* @throws SQLException |
| 82 | 82 |
*/ |
| 83 |
private boolean makeClassifications(BerlinModelImportState state) throws SQLException{
|
|
| 83 |
private void makeClassifications(BerlinModelImportState state) throws SQLException{
|
|
| 84 | 84 |
logger.info("start make classification ...");
|
| 85 | 85 |
Source source = state.getConfig().getSource(); |
| 86 | 86 |
|
| ... | ... | |
| 136 | 136 |
} |
| 137 | 137 |
logger.info("end make classification ...");
|
| 138 | 138 |
|
| 139 |
return true;
|
|
| 139 |
return; |
|
| 140 | 140 |
} |
| 141 | 141 |
|
| 142 | 142 |
/** |
| ... | ... | |
| 316 | 316 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map) |
| 317 | 317 |
*/ |
| 318 | 318 |
@Override |
| 319 |
protected boolean doInvoke(BerlinModelImportState state){
|
|
| 319 |
protected void doInvoke(BerlinModelImportState state){
|
|
| 320 | 320 |
try {
|
| 321 |
boolean success = true; |
|
| 322 |
success &= makeClassifications(state); |
|
| 323 |
success &= super.doInvoke(state); |
|
| 324 |
return success; |
|
| 321 |
makeClassifications(state); |
|
| 322 |
super.doInvoke(state); |
|
| 323 |
return; |
|
| 325 | 324 |
} catch (SQLException e) {
|
| 326 | 325 |
throw new RuntimeException(e); |
| 327 | 326 |
} |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelUserImport.java | ||
|---|---|---|
| 55 | 55 |
return validator.validate(state); |
| 56 | 56 |
} |
| 57 | 57 |
|
| 58 |
protected boolean doInvoke(BerlinModelImportState state){
|
|
| 59 |
|
|
| 58 |
protected void doInvoke(BerlinModelImportState state){
|
|
| 59 |
boolean success = true; |
|
| 60 | 60 |
MapWrapper<User> userMap = (MapWrapper<User>)state.getStore(ICdmIO.USER_STORE); |
| 61 | 61 |
|
| 62 | 62 |
BerlinModelImportConfigurator config = state.getConfig(); |
| ... | ... | |
| 65 | 65 |
String cdmAttrName; |
| 66 | 66 |
|
| 67 | 67 |
logger.info("start make "+pluralString+" ...");
|
| 68 |
boolean success = true ; |
|
| 69 |
|
|
| 70 |
|
|
| 71 | 68 |
|
| 72 | 69 |
//get data from database |
| 73 | 70 |
String strQuery = |
| ... | ... | |
| 112 | 109 |
}catch(Exception ex){
|
| 113 | 110 |
logger.error(ex.getMessage()); |
| 114 | 111 |
ex.printStackTrace(); |
| 112 |
state.setUnsuccessfull(); |
|
| 115 | 113 |
success = false; |
| 116 | 114 |
} |
| 117 | 115 |
} //while rs.hasNext() |
| 118 | 116 |
} catch (SQLException e) {
|
| 119 | 117 |
logger.error("SQLException:" + e);
|
| 120 |
return false; |
|
| 118 |
state.setUnsuccessfull(); |
|
| 119 |
return; |
|
| 121 | 120 |
} |
| 122 | 121 |
|
| 123 | 122 |
logger.info("save " + i + " "+pluralString + " ...");
|
| 124 | 123 |
getUserService().save(userMap.objects()); |
| 125 | 124 |
|
| 126 | 125 |
logger.info("end make "+pluralString+" ..." + getSuccessString(success));;
|
| 127 |
return success; |
|
| 126 |
if (!success){
|
|
| 127 |
state.setUnsuccessfull(); |
|
| 128 |
} |
|
| 129 |
return; |
|
| 128 | 130 |
} |
| 129 | 131 |
|
| 130 | 132 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelWebMarkerCategoryImport.java | ||
|---|---|---|
| 55 | 55 |
/* (non-Javadoc) |
| 56 | 56 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#doInvoke(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState) |
| 57 | 57 |
*/ |
| 58 |
protected boolean doInvoke(BerlinModelImportState state){
|
|
| 59 |
boolean result = true;
|
|
| 60 |
|
|
| 58 |
protected void doInvoke(BerlinModelImportState state){
|
|
| 59 |
boolean success = true ;
|
|
| 60 |
|
|
| 61 | 61 |
BerlinModelImportConfigurator config = state.getConfig(); |
| 62 | 62 |
Source source = config.getSource(); |
| 63 | 63 |
|
| 64 | 64 |
logger.info("start make "+pluralString+" ...");
|
| 65 |
boolean success = true ; |
|
| 66 |
|
|
| 65 |
|
|
| 67 | 66 |
ResultSet rs = source.getResultSet(getRecordQuery(config)) ; |
| 68 | 67 |
|
| 69 | 68 |
int i = 0; |
| ... | ... | |
| 94 | 93 |
} //while rs.hasNext() |
| 95 | 94 |
} catch (SQLException e) {
|
| 96 | 95 |
logger.error("SQLException:" + e);
|
| 97 |
return false; |
|
| 96 |
state.setUnsuccessfull(); |
|
| 97 |
return; |
|
| 98 | 98 |
} |
| 99 | 99 |
|
| 100 | 100 |
|
| 101 | 101 |
logger.info("save " + i + " "+pluralString + " ...");
|
| 102 | 102 |
|
| 103 | 103 |
logger.info("end make "+pluralString+" ..." + getSuccessString(success));;
|
| 104 |
return result; |
|
| 104 |
if (!success){
|
|
| 105 |
state.setUnsuccessfull(); |
|
| 106 |
} |
|
| 107 |
return; |
|
| 105 | 108 |
|
| 106 | 109 |
} |
| 107 | 110 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/validation/BerlinModelGeneralImportValidator.java | ||
|---|---|---|
| 59 | 59 |
return result; |
| 60 | 60 |
} |
| 61 | 61 |
|
| 62 |
protected boolean doInvoke(BerlinModelImportState state){
|
|
| 63 |
boolean success = true; |
|
| 62 |
protected void doInvoke(BerlinModelImportState state){
|
|
| 64 | 63 |
//do nothing |
| 65 |
return success;
|
|
| 64 |
return; |
|
| 66 | 65 |
|
| 67 | 66 |
} |
| 68 | 67 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/out/BerlinModelAuthorExport.java | ||
|---|---|---|
| 77 | 77 |
* @see eu.etaxonomy.cdm.io.berlinModel.out.BerlinModelExportBase#doInvoke(eu.etaxonomy.cdm.io.berlinModel.out.BerlinModelExportState) |
| 78 | 78 |
*/ |
| 79 | 79 |
@Override |
| 80 |
protected boolean doInvoke(BerlinModelExportState state) {
|
|
| 80 |
protected void doInvoke(BerlinModelExportState state) {
|
|
| 81 | 81 |
try{
|
| 82 |
boolean success = true; |
|
| 82 | 83 |
BerlinModelExportConfigurator bmeConfig = (BerlinModelExportConfigurator)state.getConfig(); |
| 83 | 84 |
|
| 84 | 85 |
logger.info("start make "+pluralString+" ...");
|
| 85 |
boolean success = true ; |
|
| 86 | 86 |
doDelete(bmeConfig); |
| 87 | 87 |
|
| 88 | 88 |
TransactionStatus txStatus = startTransaction(true); |
| ... | ... | |
| 103 | 103 |
|
| 104 | 104 |
commitTransaction(txStatus); |
| 105 | 105 |
logger.info("end make "+pluralString+" ..." + getSuccessString(success));
|
| 106 |
return success; |
|
| 106 |
if (!success){
|
|
| 107 |
state.setUnsuccessfull(); |
|
| 108 |
} |
|
| 109 |
return; |
|
| 107 | 110 |
}catch(SQLException e){
|
| 108 | 111 |
e.printStackTrace(); |
| 109 | 112 |
logger.error(e.getMessage()); |
| 110 |
return false; |
|
| 113 |
state.setUnsuccessfull(); |
|
| 114 |
return; |
|
| 111 | 115 |
} |
| 112 | 116 |
} |
| 113 | 117 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/out/BerlinModelAuthorTeamExport.java | ||
|---|---|---|
| 79 | 79 |
} |
| 80 | 80 |
|
| 81 | 81 |
|
| 82 |
protected boolean doInvoke(BerlinModelExportState state){
|
|
| 82 |
protected void doInvoke(BerlinModelExportState state){
|
|
| 83 | 83 |
try{
|
| 84 | 84 |
BerlinModelExportConfigurator bmeConfig = (BerlinModelExportConfigurator)state.getConfig(); |
| 85 | 85 |
|
| ... | ... | |
| 106 | 106 |
commitTransaction(txStatus); |
| 107 | 107 |
|
| 108 | 108 |
logger.info("end make "+pluralString+" ..." + getSuccessString(success));
|
| 109 |
return success; |
|
| 109 |
if (!success){
|
|
| 110 |
state.setUnsuccessfull(); |
|
| 111 |
} |
|
| 112 |
return; |
|
| 110 | 113 |
}catch(SQLException e){
|
| 111 | 114 |
e.printStackTrace(); |
| 112 | 115 |
logger.error(e.getMessage()); |
| 113 |
return false; |
|
| 116 |
state.setUnsuccessfull(); |
|
| 117 |
return; |
|
| 114 | 118 |
} |
| 115 | 119 |
} |
| 116 | 120 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/out/BerlinModelClassificationExport.java | ||
|---|---|---|
| 81 | 81 |
return mapping; |
| 82 | 82 |
} |
| 83 | 83 |
|
| 84 |
protected boolean doInvoke(BerlinModelExportState state){
|
|
| 84 |
protected void doInvoke(BerlinModelExportState state){
|
|
| 85 | 85 |
if (state.getConfig().isUseClassification() == false){
|
| 86 |
return true;
|
|
| 86 |
return; |
|
| 87 | 87 |
} |
| 88 | 88 |
|
| 89 | 89 |
try{
|
| ... | ... | |
| 111 | 111 |
} |
| 112 | 112 |
commitTransaction(txStatus); |
| 113 | 113 |
logger.info("end make " + pluralString + " ..." + getSuccessString(success));
|
| 114 |
return success; |
|
| 114 |
if (!success){
|
|
| 115 |
state.setUnsuccessfull(); |
|
| 116 |
} |
|
| 117 |
return; |
|
| 115 | 118 |
}catch(SQLException e){
|
| 116 | 119 |
e.printStackTrace(); |
| 117 | 120 |
logger.error(e.getMessage()); |
| 118 |
return false; |
|
| 121 |
state.setUnsuccessfull(); |
|
| 122 |
return; |
|
| 119 | 123 |
} |
| 120 | 124 |
} |
| 121 | 125 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/out/BerlinModelFactExport.java | ||
|---|---|---|
| 98 | 98 |
return mapping; |
| 99 | 99 |
} |
| 100 | 100 |
|
| 101 |
protected boolean doInvoke(BerlinModelExportState state){
|
|
| 101 |
protected void doInvoke(BerlinModelExportState state){
|
|
| 102 | 102 |
try{
|
| 103 | 103 |
logger.info("start make " + pluralString + " ...");
|
| 104 | 104 |
boolean success = true ; |
| ... | ... | |
| 126 | 126 |
commitTransaction(txStatus); |
| 127 | 127 |
logger.info("end make " + pluralString + " ..." + getSuccessString(success));
|
| 128 | 128 |
|
| 129 |
return success; |
|
| 129 |
if (!success){
|
|
| 130 |
state.setUnsuccessfull(); |
|
| 131 |
} |
|
| 132 |
return; |
|
| 130 | 133 |
}catch(SQLException e){
|
| 131 | 134 |
e.printStackTrace(); |
| 132 | 135 |
logger.error(e.getMessage()); |
| 133 |
return false; |
|
| 136 |
state.setUnsuccessfull(); |
|
| 137 |
return; |
|
| 134 | 138 |
} |
| 135 | 139 |
} |
| 136 | 140 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/out/BerlinModelNameRelationExport.java | ||
|---|---|---|
| 84 | 84 |
return mapping; |
| 85 | 85 |
} |
| 86 | 86 |
|
| 87 |
protected boolean doInvoke(BerlinModelExportState state){
|
|
| 87 |
protected void doInvoke(BerlinModelExportState state){
|
|
| 88 | 88 |
try{
|
| 89 | 89 |
logger.info("start make " + pluralString + " ...");
|
| 90 | 90 |
boolean success = true ; |
| ... | ... | |
| 109 | 109 |
success &= makeIsHomotypicRelation(state, mapping); |
| 110 | 110 |
|
| 111 | 111 |
logger.info("end make " + pluralString + " ..." + getSuccessString(success));
|
| 112 |
return success; |
|
| 112 |
if (!success){
|
|
| 113 |
state.setUnsuccessfull(); |
|
| 114 |
} |
|
| 115 |
return; |
|
| 113 | 116 |
}catch(SQLException e){
|
| 114 | 117 |
e.printStackTrace(); |
| 115 | 118 |
logger.error(e.getMessage()); |
| 116 |
return false; |
|
| 119 |
state.setUnsuccessfull(); |
|
| 120 |
return; |
|
| 117 | 121 |
} |
| 118 | 122 |
} |
| 119 | 123 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/out/BerlinModelReferenceExport.java | ||
|---|---|---|
| 117 | 117 |
return mapping; |
| 118 | 118 |
} |
| 119 | 119 |
|
| 120 |
protected boolean doInvoke(BerlinModelExportState state){
|
|
| 120 |
protected void doInvoke(BerlinModelExportState state){
|
|
| 121 | 121 |
try{
|
| 122 | 122 |
logger.info("start make "+pluralString+" ...");
|
| 123 | 123 |
boolean success = true ; |
| ... | ... | |
| 149 | 149 |
|
| 150 | 150 |
commitTransaction(txStatus); |
| 151 | 151 |
logger.info("end make "+pluralString+" ..." + getSuccessString(success));
|
| 152 |
|
|
| 153 |
return success; |
|
| 152 |
if (!success){
|
|
| 153 |
state.setUnsuccessfull(); |
|
| 154 |
} |
|
| 155 |
return; |
|
| 154 | 156 |
}catch(SQLException e){
|
| 155 | 157 |
e.printStackTrace(); |
| 156 | 158 |
logger.error(e.getMessage()); |
| 157 |
return false; |
|
| 159 |
state.setUnsuccessfull(); |
|
| 160 |
return; |
|
| 158 | 161 |
} |
| 159 | 162 |
} |
| 160 | 163 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/out/BerlinModelTaxonExport.java | ||
|---|---|---|
| 107 | 107 |
return mapping; |
| 108 | 108 |
} |
| 109 | 109 |
|
| 110 |
protected boolean doInvoke(BerlinModelExportState state){
|
|
| 110 |
protected void doInvoke(BerlinModelExportState state){
|
|
| 111 | 111 |
try{
|
| 112 | 112 |
logger.info("start make " + pluralString + " ...");
|
| 113 | 113 |
boolean success = true ; |
| ... | ... | |
| 127 | 127 |
} |
| 128 | 128 |
commitTransaction(txStatus); |
| 129 | 129 |
logger.info("end make " + pluralString + " ..." + getSuccessString(success));
|
| 130 |
|
|
| 131 |
return success; |
|
| 130 |
if (!success){
|
|
| 131 |
state.setUnsuccessfull(); |
|
| 132 |
} |
|
| 133 |
return; |
|
| 132 | 134 |
}catch(SQLException e){
|
| 133 | 135 |
e.printStackTrace(); |
| 134 | 136 |
logger.error(e.getMessage()); |
| 135 |
return false; |
|
| 137 |
state.setUnsuccessfull(); |
|
| 138 |
return; |
|
| 136 | 139 |
} |
| 137 | 140 |
} |
| 138 | 141 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/out/BerlinModelTaxonNameExport.java | ||
|---|---|---|
| 152 | 152 |
return mapping; |
| 153 | 153 |
} |
| 154 | 154 |
|
| 155 |
protected boolean doInvoke(BerlinModelExportState state){
|
|
| 155 |
protected void doInvoke(BerlinModelExportState state){
|
|
| 156 | 156 |
try{
|
| 157 | 157 |
logger.info("start make "+pluralString+" ...");
|
| 158 | 158 |
boolean success = true ; |
| ... | ... | |
| 174 | 174 |
commitTransaction(txStatus); |
| 175 | 175 |
logger.info("end make " + pluralString+ " ..." + getSuccessString(success));
|
| 176 | 176 |
|
| 177 |
return success; |
|
| 177 |
if (!success){
|
|
| 178 |
state.setUnsuccessfull(); |
|
| 179 |
} |
|
| 180 |
return; |
|
| 178 | 181 |
}catch(SQLException e){
|
| 179 | 182 |
e.printStackTrace(); |
| 180 | 183 |
logger.error(e.getMessage()); |
| 181 |
return false; |
|
| 184 |
state.setUnsuccessfull(); |
|
| 185 |
return; |
|
| 182 | 186 |
} |
| 183 | 187 |
} |
| 184 | 188 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/out/BerlinModelTaxonRelationExport.java | ||
|---|---|---|
| 80 | 80 |
return mapping; |
| 81 | 81 |
} |
| 82 | 82 |
|
| 83 |
protected boolean doInvoke(BerlinModelExportState state){
|
|
| 83 |
protected void doInvoke(BerlinModelExportState state){
|
|
| 84 | 84 |
try{
|
| 85 | 85 |
logger.info("start make " + pluralString + " ...");
|
| 86 | 86 |
boolean success = true ; |
| ... | ... | |
| 102 | 102 |
} |
| 103 | 103 |
commitTransaction(txStatus); |
| 104 | 104 |
logger.info("end make " + pluralString + " ..." + getSuccessString(success));
|
| 105 |
return success; |
|
| 105 |
if (!success){
|
|
| 106 |
state.setUnsuccessfull(); |
|
| 107 |
} |
|
| 108 |
return; |
|
| 106 | 109 |
}catch(SQLException e){
|
| 107 | 110 |
e.printStackTrace(); |
| 108 | 111 |
logger.error(e.getMessage()); |
| 109 |
return false; |
|
| 112 |
state.setUnsuccessfull(); |
|
| 113 |
return; |
|
| 110 | 114 |
} |
| 111 | 115 |
} |
| 112 | 116 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/CacheUpdater.java | ||
|---|---|---|
| 29 | 29 |
private static final Logger logger = Logger.getLogger(CacheUpdater.class); |
| 30 | 30 |
|
| 31 | 31 |
@Override |
| 32 |
protected boolean doInvoke(DefaultImportState<CacheUpdaterConfigurator> state) {
|
|
| 32 |
protected void doInvoke(DefaultImportState<CacheUpdaterConfigurator> state) {
|
|
| 33 | 33 |
CacheUpdaterConfigurator config = state.getConfig(); |
| 34 | 34 |
if (config.getClassList() == null || config.getClassList().isEmpty()){
|
| 35 | 35 |
//!! not yet implemented |
| ... | ... | |
| 37 | 37 |
createClassListFromBoolean(); |
| 38 | 38 |
} |
| 39 | 39 |
handleClassList(config.getClassList()); |
| 40 |
return true;
|
|
| 40 |
return; |
|
| 41 | 41 |
} |
| 42 | 42 |
|
| 43 | 43 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/CdmImportBase.java | ||
|---|---|---|
| 589 | 589 |
* @return |
| 590 | 590 |
*/ |
| 591 | 591 |
public TaxonDescription getTaxonDescription(Taxon taxon, boolean isImageGallery, boolean createNewIfNotExists) {
|
| 592 |
Reference ref = null; |
|
| 593 |
return getTaxonDescription(taxon, ref, isImageGallery, createNewIfNotExists); |
|
| 594 |
} |
|
| 595 |
|
|
| 596 |
/** |
|
| 597 |
* Like {@link #getTaxonDescription(Taxon, boolean, boolean)}
|
|
| 598 |
* Only matches a description if the given reference is a source of the description.<BR> |
|
| 599 |
* If a new description is created the given reference will be added as a source. |
|
| 600 |
* |
|
| 601 |
* @see #getTaxonDescription(Taxon, boolean, boolean) |
|
| 602 |
*/ |
|
| 603 |
public TaxonDescription getTaxonDescription(Taxon taxon, Reference ref, boolean isImageGallery, boolean createNewIfNotExists) {
|
|
| 592 | 604 |
TaxonDescription result = null; |
| 593 | 605 |
Set<TaxonDescription> descriptions= taxon.getDescriptions(); |
| 594 | 606 |
for (TaxonDescription description : descriptions){
|
| 595 | 607 |
if (description.isImageGallery() == isImageGallery){
|
| 596 |
result = description; |
|
| 597 |
break; |
|
| 608 |
if (hasCorrespondingSource(ref, description)){
|
|
| 609 |
result = description; |
|
| 610 |
break; |
|
| 611 |
} |
|
| 598 | 612 |
} |
| 599 | 613 |
} |
| 600 | 614 |
if (result == null && createNewIfNotExists){
|
| 601 | 615 |
result = TaxonDescription.NewInstance(taxon); |
| 602 | 616 |
result.setImageGallery(isImageGallery); |
| 617 |
if (ref != null){
|
|
| 618 |
result.addSource(null, null, ref, null); |
|
| 619 |
} |
|
| 603 | 620 |
} |
| 604 | 621 |
return result; |
| 605 | 622 |
} |
| 623 |
|
|
| 624 |
|
|
| 625 |
/** |
|
| 626 |
* Returns true, if this description has a source with a citation equal to the given reference. |
|
| 627 |
* Returns true if the given reference is null. |
|
| 628 |
* @param ref |
|
| 629 |
* @param description |
|
| 630 |
*/ |
|
| 631 |
private boolean hasCorrespondingSource(Reference ref, TaxonDescription description) {
|
|
| 632 |
if (ref != null){
|
|
| 633 |
for (IdentifiableSource source : description.getSources()){
|
|
| 634 |
if (ref.equals(source.getCitation())){
|
|
| 635 |
return true; |
|
| 636 |
} |
|
| 637 |
} |
|
| 638 |
return false; |
|
| 639 |
} |
|
| 640 |
return true; |
|
| 641 |
|
|
| 642 |
} |
|
| 606 | 643 |
|
| 607 | 644 |
|
| 608 | 645 |
/** |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/CdmIoBase.java | ||
|---|---|---|
| 102 | 102 |
return true; |
| 103 | 103 |
}else{
|
| 104 | 104 |
updateProgress(state, "Invoking " + ioName); |
| 105 |
return doInvoke(state); |
|
| 105 |
doInvoke(state); |
|
| 106 |
return state.isSuccess(); |
|
| 106 | 107 |
} |
| 107 | 108 |
} |
| 108 | 109 |
|
| ... | ... | |
| 111 | 112 |
* @param state |
| 112 | 113 |
* @return |
| 113 | 114 |
*/ |
| 114 |
protected abstract boolean doInvoke(STATE state);
|
|
| 115 |
protected abstract void doInvoke(STATE state);
|
|
| 115 | 116 |
|
| 116 | 117 |
|
| 117 | 118 |
@Autowired |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/ImportStateBase.java | ||
|---|---|---|
| 70 | 70 |
|
| 71 | 71 |
private Map<UUID, ReferenceSystem> referenceSystemMap = new HashMap<UUID, ReferenceSystem>(); |
| 72 | 72 |
|
| 73 |
|
|
| 74 |
|
|
| 75 | 73 |
protected ImportStateBase(CONFIG config){
|
| 76 | 74 |
this.config = config; |
| 77 | 75 |
stores.put(ICdmIO.USER_STORE, new MapWrapper<User>(service)); |
| ... | ... | |
| 286 | 284 |
this.isCheck = isCheck; |
| 287 | 285 |
} |
| 288 | 286 |
|
| 287 |
|
|
| 289 | 288 |
|
| 290 | 289 |
} |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/IoStateBase.java | ||
|---|---|---|
| 24 | 24 |
|
| 25 | 25 |
private IO currentIO; |
| 26 | 26 |
|
| 27 |
private boolean success; |
|
| 28 |
|
|
| 27 | 29 |
CONFIG config; |
| 28 | 30 |
|
| 29 | 31 |
/** |
| ... | ... | |
| 61 | 63 |
public IO getCurrentIO() {
|
| 62 | 64 |
return currentIO; |
| 63 | 65 |
} |
| 66 |
|
|
| 67 |
public void setSuccess(boolean success) {
|
|
| 68 |
this.success = success; |
|
| 69 |
} |
|
| 70 |
|
|
| 71 |
public void setUnsuccessfull(){
|
|
| 72 |
this.success = false; |
|
| 73 |
} |
|
| 74 |
|
|
| 75 |
public boolean isSuccess() {
|
|
| 76 |
return success; |
|
| 77 |
} |
|
| 64 | 78 |
|
| 65 | 79 |
|
| 66 | 80 |
} |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaDescriptionExport.java | ||
|---|---|---|
| 59 | 59 |
* @param filename |
| 60 | 60 |
*/ |
| 61 | 61 |
@Override |
| 62 |
protected boolean doInvoke(DwcaTaxExportState state){
|
|
| 62 |
protected void doInvoke(DwcaTaxExportState state){
|
|
| 63 | 63 |
DwcaTaxExportConfigurator config = state.getConfig(); |
| 64 | 64 |
TransactionStatus txStatus = startTransaction(true); |
| 65 | 65 |
|
| ... | ... | |
| 106 | 106 |
closeWriter(writer, state); |
| 107 | 107 |
} |
| 108 | 108 |
commitTransaction(txStatus); |
| 109 |
return true;
|
|
| 109 |
return; |
|
| 110 | 110 |
} |
| 111 | 111 |
|
| 112 | 112 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaDistributionExport.java | ||
|---|---|---|
| 56 | 56 |
* @param filename |
| 57 | 57 |
*/ |
| 58 | 58 |
@Override |
| 59 |
protected boolean doInvoke(DwcaTaxExportState state){
|
|
| 59 |
protected void doInvoke(DwcaTaxExportState state){
|
|
| 60 | 60 |
DwcaTaxExportConfigurator config = state.getConfig(); |
| 61 | 61 |
TransactionStatus txStatus = startTransaction(true); |
| 62 | 62 |
|
| ... | ... | |
| 103 | 103 |
closeWriter(writer, state); |
| 104 | 104 |
} |
| 105 | 105 |
commitTransaction(txStatus); |
| 106 |
return true;
|
|
| 106 |
return; |
|
| 107 | 107 |
} |
| 108 | 108 |
|
| 109 | 109 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaEmlExport.java | ||
|---|---|---|
| 63 | 63 |
* @param filename |
| 64 | 64 |
*/ |
| 65 | 65 |
@Override |
| 66 |
protected boolean doInvoke(DwcaTaxExportState state){
|
|
| 66 |
protected void doInvoke(DwcaTaxExportState state){
|
|
| 67 | 67 |
DwcaTaxExportConfigurator config = state.getConfig(); |
| 68 | 68 |
|
| 69 | 69 |
DwcaMetaDataRecord metaRecord = new DwcaMetaDataRecord(! IS_CORE, fileName, null); |
| ... | ... | |
| 73 | 73 |
|
| 74 | 74 |
DwcaEmlRecord emlRecord = config.getEmlRecord(); |
| 75 | 75 |
if (emlRecord == null){
|
| 76 |
return true;
|
|
| 76 |
return; |
|
| 77 | 77 |
} |
| 78 | 78 |
|
| 79 | 79 |
XMLStreamWriter writer = null; |
| ... | ... | |
| 128 | 128 |
closeWriter(writer, state); |
| 129 | 129 |
} |
| 130 | 130 |
|
| 131 |
return true;
|
|
| 131 |
return; |
|
| 132 | 132 |
} |
| 133 | 133 |
|
| 134 | 134 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaImageExport.java | ||
|---|---|---|
| 59 | 59 |
* @param filename |
| 60 | 60 |
*/ |
| 61 | 61 |
@Override |
| 62 |
protected boolean doInvoke(DwcaTaxExportState state){
|
|
| 62 |
protected void doInvoke(DwcaTaxExportState state){
|
|
| 63 | 63 |
DwcaTaxExportConfigurator config = state.getConfig(); |
| 64 | 64 |
TransactionStatus txStatus = startTransaction(true); |
| 65 | 65 |
|
| ... | ... | |
| 109 | 109 |
} |
| 110 | 110 |
|
| 111 | 111 |
commitTransaction(txStatus); |
| 112 |
return true;
|
|
| 112 |
return; |
|
| 113 | 113 |
} |
| 114 | 114 |
|
| 115 | 115 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaMetaDataExport.java | ||
|---|---|---|
| 47 | 47 |
* @param filename |
| 48 | 48 |
*/ |
| 49 | 49 |
@Override |
| 50 |
protected boolean doInvoke(DwcaTaxExportState state){
|
|
| 50 |
protected void doInvoke(DwcaTaxExportState state){
|
|
| 51 | 51 |
DwcaTaxExportConfigurator config = state.getConfig(); |
| 52 | 52 |
|
| 53 | 53 |
DwcaMetaDataRecord metaDataRecord = new DwcaMetaDataRecord(! IS_CORE, fileName, null); |
| ... | ... | |
| 97 | 97 |
closeWriter(writer, state); |
| 98 | 98 |
} |
| 99 | 99 |
|
| 100 |
return true;
|
|
| 100 |
return; |
|
| 101 | 101 |
} |
| 102 | 102 |
|
| 103 | 103 |
private void writeMetaDataRecord(XMLStreamWriter writer, |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaReferenceExport.java | ||
|---|---|---|
| 54 | 54 |
* @param filename |
| 55 | 55 |
*/ |
| 56 | 56 |
@Override |
| 57 |
protected boolean doInvoke(DwcaTaxExportState state){
|
|
| 57 |
protected void doInvoke(DwcaTaxExportState state){
|
|
| 58 | 58 |
DwcaTaxExportConfigurator config = state.getConfig(); |
| 59 | 59 |
TransactionStatus txStatus = startTransaction(true); |
| 60 | 60 |
|
| ... | ... | |
| 100 | 100 |
closeWriter(writer, state); |
| 101 | 101 |
} |
| 102 | 102 |
commitTransaction(txStatus); |
| 103 |
return true;
|
|
| 103 |
return; |
|
| 104 | 104 |
} |
| 105 | 105 |
|
| 106 | 106 |
private void handleReference(DwcaReferenceRecord record, Reference<?> reference, Taxon taxon) {
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaResourceRelationExport.java | ||
|---|---|---|
| 68 | 68 |
* @param filename |
| 69 | 69 |
*/ |
| 70 | 70 |
@Override |
| 71 |
protected boolean doInvoke(DwcaTaxExportState state){
|
|
| 71 |
protected void doInvoke(DwcaTaxExportState state){
|
|
| 72 | 72 |
DwcaTaxExportConfigurator config = state.getConfig(); |
| 73 | 73 |
TransactionStatus txStatus = startTransaction(true); |
| 74 | 74 |
|
| ... | ... | |
| 169 | 169 |
closeWriter(writer, state); |
| 170 | 170 |
} |
| 171 | 171 |
commitTransaction(txStatus); |
| 172 |
return true;
|
|
| 172 |
return; |
|
| 173 | 173 |
} |
| 174 | 174 |
|
| 175 | 175 |
private void handleRelationship(DwcaResourceRelationRecord record, IdentifiableEntity<?> subject, IdentifiableEntity<?> object, |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxExport.java | ||
|---|---|---|
| 68 | 68 |
* @param filename |
| 69 | 69 |
*/ |
| 70 | 70 |
@Override |
| 71 |
protected boolean doInvoke(DwcaTaxExportState state){
|
|
| 71 |
protected void doInvoke(DwcaTaxExportState state){
|
|
| 72 | 72 |
DwcaTaxExportConfigurator config = state.getConfig(); |
| 73 | 73 |
TransactionStatus txStatus = startTransaction(true); |
| 74 | 74 |
|
| ... | ... | |
| 120 | 120 |
closeWriter(writer, state); |
| 121 | 121 |
} |
| 122 | 122 |
commitTransaction(txStatus); |
| 123 |
return true;
|
|
| 123 |
return; |
|
| 124 | 124 |
|
| 125 | 125 |
} |
| 126 | 126 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTypesExport.java | ||
|---|---|---|
| 68 | 68 |
* @param filename |
| 69 | 69 |
*/ |
| 70 | 70 |
@Override |
| 71 |
protected boolean doInvoke(DwcaTaxExportState state){
|
|
| 71 |
protected void doInvoke(DwcaTaxExportState state){
|
|
| 72 | 72 |
DwcaTaxExportConfigurator config = state.getConfig(); |
| 73 | 73 |
TransactionStatus txStatus = startTransaction(true); |
| 74 | 74 |
|
| ... | ... | |
| 128 | 128 |
closeWriter(writer, state); |
| 129 | 129 |
} |
| 130 | 130 |
commitTransaction(txStatus); |
| 131 |
return true;
|
|
| 131 |
return; |
|
| 132 | 132 |
} |
| 133 | 133 |
|
| 134 | 134 |
/** |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaVernacularExport.java | ||
|---|---|---|
| 62 | 62 |
* @param filename |
| 63 | 63 |
*/ |
| 64 | 64 |
@Override |
| 65 |
protected boolean doInvoke(DwcaTaxExportState state){
|
|
| 65 |
protected void doInvoke(DwcaTaxExportState state){
|
|
| 66 | 66 |
DwcaTaxExportConfigurator config = state.getConfig(); |
| 67 | 67 |
TransactionStatus txStatus = startTransaction(true); |
| 68 | 68 |
|
| ... | ... | |
| 110 | 110 |
closeWriter(writer, state); |
| 111 | 111 |
} |
| 112 | 112 |
commitTransaction(txStatus); |
| 113 |
return true;
|
|
| 113 |
return; |
|
| 114 | 114 |
} |
| 115 | 115 |
|
| 116 | 116 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaZipExport.java | ||
|---|---|---|
| 36 | 36 |
* @param filename |
| 37 | 37 |
*/ |
| 38 | 38 |
@Override |
| 39 |
protected boolean doInvoke(DwcaTaxExportState state){
|
|
| 39 |
protected void doInvoke(DwcaTaxExportState state){
|
|
| 40 | 40 |
if (state.isZip()){
|
| 41 | 41 |
try {
|
| 42 | 42 |
state.closeZip(); |
| ... | ... | |
| 96 | 96 |
// } |
| 97 | 97 |
|
| 98 | 98 |
|
| 99 |
return true;
|
|
| 99 |
return; |
|
| 100 | 100 |
} |
| 101 | 101 |
|
| 102 | 102 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/common/ExcelImporterBase.java | ||
|---|---|---|
| 46 | 46 |
* @param stores (not used) |
| 47 | 47 |
*/ |
| 48 | 48 |
@Override |
| 49 |
protected boolean doInvoke(STATE state){
|
|
| 49 |
protected void doInvoke(STATE state){
|
|
| 50 | 50 |
|
| 51 |
boolean success = true; |
|
| 52 |
|
|
| 53 |
logger.debug("Importing excel data");
|
|
| 51 |
logger.debug("Importing excel data");
|
|
| 54 | 52 |
|
| 55 | 53 |
configurator = state.getConfig(); |
| 56 | 54 |
|
| 57 | 55 |
NomenclaturalCode nc = getConfigurator().getNomenclaturalCode(); |
| 58 | 56 |
if (nc == null && needsNomenclaturalCode()) {
|
| 59 | 57 |
logger.error("Nomenclatural code could not be determined. Skip invoke.");
|
| 60 |
return false; |
|
| 58 |
state.setUnsuccessfull(); |
|
| 59 |
return; |
|
| 61 | 60 |
} |
| 62 | 61 |
// read and save all rows of the excel worksheet |
| 63 | 62 |
URI source = state.getConfig().getSource(); |
| ... | ... | |
| 68 | 67 |
String message = "File not found: " + source; |
| 69 | 68 |
warnProgress(state, message, e); |
| 70 | 69 |
logger.error(message); |
| 71 |
return false; |
|
| 70 |
state.setUnsuccessfull(); |
|
| 71 |
return; |
|
| 72 | 72 |
} |
| 73 | 73 |
|
| 74 |
success &= handleRecordList(state, source); |
|
| 75 |
|
|
| 74 |
handleRecordList(state, source); |
|
| 76 | 75 |
logger.debug("End excel data import");
|
| 77 |
|
|
| 78 |
|
|
| 79 |
return success; |
|
| 76 |
return; |
|
| 80 | 77 |
} |
| 81 | 78 |
|
| 82 | 79 |
protected boolean needsNomenclaturalCode() {
|
| ... | ... | |
| 89 | 86 |
* @param source |
| 90 | 87 |
* @return |
| 91 | 88 |
*/ |
| 92 |
private boolean handleRecordList(STATE state, URI source) {
|
|
| 93 |
boolean success = true; |
|
| 89 |
private void handleRecordList(STATE state, URI source) {
|
|
| 94 | 90 |
Integer startingLine = 2; |
| 95 | 91 |
if (recordList != null) {
|
| 96 | 92 |
HashMap<String,String> record = null; |
| ... | ... | |
| 101 | 97 |
state.setCurrentLine(startingLine); |
| 102 | 98 |
for (int i = 0; i < recordList.size(); i++) {
|
| 103 | 99 |
record = recordList.get(i); |
| 104 |
success &= analyzeRecord(record, state);
|
|
| 100 |
analyzeRecord(record, state); |
|
| 105 | 101 |
try {
|
| 106 |
success &= firstPass(state);
|
|
| 102 |
firstPass(state); |
|
| 107 | 103 |
} catch (Exception e) {
|
| 108 | 104 |
e.printStackTrace(); |
| 109 | 105 |
}finally{
|
| ... | ... | |
| 114 | 110 |
state.setCurrentLine(startingLine); |
| 115 | 111 |
for (int i = 0; i < recordList.size(); i++) {
|
| 116 | 112 |
record = recordList.get(i); |
| 117 |
success &= analyzeRecord(record, state);
|
|
| 118 |
success &= secondPass(state);
|
|
| 113 |
analyzeRecord(record, state); |
|
| 114 |
secondPass(state); |
|
| 119 | 115 |
state.incCurrentLine(); |
| 120 | 116 |
} |
| 121 | 117 |
|
| ... | ... | |
| 123 | 119 |
}else{
|
| 124 | 120 |
logger.warn("No records found in " + source);
|
| 125 | 121 |
} |
| 126 |
return success;
|
|
| 122 |
return; |
|
| 127 | 123 |
} |
| 128 | 124 |
|
| 129 | 125 |
/** |
| ... | ... | |
| 147 | 143 |
* @param record |
| 148 | 144 |
* @return |
| 149 | 145 |
*/ |
| 150 |
protected abstract boolean analyzeRecord(HashMap<String,String> record, STATE state);
|
|
| 146 |
protected abstract void analyzeRecord(HashMap<String,String> record, STATE state);
|
|
| 151 | 147 |
|
| 152 |
protected abstract boolean firstPass(STATE state);
|
|
| 153 |
protected abstract boolean secondPass(STATE state);
|
|
| 148 |
protected abstract void firstPass(STATE state);
|
|
| 149 |
protected abstract void secondPass(STATE state);
|
|
| 154 | 150 |
|
| 155 | 151 |
|
| 156 | 152 |
public ExcelImportConfiguratorBase getConfigurator() {
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/common/ExcelTaxonOrSpecimenImportBase.java | ||
|---|---|---|
| 38 | 38 |
|
| 39 | 39 |
|
| 40 | 40 |
protected static final String CDM_UUID_COLUMN = "(?i)(CdmUuid)"; |
| 41 |
|
|
| 41 |
protected static final String IGNORE_COLUMN = "(?i)(Ignore|Not)"; |
|
| 42 |
|
|
| 42 | 43 |
|
| 43 | 44 |
protected static final String RANK_COLUMN = "(?i)(Rank)"; |
| 44 | 45 |
protected static final String FULL_NAME_COLUMN = "(?i)(FullName)"; |
| ... | ... | |
| 48 | 49 |
protected static final String INFRASPECIFIC_EPITHET_COLUMN = "(?i)(InfraSpecificEpi(thet)?)"; |
| 49 | 50 |
|
| 50 | 51 |
@Override |
| 51 |
protected boolean analyzeRecord(HashMap<String, String> record, STATE state) {
|
|
| 52 |
boolean success = true; |
|
| 53 |
Set<String> keys = record.keySet(); |
|
| 52 |
protected void analyzeRecord(HashMap<String, String> record, STATE state) {
|
|
| 53 |
Set<String> keys = record.keySet(); |
|
| 54 | 54 |
|
| 55 | 55 |
ROW row = createDataHolderRow(); |
| 56 | 56 |
state.setCurrentRow(row); |
| ... | ... | |
| 61 | 61 |
continue; |
| 62 | 62 |
} |
| 63 | 63 |
if (isBaseColumn(keyValue)){
|
| 64 |
success &= handleBaseColumn(keyValue, row);
|
|
| 64 |
handleBaseColumn(keyValue, row); |
|
| 65 | 65 |
}else{
|
| 66 |
success &= analyzeSingleValue(keyValue, state);
|
|
| 66 |
analyzeSingleValue(keyValue, state); |
|
| 67 | 67 |
} |
| 68 | 68 |
} |
| 69 |
return success;
|
|
| 69 |
return; |
|
| 70 | 70 |
} |
| 71 | 71 |
|
| 72 | 72 |
protected abstract ROW createDataHolderRow(); |
| ... | ... | |
| 77 | 77 |
* @param state |
| 78 | 78 |
* @return |
| 79 | 79 |
*/ |
| 80 |
protected abstract boolean analyzeSingleValue(KeyValue keyValue, STATE state);
|
|
| 80 |
protected abstract void analyzeSingleValue(KeyValue keyValue, STATE state);
|
|
| 81 | 81 |
|
| 82 | 82 |
/** |
| 83 | 83 |
* DataHolder class for all key and value information for a cell. |
| ... | ... | |
| 111 | 111 |
Author("RefAuthor"),
|
| 112 | 112 |
Title("RefTitle"),
|
| 113 | 113 |
Year("RefYear"),
|
| 114 |
RefExtension("RefExt(ension)?"),
|
|
| 114 | 115 |
Language("Lang") //strictly not a reference, so some refactoring/renaming is needed
|
| 115 | 116 |
; |
| 116 | 117 |
|
| ... | ... | |
| 241 | 242 |
String key = keyValue.key; |
| 242 | 243 |
if (key.matches(CDM_UUID_COLUMN)){
|
| 243 | 244 |
return true; |
| 245 |
} else if(keyValue.key.matches(IGNORE_COLUMN)) {
|
|
| 246 |
logger.debug("Ignored column" + keyValue.originalKey);
|
|
| 247 |
return true; |
|
| 244 | 248 |
} |
| 245 | 249 |
return false; |
| 246 | 250 |
} |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/distribution/DistributionImport.java | ||
|---|---|---|
| 70 | 70 |
Map<Taxon, TaxonDescription> myDescriptions = new HashMap<Taxon, TaxonDescription>(); |
| 71 | 71 |
|
| 72 | 72 |
@Override |
| 73 |
protected boolean doInvoke(ExcelImportState<ExcelImportConfiguratorBase, ExcelRowBase> state) {
|
|
| 73 |
protected void doInvoke(ExcelImportState<ExcelImportConfiguratorBase, ExcelRowBase> state) {
|
|
| 74 | 74 |
|
| 75 | 75 |
if (logger.isDebugEnabled()) { logger.debug("Importing distribution data"); }
|
| 76 | 76 |
|
| ... | ... | |
| 83 | 83 |
String message = "File not found: " + source; |
| 84 | 84 |
warnProgress(state, message, e); |
| 85 | 85 |
logger.error(message); |
| 86 |
return false; |
|
| 86 |
state.setUnsuccessfull(); |
|
| 87 |
return; |
|
| 87 | 88 |
} |
| 88 | 89 |
if (recordList != null) {
|
| 89 | 90 |
HashMap<String,String> record = null; |
| ... | ... | |
| 104 | 105 |
e.printStackTrace(); |
| 105 | 106 |
} |
| 106 | 107 |
|
| 107 |
return true;
|
|
| 108 |
return; |
|
| 108 | 109 |
} |
| 109 | 110 |
|
| 110 | 111 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImport.java | ||
|---|---|---|
| 27 | 27 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 28 | 28 |
import eu.etaxonomy.cdm.io.excel.common.ExcelRowBase.SourceDataHolder; |
| 29 | 29 |
import eu.etaxonomy.cdm.model.agent.Team; |
| 30 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
|
| 30 | 31 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 31 | 32 |
import eu.etaxonomy.cdm.model.common.DescriptionElementSource; |
| 33 |
import eu.etaxonomy.cdm.model.common.Extension; |
|
| 34 |
import eu.etaxonomy.cdm.model.common.ExtensionType; |
|
| 32 | 35 |
import eu.etaxonomy.cdm.model.common.Language; |
| 33 | 36 |
import eu.etaxonomy.cdm.model.common.TimePeriod; |
| 34 | 37 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
| ... | ... | |
| 68 | 71 |
|
| 69 | 72 |
public static Set<String> validMarkers = new HashSet<String>(Arrays.asList(new String[]{"", "valid", "accepted", "a", "v", "t"}));
|
| 70 | 73 |
public static Set<String> synonymMarkers = new HashSet<String>(Arrays.asList(new String[]{"", "invalid", "synonym", "s", "i"}));
|
| 71 |
|
|
| 74 |
public static final UUID uuidRefExtension = UUID.fromString("a46533df-7a78-448f-9b80-36d087fbdf2a");
|
|
| 72 | 75 |
|
| 73 | 76 |
/* (non-Javadoc) |
| 74 | 77 |
* @see eu.etaxonomy.cdm.io.excel.common.ExcelTaxonOrSpecimenImportBase#analyzeSingleValue(eu.etaxonomy.cdm.io.excel.common.ExcelTaxonOrSpecimenImportBase.KeyValue, eu.etaxonomy.cdm.io.excel.common.ExcelImportState) |
| 75 | 78 |
*/ |
| 76 | 79 |
@Override |
| 77 |
protected boolean analyzeSingleValue(KeyValue keyValue, TaxonExcelImportState state) {
|
|
| 78 |
boolean success = true; |
|
| 80 |
protected void analyzeSingleValue(KeyValue keyValue, TaxonExcelImportState state) {
|
|
| 79 | 81 |
|
| 80 | 82 |
NormalExplicitRow normalExplicitRow = state.getCurrentRow(); |
| 81 | 83 |
String key = keyValue.key; |
| ... | ... | |
| 124 | 126 |
}else{
|
| 125 | 127 |
String message = "Unexpected column header " + key; |
| 126 | 128 |
fireWarningEvent(message, state, 10); |
| 127 |
success = false;
|
|
| 129 |
state.setUnsuccessfull();
|
|
| 128 | 130 |
logger.error(message); |
| 129 | 131 |
} |
| 130 | 132 |
} |
| 131 |
return success;
|
|
| 133 |
return; |
|
| 132 | 134 |
} |
| 133 | 135 |
|
| 134 | 136 |
|
| 135 | 137 |
/** |
| 136 |
* Stores taxa records in DB
|
|
| 138 |
* Create base taxa and add all information attached to it's name.
|
|
| 137 | 139 |
*/ |
| 138 | 140 |
@Override |
| 139 |
protected boolean firstPass(TaxonExcelImportState state) {
|
|
| 140 |
boolean success = true; |
|
| 141 |
protected void firstPass(TaxonExcelImportState state) {
|
|
| 142 |
|
|
| 143 |
// if (1==1){
|
|
| 144 |
// return true; |
|
| 145 |
// } |
|
| 146 |
// System.out.println("FP:" + state.getCurrentLine());
|
|
| 141 | 147 |
Rank rank = null; |
| 142 | 148 |
NormalExplicitRow taxonDataHolder = state.getCurrentRow(); |
| 143 | 149 |
|
| ... | ... | |
| 161 | 167 |
try {
|
| 162 | 168 |
rank = Rank.getRankByEnglishName(rankStr, state.getConfig().getNomenclaturalCode(), false); |
| 163 | 169 |
} catch (UnknownCdmTypeException e) {
|
| 164 |
success = false;
|
|
| 170 |
state.setUnsuccessfull();
|
|
| 165 | 171 |
logger.error(rankStr + " is not a valid rank."); |
| 166 | 172 |
} |
| 167 | 173 |
} |
| ... | ... | |
| 169 | 175 |
//taxon |
| 170 | 176 |
taxonBase = createTaxon(state, rank, taxonNameStr, authorStr, nameStatus); |
| 171 | 177 |
}else{
|
| 172 |
return true;
|
|
| 178 |
return; |
|
| 173 | 179 |
} |
| 174 | 180 |
} |
| 175 | 181 |
if (taxonBase == null){
|
| 176 | 182 |
String message = "Taxon could not be created. Record will not be handled"; |
| 177 | 183 |
fireWarningEvent(message, "Record: " + state.getCurrentLine(), 6); |
| 178 | 184 |
logger.warn(message); |
| 179 |
return false; |
|
| 185 |
state.setUnsuccessfull(); |
|
| 186 |
return; |
|
| 180 | 187 |
} |
| 181 | 188 |
|
| 182 | 189 |
//protologue |
| ... | ... | |
| 190 | 197 |
} catch (URISyntaxException e) {
|
| 191 | 198 |
String warning = "URISyntaxException when trying to convert to URI: " + protologue; |
| 192 | 199 |
logger.error(warning); |
| 200 |
state.setUnsuccessfull(); |
|
| 193 | 201 |
} |
| 194 | 202 |
} |
| 195 |
|
|
| 196 |
//media |
|
| 197 |
for (String imageUrl : taxonDataHolder.getImages()){
|
|
| 198 |
//TODO |
|
| 199 |
Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
|
| 200 |
TaxonDescription td = taxon.getImageGallery(true); |
|
| 201 |
DescriptionElementBase mediaHolder; |
|
| 202 |
if (td.getElements().size() != 0){
|
|
| 203 |
mediaHolder = td.getElements().iterator().next(); |
|
| 204 |
}else{
|
|
| 205 |
mediaHolder = TextData.NewInstance(Feature.IMAGE()); |
|
| 206 |
td.addElement(mediaHolder); |
|
| 207 |
} |
|
| 208 |
try {
|
|
| 209 |
Media media = getImageMedia(imageUrl, true); |
|
| 210 |
mediaHolder.addMedia(media); |
|
| 211 |
} catch (MalformedURLException e) {
|
|
| 212 |
logger.warn("Can't add media: " + e.getMessage());
|
|
| 213 |
} |
|
| 214 |
} |
|
| 215 |
|
|
| 216 |
//tdwg label |
|
| 217 |
for (String tdwg : taxonDataHolder.getDistributions()){
|
|
| 218 |
//TODO |
|
| 219 |
Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
|
| 220 |
TaxonDescription td = this.getTaxonDescription(taxon, false, true); |
|
| 221 |
NamedArea area = TdwgArea.getAreaByTdwgAbbreviation(tdwg); |
|
| 222 |
if (area == null){
|
|
| 223 |
area = TdwgArea.getAreaByTdwgLabel(tdwg); |
|
| 224 |
} |
|
| 225 |
if (area != null){
|
|
| 226 |
Distribution distribution = Distribution.NewInstance(area, PresenceTerm.PRESENT()); |
|
| 227 |
td.addElement(distribution); |
|
| 228 |
}else{
|
|
| 229 |
String message = "TDWG area could not be recognized: " + tdwg; |
|
| 230 |
logger.warn(message); |
|
| 231 |
} |
|
| 232 |
|
|
| 233 |
} |
|
| 234 |
|
|
| 235 |
|
|
| 236 | 203 |
|
| 237 | 204 |
state.putTaxon(id, taxonBase); |
| 238 | 205 |
getTaxonService().save(taxonBase); |
Also available in: Unified diff
last updates for Taxon Excel Import and moving all success variables to state