Revision 993072c0
Added by Cherian Mathew about 10 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/AlgaTerraActivator.java | ||
|---|---|---|
| 13 | 13 |
|
| 14 | 14 |
import org.apache.log4j.Logger; |
| 15 | 15 |
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| 16 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
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import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 17 | 17 |
import eu.etaxonomy.cdm.api.service.ITermService; |
| 18 | 18 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 19 | 19 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| ... | ... | |
| 183 | 183 |
bmImport.invoke(config); |
| 184 | 184 |
|
| 185 | 185 |
if (doFacts && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT) || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ) ){
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| 186 |
ICdmApplicationDefaultConfiguration app = bmImport.getCdmAppController();
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ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
|
| 187 | 187 |
|
| 188 | 188 |
//make feature tree |
| 189 | 189 |
makeTaxonFeatureTree(config, app); |
| ... | ... | |
| 203 | 203 |
* @param config |
| 204 | 204 |
* @param app |
| 205 | 205 |
*/ |
| 206 |
private void makeTaxonFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationDefaultConfiguration app) {
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| 206 |
private void makeTaxonFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationConfiguration app) {
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| 207 | 207 |
FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList); |
| 208 | 208 |
tree.setTitleCache("AlgaTerra Taxon Feature Tree", true);
|
| 209 | 209 |
|
| ... | ... | |
| 236 | 236 |
* @param app |
| 237 | 237 |
* @param tree |
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*/ |
| 239 |
private void makeSpecimenFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationDefaultConfiguration app) {
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| 239 |
private void makeSpecimenFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationConfiguration app) {
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ITermService termService = app.getTermService(); |
| 241 | 241 |
FeatureTree specimenTree = FeatureTree.NewInstance(specimenFeatureTreeUuid); |
| 242 | 242 |
// FeatureTree specimenTree = TreeCreator.flatTree(specimenFeatureTreeUuid, config.getFeatureMap(), featureKeyList); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/CampanulaceaeActivator.java | ||
|---|---|---|
| 13 | 13 |
|
| 14 | 14 |
import org.apache.log4j.Logger; |
| 15 | 15 |
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import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
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import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 17 | 17 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 18 | 18 |
import eu.etaxonomy.cdm.app.berlinModelImport.TreeCreator; |
| 19 | 19 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| ... | ... | |
| 173 | 173 |
success &= bmImport.invoke(bmImportConfigurator); |
| 174 | 174 |
|
| 175 | 175 |
if (doFacts && (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT) || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ) ){
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| 176 |
ICdmApplicationDefaultConfiguration app = bmImport.getCdmAppController();
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ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
|
| 177 | 177 |
|
| 178 | 178 |
//make feature tree |
| 179 | 179 |
FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/EuroMedActivator.java | ||
|---|---|---|
| 13 | 13 |
|
| 14 | 14 |
import org.apache.log4j.Logger; |
| 15 | 15 |
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import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
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import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 17 | 17 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 18 | 18 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 19 | 19 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| ... | ... | |
| 229 | 229 |
bmImport.invoke(config); |
| 230 | 230 |
|
| 231 | 231 |
if (doFacts && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT) || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ) ){
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| 232 |
ICdmApplicationDefaultConfiguration app = bmImport.getCdmAppController();
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ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
|
| 233 | 233 |
|
| 234 | 234 |
//make feature tree |
| 235 | 235 |
FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/IldisActivator.java | ||
|---|---|---|
| 13 | 13 |
|
| 14 | 14 |
import org.apache.log4j.Logger; |
| 15 | 15 |
|
| 16 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
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import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 17 | 17 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 18 | 18 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 19 | 19 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| ... | ... | |
| 155 | 155 |
success &= bmImport.invoke(bmImportConfigurator); |
| 156 | 156 |
|
| 157 | 157 |
if (doFacts && (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT) || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ) ){
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ICdmApplicationDefaultConfiguration app = bmImport.getCdmAppController();
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ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
|
| 159 | 159 |
|
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//make feature tree |
| 161 | 161 |
FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/MTMooseActivator.java | ||
|---|---|---|
| 13 | 13 |
|
| 14 | 14 |
import org.apache.log4j.Logger; |
| 15 | 15 |
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import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
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import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 17 | 17 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 18 | 18 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 19 | 19 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| ... | ... | |
| 139 | 139 |
bmImport.invoke(bmImportConfigurator); |
| 140 | 140 |
|
| 141 | 141 |
if (doFacts && (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT) || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ) ){
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| 142 |
ICdmApplicationDefaultConfiguration app = bmImport.getCdmAppController();
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ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
|
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|
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//make feature tree |
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FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/MTStandardlisteActivator.java | ||
|---|---|---|
| 13 | 13 |
|
| 14 | 14 |
import org.apache.log4j.Logger; |
| 15 | 15 |
|
| 16 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
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| 16 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 17 | 17 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 18 | 18 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 19 | 19 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| ... | ... | |
| 150 | 150 |
bmImport.invoke(config); |
| 151 | 151 |
|
| 152 | 152 |
if (doFacts && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT) || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ) ){
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ICdmApplicationDefaultConfiguration app = bmImport.getCdmAppController();
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ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
|
| 154 | 154 |
|
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//make feature tree |
| 156 | 156 |
FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/CaryoActivator.java | ||
|---|---|---|
| 13 | 13 |
|
| 14 | 14 |
import org.apache.log4j.Logger; |
| 15 | 15 |
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| 16 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
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| 16 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 17 | 17 |
import eu.etaxonomy.cdm.app.berlinModelImport.SourceBase; |
| 18 | 18 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 19 | 19 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| ... | ... | |
| 82 | 82 |
|
| 83 | 83 |
//deduplicate |
| 84 | 84 |
if (doDeduplicate){
|
| 85 |
ICdmApplicationDefaultConfiguration app = myImport.getCdmAppController();
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| 85 |
ICdmApplicationConfiguration app = myImport.getCdmAppController(); |
|
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int count = app.getAgentService().deduplicate(Person.class, null, null); |
| 87 | 87 |
logger.warn("Deduplicated " + count + " persons.");
|
| 88 | 88 |
// count = app.getAgentService().deduplicate(Team.class, null, null); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java | ||
|---|---|---|
| 88 | 88 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 89 | 89 |
String cdmServer = "127.0.0.1"; |
| 90 | 90 |
String cdmDB = "dwca"; |
| 91 |
String cdmUserName = "root";
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String cdmUserName = "edit";
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return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 93 | 93 |
} |
| 94 | 94 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/common/TestActivator.java | ||
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| 16 | 16 |
import org.springframework.core.io.ClassPathResource; |
| 17 | 17 |
import org.springframework.transaction.TransactionStatus; |
| 18 | 18 |
|
| 19 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
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| 19 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 20 | 20 |
import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor; |
| 21 | 21 |
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor; |
| 22 | 22 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| ... | ... | |
| 64 | 64 |
|
| 65 | 65 |
ICdmDataSource destination = cdmDestination; |
| 66 | 66 |
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CdmApplicationDefaultController app;
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CdmApplicationController app; |
|
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|
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// applicationEventMulticaster |
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// app = CdmIoApplicationController.NewInstance(destination, dbSchemaValidation); |
| ... | ... | |
| 75 | 75 |
// ApplicationListener<?> listener = new AppImportApplicationListener(); |
| 76 | 76 |
// List<ApplicationListener> listeners = new ArrayList<ApplicationListener>(); |
| 77 | 77 |
// listeners.add(listener); |
| 78 |
// app = CdmApplicationDefaultController.NewInstance(resource, destination, dbSchemaValidation, false, progressMonitor, listeners);
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app = CdmApplicationDefaultController.NewInstance(resource, destination, dbSchemaValidation, false, progressMonitor);
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// app = CdmApplicationController.NewInstance(resource, destination, dbSchemaValidation, false, progressMonitor, listeners); |
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app = CdmApplicationController.NewInstance(resource, destination, dbSchemaValidation, false, progressMonitor); |
|
| 80 | 80 |
|
| 81 | 81 |
|
| 82 | 82 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/cyprus/CyprusActivator.java | ||
|---|---|---|
| 15 | 15 |
|
| 16 | 16 |
import org.apache.log4j.Logger; |
| 17 | 17 |
|
| 18 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
|
|
| 18 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 19 | 19 |
import eu.etaxonomy.cdm.api.service.ITermService; |
| 20 | 20 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 21 | 21 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| ... | ... | |
| 99 | 99 |
|
| 100 | 100 |
//deduplicate |
| 101 | 101 |
if (doDeduplicate){
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ICdmApplicationDefaultConfiguration app = myImport.getCdmAppController();
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| 102 |
ICdmApplicationConfiguration app = myImport.getCdmAppController(); |
|
| 103 | 103 |
int count = app.getAgentService().deduplicate(Person.class, null, null); |
| 104 | 104 |
logger.warn("Deduplicated " + count + " persons.");
|
| 105 | 105 |
// count = app.getAgentService().deduplicate(Team.class, null, null); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/dwca/DwcaImportActivator.java | ||
|---|---|---|
| 14 | 14 |
|
| 15 | 15 |
import org.apache.log4j.Logger; |
| 16 | 16 |
|
| 17 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
|
|
| 17 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 18 | 18 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 19 | 19 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 20 | 20 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| ... | ... | |
| 122 | 122 |
|
| 123 | 123 |
//deduplicate |
| 124 | 124 |
if (doDeduplicate){
|
| 125 |
ICdmApplicationDefaultConfiguration app = myImport.getCdmAppController();
|
|
| 125 |
ICdmApplicationConfiguration app = myImport.getCdmAppController(); |
|
| 126 | 126 |
int count = app.getAgentService().deduplicate(Person.class, null, null); |
| 127 | 127 |
logger.warn("Deduplicated " + count + " persons.");
|
| 128 | 128 |
// count = app.getAgentService().deduplicate(Team.class, null, null); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/globis/GlobisActivator.java | ||
|---|---|---|
| 14 | 14 |
|
| 15 | 15 |
import org.apache.log4j.Logger; |
| 16 | 16 |
|
| 17 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
|
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| 17 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 18 | 18 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 19 | 19 |
import eu.etaxonomy.cdm.app.common.CdmImportSources; |
| 20 | 20 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| ... | ... | |
| 131 | 131 |
globisImport.invoke(config); |
| 132 | 132 |
|
| 133 | 133 |
if (config.getCheck().equals(CHECK.CHECK_AND_IMPORT) || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ){
|
| 134 |
ICdmApplicationDefaultConfiguration app = globisImport.getCdmAppController();
|
|
| 134 |
ICdmApplicationConfiguration app = globisImport.getCdmAppController(); |
|
| 135 | 135 |
ISourceable obj = app.getCommonService().getSourcedObjectByIdInSource(ZoologicalName.class, "1000027", null); |
| 136 | 136 |
logger.info(obj); |
| 137 | 137 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/i4life/col/ColDwcaImportActivator.java | ||
|---|---|---|
| 14 | 14 |
|
| 15 | 15 |
import org.apache.log4j.Logger; |
| 16 | 16 |
|
| 17 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
|
|
| 17 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 18 | 18 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 19 | 19 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 20 | 20 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| ... | ... | |
| 54 | 54 |
|
| 55 | 55 |
//check - import |
| 56 | 56 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
| 57 |
static int partitionSize = 5000;
|
|
| 57 |
static int partitionSize = 1000;
|
|
| 58 | 58 |
|
| 59 | 59 |
//config |
| 60 | 60 |
static DatasetUse datasetUse = DatasetUse.ORIGINAL_SOURCE; |
| ... | ... | |
| 110 | 110 |
|
| 111 | 111 |
//deduplicate |
| 112 | 112 |
if (doDeduplicate){
|
| 113 |
ICdmApplicationDefaultConfiguration app = myImport.getCdmAppController();
|
|
| 113 |
ICdmApplicationConfiguration app = myImport.getCdmAppController(); |
|
| 114 | 114 |
int count = app.getAgentService().deduplicate(Person.class, null, null); |
| 115 | 115 |
logger.warn("Deduplicated " + count + " persons.");
|
| 116 | 116 |
// count = app.getAgentService().deduplicate(Team.class, null, null); |
| ... | ... | |
| 137 | 137 |
|
| 138 | 138 |
//CoL |
| 139 | 139 |
public static URI dwca_col_All() {
|
| 140 |
URI sourceUrl = URI.create("file:///data/dwca/xylariaceae/added.zip");
|
|
| 140 |
URI sourceUrl = URI.create("file:////Pesiimport3/col/col_20Nov2012.zip");
|
|
| 141 | 141 |
return sourceUrl; |
| 142 | 142 |
} |
| 143 | 143 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/images/AbstractImageImporter.java | ||
|---|---|---|
| 12 | 12 |
import org.apache.log4j.Logger; |
| 13 | 13 |
import org.springframework.transaction.TransactionStatus; |
| 14 | 14 |
|
| 15 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 15 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 16 | 16 |
import eu.etaxonomy.cdm.api.service.IAgentService; |
| 17 | 17 |
import eu.etaxonomy.cdm.api.service.ICommonService; |
| 18 | 18 |
import eu.etaxonomy.cdm.api.service.IDescriptionService; |
| ... | ... | |
| 31 | 31 |
public abstract class AbstractImageImporter extends CdmIoBase<ImageImportState> implements ICdmIO<ImageImportState> {
|
| 32 | 32 |
private static final Logger logger = Logger.getLogger(AbstractImageImporter.class); |
| 33 | 33 |
|
| 34 |
protected CdmApplicationDefaultController appCtr;
|
|
| 34 |
protected CdmApplicationController appCtr; |
|
| 35 | 35 |
|
| 36 |
protected CdmApplicationDefaultController cdmApp;
|
|
| 36 |
protected CdmApplicationController cdmApp; |
|
| 37 | 37 |
protected ITaxonService taxonService; |
| 38 | 38 |
protected IClassificationService classificationService; |
| 39 | 39 |
//TODO: |
| app-import/src/main/java/eu/etaxonomy/cdm/app/jaxb/JaxbExportActivator.java | ||
|---|---|---|
| 13 | 13 |
|
| 14 | 14 |
import org.apache.log4j.Logger; |
| 15 | 15 |
|
| 16 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 16 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 17 | 17 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 18 | 18 |
import eu.etaxonomy.cdm.app.util.TestDatabase; |
| 19 | 19 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| ... | ... | |
| 78 | 78 |
|
| 79 | 79 |
|
| 80 | 80 |
|
| 81 |
private CdmApplicationDefaultController initDb(ICdmDataSource db) {
|
|
| 81 |
private CdmApplicationController initDb(ICdmDataSource db) {
|
|
| 82 | 82 |
|
| 83 | 83 |
// Init source DB |
| 84 |
CdmApplicationDefaultController appCtrInit = null;
|
|
| 84 |
CdmApplicationController appCtrInit = null; |
|
| 85 | 85 |
|
| 86 | 86 |
appCtrInit = TestDatabase.initDb(db, DbSchemaValidation.VALIDATE, false); |
| 87 | 87 |
|
| ... | ... | |
| 90 | 90 |
|
| 91 | 91 |
|
| 92 | 92 |
// Load test data to DB |
| 93 |
private void loadTestData(CdmApplicationDefaultController appCtrInit) {
|
|
| 93 |
private void loadTestData(CdmApplicationController appCtrInit) {
|
|
| 94 | 94 |
TestDatabase.loadTestData("", appCtrInit);
|
| 95 | 95 |
} |
| 96 | 96 |
|
| ... | ... | |
| 104 | 104 |
ICdmDataSource source = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmSource; |
| 105 | 105 |
String file = chooseFile(args); |
| 106 | 106 |
URI uri = URI.create(file); |
| 107 |
CdmApplicationDefaultController appCtr = null;
|
|
| 107 |
CdmApplicationController appCtr = null; |
|
| 108 | 108 |
appCtr = sc.initDb(source); |
| 109 | 109 |
|
| 110 | 110 |
sc.invokeExport(source, uri); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/jaxb/JaxbImportActivator.java | ||
|---|---|---|
| 14 | 14 |
|
| 15 | 15 |
import org.apache.log4j.Logger; |
| 16 | 16 |
|
| 17 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 17 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 18 | 18 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 19 | 19 |
import eu.etaxonomy.cdm.app.util.TestDatabase; |
| 20 | 20 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| ... | ... | |
| 38 | 38 |
private static String importFileNameString = |
| 39 | 39 |
//"C:\\workspace\\cdmlib_2.2\\cdmlib-io\\src\\test\\resources\\eu\\etaxonomy\\cdm\\io\\jaxb\\export_test_app_import.xml"; |
| 40 | 40 |
// "file:/C:/export_test_app_import.xml"; |
| 41 |
"file:/C:/localCopy/Data/kr�hen/201206141338-jaxb_export-cdm.xml";
|
|
| 41 |
"file:/C:/localCopy/Data/kr?hen/201206141338-jaxb_export-cdm.xml";
|
|
| 42 | 42 |
|
| 43 | 43 |
|
| 44 | 44 |
/** NUMBER_ROWS_TO_RETRIEVE = 0 is the default case to retrieve all rows. |
| ... | ... | |
| 95 | 95 |
} |
| 96 | 96 |
|
| 97 | 97 |
|
| 98 |
private CdmApplicationDefaultController initDb(ICdmDataSource db) {
|
|
| 98 |
private CdmApplicationController initDb(ICdmDataSource db) {
|
|
| 99 | 99 |
|
| 100 | 100 |
// Init source DB |
| 101 |
CdmApplicationDefaultController appCtrInit = null;
|
|
| 101 |
CdmApplicationController appCtrInit = null; |
|
| 102 | 102 |
|
| 103 | 103 |
appCtrInit = TestDatabase.initDb(db, DbSchemaValidation.CREATE, false); |
| 104 | 104 |
|
| ... | ... | |
| 107 | 107 |
|
| 108 | 108 |
|
| 109 | 109 |
// Load test data to DB |
| 110 |
private void loadTestData(CdmApplicationDefaultController appCtrInit) {
|
|
| 110 |
private void loadTestData(CdmApplicationController appCtrInit) {
|
|
| 111 | 111 |
|
| 112 | 112 |
TestDatabase.loadTestData("", appCtrInit);
|
| 113 | 113 |
} |
| ... | ... | |
| 121 | 121 |
JaxbImportActivator jia = new JaxbImportActivator(); |
| 122 | 122 |
ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination; |
| 123 | 123 |
String file = chooseFile(args)!= null ? chooseFile(args) : importFileNameString; |
| 124 |
CdmApplicationDefaultController appCtr = null;
|
|
| 124 |
CdmApplicationController appCtr = null; |
|
| 125 | 125 |
// appCtr = jia.initDb(destination); |
| 126 | 126 |
|
| 127 | 127 |
jia.invokeImport(file, destination); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/pilotOutputHtml/SimpleDescriptionOutput.java | ||
|---|---|---|
| 115 | 115 |
|
| 116 | 116 |
SimpleDescriptionOutput sdo = new SimpleDescriptionOutput(); |
| 117 | 117 |
|
| 118 |
// CdmApplicationDefaultController appCtr = null;
|
|
| 118 |
// CdmApplicationController appCtr = null; |
|
| 119 | 119 |
// appCtr = sc.initDb(sourceDb); |
| 120 | 120 |
// sc.loadTestData(appCtr); |
| 121 | 121 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/proibiosphere/TaxonXImportLauncher.java | ||
|---|---|---|
| 121 | 121 |
log.info("End import from SpecimenData ("+ source.toString() + ")...");
|
| 122 | 122 |
|
| 123 | 123 |
// //deduplicate |
| 124 |
// ICdmApplicationDefaultConfiguration app = taxonImport.getCdmAppController();
|
|
| 124 |
// ICdmApplicationConfiguration app = taxonImport.getCdmAppController(); |
|
| 125 | 125 |
// int count = app.getAgentService().deduplicate(Person.class, null, null); |
| 126 | 126 |
// logger.warn("Deduplicated " + count + " persons.");
|
| 127 | 127 |
// count = app.getReferenceService().deduplicate(Reference.class, null, null); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/references/EndNoteImportActivator.java | ||
|---|---|---|
| 5 | 5 |
|
| 6 | 6 |
import org.apache.log4j.Logger; |
| 7 | 7 |
|
| 8 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 8 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 9 | 9 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 10 | 10 |
import eu.etaxonomy.cdm.app.util.TestDatabase; |
| 11 | 11 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| ... | ... | |
| 72 | 72 |
} |
| 73 | 73 |
|
| 74 | 74 |
|
| 75 |
private CdmApplicationDefaultController initDb(ICdmDataSource db) {
|
|
| 75 |
private CdmApplicationController initDb(ICdmDataSource db) {
|
|
| 76 | 76 |
|
| 77 | 77 |
// Init source DB |
| 78 |
CdmApplicationDefaultController appCtrInit = null;
|
|
| 78 |
CdmApplicationController appCtrInit = null; |
|
| 79 | 79 |
|
| 80 | 80 |
appCtrInit = TestDatabase.initDb(db, DbSchemaValidation.VALIDATE, true); |
| 81 | 81 |
|
| ... | ... | |
| 84 | 84 |
|
| 85 | 85 |
|
| 86 | 86 |
// Load test data to DB |
| 87 |
private void loadTestData(CdmApplicationDefaultController appCtrInit) {
|
|
| 87 |
private void loadTestData(CdmApplicationController appCtrInit) {
|
|
| 88 | 88 |
|
| 89 | 89 |
TestDatabase.loadTestData("", appCtrInit);
|
| 90 | 90 |
} |
| ... | ... | |
| 98 | 98 |
EndNoteImportActivator sc = new EndNoteImportActivator(); |
| 99 | 99 |
ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination; |
| 100 | 100 |
String file = chooseFile(args)!= null ? chooseFile(args) : importFileNameString; |
| 101 |
CdmApplicationDefaultController appCtr = null;
|
|
| 101 |
CdmApplicationController appCtr = null; |
|
| 102 | 102 |
appCtr = sc.initDb(destination); |
| 103 | 103 |
//sc.loadTestData(appCtr); |
| 104 | 104 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/SDDExportActivator.java | ||
|---|---|---|
| 91 | 91 |
CdmPersistentDataSource.save(dataSourceName, dataSource); |
| 92 | 92 |
try {
|
| 93 | 93 |
loadedDataSource = CdmPersistentDataSource.NewInstance(dataSourceName); |
| 94 |
// CdmApplicationDefaultController.NewInstance(loadedDataSource, DbSchemaValidation.CREATE);
|
|
| 94 |
// CdmApplicationController.NewInstance(loadedDataSource, DbSchemaValidation.CREATE); |
|
| 95 | 95 |
NomenclaturalCode loadedCode = loadedDataSource.getNomenclaturalCode(); |
| 96 | 96 |
|
| 97 | 97 |
Assert.assertEquals(NomenclaturalCode.ICNAFP, loadedCode); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/SDDImportActivator.java | ||
|---|---|---|
| 84 | 84 |
CdmPersistentDataSource.save(dataSourceName, dataSource); |
| 85 | 85 |
try {
|
| 86 | 86 |
loadedDataSource = CdmPersistentDataSource.NewInstance(dataSourceName); |
| 87 |
// CdmApplicationDefaultController.NewInstance(loadedDataSource, DbSchemaValidation.CREATE);
|
|
| 87 |
// CdmApplicationController.NewInstance(loadedDataSource, DbSchemaValidation.CREATE); |
|
| 88 | 88 |
NomenclaturalCode loadedCode = loadedDataSource.getNomenclaturalCode(); |
| 89 | 89 |
|
| 90 | 90 |
Assert.assertEquals(NomenclaturalCode.ICNAFP, loadedCode); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/ViolaExportActivator.java | ||
|---|---|---|
| 112 | 112 |
|
| 113 | 113 |
ViolaExportActivator vea = new ViolaExportActivator(); |
| 114 | 114 |
|
| 115 |
// CdmApplicationDefaultController appCtr = null;
|
|
| 115 |
// CdmApplicationController appCtr = null; |
|
| 116 | 116 |
// appCtr = sc.initDb(sourceDb); |
| 117 | 117 |
// sc.loadTestData(appCtr); |
| 118 | 118 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SynthesysCacheActivator.java | ||
|---|---|---|
| 21 | 21 |
import org.apache.poi.hssf.usermodel.HSSFWorkbook; |
| 22 | 22 |
import org.springframework.transaction.TransactionStatus; |
| 23 | 23 |
|
| 24 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 24 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 25 | 25 |
import eu.etaxonomy.cdm.api.service.pager.Pager; |
| 26 | 26 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 27 | 27 |
import eu.etaxonomy.cdm.app.common.CdmImportSources; |
| ... | ... | |
| 137 | 137 |
public boolean invoke(){
|
| 138 | 138 |
boolean result = true; |
| 139 | 139 |
boolean withCdm = true; |
| 140 |
CdmApplicationDefaultController app = null;
|
|
| 140 |
CdmApplicationController app = null; |
|
| 141 | 141 |
TransactionStatus tx = null; |
| 142 | 142 |
|
| 143 |
app = CdmApplicationDefaultController.NewInstance(desitination, hbm2dll);
|
|
| 143 |
app = CdmApplicationController.NewInstance(desitination, hbm2dll); |
|
| 144 | 144 |
|
| 145 | 145 |
tx = app.startTransaction(); |
| 146 | 146 |
try {
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/util/TestDatabase.java | ||
|---|---|---|
| 13 | 13 |
import org.apache.log4j.Logger; |
| 14 | 14 |
import org.springframework.transaction.TransactionStatus; |
| 15 | 15 |
|
| 16 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 16 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 17 | 17 |
import eu.etaxonomy.cdm.common.AccountStore; |
| 18 | 18 |
import eu.etaxonomy.cdm.database.CdmDataSource; |
| 19 | 19 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| ... | ... | |
| 71 | 71 |
return datasource; |
| 72 | 72 |
} |
| 73 | 73 |
|
| 74 |
public static CdmApplicationDefaultController
|
|
| 74 |
public static CdmApplicationController |
|
| 75 | 75 |
initDb(ICdmDataSource db, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading) {
|
| 76 | 76 |
|
| 77 | 77 |
logger.info("Initializing database '" + db.getName() + "'");
|
| 78 | 78 |
|
| 79 |
CdmApplicationDefaultController appCtrInit = null;
|
|
| 80 |
appCtrInit = CdmApplicationDefaultController.NewInstance(db, dbSchemaValidation, omitTermLoading);
|
|
| 79 |
CdmApplicationController appCtrInit = null; |
|
| 80 |
appCtrInit = CdmApplicationController.NewInstance(db, dbSchemaValidation, omitTermLoading); |
|
| 81 | 81 |
|
| 82 | 82 |
return appCtrInit; |
| 83 | 83 |
} |
| 84 | 84 |
|
| 85 |
public static void loadTestData(String dbname, CdmApplicationDefaultController appCtr) {
|
|
| 85 |
public static void loadTestData(String dbname, CdmApplicationController appCtr) {
|
|
| 86 | 86 |
|
| 87 | 87 |
logger.info("Loading test data into " + dbname);
|
| 88 | 88 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/util/TestTransaction.java | ||
|---|---|---|
| 12 | 12 |
import org.apache.log4j.Logger; |
| 13 | 13 |
import org.springframework.transaction.TransactionStatus; |
| 14 | 14 |
|
| 15 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 15 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 16 | 16 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 17 | 17 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 18 | 18 |
import eu.etaxonomy.cdm.model.agent.AgentBase; |
| ... | ... | |
| 51 | 51 |
*/ |
| 52 | 52 |
private void modifyDisjunctObjects() {
|
| 53 | 53 |
|
| 54 |
CdmApplicationDefaultController appCtr = null;
|
|
| 54 |
CdmApplicationController appCtr = null; |
|
| 55 | 55 |
logger.info("Test modifying disjunct objects");
|
| 56 | 56 |
|
| 57 | 57 |
try {
|
| 58 |
appCtr = CdmApplicationDefaultController.NewInstance(db, DbSchemaValidation.VALIDATE, true);
|
|
| 58 |
appCtr = CdmApplicationController.NewInstance(db, DbSchemaValidation.VALIDATE, true); |
|
| 59 | 59 |
|
| 60 | 60 |
} catch (Exception e) {
|
| 61 | 61 |
logger.error("Error creating application controller");
|
| ... | ... | |
| 129 | 129 |
*/ |
| 130 | 130 |
private void modifySharedObjects() {
|
| 131 | 131 |
|
| 132 |
CdmApplicationDefaultController appCtr = null;
|
|
| 132 |
CdmApplicationController appCtr = null; |
|
| 133 | 133 |
logger.info("Test modifying shared objects");
|
| 134 | 134 |
|
| 135 | 135 |
try {
|
| 136 |
appCtr = CdmApplicationDefaultController.NewInstance(db, DbSchemaValidation.VALIDATE, true);
|
|
| 136 |
appCtr = CdmApplicationController.NewInstance(db, DbSchemaValidation.VALIDATE, true); |
|
| 137 | 137 |
|
| 138 | 138 |
} catch (Exception e) {
|
| 139 | 139 |
logger.error("Error creating application controller");
|
| ... | ... | |
| 199 | 199 |
|
| 200 | 200 |
private void checkTransactionFacets() {
|
| 201 | 201 |
|
| 202 |
CdmApplicationDefaultController appCtr = null;
|
|
| 202 |
CdmApplicationController appCtr = null; |
|
| 203 | 203 |
logger.info("Test checking transaction facets");
|
| 204 | 204 |
|
| 205 | 205 |
try {
|
| 206 |
appCtr = CdmApplicationDefaultController.NewInstance(db, DbSchemaValidation.VALIDATE, true);
|
|
| 206 |
appCtr = CdmApplicationController.NewInstance(db, DbSchemaValidation.VALIDATE, true); |
|
| 207 | 207 |
|
| 208 | 208 |
} catch (Exception e) {
|
| 209 | 209 |
logger.error("Error creating application controller");
|
| ... | ... | |
| 216 | 216 |
|
| 217 | 217 |
TransactionStatus txStatOne = appCtr.startTransaction(); |
| 218 | 218 |
appCtr.commitTransaction(txStatOne); |
| 219 |
// set CdmApplicationDefaultController = debug in log4j.properties to see the transaction properties
|
|
| 219 |
// set CdmApplicationController = debug in log4j.properties to see the transaction properties |
|
| 220 | 220 |
appCtr.close(); |
| 221 | 221 |
logger.info("End test ask session for objects");
|
| 222 | 222 |
|
| ... | ... | |
| 228 | 228 |
|
| 229 | 229 |
private void askSessionForObjects() {
|
| 230 | 230 |
|
| 231 |
CdmApplicationDefaultController appCtr = null;
|
|
| 231 |
CdmApplicationController appCtr = null; |
|
| 232 | 232 |
logger.info("Test asking session for objects");
|
| 233 | 233 |
|
| 234 | 234 |
try {
|
| 235 |
appCtr = CdmApplicationDefaultController.NewInstance(db, DbSchemaValidation.VALIDATE, true);
|
|
| 235 |
appCtr = CdmApplicationController.NewInstance(db, DbSchemaValidation.VALIDATE, true); |
|
| 236 | 236 |
|
| 237 | 237 |
} catch (Exception e) {
|
| 238 | 238 |
logger.error("Error creating application controller");
|
| ... | ... | |
| 299 | 299 |
|
| 300 | 300 |
/* Init DB */ |
| 301 | 301 |
// initDb(ICdmDataSource db, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading) |
| 302 |
CdmApplicationDefaultController appCtrInit = TestDatabase.initDb(db, DbSchemaValidation.CREATE, false);
|
|
| 302 |
CdmApplicationController appCtrInit = TestDatabase.initDb(db, DbSchemaValidation.CREATE, false); |
|
| 303 | 303 |
|
| 304 | 304 |
/* Load test data into DB */ |
| 305 | 305 |
// TestDatabase.loadTestData(dbName, appCtrInit); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/EuroMedActivator.java | ||
|---|---|---|
| 16 | 16 |
|
| 17 | 17 |
import org.apache.log4j.Logger; |
| 18 | 18 |
|
| 19 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
|
|
| 19 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 20 | 20 |
import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources; |
| 21 | 21 |
import eu.etaxonomy.cdm.app.berlinModelImport.TreeCreator; |
| 22 | 22 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| ... | ... | |
| 231 | 231 |
bmImport.invoke(config); |
| 232 | 232 |
|
| 233 | 233 |
if (doFacts && config.getCheck().equals(CHECK.CHECK_AND_IMPORT) || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ){
|
| 234 |
ICdmApplicationDefaultConfiguration app = bmImport.getCdmAppController();
|
|
| 234 |
ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
|
| 235 | 235 |
|
| 236 | 236 |
//make feature tree |
| 237 | 237 |
FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/viennaImport/ViennaActivator.java | ||
|---|---|---|
| 17 | 17 |
|
| 18 | 18 |
import org.apache.log4j.Logger; |
| 19 | 19 |
|
| 20 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 20 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 21 | 21 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 22 | 22 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 23 | 23 |
import eu.etaxonomy.cdm.common.AccountStore; |
| ... | ... | |
| 63 | 63 |
boolean result = true; |
| 64 | 64 |
boolean withCdm = false; |
| 65 | 65 |
berlinModelSource.setQuery("SELECT * FROM vienna"); // WHERE ID1 <> 1
|
| 66 |
CdmApplicationDefaultController app = null;
|
|
| 66 |
CdmApplicationController app = null; |
|
| 67 | 67 |
|
| 68 | 68 |
|
| 69 | 69 |
try {
|
| 70 | 70 |
if (withCdm){
|
| 71 |
app = CdmApplicationDefaultController.NewInstance(CdmDestinations.localH2());
|
|
| 71 |
app = CdmApplicationController.NewInstance(CdmDestinations.localH2()); |
|
| 72 | 72 |
}else{
|
| 73 |
//app = CdmApplicationDefaultController.NewInstance(DbSchemaValidation.VALIDATE);
|
|
| 73 |
//app = CdmApplicationController.NewInstance(DbSchemaValidation.VALIDATE); |
|
| 74 | 74 |
} |
| 75 | 75 |
} catch (Exception e1) {
|
| 76 | 76 |
e1.printStackTrace(); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/CichorieaeActivator.java | ||
|---|---|---|
| 16 | 16 |
|
| 17 | 17 |
import org.apache.log4j.Logger; |
| 18 | 18 |
|
| 19 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
|
|
| 19 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 20 | 20 |
import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources; |
| 21 | 21 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 22 | 22 |
import eu.etaxonomy.cdm.app.berlinModelImport.TreeCreator; |
| ... | ... | |
| 218 | 218 |
success &= bmImport.invoke(bmImportConfigurator); |
| 219 | 219 |
|
| 220 | 220 |
if (doFacts && (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT) || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ) ){
|
| 221 |
ICdmApplicationDefaultConfiguration app = bmImport.getCdmAppController();
|
|
| 221 |
ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
|
| 222 | 222 |
ISourceable obj = app.getCommonService().getSourcedObjectByIdInSource(ZoologicalName.class, "1000027", null); |
| 223 | 223 |
logger.info(obj); |
| 224 | 224 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/TaraxacumActivator.java | ||
|---|---|---|
| 16 | 16 |
import org.apache.log4j.Logger; |
| 17 | 17 |
import org.springframework.transaction.TransactionStatus; |
| 18 | 18 |
|
| 19 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
|
|
| 19 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 20 | 20 |
import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources; |
| 21 | 21 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 22 | 22 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| ... | ... | |
| 174 | 174 |
success &= bmImport.invoke(bmImportConfigurator); |
| 175 | 175 |
|
| 176 | 176 |
if (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT) || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ){
|
| 177 |
ICdmApplicationDefaultConfiguration app = bmImport.getCdmAppController();
|
|
| 177 |
ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
|
| 178 | 178 |
TransactionStatus tx = app.startTransaction(); |
| 179 | 179 |
//make feature tree |
| 180 | 180 |
// FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList); |
| ... | ... | |
| 193 | 193 |
} |
| 194 | 194 |
|
| 195 | 195 |
|
| 196 |
public boolean mergeIntoCichorieae(ICdmApplicationDefaultConfiguration app){
|
|
| 196 |
public boolean mergeIntoCichorieae(ICdmApplicationConfiguration app){
|
|
| 197 | 197 |
boolean success = true; |
| 198 | 198 |
// String taraxTaraxacumUuidStr = "9a7bced0-fa1a-432e-9cca-57b62219cde6"; |
| 199 | 199 |
String taraxTaraxacumUuidStr = "b86f1156-091c-494d-a9c9-c84d71058f98"; |
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraActivator.java | ||
|---|---|---|
| 14 | 14 |
|
| 15 | 15 |
import org.apache.log4j.Logger; |
| 16 | 16 |
|
| 17 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
|
|
| 17 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 18 | 18 |
import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources; |
| 19 | 19 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 20 | 20 |
import eu.etaxonomy.cdm.app.berlinModelImport.TreeCreator; |
| ... | ... | |
| 183 | 183 |
success &= bmImport.invoke(bmImportConfigurator); |
| 184 | 184 |
|
| 185 | 185 |
if (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT) || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ){
|
| 186 |
ICdmApplicationDefaultConfiguration app = bmImport.getCdmAppController();
|
|
| 186 |
ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
|
| 187 | 187 |
|
| 188 | 188 |
//parse distributions |
| 189 | 189 |
if (doDistributionParser){
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraCollectionImport.java | ||
|---|---|---|
| 23 | 23 |
import org.springframework.transaction.TransactionStatus; |
| 24 | 24 |
|
| 25 | 25 |
import au.com.bytecode.opencsv.CSVReader; |
| 26 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 26 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 27 | 27 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 28 | 28 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 29 | 29 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| ... | ... | |
| 47 | 47 |
|
| 48 | 48 |
|
| 49 | 49 |
public boolean invoke(ICdmDataSource dataSource) {
|
| 50 |
CdmApplicationDefaultController cdmApp = CdmApplicationDefaultController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
|
|
| 50 |
CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
|
|
| 51 | 51 |
|
| 52 | 52 |
//create collections |
| 53 | 53 |
TransactionStatus tx = cdmApp.startTransaction(); |
| ... | ... | |
| 66 | 66 |
* @param cdmApp |
| 67 | 67 |
* @param colletionMap |
| 68 | 68 |
*/ |
| 69 |
private void addCollectionsToSpecimen(CdmApplicationDefaultController cdmApp, Map<String, Collection> colletionMap) {
|
|
| 69 |
private void addCollectionsToSpecimen(CdmApplicationController cdmApp, Map<String, Collection> colletionMap) {
|
|
| 70 | 70 |
List<SpecimenOrObservationBase> specimens = (cdmApp.getOccurrenceService().list(DerivedUnit.class, null, null, null, null)); |
| 71 | 71 |
for (SpecimenOrObservationBase<?> specOrObservBase : specimens){
|
| 72 | 72 |
if (specOrObservBase.getRecordBasis().isPreservedSpecimen()){
|
| ... | ... | |
| 186 | 186 |
/** |
| 187 | 187 |
* @param cdmApp |
| 188 | 188 |
*/ |
| 189 |
private Map<String, Collection> createCollections(CdmApplicationDefaultController cdmApp) {
|
|
| 189 |
private Map<String, Collection> createCollections(CdmApplicationController cdmApp) {
|
|
| 190 | 190 |
Map<String, Collection> collectionMap = new HashMap<String, Collection>(); |
| 191 | 191 |
List<String[]> lines = getLines(); |
| 192 | 192 |
for (String[] line:lines){
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraDistributionParser.java | ||
|---|---|---|
| 26 | 26 |
import org.apache.log4j.Logger; |
| 27 | 27 |
import org.springframework.transaction.TransactionStatus; |
| 28 | 28 |
|
| 29 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 30 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
|
|
| 29 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 30 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 31 | 31 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 32 | 32 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 33 | 33 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| ... | ... | |
| 58 | 58 |
final static String epiSplitter = "(\\s+|\\[|\\]|\\(|\\))"; //( ' '+| '(' | ')'| '[' | ']' )
|
| 59 | 59 |
static Pattern pattern = null; |
| 60 | 60 |
|
| 61 |
protected void doDistribution(ICdmApplicationDefaultConfiguration app){
|
|
| 61 |
protected void doDistribution(ICdmApplicationConfiguration app){
|
|
| 62 | 62 |
pattern = Pattern.compile(epiSplitter); |
| 63 | 63 |
TransactionStatus txStatus = app.startTransaction(); |
| 64 | 64 |
List<TaxonBase> taxa = app.getTaxonService().list(null, null, null, null, null); |
| ... | ... | |
| 415 | 415 |
* @param args |
| 416 | 416 |
*/ |
| 417 | 417 |
public static void main(String[] args) {
|
| 418 |
CdmApplicationDefaultController app = null;
|
|
| 418 |
CdmApplicationController app = null; |
|
| 419 | 419 |
DbSchemaValidation val = DbSchemaValidation.UPDATE; |
| 420 |
app = CdmApplicationDefaultController.NewInstance(cdmDestination, val);
|
|
| 420 |
app = CdmApplicationController.NewInstance(cdmDestination, val); |
|
| 421 | 421 |
|
| 422 | 422 |
DipteraDistributionParser dipDist = new DipteraDistributionParser(); |
| 423 | 423 |
if (app != null){
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraPostImportUpdater.java | ||
|---|---|---|
| 19 | 19 |
import org.apache.log4j.Logger; |
| 20 | 20 |
import org.springframework.transaction.TransactionStatus; |
| 21 | 21 |
|
| 22 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 22 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 23 | 23 |
import eu.etaxonomy.cdm.api.service.INameService; |
| 24 | 24 |
import eu.etaxonomy.cdm.api.service.pager.Pager; |
| 25 | 25 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| ... | ... | |
| 60 | 60 |
try{
|
| 61 | 61 |
logger.warn("start updating citations");
|
| 62 | 62 |
boolean result = true; |
| 63 |
CdmApplicationDefaultController cdmApp = CdmApplicationDefaultController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
|
|
| 63 |
CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
|
|
| 64 | 64 |
Set<DescriptionElementBase> citationsToSave = new HashSet<DescriptionElementBase>(); |
| 65 | 65 |
TransactionStatus tx = cdmApp.startTransaction(); |
| 66 | 66 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/palmae/PalmaeActivator.java | ||
|---|---|---|
| 16 | 16 |
|
| 17 | 17 |
import org.apache.log4j.Logger; |
| 18 | 18 |
|
| 19 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 20 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
|
|
| 19 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 20 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 21 | 21 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 22 | 22 |
import eu.etaxonomy.cdm.app.images.ImageImportConfigurator; |
| 23 | 23 |
import eu.etaxonomy.cdm.app.tcs.TcsSources; |
| ... | ... | |
| 121 | 121 |
|
| 122 | 122 |
//make feature tree |
| 123 | 123 |
logger.info("Make feature tree");
|
| 124 |
ICdmApplicationDefaultConfiguration app = tcsImport.getCdmAppController();
|
|
| 124 |
ICdmApplicationConfiguration app = tcsImport.getCdmAppController(); |
|
| 125 | 125 |
|
| 126 | 126 |
FeatureTree tree = getFeatureTree(); |
| 127 | 127 |
app.getFeatureTreeService().saveOrUpdate(tree); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/palmae/PalmaePostImportUpdater.java | ||
|---|---|---|
| 17 | 17 |
import org.apache.log4j.Logger; |
| 18 | 18 |
import org.springframework.transaction.TransactionStatus; |
| 19 | 19 |
|
| 20 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 20 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 21 | 21 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 22 | 22 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 23 | 23 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| ... | ... | |
| 53 | 53 |
try{
|
| 54 | 54 |
int count = 0; |
| 55 | 55 |
UUID featureTreeUuid = PalmaeActivator.featureTreeUuid; |
| 56 |
CdmApplicationDefaultController cdmApp = CdmApplicationDefaultController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
|
|
| 56 |
CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
|
|
| 57 | 57 |
|
| 58 | 58 |
TransactionStatus tx = cdmApp.startTransaction(); |
| 59 | 59 |
|
| ... | ... | |
| 95 | 95 |
public boolean updateNameUsage(ICdmDataSource dataSource) {
|
| 96 | 96 |
try{
|
| 97 | 97 |
boolean result = true; |
| 98 |
CdmApplicationDefaultController cdmApp = CdmApplicationDefaultController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
|
|
| 98 |
CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
|
|
| 99 | 99 |
|
| 100 | 100 |
TransactionStatus tx = cdmApp.startTransaction(); |
| 101 | 101 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/palmae/UseImport.java | ||
|---|---|---|
| 29 | 29 |
import org.apache.poi.hssf.usermodel.HSSFWorkbook; |
| 30 | 30 |
import org.apache.poi.poifs.filesystem.POIFSFileSystem; |
| 31 | 31 |
|
| 32 |
import eu.etaxonomy.cdm.api.application.CdmApplicationDefaultController;
|
|
| 32 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 33 | 33 |
import eu.etaxonomy.cdm.api.conversation.ConversationHolder; |
| 34 | 34 |
import eu.etaxonomy.cdm.api.service.IDescriptionService; |
| 35 | 35 |
import eu.etaxonomy.cdm.api.service.IFeatureTreeService; |
| ... | ... | |
| 105 | 105 |
public boolean importFromExcelSS(String xlsPath) {
|
| 106 | 106 |
boolean success = true; |
| 107 | 107 |
|
| 108 |
CdmApplicationDefaultController applicationController = CdmApplicationDefaultController.NewInstance(dataSource());
|
|
| 108 |
CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource());
|
|
| 109 | 109 |
ConversationHolder conversation = applicationController.NewConversation(); |
| 110 | 110 |
conversation.startTransaction(); |
| 111 | 111 |
|
| ... | ... | |
| 273 | 273 |
InputStream inputStream = null; |
| 274 | 274 |
|
| 275 | 275 |
|
| 276 |
CdmApplicationDefaultController applicationController = CdmApplicationDefaultController.NewInstance(dataSource());
|
|
| 276 |
CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource());
|
|
| 277 | 277 |
ConversationHolder conversation = applicationController.NewConversation(); |
| 278 | 278 |
conversation.startTransaction(); |
| 279 | 279 |
|
| ... | ... | |
| 497 | 497 |
//String xslPathString = "C://workspace//terms.xls"; |
| 498 | 498 |
String xslPathString = "//Users//alextheys//Projects//CDM_Trunk//Palm_Use_Data_Extension//CDMLib-apps//cdmlib-apps//UseImport//src//main//resources//terms.xls"; |
| 499 | 499 |
|
| 500 |
CdmApplicationDefaultController applicationController = CdmApplicationDefaultController.NewInstance(dataSource());
|
|
| 500 |
CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource());
|
|
| 501 | 501 |
ConversationHolder conversation = applicationController.NewConversation(); |
| 502 | 502 |
conversation.startTransaction(); |
| 503 | 503 |
|
| ... | ... | |
| 707 | 707 |
|
| 708 | 708 |
private boolean setupNecessaryItems() {
|
| 709 | 709 |
boolean success = false; |
| 710 |
CdmApplicationDefaultController applicationController = CdmApplicationDefaultController.NewInstance(dataSource());
|
|
| 710 |
CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource());
|
|
| 711 | 711 |
ConversationHolder conversation = applicationController.NewConversation(); |
| 712 | 712 |
|
| 713 | 713 |
|
Also available in: Unified diff
reverting back the cdm application configuration refactoring