Revision c385a1b7
Added by Andreas Müller almost 6 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/EuroMedActivator.java | ||
|---|---|---|
| 77 | 77 |
private static final Logger logger = Logger.getLogger(EuroMedActivator.class); |
| 78 | 78 |
|
| 79 | 79 |
//database validation status (create, update, validate ...) |
| 80 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
|
|
| 80 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
|
|
| 81 | 81 |
// static final Source berlinModelSource = BerlinModelSources.euroMed_Pub2(); |
| 82 | 82 |
static final Source berlinModelSource = BerlinModelSources.euroMed_BGBM42(); |
| 83 | 83 |
// static final Source berlinModelSource = BerlinModelSources.euroMed_PESI3(); |
| 84 |
|
|
| 85 |
// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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|
| 84 |
// |
|
| 85 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
|
| 86 | 86 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_euroMed(); |
| 87 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_pesi_euromed(); |
|
| 88 | 87 |
|
| 89 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_test_euromed(); |
|
| 90 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test(); |
|
| 88 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_euromed(); |
|
| 91 | 89 |
|
| 92 | 90 |
|
| 91 |
//check - import |
|
| 92 |
static final CHECK check = CHECK.CHECK_ONLY; |
|
| 93 |
|
|
| 93 | 94 |
static final boolean includePesiExport = false; |
| 94 | 95 |
|
| 95 | 96 |
static final int sourceSecId = 7000000; //500000 |
| 96 | 97 |
static final UUID classificationUuid = UUID.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");
|
| 97 | 98 |
static final boolean useSingleClassification = true; |
| 98 |
static final String classificationName = "Euro+Med 2017";
|
|
| 99 |
static final String classificationName = "Euro+Med 2018";
|
|
| 99 | 100 |
static final UUID featureTreeUuid = UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");
|
| 100 | 101 |
static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
|
| 101 | 102 |
|
| ... | ... | |
| 104 | 105 |
|
| 105 | 106 |
static final int partitionSize = 2500; |
| 106 | 107 |
|
| 107 |
//check - import |
|
| 108 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
|
| 109 | 108 |
|
| 110 | 109 |
//editor - import |
| 111 | 110 |
static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR; |
| ... | ... | |
| 144 | 143 |
static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )"; |
| 145 | 144 |
static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )"; |
| 146 | 145 |
static String webMarkerFilter = " TableNameFk <> 500 OR ( RIdentifierFk IN (SELECT RIdentifier FROM v_cdm_exp_taxaAll)) "; |
| 147 |
static String authorTeamFilter = null; // " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";
|
|
| 148 |
static String authorFilter = null; // " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) ";
|
|
| 146 |
static String authorTeamFilter = /* null; //*/ " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";
|
|
| 147 |
static String authorFilter = /* null; //*/ " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) ";
|
|
| 149 | 148 |
|
| 150 | 149 |
|
| 151 | 150 |
|
| ... | ... | |
| 162 | 161 |
static final boolean doTaxonNames = true; |
| 163 | 162 |
static final boolean doRelNames = true; |
| 164 | 163 |
static final boolean doNameStatus = true; |
| 165 |
static final boolean doTypes = false; //serious types do not exist in E+M |
|
| 164 |
static final boolean doTypes = false; //serious types do not exist in E+M except for name types which are handled in name relations
|
|
| 166 | 165 |
static final boolean doNameFacts = true; |
| 167 | 166 |
|
| 168 | 167 |
//taxa |
| 169 | 168 |
static final boolean doTaxa = true; |
| 170 | 169 |
static final boolean doFacts = true; |
| 171 |
static final boolean doCommonNames = true;
|
|
| 170 |
static final boolean doCommonNames = false;
|
|
| 172 | 171 |
static final boolean doOccurences = true; |
| 173 |
static final boolean doRelTaxa = false;
|
|
| 172 |
static final boolean doRelTaxa = true;
|
|
| 174 | 173 |
static final boolean doRunTransmissionEngine = (hbm2dll == DbSchemaValidation.VALIDATE); |
| 175 | 174 |
|
| 176 | 175 |
//etc. |
| 177 |
static final boolean doMarker = true;
|
|
| 176 |
static final boolean doMarker = false;
|
|
| 178 | 177 |
|
| 179 | 178 |
|
| 180 | 179 |
public void importEm2CDM (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
|
| ... | ... | |
| 206 | 205 |
config.setDoMarker(doMarker ^ invers); |
| 207 | 206 |
config.setDoUser(doUser ^ invers); |
| 208 | 207 |
|
| 208 |
config.setEuroMed(true); |
|
| 209 |
|
|
| 209 | 210 |
config.setUseClassification(useClassification); |
| 210 | 211 |
config.setSourceRefUuid(BerlinModelTransformer.uuidSourceRefEuroMed); |
| 211 | 212 |
config.setEditor(editor); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java | ||
|---|---|---|
| 121 | 121 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 122 | 122 |
} |
| 123 | 123 |
|
| 124 |
public static ICdmDataSource cdm_local_test_euromed(){
|
|
| 124 |
public static ICdmDataSource cdm_local_euromed(){
|
|
| 125 | 125 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 126 | 126 |
String cdmServer = "127.0.0.1"; |
| 127 | 127 |
String cdmDB = "euroMed"; |
| ... | ... | |
| 133 | 133 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 134 | 134 |
String cdmServer = "127.0.0.1"; |
| 135 | 135 |
String cdmDB = "euroMed2"; |
| 136 |
String cdmUserName = "root";
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|
| 136 |
String cdmUserName = "edit";
|
|
| 137 | 137 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 138 | 138 |
} |
| 139 | 139 |
public static ICdmDataSource cdm_local_test_euromed3(){
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/common/TestActivator.java | ||
|---|---|---|
| 39 | 39 |
@SuppressWarnings("unused")
|
| 40 | 40 |
private static final Logger logger = Logger.getLogger(TestActivator.class); |
| 41 | 41 |
|
| 42 |
//static final Source faunaEuropaeaSource = FaunaEuropaeaSources.faunEu(); |
|
| 43 | 42 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
| 44 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
|
| 45 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production();
|
|
| 43 |
// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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| 44 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_test1();
|
|
| 46 | 45 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_edit_cichorieae_preview(); |
| 47 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production(); |
|
| 46 |
|
|
| 48 | 47 |
|
| 49 | 48 |
|
| 50 | 49 |
static final int limitSave = 2000; |
| 51 | 50 |
|
| 52 | 51 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
| 53 |
// static final CHECK check = CHECK.CHECK_ONLY; |
|
| 54 |
// static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.NONE; |
|
| 55 |
// static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.UPDATE; |
|
| 56 |
static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE; |
|
| 52 |
static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE; |
|
| 57 | 53 |
static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP; |
| 58 | 54 |
|
| 59 | 55 |
|
| ... | ... | |
| 62 | 58 |
* @param args |
| 63 | 59 |
*/ |
| 64 | 60 |
public static void main(String[] args) {
|
| 61 |
new TestActivator().invoke(); |
|
| 62 |
System.exit(0); |
|
| 63 |
} |
|
| 65 | 64 |
|
| 66 |
ICdmDataSource destination = cdmDestination; |
|
| 67 |
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| 68 |
CdmApplicationController app; |
|
| 69 |
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| 70 |
// applicationEventMulticaster |
|
| 71 |
// app = CdmIoApplicationController.NewInstance(destination, dbSchemaValidation); |
|
| 72 |
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| 73 |
IProgressMonitor progressMonitor = DefaultProgressMonitor.NewInstance(); |
|
| 74 |
String resourcePath= "/eu/etaxonomy/cdm/appimportTestApplicationContext.xml"; |
|
| 75 |
ClassPathResource resource = new ClassPathResource(resourcePath); |
|
| 76 |
// ApplicationListener<?> listener = new AppImportApplicationListener(); |
|
| 77 |
// List<ApplicationListener> listeners = new ArrayList<ApplicationListener>(); |
|
| 78 |
// listeners.add(listener); |
|
| 79 |
// app = CdmApplicationController.NewInstance(resource, destination, dbSchemaValidation, false, progressMonitor, listeners); |
|
| 80 |
app = CdmApplicationController.NewInstance(resource, destination, dbSchemaValidation, false, progressMonitor); |
|
| 65 |
private void invoke(){
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| 66 |
ICdmDataSource destination = cdmDestination; |
|
| 81 | 67 |
|
| 68 |
CdmApplicationController app; |
|
| 82 | 69 |
|
| 70 |
// applicationEventMulticaster |
|
| 71 |
// app = CdmIoApplicationController.NewInstance(destination, dbSchemaValidation); |
|
| 83 | 72 |
|
| 84 |
if (true){
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| 85 |
return; |
|
| 86 |
} |
|
| 73 |
IProgressMonitor progressMonitor = DefaultProgressMonitor.NewInstance(); |
|
| 74 |
String resourcePath= "/eu/etaxonomy/cdm/appimportTestApplicationContext.xml"; |
|
| 75 |
ClassPathResource resource = new ClassPathResource(resourcePath); |
|
| 76 |
// ApplicationListener<?> listener = new AppImportApplicationListener(); |
|
| 77 |
// List<ApplicationListener> listeners = new ArrayList<>(); |
|
| 78 |
// listeners.add(listener); |
|
| 79 |
// app = CdmApplicationController.NewInstance(resource, destination, dbSchemaValidation, false, progressMonitor, listeners); |
|
| 80 |
// app = CdmApplicationController.NewInstance(resource, destination, dbSchemaValidation, false, progressMonitor); |
|
| 81 |
app = CdmApplicationController.NewInstance(destination, dbSchemaValidation, false); |
|
| 87 | 82 |
|
| 88 |
TransactionStatus tx = app.startTransaction(); |
|
| 83 |
if (true){
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| 84 |
return; |
|
| 85 |
} |
|
| 89 | 86 |
|
| 90 |
State state = (State)app.getTermService().find(UUID.fromString("881b9c80-626d-47a6-b308-a63ee5f4178f"));
|
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| 91 |
DefinedTerm modifier = (DefinedTerm)app.getTermService().find(UUID.fromString("efc38dad-205c-4028-ad9d-ae509a14b37a"));
|
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| 92 |
CategoricalData cd = CategoricalData.NewInstance(); |
|
| 93 |
StateData stateData = StateData.NewInstance(); |
|
| 94 |
stateData.setState(state); |
|
| 95 |
stateData.addModifier(modifier); |
|
| 87 |
TransactionStatus tx = app.startTransaction(); |
|
| 96 | 88 |
|
| 97 |
StateData stateData2 = StateData.NewInstance(); |
|
| 98 |
stateData2.setState(state); |
|
| 99 |
stateData2.addModifier(modifier); |
|
| 89 |
State state = (State)app.getTermService().find(UUID.fromString("881b9c80-626d-47a6-b308-a63ee5f4178f"));
|
|
| 90 |
DefinedTerm modifier = (DefinedTerm)app.getTermService().find(UUID.fromString("efc38dad-205c-4028-ad9d-ae509a14b37a"));
|
|
| 91 |
CategoricalData cd = CategoricalData.NewInstance(); |
|
| 92 |
StateData stateData = StateData.NewInstance(); |
|
| 93 |
stateData.setState(state); |
|
| 94 |
stateData.addModifier(modifier); |
|
| 100 | 95 |
|
| 101 |
cd.addStateData(stateData2); |
|
| 96 |
StateData stateData2 = StateData.NewInstance(); |
|
| 97 |
stateData2.setState(state); |
|
| 98 |
stateData2.addModifier(modifier); |
|
| 102 | 99 |
|
| 103 |
app.getDescriptionService().saveDescriptionElement(cd); |
|
| 104 |
System.out.println("Saved");
|
|
| 100 |
cd.addStateData(stateData2); |
|
| 105 | 101 |
|
| 106 |
app.commitTransaction(tx); |
|
| 102 |
app.getDescriptionService().saveDescriptionElement(cd); |
|
| 103 |
System.out.println("Saved");
|
|
| 107 | 104 |
|
| 108 |
URI uri = URI.create("file:///C:/localCopy/Data/xper/Cichorieae-DA2.sdd.xml");
|
|
| 109 |
SDDImportConfigurator configurator = SDDImportConfigurator.NewInstance(uri, destination); |
|
| 110 |
CdmDefaultImport<SDDImportConfigurator> myImport = new CdmDefaultImport<>(); |
|
| 105 |
app.commitTransaction(tx); |
|
| 111 | 106 |
|
| 112 |
myImport.setCdmAppController(app); |
|
| 107 |
URI uri = URI.create("file:///C:/localCopy/Data/xper/Cichorieae-DA2.sdd.xml");
|
|
| 108 |
SDDImportConfigurator configurator = SDDImportConfigurator.NewInstance(uri, destination); |
|
| 109 |
CdmDefaultImport<SDDImportConfigurator> myImport = new CdmDefaultImport<>(); |
|
| 113 | 110 |
|
| 114 |
ImportResult result = myImport.invoke(configurator); |
|
| 115 |
System.out.println(result.toString()); |
|
| 111 |
myImport.setCdmAppController(app); |
|
| 116 | 112 |
|
| 117 |
if (true){
|
|
| 118 |
return; |
|
| 119 |
} |
|
| 113 |
ImportResult result = myImport.invoke(configurator); |
|
| 114 |
System.out.println(result.toString()); |
|
| 120 | 115 |
|
| 116 |
if (true){
|
|
| 117 |
return; |
|
| 118 |
} |
|
| 121 | 119 |
|
| 122 | 120 |
|
| 123 | 121 |
} |
| 124 | 122 |
|
| 125 | 123 |
|
| 126 |
|
|
| 127 | 124 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/app/redlist/BfnXmlImportActivator.java | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.app.redlist; |
| 11 | 11 |
|
| 12 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand1_kriechtiere; |
|
| 13 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand1_lurche; |
|
| 14 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand1_saeugetiere; |
|
| 15 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand1_suessfische; |
|
| 16 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand2_bodenlebendenWirbellosenMeerestiere; |
|
| 17 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand2_meeresfischeUndNeunaugen; |
|
| 18 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_ameisen; |
|
| 19 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_bienen; |
|
| 20 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_binnenmollusken; |
|
| 21 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_eulenfalter; |
|
| 22 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_fransenfluegler; |
|
| 23 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_heuschrecken; |
|
| 24 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_ohrwuermer; |
|
| 25 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_pflanzenwespen; |
|
| 26 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_raubfliegen; |
|
| 27 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_schaben; |
|
| 28 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_schwebfliegen; |
|
| 29 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_spanner; |
|
| 30 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_spinner; |
|
| 31 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_tagfalter; |
|
| 32 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_tanzfliegen; |
|
| 33 |
import static eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlImportReferences.uuidBand3_zuenslerfalter; |
|
| 34 |
|
|
| 35 | 12 |
import java.net.URI; |
| 36 | 13 |
import java.util.Arrays; |
| 37 | 14 |
import java.util.Iterator; |
| ... | ... | |
| 57 | 34 |
|
| 58 | 35 |
/** |
| 59 | 36 |
* @author a.oppermann |
| 60 |
* @created 16.07.2013
|
|
| 37 |
* @since 16.07.2013
|
|
| 61 | 38 |
*/ |
| 62 | 39 |
public class BfnXmlImportActivator {
|
| 63 | 40 |
|
| ... | ... | |
| 68 | 45 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_redlist_plant_localhost(); |
| 69 | 46 |
// static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
| 70 | 47 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
| 71 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_redlist_animalia_production_final();
|
|
| 72 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_redlist_mammalia(); |
|
| 48 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_redlist_animalia_production_final(); |
|
| 49 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_redlist_mammalia();
|
|
| 73 | 50 |
|
| 74 | 51 |
private static final String sourceUriBase = "file:////BGBM-PESIHPC/RoteListen/RoteListenXml/"; |
| 75 | 52 |
|
| ... | ... | |
| 153 | 130 |
// "rldb_print_v4_0_1_0_Myxo_110708_korr_syn_neu.xml",uuidBand6_myxomyzeten.toString(), |
| 154 | 131 |
// |
| 155 | 132 |
// Animals |
| 156 |
//band1 |
|
| 157 |
"rldb_print_v4_0_1_0_Brutvoegel.xml",BfnXmlImportReferences.uuidBand1_brutvoegel.toString(), //Brutvögel |
|
| 158 |
"rldb_print_v4_0_1_0_Reptilien_1.xml",uuidBand1_kriechtiere.toString(), |
|
| 159 |
"rldb_print_v4_0_1_0_Amphibien.xml",uuidBand1_lurche.toString(), //Kriechtiere |
|
| 160 |
"RoteListe_v4_0_6_0_BFN_Saeuger_korr.xml",uuidBand1_saeugetiere.toString(), //Säugetiere |
|
| 161 |
"rldb_print_v4_0_1_0_Fische.xml",uuidBand1_suessfische.toString(), |
|
| 162 |
// |
|
| 163 |
//band2 |
|
| 164 |
"rldb_print_v4_0_1_0_artenarmeWeichtiergruppen_121127_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 165 |
"rldb_print_v4_0_1_0_Asselspinnen_120907_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 166 |
"rldb_print_v4_0_1_0_Flohkrebse_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 167 |
"rldb_print_v4_0_1_0_Igelwuermer_120907_verantw.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 168 |
"rldb_print_v4_0_1_0_Kumazeen_120709_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 169 |
"rldb_print_v4_0_1_0_Asseln_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 170 |
"rldb_print_v4_0_1_0_Moostierchen_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 171 |
"rldb_print_v4_0_1_0_Muscheln_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 172 |
"rldb_print_v4_0_1_0_Schnecken_130206_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 173 |
"rldb_print_v4_0_1_0_Meeresfische_syn.xml",uuidBand2_meeresfischeUndNeunaugen.toString(), |
|
| 174 |
"rldb_print_v4_0_1_0_Nesseltiere_130104_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 175 |
"rldb_print_v4_0_1_0_Schaedellose_120907_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), //Schädellose |
|
| 176 |
"rldb_print_v4_0_1_0_Schwaemme_121127_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), //Schwämme |
|
| 177 |
"rldb_print_v4_0_1_0_Seepocken_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 178 |
"rldb_print_v4_0_1_0_Seescheiden_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 179 |
"rldb_print_v4_0_1_0_Stachelhaeuter_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), //Stachelhäuter |
|
| 180 |
"rldb_print_v4_0_1_0_Vielborster_130206_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 181 |
"rldb_print_v4_0_1_0_Wenigborster_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 182 |
"rldb_print_v4_0_1_0_Zehnfusskrebse_130104_verantw_syn.xml", uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), |
|
| 183 |
// |
|
| 184 |
//band3 |
|
| 185 |
"rldb_print_v4_0_1_0_Ameisen_110609_rev120113_syn.xml", uuidBand3_ameisen.toString(), //Hymenoptera: Formicidae |
|
| 186 |
"rldb_print_v4_0_1_0_Bienen_PWKorr_HG_120413_DF_120612_syn.xml",uuidBand3_bienen.toString(), //Hymnenoptera: Apidae |
|
| 187 |
"rldb_print_v4_0_1_0_Binnenmollusken_0alle_120413_DF_syn.xml",uuidBand3_binnenmollusken.toString(), |
|
| 188 |
//eulenfalter - korrekt? |
|
| 189 |
"rldb_print_v4_0_1_0_Eulen_Korruebern_23-05-2012_KorrV_syn.xml",uuidBand3_eulenfalter.toString(), //Eulen & Korrübern |
|
| 190 |
"rldb_print_v4_0_1_0_Thysanoptera_120413_DF_korrV_Verantw.xml",uuidBand3_fransenfluegler.toString(), |
|
| 191 |
"rldb_print_v4_0_1_0_Heuschrecken_syn.xml",uuidBand3_heuschrecken.toString(), //Saltatoria |
|
| 192 |
"rldb_print_v4_0_1_0_Ohrwuermer_DF_syn.xml",uuidBand3_ohrwuermer.toString(), //Dermaptera |
|
| 193 |
"rldb_print_v4_0_1_0_Pflanzenwespen_280711_Autor_110815_HG2_120413_DF_syn.xml",uuidBand3_pflanzenwespen.toString(), //Hymenoptera: Symphata |
|
| 194 |
"rldb_print_v4_0_1_0_Asilidae_GMH_Wolff_110314_HGxls_120413_DF_korrV_Verantw_syn.xml",uuidBand3_raubfliegen.toString(), |
|
| 195 |
"rldb_print_v4_0_1_0_Blattoptera_140413_DF_syn.xml",uuidBand3_schaben.toString(), |
|
| 196 |
"rldb_print_v4_0_1_0_Schwebfliegen_111103_KorrAS_120413_DF_syn.xml",uuidBand3_schwebfliegen.toString(), //Diptera: Syrphidae |
|
| 197 |
//spanner - korrekt? |
|
| 198 |
"rldb_print_v4_0_1_0_Eulenspinner_Spanner_13-06-2012_KorrV_syn.xml",uuidBand3_spanner.toString(), //Eulenspinner & Spanner |
|
| 199 |
"rldb_print_v4_0_1_0_Spinner_Oktober2011_eingearbKorr_120124_Korruebern_MB_02-05-2012_KorrV_syn.xml",uuidBand3_spinner.toString(), |
|
| 200 |
"rldb_print_v4_0_1_0_Tagfalter_06-06-2012_KorrV_syn.xml",uuidBand3_tagfalter.toString(), |
|
| 201 |
"rldb_print_v4_0_1_0_Empidoidea_120413_DF.xml",uuidBand3_tanzfliegen.toString(), //Empidoidea |
|
| 202 |
//wespen - fehlen ????? => siehe auch titel des Referenz Word Files |
|
| 203 |
"rldb_print_v4_0_1_0_Pyraloidea_Februar_2012_Korruebern_MB_24-04-2012_syn.xml",uuidBand3_zuenslerfalter.toString() |
|
| 133 |
// //band1
|
|
| 134 |
// "rldb_print_v4_0_1_0_Brutvoegel.xml",BfnXmlImportReferences.uuidBand1_brutvoegel.toString(), //Brutvögel
|
|
| 135 |
// "rldb_print_v4_0_1_0_Reptilien_1.xml",uuidBand1_kriechtiere.toString(),
|
|
| 136 |
// "rldb_print_v4_0_1_0_Amphibien.xml",uuidBand1_lurche.toString(), //Kriechtiere
|
|
| 137 |
// "RoteListe_v4_0_6_0_BFN_Saeuger_korr.xml",uuidBand1_saeugetiere.toString(), //Säugetiere
|
|
| 138 |
// "rldb_print_v4_0_1_0_Fische.xml",uuidBand1_suessfische.toString(),
|
|
| 139 |
// //
|
|
| 140 |
// //band2
|
|
| 141 |
// "rldb_print_v4_0_1_0_artenarmeWeichtiergruppen_121127_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 142 |
// "rldb_print_v4_0_1_0_Asselspinnen_120907_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 143 |
// "rldb_print_v4_0_1_0_Flohkrebse_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 144 |
// "rldb_print_v4_0_1_0_Igelwuermer_120907_verantw.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 145 |
// "rldb_print_v4_0_1_0_Kumazeen_120709_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 146 |
// "rldb_print_v4_0_1_0_Asseln_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 147 |
// "rldb_print_v4_0_1_0_Moostierchen_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 148 |
// "rldb_print_v4_0_1_0_Muscheln_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 149 |
// "rldb_print_v4_0_1_0_Schnecken_130206_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 150 |
// "rldb_print_v4_0_1_0_Meeresfische_syn.xml",uuidBand2_meeresfischeUndNeunaugen.toString(),
|
|
| 151 |
// "rldb_print_v4_0_1_0_Nesseltiere_130104_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 152 |
// "rldb_print_v4_0_1_0_Schaedellose_120907_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), //Schädellose
|
|
| 153 |
// "rldb_print_v4_0_1_0_Schwaemme_121127_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), //Schwämme
|
|
| 154 |
// "rldb_print_v4_0_1_0_Seepocken_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 155 |
// "rldb_print_v4_0_1_0_Seescheiden_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 156 |
// "rldb_print_v4_0_1_0_Stachelhaeuter_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(), //Stachelhäuter
|
|
| 157 |
// "rldb_print_v4_0_1_0_Vielborster_130206_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 158 |
// "rldb_print_v4_0_1_0_Wenigborster_121128_verantw_syn.xml",uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 159 |
// "rldb_print_v4_0_1_0_Zehnfusskrebse_130104_verantw_syn.xml", uuidBand2_bodenlebendenWirbellosenMeerestiere.toString(),
|
|
| 160 |
// //
|
|
| 161 |
// //band3
|
|
| 162 |
// "rldb_print_v4_0_1_0_Ameisen_110609_rev120113_syn.xml", uuidBand3_ameisen.toString(), //Hymenoptera: Formicidae
|
|
| 163 |
// "rldb_print_v4_0_1_0_Bienen_PWKorr_HG_120413_DF_120612_syn.xml",uuidBand3_bienen.toString(), //Hymnenoptera: Apidae
|
|
| 164 |
// "rldb_print_v4_0_1_0_Binnenmollusken_0alle_120413_DF_syn.xml",uuidBand3_binnenmollusken.toString(),
|
|
| 165 |
// //eulenfalter - korrekt?
|
|
| 166 |
// "rldb_print_v4_0_1_0_Eulen_Korruebern_23-05-2012_KorrV_syn.xml",uuidBand3_eulenfalter.toString(), //Eulen & Korrübern
|
|
| 167 |
// "rldb_print_v4_0_1_0_Thysanoptera_120413_DF_korrV_Verantw.xml",uuidBand3_fransenfluegler.toString(),
|
|
| 168 |
// "rldb_print_v4_0_1_0_Heuschrecken_syn.xml",uuidBand3_heuschrecken.toString(), //Saltatoria
|
|
| 169 |
// "rldb_print_v4_0_1_0_Ohrwuermer_DF_syn.xml",uuidBand3_ohrwuermer.toString(), //Dermaptera
|
|
| 170 |
// "rldb_print_v4_0_1_0_Pflanzenwespen_280711_Autor_110815_HG2_120413_DF_syn.xml",uuidBand3_pflanzenwespen.toString(), //Hymenoptera: Symphata
|
|
| 171 |
// "rldb_print_v4_0_1_0_Asilidae_GMH_Wolff_110314_HGxls_120413_DF_korrV_Verantw_syn.xml",uuidBand3_raubfliegen.toString(),
|
|
| 172 |
// "rldb_print_v4_0_1_0_Blattoptera_140413_DF_syn.xml",uuidBand3_schaben.toString(),
|
|
| 173 |
// "rldb_print_v4_0_1_0_Schwebfliegen_111103_KorrAS_120413_DF_syn.xml",uuidBand3_schwebfliegen.toString(), //Diptera: Syrphidae
|
|
| 174 |
// //spanner - korrekt?
|
|
| 175 |
// "rldb_print_v4_0_1_0_Eulenspinner_Spanner_13-06-2012_KorrV_syn.xml",uuidBand3_spanner.toString(), //Eulenspinner & Spanner
|
|
| 176 |
// "rldb_print_v4_0_1_0_Spinner_Oktober2011_eingearbKorr_120124_Korruebern_MB_02-05-2012_KorrV_syn.xml",uuidBand3_spinner.toString(),
|
|
| 177 |
// "rldb_print_v4_0_1_0_Tagfalter_06-06-2012_KorrV_syn.xml",uuidBand3_tagfalter.toString(),
|
|
| 178 |
// "rldb_print_v4_0_1_0_Empidoidea_120413_DF.xml",uuidBand3_tanzfliegen.toString(), //Empidoidea
|
|
| 179 |
// //wespen - fehlen ????? => siehe auch titel des Referenz Word Files
|
|
| 180 |
// "rldb_print_v4_0_1_0_Pyraloidea_Februar_2012_Korruebern_MB_24-04-2012_syn.xml",uuidBand3_zuenslerfalter.toString()
|
|
| 204 | 181 |
|
| 205 | 182 |
|
| 206 | 183 |
// //the 4 first lists, THESE ARE DUPLICATES |
| 207 |
// "RoteListe_v4_0_6_0_BFN_Saeuger_korr.xml", |
|
| 208 |
// "rldb_print_v4_0_1_0_Amphibien.xml",
|
|
| 209 |
// "rldb_print_v4_0_1_0_Reptilien_1.xml",
|
|
| 210 |
// "rldb_print_v4_0_1_0_Heuschrecken_syn.xml"
|
|
| 184 |
// "RoteListe_v4_0_6_0_BFN_Saeuger_korr.xml",BfnXmlImportReferences.uuidBand1_saeugetiere.toString(),
|
|
| 185 |
"rldb_print_v4_0_1_0_Amphibien.xml",BfnXmlImportReferences.uuidBand1_lurche.toString(),
|
|
| 186 |
"rldb_print_v4_0_1_0_Reptilien_1.xml",BfnXmlImportReferences.uuidBand1_kriechtiere.toString(),
|
|
| 187 |
"rldb_print_v4_0_1_0_Heuschrecken_syn.xml", BfnXmlImportReferences.uuidBand3_heuschrecken.toString()
|
|
| 211 | 188 |
|
| 212 | 189 |
); |
| 213 | 190 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/database/update/BgbmInstancesUpdater.java | ||
|---|---|---|
| 34 | 34 |
}; |
| 35 | 35 |
|
| 36 | 36 |
private static String[] testDatabases = new String[]{
|
| 37 |
"cdm_col", |
|
| 37 |
// "cdm_col",
|
|
| 38 | 38 |
"cdm_Test_Caryophyllales", |
| 39 | 39 |
"cdm_additivity_test", |
| 40 | 40 |
"cdm_bgbm_edit_usergroup", |
| 41 | 41 |
"cdm_campanulaceae","cdm_caryo_nepenthes", |
| 42 |
"cdm_corvidae", "cdm_cyprus","cdm_edaphobase_test", |
|
| 43 |
"cdm_edit_algaterra", "cdm_edit_cichorieae", |
|
| 42 |
"cdm_caryo_spp","cdm_causcasus_workshop", |
|
| 43 |
"cdm_corvidae", "cdm_cyprus","cdm_edaphobase_test", |
|
| 44 |
"cdm_edit_algaterra", "cdm_edit_algaterranew","cdm_edit_cichorieae", |
|
| 44 | 45 |
"cdm_edit_flora_central_africa", "cdm_edit_flora_malesiana", |
| 45 | 46 |
"cdm_edit_globis", "cdm_edit_palmae", |
| 46 | 47 |
"cdm_flora_cuba", "cdm_flora_guianas", |
| ... | ... | |
| 53 | 54 |
"cdm_proibiosphere_chenopodium_pilot", |
| 54 | 55 |
"cdm_rem_conf_ak", "cdm_rem_conf_am", "cdm_rem_conf_kl", "cdm_rem_conf_pp", |
| 55 | 56 |
"cdm_rl_animalia","cdm_rl_german_sl","cdm_rl_mammalia", "cdm_rl_plantae", |
| 56 |
"cdm_salvador", |
|
| 57 |
"cdm_salvador","cdm_test1","cdm_test2",
|
|
| 57 | 58 |
"cdm_test_euromed", |
| 58 | 59 |
"cdm_vibrant_index" |
| 59 | 60 |
}; |
| ... | ... | |
| 70 | 71 |
"cdm_production_campanulaceae", |
| 71 | 72 |
"cdm_production_caryo_amaranthaceae", |
| 72 | 73 |
"cdm_production_caryo_nepenthaceae", |
| 73 |
"cdm_production_caryo_nyctaginaceae", |
|
| 74 | 74 |
"cdm_production_caryophyllales", |
| 75 | 75 |
"cdm_production_caryophyllales_spp", |
| 76 | 76 |
"cdm_production_cichorieae", |
| 77 |
"cdm_production_corvidae","cdm_production_cyprus", |
|
| 77 |
"cdm_production_corvidae", |
|
| 78 |
"cdm_production_cyprus", |
|
| 78 | 79 |
"cdm_production_diptera", |
| 79 | 80 |
"cdm_production_edaphobase", |
| 80 | 81 |
"cdm_production_euromed", |
| ... | ... | |
| 88 | 89 |
"cdm_production_flora_malesiana_prospective", |
| 89 | 90 |
"cdm_production_flore_gabon", |
| 90 | 91 |
"cdm_production_globis", |
| 92 |
"cdm_production_myristicaceae", |
|
| 91 | 93 |
"cdm_production_palmae", |
| 92 | 94 |
"cdm_production_phycobank", |
| 93 | 95 |
"cdm_production_piB_ants_pilot", |
| ... | ... | |
| 98 | 100 |
"cdm_production_piB_nephrolepis_pilot", |
| 99 | 101 |
"cdm_production_piB_spiders_pilot", |
| 100 | 102 |
"cdm_production_rl_animalia", |
| 103 |
"cdm_production_rl_animalia_final", |
|
| 101 | 104 |
"cdm_production_rl_armeria_demo", |
| 102 |
"cdm_production_rl_fungi", |
|
| 103 | 105 |
"cdm_production_rl_german_sl", |
| 104 | 106 |
"cdm_production_rl_lumbricidae", |
| 105 | 107 |
"cdm_production_rl_mammalia", |
| ... | ... | |
| 109 | 111 |
"cdm_production_rubiaceae_mexico", |
| 110 | 112 |
"cdm_production_salvador", |
| 111 | 113 |
"cdm_production_vibrant_index" |
| 112 |
};
|
|
| 114 |
}; |
|
| 113 | 115 |
|
| 114 | 116 |
|
| 115 | 117 |
static BgbmServer bgbmServer = BgbmServer.TEST; |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelCommonNamesImport.java | ||
|---|---|---|
| 86 | 86 |
if (isNotBlank(state.getConfig().getCommonNameFilter())){
|
| 87 | 87 |
result += " AND " + state.getConfig().getCommonNameFilter(); |
| 88 | 88 |
} |
| 89 |
result += " ORDER BY CommonNameId "; |
|
| 89 | 90 |
|
| 90 | 91 |
return result; |
| 91 | 92 |
} |
| ... | ... | |
| 94 | 95 |
protected String getRecordQuery(BerlinModelImportConfigurator config) {
|
| 95 | 96 |
String recordQuery = ""; |
| 96 | 97 |
recordQuery = |
| 97 |
" SELECT cn.CommonNameId, cn.CommonName, PTaxon.RIdentifier AS taxonId, cn.PTNameFk, cn.RefFk AS refId, cn.Status, cn.RegionFks, cn.MisNameRefFk, " + |
|
| 98 |
" cn.NameInSourceFk, cn.Created_When, cn.Updated_When, cn.Created_Who, cn.Updated_Who, cn.Note AS Notes, languageCommonName.Language, " + |
|
| 99 |
" languageCommonName.LanguageOriginal, languageCommonName.ISO639_1, languageCommonName.ISO639_2, " + |
|
| 100 |
" emLanguageReference.RefFk AS languageRefRefFk, emLanguageReference.ReferenceShort, emLanguageReference.ReferenceLong, " + |
|
| 101 |
" emLanguageReference.LanguageFk, languageReferenceLanguage.Language AS refLanguage, languageReferenceLanguage.ISO639_2 AS refLanguageIso639_2, "+ |
|
| 102 |
" misappliedTaxon.RIdentifier AS misappliedTaxonId " + |
|
| 103 |
" FROM PTaxon AS misappliedTaxon RIGHT OUTER JOIN " + |
|
| 104 |
" emLanguage AS languageReferenceLanguage RIGHT OUTER JOIN " + |
|
| 105 |
" emLanguageReference ON languageReferenceLanguage.LanguageId = emLanguageReference.LanguageFk RIGHT OUTER JOIN " + |
|
| 106 |
" emCommonName AS cn INNER JOIN " + |
|
| 107 |
" PTaxon ON cn.PTNameFk = PTaxon.PTNameFk AND cn.PTRefFk = PTaxon.PTRefFk ON " + |
|
| 108 |
" emLanguageReference.ReferenceId = cn.LanguageRefFk LEFT OUTER JOIN " + |
|
| 109 |
" emLanguage AS languageCommonName ON cn.LanguageFk = languageCommonName.LanguageId ON misappliedTaxon.PTNameFk = cn.NameInSourceFk AND " + |
|
| 110 |
" misappliedTaxon.PTRefFk = cn.MisNameRefFk " + |
|
| 111 |
" WHERE cn.CommonNameId IN (" + ID_LIST_TOKEN + ")";
|
|
| 98 |
" SELECT rel.RelPTaxonId, rel.RelQualifierFk, acc.RIdentifier accTaxonId, factTaxon.RIdentifier factTaxonId, accName.NameId, f.FactId, " + |
|
| 99 |
" cn.CommonNameId, cn.CommonName, tax.RIdentifier AS taxonId, cn.PTNameFk, cn.RefFk AS refId, cn.Status, cn.RegionFks, cn.MisNameRefFk, " + |
|
| 100 |
" cn.NameInSourceFk, cn.Created_When, cn.Updated_When, cn.Created_Who, cn.Updated_Who, cn.Note AS Notes, languageCommonName.Language, " + |
|
| 101 |
" languageCommonName.LanguageOriginal, languageCommonName.ISO639_1, languageCommonName.ISO639_2, " + |
|
| 102 |
" emLanguageReference.RefFk AS languageRefRefFk, emLanguageReference.ReferenceShort, emLanguageReference.ReferenceLong, " + |
|
| 103 |
" emLanguageReference.LanguageFk, languageReferenceLanguage.Language AS refLanguage, languageReferenceLanguage.ISO639_2 AS refLanguageIso639_2, "+ |
|
| 104 |
" misappliedTaxon.RIdentifier AS misappliedTaxonId " + |
|
| 105 |
" FROM PTaxon AS misappliedTaxon RIGHT OUTER JOIN " + |
|
| 106 |
" emLanguage AS languageReferenceLanguage RIGHT OUTER JOIN " + |
|
| 107 |
" emLanguageReference ON languageReferenceLanguage.LanguageId = emLanguageReference.LanguageFk RIGHT OUTER JOIN " + |
|
| 108 |
" emCommonName AS cn INNER JOIN " + |
|
| 109 |
" PTaxon AS tax ON cn.PTNameFk = tax.PTNameFk AND cn.PTRefFk = tax.PTRefFk ON " + |
|
| 110 |
" emLanguageReference.ReferenceId = cn.LanguageRefFk LEFT OUTER JOIN " + |
|
| 111 |
" emLanguage AS languageCommonName ON cn.LanguageFk = languageCommonName.LanguageId ON misappliedTaxon.PTNameFk = cn.NameInSourceFk AND " + |
|
| 112 |
" misappliedTaxon.PTRefFk = cn.MisNameRefFk " + |
|
| 113 |
|
|
| 114 |
" LEFT OUTER JOIN Fact f ON cn.CommonNameId = f.ExtensionFk " + |
|
| 115 |
" LEFT OUTER JOIN PTaxon factTaxon ON factTaxon.PTNameFk = f.PTNameFk AND factTaxon.PTRefFk = f.PTRefFk " + |
|
| 116 |
" LEFT OUTER JOIN RelPTaxon rel ON rel.PTNameFk1 = tax.PTNameFk AND rel.PTRefFk1 = tax.PTRefFk AND rel.RelQualifierFk IN (2,6,7) " + |
|
| 117 |
" LEFT OUTER JOIN PTaxon acc ON rel.PTNameFk2 = acc.PTNameFk AND rel.PTRefFk2 = acc.PTRefFk " + |
|
| 118 |
" LEFT OUTER JOIN Name accName ON accName.NameId = acc.PTNameFk " + |
|
| 119 |
" WHERE cn.CommonNameId IN (" + ID_LIST_TOKEN + ") " +
|
|
| 120 |
" ORDER BY cn.CommonNameId "; |
|
| 121 |
|
|
| 112 | 122 |
return recordQuery; |
| 113 | 123 |
} |
| 114 | 124 |
|
| ... | ... | |
| 174 | 184 |
// logger.warn("MisappliedNameRefFk not yet implemented for Common Names");
|
| 175 | 185 |
|
| 176 | 186 |
ResultSet rs = partitioner.getResultSet(); |
| 187 |
Integer lastCommonNameId = null; |
|
| 177 | 188 |
try{
|
| 178 | 189 |
while (rs.next()){
|
| 179 | 190 |
|
| 180 | 191 |
//create TaxonName element |
| 181 | 192 |
Integer commonNameId = rs.getInt("CommonNameId");
|
| 182 | 193 |
int taxonId = rs.getInt("taxonId");
|
| 194 |
Integer factTaxonId = nullSafeInt(rs, "factTaxonId"); |
|
| 195 |
Integer accTaxonId = nullSafeInt(rs, "accTaxonId"); //if common name is related to synonym this is the accepted taxon id |
|
| 196 |
|
|
| 183 | 197 |
Integer refId = nullSafeInt(rs, "refId"); |
| 184 | 198 |
// Integer ptNameFk = nullSafeInt(rs,"PTNameFk"); |
| 185 | 199 |
String commonNameString = rs.getString("CommonName");
|
| ... | ... | |
| 195 | 209 |
Integer nameInSourceFk = nullSafeInt( rs, "NameInSourceFk"); |
| 196 | 210 |
Integer misappliedTaxonId = nullSafeInt( rs, "misappliedTaxonId"); |
| 197 | 211 |
|
| 212 |
if (commonNameId == lastCommonNameId){
|
|
| 213 |
logger.warn("CommonNameId >1 times in query. This may happen due to LEFT JOINS to fact and/or accepted taxon and e.g. multiple taxon relationships. 2018-04-01 no such double relation existed in E+M. ");
|
|
| 214 |
}else{
|
|
| 215 |
lastCommonNameId = commonNameId; |
|
| 216 |
} |
|
| 217 |
|
|
| 198 | 218 |
//regions |
| 199 | 219 |
String regionFks = rs.getString("RegionFks");
|
| 200 |
String[] regionFkSplit = regionFks.split(",");
|
|
| 220 |
String[] regionFkSplit = (regionFks==null)? new String[0] : regionFks.split(",");
|
|
| 201 | 221 |
|
| 202 | 222 |
//commonNameString |
| 203 | 223 |
if (isBlank(commonNameString)){
|
| ... | ... | |
| 212 | 232 |
if (taxonBase == null){
|
| 213 | 233 |
logger.warn("Taxon (" + taxonId + ") could not be found. Common name " + commonNameString + "(" + commonNameId + ") not imported");
|
| 214 | 234 |
continue; |
| 215 |
}else if (! taxonBase.isInstanceOf(Taxon.class)){
|
|
| 216 |
logger.warn("taxon (" + taxonId + ") is not accepted. Can't import common name " + commonNameId);
|
|
| 217 |
continue; |
|
| 235 |
}else if (taxonBase.isInstanceOf(Taxon.class)){
|
|
| 236 |
taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
|
| 237 |
if (factTaxonId != null && !factTaxonId.equals(taxonId)){
|
|
| 238 |
logger.warn("Fact taxon ("+factTaxonId+") for common name "+commonNameId+" differs from common name taxon " + taxonId);
|
|
| 239 |
} |
|
| 218 | 240 |
}else{
|
| 219 |
taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
|
| 241 |
Taxon factTaxon = null; |
|
| 242 |
if (factTaxonId != null && factTaxonId.equals(accTaxonId)){
|
|
| 243 |
factTaxon = taxonMap.get(String.valueOf(factTaxonId)); |
|
| 244 |
} |
|
| 245 |
if (factTaxon != null){
|
|
| 246 |
taxon = factTaxon; |
|
| 247 |
}else{
|
|
| 248 |
logger.warn("taxon (" + taxonId + ") is not accepted. Can't import common name " + commonNameId + ". FactTaxonId= " + factTaxonId + "; accTaxonId = " + accTaxonId);
|
|
| 249 |
continue; |
|
| 250 |
} |
|
| 220 | 251 |
} |
| 221 | 252 |
|
| 222 | 253 |
//Language |
| ... | ... | |
| 253 | 284 |
if (languageRefRefFk == null){
|
| 254 | 285 |
languageRefRefFk = refId; |
| 255 | 286 |
}else{
|
| 256 |
logger.warn("CommonName.RefFk (" + CdmUtils.Nz(refId) + ") and LanguageReference.RefFk " + (languageRefRefFk==null? "null" : languageRefRefFk) + " are not equal. I will import only languageReference.RefFk");
|
|
| 287 |
logger.warn("CommonName.RefFk (" + CdmUtils.Nz(refId) + ") and LanguageReference.RefFk " + languageRefRefFk + " are not equal. I will import only languageReference.RefFk");
|
|
| 257 | 288 |
} |
| 258 | 289 |
} |
| 259 | 290 |
|
| ... | ... | |
| 268 | 299 |
if (nameInSourceFk != null && nameUsedInSource == null){
|
| 269 | 300 |
logger.warn("Name used in source (" + nameInSourceFk + ") was not found for common name " + commonNameId);
|
| 270 | 301 |
} |
| 271 |
DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(reference, microCitation, nameUsedInSource, originalNameString); |
|
| 272 | 302 |
for (CommonTaxonName commonTaxonName : commonTaxonNames){
|
| 273 |
commonTaxonName.addSource(source); |
|
| 303 |
DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(reference, microCitation, nameUsedInSource, originalNameString); |
|
| 304 |
commonTaxonName.addSource(source); |
|
| 274 | 305 |
} |
| 275 | 306 |
|
| 276 | 307 |
|
| ... | ... | |
| 315 | 346 |
misappliedNameDescription.addElement(commonNameClone); |
| 316 | 347 |
} |
| 317 | 348 |
}else{
|
| 318 |
logger.warn("Misapplied name is null for common name " + commonNameId);
|
|
| 349 |
//wird schon oben gelogged |
|
| 350 |
//logger.warn("Misapplied name is null for common name " + commonNameId);
|
|
| 319 | 351 |
} |
| 320 | 352 |
|
| 321 | 353 |
} |
| ... | ... | |
| 358 | 390 |
return false; |
| 359 | 391 |
} catch (ClassCastException e) {
|
| 360 | 392 |
e.printStackTrace(); |
| 361 |
} |
|
| 393 |
} catch (Exception e) {
|
|
| 394 |
throw e; |
|
| 395 |
} |
|
| 362 | 396 |
|
| 363 | 397 |
// logger.info( i + " names handled"); |
| 364 | 398 |
getTaxonService().save(taxaToSave); |
| ... | ... | |
| 507 | 541 |
NamedArea newArea = getNamedArea(state, null, region, "Language region '" + region + "'", null, null, null); |
| 508 | 542 |
// getTermService().save(newArea); |
| 509 | 543 |
regionMap.put(String.valueOf(regionId), newArea); |
| 510 |
logger.warn("Found new area: " + region);
|
|
| 544 |
logger.info("Found new area: " + region);
|
|
| 511 | 545 |
}else if (splitRegion.length == 2){
|
| 512 | 546 |
String emCode = splitRegion[1].trim(); |
| 513 | 547 |
String tdwgCode = emTdwgMap.get(emCode); |
| ... | ... | |
| 547 | 581 |
area = Country.RUSSIANFEDERATION(); |
| 548 | 582 |
}else if (tdwgCode.equalsIgnoreCase("Gg")){
|
| 549 | 583 |
area = Country.GEORGIA(); |
| 550 |
}else{
|
|
| 584 |
}else if (tdwgCode.equalsIgnoreCase("SM")){
|
|
| 585 |
area = getNamedArea(state, BerlinModelTransformer.uuidSM , "Serbia & Montenegro", "Serbia & Montenegro", "SM", null, null); |
|
| 586 |
getTermService().saveOrUpdate(area); |
|
| 587 |
}else if (tdwgCode.equalsIgnoreCase("Tu")){
|
|
| 588 |
area = Country.TURKEYREPUBLICOF(); |
|
| 589 |
}else{
|
|
| 551 | 590 |
area = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwgCode); |
| 552 | 591 |
} |
| 553 | 592 |
if (area == null){
|
| ... | ... | |
| 588 | 627 |
if (isNotBlank(emCode) ){
|
| 589 | 628 |
emCode = emCode.trim(); |
| 590 | 629 |
if (emCode.equalsIgnoreCase("Ab") || emCode.equalsIgnoreCase("Rf")||
|
| 591 |
emCode.equalsIgnoreCase("Uk") || emCode.equalsIgnoreCase("Gg")){
|
|
| 630 |
emCode.equalsIgnoreCase("Uk") || emCode.equalsIgnoreCase("Gg")
|
|
| 631 |
|| emCode.equalsIgnoreCase("SM") || emCode.equalsIgnoreCase("Tu")){
|
|
| 592 | 632 |
emTdwgMap.put(emCode, emCode); |
| 593 | 633 |
}else if (isNotBlank(TDWGCode)){
|
| 594 | 634 |
emTdwgMap.put(emCode, TDWGCode.trim()); |
| ... | ... | |
| 601 | 641 |
emTdwgMap.put("Uk / Uk(U)", "Uk");
|
| 602 | 642 |
emTdwgMap.put("Ar / Ar(A)", "TCS-AR");
|
| 603 | 643 |
emTdwgMap.put("Hs / Hs(S)", "SPA-SP");
|
| 644 |
emTdwgMap.put("Hb / Hb(E)", "IRE-IR");
|
|
| 604 | 645 |
|
| 605 | 646 |
return emTdwgMap; |
| 606 | 647 |
} |
| ... | ... | |
| 638 | 679 |
Set<String> referenceIdSet = new HashSet<>(); |
| 639 | 680 |
while (rs.next()){
|
| 640 | 681 |
handleForeignKey(rs, taxonIdSet, "taxonId"); |
| 641 |
handleForeignKey(rs, taxonIdSet, "misappliedTaxonId"); |
|
| 682 |
handleForeignKey(rs, taxonIdSet, "factTaxonId"); |
|
| 683 |
handleForeignKey(rs, taxonIdSet, "misappliedTaxonId"); |
|
| 642 | 684 |
handleForeignKey(rs, referenceIdSet, "refId"); |
| 643 | 685 |
handleForeignKey(rs, referenceIdSet, "languageRefRefFk"); |
| 644 | 686 |
handleForeignKey(rs, nameIdSet, "NameInSourceFk"); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelImportBase.java | ||
|---|---|---|
| 34 | 34 |
import eu.etaxonomy.cdm.model.location.Country; |
| 35 | 35 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 36 | 36 |
import eu.etaxonomy.cdm.model.location.NamedAreaType; |
| 37 |
import eu.etaxonomy.cdm.model.name.Rank; |
|
| 38 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
| 39 | 37 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 40 | 38 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 41 | 39 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| ... | ... | |
| 44 | 42 |
* @author a.mueller |
| 45 | 43 |
* @since 20.03.2008 |
| 46 | 44 |
*/ |
| 47 |
public abstract class BerlinModelImportBase extends DbImportBase<BerlinModelImportState, BerlinModelImportConfigurator> implements ICdmIO<BerlinModelImportState>, IPartitionedIO<BerlinModelImportState> {
|
|
| 45 |
public abstract class BerlinModelImportBase |
|
| 46 |
extends DbImportBase<BerlinModelImportState, BerlinModelImportConfigurator> |
|
| 47 |
implements ICdmIO<BerlinModelImportState>, IPartitionedIO<BerlinModelImportState> {
|
|
| 48 | 48 |
private static final long serialVersionUID = -4982506434258587864L; |
| 49 | 49 |
private static final Logger logger = Logger.getLogger(BerlinModelImportBase.class); |
| 50 | 50 |
|
| ... | ... | |
| 192 | 192 |
TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(taxonId)); |
| 193 | 193 |
|
| 194 | 194 |
//TODO for testing |
| 195 |
if (taxonBase == null && ! state.getConfig().isDoTaxa()){
|
|
| 196 |
taxonBase = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null); |
|
| 197 |
} |
|
| 195 |
// if (taxonBase == null && ! state.getConfig().isDoTaxa()){
|
|
| 196 |
// taxonBase = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null);
|
|
| 197 |
// }
|
|
| 198 | 198 |
|
| 199 | 199 |
Taxon taxon; |
| 200 | 200 |
if ( taxonBase instanceof Taxon ) {
|
| ... | ... | |
| 376 | 376 |
return getNamedArea(state, BerlinModelTransformer.uuidTerceira, "Menorca", "Euro+Med area 'Menorca'", "Bl(N)", null, null); |
| 377 | 377 |
} |
| 378 | 378 |
|
| 379 |
logger.warn("Area(em: '" + em + "', tdwg: '" + tdwg +"') could not be found for occurrence import");
|
|
| 379 |
logger.warn("Area(em: '" + em + "', tdwg: '" + tdwg +"') could not be found");
|
|
| 380 | 380 |
|
| 381 | 381 |
return null; |
| 382 | 382 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelImportConfigurator.java | ||
|---|---|---|
| 57 | 57 |
private boolean doTypes = true; |
| 58 | 58 |
|
| 59 | 59 |
private boolean isSalvador = false; |
| 60 |
private boolean isEuroMed = false; |
|
| 60 | 61 |
|
| 61 | 62 |
//taxa |
| 62 | 63 |
private boolean doTaxa = true; |
| ... | ... | |
| 641 | 642 |
public boolean isSalvador() {return isSalvador;}
|
| 642 | 643 |
public void setSalvador(boolean isSalvador) {this.isSalvador = isSalvador;}
|
| 643 | 644 |
|
| 645 |
public boolean isEuroMed() {return isEuroMed;}
|
|
| 646 |
public void setEuroMed(boolean isEuroMed) {this.isEuroMed = isEuroMed;}
|
|
| 647 |
|
|
| 644 | 648 |
public UUID getFeatureTreeUuid() {
|
| 645 | 649 |
return featureTreeUuid; |
| 646 | 650 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelOccurrenceSourceImport.java | ||
|---|---|---|
| 238 | 238 |
if (names.size() == 1){
|
| 239 | 239 |
return names.get(0); |
| 240 | 240 |
}else {
|
| 241 |
if (names.size()> 2){
|
|
| 241 |
if (names.size()> 1){
|
|
| 242 | 242 |
logger.info("There is more than one name matching oldName: " + oldName + ".");
|
| 243 | 243 |
} |
| 244 |
return null;
|
|
| 244 |
return names.get(0);
|
|
| 245 | 245 |
//taxonName = nameParser.parseSimpleName(oldName); |
| 246 | 246 |
} |
| 247 | 247 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonImport.java | ||
|---|---|---|
| 104 | 104 |
protected String getRecordQuery(BerlinModelImportConfigurator config) {
|
| 105 | 105 |
String sqlSelect = " SELECT pt.* "; |
| 106 | 106 |
String sqlFrom = " FROM PTaxon pt "; |
| 107 |
if (isEuroMed(config) ){
|
|
| 107 |
if (config.isEuroMed()){
|
|
| 108 | 108 |
sqlFrom = " FROM PTaxon AS pt " + |
| 109 | 109 |
" INNER JOIN v_cdm_exp_taxaAll AS em ON pt.RIdentifier = em.RIdentifier " + |
| 110 | 110 |
" LEFT OUTER JOIN Reference r ON pt.LastScrutinyFk = r.RefId "; |
| ... | ... | |
| 121 | 121 |
return strRecordQuery; |
| 122 | 122 |
} |
| 123 | 123 |
|
| 124 |
private boolean isEuroMed(BerlinModelImportConfigurator config) {
|
|
| 125 |
return config.getTaxonTable().trim().equals("v_cdm_exp_taxaAll");
|
|
| 126 |
} |
|
| 127 |
|
|
| 128 | 124 |
@Override |
| 129 | 125 |
protected boolean doCheck(BerlinModelImportState state){
|
| 130 | 126 |
IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonImportValidator(); |
| ... | ... | |
| 143 | 139 |
ResultSet rs = partitioner.getResultSet(); |
| 144 | 140 |
try{
|
| 145 | 141 |
boolean publishFlagExists = state.getConfig().getSource().checkColumnExists("PTaxon", "PublishFlag");
|
| 146 |
boolean isEuroMed = isEuroMed(state.getConfig());
|
|
| 142 |
boolean isEuroMed = config.isEuroMed();
|
|
| 147 | 143 |
while (rs.next()){
|
| 148 | 144 |
|
| 149 | 145 |
// if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("PTaxa handled: " + (i-1));}
|
| ... | ... | |
| 183 | 179 |
Taxon taxon; |
| 184 | 180 |
try {
|
| 185 | 181 |
logger.debug(statusFk); |
| 186 |
if (statusFk == T_STATUS_ACCEPTED || statusFk == T_STATUS_UNRESOLVED ){
|
|
| 182 |
if (statusFk == T_STATUS_ACCEPTED || statusFk == T_STATUS_UNRESOLVED |
|
| 183 |
|| statusFk == T_STATUS_PRO_PARTE_SYN || statusFk == T_STATUS_PARTIAL_SYN ){
|
|
| 187 | 184 |
taxon = Taxon.NewInstance(taxonName, reference); |
| 188 | 185 |
taxonBase = taxon; |
| 189 | 186 |
if (statusFk == T_STATUS_UNRESOLVED){
|
| 190 | 187 |
taxon.setTaxonStatusUnknown(true); |
| 191 | 188 |
} |
| 192 |
}else if (statusFk == T_STATUS_SYNONYM || statusFk == T_STATUS_PRO_PARTE_SYN || statusFk == T_STATUS_PARTIAL_SYN){
|
|
| 189 |
//TODO marker for pp and partial? |
|
| 190 |
}else if (statusFk == T_STATUS_SYNONYM ){
|
|
| 193 | 191 |
synonym = Synonym.NewInstance(taxonName, reference); |
| 194 | 192 |
taxonBase = synonym; |
| 195 |
if (statusFk == T_STATUS_PRO_PARTE_SYN){
|
|
| 196 |
synonym.setProParte(true); |
|
| 197 |
} |
|
| 198 |
if (statusFk == T_STATUS_PARTIAL_SYN){
|
|
| 199 |
synonym.setPartial(true); |
|
| 200 |
} |
|
| 193 |
// if (statusFk == T_STATUS_PRO_PARTE_SYN){
|
|
| 194 |
// synonym.setProParte(true);
|
|
| 195 |
// }
|
|
| 196 |
// if (statusFk == T_STATUS_PARTIAL_SYN){
|
|
| 197 |
// synonym.setPartial(true);
|
|
| 198 |
// }
|
|
| 201 | 199 |
}else{
|
| 202 | 200 |
logger.warn("TaxonStatus " + statusFk + " not yet implemented. Taxon (RIdentifier = " + taxonId + ") left out.");
|
| 203 | 201 |
success = false; |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonNameImport.java | ||
|---|---|---|
| 33 | 33 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 34 | 34 |
import eu.etaxonomy.cdm.model.agent.Team; |
| 35 | 35 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| 36 |
import eu.etaxonomy.cdm.model.common.Annotation; |
|
| 36 | 37 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 37 | 38 |
import eu.etaxonomy.cdm.model.common.Extension; |
| 38 | 39 |
import eu.etaxonomy.cdm.model.common.ExtensionType; |
| ... | ... | |
| 260 | 261 |
|
| 261 | 262 |
//created, notes |
| 262 | 263 |
boolean excludeUpdated = true; |
| 263 |
success &= doIdCreatedUpdatedNotes(state, taxonName, rs, nameId, NAMESPACE, excludeUpdated, false); |
|
| 264 |
boolean excludeNotes = true; |
|
| 265 |
success &= doIdCreatedUpdatedNotes(state, taxonName, rs, nameId, NAMESPACE, excludeUpdated, excludeNotes); |
|
| 266 |
handleNameNotes(state, taxonName, rs, nameId); |
|
| 264 | 267 |
|
| 265 | 268 |
//NonViralName |
| 266 | 269 |
if (taxonName.isNonViral()){
|
| ... | ... | |
| 326 | 329 |
} |
| 327 | 330 |
|
| 328 | 331 |
|
| 329 |
private Rank handleProlesAndRaceSublusus(BerlinModelImportState state, ResultSet rs, Rank rank) throws SQLException {
|
|
| 332 |
/** |
|
| 333 |
* @param state |
|
| 334 |
* @param taxonName |
|
| 335 |
* @param rs |
|
| 336 |
* @param nameId |
|
| 337 |
* @throws SQLException |
|
| 338 |
*/ |
|
| 339 |
private void handleNameNotes(BerlinModelImportState state, TaxonName taxonName, ResultSet rs, int nameId) throws SQLException {
|
|
| 340 |
String notesOrig = rs.getString("notes");
|
|
| 341 |
String notes = filterNotes(notesOrig, nameId); |
|
| 342 |
if (isNotBlank(notes) && taxonName != null ){
|
|
| 343 |
String notesString = String.valueOf(notes); |
|
| 344 |
if (notesString.length() > 65530 ){
|
|
| 345 |
notesString = notesString.substring(0, 65530) + "..."; |
|
| 346 |
logger.warn("Notes string is longer than 65530 and was truncated: " + taxonName);
|
|
| 347 |
} |
|
| 348 |
Annotation notesAnnotation = Annotation.NewInstance(notesString, Language.DEFAULT()); |
|
| 349 |
//notesAnnotation.setAnnotationType(AnnotationType.EDITORIAL()); |
|
| 350 |
//notes.setCommentator(bmiConfig.getCommentator()); |
|
| 351 |
taxonName.addAnnotation(notesAnnotation); |
|
| 352 |
} |
|
| 353 |
|
|
| 354 |
} |
|
| 355 |
|
|
| 356 |
private static final String MCL = "MCL\\s?[0-9]{1,3}(\\-[0-9]{1,4}(\\-[0-9]{1,4}(\\-[0-9]{1,4}(\\-[0-9]{1,3})?)?)?)?";
|
|
| 357 |
/** |
|
| 358 |
* @param notes |
|
| 359 |
*/ |
|
| 360 |
private String filterNotes(String notes, int nameId) {
|
|
| 361 |
String result; |
|
| 362 |
if (isBlank(notes)){
|
|
| 363 |
result = null; |
|
| 364 |
}else if (notes.matches("Acc:.*")){
|
|
| 365 |
if (notes.matches("Acc: .*\\$$") || (notes.matches("Acc: .*"+MCL))){
|
|
| 366 |
result = null; |
|
| 367 |
}else if (notes.matches("Acc: .*(\\$|"+MCL+")\\s*\\{.*\\}")){
|
|
| 368 |
notes = notes.substring(notes.indexOf("{")+1, notes.length()-1);
|
|
| 369 |
result = notes; |
|
| 370 |
}else if (notes.matches("Acc: .*(\\$|"+MCL+")\\s*\\[.*\\]")){
|
|
| 371 |
notes = notes.substring(notes.indexOf("[")+1, notes.length()-1);
|
|
| 372 |
result = notes; |
|
| 373 |
}else{
|
|
| 374 |
logger.warn("Name id: " + nameId + ". Namenote: " + notes);
|
|
| 375 |
result = notes; |
|
| 376 |
} |
|
| 377 |
}else if (notes.matches("Syn:.*")){
|
|
| 378 |
if (notes.matches("Syn: .*\\$$") || (notes.matches("Syn: .*"+MCL))){
|
|
| 379 |
result = null; |
|
| 380 |
}else if (notes.matches("Syn: .*(\\$|"+MCL+")\\s*\\{.*\\}")){
|
|
| 381 |
notes = notes.substring(notes.indexOf("{")+1, notes.length()-1);
|
|
| 382 |
result = notes; |
|
| 383 |
}else if (notes.matches("Syn: .*(\\$|"+MCL+")\\s*\\[.*\\]")){
|
|
| 384 |
notes = notes.substring(notes.indexOf("[")+1, notes.length()-1);
|
|
| 385 |
result = notes; |
|
| 386 |
}else{
|
|
| 387 |
logger.warn("Name id: " + nameId + ". Namenote: " + notes);
|
|
| 388 |
result = notes; |
|
| 389 |
} |
|
| 390 |
}else{
|
|
| 391 |
result = notes; |
|
| 392 |
} |
|
| 393 |
return result; |
|
| 394 |
} |
|
| 395 |
|
|
| 396 |
|
|
| 397 |
private Rank handleProlesAndRaceSublusus(BerlinModelImportState state, ResultSet rs, Rank rank) throws SQLException {
|
|
| 330 | 398 |
Rank result; |
| 331 | 399 |
String rankAbbrev = rs.getString("RankAbbrev");
|
| 332 | 400 |
// String rankStr = rs.getString("Rank");
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonNameRelationImport.java | ||
|---|---|---|
| 36 | 36 |
import java.util.Map; |
| 37 | 37 |
import java.util.Set; |
| 38 | 38 |
|
| 39 |
import org.apache.commons.lang.StringUtils; |
|
| 40 | 39 |
import org.apache.log4j.Logger; |
| 41 | 40 |
import org.springframework.stereotype.Component; |
| 42 | 41 |
|
| ... | ... | |
| 46 | 45 |
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
| 47 | 46 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 48 | 47 |
import eu.etaxonomy.cdm.model.common.AnnotatableEntity; |
| 48 |
import eu.etaxonomy.cdm.model.common.Annotation; |
|
| 49 |
import eu.etaxonomy.cdm.model.common.AnnotationType; |
|
| 49 | 50 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 50 | 51 |
import eu.etaxonomy.cdm.model.name.HybridRelationshipType; |
| 51 | 52 |
import eu.etaxonomy.cdm.model.name.IBotanicalName; |
| ... | ... | |
| 77 | 78 |
|
| 78 | 79 |
@Override |
| 79 | 80 |
protected String getIdQuery(BerlinModelImportState state) {
|
| 80 |
if (StringUtils.isNotBlank(state.getConfig().getNameIdTable())){
|
|
| 81 |
String result = super.getIdQuery(state); |
|
| 82 |
result += " WHERE nameFk1 IN (SELECT NameId FROM %s) OR "; |
|
| 83 |
result += " nameFk2 IN (SELECT NameId FROM %s)"; |
|
| 84 |
result = String.format(result, state.getConfig().getNameIdTable(),state.getConfig().getNameIdTable() ); |
|
| 85 |
return result; |
|
| 81 |
String nameIdTable = state.getConfig().getNameIdTable(); |
|
| 82 |
String result = super.getIdQuery(state); |
|
| 83 |
if (isNotBlank(nameIdTable)){
|
|
| 84 |
if (state.getConfig().isEuroMed()){
|
|
| 85 |
result += " WHERE nameFk1 IN (SELECT NameId FROM %s) AND RelNameQualifierFk NOT IN (1, 3, 9, 10, 16, 6, 61) OR "; |
|
| 86 |
result += " nameFk2 IN (SELECT NameId FROM %s) AND RelNameQualifierFk NOT IN (2) "; |
|
| 87 |
//2 is unclear, 17 should be in both, 62 links names to itself |
|
| 88 |
result = String.format(result, nameIdTable, nameIdTable); |
|
| 89 |
}else{
|
|
| 90 |
result += " WHERE nameFk1 IN (SELECT NameId FROM %s) OR "; |
|
| 91 |
result += " nameFk2 IN (SELECT NameId FROM %s) "; |
|
| 92 |
result = String.format(result, nameIdTable, nameIdTable ); |
|
| 93 |
} |
|
| 94 |
|
|
| 86 | 95 |
}else{
|
| 87 |
return super.getIdQuery(state);
|
|
| 96 |
//
|
|
| 88 | 97 |
} |
| 98 |
return result; |
|
| 89 | 99 |
} |
| 90 | 100 |
|
| 91 | 101 |
|
| ... | ... | |
| 143 | 153 |
|
| 144 | 154 |
if (nameFrom != null && nameTo != null){
|
| 145 | 155 |
success = handleNameRelationship(success, config, name1Id, name2Id, relQualifierFk, |
| 146 |
notes, nameFrom, nameTo, citation, microcitation, rule); |
|
| 156 |
notes, nameFrom, nameTo, citation, microcitation, rule, relNameId);
|
|
| 147 | 157 |
|
| 148 | 158 |
if (! nameFrom.isProtectedTitleCache()){
|
| 149 | 159 |
nameFrom.setTitleCache(null); |
| ... | ... | |
| 195 | 205 |
* @param citation |
| 196 | 206 |
* @param microcitation |
| 197 | 207 |
* @param rule |
| 208 |
* @param relNameId |
|
| 198 | 209 |
* @return |
| 199 | 210 |
*/ |
| 200 | 211 |
private boolean handleNameRelationship(boolean success, |
| 201 | 212 |
BerlinModelImportConfigurator config, int name1Id, int name2Id, |
| 202 | 213 |
int relQualifierFk, String notes, TaxonName nameFrom, |
| 203 | 214 |
TaxonName nameTo, Reference citation, |
| 204 |
String microcitation, String rule) {
|
|
| 215 |
String microcitation, String rule, int relNameId) {
|
|
| 205 | 216 |
AnnotatableEntity nameRelationship = null; |
| 206 | 217 |
if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
|
| 207 | 218 |
nameRelationship = nameTo.addBasionym(nameFrom, citation, microcitation, rule); |
| ... | ... | |
| 240 | 251 |
if (isLectoType){
|
| 241 | 252 |
status = NameTypeDesignationStatus.LECTOTYPE(); |
| 242 | 253 |
} |
| 243 |
nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, isRejectedType, isConservedType, /*isLectoType,*/ isNotDesignated, addToAllNames); |
|
| 254 |
if (isNotDesignated && nameTo == nameFrom){
|
|
| 255 |
nameFrom = null; //E+M case |
|
| 256 |
} |
|
| 257 |
|
|
| 258 |
nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, isRejectedType, isConservedType, isNotDesignated, addToAllNames); |
|
| 244 | 259 |
} |
| 245 | 260 |
|
| 246 | 261 |
}else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
|
| ... | ... | |
| 276 | 291 |
success = false; |
| 277 | 292 |
} |
| 278 | 293 |
} |
| 279 |
doNotes(nameRelationship, notes); |
|
| 294 |
Annotation annotation = doNotes(nameRelationship, notes); |
|
| 295 |
if (config.isEuroMed() && annotation != null){
|
|
| 296 |
if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
|
|
| 297 |
annotation.setAnnotationType(AnnotationType.TECHNICAL()); |
|
| 298 |
}else if ((relQualifierFk == NAME_REL_IS_LECTOTYPE_OF) && !notes.contains("designated")){
|
|
| 299 |
annotation.setAnnotationType(AnnotationType.TECHNICAL()); |
|
| 300 |
}else{
|
|
| 301 |
logger.warn("Annotation type not defined for name relationship " + relNameId);
|
|
| 302 |
} |
|
| 303 |
}else if (annotation != null){
|
|
| 304 |
logger.warn("Annotation type not defined for name relationship " + relNameId);
|
|
| 305 |
} |
|
| 280 | 306 |
return success; |
| 281 | 307 |
} |
| 282 | 308 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonRelationImport.java | ||
|---|---|---|
| 293 | 293 |
taxonRelationship = makeTaxonomicallyIncluded(state, classificationMap, treeRefFk, fromTaxon, toTaxon, citation, microcitation); |
| 294 | 294 |
}else if (relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){
|
| 295 | 295 |
taxonRelationship = toTaxon.addMisappliedName(fromTaxon, citation, microcitation); |
| 296 |
}else{
|
|
| 296 |
}else if (relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF || |
|
| 297 |
//TODO homo/hetero |
|
| 298 |
relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF || |
|
| 299 |
relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ){
|
|
| 300 |
toTaxon.addProparteSynonym(fromTaxon, citation, microcitation); |
|
| 301 |
}else if(relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF || |
|
| 302 |
//TODO homo/hetero |
|
| 303 |
relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF || |
|
| 304 |
relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF ){
|
|
| 305 |
toTaxon.addPartialSynonym(fromTaxon, citation, microcitation); |
|
| 306 |
}else{
|
|
| 297 | 307 |
handleAllRelatedTaxa(state, fromTaxon, classificationMap, fromRefFk); |
| 298 | 308 |
handleAllRelatedTaxa(state, toTaxon, classificationMap, treeRefFk); |
| 299 | 309 |
logger.warn("Unhandled taxon relationship: RelId:" + relPTaxonId + "; QualifierId: " + relQualifierFk);
|
| ... | ... | |
| 316 | 326 |
relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF || |
| 317 | 327 |
relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF){
|
| 318 | 328 |
//pro parte already set by taxon mapping |
| 319 |
}else if (relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF || |
|
| 320 |
relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF || |
|
| 321 |
relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ){
|
|
| 322 |
synonym.setProParte(true); |
|
| 323 |
}else if(relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF || |
|
| 324 |
relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF || |
|
| 325 |
relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF ){
|
|
| 326 |
synonym.setPartial(true); |
|
| 329 |
// }else if (relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF ||
|
|
| 330 |
// relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF ||
|
|
| 331 |
// relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ){
|
|
| 332 |
// synonym.setProParte(true);
|
|
| 333 |
// }else if(relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF ||
|
|
| 334 |
// relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF ||
|
|
| 335 |
// relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF ){
|
|
| 336 |
// synonym.setPartial(true);
|
|
| 327 | 337 |
}else{
|
| 328 | 338 |
success = false; |
| 329 | 339 |
logger.warn("Synonym relationship type not yet implemented: " + relQualifierFk);
|
| ... | ... | |
| 610 | 620 |
if (relQualifierFk == TAX_REL_IS_INCLUDED_IN || |
| 611 | 621 |
relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){
|
| 612 | 622 |
return true; |
| 623 |
}else if (relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF || |
|
| 624 |
relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF || |
|
| 625 |
relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF || |
|
| 626 |
relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF || |
|
| 627 |
relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF || |
|
| 628 |
relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF |
|
| 629 |
){
|
|
| 630 |
return true; |
|
| 631 |
|
|
| 613 | 632 |
}else{
|
| 614 | 633 |
return false; |
| 615 | 634 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/germanSL/GermanSLImporBase.java | ||
|---|---|---|
| 1 |
/** |
|
| 2 |
* Copyright (C) 2018 EDIT |
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 |
* http://www.e-taxonomy.eu |
|
| 5 |
* |
|
| 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 8 |
*/ |
|
| 9 |
package eu.etaxonomy.cdm.io.redlist.germanSL; |
|
| 10 |
|
|
| 11 |
import org.apache.log4j.Logger; |
|
| 12 |
|
|
| 13 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport; |
|
| 14 |
import eu.etaxonomy.cdm.model.name.IBotanicalName; |
|
| 15 |
|
|
| 16 |
/** |
|
| 17 |
* @author a.mueller |
|
| 18 |
* @since 15.05.2018 |
|
| 19 |
* |
|
| 20 |
*/ |
|
| 21 |
public abstract class GermanSLImporBase |
|
| 22 |
extends SimpleExcelTaxonImport<GermanSLImportConfigurator> {
|
|
| 23 |
|
|
| 24 |
private static final long serialVersionUID = 236093186271666895L; |
|
| 25 |
|
|
| 26 |
private static final Logger logger = Logger.getLogger(GermanSLImporBase.class); |
|
| 27 |
|
|
| 28 |
|
|
| 29 |
protected class NameResult{
|
|
| 30 |
IBotanicalName name; |
|
| 31 |
boolean proParte = false; |
|
| 32 |
String sensu = null; |
|
| 33 |
String auct = null; |
|
| 34 |
} |
|
| 35 |
|
|
| 36 |
protected boolean isAccepted(String statusStr, NameResult nameResult){
|
|
| 37 |
if (nameResult.proParte){
|
|
| 38 |
return true; //pro parte synonyms and misapplied names are always handled as concept relationships |
|
| 39 |
//and therefore need to be accepted |
|
| 40 |
}else if ("FALSE()".equals(statusStr) || "0".equals(statusStr) || "false".equalsIgnoreCase(statusStr)){
|
|
| 41 |
return true; |
|
| 42 |
} else if ("TRUE()".equals(statusStr) || "1".equals(statusStr)|| "true".equalsIgnoreCase(statusStr)){
|
|
| 43 |
return false; |
|
| 44 |
}else{
|
|
| 45 |
logger.warn("Unhandled taxon status: " + statusStr);
|
|
| 46 |
return false; |
|
| 47 |
} |
|
| 48 |
} |
|
| 49 |
} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/germanSL/GermanSLTaxonImport.java | ||
|---|---|---|
| 20 | 20 |
|
| 21 | 21 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 22 | 22 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| 23 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport; |
|
| 24 | 23 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 25 | 24 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 26 | 25 |
import eu.etaxonomy.cdm.model.common.DefinedTerm; |
| ... | ... | |
| 46 | 45 |
* |
| 47 | 46 |
*/ |
| 48 | 47 |
@Component |
| 49 |
public class GermanSLTaxonImport<CONFIG extends GermanSLImportConfigurator>
|
|
| 50 |
extends SimpleExcelTaxonImport<CONFIG> {
|
|
| 48 |
public class GermanSLTaxonImport |
|
| 49 |
extends GermanSLImporBase {
|
|
| 51 | 50 |
|
| 52 | 51 |
private static final long serialVersionUID = 236093186271666895L; |
| 53 | 52 |
|
| ... | ... | |
| 99 | 98 |
|
| 100 | 99 |
|
| 101 | 100 |
@Override |
| 102 |
protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {
|
|
| 101 |
protected void firstPass(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state) {
|
|
| 103 | 102 |
String line = state.getCurrentLine() + ": "; |
| 104 | 103 |
HashMap<String, String> record = state.getOriginalRecord(); |
| 105 | 104 |
|
| ... | ... | |
| 119 | 118 |
//status |
| 120 | 119 |
String statusStr = getValue(record, SYNONYM); |
| 121 | 120 |
TaxonBase<?> taxonBase; |
| 122 |
if (isAccepted(statusStr)){
|
|
| 121 |
if (isAccepted(statusStr, nameResult)){
|
|
| 123 | 122 |
taxonBase = Taxon.NewInstance(taxonName, sec); |
| 124 |
if (nameResult.proParte){
|
|
| 125 |
logger.warn(line + "accepted taxon can not be pro parte");
|
|
| 126 |
} |
|
| 123 |
// if (nameResult.proParte){
|
|
| 124 |
// logger.warn(line + "accepted taxon can not be pro parte in GermanSL");
|
|
| 125 |
// }
|
|
| 127 | 126 |
}else{
|
| 128 | 127 |
Synonym syn = Synonym.NewInstance(taxonName, sec); |
| 129 |
if (nameResult.proParte){
|
|
| 130 |
syn.setProParte(true); |
|
| 131 |
} |
|
| 128 |
// if (nameResult.proParte){
|
|
| 129 |
// syn.setProParte(true);
|
|
| 130 |
// }
|
|
| 132 | 131 |
taxonBase = syn; |
| 133 | 132 |
} |
| 134 | 133 |
if (!isBlank(nameResult.sensu)){
|
| ... | ... | |
| 217 | 216 |
* @param secRefStr |
| 218 | 217 |
* @return |
| 219 | 218 |
*/ |
| 220 |
private Reference getSecRef(SimpleExcelTaxonImportState<CONFIG> state, String secRefStr, String line) {
|
|
| 219 |
private Reference getSecRef(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state, String secRefStr, String line) {
|
|
| 221 | 220 |
Reference result = state.getReference(secRefStr); |
| 222 | 221 |
if (result == null && secRefStr != null){
|
| 223 | 222 |
result = ReferenceFactory.newGeneric(); |
| ... | ... | |
| 261 | 260 |
} |
| 262 | 261 |
|
| 263 | 262 |
|
| 264 |
private class NameResult{
|
|
| 265 |
IBotanicalName name; |
|
| 266 |
boolean proParte = false; |
|
| 267 |
String sensu = null; |
|
| 268 |
String auct = null; |
|
| 269 |
} |
|
| 270 | 263 |
|
| 271 | 264 |
/** |
| 272 | 265 |
* @param record |
| 273 | 266 |
* @param state |
| 274 | 267 |
* @return |
| 275 | 268 |
*/ |
| 276 |
private NameResult makeName(String line, HashMap<String, String> record, SimpleExcelTaxonImportState<CONFIG> state) {
|
|
| 269 |
public NameResult makeName(String line, HashMap<String, String> record, SimpleExcelTaxonImportState<GermanSLImportConfigurator> state) {
|
|
| 277 | 270 |
|
| 278 | 271 |
String specieNrStr = getValue(record, SPECIES_NR); |
| 279 | 272 |
String nameStr = getValue(record, ABBREVIAT); |
| ... | ... | |
| 335 | 328 |
* @param rankStr |
| 336 | 329 |
* @return |
| 337 | 330 |
*/ |
| 338 |
private Rank makeRank(String line, SimpleExcelTaxonImportState<CONFIG> state, String rankStr) {
|
|
| 331 |
private Rank makeRank(String line, SimpleExcelTaxonImportState<GermanSLImportConfigurator> state, String rankStr) {
|
|
| 339 | 332 |
Rank rank = null; |
| 340 | 333 |
try {
|
| 341 | 334 |
rank = state.getTransformer().getRankByKey(rankStr); |
| ... | ... | |
| 386 | 379 |
* @param fullName |
| 387 | 380 |
* @return |
| 388 | 381 |
*/ |
| 389 |
private IBotanicalName getExistingName(SimpleExcelTaxonImportState<CONFIG> state, IBotanicalName fullName) {
|
|
| 382 |
private IBotanicalName getExistingName(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state, IBotanicalName fullName) {
|
|
| 390 | 383 |
initExistinNames(state); |
| 391 | 384 |
return (IBotanicalName)state.getName(fullName.getTitleCache()); |
| 392 | 385 |
} |
| ... | ... | |
| 395 | 388 |
* @param state |
| 396 | 389 |
*/ |
| 397 | 390 |
@SuppressWarnings("rawtypes")
|
| 398 |
private void initExistinNames(SimpleExcelTaxonImportState<CONFIG> state) {
|
|
| 391 |
private void initExistinNames(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state) {
|
|
| 399 | 392 |
if (!nameMapIsInitialized){
|
| 400 | 393 |
List<String> propertyPaths = Arrays.asList("");
|
| 401 | 394 |
List<TaxonName> existingNames = this.getNameService().list(null, null, null, null, propertyPaths); |
| ... | ... | |
| 429 | 422 |
} |
| 430 | 423 |
|
| 431 | 424 |
|
| 432 |
|
|
| 433 |
private boolean isAccepted(String statusStr){
|
|
| 434 |
if ("FALSE()".equals(statusStr) || "0".equals(statusStr) || "false".equalsIgnoreCase(statusStr)){
|
|
| 435 |
return true; |
|
| 436 |
} else if ("TRUE()".equals(statusStr) || "1".equals(statusStr)|| "true".equalsIgnoreCase(statusStr)){
|
|
| 437 |
return false; |
|
| 438 |
}else{
|
|
| 439 |
logger.warn("Unhandled taxon status: " + statusStr);
|
|
| 440 |
return false; |
|
| 441 |
} |
|
| 442 |
} |
|
| 443 |
|
|
| 444 |
|
|
| 445 | 425 |
/** |
| 446 | 426 |
* @param next |
| 447 | 427 |
* @return |
| ... | ... | |
| 457 | 437 |
|
| 458 | 438 |
|
| 459 | 439 |
@Override |
| 460 |
protected boolean isIgnore(SimpleExcelTaxonImportState<CONFIG> state) {
|
|
| 440 |
protected boolean isIgnore(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state) {
|
|
| 461 | 441 |
return ! state.getConfig().isDoTaxa(); |
| 462 | 442 |
} |
| 463 | 443 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/germanSL/GermanSLTaxonRelationImport.java | ||
|---|---|---|
| 15 | 15 |
import org.apache.log4j.Logger; |
| 16 | 16 |
import org.springframework.stereotype.Component; |
| 17 | 17 |
|
| 18 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport; |
|
| 19 | 18 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 20 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
|
| 21 | 19 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 22 | 20 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 23 | 21 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| ... | ... | |
| 31 | 29 |
* |
| 32 | 30 |
*/ |
| 33 | 31 |
@Component |
| 34 |
public class GermanSLTaxonRelationImport<CONFIG extends GermanSLImportConfigurator> |
|
| 35 |
extends SimpleExcelTaxonImport<CONFIG> {
|
|
| 32 |
public class GermanSLTaxonRelationImport extends GermanSLImporBase {
|
|
| 36 | 33 |
|
| 37 | 34 |
private static final long serialVersionUID = 3381597141845204995L; |
| 38 | 35 |
|
| ... | ... | |
| 50 | 47 |
private int count = 0; |
| 51 | 48 |
|
| 52 | 49 |
@Override |
| 53 |
protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {
|
|
| 50 |
protected void firstPass(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state) {
|
|
| 54 | 51 |
count++; |
| 55 | 52 |
Map<String, String> record = state.getOriginalRecord(); |
| 56 | 53 |
String line = state.getCurrentLine() + ": "; |
| ... | ... | |
| 59 | 56 |
String acceptedStr = getValue(record, GermanSLTaxonImport.VALID_NR); |
| 60 | 57 |
String idStr = getValue(record, GermanSLTaxonImport.SPECIES_NR); |
| 61 | 58 |
String statusStr = getValue(record, GermanSLTaxonImport.SYNONYM); |
| 59 |
NameResult nameResult = GermanSLTaxonImport.makeName (line, record, state); |
|
| 62 | 60 |
|
| 63 | 61 |
Classification classification = getClassification(state); |
| 64 | 62 |
TaxonBase<?> taxonBase = GermanSLTaxonImport.taxonIdMap.get(idStr); |
| 65 | 63 |
Taxon parent; |
| 66 |
if (isAccepted(statusStr)){
|
|
| 64 |
if (isAccepted(statusStr, nameResult)){
|
|
| 67 | 65 |
TaxonBase<?> parentTmp = GermanSLTaxonImport.taxonIdMap.get(parentStr); |
| 68 | 66 |
if (parentTmp == null){
|
| 69 | 67 |
logger.warn(line + "Parent is missing: "+ parentStr); |
| ... | ... | |
| 100 | 98 |
} |
| 101 | 99 |
|
| 102 | 100 |
|
| 103 |
private boolean isAccepted(String statusStr){
|
|
| 104 |
if ("FALSE()".equals(statusStr) || "0".equals(statusStr) || "false".equalsIgnoreCase(statusStr)){
|
|
| 105 |
return true; |
|
| 106 |
} else if ("TRUE()".equals(statusStr) || "1".equals(statusStr)|| "true".equalsIgnoreCase(statusStr)){
|
|
| 107 |
return false; |
|
| 108 |
}else{
|
|
| 109 |
logger.warn("Unhandled taxon status: " + statusStr);
|
|
| 110 |
return false; |
|
| 111 |
} |
|
| 112 |
} |
|
| 113 |
|
|
| 114 |
|
|
| 115 |
/** |
|
| 116 |
* @param next |
|
| 117 |
* @return |
|
| 118 |
*/ |
|
| 119 |
private Taxon getAccepted(TaxonBase<?> taxonBase) {
|
|
| 120 |
if (taxonBase.isInstanceOf(Taxon.class)){
|
|
| 121 |
return CdmBase.deproxy(taxonBase, Taxon.class); |
|
| 122 |
}else{
|
|
| 123 |
Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class); |
|
| 124 |
return syn.getAcceptedTaxon(); |
|
| 125 |
} |
|
| 126 |
} |
|
| 127 |
|
|
| 128 |
|
|
| 129 | 101 |
boolean needsFinalSave = true; |
| 130 | 102 |
/** |
| 131 | 103 |
* {@inheritDoc}
|
| 132 | 104 |
*/ |
| 133 | 105 |
@Override |
| 134 |
protected void secondPass(SimpleExcelTaxonImportState<CONFIG> state) {
|
|
| 106 |
protected void secondPass(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state) {
|
|
| 135 | 107 |
if (needsFinalSave){
|
| 136 | 108 |
getTaxonService().saveOrUpdate(taxaToSave); |
| 137 | 109 |
needsFinalSave = false; |
| ... | ... | |
| 142 | 114 |
/** |
| 143 | 115 |
* @return |
| 144 | 116 |
*/ |
| 145 |
private Classification getClassification(SimpleExcelTaxonImportState<CONFIG> state) {
|
|
| 117 |
private Classification getClassification(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state) {
|
|
| 146 | 118 |
if (classification == null){
|
| 147 | 119 |
GermanSLImportConfigurator config = state.getConfig(); |
| 148 | 120 |
classification = Classification.NewInstance(config.getClassificationName()); |
| ... | ... | |
| 154 | 126 |
} |
| 155 | 127 |
|
| 156 | 128 |
@Override |
| 157 |
protected boolean isIgnore(SimpleExcelTaxonImportState<CONFIG> state) {
|
|
| 129 |
protected boolean isIgnore(SimpleExcelTaxonImportState<GermanSLImportConfigurator> state) {
|
|
| 158 | 130 |
return ! state.getConfig().isDoTaxa(); |
| 159 | 131 |
} |
| 160 | 132 |
} |
| app-import/src/test/resources/eu/etaxonomy/cdm/io/PUBLIC.xsd | ||
|---|---|---|
| 12 | 12 |
<xsd:element name="COLLECTION_EXTENSION" type="COLLECTION_EXTENSION__type" /> |
| 13 | 13 |
<xsd:element name="AGENTBASE_CONTACT_URLS_AUD" type="AGENTBASE_CONTACT_URLS_AUD__type" /> |
| 14 | 14 |
<xsd:element name="STATISTICALMEASUREMENTVALUE_DEFINEDTERMBASE_AUD" type="STATISTICALMEASUREMENTVALUE_DEFINEDTERMBASE_AUD__type" /> |
| 15 |
<xsd:element name="WORKINGSET_TAXONBASE_AUD" type="WORKINGSET_TAXONBASE_AUD__type" />
|
|
| 15 |
<xsd:element name="DESCRIPTIVEDATASET_TAXONBASE_AUD" type="DESCRIPTIVEDATASET_TAXONBASE_AUD__type" />
|
|
| 16 | 16 |
<xsd:element name="FEATURETREE_RIGHTS" type="FEATURETREE_RIGHTS__type" /> |
| 17 | 17 |
<xsd:element name="COLLECTION_MEDIA_AUD" type="COLLECTION_MEDIA_AUD__type" /> |
| 18 | 18 |
<xsd:element name="REFERENCE_EXTENSION" type="REFERENCE_EXTENSION__type" /> |
| 19 | 19 |
<xsd:element name="CDM_VIEW_CDM_VIEW" type="CDM_VIEW_CDM_VIEW__type" /> |
| 20 | 20 |
<xsd:element name="REFERENCE_ANNOTATION" type="REFERENCE_ANNOTATION__type" /> |
| 21 | 21 |
<xsd:element name="DESCRIPTIONBASE_SPECIMENOROBSERVATIONBASE" type="DESCRIPTIONBASE_SPECIMENOROBSERVATIONBASE__type" /> |
| 22 |
<xsd:element name="WORKINGSET_REPRESENTATION" type="WORKINGSET_REPRESENTATION__type" />
|
|
| 22 |
<xsd:element name="DESCRIPTIVEDATASET_REPRESENTATION" type="DESCRIPTIVEDATASET_REPRESENTATION__type" />
|
|
| 23 | 23 |
<xsd:element name="TERMVOCABULARY_MARKER" type="TERMVOCABULARY_MARKER__type" /> |
| 24 | 24 |
<xsd:element name="TAXONRELATIONSHIP_ANNOTATION_AUD" type="TAXONRELATIONSHIP_ANNOTATION_AUD__type" /> |
| 25 | 25 |
<xsd:element name="MEDIA_MARKER_AUD" type="MEDIA_MARKER_AUD__type" /> |
| ... | ... | |
| 133 | 133 |
<xsd:element name="SPECIMENOROBSERVATIONBASE_MEDIA_AUD" type="SPECIMENOROBSERVATIONBASE_MEDIA_AUD__type" /> |
| 134 | 134 |
<xsd:element name="TAXONBASE_MARKER" type="TAXONBASE_MARKER__type" /> |
| 135 | 135 |
<xsd:element name="DEFINEDTERMBASE_MARKER_AUD" type="DEFINEDTERMBASE_MARKER_AUD__type" /> |
| 136 |
<xsd:element name="WORKINGSET_DESCRIPTIONBASE_AUD" type="WORKINGSET_DESCRIPTIONBASE_AUD__type" />
|
|
| 136 |
<xsd:element name="DESCRIPTIVEDATASET_DESCRIPTIONBASE_AUD" type="DESCRIPTIVEDATASET_DESCRIPTIONBASE_AUD__type" />
|
|
| 137 | 137 |
<xsd:element name="TAXONNAMEBASE_EXTENSION_AUD" type="TAXONNAMEBASE_EXTENSION_AUD__type" /> |
| 138 | 138 |
<xsd:element name="DETERMINATIONEVENT_MARKER_AUD" type="DETERMINATIONEVENT_MARKER_AUD__type" /> |
| 139 | 139 |
<xsd:element name="CLASSIFICATION_ORIGINALSOURCEBASE" type="CLASSIFICATION_ORIGINALSOURCEBASE__type" /> |
| ... | ... | |
| 158 | 158 |
<xsd:element name="AGENTBASE_CREDIT" type="AGENTBASE_CREDIT__type" /> |
| 159 | 159 |
<xsd:element name="DEFINEDTERMBASE_ORIGINALSOURCEBASE" type="DEFINEDTERMBASE_ORIGINALSOURCEBASE__type" /> |
| 160 | 160 |
<xsd:element name="AGENTBASE_CONTACT_PHONENUMBERS" type="AGENTBASE_CONTACT_PHONENUMBERS__type" /> |
| 161 |
<xsd:element name="WORKINGSET_MARKER_AUD" type="WORKINGSET_MARKER_AUD__type" />
|
|
| 161 |
<xsd:element name="DESCRIPTIVEDATASET_MARKER_AUD" type="DESCRIPTIVEDATASET_MARKER_AUD__type" />
|
|
| 162 | 162 |
<xsd:element name="TERMVOCABULARY_EXTENSION_AUD" type="TERMVOCABULARY_EXTENSION_AUD__type" /> |
| 163 | 163 |
<xsd:element name="SPECIMENOROBSERVATIONBASE_MARKER" type="SPECIMENOROBSERVATIONBASE_MARKER__type" /> |
| 164 | 164 |
<xsd:element name="PERMISSIONGROUP_GRANTEDAUTHORITYIMPL" type="PERMISSIONGROUP_GRANTEDAUTHORITYIMPL__type" /> |
| ... | ... | |
| 185 | 185 |
<xsd:element name="COLLECTION_RIGHTS_AUD" type="COLLECTION_RIGHTS_AUD__type" /> |
| 186 | 186 |
<xsd:element name="INDIVIDUALASSOCIATION_LANGUAGESTRING_AUD" type="INDIVIDUALASSOCIATION_LANGUAGESTRING_AUD__type" /> |
| 187 | 187 |
<xsd:element name="AGENTBASE_DEFINEDTERMBASE_AUD" type="AGENTBASE_DEFINEDTERMBASE_AUD__type" /> |
| 188 |
<xsd:element name="WORKINGSET_DESCRIPTIONBASE" type="WORKINGSET_DESCRIPTIONBASE__type" />
|
|
| 188 |
<xsd:element name="DESCRIPTIVEDATASET_DESCRIPTIONBASE" type="DESCRIPTIVEDATASET_DESCRIPTIONBASE__type" />
|
|
| 189 | 189 |
<xsd:element name="GENBANKACCESSION_AUD" type="GENBANKACCESSION_AUD__type" /> |
| 190 | 190 |
<xsd:element name="POLYTOMOUSKEY_EXTENSION_AUD" type="POLYTOMOUSKEY_EXTENSION_AUD__type" /> |
| 191 | 191 |
<xsd:element name="DESCRIPTIONELEMENTBASE_STATEDATA_AUD" type="DESCRIPTIONELEMENTBASE_STATEDATA_AUD__type" /> |
| 192 |
<xsd:element name="WORKINGSET_ANNOTATION" type="WORKINGSET_ANNOTATION__type" />
|
|
| 192 |
<xsd:element name="DESCRIPTIVEDATASET_ANNOTATION" type="DESCRIPTIVEDATASET_ANNOTATION__type" />
|
|
| 193 | 193 |
<xsd:element name="FEATURETREE_ORIGINALSOURCEBASE" type="FEATURETREE_ORIGINALSOURCEBASE__type" /> |
| 194 | 194 |
<xsd:element name="TAXONBASE_MARKER_AUD" type="TAXONBASE_MARKER_AUD__type" /> |
| 195 | 195 |
<xsd:element name="MEDIA_ANNOTATION_AUD" type="MEDIA_ANNOTATION_AUD__type" /> |
| ... | ... | |
| 212 | 212 |
<xsd:element name="CDMMETADATA" type="CDMMETADATA__type" /> |
| 213 | 213 |
<xsd:element name="RELATIONSHIPTERMBASE_INVERSEREPRESENTATION_AUD" type="RELATIONSHIPTERMBASE_INVERSEREPRESENTATION_AUD__type" /> |
| 214 | 214 |
<xsd:element name="SPECIMENOROBSERVATIONBASE" type="SPECIMENOROBSERVATIONBASE__type" /> |
| 215 |
<xsd:element name="WORKINGSET" type="WORKINGSET__type" />
|
|
| 215 |
<xsd:element name="DESCRIPTIVEDATASET" type="DESCRIPTIVEDATASET__type" />
|
|
| 216 | 216 |
<xsd:element name="MEDIA_SEQUENCE" type="MEDIA_SEQUENCE__type" /> |
| 217 | 217 |
<xsd:element name="TERMVOCABULARY_RIGHTS_AUD" type="TERMVOCABULARY_RIGHTS_AUD__type" /> |
| 218 | 218 |
<xsd:element name="FEATURENODE_DEFINEDTERMBASE_ONLYAPPLICABLE" type="FEATURENODE_DEFINEDTERMBASE_ONLYAPPLICABLE__type" /> |
| ... | ... | |
| 228 | 228 |
<xsd:element name="TYPEDESIGNATIONBASE_ANNOTATION" type="TYPEDESIGNATIONBASE_ANNOTATION__type" /> |
| 229 | 229 |
<xsd:element name="NAMERELATIONSHIP_ANNOTATION" type="NAMERELATIONSHIP_ANNOTATION__type" /> |
| 230 | 230 |
<xsd:element name="ADDRESS" type="ADDRESS__type" /> |
| 231 |
<xsd:element name="MULTIACCESSKEY_COVEREDTAXON" type="WORKINGSET_TAXONBASE__type" /> |
|
| 231 |
<xsd:element name="MULTIACCESSKEY_COVEREDTAXON" type="DESCRIPTIVEDATASET_TAXONBASE__type" /> |
|
Also available in: Unified diff
latest changes to BgbmInstancesUpdater, E+M Import, GermanSL Import, etct