From c193fda8ec2b8625d40a00aa514f8079a0ba4b2d Mon Sep 17 00:00:00 2001 From: =?utf8?q?Andreas=20M=C3=BCller?= Date: Sat, 27 Aug 2022 18:19:31 +0200 Subject: [PATCH] ref #4670 fix further E+M problems in BerlinModelImport --- .../berlinModelImport/MTMooseActivator.java | 12 +++++++++--- .../berlinModel/in/BerlinModelAreaImport.java | 11 +---------- .../in/BerlinModelTaxonRelationImport.java | 18 ++++++++++-------- 3 files changed, 20 insertions(+), 21 deletions(-) diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/MTMooseActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/MTMooseActivator.java index 7196a6f1..f671b6e5 100644 --- a/app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/MTMooseActivator.java +++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/MTMooseActivator.java @@ -40,9 +40,9 @@ public class MTMooseActivator { static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; static final Source berlinModelSource = BerlinModelSources.MT_MOOSE(); -// static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); + static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); // static final ICdmDataSource cdmDestination = CdmDestinations.cdm_redlist_moose_production(); - static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test(); +// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test(); static final UUID classificationUuid = UUID.fromString("601d8a00-cffe-4509-af93-b15b543ccf8d"); static final UUID sourceRefUuid = UUID.fromString("601d8a00-cffe-4509-af93-b15b543ccf8d"); @@ -80,7 +80,9 @@ public class MTMooseActivator { static final boolean doTaxa = true; static final boolean doRelTaxa = true; static final boolean doFacts = false; //no facts exist + static final boolean doNamedAreas = false; //no areas exist static final boolean doOccurences = false; //no occurrences exist + static final boolean doOccurenceSources = false; //no occurrences exist static final boolean doCommonNames = false; //no common names exist // ************************ NONE **************************************** // @@ -100,8 +102,10 @@ public class MTMooseActivator { // static final boolean doTaxa = false; // static final boolean doRelTaxa = false; // static final boolean doFacts = false; +// static final boolean doNamedAreas = false; // static final boolean doOccurences = false; -// static final boolean doCommonNames = false; +// static final boolean doOccurenceSources = false; +// static final boolean doCommonNames = false; public void invoke(String[] args){ @@ -130,7 +134,9 @@ public class MTMooseActivator { config.setDoTaxa(doTaxa); config.setDoRelTaxa(doRelTaxa); config.setDoFacts(doFacts); + config.setDoNamedAreas(doNamedAreas); config.setDoOccurrence(doOccurences); + config.setDoOccurrenceSources(doOccurenceSources); config.setDoCommonNames(doCommonNames); config.setSourceRefUuid(sourceRefUuid); config.setRelTaxaIdQuery(relPTaxonIdQuery); diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelAreaImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelAreaImport.java index 4a02970c..52e1ebca 100644 --- a/app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelAreaImport.java +++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelAreaImport.java @@ -87,10 +87,6 @@ public class BerlinModelAreaImport extends BerlinModelImportBase { private Map euroMedAreas = new HashMap<>(); - - /** - * {@inheritDoc} - */ @Override public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) { // not relevant @@ -112,8 +108,6 @@ public class BerlinModelAreaImport extends BerlinModelImportBase { return; } - - private TermVocabulary createEuroMedAreas(BerlinModelImportState state) throws SQLException { logger.warn("Start creating E+M areas"); @@ -509,7 +503,6 @@ public class BerlinModelAreaImport extends BerlinModelImportBase { return validator.validate(state); } - @Override protected boolean isIgnore(BerlinModelImportState state){ if (state.getConfig().isDoNamedAreas()){ @@ -526,6 +519,4 @@ public class BerlinModelAreaImport extends BerlinModelImportBase { } } } - - -} +} \ No newline at end of file diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonRelationImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonRelationImport.java index cfbf6429..eb1758b8 100644 --- a/app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonRelationImport.java +++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonRelationImport.java @@ -6,7 +6,6 @@ * The contents of this file are subject to the Mozilla Public License Version 1.1 * See LICENSE.TXT at the top of this package for the full license terms. */ - package eu.etaxonomy.cdm.io.berlinModel.in; import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_HETEROTYPIC_SYNONYM_OF; @@ -80,6 +79,7 @@ public class BerlinModelTaxonRelationImport extends BerlinModelImportBase { private static final String pluralString = "taxon relations"; private static final String dbTableName = "RelPTaxon"; + private boolean hasProvisional = true; public BerlinModelTaxonRelationImport(){ super(dbTableName, pluralString); @@ -301,7 +301,7 @@ public class BerlinModelTaxonRelationImport extends BerlinModelImportBase { } Taxon fromTaxon = (Taxon)taxon1; if (relQualifierFk == TAX_REL_IS_INCLUDED_IN){ - Boolean provisional = rs.getBoolean("Provisional"); + Boolean provisional = makeProvisional(rs); taxonRelationship = makeTaxonomicallyIncluded(state, classificationMap, treeRefFk, fromTaxon, toTaxon, citation, microcitation, provisional); }else if (relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){ boolean isProParte = "p.p.".equals(notes); @@ -463,13 +463,15 @@ public class BerlinModelTaxonRelationImport extends BerlinModelImportBase { return success; } + private boolean makeProvisional(ResultSet rs){ + try { + return hasProvisional? rs.getBoolean("Provisional") : false; + } catch (SQLException e) { + hasProvisional = false; + return false; + } + } - /** - * @param toTaxon - * @param synonym - * @param notes - * @return - */ private String handleSynonymNotes(BerlinModelImportState state, Taxon toTaxon, Synonym synonym, String notes, int relId) { if (state.getConfig().isEuroMed() && isNotBlank(notes)){ notes = notes.trim(); -- 2.34.1