From: Andreas Kohlbecker Date: Thu, 8 Oct 2009 09:15:51 +0000 (+0000) Subject: final commit of Taraxacum import on behalf of anahit X-Git-Tag: 3.0.3~1651 X-Git-Url: https://dev.e-taxonomy.eu/gitweb/cdmlib.git/commitdiff_plain/ff1a69fbb4a1acfc4a91e0e73c958046a0f5b942 final commit of Taraxacum import on behalf of anahit --- diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java index b5d90129ee..c7e0f41dbf 100644 --- a/app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java +++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java @@ -244,6 +244,59 @@ public class CdmDestinations { return makeDestination(cdmServer, cdmDB, -1, cdmUserName, null); } + public static ICdmDataSource cdm_bgbm24_palmae_a(){ + DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; + String cdmServer = "192.168.2.10"; + int port = 3306; + String cdmDB = "cdm_edit_palmae_a"; + String cdmUserName = "edit"; + return makeDestination(cdmServer, cdmDB, port, cdmUserName, null); + } + + public static ICdmDataSource cdm_bgbm24_cichorieae_a(){ + DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; + String cdmServer = "192.168.2.10"; + int port = 3306; + String cdmDB = "cdm_edit_cichorieae_a"; + String cdmUserName = "edit"; + return makeDestination(cdmServer, cdmDB, port, cdmUserName, null); + } + + public static ICdmDataSource cdm_bgbm24_dipera_a(){ + DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; + String cdmServer = "192.168.2.10"; + int port = 3306; + String cdmDB = "cdm_edit_diptera_a"; + String cdmUserName = "edit"; + return makeDestination(cdmServer, cdmDB, port, cdmUserName, null); + } + public static ICdmDataSource cdm_bgbm24_palmae_b(){ + DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; + String cdmServer = "192.168.2.10"; + int port = 3306; + String cdmDB = "cdm_edit_palmae_b"; + String cdmUserName = "edit"; + return makeDestination(cdmServer, cdmDB, port, cdmUserName, null); + } + + public static ICdmDataSource cdm_bgbm24_cichorieae_b(){ + DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; + String cdmServer = "192.168.2.10"; + int port = 3306; + String cdmDB = "cdm_edit_cichorieae_b"; + String cdmUserName = "edit"; + return makeDestination(cdmServer, cdmDB, port , cdmUserName, null); + } + + public static ICdmDataSource cdm_bgbm24_dipera_b(){ + DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; + String cdmServer = "127.0.0.1"; + int port = 3306; + String cdmDB = "cdm_edit_diptera_b"; + String cdmUserName = "edit"; + return makeDestination(cdmServer, cdmDB, port, cdmUserName, null); + } + public static ICdmDataSource cdm_local_palmae(){ DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; String cdmServer = "127.0.0.1"; diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/CichorieaeActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/CichorieaeActivator.java index 64ca2d6b00..a33f16f420 100644 --- a/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/CichorieaeActivator.java +++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/CichorieaeActivator.java @@ -52,7 +52,7 @@ public class CichorieaeActivator { //database validation status (create, update, validate ...) static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; static final Source berlinModelSource = BerlinModelSources.EDIT_CICHORIEAE(); - static final ICdmDataSource cdmDestination = CdmDestinations.localH2Cichorieae(); + static final ICdmDataSource cdmDestination = CdmDestinations.cdm_bgbm24_cichorieae_b(); static final UUID secUuid = UUID.fromString("6924c75d-e0d0-4a6d-afb7-3dd8c71195ca"); static final UUID taxonomicTreeUuid = UUID.fromString("534e190f-3339-49ba-95d9-fa27d5493e3e"); diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/CichorieaeImageActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/CichorieaeImageActivator.java index 1fa23b6248..242c796241 100644 --- a/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/CichorieaeImageActivator.java +++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/CichorieaeImageActivator.java @@ -32,7 +32,7 @@ public class CichorieaeImageActivator { public static final File sourceFolder = new File("\\\\media\\editwp6\\photos"); // private static final File sourceFile = new File("src/main/resources/images/images_cich.xls"); - private static final ICdmDataSource cdmDestination = CdmDestinations.localH2Cichorieae(); + private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_bgbm24_cichorieae_b(); // private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_import_cichorieae(); static final UUID secUuid = UUID.fromString("6924c75d-e0d0-4a6d-afb7-3dd8c71195ca"); diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/TaraxacumActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/TaraxacumActivator.java index 1bbc710825..0a49e56c52 100644 --- a/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/TaraxacumActivator.java +++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/TaraxacumActivator.java @@ -51,10 +51,12 @@ public class TaraxacumActivator { //database validation status (create, update, validate ...) static DbSchemaValidation hbm2dll = DbSchemaValidation.UPDATE; static final Source berlinModelSource = BerlinModelSources.EDIT_Taraxacum(); - static final ICdmDataSource cdmDestination = CdmDestinations.cdm_import_cichorieae(); + static final ICdmDataSource cdmDestination = CdmDestinations.cdm_bgbm24_cichorieae_b(); org.h2.jdbc.JdbcSQLException h; - static final UUID treeUuid = UUID.fromString("ba7120ce-4fab-49dc-aaa4-f36276426aa8"); + static final UUID treeUuid = UUID.fromString("019c4b4d-736b-4d2e-883c-e3244167080a"); +// static final UUID treeUuid = UUID.fromString("00db28a7-50e1-4abc-86ec-b2a8ce870de9"); +// static final UUID treeUuid = UUID.fromString("534e190f-3339-49ba-95d9-fa27d5493e3e"); static final int sourceSecId = 7700000; static final UUID featureTreeUuid = UUID.fromString("ab007336-d853-4f2f-a490-7c8232eafe7b"); @@ -82,7 +84,7 @@ public class TaraxacumActivator { // **************** ALL ********************* -//// authors + //authors static final boolean doAuthors = true; //references static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; @@ -105,17 +107,17 @@ public class TaraxacumActivator { // //authors // static final boolean doAuthors = false; // //references -// static final DO_REFERENCES doReferences = DO_REFERENCES.NONE; +// static final DO_REFERENCES doReferences = DO_REFERENCES.CONCEPT_REFERENCES; // //names -// static final boolean doTaxonNames = false; +// static final boolean doTaxonNames = true; // static final boolean doRelNames = false; // static final boolean doNameStatus = false; // static final boolean doTypes = false; // static final boolean doNameFacts = false; // // //taxa -// static final boolean doTaxa = false; -// static final boolean doRelTaxa = false; +// static final boolean doTaxa = true; +// static final boolean doRelTaxa = true; // static final boolean doFacts = false; // static final boolean doOccurences = false; @@ -131,6 +133,7 @@ public class TaraxacumActivator { BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source, destination); + bmImportConfigurator.setTreeUuid(treeUuid); // bmImportConfigurator.setSecUuid(secUuid); bmImportConfigurator.setSourceSecId(sourceSecId); @@ -177,7 +180,9 @@ public class TaraxacumActivator { FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE()); tree.getRoot().addChild(imageNode); FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); - tree.getRoot().addChild(distributionNode, 2); + FeatureNode featureNode = tree.getRoot(); +// tree.getRoot().addChild(distributionNode, 2); + tree.getRoot().addChild(distributionNode, featureNode.getChildCount() + 1); app.getDescriptionService().saveFeatureTree(tree); mergeIntoCichorieae(app); app.commitTransaction(tx); @@ -186,7 +191,7 @@ public class TaraxacumActivator { logger.info("End import from BerlinModel ("+ source.getDatabase() + ")..."); } - public void mergeIntoCichorieae(CdmApplicationController app){ + public void mergeIntoCichorieae(CdmApplicationController app){ String taraxTaraxacum = "9a7bced0-fa1a-432e-9cca-57b62219cde6"; String cichTaraxacum = "c946ac62-b6c6-493b-8ed9-278fa38b931a"; @@ -194,22 +199,39 @@ public class TaraxacumActivator { Taxon taraxacumInCich = (Taxon)app.getTaxonService().findByUuid(taraxacumCichUUID); if (taraxacumInCich != null) { logger.info("Merge Taraxacum"); - Taxon parent = taraxacumInCich.getTaxonomicParent(); - Set parentNodes = parent.getTaxonNodes(); - if(parentNodes.size() != 1){ - throw new RuntimeException("Exactly one Taxon Node expected, but found " + parentNodes.size()); + Set taxonNodesInCich = taraxacumInCich.getTaxonNodes(); + TaxonNode taxonNodeInCich = null; + TaxonNode parentNodeInCich = null; + Taxon parentInCich = null; + + if (taxonNodesInCich == null) { + logger.error("No taxon nodes found for Taraxacum in Cich DB"); + } else { + logger.info(taxonNodesInCich .size()+ " taxon node(s) found for Taraxacum in Cich DB"); + taxonNodeInCich = taxonNodesInCich.iterator().next(); + parentNodeInCich = taxonNodeInCich.getParent(); + parentInCich = parentNodeInCich.getTaxon(); } - TaxonNode parentNode = parentNodes.iterator().next(); + UUID taraxacumTaraxUUID = UUID.fromString(taraxTaraxacum); Taxon taraxacumInTarax = (Taxon)app.getTaxonService().findByUuid(taraxacumTaraxUUID); + + Set taxonNodesInTarax = taraxacumInTarax.getTaxonNodes(); + + if (taxonNodesInTarax == null) { + logger.warn("No taxon nodes found for Taraxacum in Taraxacum DB"); + } //TODO reference ReferenceBase citation = null; String microcitation = null; - parentNode.addChild(taraxacumInTarax, citation, microcitation); - app.getTaxonService().save(parent); - TaxonNode taraxacumInCichNode = parentNode.getTaxonomicTree().getNode(taraxacumInCich); - parentNode.removeChild(taraxacumInCichNode); + + TaxonNode taxonNodeInTarax = + parentNodeInCich.addChild(taraxacumInTarax, citation, microcitation); + parentNodeInCich.getTaxonomicTree().addParentChild(parentInCich, taraxacumInTarax, null, null); + parentNodeInCich.removeChild(taxonNodeInCich); + + app.getTaxonService().save(parentInCich); app.getTaxonService().delete(taraxacumInCich); } }