--- /dev/null
+/**
+* Copyright (C) 2007 EDIT
+* European Distributed Institute of Taxonomy
+* http://www.e-taxonomy.eu
+*
+* 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.app.berlinModelImport;
+
+import java.util.List;
+import java.util.Set;
+import java.util.UUID;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.security.core.GrantedAuthority;
+import org.springframework.transaction.TransactionStatus;
+
+import eu.etaxonomy.cdm.api.application.FirstDataInserter;
+import eu.etaxonomy.cdm.api.application.ICdmRepository;
+import eu.etaxonomy.cdm.api.service.IGroupService;
+import eu.etaxonomy.cdm.app.common.CdmDestinations;
+import eu.etaxonomy.cdm.database.DbSchemaValidation;
+import eu.etaxonomy.cdm.database.ICdmDataSource;
+import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
+import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
+import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
+import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
+import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
+import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
+import eu.etaxonomy.cdm.io.common.Source;
+import eu.etaxonomy.cdm.model.agent.Person;
+import eu.etaxonomy.cdm.model.description.Feature;
+import eu.etaxonomy.cdm.model.metadata.CdmPreference;
+import eu.etaxonomy.cdm.model.metadata.PreferencePredicate;
+import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
+import eu.etaxonomy.cdm.model.permission.GrantedAuthorityImpl;
+import eu.etaxonomy.cdm.model.permission.Group;
+import eu.etaxonomy.cdm.model.permission.User;
+import eu.etaxonomy.cdm.model.taxon.Taxon;
+import eu.etaxonomy.cdm.model.taxon.TaxonNode;
+import eu.etaxonomy.cdm.model.term.TermTree;
+import eu.etaxonomy.cdm.persistence.permission.Role;
+import eu.etaxonomy.cdm.persistence.query.MatchMode;
+
+/**
+ * TODO add the following to a wiki page:
+ * HINT: If you are about to import into a mysql data base running under windows and if you wish to
+ * dump and restore the resulting data bas under another operation systen
+ * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
+ *
+ * @author a.mueller
+ */
+public class MclActivator {
+
+ private static final Logger logger = LogManager.getLogger();
+
+ //database validation status (create, update, validate ...)
+ static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
+ static final Source berlinModelSource = BerlinModelSources.mcl();
+
+ static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
+// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_medchecklist();
+// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_medchecklist();
+// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_medchecklist();
+
+ //check - import
+ static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
+
+ static final boolean doUser = false;
+// //authors
+ static final boolean doAuthors = true;
+ //references
+ static final DO_REFERENCES doReferences = DO_REFERENCES.ALL;
+ //names
+ static final boolean doTaxonNames = true;
+ static final boolean doRelNames = true;
+ static final boolean doNameStatus = true;
+ static final boolean doNameFacts = true;
+
+ //taxa
+ static final boolean doTaxa = true;
+ static final boolean doFacts = true;
+ static final boolean doRelTaxa = true;
+ static final boolean doOccurrences = true;
+ static final boolean doOccurrenceSources = true;
+ static final boolean doCommonNames = true;
+
+ static final boolean doNamedAreas = true;
+
+ //serious types do not exist in MCL
+ static final boolean doTypes = false;
+
+ static final boolean doRunTransmissionEngine = false; // (hbm2dll == DbSchemaValidation.VALIDATE);
+
+ //etc.
+ static final boolean doMarker = false; //no relevant markers exist
+
+ boolean invers = !(hbm2dll == DbSchemaValidation.CREATE);
+
+ boolean doPreliminaryRefDetailsWithNames = true;
+
+ boolean logNotMatchingOldNames = false;
+ boolean logMatchingNotExportedOldNames = false; //true
+ boolean checkOldNameIsSynonym = false;
+ boolean includeMANsForOldNameCheck = true;
+
+ static final int sourceSecId = 7000000; //500000
+ static final UUID classificationUuid = UUID.fromString("f65a592d-a430-4db9-b994-39c181c34abe");
+ static final boolean useSingleClassification = true;
+ static final String classificationName = "Med-Checklist";
+ static final UUID featureTreeUuid = UUID.fromString("be5851fb-ddb7-4e30-a375-57d98cf30c40");
+ static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
+
+ // set to zero for unlimited nameFacts
+ static final int maximumNumberOfNameFacts = 0;
+
+ static final int partitionSize = 2500;
+
+
+ //editor - import
+ static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
+
+ //NomenclaturalCode
+ static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
+
+ //ignore null
+ static final boolean ignoreNull = false;
+
+ static final boolean switchSpeciesGroup = true;
+
+ static boolean useClassification = true;
+
+ static boolean isSplitTdwgCodes = false;
+// static boolean useEmAreaVocabulary = true;
+
+ private final boolean removeHttpMapsAnchor = true;
+
+
+ static final String infrGenericRankAbbrev = "[unranked]";
+ static final String infrSpecificRankAbbrev = "[unranked]";
+
+ static boolean useLastScrutinyAsSec = false;
+ static boolean warnForDifferingSynonymReference = false;
+
+
+// **************** ALL *********************
+
+ public void importEm2CDM (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
+ System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
+ //make BerlinModel Source
+
+ BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source, destination);
+
+ config.setClassificationName(classificationName);
+
+ config.setClassificationUuid(classificationUuid);
+ config.setSourceSecId(sourceSecId);
+ config.setNomenclaturalCode(nomenclaturalCode);
+ config.setIgnoreNull(ignoreNull);
+
+ config.setDoAuthors(doAuthors ^ invers);
+ config.setDoReferences(invers ? doReferences.invers() : doReferences);
+ config.setDoTaxonNames(doTaxonNames ^ invers);
+ config.setDoRelNames(doRelNames ^ invers);
+ config.setDoNameStatus(doNameStatus ^ invers);
+ config.setDoTypes(doTypes); //always false
+ config.setDoNameFacts(doNameFacts ^ invers);
+ config.setDoTaxa(doTaxa ^ invers);
+ config.setDoRelTaxa(doRelTaxa ^ invers);
+ config.setDoFacts(doFacts ^ invers);
+ config.setDoOccurrence(doOccurrences ^ invers);
+ config.setDoOccurrenceSources(doOccurrenceSources ^ invers);
+ config.setDoCommonNames(doCommonNames ^ invers);
+ config.setDoNamedAreas(doNamedAreas ^ invers);
+
+ config.setDoMarker(doMarker);
+ config.setDoUser(doUser ^ invers);
+
+ config.setMcl(true);
+ config.setDoSourceNumber(true);
+
+ config.setLogNotMatchingOldNames(logNotMatchingOldNames);
+ config.setLogMatchingNotExportedOldNames(logMatchingNotExportedOldNames);
+ config.setCheckOldNameIsSynonym(checkOldNameIsSynonym);
+ config.setIncludeMANsForOldNameCheck(includeMANsForOldNameCheck);
+
+ config.setUseClassification(useClassification);
+ config.setSourceRefUuid(BerlinModelTransformer.uuidSourceRefEuroMed);
+ config.setEditor(editor);
+ config.setDbSchemaValidation(hbm2dll);
+ config.setUseLastScrutinyAsSec(useLastScrutinyAsSec);
+ config.setWarnForDifferingSynonymReference(warnForDifferingSynonymReference);
+
+ // maximum number of name facts to import
+ config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
+
+ config.setInfrGenericRankAbbrev(infrGenericRankAbbrev);
+ config.setInfrSpecificRankAbbrev(infrSpecificRankAbbrev);
+ config.setRemoveHttpMapsAnchor(removeHttpMapsAnchor);
+
+ config.setDoPreliminaryRefDetailsWithNames(doPreliminaryRefDetailsWithNames);
+
+// filter
+// config.setTaxonTable(taxonTable);
+// config.setClassificationQuery(classificationQuery);
+// config.setRelTaxaIdQuery(relPTaxonIdQuery);
+// config.setNameIdTable(nameIdTable);
+// config.setReferenceIdTable(referenceIdTable);
+// config.setAuthorTeamFilter(authorTeamFilter);
+// config.setAuthorFilter(authorFilter);
+// config.setFactFilter(factFilter);
+// config.setRefDetailFilter(refDetailFilter);
+// config.setCommonNameFilter(commonNameFilter);
+// config.setOccurrenceFilter(occurrenceFilter);
+// config.setOccurrenceSourceFilter(occurrenceSourceFilter);
+// config.setWebMarkerFilter(webMarkerFilter);
+ config.setUseSingleClassification(useSingleClassification);
+
+ //TDWG codes
+ config.setSplitTdwgCodes(isSplitTdwgCodes);
+// config.setUseEmAreaVocabulary(useEmAreaVocabulary);
+
+ config.setCheck(check);
+ config.setEditor(editor);
+ config.setRecordsPerTransaction(partitionSize);
+
+ config.setSwitchSpeciesGroup(switchSpeciesGroup);
+
+ // invoke import
+ CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<>();
+ bmImport.invoke(config);
+
+// renameRanks(config, bmImport);
+
+ createFeatureTree(config, bmImport);
+
+// changeCommonNameLabel(config, bmImport);
+
+// createUsersAndRoles(config, bmImport);
+
+// runTransmissionEngine(config, bmImport);
+
+// importShapefile(config, bmImport);
+
+// createPreferences(config, bmImport); => manual
+
+// markAreasAsHidden(config, bmImport); //has been moved to BM occurrence import
+
+ System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
+ }
+
+ private void createPreferences(BerlinModelImportConfigurator config,
+ CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
+
+ if (config.isDoUser() && (config.getCheck().isImport() )){
+ ICdmRepository app = bmImport.getCdmAppController();
+
+ //area vocs
+ CdmPreference preference = CdmPreference.NewTaxEditorInstance(PreferencePredicate.AvailableDistributionAreaVocabularies, BerlinModelTransformer.uuidVocCaucasusAreas.toString()+";" + BerlinModelTransformer.uuidVocEuroMedAreas.toString());
+ preference.setAllowOverride(false);
+ app.getPreferenceService().set(preference);
+
+ //occ status list
+ String status ="42946bd6-9c22-45ad-a910-7427e8f60bfd;9eb99fe6-59e2-4445-8e6a-478365bd0fa9;c3ee7048-15b7-4be1-b687-9ce9c1a669d6;643cf9d1-a5f1-4622-9837-82ef961e880b;0c54761e-4887-4788-9dfa-7190c88746e3;83eb0aa0-1a45-495a-a3ca-bf6958b74366;aeec2947-2700-4623-8e32-9e3a430569d1;ddeac4f2-d8fa-43b8-ad7e-ca13abdd32c7;310373bf-7df4-4d02-8cb3-bcc7448805fc;5c397f7b-59ef-4c11-a33c-45691ceda91b;925662c1-bb10-459a-8c53-da5a738ac770;61cee840-801e-41d8-bead-015ad866c2f1;e191e89a-a751-4b0c-b883-7f1de70915c9";
+ CdmPreference statusListPref = CdmPreference.NewTaxEditorInstance(PreferencePredicate.AvailableDistributionAreaVocabularies, status);
+ statusListPref.setAllowOverride(false);
+ app.getPreferenceService().set(statusListPref);
+
+ //distr. editor activated
+ CdmPreference distrEditorActive = CdmPreference.NewTaxEditorInstance(PreferencePredicate.DistributionEditorActivated, "true");
+ statusListPref.setAllowOverride(true);
+ app.getPreferenceService().set(distrEditorActive);
+
+// //idInVoc for areas
+// CdmPreference distrEditorShowIdInVocForAreas = CdmPreference.NewTaxEditorInstance(PreferencePredicate.Sho.ShowIdInVocabulary, "true");
+// distrEditorShowIdInVocForAreas.setAllowOverride(true);
+// app.getPreferenceService().set(distrEditorShowIdInVocForAreas);
+//
+// //areas sort order
+// //?? correct?
+// CdmPreference distrEditorSorted = CdmPreference.NewTaxEditorInstance(PreferencePredicate.AreasSortedByIdInVocabulary, "true");
+// distrEditorSorted.setAllowOverride(true);
+// app.getPreferenceService().set(distrEditorSorted);
+//
+// //distr. status uses symbol
+// //?? correct?
+// CdmPreference distrEditorStatusUseSymbols = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowSymbolForStatus, "false");
+// distrEditorStatusUseSymbols.setAllowOverride(true);
+// app.getPreferenceService().set(distrEditorStatusUseSymbols);
+
+ //media view
+ CdmPreference showMediaView = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowMediaView, "false");
+ showMediaView.setAllowOverride(false);
+ app.getPreferenceService().set(showMediaView);
+
+ //multi classification
+ CdmPreference multiClassification = CdmPreference.NewTaxEditorInstance(PreferencePredicate.DisableMultiClassification, "true");
+ multiClassification.setAllowOverride(false);
+ app.getPreferenceService().set(multiClassification);
+
+ //taxon node wizard
+ CdmPreference showTaxonNodeWizard = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowTaxonNodeWizard, "false");
+ showTaxonNodeWizard.setAllowOverride(false);
+ app.getPreferenceService().set(showTaxonNodeWizard);
+
+ //import+export
+ CdmPreference showImportExportMenu = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowImportExportMenu, "false");
+ showImportExportMenu.setAllowOverride(true);
+ app.getPreferenceService().set(showImportExportMenu);
+
+ //show specimen
+ CdmPreference showSpecimen = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowSpecimen, "false");
+ showSpecimen.setAllowOverride(false);
+ app.getPreferenceService().set(showSpecimen);
+
+ }
+
+ }
+
+ //create feature tree
+ private void createFeatureTree(BerlinModelImportConfigurator config,
+ CdmDefaultImport<BerlinModelImportConfigurator> bmImport){
+ if (config.isDoFacts() && (config.getCheck().isImport() ) ){
+ try {
+ ICdmRepository app = bmImport.getCdmAppController();
+ TransactionStatus tx = app.startTransaction();
+
+ //make feature tree
+ TermTree<Feature> tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
+ tree.setTitleCache("Euro+Med Feature Tree", true);
+ tree.getRoot().addChild(Feature.IMAGE());
+ tree.getRoot().addChild(Feature.DISTRIBUTION(), 1);
+ tree.getRoot().addChild(Feature.COMMON_NAME(), 2);
+ app.getTermTreeService().saveOrUpdate(tree);
+
+ app.commitTransaction(tx);
+ } catch (Exception e) {
+ e.printStackTrace();
+ logger.error("Exception in createFeatureTree: " + e.getMessage());
+ }
+ }
+ }
+
+
+
+ //4. Create users and assign roles #3979
+ private void createUsersAndRoles(BerlinModelImportConfigurator config,
+ CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
+
+ try {
+ if (config.isDoRelTaxa() && (config.getCheck().isImport())){
+ ICdmRepository app = bmImport.getCdmAppController();
+ TransactionStatus tx = app.startTransaction();
+
+ //eraabstraube
+ String eraabstraube = "e.raabstraube";
+ List<User> users = app.getUserService().listByUsername(eraabstraube, MatchMode.EXACT, null, null, null, null, null);
+ User userEraabStraube;
+ if (users.isEmpty()){
+ userEraabStraube = User.NewInstance(eraabstraube, eraabstraube);
+ }else{
+ userEraabStraube = users.get(0);
+ }
+ if (userEraabStraube.getPerson() == null){
+ Person eckhard = Person.NewInstance();
+ eckhard.setFamilyName("von Raab-Straube");
+ eckhard.setGivenName("Eckhard");
+ eckhard.setPrefix("Dr.");
+ userEraabStraube.setPerson(eckhard);
+ }
+ app.getUserService().saveOrUpdate(userEraabStraube);
+
+ //groups
+ Group groupEditor = app.getGroupService().load(Group.GROUP_EDITOR_UUID);
+ groupEditor.addMember(userEraabStraube);
+ app.getGroupService().saveOrUpdate(groupEditor);
+
+ Group groupProjectManager = app.getGroupService().load(Group.GROUP_PROJECT_MANAGER_UUID);
+ groupProjectManager.addMember(userEraabStraube);
+ app.getGroupService().saveOrUpdate(groupProjectManager);
+
+ String[] publishRoles = new String[]{Role.ROLE_PUBLISH.toString()};
+ Group groupPublisher = checkGroup(app.getGroupService(), Group.GROUP_PUBLISH_UUID, "Publisher", publishRoles);
+ groupPublisher.addMember(userEraabStraube);
+ app.getGroupService().saveOrUpdate(groupPublisher);
+
+ UUID uuidEuroMedPlantBaseGroup = UUID.fromString("91be42ea-ad04-4458-9836-389277e773db");
+ String[] emPlantBaseRoles = new String[]{"TAXONNODE.[CREATE,READ,UPDATE,DELETE]"};
+ Group euroMedPlantbase = checkGroup(app.getGroupService(), uuidEuroMedPlantBaseGroup, "Euro+Med Plantbase", emPlantBaseRoles);
+ euroMedPlantbase.addMember(userEraabStraube);
+ app.getGroupService().saveOrUpdate(euroMedPlantbase);
+
+ //cichorieae-editor
+ String cichorieaeEditor = "cichorieae-editor";
+ app.getUserService().listByUsername(cichorieaeEditor, MatchMode.EXACT, null, null, null, null, null);
+ User userCichEditor;
+ if (users.isEmpty()){
+ userCichEditor = User.NewInstance(cichorieaeEditor, cichorieaeEditor);
+ }else{
+ userCichEditor = users.get(0);
+ }
+ app.getUserService().saveOrUpdate(userCichEditor);
+
+ //groups
+ groupEditor.addMember(userCichEditor);
+ app.getGroupService().saveOrUpdate(groupEditor);
+
+ UUID uuidCichorieaeSubtree = null;
+ UUID uuidCichorieae = UUID.fromString("63c7dbeb-b9a2-48b8-a75f-e3fe5e161f7c");
+ Taxon cich = (Taxon)app.getTaxonService().find(uuidCichorieae);
+ if (cich != null){
+ if (!cich.getTaxonNodes().isEmpty()){
+ TaxonNode cichNode = cich.getTaxonNodes().iterator().next();
+ uuidCichorieaeSubtree = cichNode.getUuid();
+ }
+ }
+
+ String[] cichorieaeRoles = new String[]{};
+ if (uuidCichorieaeSubtree != null){
+ cichorieaeRoles = new String[]{"TAXONNODE.[CREATE,READ,UPDATE,DELETE]{"+uuidCichorieaeSubtree.toString()+"}"};
+ }else{
+ String message = "Cichorieae node could not be found for cichorieae-editor role";
+ logger.warn(message);
+ System.out.println(message);
+ }
+ UUID uuidCichorieaeGroup = UUID.fromString("a630938d-dd4f-48c2-9406-91def487b11e");
+ String cichorieaeGroupName = "Cichorieae";
+ Group cichorieaeGroup = checkGroup(app.getGroupService(), uuidCichorieaeGroup, cichorieaeGroupName, cichorieaeRoles);
+ cichorieaeGroup.addMember(userCichEditor);
+ app.getGroupService().saveOrUpdate(cichorieaeGroup);
+
+ app.commitTransaction(tx);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ logger.error("Exception in createUsersAndRoles: " + e.getMessage());
+ }
+ }
+
+ /**
+ * copied from {@link FirstDataInserter#checkGroup}
+ */
+ private Group checkGroup(IGroupService groupService, UUID groupUuid, String groupName, String[] requiredAuthorities) {
+ Group group = groupService.load(groupUuid);
+ if(group == null){
+ group = Group.NewInstance();
+ group.setUuid(groupUuid);
+ logger.info("New Group '" + groupName + "' created");
+ }
+ group.setName(groupName); // force name
+
+ Set<GrantedAuthority> grantedAuthorities = group.getGrantedAuthorities();
+
+ for(String a : requiredAuthorities){
+ boolean isMissing = true;
+ for(GrantedAuthority ga : grantedAuthorities){
+ if(a.equals(ga.getAuthority())){
+ isMissing = false;
+ break;
+ }
+ }
+ if(isMissing){
+ GrantedAuthorityImpl newGa = GrantedAuthorityImpl.NewInstance(a);
+ group.addGrantedAuthority(newGa);
+ logger.info("New GrantedAuthority '" + a + "' added to '" + groupName + "'");
+ }
+ }
+ groupService.saveOrUpdate(group);
+ logger.info("Check of group '" + groupName + "' done");
+ return group;
+ }
+
+
+ /**
+ * @param args
+ */
+ public static void main(String[] args) {
+ MclActivator importActivator = new MclActivator();
+ Source source = berlinModelSource;
+ ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
+
+ importActivator.importEm2CDM(source, cdmRepository, hbm2dll);
+ System.exit(0);
+ }
+
+}
BGBM BDI Projects / cdmlib-apps.git / commitdiff