package eu.etaxonomy.cdm.database.update.v33_34;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import org.apache.log4j.Logger;
+import org.hibernate.loader.custom.ColumnCollectionAliases;
import eu.etaxonomy.cdm.database.update.ColumnAdder;
import eu.etaxonomy.cdm.database.update.ISchemaUpdater;
import eu.etaxonomy.cdm.database.update.ISchemaUpdaterStep;
import eu.etaxonomy.cdm.database.update.SchemaUpdaterBase;
+import eu.etaxonomy.cdm.database.update.SimpleSchemaUpdaterStep;
+import eu.etaxonomy.cdm.database.update.TableCreator;
import eu.etaxonomy.cdm.database.update.TableDroper;
/**
String stepName;
String tableName;
ISchemaUpdaterStep step;
- String columnName;
+// String columnName;
String newColumnName;
- String oldColumnName;
+// String oldColumnName;
+ String query;
List<ISchemaUpdaterStep> stepList = new ArrayList<ISchemaUpdaterStep>();
stepList.add(step);
//Institution for DerivationEvent
- //TODO H2 / PostGreSQL / SQL Server
stepName = "Add foreign key for DerivationEvent.institution";
tableName = "DerivationEvent";
newColumnName = "institution_id";
stepList.add(step);
//Institution for Amplication
- //TODO H2 / PostGreSQL / SQL Server
stepName = "Add foreign key for Amplification.institution";
tableName = "Amplification";
newColumnName = "institution_id";
step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, notNull, referencedTable);
stepList.add(step);
- //Institution for Amplification
- //TODO H2 / PostGreSQL / SQL Server
- stepName = "Add foreign key for DerivationEvent.taxonName";
- tableName = "DerivationEvent";
+ //TaxonName for DeterminationEvent
+ stepName = "Add foreign key for DeterminationEvent.taxonName";
+ tableName = "DeterminationEvent";
newColumnName = "taxonname_id";
referencedTable = "TaxonNameBase";
step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, notNull, referencedTable);
stepList.add(step);
-
-
-
-// xxx update data
-//
+ //FIXME H2, SQL Server, PostGres
+ //update DerivationEvent.taxonname_id
+ stepName = "Update taxon name in derivation event";
+ query = "UPDATE DeterminationEvent dev " +
+ " SET taxonname_id = (SELECT name_id FROM TaxonBase tb WHERE tb.id = dev.taxon_id) " +
+ " WHERE taxon_id IS NOT NULL ";
+ tableName = "DeterminationEvent";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "", -99);
+ stepList.add(step);
+
+
+ //PAT
+ //ad absence term
+ stepName = "Create absenceterm column";
+ tableName = "DefinedTermBase";
+ newColumnName = "absenceterm";
+ step = ColumnAdder.NewBooleanInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, null);
+ stepList.add(step);
+
+ //set default value
+ stepName ="Update AbsenceTerm vocabulary";
+ tableName = "DefinedTermBase";
+ query = " UPDATE @@DefinedTermBase@@ " +
+ " SET absenceterm = @@FALSE@@ " +
+ " WHERE termType = 'PAT' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, tableName, 99);
+ stepList.add(step);
- //Rename Sequence_SingleRead
-
-
- //Add fields
-
+ //vocabulary for absence terms
+ stepName ="Update AbsenceTerm vocabulary";
+ tableName = "DefinedTermBase";
+ query = " UPDATE @@DefinedTermBase@@ " +
+ " SET absenceterm = @@TRUE@@, "
+ + " vocabulary_id = "
+ + "(SELECT id FROM @@TermVocabulary@@ "
+ + " WHERE uuid = 'adbbbe15-c4d3-47b7-80a8-c7d104e53a05'),"
+ + " orderindex = orderindex + "
+ + " (SELECT max(orderindex) FROM "
+ + " (SELECT * FROM DefinedTermBase dtb2 "
+ + " WHERE dtb2.termtype = 'PAT' AND dtb2.absenceterm = 0 "
+ + ") as tmp )" +
+ " WHERE DTYPE = 'AbsenceTerm' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, tableName, 99);
+ stepList.add(step);
+
+ //PAT - DTYPE
+ stepName ="Update PresenceAbsenceTerms DTYPE";
+ tableName = "DefinedTermBase";
+ query = " UPDATE @@DefinedTermBase@@ " +
+ " SET DTYPE = 'PresenceAbsenceTerm' " +
+ " WHERE termType = 'PAT' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, tableName, 99);
+ stepList.add(step);
+
+ //PAT - remove absence vocabulary
+ stepName ="Remove Absence Vocabulary I";
+ tableName = "TermVocabulary_Representation";
+ query = " DELETE FROM TermVocabulary_Representation " +
+ " WHERE TermVocabulary_id in (SELECT id FROM TermVocabulary WHERE uuid = '5cd438c8-a8a1-4958-842e-169e83e2ceee') ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, tableName, 99);
+ stepList.add(step);
+
+ //PAT - remove absence vocabulary
+ stepName ="Remove Absence Vocabulary II";
+ tableName = "TermVocabulary_Representation";
+ query = " DELETE FROM TermVocabulary"
+ + " WHERE uuid = '5cd438c8-a8a1-4958-842e-169e83e2ceee' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, tableName, 99);
+ stepList.add(step);
+
+ //PAT - remove absence vocabulary
+ stepName ="Remove Absence Vocabulary III";
+ tableName = "Representation";
+ query = " DELETE FROM Representation "
+ + " WHERE text = 'AbsenceTerm' AND label = 'AbsenceTerm' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, tableName, 99);
+ stepList.add(step);
+
+ //PAT - update representation
+ stepName ="Update Presence Absence vocabulary representation";
+ tableName = "Representation";
+ query = " UPDATE Representation "
+ + " SET text = 'Presence Absence Term', label = 'Presence Absence Term' "
+ + " WHERE text = 'Presence Term' AND label = 'Presence Term' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, tableName, 99);
+ stepList.add(step);
+
+ //PAT - update titlecache
+ stepName ="Update Presence Absence vocabulary titlecache";
+ tableName = "TermVocabulary";
+ query = " UPDATE TermVocabulary "
+ + " SET titleCache = 'Presence Absence Term' "
+ + " WHERE uuid = 'adbbbe15-c4d3-47b7-80a8-c7d104e53a05' ";
+ step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, tableName, 99);
+ stepList.add(step);
+
+ //SingleReadAlignment
+ stepName = "Remove Sequence_SingleRead"; //we assume that this field is not yet used
+ tableName = "Sequence_SingleRead";
+ step = TableDroper.NewInstance(stepName, tableName, INCLUDE_AUDIT, true);
+ stepList.add(step);
+
+ //Add SingleReadAlignment
+ stepName = "Add SingleReadAlignment";
+ tableName = "SingleReadAlignment";
+ String[] columnNames = new String[]{"shifts","editedsequence",
+ "consensusalignment_id","singleread_id"};
+ String[] columnTypes = new String[]{"clob","clob","int","int"};
+ String[] referencedTables = new String[]{null, null,"Sequence","SingleRead"};
+ step = TableCreator.NewInstance(stepName, tableName, columnNames, columnTypes,
+ referencedTables, INCLUDE_AUDIT, true);
+ stepList.add(step);
+
+
//SpecimenOrObservationBase_Sequence (was incorrect mapping before)
stepName = "Remove SpecimenOrObservationBase_Sequence";
tableName = "SpecimenOrObservationBase_Sequence";
BGBM BDI Projects / cdmlib.git / blobdiff