diff --git a/microscopy-migration-tool/src/ethz/ch/Main.java b/microscopy-migration-tool/src/ethz/ch/Main.java
index 12ef35dffccc0da8eddb91138d6eb02e8e1fb94f..30b1643c7e8527be582d31274e12f23a9bc8276b 100644
--- a/microscopy-migration-tool/src/ethz/ch/Main.java
+++ b/microscopy-migration-tool/src/ethz/ch/Main.java
@@ -194,6 +194,10 @@ public class Main
total++;
System.out.println("[DONE] " + config.getTypeCode() + "\t" + total + "/" + experiments.getTotalCount());
}
+ // Delete old experiment type
+ MasterdataHelper.deleteExperimentType(sessionToken, v3, config.getTypeCode());
+ // Delete old name property from new sample type
+ config.getSamplePropertyDelete().deleteOldPropertyType(sessionToken, v3);
}
System.out.println("4. Translate Properties to Samples");
@@ -234,6 +238,8 @@ public class Main
total++;
System.out.println("[DONE] " + config.getOldSampleTypeCode() + "\t" + total + "/" + samples.getTotalCount());
}
+ // Delete old copied property that become a sample
+ config.getEntityPropertyDelete().deleteOldPropertyType(sessionToken, v3);
}
System.out.println("5. Copy Property A to Property B on Samples and DataSets");
@@ -259,6 +265,8 @@ public class Main
for (EntityPropertyCopy config:propertyCopiesMigrationConfig) {
config.copy(sessionToken, v3);
+ // Delete old copied name property
+ config.getEntityPropertyDelete().deleteOldPropertyType(sessionToken, v3);
}
}
}
diff --git a/microscopy-migration-tool/src/ethz/ch/MasterdataHelper.java b/microscopy-migration-tool/src/ethz/ch/MasterdataHelper.java
index 03bc5663b0d4a345b64626401246beec491fd9e4..e5fe6562da9410e463ce44ffa1817ca21ed89e4c 100644
--- a/microscopy-migration-tool/src/ethz/ch/MasterdataHelper.java
+++ b/microscopy-migration-tool/src/ethz/ch/MasterdataHelper.java
@@ -8,10 +8,12 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.DataSetTypeCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.update.DataSetTypeUpdate;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.EntityKind;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.IEntityTypeId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.create.ExperimentTypeCreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.delete.ExperimentTypeDeletionOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search.ExperimentTypeSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.DataType;
@@ -19,7 +21,9 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.create.PropertyAssignmentCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.create.PropertyTypeCreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.delete.PropertyTypeDeletionOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.fetchoptions.PropertyTypeFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.PropertyAssignmentPermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.PropertyTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search.PropertyTypeSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType;
@@ -184,30 +188,69 @@ public class MasterdataHelper
// Update
//
- public static void updateSampleType(String sessionToken, IApplicationServerApi v3, String typeCode, int addOrder, String addPropertyTypeCode) {
+ public enum PropertyTypeUpdateAction { ADD, REMOVE}
+
+ public static void updateSampleType(String sessionToken, IApplicationServerApi v3, String typeCode, PropertyTypeUpdateAction updateAction, int addOrder, String addPropertyTypeCode) {
SampleTypeUpdate update = new SampleTypeUpdate();
update.setTypeId(new EntityTypePermId(typeCode));
- ListUpdateValue.ListUpdateActionAdd add = new ListUpdateValue.ListUpdateActionAdd();
- PropertyAssignmentCreation propertyAssignmentCreation = new PropertyAssignmentCreation();
- propertyAssignmentCreation.setOrdinal(addOrder);
- propertyAssignmentCreation.setPropertyTypeId(new PropertyTypePermId(addPropertyTypeCode));
- add.setItems(Arrays.asList(propertyAssignmentCreation));
- update.setPropertyAssignmentActions(Arrays.asList(add));
+ ListUpdateValue.ListUpdateAction action = null;
+ switch (updateAction) {
+ case ADD:
+ action = new ListUpdateValue.ListUpdateActionAdd();
+ PropertyAssignmentCreation propertyAssignmentCreation = new PropertyAssignmentCreation();
+ propertyAssignmentCreation.setOrdinal(addOrder);
+ propertyAssignmentCreation.setPropertyTypeId(new PropertyTypePermId(addPropertyTypeCode));
+ action.setItems(Arrays.asList(propertyAssignmentCreation));
+ break;
+ case REMOVE:
+ action = new ListUpdateValue.ListUpdateActionRemove();
+ action.setItems(Arrays.asList(new PropertyAssignmentPermId(new EntityTypePermId(typeCode, EntityKind.SAMPLE), new PropertyTypePermId(addPropertyTypeCode))));
+ update.getPropertyAssignments().setForceRemovingAssignments(true);
+ break;
+ }
+ update.setPropertyAssignmentActions(Arrays.asList(action));
v3.updateSampleTypes(sessionToken, Arrays.asList(update));
}
- public static void updateDataSetType(String sessionToken, IApplicationServerApi v3, String typeCode, int addOrder, String addPropertyTypeCode) {
+ public static void updateDataSetType(String sessionToken, IApplicationServerApi v3, String typeCode, PropertyTypeUpdateAction updateAction, int addOrder, String addPropertyTypeCode) {
DataSetTypeUpdate update = new DataSetTypeUpdate();
update.setTypeId(new EntityTypePermId(typeCode));
- ListUpdateValue.ListUpdateActionAdd add = new ListUpdateValue.ListUpdateActionAdd();
- PropertyAssignmentCreation propertyAssignmentCreation = new PropertyAssignmentCreation();
- propertyAssignmentCreation.setOrdinal(addOrder);
- propertyAssignmentCreation.setPropertyTypeId(new PropertyTypePermId(addPropertyTypeCode));
- add.setItems(Arrays.asList(propertyAssignmentCreation));
- update.setPropertyAssignmentActions(Arrays.asList(add));
+ ListUpdateValue.ListUpdateAction action = null;
+ switch (updateAction) {
+ case ADD:
+ action = new ListUpdateValue.ListUpdateActionAdd();
+ PropertyAssignmentCreation propertyAssignmentCreation = new PropertyAssignmentCreation();
+ propertyAssignmentCreation.setOrdinal(addOrder);
+ propertyAssignmentCreation.setPropertyTypeId(new PropertyTypePermId(addPropertyTypeCode));
+ action.setItems(Arrays.asList(propertyAssignmentCreation));
+ break;
+ case REMOVE:
+ action = new ListUpdateValue.ListUpdateActionRemove();
+ action.setItems(Arrays.asList(new PropertyAssignmentPermId(new EntityTypePermId(typeCode, EntityKind.DATA_SET), new PropertyTypePermId(addPropertyTypeCode))));
+ update.getPropertyAssignments().setForceRemovingAssignments(true);
+ break;
+ }
+
+ update.setPropertyAssignmentActions(Arrays.asList(action));
v3.updateDataSetTypes(sessionToken, Arrays.asList(update));
}
+ //
+ // Delete
+ //
+
+ public static void deletePropertyType(String sessionToken, IApplicationServerApi v3, String propertyTypeCode) {
+ PropertyTypeDeletionOptions propertyTypeDeletionOptions = new PropertyTypeDeletionOptions();
+ propertyTypeDeletionOptions.setReason("Microscopy Migration");
+ v3.deletePropertyTypes(sessionToken, Arrays.asList(new PropertyTypePermId(propertyTypeCode)), propertyTypeDeletionOptions);
+ }
+
+ public static void deleteExperimentType(String sessionToken, IApplicationServerApi v3, String typeCode) {
+ ExperimentTypeDeletionOptions experimentTypeDeletionOptions = new ExperimentTypeDeletionOptions();
+ experimentTypeDeletionOptions.setReason("Microscopy Migration");
+ v3.deleteExperimentTypes(sessionToken, Arrays.asList(new EntityTypePermId(typeCode, EntityKind.EXPERIMENT)), experimentTypeDeletionOptions);
+ }
+
//
// Type to translate Attachments to DataSets
//
diff --git a/microscopy-migration-tool/src/ethz/ch/dataset/DataSetPropertyCopy.java b/microscopy-migration-tool/src/ethz/ch/dataset/DataSetPropertyCopy.java
index 03b180618f530228f5c54c5901e57b6fa81d0eb3..cf3f8f8d3fc75e2fa79f54c4f75587e36d15dcf4 100644
--- a/microscopy-migration-tool/src/ethz/ch/dataset/DataSetPropertyCopy.java
+++ b/microscopy-migration-tool/src/ethz/ch/dataset/DataSetPropertyCopy.java
@@ -6,6 +6,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
import ethz.ch.MasterdataHelper;
import ethz.ch.MetadataHelper;
import ethz.ch.property.EntityPropertyCopy;
+import ethz.ch.property.EntityPropertyDelete;
import java.util.List;
@@ -22,7 +23,7 @@ public class DataSetPropertyCopy extends EntityPropertyCopy<DataSet> {
@Override
public void updatePropertyAssignmentsHolder(String sessionToken, IApplicationServerApi v3) {
- MasterdataHelper.updateDataSetType(sessionToken, v3, typeCode, 1, newPropertyCode);
+ MasterdataHelper.updateDataSetType(sessionToken, v3, typeCode, MasterdataHelper.PropertyTypeUpdateAction.ADD,1, newPropertyCode);
}
@Override
@@ -34,4 +35,9 @@ public class DataSetPropertyCopy extends EntityPropertyCopy<DataSet> {
public void updateEntityProperty(String sessionToken, IApplicationServerApi v3, DataSet entity) {
MetadataHelper.updateDataSetProperty(sessionToken, v3, entity.getPermId().getPermId(), newPropertyCode, entity.getProperty(oldPropertyCode));
}
+
+ @Override
+ public EntityPropertyDelete getEntityPropertyDelete() {
+ return new DataSetPropertyDelete(typeCode, oldPropertyCode);
+ }
}
diff --git a/microscopy-migration-tool/src/ethz/ch/dataset/DataSetPropertyDelete.java b/microscopy-migration-tool/src/ethz/ch/dataset/DataSetPropertyDelete.java
new file mode 100644
index 0000000000000000000000000000000000000000..b63a91ca3266c0c6c97c057b64a64b2bf53c33a0
--- /dev/null
+++ b/microscopy-migration-tool/src/ethz/ch/dataset/DataSetPropertyDelete.java
@@ -0,0 +1,31 @@
+package ethz.ch.dataset;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
+import ethz.ch.MasterdataHelper;
+import ethz.ch.property.EntityPropertyDelete;
+
+public class DataSetPropertyDelete extends EntityPropertyDelete {
+
+ public DataSetPropertyDelete(String typeCode, String propertyCode) {
+ super(typeCode, propertyCode);
+ }
+
+ @Override
+ public void deleteOldPropertyType(String sessionToken, IApplicationServerApi v3) {
+ DataSetType type = MasterdataHelper.getDataSetType(sessionToken, v3, typeCode);
+ boolean found = false;
+ for(PropertyAssignment propertyAssignment:type.getPropertyAssignments()) {
+ found = propertyAssignment.getPropertyType().getCode().equals(propertyCode);
+ if (found) {
+ break;
+ }
+ }
+ if (found) {
+ MasterdataHelper.updateDataSetType(sessionToken, v3, typeCode, MasterdataHelper.PropertyTypeUpdateAction.REMOVE, 1, propertyCode);
+ MasterdataHelper.deletePropertyType(sessionToken, v3, propertyCode);
+ System.out.println("[PROPERTY DELETE] " + "\t" + propertyCode);
+ }
+ }
+}
diff --git a/microscopy-migration-tool/src/ethz/ch/experiment/ExperimentType2SampleType.java b/microscopy-migration-tool/src/ethz/ch/experiment/ExperimentType2SampleType.java
index a2d8988776efed0dac4955e18c34425dc6bf543b..bcea5c9d60b3d4d16482a6c9f87abc57a848fde8 100644
--- a/microscopy-migration-tool/src/ethz/ch/experiment/ExperimentType2SampleType.java
+++ b/microscopy-migration-tool/src/ethz/ch/experiment/ExperimentType2SampleType.java
@@ -1,5 +1,7 @@
package ethz.ch.experiment;
+import ethz.ch.sample.SamplePropertyDelete;
+
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
@@ -33,8 +35,7 @@ public class ExperimentType2SampleType {
return propertyTypesFromTo;
}
- public List<String> getPropertyTypesToDeleteAfterMigration()
- {
- return propertyTypesToDeleteAfterMigration;
+ public SamplePropertyDelete getSamplePropertyDelete() {
+ return new SamplePropertyDelete(typeCode, propertyTypesToDeleteAfterMigration.get(0));
}
}
\ No newline at end of file
diff --git a/microscopy-migration-tool/src/ethz/ch/property/EntityPropertyCopy.java b/microscopy-migration-tool/src/ethz/ch/property/EntityPropertyCopy.java
index b4232ed199837fab316cc33c60d6435bf92b75b4..4533086b38cd052af2f546f74240587fa1a1531c 100644
--- a/microscopy-migration-tool/src/ethz/ch/property/EntityPropertyCopy.java
+++ b/microscopy-migration-tool/src/ethz/ch/property/EntityPropertyCopy.java
@@ -8,9 +8,9 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
import java.util.List;
public abstract class EntityPropertyCopy<ENTITY extends IPermIdHolder & IPropertiesHolder> {
- protected String typeCode;
- protected String oldPropertyCode;
- protected String newPropertyCode;
+ protected final String typeCode;
+ protected final String oldPropertyCode;
+ protected final String newPropertyCode;
public EntityPropertyCopy(String typeCode, String oldPropertyCode, String newPropertyCode) {
this.typeCode = typeCode;
@@ -18,6 +18,18 @@ public abstract class EntityPropertyCopy<ENTITY extends IPermIdHolder & IPropert
this.newPropertyCode = newPropertyCode;
}
+ public String getTypeCode() {
+ return typeCode;
+ }
+
+ public String getOldPropertyCode() {
+ return oldPropertyCode;
+ }
+
+ public String getNewPropertyCode() {
+ return newPropertyCode;
+ }
+
public abstract IPropertyAssignmentsHolder getPropertyAssignmentsHolder(String sessionToken, IApplicationServerApi v3);
public abstract void updatePropertyAssignmentsHolder(String sessionToken, IApplicationServerApi v3);
@@ -26,6 +38,8 @@ public abstract class EntityPropertyCopy<ENTITY extends IPermIdHolder & IPropert
public abstract void updateEntityProperty(String sessionToken, IApplicationServerApi v3, ENTITY entity);
+ public abstract EntityPropertyDelete getEntityPropertyDelete();
+
public void copy(String sessionToken, IApplicationServerApi v3) {
// Is Property B assigned to the type? If not Do
System.out.println("5. Copy Property " + oldPropertyCode + " to Property " + newPropertyCode + " on " + typeCode);
@@ -51,14 +65,14 @@ public abstract class EntityPropertyCopy<ENTITY extends IPermIdHolder & IPropert
if (entity.getProperty(oldPropertyCode) != null) {
if(!entity.getProperty(oldPropertyCode).equals(entity.getProperty(newPropertyCode))) {
updateEntityProperty(sessionToken, v3, entity);
- System.out.println("[PREPARING] " + entity.getPermId() + "\t" + entity.getProperty(oldPropertyCode) + "\t" + total + "/" + entities.size());
+ System.out.println("[PREPARING COPY] " + entity.getPermId() + "\t" + entity.getProperty(oldPropertyCode) + "\t" + total + "/" + entities.size());
} else {
- System.out.println("[SKIP] " + entity.getPermId() + "\t" + entity.getProperty(oldPropertyCode) + "\t" + total + "/" + entities.size());
+ System.out.println("[SKIP COPY] " + entity.getPermId() + "\t" + entity.getProperty(oldPropertyCode) + "\t" + total + "/" + entities.size());
}
}
total++;
}
- System.out.println("[DONE] " + total + "/" + entities.size());
+ System.out.println("[DONE COPY] " + total + "/" + entities.size());
}
}
diff --git a/microscopy-migration-tool/src/ethz/ch/property/EntityPropertyDelete.java b/microscopy-migration-tool/src/ethz/ch/property/EntityPropertyDelete.java
new file mode 100644
index 0000000000000000000000000000000000000000..c876c7d6b37b7041a0614027770df5b888b0b3b3
--- /dev/null
+++ b/microscopy-migration-tool/src/ethz/ch/property/EntityPropertyDelete.java
@@ -0,0 +1,16 @@
+package ethz.ch.property;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+
+public abstract class EntityPropertyDelete {
+
+ protected final String typeCode;
+ protected final String propertyCode;
+
+ public EntityPropertyDelete(String typeCode, String propertyCode) {
+ this.typeCode = typeCode;
+ this.propertyCode = propertyCode;
+ }
+
+ public abstract void deleteOldPropertyType(String sessionToken, IApplicationServerApi v3);
+}
diff --git a/microscopy-migration-tool/src/ethz/ch/property/PropertyType2SampleType.java b/microscopy-migration-tool/src/ethz/ch/property/PropertyType2SampleType.java
index 935ffbdd687bbfe23f4c70615b1d31e8c4edcd13..bed6b62795c30f76013166a06d72b7a328aecb53 100644
--- a/microscopy-migration-tool/src/ethz/ch/property/PropertyType2SampleType.java
+++ b/microscopy-migration-tool/src/ethz/ch/property/PropertyType2SampleType.java
@@ -1,5 +1,7 @@
package ethz.ch.property;
+import ethz.ch.sample.SamplePropertyDelete;
+
public class PropertyType2SampleType
{
private String oldSampleTypeCode;
@@ -35,5 +37,9 @@ public class PropertyType2SampleType
{
return newPropertyCode;
}
+
+ public EntityPropertyDelete getEntityPropertyDelete() {
+ return new SamplePropertyDelete(oldSampleTypeCode, oldPropertyCode);
+ }
}
\ No newline at end of file
diff --git a/microscopy-migration-tool/src/ethz/ch/sample/SamplePropertyCopy.java b/microscopy-migration-tool/src/ethz/ch/sample/SamplePropertyCopy.java
index 76dbc7b2f7c3648f92ab8740232224af78ca498e..d820b3e2591a74f8da60eeaa4dacc74a9f6c98d7 100644
--- a/microscopy-migration-tool/src/ethz/ch/sample/SamplePropertyCopy.java
+++ b/microscopy-migration-tool/src/ethz/ch/sample/SamplePropertyCopy.java
@@ -6,6 +6,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
import ethz.ch.MasterdataHelper;
import ethz.ch.MetadataHelper;
import ethz.ch.property.EntityPropertyCopy;
+import ethz.ch.property.EntityPropertyDelete;
import java.util.List;
@@ -22,7 +23,7 @@ public class SamplePropertyCopy extends EntityPropertyCopy<Sample> {
@Override
public void updatePropertyAssignmentsHolder(String sessionToken, IApplicationServerApi v3) {
- MasterdataHelper.updateSampleType(sessionToken, v3, typeCode, 1, newPropertyCode);
+ MasterdataHelper.updateSampleType(sessionToken, v3, typeCode, MasterdataHelper.PropertyTypeUpdateAction.ADD,1, newPropertyCode);
}
@Override
@@ -34,4 +35,9 @@ public class SamplePropertyCopy extends EntityPropertyCopy<Sample> {
public void updateEntityProperty(String sessionToken, IApplicationServerApi v3, Sample entity) {
MetadataHelper.updateSampleProperty(sessionToken, v3, entity.getPermId().getPermId(), newPropertyCode, entity.getProperty(oldPropertyCode));
}
+
+ @Override
+ public EntityPropertyDelete getEntityPropertyDelete() {
+ return new SamplePropertyDelete(typeCode, oldPropertyCode);
+ }
}
diff --git a/microscopy-migration-tool/src/ethz/ch/sample/SamplePropertyDelete.java b/microscopy-migration-tool/src/ethz/ch/sample/SamplePropertyDelete.java
new file mode 100644
index 0000000000000000000000000000000000000000..2884399846bea8791b32410b3cdb12bc19f429ad
--- /dev/null
+++ b/microscopy-migration-tool/src/ethz/ch/sample/SamplePropertyDelete.java
@@ -0,0 +1,31 @@
+package ethz.ch.sample;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType;
+import ethz.ch.MasterdataHelper;
+import ethz.ch.property.EntityPropertyDelete;
+
+public class SamplePropertyDelete extends EntityPropertyDelete {
+
+ public SamplePropertyDelete(String typeCode, String propertyCode) {
+ super(typeCode, propertyCode);
+ }
+
+ @Override
+ public void deleteOldPropertyType(String sessionToken, IApplicationServerApi v3) {
+ SampleType type = MasterdataHelper.getSampleType(sessionToken, v3, typeCode);
+ boolean found = false;
+ for(PropertyAssignment propertyAssignment:type.getPropertyAssignments()) {
+ found = propertyAssignment.getPropertyType().getCode().equals(propertyCode);
+ if (found) {
+ break;
+ }
+ }
+ if (found) {
+ MasterdataHelper.updateSampleType(sessionToken, v3, typeCode, MasterdataHelper.PropertyTypeUpdateAction.REMOVE, 1, propertyCode);
+ MasterdataHelper.deletePropertyType(sessionToken, v3, propertyCode);
+ System.out.println("[PROPERTY DELETE] " + "\t" + propertyCode);
+ }
+ }
+}