diff --git a/microscopy-migration-tool/src/ethz/ch/Main.java b/microscopy-migration-tool/src/ethz/ch/Main.java
index ebfdf38bc65c0baad9e61730bc73afb39847c165..12ef35dffccc0da8eddb91138d6eb02e8e1fb94f 100644
--- a/microscopy-migration-tool/src/ethz/ch/Main.java
+++ b/microscopy-migration-tool/src/ethz/ch/Main.java
@@ -1,9 +1,6 @@
package ethz.ch;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
@@ -21,13 +18,16 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.fetchoptions.SpaceFetchOpt
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.search.SpaceSearchCriteria;
import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
+import ethz.ch.dataset.DataSetPropertyCopy;
import ethz.ch.dataset.DatasetCreationHelper;
import ethz.ch.experiment.Experiment2Sample;
import ethz.ch.experiment.Experiment2SampleTranslator;
import ethz.ch.experiment.ExperimentType2SampleType;
import ethz.ch.property.Property2Sample;
import ethz.ch.property.Property2SampleTranslator;
+import ethz.ch.property.EntityPropertyCopy;
import ethz.ch.property.PropertyType2SampleType;
+import ethz.ch.sample.SamplePropertyCopy;
import ethz.ch.ssl.SslCertificateHelper;
import ethz.ch.tag.Tag2SampleTranslator;
@@ -56,6 +56,9 @@ public class Main
doTheWork(true, AS_URL, DSS_URL, user, pass, true, true, true);
} else {
+ String AS_URL = OPENBIS_LOCAL_DEV + "/openbis/openbis" + IApplicationServerApi.SERVICE_URL;
+ String DSS_URL = DSS_LOCAL_DEV + "/datastore_server" + IDataStoreServerApi.SERVICE_URL;
+ doTheWork(true, AS_URL, DSS_URL, "pontia", "a", true, true, true);
System.out.println("Example: java -jar microscopy_migration_tool.jar https://openbis-as-domain.ethz.ch https://openbis-dss-domain.ethz.ch user password");
}
}
@@ -90,23 +93,23 @@ public class Main
}
private static void migrate(String sessionToken, IApplicationServerApi v3, IDataStoreServerApi v3dss,boolean COMMIT_CHANGES_TO_OPENBIS) throws Exception {
-
+
//
// Experiment types to migrate as samples
//
-
+
ExperimentType2SampleType MICROSCOPY_EXPERIMENT = new ExperimentType2SampleType("MICROSCOPY_EXPERIMENT", "MICROSCOPY_EXPERIMENTS_COLLECTION", "MICROSCOPY_EXPERIMENT_NAME");
ExperimentType2SampleType FACS_ARIA_EXPERIMENT = new ExperimentType2SampleType("FACS_ARIA_EXPERIMENT", "FLOW_SORTERS_EXPERIMENTS_COLLECTION", "FACS_ARIA_EXPERIMENT_NAME");
ExperimentType2SampleType INFLUX_EXPERIMENT = new ExperimentType2SampleType("INFLUX_EXPERIMENT", "FLOW_SORTERS_EXPERIMENTS_COLLECTION", "INFLUX_EXPERIMENT_NAME");
ExperimentType2SampleType LSR_FORTESSA_EXPERIMENT = new ExperimentType2SampleType("LSR_FORTESSA_EXPERIMENT","FLOW_ANALYZERS_EXPERIMENTS_COLLECTION", "LSR_FORTESSA_EXPERIMENT_NAME");
ExperimentType2SampleType MOFLO_XDP_EXPERIMENT = new ExperimentType2SampleType("MOFLO_XDP_EXPERIMENT", "FLOW_SORTERS_EXPERIMENTS_COLLECTION", "MOFLO_XDP_EXPERIMENT_NAME");
ExperimentType2SampleType S3E_EXPERIMENT = new ExperimentType2SampleType("S3E_EXPERIMENT", "FLOW_SORTERS_EXPERIMENTS_COLLECTION", "S3E_EXPERIMENT_NAME");
-
+
//
// 1. Installing new sample types
//
System.out.println("1. Installing types");
-
+
// Install Sample Types for Experiment Types
List<ExperimentType2SampleType> experimentMigrationConfigs = Arrays.asList(MICROSCOPY_EXPERIMENT,
FACS_ARIA_EXPERIMENT,
@@ -114,7 +117,7 @@ public class Main
LSR_FORTESSA_EXPERIMENT,
MOFLO_XDP_EXPERIMENT,
S3E_EXPERIMENT);
-
+
for(ExperimentType2SampleType experimentMigrationConfig:experimentMigrationConfigs) {
if(COMMIT_CHANGES_TO_OPENBIS && !MasterdataHelper.doSampleTypeExist(sessionToken, v3, experimentMigrationConfig.getTypeCode())) {
MasterdataHelper.createSampleTypesFromExperimentTypes(sessionToken, v3, Arrays.asList(experimentMigrationConfig.getTypeCode()));
@@ -123,38 +126,38 @@ public class Main
System.out.println(experimentMigrationConfig.getTypeCode() + " Sample Type installation skipped.");
}
}
-
+
// Install Sample Type ORGANIZATION_UNIT
if(COMMIT_CHANGES_TO_OPENBIS && !MasterdataHelper.doSampleTypeExist(sessionToken, v3, "ORGANIZATION_UNIT")) {
v3.createSampleTypes(sessionToken, Collections.singletonList(MasterdataHelper.getSampleTypeORGANIZATION_UNIT()));
}
System.out.println("ORGANIZATION_UNIT Sample Type installed.");
-
+
if(COMMIT_CHANGES_TO_OPENBIS && !MasterdataHelper.doDataSetTypeExist(sessionToken, v3, "ATTACHMENT")) {
v3.createDataSetTypes(sessionToken, Collections.singletonList(MasterdataHelper.getDataSetTypeATTACHMENT()));
}
-
+
System.out.println("ATTACHMENT DataSet Type installed.");
-
+
//
// 2. Creating new ORGANIZATION_UNITS_COLLECTION and MICROSCOPY_EXPERIMENTS_COLLECTION
//
System.out.println("2. Creating new ORGANIZATION_UNITS_COLLECTION and MICROSCOPY_EXPERIMENTS_COLLECTION");
-
+
// Create General ORGANIZATION_UNIT Collection for every PROJECT following the pattern /SPACE/PROJECT/ORGANIZATION_UNIT_COLLECTION
// Create General ORGANIZATION_UNIT Collection for every SPACE following the pattern /SPACE/COMMON_ORGANIZATION_UNITS/ORGANIZATION_UNIT_COLLECTION
SpaceFetchOptions spaceFetchOptions = new SpaceFetchOptions();
spaceFetchOptions.withProjects();
-
+
SearchResult<Space> spaces = v3.searchSpaces(sessionToken, new SpaceSearchCriteria(), spaceFetchOptions);
-
+
for(Space space:spaces.getObjects()) {
String spaceCode = space.getCode();
if(!EXCLUDE_SPACES.contains(spaceCode)) {
// Install Project level collection
ProjectSearchCriteria projectSearchCriteria = new ProjectSearchCriteria();
projectSearchCriteria.withSpace().withCode().equals(spaceCode);
-
+
for(Project project:space.getProjects()) {
String experimentIdentifierOU = "/" + spaceCode + "/" + project.getCode() + "/ORGANIZATION_UNITS_COLLECTION";
if(COMMIT_CHANGES_TO_OPENBIS && !MetadataHelper.doExperimentExist(v3, sessionToken, experimentIdentifierOU)) {
@@ -162,14 +165,14 @@ public class Main
}
System.out.println("Project Experiment Created: " + experimentIdentifierOU);
}
-
+
// Install Space level project and collection
String projectIdentifier = "/" + spaceCode + "/COMMON_ORGANIZATION_UNITS";
if(COMMIT_CHANGES_TO_OPENBIS && !MetadataHelper.doProjectExist(v3, sessionToken, projectIdentifier)) {
v3.createProjects(sessionToken, Collections.singletonList(MetadataHelper.getProjectCreation(spaceCode, "COMMON_ORGANIZATION_UNITS", "Folder to share common organization units collections.")));
}
System.out.println("Space Project Created: " + projectIdentifier);
-
+
String experimentIdentifier = "/" + spaceCode + "/COMMON_ORGANIZATION_UNITS/ORGANIZATION_UNITS_COLLECTION";
if(COMMIT_CHANGES_TO_OPENBIS && !MetadataHelper.doExperimentExist(v3, sessionToken, experimentIdentifier)) {
v3.createExperiments(sessionToken, Collections.singletonList(MetadataHelper.getOrganizationUnitCollectionCreation(new ProjectIdentifier("/" + spaceCode + "/COMMON_ORGANIZATION_UNITS"), "ORGANIZATION_UNITS_COLLECTION")));
@@ -177,9 +180,9 @@ public class Main
System.out.println("Space Experiment Created: " + experimentIdentifier);
}
}
-
+
System.out.println("3. Translate Experiment to Samples");
-
+
for(ExperimentType2SampleType config:experimentMigrationConfigs) {
int total = 0;
ExperimentSearchCriteria experimentSearchCriteria = new ExperimentSearchCriteria();
@@ -192,7 +195,7 @@ public class Main
System.out.println("[DONE] " + config.getTypeCode() + "\t" + total + "/" + experiments.getTotalCount());
}
}
-
+
System.out.println("4. Translate Properties to Samples");
PropertyType2SampleType FACS_ARIA_TUBE = new PropertyType2SampleType( "FACS_ARIA_TUBE", "FACS_ARIA_SPECIMEN", "FACS_ARIA_SPECIMEN", "$NAME");
@@ -201,16 +204,16 @@ public class Main
PropertyType2SampleType LSR_FORTESSA_TUBE = new PropertyType2SampleType( "LSR_FORTESSA_TUBE","LSR_FORTESSA_SPECIMEN","LSR_FORTESSA_SPECIMEN","$NAME");
PropertyType2SampleType LSR_FORTESSA_WELL = new PropertyType2SampleType( "LSR_FORTESSA_WELL","LSR_FORTESSA_SPECIMEN","LSR_FORTESSA_SPECIMEN","$NAME");
PropertyType2SampleType MOFLO_XDP_TUBE = new PropertyType2SampleType( "MOFLO_XDP_TUBE", "MOFLO_XDP_SPECIMEN", "MOFLO_XDP_SPECIMEN", "$NAME");
- PropertyType2SampleType SE3_TUBE = new PropertyType2SampleType( "SE3_TUBE", "SE3_SPECIMEN", "SE3_SPECIMEN", "$NAME");
-
+ PropertyType2SampleType S3E_TUBE = new PropertyType2SampleType( "S3E_TUBE", "S3E_SPECIMEN", "S3E_SPECIMEN", "$NAME");
+
List<PropertyType2SampleType> propertiesMigrationConfigs = Arrays.asList(FACS_ARIA_TUBE,
FACS_ARIA_WELL,
INFLUX_TUBE,
LSR_FORTESSA_TUBE,
LSR_FORTESSA_WELL,
MOFLO_XDP_TUBE,
- SE3_TUBE);
-
+ S3E_TUBE);
+
for(PropertyType2SampleType propertyMigrationConfigs:propertiesMigrationConfigs) {
if(COMMIT_CHANGES_TO_OPENBIS && !MasterdataHelper.doSampleTypeExist(sessionToken, v3, propertyMigrationConfigs.getNewSampleTypeCode())) {
MasterdataHelper.createDefaultSampleType(sessionToken, v3, propertyMigrationConfigs.getNewSampleTypeCode());
@@ -219,7 +222,7 @@ public class Main
System.out.println(propertyMigrationConfigs.getNewSampleTypeCode() + " Sample Type installation skipped.");
}
}
-
+
for(PropertyType2SampleType config:propertiesMigrationConfigs) {
int total = 0;
SampleSearchCriteria sampleSearchCriteria = new SampleSearchCriteria();
@@ -232,5 +235,30 @@ public class Main
System.out.println("[DONE] " + config.getOldSampleTypeCode() + "\t" + total + "/" + samples.getTotalCount());
}
}
+
+ System.out.println("5. Copy Property A to Property B on Samples and DataSets");
+ EntityPropertyCopy LSR_FORTESSA_PLATE_p = new SamplePropertyCopy( "LSR_FORTESSA_PLATE", "LSR_FORTESSA_PLATE_NAME", "$NAME");
+ EntityPropertyCopy LSR_FORTESSA_TUBE_p = new SamplePropertyCopy( "LSR_FORTESSA_TUBE", "LSR_FORTESSA_TUBE_NAME", "$NAME");
+ EntityPropertyCopy LSR_FORTESSA_WELL_p = new SamplePropertyCopy( "LSR_FORTESSA_WELL", "LSR_FORTESSA_WELL_NAME", "$NAME");
+ EntityPropertyCopy FACS_ARIA_TUBE_p = new SamplePropertyCopy( "FACS_ARIA_TUBE", "FACS_ARIA_TUBE_NAME", "$NAME");
+ EntityPropertyCopy INFLUX_TUBE_p = new SamplePropertyCopy( "INFLUX_TUBE", "INFLUX_TUBE_NAME", "$NAME");
+ EntityPropertyCopy MOFLO_XDP_TUBE_p = new SamplePropertyCopy( "MOFLO_XDP_TUBE", "MOFLO_XDP_TUBE_NAME", "$NAME");
+ EntityPropertyCopy S3E_TUBE_p = new SamplePropertyCopy( "S3E_TUBE", "S3E_NAME", "$NAME");
+ EntityPropertyCopy MICROSCOPY_SAMPLE_TYPE_p = new SamplePropertyCopy( "MICROSCOPY_SAMPLE_TYPE", "MICROSCOPY_SAMPLE_NAME", "$NAME");
+ EntityPropertyCopy MICROSCOPY_ACCESSORY_FILE_p = new DataSetPropertyCopy("MICROSCOPY_ACCESSORY_FILE","MICROSCOPY_ACCESSORY_FILE_NAME", "$NAME");
+
+ List<EntityPropertyCopy> propertyCopiesMigrationConfig = Arrays.asList(LSR_FORTESSA_PLATE_p,
+ LSR_FORTESSA_TUBE_p,
+ LSR_FORTESSA_WELL_p,
+ FACS_ARIA_TUBE_p,
+ INFLUX_TUBE_p,
+ MOFLO_XDP_TUBE_p,
+ S3E_TUBE_p,
+ MICROSCOPY_SAMPLE_TYPE_p,
+ MICROSCOPY_ACCESSORY_FILE_p);
+
+ for (EntityPropertyCopy config:propertyCopiesMigrationConfig) {
+ config.copy(sessionToken, v3);
+ }
}
}
diff --git a/microscopy-migration-tool/src/ethz/ch/MasterdataHelper.java b/microscopy-migration-tool/src/ethz/ch/MasterdataHelper.java
index 3f8e1f580d9187e0cb617f3d7b418874c0e4021d..03bc5663b0d4a345b64626401246beec491fd9e4 100644
--- a/microscopy-migration-tool/src/ethz/ch/MasterdataHelper.java
+++ b/microscopy-migration-tool/src/ethz/ch/MasterdataHelper.java
@@ -1,15 +1,15 @@
package ethz.ch;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.update.ListUpdateValue;
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.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.fetchoptions.ExperimentTypeFetchOptions;
@@ -25,6 +25,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search.PropertyTypeSear
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.create.SampleTypeCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleTypeFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.update.SampleTypeUpdate;
public class MasterdataHelper
{
@@ -158,7 +159,55 @@ public class MasterdataHelper
createExperimentTypeIfMissing(sessionToken, v3, creation);
}
-
+
+ //
+ // Get
+ //
+
+ public static SampleType getSampleType(String sessionToken, IApplicationServerApi v3, String typeCode) {
+ EntityTypePermId id = new EntityTypePermId(typeCode);
+ SampleTypeFetchOptions fetchOptions = new SampleTypeFetchOptions();
+ fetchOptions.withPropertyAssignments().withPropertyType();
+ Map<IEntityTypeId, SampleType> types = v3.getSampleTypes(sessionToken, Arrays.asList(id), fetchOptions);
+ return types.get(id);
+ }
+
+ public static DataSetType getDataSetType(String sessionToken, IApplicationServerApi v3, String typeCode) {
+ EntityTypePermId id = new EntityTypePermId(typeCode);
+ DataSetTypeFetchOptions fetchOptions = new DataSetTypeFetchOptions();
+ fetchOptions.withPropertyAssignments().withPropertyType();
+ Map<IEntityTypeId, DataSetType> types = v3.getDataSetTypes(sessionToken, Arrays.asList(id), fetchOptions);
+ return types.get(id);
+ }
+
+ //
+ // Update
+ //
+
+ public static void updateSampleType(String sessionToken, IApplicationServerApi v3, String typeCode, 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));
+ v3.updateSampleTypes(sessionToken, Arrays.asList(update));
+ }
+
+ public static void updateDataSetType(String sessionToken, IApplicationServerApi v3, String typeCode, 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));
+ v3.updateDataSetTypes(sessionToken, Arrays.asList(update));
+ }
+
//
// Type to translate Attachments to DataSets
//
diff --git a/microscopy-migration-tool/src/ethz/ch/MetadataHelper.java b/microscopy-migration-tool/src/ethz/ch/MetadataHelper.java
index cb01dfd1f6aaf6a10c6cd50e97549f1115628d72..aacbf6f9754b0250ec1113d57b2ba51c938e5144 100644
--- a/microscopy-migration-tool/src/ethz/ch/MetadataHelper.java
+++ b/microscopy-migration-tool/src/ethz/ch/MetadataHelper.java
@@ -9,6 +9,10 @@ import java.util.List;
import java.util.Map;
import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search.DataSetSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.update.DataSetUpdate;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
@@ -27,6 +31,8 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.create.SampleCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.ISampleId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SampleIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search.SampleSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.update.SampleUpdate;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.id.SpacePermId;
@@ -133,7 +139,23 @@ public class MetadataHelper
//
// Gets
//
-
+
+ public static List<Sample> getSamples(String sessionToken, IApplicationServerApi v3, String typeCode) {
+ SampleSearchCriteria sampleSearchCriteria = new SampleSearchCriteria();
+ sampleSearchCriteria.withType().withCode().thatEquals(typeCode);
+ SampleFetchOptions fetchOptions = new SampleFetchOptions();
+ fetchOptions.withProperties();
+ return v3.searchSamples(sessionToken, sampleSearchCriteria, fetchOptions).getObjects();
+ }
+
+ public static List<DataSet> getDataSets(String sessionToken, IApplicationServerApi v3, String typeCode) {
+ DataSetSearchCriteria searchCriteria = new DataSetSearchCriteria();
+ searchCriteria.withType().withCode().thatEquals(typeCode);
+ DataSetFetchOptions fetchOptions = new DataSetFetchOptions();
+ fetchOptions.withProperties();
+ return v3.searchDataSets(sessionToken, searchCriteria, fetchOptions).getObjects();
+ }
+
public static Sample getSample(String sessionToken, IApplicationServerApi v3, ISampleId sampleId) {
SampleFetchOptions fo = new SampleFetchOptions();
fo.withProperties();
@@ -166,5 +188,22 @@ public class MetadataHelper
throw new RuntimeException("Experiment with PermId not found: " + permId.getPermId());
}
}
-
+
+ //
+ // Update
+ //
+
+ public static void updateSampleProperty(String sessionToken, IApplicationServerApi v3, String permId, String propertyCode, String propertyValue) {
+ SampleUpdate update = new SampleUpdate();
+ update.setSampleId(new SamplePermId(permId));
+ update.setProperty(propertyCode, propertyValue);
+ v3.updateSamples(sessionToken, Arrays.asList(update));
+ }
+
+ public static void updateDataSetProperty(String sessionToken, IApplicationServerApi v3, String permId, String propertyCode, String propertyValue) {
+ DataSetUpdate update = new DataSetUpdate();
+ update.setDataSetId(new DataSetPermId(permId));
+ update.setProperty(propertyCode, propertyValue);
+ v3.updateDataSets(sessionToken, Arrays.asList(update));
+ }
}
diff --git a/microscopy-migration-tool/src/ethz/ch/dataset/DataSetPropertyCopy.java b/microscopy-migration-tool/src/ethz/ch/dataset/DataSetPropertyCopy.java
new file mode 100644
index 0000000000000000000000000000000000000000..03b180618f530228f5c54c5901e57b6fa81d0eb3
--- /dev/null
+++ b/microscopy-migration-tool/src/ethz/ch/dataset/DataSetPropertyCopy.java
@@ -0,0 +1,37 @@
+package ethz.ch.dataset;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IPropertyAssignmentsHolder;
+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 java.util.List;
+
+public class DataSetPropertyCopy extends EntityPropertyCopy<DataSet> {
+
+ public DataSetPropertyCopy(String typeCode, String oldPropertyCode, String newPropertyCode) {
+ super(typeCode, oldPropertyCode, newPropertyCode);
+ }
+
+ @Override
+ public IPropertyAssignmentsHolder getPropertyAssignmentsHolder(String sessionToken, IApplicationServerApi v3) {
+ return MasterdataHelper.getDataSetType(sessionToken, v3, typeCode);
+ }
+
+ @Override
+ public void updatePropertyAssignmentsHolder(String sessionToken, IApplicationServerApi v3) {
+ MasterdataHelper.updateDataSetType(sessionToken, v3, typeCode, 1, newPropertyCode);
+ }
+
+ @Override
+ public List<DataSet> getEntities(String sessionToken, IApplicationServerApi v3) {
+ return MetadataHelper.getDataSets(sessionToken, v3, typeCode);
+ }
+
+ @Override
+ public void updateEntityProperty(String sessionToken, IApplicationServerApi v3, DataSet entity) {
+ MetadataHelper.updateDataSetProperty(sessionToken, v3, entity.getPermId().getPermId(), newPropertyCode, entity.getProperty(oldPropertyCode));
+ }
+}
diff --git a/microscopy-migration-tool/src/ethz/ch/property/EntityPropertyCopy.java b/microscopy-migration-tool/src/ethz/ch/property/EntityPropertyCopy.java
new file mode 100644
index 0000000000000000000000000000000000000000..b4232ed199837fab316cc33c60d6435bf92b75b4
--- /dev/null
+++ b/microscopy-migration-tool/src/ethz/ch/property/EntityPropertyCopy.java
@@ -0,0 +1,64 @@
+package ethz.ch.property;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IPermIdHolder;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IPropertiesHolder;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IPropertyAssignmentsHolder;
+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;
+
+ public EntityPropertyCopy(String typeCode, String oldPropertyCode, String newPropertyCode) {
+ this.typeCode = typeCode;
+ this.oldPropertyCode = oldPropertyCode;
+ this.newPropertyCode = newPropertyCode;
+ }
+
+ public abstract IPropertyAssignmentsHolder getPropertyAssignmentsHolder(String sessionToken, IApplicationServerApi v3);
+
+ public abstract void updatePropertyAssignmentsHolder(String sessionToken, IApplicationServerApi v3);
+
+ public abstract List<ENTITY> getEntities(String sessionToken, IApplicationServerApi v3);
+
+ public abstract void updateEntityProperty(String sessionToken, IApplicationServerApi v3, ENTITY entity);
+
+ 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);
+ IPropertyAssignmentsHolder propertyAssignmentsHolder = getPropertyAssignmentsHolder(sessionToken, v3);
+ boolean found = false;
+ for (PropertyAssignment propertyAssignment:propertyAssignmentsHolder.getPropertyAssignments()) {
+ found = propertyAssignment.getPropertyType().getCode().equals(newPropertyCode);
+ if (found) {
+ break;
+ }
+ }
+ if (!found) {
+ System.out.println("Property Type " + newPropertyCode + " not found on " + typeCode);
+ updatePropertyAssignmentsHolder(sessionToken, v3);
+ System.out.println("Property Type " + newPropertyCode + " created on " + typeCode);
+ }
+
+ // Copy
+ int total = 0;
+ List<ENTITY> entities = getEntities(sessionToken, v3);
+
+ for(ENTITY entity:entities) {
+ 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());
+ } else {
+ System.out.println("[SKIP] " + entity.getPermId() + "\t" + entity.getProperty(oldPropertyCode) + "\t" + total + "/" + entities.size());
+ }
+ }
+ total++;
+ }
+ System.out.println("[DONE] " + total + "/" + entities.size());
+
+ }
+}
diff --git a/microscopy-migration-tool/src/ethz/ch/sample/SamplePropertyCopy.java b/microscopy-migration-tool/src/ethz/ch/sample/SamplePropertyCopy.java
new file mode 100644
index 0000000000000000000000000000000000000000..76dbc7b2f7c3648f92ab8740232224af78ca498e
--- /dev/null
+++ b/microscopy-migration-tool/src/ethz/ch/sample/SamplePropertyCopy.java
@@ -0,0 +1,37 @@
+package ethz.ch.sample;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IPropertyAssignmentsHolder;
+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 java.util.List;
+
+public class SamplePropertyCopy extends EntityPropertyCopy<Sample> {
+
+ public SamplePropertyCopy(String typeCode, String oldPropertyCode, String newPropertyCode) {
+ super(typeCode, oldPropertyCode, newPropertyCode);
+ }
+
+ @Override
+ public IPropertyAssignmentsHolder getPropertyAssignmentsHolder(String sessionToken, IApplicationServerApi v3) {
+ return MasterdataHelper.getSampleType(sessionToken, v3, typeCode);
+ }
+
+ @Override
+ public void updatePropertyAssignmentsHolder(String sessionToken, IApplicationServerApi v3) {
+ MasterdataHelper.updateSampleType(sessionToken, v3, typeCode, 1, newPropertyCode);
+ }
+
+ @Override
+ public List<Sample> getEntities(String sessionToken, IApplicationServerApi v3) {
+ return MetadataHelper.getSamples(sessionToken, v3, typeCode);
+ }
+
+ @Override
+ public void updateEntityProperty(String sessionToken, IApplicationServerApi v3, Sample entity) {
+ MetadataHelper.updateSampleProperty(sessionToken, v3, entity.getPermId().getPermId(), newPropertyCode, entity.getProperty(oldPropertyCode));
+ }
+}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/error.png b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/error.png
deleted file mode 100644
index 5c832c00dc0500c8e7a14961aa0088bcceabc6a1..0000000000000000000000000000000000000000
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/error.png and /dev/null differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/wait.png b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/wait.png
deleted file mode 100644
index 0fe45f49527805aa459580082564916ce59934d4..0000000000000000000000000000000000000000
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/wait.png and /dev/null differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js
index d0d3d304695147ff5716ba69fbf0b767dc535f28..6d3ba47ce6d3e13eda32d40fdbd8c53b9b37833b 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js
@@ -193,7 +193,7 @@ $.extend(MicroscopyTechnology.prototype, ELNLIMSPlugin.prototype, {
// we will replace it asynchronously.
var thumbnailImage = $("<img />",
{
- src: "./img/wait.png",
+ src: "./img/image_loading.gif",
class: "img-responsive",
display: "inline",
"text-align": "center",
@@ -296,7 +296,7 @@ $.extend(MicroscopyTechnology.prototype, ELNLIMSPlugin.prototype, {
if (result.getTotalCount() == 0) {
// Thumbnail not found!
- imD.attr("src", "./img/error.png");
+ imD.attr("src", "./img/image_unavailable.png");
imD.attr("title", "Could not find a thumbnail for this dataset!");
return;