diff --git a/common/source/java/ch/systemsx/cisd/common/spring/ExposablePropertyPlaceholderConfigurer.java b/common/source/java/ch/systemsx/cisd/common/spring/ExposablePropertyPlaceholderConfigurer.java
index 8fe737b91f516740a854d73513cc4451e03c128a..8dce3f7fc599daf9a468c0427aac278ca7fa6ba8 100644
--- a/common/source/java/ch/systemsx/cisd/common/spring/ExposablePropertyPlaceholderConfigurer.java
+++ b/common/source/java/ch/systemsx/cisd/common/spring/ExposablePropertyPlaceholderConfigurer.java
@@ -24,6 +24,8 @@ import org.springframework.beans.BeansException;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.beans.factory.config.PropertyPlaceholderConfigurer;
import org.springframework.core.Constants;
+import org.springframework.util.PropertyPlaceholderHelper;
+import org.springframework.util.PropertyPlaceholderHelper.PlaceholderResolver;
import org.springframework.util.StringUtils;
import ch.systemsx.cisd.common.properties.ExtendedProperties;
@@ -111,6 +113,16 @@ public class ExposablePropertyPlaceholderConfigurer extends PropertyPlaceholderC
private String getResolvedProperty(final Properties props, final String key)
{
- return resolvePlaceholder(key, props, systemPropertiesMode);
+ PropertyPlaceholderHelper helper = new PropertyPlaceholderHelper(
+ placeholderPrefix, placeholderSuffix, valueSeparator, ignoreUnresolvablePlaceholders);
+ String resolvedPlaceholder = resolvePlaceholder(key, props, systemPropertiesMode);
+ return helper.replacePlaceholders(resolvedPlaceholder, new PlaceholderResolver()
+ {
+ @Override
+ public String resolvePlaceholder(String placeholderName)
+ {
+ return ExposablePropertyPlaceholderConfigurer.this.resolvePlaceholder(placeholderName, props, systemPropertiesMode);
+ }
+ });
}
}
\ No newline at end of file
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponentTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponentTest.java
index 8ab94d1ec734279521a71fcf2bf5187d3264542b..9edca33bbdf825357af3112281b8fe8852ccad5c 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponentTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponentTest.java
@@ -119,6 +119,8 @@ public class DssComponentTest extends AbstractFileSystemTestCase
private IShareIdManager shareIdManager;
+ private StaticListableBeanFactory applicationContext;
+
@SuppressWarnings("unchecked")
private <T extends IRpcService> T getAdvisedDssService(final T service)
{
@@ -140,6 +142,7 @@ public class DssComponentTest extends AbstractFileSystemTestCase
{ advisor };
}
};
+ ((AbstractAutoProxyCreator) processor).setBeanFactory(applicationContext);
final Object proxy =
processor.postProcessAfterInitialization(service, "proxy of "
+ service.getClass().getName());
@@ -157,7 +160,7 @@ public class DssComponentTest extends AbstractFileSystemTestCase
{
super.setUp();
DssSessionAuthorizationHolder.setAuthorizer(new DatasetSessionAuthorizer());
- final StaticListableBeanFactory applicationContext = new StaticListableBeanFactory();
+ applicationContext = new StaticListableBeanFactory();
ServiceProviderTestWrapper.setApplicationContext(applicationContext);
context = new Mockery();
openBisService = context.mock(IGeneralInformationService.class);
diff --git a/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/deserializer/JsonTypeAndClassDeserializer.java b/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/deserializer/JsonTypeAndClassDeserializer.java
index 27059d1aaca16706087b1cd3749986ae52125df9..9fd9eccc1c6c7a678f4fd32597b179078182a3ba 100644
--- a/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/deserializer/JsonTypeAndClassDeserializer.java
+++ b/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/deserializer/JsonTypeAndClassDeserializer.java
@@ -161,7 +161,7 @@ public class JsonTypeAndClassDeserializer extends AsPropertyTypeDeserializer
{ // need to merge id back in JSON input?
if (actualTb == null)
{
- actualTb = new TokenBuffer(null);
+ actualTb = new TokenBuffer(null, false);
}
actualTb.writeFieldName(actualJp.getCurrentName());
actualTb.writeString(type);
diff --git a/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/deserializer/JsonTypeAndClassSerializer.java b/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/deserializer/JsonTypeAndClassSerializer.java
index 599133b64d34744f6733a0e6b4795385753394b4..fe00ce1c8e16b0d7c0258e02f613e85b62a6c42f 100644
--- a/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/deserializer/JsonTypeAndClassSerializer.java
+++ b/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/deserializer/JsonTypeAndClassSerializer.java
@@ -19,7 +19,8 @@ package ch.systemsx.cisd.openbis.common.api.server.json.deserializer;
import java.io.IOException;
import com.fasterxml.jackson.core.JsonGenerator;
-import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.core.JsonToken;
+import com.fasterxml.jackson.core.type.WritableTypeId;
import com.fasterxml.jackson.databind.BeanProperty;
import com.fasterxml.jackson.databind.jsontype.TypeIdResolver;
import com.fasterxml.jackson.databind.jsontype.impl.AsPropertyTypeSerializer;
@@ -46,58 +47,55 @@ public class JsonTypeAndClassSerializer extends AsPropertyTypeSerializer
}
@Override
- public void writeTypePrefixForObject(Object value, JsonGenerator jgen) throws IOException,
- JsonProcessingException
+ public WritableTypeId writeTypePrefix(JsonGenerator g, WritableTypeId idMetadata) throws IOException
{
- if (isValueWithType(value))
+ Object value = idMetadata.forValue;
+ JsonToken valueShape = idMetadata.valueShape;
+ if (JsonToken.START_OBJECT == valueShape)
{
- jgen.writeStartObject();
- jgen.writeStringField(_typePropertyName, idFromValue(value));
+ g.writeStartObject();
+ if (isValueWithType(value))
+ {
+ g.writeStringField(_typePropertyName, idFromValue(value));
+ }
+ } else if (JsonToken.VALUE_STRING == valueShape)
+ {
+ if (isValueWithType(value))
+ {
+ g.writeTypePrefix(idMetadata);
+ }
+ } else if (JsonToken.START_ARRAY == valueShape)
+ {
+ g.writeStartArray();
} else
{
- jgen.writeStartObject();
+ g.writeTypePrefix(idMetadata);
}
+ return idMetadata;
}
@Override
- public void writeTypeSuffixForObject(Object value, JsonGenerator jgen) throws IOException,
- JsonProcessingException
- {
- jgen.writeEndObject();
- }
-
- @Override
- public void writeTypePrefixForScalar(Object value, JsonGenerator jgen) throws IOException,
- JsonProcessingException
+ public WritableTypeId writeTypeSuffix(JsonGenerator g, WritableTypeId idMetadata) throws IOException
{
- if (isValueWithType(value))
+ Object value = idMetadata.forValue;
+ JsonToken valueShape = idMetadata.valueShape;
+ if (JsonToken.START_OBJECT == valueShape)
{
- super.writeTypePrefixForScalar(value, jgen);
- }
- }
-
- @Override
- public void writeTypeSuffixForScalar(Object value, JsonGenerator jgen) throws IOException,
- JsonProcessingException
- {
- if (isValueWithType(value))
+ g.writeEndObject();
+ } else if (JsonToken.VALUE_STRING == valueShape)
{
- super.writeTypeSuffixForScalar(value, jgen);
+ if (isValueWithType(value))
+ {
+ g.writeTypeSuffix(idMetadata);
+ }
+ } else if (JsonToken.START_ARRAY == valueShape)
+ {
+ g.writeEndArray();
+ } else
+ {
+ g.writeTypeSuffix(idMetadata);
}
- }
-
- @Override
- public void writeTypePrefixForArray(Object value, JsonGenerator jgen) throws IOException,
- JsonProcessingException
- {
- jgen.writeStartArray();
- }
-
- @Override
- public void writeTypeSuffixForArray(Object value, JsonGenerator jgen) throws IOException,
- JsonProcessingException
- {
- jgen.writeEndArray();
+ return idMetadata;
}
private boolean isValueWithType(Object value)
diff --git a/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/introspector/JsonTypeAndClassAnnotationIntrospector.java b/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/introspector/JsonTypeAndClassAnnotationIntrospector.java
index 9b62e3fa8985e66b0f528e0b8d5dcba140647862..b27735b9dda230dd47b91299d230b3ebac4125b6 100644
--- a/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/introspector/JsonTypeAndClassAnnotationIntrospector.java
+++ b/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/introspector/JsonTypeAndClassAnnotationIntrospector.java
@@ -27,6 +27,7 @@ import com.fasterxml.jackson.databind.cfg.MapperConfig;
import com.fasterxml.jackson.databind.introspect.Annotated;
import com.fasterxml.jackson.databind.introspect.AnnotatedClass;
import com.fasterxml.jackson.databind.introspect.JacksonAnnotationIntrospector;
+import com.fasterxml.jackson.databind.introspect.NopAnnotationIntrospector;
import com.fasterxml.jackson.databind.introspect.ObjectIdInfo;
import com.fasterxml.jackson.databind.jsontype.TypeResolverBuilder;
@@ -59,7 +60,7 @@ public class JsonTypeAndClassAnnotationIntrospector extends JacksonAnnotationInt
{
return null;
}
- JsonObject tn = ac.getAnnotation(JsonObject.class);
+ JsonObject tn = _findAnnotation(ac, JsonObject.class);
return (tn == null) ? null : tn.value();
}
@@ -87,8 +88,7 @@ public class JsonTypeAndClassAnnotationIntrospector extends JacksonAnnotationInt
private boolean useCustomResolver(JavaType type)
{
return type.getRawClass().equals(Object.class)
- || (type.getRawClass().isAnnotationPresent(JsonObject.class) && !type.getRawClass()
- .isEnum());
+ || (type.getRawClass().isAnnotationPresent(JsonObject.class) && false == type.getRawClass().isEnum());
}
}
diff --git a/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/resolver/JsonTypeAndClassResolverBuilder.java b/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/resolver/JsonTypeAndClassResolverBuilder.java
index deecd77f3ccf7d8add2fd3a5decae43281692949..5f4aeedd8170e6426bb4dfc16994045b1d481f18 100644
--- a/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/resolver/JsonTypeAndClassResolverBuilder.java
+++ b/openbis-common/source/java/ch/systemsx/cisd/openbis/common/api/server/json/resolver/JsonTypeAndClassResolverBuilder.java
@@ -22,12 +22,16 @@ import com.fasterxml.jackson.annotation.JsonTypeInfo.As;
import com.fasterxml.jackson.annotation.JsonTypeInfo.Id;
import com.fasterxml.jackson.databind.DeserializationConfig;
import com.fasterxml.jackson.databind.JavaType;
+import com.fasterxml.jackson.databind.SerializationConfig;
import com.fasterxml.jackson.databind.jsontype.NamedType;
import com.fasterxml.jackson.databind.jsontype.TypeDeserializer;
import com.fasterxml.jackson.databind.jsontype.TypeIdResolver;
+import com.fasterxml.jackson.databind.jsontype.TypeSerializer;
import com.fasterxml.jackson.databind.jsontype.impl.StdTypeResolverBuilder;
+import ch.systemsx.cisd.openbis.common.api.server.json.common.JsonConstants;
import ch.systemsx.cisd.openbis.common.api.server.json.deserializer.JsonTypeAndClassDeserializer;
+import ch.systemsx.cisd.openbis.common.api.server.json.deserializer.JsonTypeAndClassSerializer;
import ch.systemsx.cisd.openbis.common.api.server.json.mapping.IJsonClassValueToClassObjectsMapping;
/**
@@ -58,4 +62,11 @@ public class JsonTypeAndClassResolverBuilder extends StdTypeResolverBuilder
return deserializer;
}
+ @Override
+ public TypeSerializer buildTypeSerializer(SerializationConfig config, JavaType baseType, Collection<NamedType> subtypes)
+ {
+ TypeIdResolver resolver = idResolver(config, baseType, subtypes, true, false);
+ return new JsonTypeAndClassSerializer(resolver, null, JsonConstants.getTypeField());
+ }
+
}
diff --git a/openbis-common/sourceTest/java/ch/systemsx/cisd/openbis/common/api/server/json/JsonSerializationTest.java b/openbis-common/sourceTest/java/ch/systemsx/cisd/openbis/common/api/server/json/JsonSerializationTest.java
index 8c3922fcf20350551a09d088de0d798d42da62e7..f999b143e24b47f3eca01e64187496730bed94a4 100644
--- a/openbis-common/sourceTest/java/ch/systemsx/cisd/openbis/common/api/server/json/JsonSerializationTest.java
+++ b/openbis-common/sourceTest/java/ch/systemsx/cisd/openbis/common/api/server/json/JsonSerializationTest.java
@@ -16,6 +16,14 @@
package ch.systemsx.cisd.openbis.common.api.server.json;
+import static org.testng.Assert.assertEquals;
+
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
import org.testng.Assert;
import org.testng.annotations.Test;
@@ -48,7 +56,6 @@ import ch.systemsx.cisd.openbis.common.api.server.json.object.ObjectWithTypeFact
*/
public class JsonSerializationTest
{
-
@Test
public void testSerializeRootType() throws Exception
{
@@ -169,6 +176,19 @@ public class JsonSerializationTest
testSerialize(new ObjectWithReusedReferencesFactory());
}
+ @Test
+ public void testMapWithValueOfTypeList() throws Exception
+ {
+ Map<String, List<String>> map = new LinkedHashMap<>();
+ map.put("abc", Arrays.asList("A", "B", "C"));
+
+ String jsonFromObject = new JsonTestObjectMapper().writeValueAsString(map);
+
+ assertEquals(jsonFromObject, "{\"abc\":[\"A\",\"B\",\"C\"]}");
+ Map<String, Set<String>> recreatedMap = new JsonTestObjectMapper().readValue(jsonFromObject, LinkedHashMap.class);
+ assertEquals(recreatedMap.toString(), map.toString());
+ }
+
private void testSerialize(ObjectFactory<?> factory) throws Exception
{
Object object = factory.createObjectToSerialize();
@@ -177,7 +197,7 @@ public class JsonSerializationTest
Object expectedObject = factory.createExpectedMapAfterSerialization(new ObjectCounter());
String jsonFromExpectedMap = new ObjectMapper().writeValueAsString(expectedObject);
- Assert.assertEquals(jsonFromObject, jsonFromExpectedMap);
+ assertEquals(jsonFromObject, jsonFromExpectedMap);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java
index 8a9a8f495f872d5c4e6f1de67931306befd4aecc..0f2f6bd1f0c221d68308b847d28cd5645c671c08 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java
@@ -529,7 +529,6 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
return entity;
}
- @SuppressWarnings({ "unchecked", "rawtypes" })
@Override
public void updateDataSetStatuses(final List<String> dataSetCodes,
final DataSetArchivingStatus status)
@@ -558,55 +557,14 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
{
final int startIndexFinal = startIndex;
final int endIndexFinal = endIndex;
- updatedRows += (Integer) hibernateTemplate.execute(new HibernateCallback()
- {
-
- //
- // HibernateCallback
- //
-
- @Override
- public final Object doInHibernate(final Session session)
- throws HibernateException
- {
- // NOTE: 'VERSIONED' makes modification time modified too
- return session
- .createQuery(
- "UPDATE VERSIONED "
- + EXTERNAL_DATA_TABLE_NAME
- + " SET status = :status WHERE code IN (:codes) ")
- .setParameter("status", status)
- .setParameterList("codes",
- dataSetCodes.subList(startIndexFinal, endIndexFinal))
- .executeUpdate();
- }
- });
+ List<String> codes = dataSetCodes.subList(startIndexFinal, endIndexFinal);
+ updatedRows += updateStatus(hibernateTemplate, status, codes);
startIndex = endIndex;
endIndex = Math.min(endIndex + MAX_BATCH_SIZE, len);
}
} else
{
- updatedRows = (Integer) hibernateTemplate.execute(new HibernateCallback()
- {
-
- //
- // HibernateCallback
- //
-
- @Override
- public final Object doInHibernate(final Session session)
- throws HibernateException
- {
- // NOTE: 'VERSIONED' makes modification time modified too
- return session
- .createQuery(
- "UPDATE VERSIONED " + EXTERNAL_DATA_TABLE_NAME
- + " SET status = :status WHERE code IN (:codes) ")
- .setParameter("status", status)
- .setParameterList("codes", dataSetCodes).executeUpdate();
- }
-
- });
+ updatedRows = updateStatus(hibernateTemplate, status, dataSetCodes);
}
scheduleDynamicPropertiesEvaluationForDataSets(dataSetCodes);
hibernateTemplate.flush();
@@ -619,6 +577,45 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
}
}
+ @SuppressWarnings({ "unchecked", "rawtypes" })
+ private Integer updateStatus(final HibernateTemplate hibernateTemplate, final DataSetArchivingStatus status, List<String> codes)
+ {
+ return (Integer) hibernateTemplate.execute(new HibernateCallback()
+ {
+ @Override
+ public final Object doInHibernate(final Session session)
+ throws HibernateException
+ {
+ int result = session.createQuery(
+ "UPDATE " + EXTERNAL_DATA_TABLE_NAME + " SET status = :status WHERE code IN (:codes) ")
+ .setParameter("status", status)
+ .setParameterList("codes", codes)
+ .executeUpdate();
+ updateVersion(session, codes);
+ return result;
+ /*
+ // NOTE: 'VERSIONED' makes modification time modified too
+ return session
+ .createQuery(
+ "UPDATE VERSIONED "
+ + EXTERNAL_DATA_TABLE_NAME
+ + " SET status = :status WHERE code IN (:codes) ")
+ .setParameter("status", status)
+ .setParameterList("codes", codes)
+ .executeUpdate();
+ */
+ }
+ });
+ }
+
+ private static int updateVersion(final Session session, List<String> codes)
+ {
+ return session.createQuery(
+ "UPDATE " + TABLE_NAME + " SET version = version + 1 WHERE code IN (:codes) ")
+ .setParameterList("codes", codes)
+ .executeUpdate();
+ }
+
@SuppressWarnings({ "unchecked", "rawtypes" })
@Override
public void updateSizes(final Map<String, Long> sizeMap)
@@ -828,7 +825,7 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
{
query = session
.createQuery(
- "UPDATE VERSIONED "
+ "UPDATE "
+ EXTERNAL_DATA_TABLE_NAME
+ " SET status = :status, presentInArchive = :presentInArchive, "
+ " archivingRequested = 'f'"
@@ -837,17 +834,20 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
{
query = session
.createQuery(
- "UPDATE VERSIONED "
+ "UPDATE "
+ EXTERNAL_DATA_TABLE_NAME
+ " SET status = :status, presentInArchive = :presentInArchive"
+ " WHERE code IN (:codes) ");
}
- return query
+ int result = query
.setParameter("status", status)
.setParameter("presentInArchive", presentInArchive)
.setParameterList("codes", codes)
.executeUpdate();
+ System.err.println(result+" UPDATED "+codes);
+ updateVersion(session, codes);
+ return result;
}
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ProjectSampleTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ProjectSampleTest.java
index f6700b590d0c853615e8e9b9ee708b6dc9534a05..47680b279f87ef1bf684374f01276a6819d3b7c0 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ProjectSampleTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ProjectSampleTest.java
@@ -82,7 +82,7 @@ import ch.systemsx.cisd.openbis.systemtest.base.builder.SessionBuilder;
* @author Franz-Josef Elmer
*/
@Transactional(transactionManager = "transaction-manager")
-@Rollback
+@Rollback(false)
@Test(groups = "project-samples")
public class ProjectSampleTest extends BaseTest
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractAssignmentSampleToExperimentTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractAssignmentSampleToExperimentTestCase.java
index f183a91a6816c8e175a260626dd4c62d6ed6ddb9..0fef1ce6322c19949813ba2b79fd19ce94996a57 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractAssignmentSampleToExperimentTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractAssignmentSampleToExperimentTestCase.java
@@ -55,7 +55,7 @@ import ch.systemsx.cisd.openbis.systemtest.base.auth.SpaceDomain;
* @author Franz-Josef Elmer
*/
@Transactional(transactionManager = "transaction-manager")
-@Rollback
+@Rollback(false)
public abstract class AbstractAssignmentSampleToExperimentTestCase extends BaseTest
{
Experiment sourceExperiment;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractDataSetAssignmentTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractDataSetAssignmentTestCase.java
index cc8875f09c7b610b79cbbfe0dfa674846d9a2855..7454e505038e938f92fc9d92bccc11773493f099 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractDataSetAssignmentTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractDataSetAssignmentTestCase.java
@@ -53,7 +53,7 @@ import ch.systemsx.cisd.openbis.systemtest.base.auth.SpaceDomain;
* @author Franz-Josef Elmer
*/
@Transactional(transactionManager = "transaction-manager")
-@Rollback
+@Rollback(false)
public abstract class AbstractDataSetAssignmentTestCase extends BaseTest
{
Sample sourceSample;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractEntityDeletionTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractEntityDeletionTestCase.java
index 2c78dd56bd5b878d8352bcb0479345a1f1751185..ec2ae1e37a4e05d0fa87550540eb4b6fbe12c15b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractEntityDeletionTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractEntityDeletionTestCase.java
@@ -44,7 +44,7 @@ import ch.systemsx.cisd.openbis.systemtest.base.builder.SessionBuilder;
* @author Franz-Josef Elmer
*/
@Transactional(transactionManager = "transaction-manager")
-@Rollback
+@Rollback(false)
public abstract class AbstractEntityDeletionTestCase extends BaseTest
{
@Test
diff --git a/openbis_standard_technologies/.dynamic_property_evaluator_queue b/openbis_standard_technologies/.dynamic_property_evaluator_queue
new file mode 100644
index 0000000000000000000000000000000000000000..2e08dce276e43c677d121d627a250d1710fed824
Binary files /dev/null and b/openbis_standard_technologies/.dynamic_property_evaluator_queue differ
diff --git a/openbis_standard_technologies/build.gradle b/openbis_standard_technologies/build.gradle
index 5d823361a6a0bdfb21f9b692075006e0e71d75a0..b5cf66c440696ed75b1d0d0140d76b06dbce84db 100644
--- a/openbis_standard_technologies/build.gradle
+++ b/openbis_standard_technologies/build.gradle
@@ -108,6 +108,19 @@ dependencies {
javadoc_compilation project(path:':rtd_phosphonetx'),
project(path:':screening')
+
+ testCompile (project(path: ':openbis', configuration: 'tests')) {
+ exclude group: 'google', module: 'gwt-user'
+ }
+
+}
+
+sourceSets {
+ test {
+ resources {
+ srcDirs = ['source/java', 'sourceTest/java']
+ }
+ }
}
task compileGwt (dependsOn: classes, type: JavaExec) {
diff --git a/openbis_standard_technologies/dist/core-plugins/core-plugins.properties b/openbis_standard_technologies/dist/core-plugins/core-plugins.properties
new file mode 100644
index 0000000000000000000000000000000000000000..77fe9f20e507ac4dc02ef2ae23706d7f9f36fb00
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/core-plugins.properties
@@ -0,0 +1 @@
+enabled-modules = dev-.*
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchController.js
index 25b7daad6b40f0d9659da200406abfc2444bc26a..1b08ef8f11236de7f2248b17025f8cc3ea9a2cba 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchController.js
@@ -227,7 +227,7 @@ function AdvancedSearchController(mainController, forceSearch) {
this.selectSavedSearch = function(selcetedSavedSearchIndex) {
var savedSearch = this._advancedSearchModel.savedSearches[selcetedSavedSearchIndex];
this._advancedSearchModel.selcetedSavedSearchIndex = selcetedSavedSearchIndex;
- this._advancedSearchModel.criteria = savedSearch.criteria;
+ this._advancedSearchModel.criteria = this._clone(savedSearch.criteria);
this._advancedSearchModel.forceLoadCriteria = true;
this._advancedSearchView.repaintContent();
}
@@ -271,6 +271,7 @@ function AdvancedSearchController(mainController, forceSearch) {
}, function(success) {
if (success) {
Util.showSuccess('Search updated.');
+ savedSearch.criteria = _this._clone(_this._advancedSearchModel.criteria);
}
callback();
});
@@ -296,6 +297,11 @@ function AdvancedSearchController(mainController, forceSearch) {
);
}
+ this.clearSelection = function() {
+ this._advancedSearchModel.selcetedSavedSearchIndex = -1;
+ this._advancedSearchView.repaintContent();
+ }
+
this._loadSavedSearches = function(callback) {
var _this = this;
this._mainController.serverFacade.searchSamplesV3('SEARCH_QUERY', function(result) {
@@ -399,4 +405,8 @@ function AdvancedSearchController(mainController, forceSearch) {
}
});
}
+
+ this._clone = function(object) {
+ return JSON.parse(JSON.stringify(object));
+ }
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchModel.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchModel.js
index 0bc09d820013cdd67a1ca9f2a668a6f9bc97fbbc..e75a6608e04d9a94bc05834e8e5753bbc28c2a51 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchModel.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchModel.js
@@ -47,7 +47,17 @@ function AdvancedSearchModel(forceSearch) {
this.setEntityKind = function(entityKind) {
this.criteria.entityKind = entityKind;
}
-
+
+ // a hidden object type rule is used for the "Search For" dropdown
+ this.getHiddenRule = function() {
+ for(var ruleKey in this.criteria.rules) {
+ if (this.criteria.rules[ruleKey].hidden) {
+ return this.criteria.rules[ruleKey];
+ }
+ }
+ return null;
+ }
+
this.resetModel = function(entityKind) {
this.criteria.entityKind = entityKind;
this.criteria.rules = {};
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchView.js
index 643c801d6f82f8d5d6cfb8f81f0080e39370aca5..15505da7ca0ef64fd898aadeb9754f94877147e6 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/AdvancedSearch/AdvancedSearchView.js
@@ -21,6 +21,7 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
this._$andOrDropdownComponent = null;
this._$menuPanelContainer = null;
this._$searchCriteriaPanelContainer = null;
+ this._$rulesPanelContainer = null;
this._$tbody = null;
this._$dataGridContainer = null;
this._$saveLoadContainer = null;
@@ -67,19 +68,28 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
//Triggers Layout refresh
$container.append($mainPanel);
- if(this._advancedSearchModel.forceLoadCriteria) {
- this._$entityTypeDropdown.val(this._advancedSearchModel.criteria.entityKind);
- this._$andOrDropdownComponent.val(this._advancedSearchModel.criteria.logicalOperator);
- this._advancedSearchModel.forceLoadCriteria = undefined;
- }
-
+ this._updateEntityTypeAndUsingDropdownValues();
}
this.repaintContent = function() {
this._paintSaveLoadPanel(this._$saveLoadContainer);
this._paintCriteriaPanel(this._$searchCriteriaPanelContainer);
+ this._updateEntityTypeAndUsingDropdownValues();
}
+ this._updateEntityTypeAndUsingDropdownValues = function() {
+ if(this._advancedSearchModel.forceLoadCriteria) {
+ var hiddenRule = this._advancedSearchModel.getHiddenRule();
+ if (hiddenRule) {
+ this._$entityTypeDropdown.val('SAMPLE$' + hiddenRule.value);
+ } else {
+ this._$entityTypeDropdown.val(this._advancedSearchModel.criteria.entityKind);
+ }
+ this._$andOrDropdownComponent.val(this._advancedSearchModel.criteria.logicalOperator);
+ this._advancedSearchModel.forceLoadCriteria = undefined;
+ }
+ }
+
//
// Repaint Panels Methods
//
@@ -176,6 +186,13 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
theme: "bootstrap"
});
+ if (_this._advancedSearchModel.selcetedSavedSearchIndex > -1) {
+ var $buttonClear = FormUtil.getButtonWithIcon('glyphicon-remove', function() {
+ _this._advancedSearchController.clearSelection();
+ }, null, 'Clear selection');
+ $container.append($buttonClear);
+ }
+
var $buttonSave = FormUtil.getButtonWithIcon('glyphicon-floppy-disk', function() {
_this._save();
}, 'Save');
@@ -227,6 +244,15 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
this._paintTypeSelectionPanel(this._$searchCriteriaPanelContainer);
+ // TODO put the rest in separate panel
+ this._$rulesPanelContainer = $("<div>");
+ this._paintRulesPanel(this._$rulesPanelContainer);
+ $searchCriteriaPanelContainer.append(this._$rulesPanelContainer);
+ }
+
+
+ this._paintRulesPanel = function($container) {
+ $container.empty();
var _this = this;
var $table = $("<table>", { class : "table table-bordered"});
$table.css({ 'margin-top': '10px' });
@@ -250,24 +276,31 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
.append($("<th>").text("Field Value"))
.append($("<th>", { "style" : "width : 56px !important;" }).append(this._$addButton))
);
-
- this._paintInputRow();
-
- $searchCriteriaPanelContainer.append($table);
+
+ if ($.isEmptyObject(this._advancedSearchModel.criteria.rules)) {
+ this._paintInputRow();
+ } else {
+ for(var ruleKey in this._advancedSearchModel.criteria.rules) {
+ if ( ! this._advancedSearchModel.criteria.rules[ruleKey].hidden) {
+ this._paintInputRow(ruleKey);
+ }
+ }
+ }
+
+ $container.append($table);
}
//
// Auxiliar Components Methods
//
-
- this._paintInputRow = function() {
+
+ // paints a row for the given ruleKey or a new empty row if no ruleKey is given
+ this._paintInputRow = function(ruleKey) {
var _this = this;
-
- if(this._advancedSearchModel.forceLoadCriteria) {
- var uuidValue = null;
- for(var ruleKey in this._advancedSearchModel.criteria.rules) {
- uuidValue = ruleKey;
- }
+
+ var uuidValue = null;
+ if (ruleKey) {
+ uuidValue = ruleKey;
} else {
var uuidValue = Util.guid();
this._advancedSearchModel.criteria.rules[uuidValue] = { };
@@ -313,13 +346,11 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
}
if(this._advancedSearchModel.forceLoadCriteria) {
- for(var ruleKey in this._advancedSearchModel.criteria.rules) {
- var rule = this._advancedSearchModel.criteria.rules[ruleKey];
- $fieldTypeDropdown.val(rule.type).change();
- $fieldValue.val(rule.value);
- var $fieldNameDropdown = $($newFieldNameContainer.children()[0]);
- $fieldNameDropdown.val(rule.name);
- }
+ var rule = this._advancedSearchModel.criteria.rules[uuidValue];
+ $fieldTypeDropdown.val(rule.type).change();
+ $fieldValue.val(rule.value);
+ var $fieldNameDropdown = $($newFieldNameContainer.children()[0]);
+ $fieldNameDropdown.val(rule.name);
}
}
@@ -631,7 +662,7 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
}
} else {
_this._advancedSearchModel.resetModel(kindAndType[0]); //Restart model
- _this._paintCriteriaPanel(_this._$searchCriteriaPanelContainer); //Restart view
+ _this._paintRulesPanel(_this._$rulesPanelContainer);
}
if(kindAndType.length === 2) {
@@ -640,6 +671,7 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
_this._advancedSearchModel.criteria.rules[uuidValue].type = 'Attribute';
_this._advancedSearchModel.criteria.rules[uuidValue].name = 'ATTR.SAMPLE_TYPE';
_this._advancedSearchModel.criteria.rules[uuidValue].value = kindAndType[1];
+ _this._advancedSearchModel.criteria.rules[uuidValue].hidden = true;
_this._advancedSearchModel.isSampleTypeForced = true;
} else {
_this._advancedSearchModel.isSampleTypeForced = false;
@@ -897,4 +929,4 @@ function AdvancedSearchView(advancedSearchController, advancedSearchModel) {
return dataGrid;
}
-}
\ No newline at end of file
+}
diff --git a/openbis_standard_technologies/source/java/service.properties b/openbis_standard_technologies/source/java/service.properties
index e8586097f09ecde472f31d671d52d7dcc0c13ad4..ca515e360564c0f113dea8f8e4d273c487fd2610 100644
--- a/openbis_standard_technologies/source/java/service.properties
+++ b/openbis_standard_technologies/source/java/service.properties
@@ -77,7 +77,7 @@ hibernate.search.worker.execution=async
web-client-configuration-file = etc/web-client.properties
-core-plugins-folder=source/core-plugins
+core-plugins-folder=dist/core-plugins
# Database Configurations for Query module
query-databases = 1
diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/AbstractImportTest.java b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/AbstractImportTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..f7819e2ba882e4e25e8ecc774bdb685fcaa4d8c7
--- /dev/null
+++ b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/AbstractImportTest.java
@@ -0,0 +1,23 @@
+package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
+
+import org.springframework.test.context.testng.AbstractTransactionalTestNGSpringContextTests;
+import org.testng.annotations.BeforeSuite;
+
+import ch.systemsx.cisd.openbis.generic.server.util.TestInitializer;
+import ch.systemsx.cisd.openbis.generic.shared.Constants;
+import ch.systemsx.cisd.openbis.generic.shared.coreplugin.CorePluginsUtils;
+
+public class AbstractImportTest extends AbstractTransactionalTestNGSpringContextTests
+{
+
+ protected String FILES_DIR;
+
+ @BeforeSuite
+ public void setupSuite()
+ {
+ System.setProperty(CorePluginsUtils.CORE_PLUGINS_FOLDER_KEY, "dist/core-plugins");
+ System.setProperty(Constants.ENABLED_MODULES_KEY, "xls-import");
+ TestInitializer.initEmptyDbNoIndex();
+ }
+
+}
diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportDatasetTypesTest.java b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportDatasetTypesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..f5436657b69312da800689c90793c6e97a1f372b
--- /dev/null
+++ b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportDatasetTypesTest.java
@@ -0,0 +1,107 @@
+package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
+
+import static org.testng.Assert.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+import org.apache.commons.io.FilenameUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.transaction.annotation.Transactional;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+@ContextConfiguration(locations = "classpath:applicationContext.xml")
+@Transactional(transactionManager = "transaction-manager")
+@Rollback
+public class ImportDatasetTypesTest extends AbstractImportTest
+{
+
+ @Autowired
+ private IApplicationServerInternalApi v3api;
+
+ private static final String TEST_USER = "test";
+
+ private static final String PASSWORD = "password";
+
+ private static final String DATASET_TYPES_XLS = "dataset_types/normal_dataset.xls";
+
+ private static final String DATASET_NO_CODE = "dataset_types/no_code.xls";
+
+ private static final String DATASET_WITH_VALIDATION_SCRIPT = "dataset_types/with_validation.xls";
+
+ private static final String DATASET_WITHOUT_PROPERTIES = "dataset_types/no_properties.xls";
+
+ private static String FILES_DIR;
+
+ private String sessionToken;
+
+ @BeforeClass
+ public void setupClass() throws IOException
+ {
+ String f = ImportDatasetTypesTest.class.getName().replace(".", "/");
+ FILES_DIR = f.substring(0, f.length() - ImportDatasetTypesTest.class.getSimpleName().length()) + "/test_files/";
+ System.out.println(FILES_DIR);
+ System.out.println("SEE ME MY DEAR FRIEND");
+ }
+
+ @BeforeMethod
+ public void beforeTest()
+ {
+ sessionToken = v3api.login(TEST_USER, PASSWORD);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testNormalDatasetsTypesAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, DATASET_TYPES_XLS)));
+ // WHEN
+ DataSetType rawData = TestUtils.getDatasetType(v3api, sessionToken, "RAW_DATA");
+ // THEN
+ assertEquals(rawData.getCode(), "RAW_DATA");
+ assertEquals(rawData.getPropertyAssignments().size(), 2);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testDatasetsWithoutPropertiesTypesAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, DATASET_WITHOUT_PROPERTIES)));
+ // WHEN
+ DataSetType rawData = TestUtils.getDatasetType(v3api, sessionToken, "RAW_DATA");
+ // THEN
+ assertEquals(rawData.getCode(), "RAW_DATA");
+ assertEquals(rawData.getPropertyAssignments().size(), 0);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSampleTypesWithValidationScript() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, TestUtils.getValidationPluginMap(),
+ Paths.get(FilenameUtils.concat(FILES_DIR, DATASET_WITH_VALIDATION_SCRIPT)));
+ // WHEN
+ DataSetType collection = TestUtils.getDatasetType(v3api, sessionToken, "RAW_DATA");
+ // THEN
+ assertEquals(collection.getValidationPlugin().getName().toUpperCase(), "RAW_DATA.VALID");
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfNoSampleCode() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, DATASET_NO_CODE)));
+ }
+
+}
diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentTypesTest.java b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentTypesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..99010317951ca59f376a98f62e0bed6b8d29e0e0
--- /dev/null
+++ b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentTypesTest.java
@@ -0,0 +1,88 @@
+package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
+
+import static org.testng.Assert.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+import org.apache.commons.io.FilenameUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.transaction.annotation.Transactional;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+@ContextConfiguration(locations = "classpath:applicationContext.xml")
+@Transactional(transactionManager = "transaction-manager")
+@Rollback
+public class ImportExperimentTypesTest extends AbstractImportTest
+{
+ @Autowired
+ private IApplicationServerInternalApi v3api;
+
+ private static final String TEST_USER = "test";
+
+ private static final String PASSWORD = "password";
+
+ private static final String EXPERIMENT_TYPES_XLS = "experiment_types/normal_experiment.xls";
+
+ private static final String EXPERIMENT_NO_CODE = "experiment_types/no_code.xls";
+
+ private static final String EXPERIMENT_WITH_VALIDATION_SCRIPT = "experiment_types/with_validation_script.xls";
+
+ private static String FILES_DIR;
+
+ private String sessionToken;
+
+ @BeforeClass
+ public void setupClass() throws IOException
+ {
+ String f = ImportExperimentTypesTest.class.getName().replace(".", "/");
+ FILES_DIR = f.substring(0, f.length() - ImportExperimentTypesTest.class.getSimpleName().length()) + "/test_files/";
+ }
+
+ @BeforeMethod
+ public void beforeTest()
+ {
+ sessionToken = v3api.login(TEST_USER, PASSWORD);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testNormalExperimentTypesAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPES_XLS)));
+ // WHEN
+ ExperimentType collection = TestUtils.getExperimentType(v3api, sessionToken, "COLLECTION");
+ // THEN
+ assertEquals(collection.getCode(), "COLLECTION");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testExperimentTypesWithValidationScript() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, TestUtils.getValidationPluginMap(),
+ Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_WITH_VALIDATION_SCRIPT)));
+ // WHEN
+ ExperimentType collection = TestUtils.getExperimentType(v3api, sessionToken, "COLLECTION");
+ // THEN
+ assertEquals(collection.getValidationPlugin().getName().toUpperCase(), "COLLECTION.VALID");
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfNoSampleCode() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_NO_CODE)));
+ }
+
+}
diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentsTest.java b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentsTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..cbf5a4114bb870ebbbaca669283fc3ac1994d5e5
--- /dev/null
+++ b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportExperimentsTest.java
@@ -0,0 +1,329 @@
+package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
+
+import static org.testng.Assert.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+import org.apache.commons.io.FilenameUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.transaction.annotation.Transactional;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+@ContextConfiguration(locations = "classpath:applicationContext.xml")
+@Transactional(transactionManager = "transaction-manager")
+@Rollback
+public class ImportExperimentsTest extends AbstractImportTest
+{
+ @Autowired
+ private IApplicationServerInternalApi v3api;
+
+ private static final String TEST_USER = "test";
+
+ private static final String PASSWORD = "password";
+
+ private static final String EXPERIMENT_XLS = "experiments/all_inside.xls";
+
+ private static final String EXPERIMENTS_ALL_ELSEWHERE = "experiments/all_elsewhere.xls";
+
+ private static final String EXPERIMENTS_WITH_TYPE_ELSEWHERE = "experiments/experiment_type_elsewhere.xls";
+
+ private static final String EXPERIMENTS_NO_CODE = "experiments/no_code.xls";
+
+ private static final String EXPERIMENTS_WITH_NON_MANDATORY_PROPERTY_MISSING = "experiments/no_non_mandatory_property.xls";
+
+ private static final String EXPERIMENTS_NO_PROJECT_ATTRIBUTE = "experiments/no_project.xls";
+
+ private static final String EXPERIMENTS_WITH_SPACE_AND_PROJECT_ELSEWHERE = "experiments/space_and_project_elsewhere.xls";
+
+ private static final String EXPERIMENTS_SPACE_ELSEWHERE = "experiments/space_elsewhere.xls";
+
+ private static final String EXPERIMENTS_WITH_TYPE_AND_SPACE_ELSEWHERE = "experiments/type_and_space_elsewhere.xls";
+
+ private static final String EXPERIMENTS_WITH_MANDATORY_PROPERTY_MISSING = "experiments/with_mandatory_property_missing.xls";
+
+ private static final String EXPERIMENTS_WITH_MANDATORY_PROPERTY_PRESENT = "experiments/with_mandatory_property.xls";
+
+ private static final String EXPERIMENTS_PROPERTIES_COLUMNS_AS_LABELS = "experiments/with_properties_as_labels.xls";
+
+ private static final String EXPERIMENTS_PROPERTIES_COLUMNS_AS_LABELS_TYPE_ON_SERVER = "experiments/with_properties_as_labels_type_elsewhere.xls";
+
+ private static final String SPACE = "experiments/space.xls";
+
+ private static final String PROJECT = "experiments/project.xls";
+
+ private static final String EXPERIMENT_TYPE = "experiments/experiment_type.xls";
+
+ private static String FILES_DIR;
+
+ private String sessionToken;
+
+ @BeforeClass
+ public void setupClass() throws IOException
+ {
+ String f = ImportExperimentsTest.class.getName().replace(".", "/");
+ FILES_DIR = f.substring(0, f.length() - ImportExperimentsTest.class.getSimpleName().length()) + "/test_files/";
+ }
+
+ @BeforeMethod
+ public void beforeTest()
+ {
+ sessionToken = v3api.login(TEST_USER, PASSWORD);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_XLS)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), "Value");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedSecondExperiment() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_XLS)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT2", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT2");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), "Other Value");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "Random string");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedWithEverythingOnServer() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECT)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_ALL_ELSEWHERE)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), "Value");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedWithEverythingOnServerAndInXls() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECT)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_XLS)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), "Value");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfExperimentTypeDoesntExist() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECT)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_ALL_ELSEWHERE)));
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfProjectDoesntExist() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_ALL_ELSEWHERE)));
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedWithTypeOnServer() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_TYPE_ELSEWHERE)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), "Value");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedWithTypeOnServerAndInXls() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECT)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_TYPE_ELSEWHERE)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), "Value");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfExperimentNoCode() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_NO_CODE)));
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedWhenNonMandatoryPropertiesAreNotProvided() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_NON_MANDATORY_PROPERTY_MISSING)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), null);
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfExperimentNoProject() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_NO_PROJECT_ATTRIBUTE)));
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedWithSpaceAndProjectOnServer() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECT)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_SPACE_AND_PROJECT_ELSEWHERE)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), "Value");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedWithSpaceOnServer() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_SPACE_ELSEWHERE)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), "Value");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedWithTypeAndSpaceOnServer() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_TYPE_AND_SPACE_ELSEWHERE)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), "Value");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfMandatoryPropertyMissing() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_MANDATORY_PROPERTY_MISSING)));
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedIfMandatoryPropertyArePresent() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_WITH_MANDATORY_PROPERTY_PRESENT)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), "Value");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedWhenPropertiesAreAddressedByLabelsWithTypeInXls() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_PROPERTIES_COLUMNS_AS_LABELS)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), "Value");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedWhenPropertiesAreAddressedByLabelsWithTypeOnServer() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENT_TYPE)));
+ TestUtils.createFrom(v3api, sessionToken,
+ Paths.get(FilenameUtils.concat(FILES_DIR, EXPERIMENTS_PROPERTIES_COLUMNS_AS_LABELS_TYPE_ON_SERVER)));
+ // WHEN
+ Experiment experiment = TestUtils.getExperiment(v3api, sessionToken, "TEST_EXPERIMENT", "TEST_PROJECT", "TEST_SPACE");
+ // THEN
+ assertEquals(experiment.getCode(), "TEST_EXPERIMENT");
+ assertEquals(experiment.getProject().getCode(), "TEST_PROJECT");
+ assertEquals(experiment.getProperties().get("$NAME"), "Value");
+ assertEquals(experiment.getProperties().get("DEFAULT_OBJECT_TYPE"), "OBJECT_TYPE");
+ }
+
+}
diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportProjectsTest.java b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportProjectsTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..7b06530d87c6fa5575741a913414f78c8937692d
--- /dev/null
+++ b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportProjectsTest.java
@@ -0,0 +1,132 @@
+package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
+
+import static org.testng.Assert.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+import org.apache.commons.io.FilenameUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.transaction.annotation.Transactional;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.Project;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+@ContextConfiguration(locations = "classpath:applicationContext.xml")
+@Transactional(transactionManager = "transaction-manager")
+@Rollback
+public class ImportProjectsTest extends AbstractImportTest
+{
+ @Autowired
+ private IApplicationServerInternalApi v3api;
+
+ private static final String TEST_USER = "test";
+
+ private static final String PASSWORD = "password";
+
+ private static final String PROJECTS_XLS = "projects/with_spaces.xls";
+
+ private static final String PROJECTS_NO_CODE = "projects/no_code.xls";
+
+ private static final String PROJECTS_NO_DESCRIPTION = "projects/no_desc.xls";
+
+ private static final String PROJECTS_NO_SPACE = "projects/no_space.xls";
+
+ private static final String PROJECTS_WITH_SPACES_ON_SERVER = "projects/with_spaces_on_server.xls";
+
+ private static final String SPACES = "projects/spaces.xls";
+
+ private static String FILES_DIR;
+
+ private String sessionToken;
+
+ @BeforeClass
+ public void setupClass() throws IOException
+ {
+ String f = ImportProjectsTest.class.getName().replace(".", "/");
+ FILES_DIR = f.substring(0, f.length() - ImportProjectsTest.class.getSimpleName().length()) + "/test_files/";
+ }
+
+ @BeforeMethod
+ public void beforeTest()
+ {
+ sessionToken = v3api.login(TEST_USER, PASSWORD);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_XLS)));
+ // WHEN
+ Project project = TestUtils.getProject(v3api, sessionToken, "TEST_PROJECT");
+ // THEN
+ assertEquals(project.getCode(), "TEST_PROJECT");
+ assertEquals(project.getDescription(), "TEST");
+ assertEquals(project.getSpace().getCode(), "TEST_SPACE");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedSecondProject() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_XLS)));
+ // WHEN
+ Project project = TestUtils.getProject(v3api, sessionToken, "TEST_PROJECT2");
+ // THEN
+ assertEquals(project.getCode(), "TEST_PROJECT2");
+ assertEquals(project.getDescription(), "description of another project");
+ assertEquals(project.getSpace().getCode(), "TEST_SPACE2");
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfNoProjectCode() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_NO_CODE)));
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedNoDescription() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_NO_DESCRIPTION)));
+ // WHEN
+ Project project = TestUtils.getProject(v3api, sessionToken, "TEST_PROJECT");
+ // THEN
+ assertEquals(project.getCode(), "TEST_PROJECT");
+ assertEquals(project.getDescription(), null);
+ assertEquals(project.getSpace().getCode(), "TEST_SPACE");
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfNoProjectSpace() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_NO_SPACE)));
+ }
+
+ @Test
+ @DirtiesContext
+ public void testProjectsAreCreatedSpaceOnServer() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACES)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROJECTS_WITH_SPACES_ON_SERVER)));
+ // WHEN
+ Project project = TestUtils.getProject(v3api, sessionToken, "TEST_PROJECT");
+ // THEN
+ assertEquals(project.getCode(), "TEST_PROJECT");
+ assertEquals(project.getDescription(), "TEST");
+ assertEquals(project.getSpace().getCode(), "TEST_SPACE");
+ }
+
+}
diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportPropertyTypesTest.java b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportPropertyTypesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..8b0def35d27e07b085af53fe2dce981ace80eb7d
--- /dev/null
+++ b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportPropertyTypesTest.java
@@ -0,0 +1,148 @@
+package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+import org.apache.commons.io.FilenameUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.transaction.annotation.Transactional;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.DataType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyType;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+@ContextConfiguration(locations = "classpath:applicationContext.xml")
+@Transactional(transactionManager = "transaction-manager")
+@Rollback
+public class ImportPropertyTypesTest extends AbstractImportTest
+{
+
+ @Autowired
+ private IApplicationServerInternalApi v3api;
+
+ private static final String TEST_USER = "test";
+
+ private static final String PASSWORD = "password";
+
+ private static final String PROPERTY_TYPES_XLS = "property_types/normal_property_type.xls";
+
+ private static final String PROPERTY_NO_CODE = "property_types/no_code.xls";
+
+ private static final String PROPERTY_NO_DATA_TYPE = "property_types/no_data_type.xls";
+
+ private static final String PROPERTY_NO_DESCRIPTION = "property_types/no_desc.xls";
+
+ private static final String PROPERTY_NO_LABEL = "property_types/no_label.xls";
+
+ private static final String PROPERTY_VOCAB_TYPE_NO_VOCABULARY_CODE = "property_types/no_vocab_code.xls";
+
+ private static final String PROPERTY_NON_VOCAB_TYPE_VOCABULARY_CODE = "property_types/vocabcode_when_not_vocabtype.xls";
+
+ private static final String PROPERTY_VOCABULARY_ON_SERVER = "property_types/with_vocab_on_server.xls";
+
+ private static final String PROPERTY_VOCAB_TYPE = "property_types/with_vocab.xls";
+
+ private static final String VOCABULARY_DETECTION = "property_types/vocabulary_detection.xls";
+
+ private static String FILES_DIR;
+
+ private String sessionToken;
+
+ @BeforeClass
+ public void setupClass() throws IOException
+ {
+ String f = ImportPropertyTypesTest.class.getName().replace(".", "/");
+ FILES_DIR = f.substring(0, f.length() - ImportPropertyTypesTest.class.getSimpleName().length()) + "/test_files/";
+ }
+
+ @BeforeMethod
+ public void beforeTest()
+ {
+ sessionToken = v3api.login(TEST_USER, PASSWORD);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testNormalPropertyTypesAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_XLS)));
+ // WHEN
+ PropertyType notes = TestUtils.getPropertyType(v3api, sessionToken, "NOTES");
+ // THEN
+ assertEquals(notes.getCode(), "NOTES");
+ assertEquals(notes.getLabel(), "Notes");
+ assertEquals(notes.getDataType(), DataType.MULTILINE_VARCHAR);
+ assertEquals(notes.getDescription(), "Notes Descripton");
+ assertFalse(notes.isInternalNameSpace());
+ assertFalse(notes.isManagedInternally());
+ assertNull(notes.getVocabulary());
+ }
+
+ @Test
+ @DirtiesContext
+ public void testInternalPropertyTypesAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_TYPES_XLS)));
+ // WHEN
+ PropertyType notes = TestUtils.getPropertyType(v3api, sessionToken, "$INTERNAL_PROP");
+ // THEN
+ assertEquals(notes.getCode(), "$INTERNAL_PROP");
+ assertEquals(notes.getLabel(), "Name");
+ assertEquals(notes.getDataType(), DataType.VARCHAR);
+ assertEquals(notes.getDescription(), "Name");
+ assertTrue(notes.isInternalNameSpace());
+ assertFalse(notes.isManagedInternally());
+ assertNull(notes.getVocabulary());
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void testPropertyTypeNoCode() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_NO_CODE)));
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void testPropertyTypeNoLabel() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_NO_LABEL)));
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void testPropertyTypeNoVocabularyCodeWhenVocabularyType() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_VOCAB_TYPE_NO_VOCABULARY_CODE)));
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void testPropertyTypeNoDataType() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_NO_DATA_TYPE)));
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void testPropertyTypeNoDescription() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_NO_DESCRIPTION)));
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void testPropertyTypeVocabularyCodeToNonVocabularyType() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, PROPERTY_NON_VOCAB_TYPE_VOCABULARY_CODE)));
+ }
+
+}
diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSampleTypesTest.java b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSampleTypesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..78c3538bf5c6fcc708c07b90dfd5d8c569b93112
--- /dev/null
+++ b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSampleTypesTest.java
@@ -0,0 +1,233 @@
+package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+import org.apache.commons.io.FilenameUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.transaction.annotation.Transactional;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.Plugin;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.PluginType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+@ContextConfiguration(locations = "classpath:applicationContext.xml")
+@Transactional(transactionManager = "transaction-manager")
+@Rollback
+public class ImportSampleTypesTest extends AbstractImportTest
+{
+
+ private static final String SAMPLE_TYPES_XLS = "sample_types/normal_samples.xls";
+
+ private static final String SAMPLE_TYPES_XLS_DIFFERENT_PROPERTY_ASSIGN = "sample_types/normal_samples_v2.xls";
+
+ private static final String SAMPLE_TYPES_WITH_DYNAMIC_SCRIPT = "sample_types/with_dynamic_script.xls";
+
+ private static final String SAMPLE_TYPES_WITH_VALIDATION_SCRIPT = "sample_types/with_validation_script.xls";
+
+ private static final String SAMPLE_TYPES_WITH_VOCABULARY = "sample_types/with_vocabulary_in_xls.xls";
+
+ private static final String SAMPLE_TYPES_WITH_VOCABULARY_ON_SERVER = "sample_types/with_vocabulary_on_server.xls";
+
+ private static final String VOCABULARY_DETECTION = "sample_types/vocabulary_detection.xls";
+
+ private static final String SAMPLE_TYPES_WITH_AUTO_GENERATED_CODES = "sample_types/with_auto_generated_codes.xls";
+
+ private static final String SAMPLE_TYPE_NO_CODE = "sample_types/no_code.xls";
+
+ @Autowired
+ private IApplicationServerInternalApi v3api;
+
+ private static final String TEST_USER = "test";
+
+ private static final String PASSWORD = "password";
+
+ private static String FILES_DIR;
+
+ private String sessionToken;
+
+ @BeforeClass
+ public void setupClass() throws IOException
+ {
+ String f = ImportSampleTypesTest.class.getName().replace(".", "/");
+ FILES_DIR = f.substring(0, f.length() - ImportSampleTypesTest.class.getSimpleName().length()) + "/test_files/";
+ }
+
+ @BeforeMethod
+ public void beforeTest()
+ {
+ sessionToken = v3api.login(TEST_USER, PASSWORD);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testNormalSampleTypesAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_XLS)));
+ // WHEN
+ SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+ // THEN
+ assertFalse(antibody.isAutoGeneratedCode());
+ }
+
+ @Test
+ @DirtiesContext
+ public void testPropertyTypeAssignmentsFromNormalSampleTypesAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_XLS)));
+ // WHEN
+ SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+ // THEN
+ boolean allMandatory = antibody.getPropertyAssignments().stream().allMatch(propAssignment -> propAssignment.isMandatory() == true);
+ boolean allShownInEditView =
+ antibody.getPropertyAssignments().stream().allMatch(propAssignment -> propAssignment.isShowInEditView() == true);
+ boolean generalInformationExists =
+ antibody.getPropertyAssignments().stream().anyMatch(propAssignment -> propAssignment.getSection().equals("General information"));
+ boolean someOtherSectionExists =
+ antibody.getPropertyAssignments().stream().anyMatch(propAssignment -> propAssignment.getSection().equals("Some other section"));
+ boolean threePropertyAssignments = antibody.getPropertyAssignments().size() == 3;
+ assertTrue(threePropertyAssignments);
+ assertTrue(generalInformationExists);
+ assertTrue(someOtherSectionExists);
+ assertTrue(allShownInEditView);
+ assertTrue(allMandatory);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testPropertyTypeAssignmentsFromNormalv2SampleTypesAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_XLS_DIFFERENT_PROPERTY_ASSIGN)));
+ // WHEN
+ SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+ // THEN
+ boolean allNotMandatory = antibody.getPropertyAssignments().stream().allMatch(propAssignment -> propAssignment.isMandatory() == false);
+ boolean allNotShownInEditView =
+ antibody.getPropertyAssignments().stream().allMatch(propAssignment -> propAssignment.isShowInEditView() == false);
+ boolean threePropertyAssignments = antibody.getPropertyAssignments().size() == 3;
+ assertTrue(threePropertyAssignments);
+ assertTrue(allNotShownInEditView);
+ assertTrue(allNotMandatory);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testPropertyTypesFromNormalSampleTypesAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_XLS)));
+ // WHEN
+ SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+ // THEN
+ boolean namePropertyExists =
+ antibody.getPropertyAssignments().stream().anyMatch(propAssignment -> propAssignment.getPropertyType().getCode().equals("$NAME"));
+ boolean forWhatPropertyExists =
+ antibody.getPropertyAssignments().stream().anyMatch(propAssignment -> propAssignment.getPropertyType().getCode().equals("FOR_WHAT"));
+ boolean epitopePropertyExists =
+ antibody.getPropertyAssignments().stream().anyMatch(propAssignment -> propAssignment.getPropertyType().getCode().equals("EPITOPE"));
+
+ assertNotNull(antibody);
+ assertTrue(namePropertyExists);
+ assertTrue(forWhatPropertyExists);
+ assertTrue(epitopePropertyExists);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSampleTypesWithPropertyHavingDynamicScript() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, TestUtils.getDynamicPluginMap(),
+ Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_DYNAMIC_SCRIPT)));
+ // WHEN
+ SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+ // THEN
+ Plugin dynamicScript = antibody.getPropertyAssignments().get(0).getPlugin();
+ assertNotNull(dynamicScript);
+ assertEquals(dynamicScript.getName().toUpperCase(), "$NAME.DYNAMIC");
+ assertEquals(dynamicScript.getScript(), TestUtils.getDynamicScript());
+ assertEquals(dynamicScript.getPluginType(), PluginType.DYNAMIC_PROPERTY);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSampleTypesWithPropertyHavingValidationScript() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, TestUtils.getValidationPluginMap(),
+ Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_VALIDATION_SCRIPT)));
+ // WHEN
+ SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+ // THEN
+ Plugin validationScript = antibody.getValidationPlugin();
+ assertNotNull(validationScript);
+ assertEquals(validationScript.getName().toUpperCase(), "ANTIBODY.VALID");
+ assertEquals(validationScript.getScript(), TestUtils.getValidationScript());
+ assertEquals(validationScript.getPluginType(), PluginType.ENTITY_VALIDATION);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSampleTypesWithVocabularyInXls() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_VOCABULARY)));
+ // WHEN
+ SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+ // THEN
+ PropertyAssignment propertyAssignment = antibody.getPropertyAssignments().get(0);
+ assertNotNull(propertyAssignment);
+ assertEquals(propertyAssignment.getPropertyType().getVocabulary().getCode(), "DETECTION");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSampleTypesWithVocabularyOnServer() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARY_DETECTION)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_VOCABULARY_ON_SERVER)));
+ // WHEN
+ SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "ANTIBODY");
+ // THEN
+ PropertyAssignment propertyAssignment = antibody.getPropertyAssignments().get(0);
+ assertNotNull(propertyAssignment);
+ assertEquals(propertyAssignment.getPropertyType().getVocabulary().getCode(), "DETECTION");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSampleTypesWithAutoGeneratedCodeAttribute() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPES_WITH_AUTO_GENERATED_CODES)));
+ // WHEN
+ SampleType antibody = TestUtils.getSampleType(v3api, sessionToken, "SECONDBODY");
+ // THEN
+ assertTrue(antibody.isAutoGeneratedCode());
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfNoSampleCode() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE_NO_CODE)));
+ }
+
+}
diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSamplesTest.java b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSamplesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..f83fb7839c5e85bc3e832ed6d54b4e3ee3802752
--- /dev/null
+++ b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSamplesTest.java
@@ -0,0 +1,313 @@
+package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+import org.apache.commons.io.FilenameUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.transaction.annotation.Transactional;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+@ContextConfiguration(locations = "classpath:applicationContext.xml")
+@Transactional(transactionManager = "transaction-manager")
+@Rollback
+public class ImportSamplesTest extends AbstractImportTest
+{
+ @Autowired
+ private IApplicationServerInternalApi v3api;
+
+ private static final String TEST_USER = "test";
+
+ private static final String PASSWORD = "password";
+
+ private static final String SAMPLES_XLS = "samples/all_in.xls";
+
+ private static final String SAMPLES_SPACE_ELSEWHERE = "samples/space_elsewhere.xls";
+
+ private static final String SAMPLES_SAMPLE_TYPE_ELSWHERE = "samples/sample_type_elsewhere.xls";
+
+ private static final String SAMPLES_SPACE_PROJECT_EXPERIMENT_ELSEWHERE = "samples/space_project_experiment_elsewhere.xls";
+
+ private static final String SPACE = "samples/space.xls";
+
+ private static final String SAMPLE_TYPE = "samples/sample_type.xls";
+
+ private static final String VOCABULARY_TYPE = "samples/vocab_type.xls";
+
+ private static final String CHILD_AS_CODE = "samples/child_as_code.xls";
+
+ private static final String CHILD_AS_DOLLARTAG = "samples/child_as_dollartag.xls";
+
+ private static final String PARENT_AS_CODE = "samples/parent_as_code.xls";
+
+ private static final String PARENT_AS_DOLLARTAG = "samples/parent_as_dollartag.xls";
+
+ private static final String MANDATORY_FIELD_MISSING = "samples/mandatory_field_missing.xls";
+
+ private static final String NON_MANDATORY_FIELD_MISSING = "samples/non_mandatory_field_missing.xls";
+
+ private static final String AUTO_GENERATED_SAMPLE_LEVEL = "samples/with_auto_generated_code_sample_level.xls";
+
+ private static final String AUTO_GENERATED_SAMPLE_TYPE_LEVEL = "samples/with_auto_generated_code_sampletype_level.xls";
+
+ private static String FILES_DIR;
+
+ private String sessionToken;
+
+ @BeforeClass
+ public void setupClass() throws IOException
+ {
+ String f = ImportSamplesTest.class.getName().replace(".", "/");
+ FILES_DIR = f.substring(0, f.length() - ImportSamplesTest.class.getSimpleName().length()) + "/test_files/";
+ }
+
+ @BeforeMethod
+ public void beforeTest()
+ {
+ sessionToken = v3api.login(TEST_USER, PASSWORD);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSamplesAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_XLS)));
+ // WHEN
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "AAA", "TEST_SPACE");
+ // THEN
+ assertEquals(sample.getCode(), "AAA");
+ assertEquals(sample.getProject(), null);
+ assertEquals(sample.getExperiment().getCode(), "TEST_EXPERIMENT2");
+ assertEquals(sample.getSpace().getCode(), "TEST_SPACE");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSamplesAreCreatedSecondSample() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_XLS)));
+ // WHEN
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ // THEN
+ assertEquals(sample.getCode(), "VVV");
+ assertEquals(sample.getProject(), null);
+ assertEquals(sample.getExperiment().getCode(), "TEST_EXPERIMENT");
+ assertEquals(sample.getSpace().getCode(), "TEST_SPACE");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSamplesAreCreatedThirdSample() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_XLS)));
+ // WHEN
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "S1", "TEST_SPACE");
+ // THEN
+ assertEquals(sample.getCode(), "S1");
+ assertEquals(sample.getProject(), null);
+ assertEquals(sample.getExperiment().getCode(), "TEST_EXPERIMENT");
+ assertEquals(sample.getSpace().getCode(), "TEST_SPACE");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSamplesAreCreatedWhenSpaceOnServer() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SPACE_ELSEWHERE)));
+ // WHEN
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ // THEN
+ assertNotNull(sample);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSamplesAreCreatedWhenSpaceInSeparateXls() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken,
+ Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SPACE_ELSEWHERE)),
+ Paths.get(FilenameUtils.concat(FILES_DIR, SPACE)));
+ // WHEN
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ // THEN
+ assertNotNull(sample);
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfSpaceDoesntExist() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SPACE_ELSEWHERE)));
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSamplesAreCreatedWhenSampleTypeOnServer() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken,
+ Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARY_TYPE)),
+ Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE)));
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SAMPLE_TYPE_ELSWHERE)));
+ // WHEN
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ // THEN
+ assertNotNull(sample);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSamplesAreCreatedWhenSampleTypeInSeparateXls() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken,
+ Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SAMPLE_TYPE_ELSWHERE)),
+ Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLE_TYPE)));
+ // WHEN
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ // THEN
+ assertNotNull(sample);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSamplesChildrenAreAssignedWhenAddressedByCodeInXls() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken,
+ Paths.get(FilenameUtils.concat(FILES_DIR, CHILD_AS_CODE)));
+ // WHEN
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ // THEN
+ assertNotNull(sample);
+ assertEquals(sample.getChildren().size(), 1);
+ assertEquals(sample.getChildren().get(0).getCode(), "AAA");
+ assertEquals(sample.getChildren().get(0).getSpace().getCode(), "TEST_SPACE");
+ assertEquals(sample.getChildren().get(0).getExperiment().getCode(), "TEST_EXPERIMENT2");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSamplesParentsAreAssignedWhenAddressedByCodeInXls() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken,
+ Paths.get(FilenameUtils.concat(FILES_DIR, PARENT_AS_CODE)));
+ // WHEN
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ // THEN
+ assertNotNull(sample);
+ assertEquals(sample.getParents().size(), 1);
+ assertEquals(sample.getParents().get(0).getCode(), "AAA");
+ assertEquals(sample.getParents().get(0).getSpace().getCode(), "TEST_SPACE");
+ assertEquals(sample.getParents().get(0).getExperiment().getCode(), "TEST_EXPERIMENT2");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSamplesChildrenAreAssignedWhenAddressedByDollartagInXls() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken,
+ Paths.get(FilenameUtils.concat(FILES_DIR, CHILD_AS_DOLLARTAG)));
+ // WHEN
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ // THEN
+ assertNotNull(sample);
+ assertEquals(sample.getChildren().size(), 1);
+ assertEquals(sample.getChildren().get(0).getCode(), "AAA");
+ assertEquals(sample.getChildren().get(0).getSpace().getCode(), "TEST_SPACE");
+ assertEquals(sample.getChildren().get(0).getExperiment().getCode(), "TEST_EXPERIMENT2");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testSamplesParentsAreAssignedWhenAddressedByDollartagInXls() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken,
+ Paths.get(FilenameUtils.concat(FILES_DIR, PARENT_AS_DOLLARTAG)));
+ // WHEN
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "VVV", "TEST_SPACE");
+ // THEN
+ assertNotNull(sample);
+ assertEquals(sample.getParents().size(), 1);
+ assertEquals(sample.getParents().get(0).getCode(), "AAA");
+ assertEquals(sample.getParents().get(0).getSpace().getCode(), "TEST_SPACE");
+ assertEquals(sample.getParents().get(0).getExperiment().getCode(), "TEST_EXPERIMENT2");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testCreatesSampleWithNonMandatoryFieldsMissing() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken,
+ Paths.get(FilenameUtils.concat(FILES_DIR, NON_MANDATORY_FIELD_MISSING)));
+ // WHEN
+ Sample sample = TestUtils.getSample(v3api, sessionToken, "AAA", "TEST_SPACE");
+ // THEN
+ assertNotNull(sample);
+ assertEquals(sample.getProperties().get("FOR_WHAT"), null);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testCreatesSampleWithAutogeneratedCodeWhenOnPerSampleLevel() throws IOException
+ {
+ // GIVEN
+ String result = TestUtils.createFrom(v3api, sessionToken,
+ Paths.get(FilenameUtils.concat(FILES_DIR, AUTO_GENERATED_SAMPLE_LEVEL)));
+ String permId = TestUtils.extractSamplePermIdFromResults(result);
+ // WHEN
+ Sample sample = TestUtils.getSampleByPermId(v3api, sessionToken, permId);
+ // THEN
+ assertNotNull(sample.getCode());
+ assertEquals(sample.getType().getCode(), "ANTIBODY");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testCreatesSampleWithAutogeneratedCodeWhenOnSampleTypeLevel() throws IOException
+ {
+ // GIVEN
+ String result = TestUtils.createFrom(v3api, sessionToken,
+ Paths.get(FilenameUtils.concat(FILES_DIR, AUTO_GENERATED_SAMPLE_TYPE_LEVEL)));
+ String permId = TestUtils.extractSamplePermIdFromResults(result);
+ // WHEN
+ Sample sample = TestUtils.getSampleByPermId(v3api, sessionToken, permId);
+ // THEN
+ assertNotNull(sample);
+ assertEquals(sample.getType().getCode(), "ANTIBODY");
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfSamplesSpaceProjectDoesntExist() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SAMPLES_SPACE_PROJECT_EXPERIMENT_ELSEWHERE)));
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfMandatoryPropertyIsMissing() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, MANDATORY_FIELD_MISSING)));
+ }
+
+}
diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSpacesTest.java b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSpacesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..c76bf95b2505429d0711af6453ffebf7dbdd9fc8
--- /dev/null
+++ b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportSpacesTest.java
@@ -0,0 +1,102 @@
+package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
+
+import static org.testng.Assert.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+import org.apache.commons.io.FilenameUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.transaction.annotation.Transactional;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.Space;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+@ContextConfiguration(locations = "classpath:applicationContext.xml")
+@Transactional(transactionManager = "transaction-manager")
+@Rollback
+public class ImportSpacesTest extends AbstractImportTest
+{
+ @Autowired
+ private IApplicationServerInternalApi v3api;
+
+ private static final String TEST_USER = "test";
+
+ private static final String PASSWORD = "password";
+
+ private static final String SPACES_XLS = "spaces/normal_spaces.xls";
+
+ private static final String SPACES_NO_CODE = "spaces/no_code.xls";
+
+ private static final String SPACES_NO_DESCRIPTION = "spaces/no_desc.xls";
+
+ private static String FILES_DIR;
+
+ private String sessionToken;
+
+ @BeforeClass
+ public void setupClass() throws IOException
+ {
+ String f = ImportSpacesTest.class.getName().replace(".", "/");
+ FILES_DIR = f.substring(0, f.length() - ImportSpacesTest.class.getSimpleName().length()) + "/test_files/";
+ }
+
+ @BeforeMethod
+ public void beforeTest()
+ {
+ sessionToken = v3api.login(TEST_USER, PASSWORD);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testNormalSpacesAreCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACES_XLS)));
+ // WHEN
+ Space rawData = TestUtils.getSpace(v3api, sessionToken, "TEST_SPACE");
+ // THEN
+ assertEquals(rawData.getCode(), "TEST_SPACE");
+ assertEquals(rawData.getDescription(), "TEST");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testNormalSpacesAreCreatedSecondSpace() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACES_XLS)));
+ // WHEN
+ Space space = TestUtils.getSpace(v3api, sessionToken, "TEST_SPACE2");
+ // THEN
+ assertEquals(space.getCode(), "TEST_SPACE2");
+ assertEquals(space.getDescription(), "TEST desc");
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfNoSpaceCode() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACES_NO_CODE)));
+ }
+
+ @Test
+ @DirtiesContext
+ public void shouldCreateSpaceWhenNoDescription() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, SPACES_NO_DESCRIPTION)));
+ // WHEN
+ Space space = TestUtils.getSpace(v3api, sessionToken, "TEST_SPACE");
+ // THEN
+ assertEquals(space.getCode(), "TEST_SPACE");
+ assertEquals(space.getDescription(), null);
+ }
+
+}
diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportVocabularyTypesTest.java b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportVocabularyTypesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..4a8f9088f44b3de91fbf0614bb0d1f088b6556d3
--- /dev/null
+++ b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/ImportVocabularyTypesTest.java
@@ -0,0 +1,205 @@
+/*
+ * Copyright 2015 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+import java.util.List;
+
+import org.apache.commons.io.FilenameUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.transaction.annotation.Transactional;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.Vocabulary;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.VocabularyTerm;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+@ContextConfiguration(locations = "classpath:applicationContext.xml")
+@Transactional(transactionManager = "transaction-manager")
+@Rollback
+public class ImportVocabularyTypesTest extends AbstractImportTest
+{
+
+ private static final String VOCABULARIES_TYPES_XLS = "vocabularies/normal_vocab.xls";
+
+ private static final String VOCABULARIES_NO_CODE = "vocabularies/vocab_no_code.xlsx";
+
+ private static final String VOCABULARIES_NO_DESCRIPTION = "vocabularies/vocab_no_desc.xlsx";
+
+ private static final String VOCABULARIES_NO_TERM_CODE = "vocabularies/vocab_no_term_code.xlsx";
+
+ private static final String VOCABULARIES_NO_TERM_DESCRIPTION = "vocabularies/vocab_no_term_desc.xlsx";
+
+ private static final String VOCABULARIES_NO_TERM_LABEL = "vocabularies/vocab_no_term_label.xlsx";
+
+ private static final String VOCABULARIES_NO_TERMS = "vocabularies/vocab_no_term_label.xlsx";
+
+ @Autowired
+ private IApplicationServerInternalApi v3api;
+
+ private static final String TEST_USER = "test";
+
+ private static final String PASSWORD = "password";
+
+ private static String FILES_DIR;
+
+ private String sessionToken;
+
+ @BeforeClass
+ public void setupClass() throws IOException
+ {
+ String f = ImportVocabularyTypesTest.class.getName().replace(".", "/");
+ FILES_DIR = f.substring(0, f.length() - ImportVocabularyTypesTest.class.getSimpleName().length()) + "/test_files/";
+
+ }
+
+ @BeforeMethod
+ public void beforeTest()
+ {
+ sessionToken = v3api.login(TEST_USER, PASSWORD);
+ }
+
+ @Test
+ @DirtiesContext
+ public void testNormalVocabularyCreationIsCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_TYPES_XLS)));
+ // WHEN
+ Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+ // THEN
+ assertNotNull(detection);
+ assertEquals(detection.getDescription(), "Protein detection system");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testNormalVocabularyHasFirstTermCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_TYPES_XLS)));
+ // WHEN
+ Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+ // THEN
+ VocabularyTerm term = detection.getTerms().get(0);
+ assertEquals(term.getCode(), "HRP");
+ assertEquals(term.getDescription(), "The antibody is conjugated with the horseradish peroxydase");
+ assertEquals(term.getLabel(), "horseradish peroxydase");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testNormalVocabularyCreatedNoExtraVocabulary() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_TYPES_XLS)));
+ // WHEN
+ List<Vocabulary> vocabularies = TestUtils.getAllVocabularies(v3api, sessionToken);
+ // THEN
+ assertEquals(vocabularies.size(), 3); // 2 created + 1 default
+ }
+
+ @Test
+ @DirtiesContext
+ public void testNormalVocabularyHasSecondTermCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_TYPES_XLS)));
+ // WHEN
+ Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+ // THEN
+ VocabularyTerm term = detection.getTerms().get(1);
+ assertEquals(term.getCode(), "TEST_VOC");
+ assertEquals(term.getDescription(), "some focabulary that is used in tests and nothing else");
+ assertEquals(term.getLabel(), "vocabulary for tests");
+ }
+
+ @Test
+ @DirtiesContext
+ public void testVocabularyWithNoTermDescriptionShouldBeCreated() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_TERM_DESCRIPTION)));
+ // WHEN
+ Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+ // THEN
+ assertNotNull(detection);
+ assertNull(detection.getTerms().get(0).getDescription());
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfNoVocabularyCode() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_CODE)));
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void shouldThrowExceptionIfNoTermCode() throws IOException
+ {
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_TERM_CODE)));
+ }
+
+ @Test
+ @DirtiesContext
+ public void shouldNotThrowExceptionIfNoVocabularyDescription() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_DESCRIPTION)));
+ // WHEN
+ Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+ // THEN
+ assertNotNull(detection);
+ assertNull(detection.getDescription());
+ }
+
+ @Test
+ @DirtiesContext
+ public void shouldNotThrowExceptionIfNoTermLabel() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_TERM_LABEL)));
+ // WHEN
+ Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+ // THEN
+ assertNotNull(detection);
+ assertNull(detection.getTerms().get(0).getLabel());
+ }
+
+ @Test
+ @DirtiesContext
+ public void shouldNotThrowExceptionIfNoTerms() throws IOException
+ {
+ // GIVEN
+ TestUtils.createFrom(v3api, sessionToken, Paths.get(FilenameUtils.concat(FILES_DIR, VOCABULARIES_NO_TERMS)));
+ // WHEN
+ Vocabulary detection = TestUtils.getVocabulary(v3api, sessionToken, "DETECTION");
+ // THEN
+ assertNotNull(detection);
+ }
+
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/TestUtils.java b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/TestUtils.java
new file mode 100644
index 0000000000000000000000000000000000000000..cd10c5cf5514ca8d6935c14eb09f88e47b10f905
--- /dev/null
+++ b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/TestUtils.java
@@ -0,0 +1,366 @@
+package ch.ethz.sis.openbis.systemtest.plugin.excelimport;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetTypeFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search.DataSetTypeSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentTypeFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.IExperimentId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search.ExperimentTypeSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.Project;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.fetchoptions.ProjectFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.search.ProjectSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.fetchoptions.PropertyAssignmentFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.fetchoptions.PropertyTypeFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search.PropertyTypeSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleTypeFetchOptions;
+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.SampleTypeSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.CustomASServiceExecutionOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id.CustomASServiceCode;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.Space;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.fetchoptions.SpaceFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.search.SpaceSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.Vocabulary;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.fetchoptions.VocabularyFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.id.VocabularyPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.search.VocabularySearchCriteria;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.IApplicationServerInternalApi;
+
+public class TestUtils
+{
+
+ public static final String XLS_PARAM = "xls";
+
+ public static final String SCRIPTS_PARAM = "scripts";
+
+ public static final String XLS_IMPORT_API = "xls-import-api";
+
+ static Vocabulary getVocabulary(IApplicationServerInternalApi v3api, String sessionToken, String code)
+ {
+ VocabularySearchCriteria criteria = new VocabularySearchCriteria();
+ criteria.withId().thatEquals(new VocabularyPermId(code));
+
+ VocabularyFetchOptions fo = new VocabularyFetchOptions();
+ fo.withTerms();
+
+ SearchResult<Vocabulary> result = v3api.searchVocabularies(sessionToken, criteria, fo);
+
+ if (result.getObjects().size() > 0)
+ {
+ return result.getObjects().get(0);
+ } else
+ {
+ return null;
+ }
+ }
+
+ static List<Vocabulary> getAllVocabularies(IApplicationServerInternalApi v3api, String sessionToken)
+ {
+ VocabularySearchCriteria criteria = new VocabularySearchCriteria();
+ VocabularyFetchOptions fo = new VocabularyFetchOptions();
+ fo.withTerms();
+
+ SearchResult<Vocabulary> result = v3api.searchVocabularies(sessionToken, criteria, fo);
+
+ if (result.getObjects().size() > 0)
+ {
+ return result.getObjects();
+ } else
+ {
+ return null;
+ }
+ }
+
+ static SampleType getSampleType(IApplicationServerInternalApi v3api, String sessionToken, String code)
+ {
+ SampleTypeSearchCriteria criteria = new SampleTypeSearchCriteria();
+ criteria.withCode().thatEquals(code);
+
+ SampleTypeFetchOptions fo = new SampleTypeFetchOptions();
+ fo.withValidationPlugin().withScript();
+ PropertyAssignmentFetchOptions propCriteria = fo.withPropertyAssignments();
+ propCriteria.withPlugin().withScript();
+ propCriteria.withPropertyType().withVocabulary();
+
+ SearchResult<SampleType> result = v3api.searchSampleTypes(sessionToken, criteria, fo);
+
+ if (result.getObjects().size() > 0)
+ {
+ return result.getObjects().get(0);
+ } else
+ {
+ return null;
+ }
+ }
+
+ static ExperimentType getExperimentType(IApplicationServerInternalApi v3api, String sessionToken, String code)
+ {
+ ExperimentTypeSearchCriteria criteria = new ExperimentTypeSearchCriteria();
+ criteria.withCode().thatEquals(code);
+
+ ExperimentTypeFetchOptions fo = new ExperimentTypeFetchOptions();
+ fo.withValidationPlugin().withScript();
+ PropertyAssignmentFetchOptions propCriteria = fo.withPropertyAssignments();
+ propCriteria.withPlugin().withScript();
+ propCriteria.withPropertyType().withVocabulary();
+
+ SearchResult<ExperimentType> result = v3api.searchExperimentTypes(sessionToken, criteria, fo);
+
+ if (result.getObjects().size() > 0)
+ {
+ return result.getObjects().get(0);
+ } else
+ {
+ return null;
+ }
+ }
+
+ static DataSetType getDatasetType(IApplicationServerInternalApi v3api, String sessionToken, String code)
+ {
+ DataSetTypeSearchCriteria criteria = new DataSetTypeSearchCriteria();
+ criteria.withCode().thatEquals(code);
+
+ DataSetTypeFetchOptions fo = new DataSetTypeFetchOptions();
+ fo.withValidationPlugin().withScript();
+ PropertyAssignmentFetchOptions propCriteria = fo.withPropertyAssignments();
+ propCriteria.withPlugin().withScript();
+ propCriteria.withPropertyType().withVocabulary();
+
+ SearchResult<DataSetType> result = v3api.searchDataSetTypes(sessionToken, criteria, fo);
+
+ if (result.getObjects().size() > 0)
+ {
+ return result.getObjects().get(0);
+ } else
+ {
+ return null;
+ }
+ }
+
+ static PropertyType getPropertyType(IApplicationServerInternalApi v3api, String sessionToken, String code)
+ {
+ PropertyTypeSearchCriteria criteria = new PropertyTypeSearchCriteria();
+ criteria.withCode().thatEquals(code);
+
+ PropertyTypeFetchOptions fo = new PropertyTypeFetchOptions();
+ fo.withVocabulary();
+
+ SearchResult<PropertyType> result = v3api.searchPropertyTypes(sessionToken, criteria, fo);
+
+ if (result.getObjects().size() > 0)
+ {
+ return result.getObjects().get(0);
+ } else
+ {
+ return null;
+ }
+ }
+
+ static Space getSpace(IApplicationServerInternalApi v3api, String sessionToken, String code)
+ {
+ SpaceSearchCriteria criteria = new SpaceSearchCriteria();
+ criteria.withCode().thatEquals(code);
+
+ SpaceFetchOptions fo = new SpaceFetchOptions();
+
+ SearchResult<Space> result = v3api.searchSpaces(sessionToken, criteria, fo);
+
+ if (result.getObjects().size() > 0)
+ {
+ return result.getObjects().get(0);
+ } else
+ {
+ return null;
+ }
+ }
+
+ static Project getProject(IApplicationServerInternalApi v3api, String sessionToken, String code)
+ {
+ ProjectSearchCriteria criteria = new ProjectSearchCriteria();
+ criteria.withCode().thatEquals(code);
+
+ ProjectFetchOptions fo = new ProjectFetchOptions();
+ fo.withSpace();
+
+ SearchResult<Project> result = v3api.searchProjects(sessionToken, criteria, fo);
+
+ if (result.getObjects().size() > 0)
+ {
+ return result.getObjects().get(0);
+ } else
+ {
+ return null;
+ }
+ }
+
+ static Experiment getExperiment(IApplicationServerInternalApi v3api, String sessionToken, String experimentCode, String projectCode,
+ String spaceCode)
+ {
+ List<IExperimentId> ids = new ArrayList<>();
+ ids.add(new ExperimentIdentifier(spaceCode, projectCode, experimentCode));
+
+ ExperimentFetchOptions fo = new ExperimentFetchOptions();
+ fo.withProject();
+ fo.withProperties();
+ fo.withType();
+
+ List<Experiment> result = v3api.getExperiments(sessionToken, ids, fo).values().stream().collect(Collectors.toList());
+
+ if (result.size() > 0)
+ {
+ return result.get(0);
+ } else
+ {
+ return null;
+ }
+ }
+
+ static Sample getSample(IApplicationServerInternalApi v3api, String sessionToken, String sampleCode, String spaceCode)
+ {
+ List<ISampleId> ids = new ArrayList<>();
+ ids.add(new SampleIdentifier(spaceCode, null, null, sampleCode));
+
+ return getSamples(v3api, sessionToken, ids);
+ }
+
+ static Sample getSampleByPermId(IApplicationServerInternalApi v3api, String sessionToken, String permId)
+ {
+ List<ISampleId> ids = new ArrayList<>();
+ ids.add(new SamplePermId(permId));
+
+ return getSamples(v3api, sessionToken, ids);
+ }
+
+ private static Sample getSamples(IApplicationServerInternalApi v3api, String sessionToken, List<ISampleId> ids)
+ {
+ SampleFetchOptions fo = new SampleFetchOptions();
+ SampleFetchOptions childrenFo = fo.withChildren();
+ childrenFo.withSpace();
+ childrenFo.withExperiment();
+ SampleFetchOptions parentsFo = fo.withParents();
+ parentsFo.withSpace();
+ parentsFo.withExperiment();
+ fo.withExperiment();
+ fo.withProject();
+ fo.withProperties();
+ fo.withSpace();
+ fo.withType();
+
+ List<Sample> result = v3api.getSamples(sessionToken, ids, fo).values().stream().collect(Collectors.toList());
+
+ if (result.size() > 0)
+ {
+ return result.get(0);
+ } else
+ {
+ return null;
+ }
+ }
+
+ static String createFrom(IApplicationServerInternalApi v3api, String sessionToken, Path... xls_paths) throws IOException
+ {
+ List<byte[]> excels = new ArrayList<>();
+ for (Path xls_path : xls_paths)
+ {
+ byte[] xls = readData(xls_path);
+ excels.add(xls);
+ }
+ CustomASServiceExecutionOptions options = new CustomASServiceExecutionOptions();
+ options.withParameter(XLS_PARAM, excels);
+ return (String) v3api.executeCustomASService(sessionToken, new CustomASServiceCode(XLS_IMPORT_API), options);
+ }
+
+ static String createFrom(IApplicationServerInternalApi v3api, String sessionToken, Map<String, String> scripts, Path... xls_paths)
+ throws IOException
+ {
+ List<byte[]> excels = new ArrayList<>();
+ for (Path xls_path : xls_paths)
+ {
+ byte[] xls = readData(xls_path);
+ excels.add(xls);
+ }
+ CustomASServiceExecutionOptions options = new CustomASServiceExecutionOptions();
+ options.withParameter(XLS_PARAM, excels);
+ options.withParameter(SCRIPTS_PARAM, scripts);
+ return (String) v3api.executeCustomASService(sessionToken, new CustomASServiceCode(XLS_IMPORT_API), options);
+ }
+
+ static String getValidationScript()
+ {
+ return "def validate(entity, isNew):\n if isNew:\n return";
+ }
+
+ static String getDynamicScript()
+ {
+ return "def calculate():\n return 1";
+ }
+
+ static Map<String, String> getValidationPluginMap()
+ {
+ String dynamicScriptString = getValidationScript();
+ Map<String, String> scriptsMap = new HashMap<>();
+ scriptsMap.put("valid.py", dynamicScriptString);
+
+ return scriptsMap;
+ }
+
+ static Map<String, String> getDynamicPluginMap()
+ {
+ String dynamicScriptString = getDynamicScript();
+ Map<String, String> scriptsMap = new HashMap<>();
+ scriptsMap.put("dynamic/dynamic.py", dynamicScriptString);
+
+ return scriptsMap;
+ }
+
+ static String extractSamplePermIdFromResults(String result)
+ {
+ // Note this will work only if we created single sample!!
+ String permId = result.substring(result.indexOf("CreateSamplesOperationResult") + "CreateSamplesOperationResult".length());
+ permId = StringUtils.strip(permId, "[]");
+ return permId;
+ }
+
+ private static byte[] readData(Path xls_path) throws IOException
+ {
+ String path = xls_path.toString();
+ InputStream resourceAsStream = TestUtils.class.getClassLoader().getResourceAsStream(path);
+ try
+ {
+ ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+ IOUtils.copy(resourceAsStream, byteArrayOutputStream);
+ return byteArrayOutputStream.toByteArray();
+ } finally
+ {
+ if (resourceAsStream != null)
+ {
+ resourceAsStream.close();
+ }
+ }
+ }
+
+}
diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/dataset_types/no_code.xls b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/dataset_types/no_code.xls
new file mode 100644
index 0000000000000000000000000000000000000000..d54b992af7d5ef3497b591b71b0a937aeecee4c6
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\ No newline at end of file
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+def validate(entity, isNew):
+ if isNew:
+ return
\ No newline at end of file
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diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/vocabularies/vocab_no_term_code.xlsx b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/vocabularies/vocab_no_term_code.xlsx
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diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/vocabularies/vocab_no_term_desc.xlsx b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/vocabularies/vocab_no_term_desc.xlsx
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diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/vocabularies/vocab_no_term_label.xlsx b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/vocabularies/vocab_no_term_label.xlsx
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diff --git a/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/vocabularies/vocab_no_terms.xlsx b/openbis_standard_technologies/sourceTest/java/ch/ethz/sis/openbis/systemtest/plugin/excelimport/test_files/vocabularies/vocab_no_terms.xlsx
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diff --git a/openbis_standard_technologies/sourceTest/java/tests.xml b/openbis_standard_technologies/sourceTest/java/tests.xml
index 63c73169b0852cdd4fb77366cccf07c26ba3b6e0..a198fbcfdb1da92cb07df9f7fcc71c7bf4b604f4 100644
--- a/openbis_standard_technologies/sourceTest/java/tests.xml
+++ b/openbis_standard_technologies/sourceTest/java/tests.xml
@@ -1,11 +1,12 @@
-<suite name="All" verbose="2" >
- <test name="All" annotations="JDK">
- <groups>
- <run>
- <exclude name="broken" />
- </run>
- </groups>
- <packages>
- </packages>
- </test>
+<suite name="All" verbose="2">
+ <test name="All" annotations="JDK">
+ <groups>
+ <run>
+ <exclude name="broken" />
+ </run>
+ </groups>
+ <packages>
+ <package name="ch.ethz.sis.openbis.systemtest.plugin.*" />
+ </packages>
+ </test>
</suite>