package org.molgenis.integrationtest.platform.datatypeediting;
import org.molgenis.data.DataService;
import org.molgenis.data.Entity;
import org.molgenis.data.EntityManager;
import org.molgenis.data.elasticsearch.index.job.IndexService;
import org.molgenis.data.meta.AttributeType;
import org.molgenis.data.meta.MetaDataService;
import org.molgenis.data.meta.model.Attribute;
import org.molgenis.data.meta.model.AttributeFactory;
import org.molgenis.data.meta.model.EntityType;
import org.molgenis.data.meta.model.EntityTypeFactory;
import org.molgenis.data.postgresql.PostgreSqlRepositoryCollection;
import org.molgenis.data.validation.MolgenisValidationException;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.authentication.TestingAuthenticationToken;
import org.springframework.security.core.GrantedAuthority;
import org.springframework.security.core.authority.SimpleGrantedAuthority;
import org.springframework.test.context.testng.AbstractTestNGSpringContextTests;
import java.util.List;
import java.util.stream.Stream;
import static com.google.common.collect.Lists.newArrayList;
import static java.util.Collections.emptyList;
import static org.molgenis.data.EntityManager.CreationMode.NO_POPULATE;
import static org.molgenis.data.meta.AttributeType.*;
import static org.molgenis.data.meta.model.AttributeMetadata.ATTRIBUTE_META_DATA;
import static org.molgenis.data.meta.model.EntityTypeMetadata.ENTITY_TYPE_META_DATA;
import static org.molgenis.data.meta.model.EntityTypeMetadata.PACKAGE;
import static org.molgenis.security.core.runas.RunAsSystemProxy.runAsSystem;
import static org.slf4j.LoggerFactory.getLogger;
import static org.springframework.security.core.context.SecurityContextHolder.getContext;
public abstract class AbstractAttributeTypeUpdateTest extends AbstractTestNGSpringContextTests
{
private final Logger LOG = getLogger(AbstractAttributeTypeUpdateTest.class);
private static final List<AttributeType> referencingTypes = newArrayList(MREF, XREF, CATEGORICAL, CATEGORICAL_MREF,
FILE);
private static final List<String> enumOptions = newArrayList("1", "2b", "abc");
private static final String MAIN_ENTITY = "MAIN_ENTITY";
private static final String REFERENCE_ENTITY = "REFERENCE_ENTITY";
private static final String MAIN_ENTITY_ID_VALUE = "1";
@Autowired
IndexService indexService;
@Autowired
AttributeFactory attributeFactory;
@Autowired
EntityTypeFactory entityTypeFactory;
@Autowired
DataService dataService;
@Autowired
EntityManager entityManager;
@Autowired
MetaDataService metaDataService;
private EntityType entityType;
private String mainId = "id";
private String mainAttribute = "mainAttribute";
private EntityType referenceEntityType;
private String refId = "id";
private String refLabel = "label";
List<GrantedAuthority> setAuthorities()
{
List<GrantedAuthority> authorities = newArrayList();
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_WRITE_" + ENTITY_TYPE_META_DATA));
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_READ_" + ENTITY_TYPE_META_DATA));
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_WRITE_" + ATTRIBUTE_META_DATA));
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_READ_" + ATTRIBUTE_META_DATA));
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_WRITE_" + PACKAGE));
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_READ_" + PACKAGE));
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_READ_" + "sys_sec_UserAuthority"));
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_WRITEMETA_" + MAIN_ENTITY));
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_WRITE_" + MAIN_ENTITY));
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_READ_" + MAIN_ENTITY));
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_WRITEMETA_" + REFERENCE_ENTITY));
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_WRITE_" + REFERENCE_ENTITY));
authorities.add(new SimpleGrantedAuthority("ROLE_ENTITY_READ_" + REFERENCE_ENTITY));
return authorities;
}
/**
* setup method to configure the entities for AttributeType editing
*
* @param type The main AttributeType, which will be converted to all other types
* @param refIdType The type of the reference ID attribute, used for testing valid and invalid XREF conversions
*/
void setup(AttributeType type, AttributeType refIdType)
{
List<GrantedAuthority> authorities = setAuthorities();
getContext().setAuthentication(new TestingAuthenticationToken("user", "user", authorities));
entityType = entityTypeFactory.create("1");
entityType.setName(MAIN_ENTITY);
entityType.setBackend(PostgreSqlRepositoryCollection.POSTGRESQL);
referenceEntityType = entityTypeFactory.create("2");
referenceEntityType.setName(REFERENCE_ENTITY);
referenceEntityType.setBackend(PostgreSqlRepositoryCollection.POSTGRESQL);
Attribute mainIdAttribute = attributeFactory.create().setName(mainId).setIdAttribute(true);
Attribute mainAttributeAttribute = attributeFactory.create().setDataType(type).setName(mainAttribute)
.setNillable(false);
if (referencingTypes.contains(type))
{
mainAttributeAttribute.setRefEntity(referenceEntityType);
}
else if (type.equals(ENUM))
{
mainAttributeAttribute.setEnumOptions(enumOptions);
}
Attribute refIdAttribute = attributeFactory.create().setName(refId).setDataType(refIdType).setIdAttribute(true);
Attribute refLabelAttribute = attributeFactory.create().setName(refLabel).setLabelAttribute(true)
.setNillable(false);
entityType.addAttributes(newArrayList(mainIdAttribute, mainAttributeAttribute));
referenceEntityType.addAttributes(newArrayList(refIdAttribute, refLabelAttribute));
metaDataService.upsertEntityTypes(newArrayList(entityType, referenceEntityType));
Entity refEntity_1 = entityManager.create(referenceEntityType, NO_POPULATE);
Entity refEntity_2 = entityManager.create(referenceEntityType, NO_POPULATE);
Entity refEntity_3 = entityManager.create(referenceEntityType, NO_POPULATE);
if (refIdType == INT)
{
refEntity_1.set(refId, 1);
refEntity_2.set(refId, 23);
refEntity_3.set(refId, 42);
}
else if (refIdType == LONG)
{
refEntity_1.set(refId, 1L);
refEntity_2.set(refId, 3432453425L);
refEntity_3.set(refId, 42L);
}
else
{
refEntity_1.set(refId, "1");
refEntity_2.set(refId, "molgenis@test.org");
refEntity_3.set(refId, "https://www.google.com");
}
refEntity_1.set(refLabel, "label1");
refEntity_2.set(refLabel, "email label");
refEntity_3.set(refLabel, "hyperlink label");
dataService.add(REFERENCE_ENTITY, Stream.of(refEntity_1, refEntity_2, refEntity_3));
}
void testTypeConversion(Object valueToConvert, AttributeType typeToConvertTo) throws MolgenisValidationException
{
// Add a data row to the EntityType
Entity entity = entityManager.create(entityType, NO_POPULATE);
entity.set(mainId, MAIN_ENTITY_ID_VALUE);
entity.set(mainAttribute, valueToConvert);
// Add one entity row
dataService.add(MAIN_ENTITY, entity);
// Update EntityType
convert(typeToConvertTo);
metaDataService.updateEntityType(entityType);
}
private void convert(AttributeType typeToConvertTo) throws MolgenisValidationException
{
Attribute attribute = entityType.getAttribute(mainAttribute);
if (referencingTypes.contains(typeToConvertTo)) attribute.setRefEntity(referenceEntityType);
else attribute.setRefEntity(null);
if (typeToConvertTo.equals(AttributeType.ENUM)) attribute.setEnumOptions(enumOptions);
else attribute.setEnumOptions(emptyList());
attribute.setDataType(typeToConvertTo);
metaDataService.updateEntityType(entityType);
}
Object getActualValue()
{
Object actualValue = dataService.findOneById(MAIN_ENTITY, MAIN_ENTITY_ID_VALUE).get(mainAttribute);
if (actualValue instanceof Entity) return ((Entity) actualValue).getLabelValue();
return actualValue;
}
AttributeType getActualDataType()
{
return metaDataService.getEntityType(MAIN_ENTITY).getAttribute(mainAttribute).getDataType();
}
void afterMethod(AttributeType type)
{
// Delete rows of data
dataService.deleteAll(MAIN_ENTITY);
// Remove attribute, some conversions back to the main attribute are not allowed
Attribute attribute = entityType.getAttribute(mainAttribute);
entityType.removeAttribute(attribute);
metaDataService.updateEntityType(entityType);
// Add the main attribute again, with the original type
Attribute mainAttributeAttribute = attributeFactory.create().setDataType(type).setName(mainAttribute);
if (referencingTypes.contains(type)) mainAttributeAttribute.setRefEntity(referenceEntityType);
else if (type.equals(ENUM)) mainAttributeAttribute.setEnumOptions(enumOptions);
entityType.addAttribute(mainAttributeAttribute);
metaDataService.updateEntityType(entityType);
}
void afterClass()
{
runAsSystem(() ->
{
dataService.deleteAll(MAIN_ENTITY);
dataService.deleteAll(REFERENCE_ENTITY);
metaDataService.deleteEntityType(MAIN_ENTITY);
metaDataService.deleteEntityType(REFERENCE_ENTITY);
});
}
}