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https://issues.apache.org/jira/browse/AIRAVATA-2728?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16458931#comment-16458931
]
ASF GitHub Bot commented on AIRAVATA-2728:
------------------------------------------
machristie commented on a change in pull request #191: [AIRAVATA-2728]
Refactoring Experiment Catalog Implementation
URL: https://github.com/apache/airavata/pull/191#discussion_r185076121
##########
File path:
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentRepository.java
##########
@@ -20,82 +20,413 @@
*/
package org.apache.airavata.registry.core.repositories.expcatalog;
+import org.apache.airavata.model.application.io.InputDataObjectType;
+import org.apache.airavata.model.application.io.OutputDataObjectType;
+import org.apache.airavata.model.commons.ErrorModel;
import org.apache.airavata.model.experiment.ExperimentModel;
-import org.apache.airavata.registry.core.entities.expcatalog.ExperimentEntity;
-import org.apache.airavata.registry.core.repositories.AbstractRepository;
-import org.apache.airavata.registry.core.utils.JPAUtils;
+import org.apache.airavata.model.experiment.UserConfigurationDataModel;
+import org.apache.airavata.model.status.*;
+import org.apache.airavata.registry.core.entities.expcatalog.*;
+import org.apache.airavata.registry.core.utils.DBConstants;
+import org.apache.airavata.registry.core.utils.ExpCatalogUtils;
import org.apache.airavata.registry.core.utils.ObjectMapperSingleton;
+import org.apache.airavata.registry.core.utils.QueryConstants;
+import org.apache.airavata.registry.cpi.*;
import org.dozer.Mapper;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import java.util.List;
+import java.sql.Timestamp;
+import java.util.*;
-public class ExperimentRepository extends AbstractRepository<ExperimentModel,
ExperimentEntity, String> {
+public class ExperimentRepository extends
ExpCatAbstractRepository<ExperimentModel, ExperimentEntity, String> {
private final static Logger logger =
LoggerFactory.getLogger(ExperimentRepository.class);
- public ExperimentRepository(Class<ExperimentModel> thriftGenericClass,
Class<ExperimentEntity> dbEntityGenericClass) {
- super(thriftGenericClass, dbEntityGenericClass);
+ public ExperimentRepository() {
+ super(ExperimentModel.class, ExperimentEntity.class);
}
- @Override
- public ExperimentModel create(ExperimentModel experiment){
- return update(experiment);
+ protected String saveExperimentModelData(ExperimentModel experimentModel)
throws RegistryException {
+ ExperimentEntity experimentEntity = saveExperiment(experimentModel);
+ return experimentEntity.getExperimentId();
}
- @Override
- public ExperimentModel update(ExperimentModel experiment){
- String experimentId = experiment.getExperimentId();
+ protected ExperimentEntity saveExperiment(ExperimentModel experimentModel)
throws RegistryException {
+ if (experimentModel.getExperimentId() == null ||
experimentModel.getExperimentId().equals("DO_NOT_SET_AT_CLIENTS")) {
+ logger.debug("Setting the Experiment's ExperimentId");
+
experimentModel.setExperimentId(ExpCatalogUtils.getID(experimentModel.getExperimentName()));
+ }
+
+ String experimentId = experimentModel.getExperimentId();
Mapper mapper = ObjectMapperSingleton.getInstance();
- ExperimentEntity entity = mapper.map(experiment,
ExperimentEntity.class);
-
- if(entity.getUserConfigurationData() != null) {
- entity.getUserConfigurationData().setExperimentId(experimentId);
- if
(entity.getUserConfigurationData().getComputeResourceSchedulingEntity() != null)
-
entity.getUserConfigurationData().getComputeResourceSchedulingEntity().setExperimentId(experimentId);
- }
- if(entity.getExperimentInputs() != null)
-
entity.getExperimentInputs().forEach(expIn->expIn.setExperimentId(experimentId));
- if(entity.getExperimentOutputs() != null)
-
entity.getExperimentOutputs().forEach(expOut->expOut.setExperimentId(experimentId));
- if(entity.getExperimentErrors() != null)
-
entity.getExperimentErrors().forEach(expErr->expErr.setExperimentId(experimentId));
- if(entity.getExperimentStatuses() != null)
-
entity.getExperimentStatuses().forEach(expStatus->expStatus.setExperimentId(experimentId));
-
- if(entity.getProcesses() != null){
- entity.getProcesses().forEach(process->{
- process.setExperimentId(experimentId);
- String processId = process.getProcessId();
- if(process.getProcessResourceSchedule() != null)
-
process.getProcessResourceSchedule().setProcessId(processId);
- if(process.getProcessInputs() != null)
-
process.getProcessInputs().forEach(proInput->proInput.setProceseId(processId));
- if(process.getProcessOutputs() != null)
-
process.getProcessOutputs().forEach(proOutput->proOutput.setProcessId(processId));
- if(process.getProcessErrors() != null)
-
process.getProcessErrors().forEach(processErr->processErr.setProcessId(processId));
- if(process.getProcessStatuses() != null)
-
process.getProcessStatuses().forEach(processStat->processStat.setProcessId(processId));
-
- if(process.getTasks() != null){
- process.getTasks().forEach(task->{
- String taskId = task.getTaskId();
- task.setParentProcessId(processId);
-
-
- });
- }
- });
- }
-
- ExperimentEntity persistedCopy = JPAUtils.execute(entityManager ->
entityManager.merge(entity));
- return mapper.map(persistedCopy, ExperimentModel.class);
- }
-
- @Override
- public List<ExperimentModel> select(String criteria, int offset, int
limit){
- throw new UnsupportedOperationException("Due to performance overheads
this method is not supported. Instead use" +
- " ExperimentSummaryRepository");
+ ExperimentEntity experimentEntity = mapper.map(experimentModel,
ExperimentEntity.class);
+
+ if (experimentEntity.getUserConfigurationData() != null) {
+ logger.debug("Populating the Primary Key of UserConfigurationData
object for the Experiment");
+
experimentEntity.getUserConfigurationData().setExperimentId(experimentId);
+ }
+
+ if (experimentEntity.getExperimentInputs() != null) {
+ logger.debug("Populating the Primary Key of ExperimentInput
objects for the Experiment");
+
experimentEntity.getExperimentInputs().forEach(experimentInputEntity ->
experimentInputEntity.setExperimentId(experimentId));
+ }
+
+ if (experimentEntity.getExperimentOutputs() != null) {
+ logger.debug("Populating the Primary Key of ExperimentOutput
objects for the Experiment");
+
experimentEntity.getExperimentOutputs().forEach(experimentOutputEntity ->
experimentOutputEntity.setExperimentId(experimentId));
+ }
+
+ if (experimentEntity.getExperimentStatus() != null) {
+ logger.debug("Populating the Primary Key of ExperimentStatus
objects for the Experiment");
+
experimentEntity.getExperimentStatus().forEach(experimentStatusEntity ->
experimentStatusEntity.setExperimentId(experimentId));
+ }
+
+ if (experimentEntity.getErrors() != null) {
+ logger.debug("Populating the Primary Key of ExperimentError
objects for the Experiment");
+ experimentEntity.getErrors().forEach(experimentErrorEntity ->
experimentErrorEntity.setExperimentId(experimentId));
+ }
+
+ if (experimentEntity.getProcesses() != null) {
+ logger.debug("Populating the Process objects' Experiment ID for
the Experiment");
+ experimentEntity.getProcesses().forEach(processEntity ->
processEntity.setExperimentId(experimentId));
+ }
+
+ if (!isExperimentExist(experimentId)) {
+ logger.debug("Checking if the Experiment already exists");
+ experimentEntity.setCreationTime(new
Timestamp((System.currentTimeMillis())));
+ }
+
+ return execute(entityManager -> entityManager.merge(experimentEntity));
+ }
+
+ public String addExperiment(ExperimentModel experimentModel) throws
RegistryException {
+ return saveExperimentModelData(experimentModel);
+ }
+
+ public void updateExperiment(ExperimentModel updatedExperimentModel,
String experimentId) throws RegistryException {
+ saveExperimentModelData(updatedExperimentModel);
+ }
+
+ public ExperimentModel getExperiment(String experimentId) throws
RegistryException {
+ return get(experimentId);
+ }
+
+ public String addUserConfigurationData(UserConfigurationDataModel
userConfigurationDataModel, String experimentId) throws RegistryException {
+ ExperimentModel experimentModel = getExperiment(experimentId);
+ experimentModel.setUserConfigurationData(userConfigurationDataModel);
+ updateExperiment(experimentModel, experimentId);
+ return experimentId;
+ }
+
+ public String updateUserConfigurationData(UserConfigurationDataModel
updatedUserConfigurationDataModel, String experimentId) throws
RegistryException {
+ return addUserConfigurationData(updatedUserConfigurationDataModel,
experimentId);
+ }
+
+ public UserConfigurationDataModel getUserConfigurationData(String
experimentId) throws RegistryException {
+ ExperimentModel experimentModel = getExperiment(experimentId);
+ return experimentModel.getUserConfigurationData();
+ }
+
+ public String addExperimentInputs(List<InputDataObjectType>
experimentInputs, String experimentId) throws RegistryException {
+ ExperimentModel experimentModel = getExperiment(experimentId);
+ List<InputDataObjectType> inputDataObjectTypeList =
experimentModel.getExperimentInputs();
+
+ for (InputDataObjectType input : experimentInputs) {
+
+ if (inputDataObjectTypeList != null &&
!inputDataObjectTypeList.contains(input)) {
+ logger.debug("Adding the ExperimentInput to the list");
+ inputDataObjectTypeList.add(input);
+ experimentModel.setExperimentInputs(inputDataObjectTypeList);
+ updateExperiment(experimentModel, experimentId);
+ }
+
+ }
+
+ return experimentId;
+ }
+
+ public void updateExperimentInputs(List<InputDataObjectType>
updatedExperimentInputs, String experimentId) throws RegistryException {
+ addExperimentInputs(updatedExperimentInputs, experimentId);
+ }
+
+ public List<InputDataObjectType> getExperimentInputs(String experimentId)
throws RegistryException {
+ ExperimentModel experimentModel = getExperiment(experimentId);
+ return experimentModel.getExperimentInputs();
+ }
+
+ public String addExperimentOutputs(List<OutputDataObjectType>
experimentOutputs, String experimentId) throws RegistryException {
+ ExperimentModel experimentModel = getExperiment(experimentId);
+ List<OutputDataObjectType> outputDataObjectTypeList =
experimentModel.getExperimentOutputs();
+
+ for (OutputDataObjectType output : experimentOutputs) {
+
+ if (outputDataObjectTypeList != null &&
!outputDataObjectTypeList.contains(output)) {
+ logger.debug("Adding the ExperimentOutput to the list");
+ outputDataObjectTypeList.add(output);
+ experimentModel.setExperimentOutputs(outputDataObjectTypeList);
+ updateExperiment(experimentModel, experimentId);
+ }
+
+ }
+
+ return experimentId;
+ }
+
+ public void updateExperimentOutputs(List<OutputDataObjectType>
updatedExperimentOutputs, String experimentId) throws RegistryException {
+ addExperimentOutputs(updatedExperimentOutputs, experimentId);
+ }
+
+ public List<OutputDataObjectType> getExperimentOutputs(String
experimentId) throws RegistryException {
+ ExperimentModel experimentModel = getExperiment(experimentId);
+ return experimentModel.getExperimentOutputs();
+ }
+
+ public String addExperimentStatus(ExperimentStatus experimentStatus,
String experimentId) throws RegistryException {
+ ExperimentModel experimentModel = getExperiment(experimentId);
+ List<ExperimentStatus> experimentStatusList =
experimentModel.getExperimentStatus();
+
+ if (experimentStatusList.size() == 0 ||
!experimentStatusList.contains(experimentStatus)) {
+
+ if (experimentStatus.getStatusId() == null) {
+ logger.debug("Set ExperimentStatus's StatusId");
+ experimentStatus.setStatusId(ExpCatalogUtils.getID("STATUS"));
+ }
+
+ logger.debug("Adding the ExperimentStatus to the list");
+ experimentStatusList.add(experimentStatus);
+ }
+
+ experimentModel.setExperimentStatus(experimentStatusList);
+ updateExperiment(experimentModel, experimentId);
+ return experimentStatus.getStatusId();
+ }
+
+ public String updateExperimentStatus(ExperimentStatus
updatedExperimentStatus, String experimentId) throws RegistryException {
+ ExperimentModel experimentModel = getExperiment(experimentId);
+ List<ExperimentStatus> experimentStatusList =
experimentModel.getExperimentStatus();
+
+ for (ExperimentStatus retrievedExperimentStatus :
experimentStatusList) {
+
+ if
(retrievedExperimentStatus.getStatusId().equals(updatedExperimentStatus.getStatusId()))
{
+ logger.debug("Updating the ExperimentStatus");
+ experimentStatusList.remove(retrievedExperimentStatus);
Review comment:
You want to use an Iterator to remove from a collection you are also
currently looping over, see https://stackoverflow.com/a/1196612/1419499. Or you
might just have a second list that you add entries to.
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> Refactoring Experiment Catalog Implementation
> ---------------------------------------------
>
> Key: AIRAVATA-2728
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2728
> Project: Airavata
> Issue Type: Improvement
> Components: Registry API
> Reporter: Sneha Tilak
> Assignee: Sneha Tilak
> Priority: Major
>
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