diff --git a/pom.xml b/pom.xml
index 0c3f8a8c2b04bbf95b26ce18c1e75b9549780ac9..97d528b788f61fa50b570ece91b38ade11cfc6d9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -251,20 +251,31 @@
<artifactId>java-jwt</artifactId>
<version>3.11.0</version>
</dependency>
- </dependencies>
- <build>
- <finalName>portal-backend</finalName>
- <resources>
- <resource>
- <directory>src/main/resources</directory>
- <includes>
- <include>**/*.xml</include>
- <include>**/*.json</include>
- <include>**/*.csv</include>
- <include>**/*.sql</include>
- <include>**/*.conf</include>
- <include>**/*.yml</include> <!-- Only for development -->
+ <dependency>
+ <groupId>com.google.code.svenson</groupId>
+ <artifactId>svenson</artifactId>
+ <version>1.5.8</version>
+ </dependency>
+ <!--<dependency>
+ <groupId>eu.hbp.mip</groupId>
+ <artifactId>portal-backend</artifactId>
+ <version>4.0.0</version>
+ </dependency>-->
+ </dependencies>
+
+ <build>
+ <finalName>portal-backend</finalName>
+ <resources>
+ <resource>
+ <directory>src/main/resources</directory>
+ <includes>
+ <include>**/*.xml</include>
+ <include>**/*.json</include>
+ <include>**/*.csv</include>
+ <include>**/*.sql</include>
+ <include>**/*.conf</include>
+ <!-- <include>**/*.yml</include> Only for development -->
</includes>
<filtering>true</filtering>
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index 322f33f4f5a8a08dff189b9e76a332e2983317bb..803c475723eb1a86bdc4f75e5112d67994de981d 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -1,13 +1,11 @@
package eu.hbp.mip.controllers;
import eu.hbp.mip.model.DTOs.ExperimentDTO;
-import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.services.ExperimentService;
import eu.hbp.mip.utils.JsonConverters;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.security.core.Authentication;
@@ -27,23 +25,34 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/experiments")
public class ExperimentApi {
- @Autowired
- private UserInfo userInfo;
+ private final ExperimentService experimentService;
- @Autowired
- private ExperimentService experimentService;
+ public ExperimentApi(ExperimentService experimentService) {
+ this.experimentService = experimentService;
+ }
- @ApiOperation(value = "Get experiments", response = ExperimentDTO.class, responseContainer = "List")
+ @ApiOperation(value = "Get experiments", response = Map.class, responseContainer = "List")
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<String> getExperiments(
@RequestParam(name = "name", required = false) String name,
@RequestParam(name = "algorithm", required = false) String algorithm,
@RequestParam(name = "shared", required = false) Boolean shared,
@RequestParam(name = "viewed", required = false) Boolean viewed,
+ @RequestParam(name = "orderBy", required = false, defaultValue = "created") String orderBy,
+ @RequestParam(name = "descending", required = false, defaultValue = "true") Boolean descending,
@RequestParam(defaultValue = "0") int page,
@RequestParam(defaultValue = "3") int size
) {
- Map experiments = experimentService.getExperiments(name, algorithm, shared, viewed, page, size, "(GET) /experiments");
+ Map experiments = experimentService.getExperiments(
+ name,
+ algorithm,
+ shared,
+ viewed,
+ page,
+ size,
+ orderBy,
+ descending,
+ "(GET) /experiments");
return new ResponseEntity(experiments, HttpStatus.OK);
}
@@ -66,7 +75,7 @@ public class ExperimentApi {
@ApiOperation(value = "Create a transient experiment", response = ExperimentDTO.class)
- @RequestMapping(value = "/{transient}",method = RequestMethod.POST)
+ @RequestMapping(value = "/transient",method = RequestMethod.POST)
public ResponseEntity<String> createTransientExperiment(Authentication authentication, @RequestBody ExperimentDTO experimentDTO) {
experimentDTO = experimentService.createTransientExperiment(authentication, experimentDTO, "(POST) /experiments/transient");
diff --git a/src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java b/src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java
index 2ee8e0ba401191508fa72258d35f997f8fba9509..f10f887426f189917fe2dd9f632a21e95df6192d 100644
--- a/src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java
+++ b/src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java
@@ -7,10 +7,10 @@ import eu.hbp.mip.model.DTOs.AlgorithmDTO;
import eu.hbp.mip.model.DTOs.ExperimentDTO;
import eu.hbp.mip.utils.JsonConverters;
import io.swagger.annotations.ApiModel;
+import org.svenson.JSONParser;
import javax.persistence.*;
-import java.util.Date;
-import java.util.UUID;
+import java.util.*;
/**
* Created by habfast on 21/04/16.
@@ -65,6 +65,10 @@ public class ExperimentDAO {
@Expose
@Column(columnDefinition = "TIMESTAMP WITHOUT TIME ZONE")
private Date created = new Date();
+
+ @Expose
+ @Column(columnDefinition = "TIMESTAMP WITHOUT TIME ZONE")
+ private Date updated;
@Expose
@Column(columnDefinition = "BOOLEAN")
@@ -81,7 +85,7 @@ public class ExperimentDAO {
success
}
- public enum MimeTypes {
+ public enum Type {
ERROR("text/plain+error"),
WARNING("text/plain+warning"),
USER_WARNING("text/plain+user_error"),
@@ -93,15 +97,15 @@ public class ExperimentDAO {
HTML("text/html"),
TEXT("text/plain");
- private String types;
+ private String type;
//Constructor to initialize the instance variable
- MimeTypes(String types) {
- this.types = types;
+ Type(String type) {
+ this.type = type;
}
- public String getTypes() {
- return this.types;
+ public String getType() {
+ return this.type;
}
}
@@ -116,15 +120,25 @@ public class ExperimentDAO {
ExperimentDTO experimentDTO = new ExperimentDTO();
experimentDTO.setAlgorithmDetails(JsonConverters.convertJsonStringToObject(this.algorithmDetails, AlgorithmDTO.class));
experimentDTO.setCreated(this.created);
+ experimentDTO.setUpdated(this.updated);
+ experimentDTO.setFinished(this.finished);
experimentDTO.setCreatedBy(this.createdBy.getUsername());
experimentDTO.setName(this.name);
- experimentDTO.setResult(JsonConverters.convertJsonStringToObject(this.result, ExperimentDTO.ResultDTO.class));
+ experimentDTO.setResult(convertJsonStringToResult(this.result));
+ experimentDTO.setStatus(this.status);
experimentDTO.setShared(this.shared);
experimentDTO.setUuid(this.uuid);
experimentDTO.setViewed(this.viewed);
return experimentDTO;
}
+ public static Map convertJsonStringToResult(String jsonResult) {
+ if(jsonResult == null || jsonResult.isEmpty())
+ return null;
+ JSONParser parser = new JSONParser();
+ parser.addTypeHint("Result[]", ExperimentDTO.ResultDTO.class);
+ return parser.parse(Map.class, jsonResult);
+ }
public String getAlgorithmDetails() {
return algorithmDetails;
}
@@ -180,6 +194,14 @@ public class ExperimentDAO {
public void setCreated(Date created) {
this.created = created;
}
+
+ public Date getUpdated() {
+ return updated;
+ }
+
+ public void setUpdated(Date updated) {
+ this.updated = updated;
+ }
public UUID getUuid() {
return uuid;
diff --git a/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java b/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java
index 64ade455bc623298c173edad1ddd60919517bc1c..037ab5767cec70daa49320fa228c73cc5b1f7a8e 100644
--- a/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java
+++ b/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java
@@ -3,7 +3,7 @@ package eu.hbp.mip.model.DTOs;
import eu.hbp.mip.model.DAOs.ExperimentDAO;
import java.util.Date;
-import java.util.List;
+import java.util.Map;
import java.util.UUID;
public class ExperimentDTO {
@@ -12,9 +12,11 @@ public class ExperimentDTO {
private String name;
private String createdBy;
private Date created;
+ private Date updated;
+ private Date finished;
private Boolean shared;
private Boolean viewed;
- private ExperimentDTO.ResultDTO result;
+ private Map result;
private ExperimentDAO.Status status;
private String algorithm;
@@ -71,6 +73,22 @@ public class ExperimentDTO {
public void setCreated(Date created) {
this.created = created;
}
+
+ public Date getUpdated() {
+ return updated;
+ }
+
+ public void setUpdated(Date updated) {
+ this.updated = updated;
+ }
+
+ public Date getFinished() {
+ return finished;
+ }
+
+ public void setFinished(Date finished) {
+ this.finished = finished;
+ }
public Boolean getShared() {
return shared;
@@ -88,11 +106,11 @@ public class ExperimentDTO {
this.viewed = viewed;
}
- public ExperimentDTO.ResultDTO getResult() {
+ public Map getResult() {
return result;
}
- public void setResult(ExperimentDTO.ResultDTO result) {
+ public void setResult(Map result) {
this.result = result;
}
@@ -104,37 +122,25 @@ public class ExperimentDTO {
this.status = status;
}
- public static class OutputDTO {
+ public static class ResultDTO {
- private String data;
- private ExperimentDAO.MimeTypes mimeTypes;
+ private Object data;
+ private ExperimentDAO.Type type;
- public String getData() {
+ public Object getData() {
return this.data;
}
- public void setData(String data) {
+ public void setData(Object data) {
this.data = data;
}
- public ExperimentDAO.MimeTypes getMimeTypes() {
- return mimeTypes;
- }
-
- public void setMimeTypes(ExperimentDAO.MimeTypes mimeTypes) {
- this.mimeTypes = mimeTypes;
- }
- }
-
- public static class ResultDTO {
- private List<OutputDTO> result;
-
- public List<OutputDTO> getResult() {
- return this.result;
+ public ExperimentDAO.Type getType() {
+ return type;
}
- public void setResult(List<OutputDTO> result) {
- this.result = result;
+ public void setType(ExperimentDAO.Type type) {
+ this.type = type;
}
}
}
diff --git a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
index 5f2c8dc7643799b1a2f5a7a15773140376ff5756..7b30600e5d5575aa9a2b2f12909820382aec2142 100644
--- a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
@@ -13,5 +13,5 @@ import java.util.UUID;
public interface ExperimentRepository extends CrudRepository<ExperimentDAO, UUID>, JpaSpecificationExecutor<ExperimentDAO>
{
- Optional<ExperimentDAO> findByUuid(UUID experimentUuid);
+ ExperimentDAO findByUuid(UUID experimentUuid);
}
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index 2590e1edd05843edb56ef45b1d16e26eaa0f4415..12c0d126942063868c09334bc8fe456489d95238 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -27,7 +27,7 @@ import eu.hbp.mip.utils.JsonConverters;
import eu.hbp.mip.utils.Logging;
import org.codehaus.jettison.json.JSONException;
import org.codehaus.jettison.json.JSONObject;
-import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
@@ -46,8 +46,6 @@ import static java.lang.Thread.sleep;
@Service
public class ExperimentService {
- @Autowired
- private UserInfo userInfo;
@Value("#{'${services.exareme.queryExaremeUrl}'}")
private String queryExaremeUrl;
@@ -62,11 +60,16 @@ public class ExperimentService {
@Value("#{'${hbp.authentication.enabled:1}'}")
private boolean authenticationIsEnabled;
- @Autowired
- private ExperimentRepository experimentRepository;
-
private static final Gson gson = new Gson();
+ private final UserInfo userInfo;
+ private final ExperimentRepository experimentRepository;
+
+ public ExperimentService(@Qualifier("userInfo") UserInfo userInfo, ExperimentRepository experimentRepository) {
+ this.userInfo = userInfo;
+ this.experimentRepository = experimentRepository;
+ }
+
/**
* The getExperiments will retrieve the experiments from database according to the filters.
*
@@ -76,23 +79,26 @@ public class ExperimentService {
* @param viewed is optional, in case it is required to filter the experiments by viewed
* @param page is the page that is required to be retrieve
* @param size is the size of each page
+ * @param orderBy is the column that is required to ordered by
+ * @param descending is a boolean to determine if the experiments will be order by descending or ascending
* @param endpoint is the endpoint that called the function
* @return a list of mapped experiments
*/
- public Map getExperiments(String name,String algorithm, Boolean shared,Boolean viewed, int page, int size, String endpoint) {
+ public Map getExperiments(String name,String algorithm, Boolean shared,Boolean viewed, int page, int size, String orderBy, Boolean descending, String endpoint) {
UserDAO user = userInfo.getUser();
Logging.LogUserAction(user.getUsername(), endpoint, "Listing my experiments.");
if(size > 10 )
throw new BadRequestException("Invalid size input, max size is 10.");
-
- Specification<ExperimentDAO> spec = Specification.where(new ExperimentSpecifications.ExperimentWithName(name))
+ Specification<ExperimentDAO> spec = Specification
+ .where(new ExperimentSpecifications.ExperimentWithName(name))
.and(new ExperimentSpecifications.ExperimentWithAlgorithm(algorithm))
.and(new ExperimentSpecifications.ExperimentWithShared(shared))
- .and(new ExperimentSpecifications.ExperimentWithViewed(viewed));
+ .and(new ExperimentSpecifications.ExperimentWithViewed(viewed))
+ .and(new ExperimentSpecifications.ExperimentOrderBy(orderBy, descending));
Pageable paging = PageRequest.of(page, size);
- Page<ExperimentDAO> pageExperiments = experimentRepository.findAll(spec, paging);
+ Page<ExperimentDAO> pageExperiments = experimentRepository.findAll(spec, paging);
List<ExperimentDAO> experimentDAOs = pageExperiments.getContent();
if (experimentDAOs.isEmpty())
@@ -124,7 +130,7 @@ public class ExperimentService {
Logging.LogUserAction(user.getUsername(), endpoint, "Loading Experiment with uuid : " + uuid);
- experimentDAO = loadExperiment(uuid).orElseThrow(() -> new ExperimentNotFoundException("Not found Experimnet with id = " + uuid));
+ experimentDAO = loadExperiment(uuid, endpoint);
if (!experimentDAO.isShared() && !experimentDAO.getCreatedBy().getUsername().equals(user.getUsername())) {
Logging.LogUserAction(user.getUsername(), endpoint, "Accessing Experiment is unauthorized.");
@@ -148,45 +154,16 @@ public class ExperimentService {
UserDAO user = userInfo.getUser();
//Checking if check (POST) /experiments has proper input.
- if (checkPostExperimentProperInput(experimentDTO)){
- Logging.LogUserAction(user.getUsername(), endpoint,
- "Invalid input.");
- throw new BadRequestException("Please provide proper input.");
- }
+ checkPostExperimentProperInput(experimentDTO, endpoint);
+
// Get the type and name of algorithm
String algorithmType = experimentDTO.getAlgorithmDetails().getType();
- String algorithmName = experimentDTO.getAlgorithmDetails().getName();
- StringBuilder parametersLogMessage = new StringBuilder(", Parameters:\n");
- experimentDTO.getAlgorithmDetails().getParameters().forEach(
- params -> parametersLogMessage
- .append(" ")
- .append(params.getLabel())
- .append(" -> ")
- .append(params.getValue())
- .append("\n") );
- Logging.LogUserAction(user.getUsername(), endpoint, "Executing " + algorithmName + parametersLogMessage);
+ algorithmParametersLogging(experimentDTO, endpoint);
if (authenticationIsEnabled) {
- // Getting the dataset from the experiment parameters
- String experimentDatasets = null;
- for (AlgorithmDTO.AlgorithmParamDTO parameter : experimentDTO.getAlgorithmDetails().getParameters()) {
- if (parameter.getLabel().equals("dataset")) {
- experimentDatasets = parameter.getValue();
- break;
- }
- }
-
- if (experimentDatasets == null || experimentDatasets.equals("")) {
- Logging.LogUserAction(user.getUsername(), endpoint,
- "A dataset should be specified to run an algorithm.");
- throw new BadRequestException("Please provide at least one dataset to run the algorithm.");
- }
-
- // --- Validating proper access rights on the datasets ---
- if (!ClaimUtils.userHasDatasetsAuthorization(user.getUsername(), authentication.getAuthorities(), experimentDatasets)) {
- throw new BadRequestException("You are not authorized to use these datasets.");
- }
+ String experimentDatasets = getDatasetFromExperimentParameters(experimentDTO, endpoint);
+ ClaimUtils.validateAccessRightsOnDatasets(user.getUsername(), authentication.getAuthorities(), experimentDatasets);
}
// Run with the appropriate engine
@@ -211,11 +188,7 @@ public class ExperimentService {
UserDAO user = userInfo.getUser();
//Checking if check (POST) /experiments has proper input.
- if (checkPostExperimentProperInput(experimentDTO)){
- Logging.LogUserAction(user.getUsername(), endpoint,
- "Invalid input.");
- throw new BadRequestException("Please provide proper input.");
- }
+ checkPostExperimentProperInput(experimentDTO, endpoint);
// Get the parameters
List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
@@ -224,42 +197,17 @@ public class ExperimentService {
// Get the type and name of algorithm
String algorithmName = experimentDTO.getAlgorithmDetails().getName();
- if (!loadProperAlgorithms().contains(algorithmName)){
+ if (!allowedTransientAlgorithms(algorithmName)){
Logging.LogUserAction(user.getUsername(), endpoint,
"Not proper algorithm.");
throw new BadRequestException("Please provide proper algorithm.");
}
- StringBuilder parametersLogMessage = new StringBuilder(", Parameters:\n");
- experimentDTO.getAlgorithmDetails().getParameters().forEach(
- params -> parametersLogMessage
- .append(" ")
- .append(params.getLabel())
- .append(" -> ")
- .append(params.getValue())
- .append("\n") );
- Logging.LogUserAction(user.getUsername(), endpoint, "Executing " + algorithmName + parametersLogMessage);
+ algorithmParametersLogging(experimentDTO, endpoint);
if (authenticationIsEnabled) {
- // Getting the dataset from the experiment parameters
- String experimentDatasets = null;
- for (AlgorithmDTO.AlgorithmParamDTO parameter : experimentDTO.getAlgorithmDetails().getParameters()) {
- if (parameter.getLabel().equals("dataset")) {
- experimentDatasets = parameter.getValue();
- break;
- }
- }
-
- if (experimentDatasets == null || experimentDatasets.equals("")) {
- Logging.LogUserAction(user.getUsername(), endpoint,
- "A dataset should be specified to run an algorithm.");
- throw new BadRequestException("Please provide at least one dataset to run the algorithm.");
- }
-
- // --- Validating proper access rights on the datasets ---
- if (!ClaimUtils.userHasDatasetsAuthorization(user.getUsername(), authentication.getAuthorities(), experimentDatasets)) {
- throw new BadRequestException("You are not authorized to use these datasets.");
- }
+ String experimentDatasets = getDatasetFromExperimentParameters(experimentDTO, endpoint);
+ ClaimUtils.validateAccessRightsOnDatasets(user.getUsername(), authentication.getAuthorities(), experimentDatasets);
}
String body = gson.toJson(algorithmParameters);
@@ -271,8 +219,11 @@ public class ExperimentService {
// Results are stored in the experiment object
ExaremeResult exaremeResult = runExaremeExperiment(url, body, experimentDTO);
- experimentDTO.setResult(exaremeResult.result);
- experimentDTO.setStatus((exaremeResult.code>= 400)? ExperimentDAO.Status.error: ExperimentDAO.Status.success);
+
+ Logging.LogUserAction(user.getUsername(), endpoint, "Experiment with uuid: " + experimentDTO.getUuid() + "gave response code: " +exaremeResult.getCode() + " and result: "+ exaremeResult.getResults());
+
+ experimentDTO.setResult((exaremeResult.getCode()>= 400)? null: exaremeResult.getResults());
+ experimentDTO.setStatus((exaremeResult.getCode()>= 400)? ExperimentDAO.Status.error: ExperimentDAO.Status.success);
return experimentDTO;
}
@@ -289,41 +240,26 @@ public class ExperimentService {
{
ExperimentDAO experimentDAO;
UserDAO user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), endpoint, "Updating experiment with uuid : " + experimentDTO.getUuid() + ".");
- //Checking if check (PUT) /experiments has proper input.
- if (checkPutExperimentProperInput(experimentDTO)){
- Logging.LogUserAction(user.getUsername(), endpoint,
- "Invalid input.");
- throw new BadRequestException("Please provide proper input.");
- }
-
- if((experimentDTO.getName() == null || experimentDTO.getName().length() == 0)
- && experimentDTO.getShared() == null
- && experimentDTO.getViewed() == null
- && experimentDTO.getAlgorithmDetails() == null)
- {
- throw new BadRequestException("Input is required.");
- }
+ Logging.LogUserAction(user.getUsername(), endpoint, "Updating experiment with uuid : " + uuid + ".");
- experimentDAO = loadExperiment(uuid).orElseThrow(() -> new ExperimentNotFoundException("Not found Experimnet with id = " + uuid));
+ experimentDAO = loadExperiment(uuid, endpoint);
+ //Verify (PATCH) /experiments non editable fields.
+ verifyPatchExperimentNonEditableFields(uuid, experimentDTO, experimentDAO, endpoint);
+
if (!experimentDAO.getCreatedBy().getUsername().equals(user.getUsername()))
throw new UnauthorizedException("You don't have access to the experiment.");
if(experimentDTO.getName() != null && experimentDTO.getName().length() != 0)
- {
experimentDAO.setName(experimentDTO.getName());
- }
if(experimentDTO.getShared() != null)
- {
experimentDAO.setShared(experimentDTO.getShared());
- }
if(experimentDTO.getViewed() != null)
- {
experimentDAO.setViewed(experimentDTO.getViewed());
- }
+
+ experimentDAO.setUpdated(new Date());
try {
experimentRepository.save(experimentDAO);
@@ -332,7 +268,8 @@ public class ExperimentService {
Logging.LogUserAction(user.getUsername(), endpoint, "Attempted to save changes to database but an error ocurred : " + e.getMessage() + ".");
throw new InternalServerError(e.getMessage());
}
- Logging.LogUserAction(user.getUsername(), endpoint, "Updated experiment with uuid : " + experimentDTO.getUuid() + ".");
+
+ Logging.LogUserAction(user.getUsername(), endpoint, "Updated experiment with uuid : " + uuid + ".");
experimentDTO = experimentDAO.convertToDTO();
return experimentDTO;
@@ -350,42 +287,125 @@ public class ExperimentService {
UserDAO user = userInfo.getUser();
Logging.LogUserAction(user.getUsername(), endpoint, "Deleting experiment with uuid : " + uuid + ".");
- experimentDAO = loadExperiment(uuid).orElseThrow(() -> new ExperimentNotFoundException("Not found Experimnet with id = " + uuid));
+ experimentDAO = loadExperiment(uuid, endpoint);
if (!experimentDAO.getCreatedBy().getUsername().equals(user.getUsername()))
throw new UnauthorizedException("You don't have access to the experiment.");
- experimentRepository.delete(experimentDAO);
+ try {
+ experimentRepository.delete(experimentDAO);
+ }
+ catch (Exception e){
+ Logging.LogUserAction(user.getUsername(), endpoint, "Attempted to delete an experiment to database but an error ocurred : " + e.getMessage() + ".");
+ throw new InternalServerError(e.getMessage());
+ }
Logging.LogUserAction(user.getUsername(), endpoint, "Deleted experiment with uuid : " + uuid + ".");
}
// /* ------------------------------- PRIVATE METHODS ----------------------------------------------------*/
- private boolean checkPostExperimentProperInput(ExperimentDTO experimentDTO)
+
+ private void checkPostExperimentProperInput(ExperimentDTO experimentDTO, String endpoint)
{
- return experimentDTO.getShared() != null
- || experimentDTO.getViewed() != null
- || experimentDTO.getCreated() != null
- || experimentDTO.getCreatedBy() != null
- || experimentDTO.getResult() != null
- || experimentDTO.getStatus() != null
- || experimentDTO.getUuid() != null;
+
+ boolean properInput =
+ experimentDTO.getShared() == null
+ && experimentDTO.getViewed() == null
+ && experimentDTO.getCreated() == null
+ && experimentDTO.getCreatedBy() == null
+ && experimentDTO.getResult() == null
+ && experimentDTO.getStatus() == null
+ && experimentDTO.getUuid() == null;
+
+ if (!properInput){
+ Logging.LogUserAction(userInfo.getUser().getUsername(), endpoint, "Invalid input.");
+ throw new BadRequestException("Please provide proper input.");
+ }
}
- private List<String> loadProperAlgorithms()
+ private boolean allowedTransientAlgorithms(String algorithmName)
{
List<String> properAlgorithms = new ArrayList<>();
- properAlgorithms.add("histograms");
- properAlgorithms.add("descriptive_stats");
- return properAlgorithms;
+ properAlgorithms.add("MULTIPLE_HISTOGRAMS");
+ properAlgorithms.add("DESCRIPTIVE_STATS");
+ return properAlgorithms.contains(algorithmName);
}
- private boolean checkPutExperimentProperInput(ExperimentDTO experimentDTO)
+ private void verifyPatchExperimentNonEditableFields(String uuid , ExperimentDTO experimentDTO, ExperimentDAO experimentDAO, String endpoint)
{
- return experimentDTO.getUuid() != null
- || experimentDTO.getCreated() != null
- || experimentDTO.getResult() != null
- || experimentDTO.getStatus() != null;
+ if(experimentDTO.getUuid() != null && experimentDTO.getUuid().toString().compareTo(uuid) != 0){
+ Logging.LogUserAction(userInfo.getUser().getUsername(), endpoint, "Uuid is not editable.");
+ throw new BadRequestException("Uuid is not editable.");
+ }
+
+ if(experimentDTO.getAlgorithm() != null && experimentDTO.getAlgorithm().compareTo(experimentDAO.getAlgorithm()) != 0){
+ Logging.LogUserAction(userInfo.getUser().getUsername(), endpoint, "Algorithm is not editable.");
+ throw new BadRequestException("Algorithm is not editable.");
+ }
+
+ if(experimentDTO.getCreated() != null && experimentDTO.getCreatedBy().compareTo(experimentDAO.getCreatedBy().getUsername()) != 0){
+ Logging.LogUserAction(userInfo.getUser().getUsername(), endpoint, "CreatedBy is not editable.");
+ throw new BadRequestException("CreatedBy is not editable.");
+ }
+
+ if(experimentDTO.getAlgorithmDetails() != null && JsonConverters.convertObjectToJsonString(experimentDTO.getAlgorithmDetails()).compareTo(experimentDAO.getAlgorithmDetails()) != 0){
+ Logging.LogUserAction(userInfo.getUser().getUsername(), endpoint, "AlgorithmDetails is not editable.");
+ throw new BadRequestException("AlgorithmDetails is not editable.");
+ }
+
+ if(experimentDTO.getCreated() != null && experimentDTO.getAlgorithm().compareTo(experimentDAO.getAlgorithm()) != 0){
+ Logging.LogUserAction(userInfo.getUser().getUsername(), endpoint, "Created is not editable.");
+ throw new BadRequestException("Created is not editable.");
+ }
+
+ if(experimentDTO.getResult() != null && JsonConverters.convertObjectToJsonString(experimentDTO.getResult()).compareTo(experimentDAO.getResult()) != 0){
+ Logging.LogUserAction(userInfo.getUser().getUsername(), endpoint, "Status is not editable.");
+ throw new BadRequestException("Status is not editable.");
+ }
+
+ if(experimentDTO.getStatus() != null && experimentDTO.getStatus().compareTo(experimentDAO.getStatus()) != 0){
+ Logging.LogUserAction(userInfo.getUser().getUsername(), endpoint, "Status is not editable.");
+ throw new BadRequestException("Status is not editable.");
+ }
+ }
+
+ private void algorithmParametersLogging(ExperimentDTO experimentDTO, String endpoint) {
+ UserDAO user = userInfo.getUser() ;
+ String algorithmName = experimentDTO.getAlgorithm();
+ StringBuilder parametersLogMessage = new StringBuilder(", Parameters:\n");
+ experimentDTO.getAlgorithmDetails().getParameters().forEach(
+ params -> parametersLogMessage
+ .append(" ")
+ .append(params.getLabel())
+ .append(" -> ")
+ .append(params.getValue())
+ .append("\n") );
+ Logging.LogUserAction(user.getUsername(), endpoint, "Executing " + algorithmName + parametersLogMessage);
+ }
+
+ /**
+ * The getDatasetFromExperimentParameters will retrieve the dataset from the experiment parameters
+ *
+ * @param experimentDTO is the experiment information
+ * @param endpoint is the endpoint that called the function
+ * @return the dataset from the experiment
+ */
+ private String getDatasetFromExperimentParameters(ExperimentDTO experimentDTO, String endpoint) {
+
+ String experimentDatasets = null;
+ for (AlgorithmDTO.AlgorithmParamDTO parameter : experimentDTO.getAlgorithmDetails().getParameters()) {
+ if (parameter.getLabel().equals("dataset")) {
+ experimentDatasets = parameter.getValue();
+ break;
+ }
+ }
+
+ if (experimentDatasets == null || experimentDatasets.equals("")) {
+ Logging.LogUserAction(userInfo.getUser().getUsername(), endpoint,
+ "A dataset should be specified to run an algorithm.");
+ throw new BadRequestException("Please provide at least one dataset to run the algorithm.");
+ }
+ return experimentDatasets;
}
/**
@@ -394,14 +414,26 @@ public class ExperimentService {
* @param uuid is the id of the experiment to be retrieved
* @return the experiment information that was retrieved from database
*/
- private Optional<ExperimentDAO> loadExperiment(String uuid){
-
-
+ private ExperimentDAO loadExperiment(String uuid, String endpoint){
UUID experimentUuid ;
+ ExperimentDAO experimentDAO;
+
+ try {
+ experimentUuid = UUID.fromString(uuid);
+ }
+ catch (Exception e)
+ {
+ Logging.LogUserAction(userInfo.getUser().getUsername(), endpoint, e.getMessage());
+ throw new BadRequestException(e.getMessage());
+ }
- experimentUuid = Optional.of(UUID.fromString(uuid)).orElseThrow(() -> new IllegalArgumentException("Invalid input uuid:"+ uuid));
+ experimentDAO = experimentRepository.findByUuid(experimentUuid);
+ if (experimentDAO == null){
+ Logging.LogUserAction(userInfo.getUser().getUsername(), endpoint, "Experiment with uuid : " + uuid + "was not found.");
+ throw new ExperimentNotFoundException("Experiment with uuid : " + uuid + " was not found.");
+ }
- return experimentRepository.findByUuid(experimentUuid);
+ return experimentDAO;
}
/**
@@ -411,6 +443,7 @@ public class ExperimentService {
* @return the experiment information that was inserted into the database
*/
private ExperimentDAO createExperimentInTheDatabase(ExperimentDTO experimentDTO, String endpoint) {
+
UserDAO user = userInfo.getUser();
ExperimentDAO experimentDAO = new ExperimentDAO();
@@ -420,6 +453,7 @@ public class ExperimentService {
experimentDAO.setAlgorithm(experimentDTO.getAlgorithm());
experimentDAO.setName(experimentDTO.getName());
experimentDAO.setStatus(ExperimentDAO.Status.pending);
+
try {
experimentRepository.save(experimentDAO);
}
@@ -456,6 +490,7 @@ public class ExperimentService {
private void finishExperiment(ExperimentDAO experimentDAO, String endpoint) {
experimentDAO.setFinished(new Date());
+
try {
experimentRepository.save(experimentDAO);
}
@@ -508,8 +543,10 @@ public class ExperimentService {
// Results are stored in the experiment object
ExaremeResult exaremeResult = runExaremeExperiment(url, body, finalExperimentDTO);
- experimentDAO.setResult(JsonConverters.convertObjectToJsonString(exaremeResult.result));
- experimentDAO.setStatus((exaremeResult.code>= 400)? ExperimentDAO.Status.error: ExperimentDAO.Status.success);
+ Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Experiment with uuid: " + experimentDAO.getUuid() + "gave response code: " +exaremeResult.getCode() + " and result: "+ exaremeResult.getResults());
+
+ experimentDAO.setResult((exaremeResult.getCode()>= 400)? null : JsonConverters.convertObjectToJsonString(exaremeResult.getResults()));
+ experimentDAO.setStatus((exaremeResult.getCode()>= 400)? ExperimentDAO.Status.error: ExperimentDAO.Status.success);
} catch (Exception e) {
Logging.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "There was an exception: " + e.getMessage());
@@ -539,13 +576,13 @@ public class ExperimentService {
code = HTTPUtil.sendPost(url, body, results);
}
catch (Exception e){
- throw new InternalServerError("Error occured : "+ e.getMessage());
+ throw new InternalServerError("Error occurred : "+ e.getMessage());
}
Logging.LogExperimentAction(experimentDTO.getName(), experimentDTO.getUuid(), "Algorithm finished with code: " + code);
// Results are stored in the experiment object
- ExperimentDTO.ResultDTO resultDTO = JsonConverters.convertJsonStringToObject(String.valueOf(results), ExperimentDTO.ResultDTO.class);
- return new ExaremeResult(code, resultDTO);
+ Map resultsDTO = ExperimentDAO.convertJsonStringToResult(String.valueOf(results));
+ return new ExaremeResult(code, resultsDTO);
}
@@ -952,21 +989,21 @@ public class ExperimentService {
return returnError;
}
- final class ExaremeResult {
- private final int code;
- private final ExperimentDTO.ResultDTO result;
+ static class ExaremeResult {
+ private int code;
+ private Map results;
- public ExaremeResult(int code, ExperimentDTO.ResultDTO result) {
+ public ExaremeResult(int code, Map results) {
this.code = code;
- this.result = result;
+ this.results = results;
}
public int getCode() {
return code;
}
- public ExperimentDTO.ResultDTO getResult() {
- return result;
+ public Map getResults() {
+ return results;
}
}
}
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java b/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java
index 076249e0becac36fbb64db83eae5e758c56d4161..f59faa9ed73017bd9662f15a382fe1252925c2a4 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java
@@ -1,12 +1,15 @@
package eu.hbp.mip.services;
import eu.hbp.mip.model.DAOs.ExperimentDAO;
+import eu.hbp.mip.utils.Exceptions.BadRequestException;
import org.springframework.data.jpa.domain.Specification;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
+import java.util.ArrayList;
+import java.util.List;
public class ExperimentSpecifications {
public static class ExperimentWithName implements Specification<ExperimentDAO> {
@@ -65,7 +68,7 @@ public class ExperimentSpecifications {
}
}
- public static class ExperimentWithShared implements org.springframework.data.jpa.domain.Specification<ExperimentDAO> {
+ public static class ExperimentWithShared implements Specification<ExperimentDAO> {
private Boolean shared;
@@ -79,7 +82,47 @@ public class ExperimentSpecifications {
}
return cb.equal(root.get("shared"), this.shared);
}
+ }
+
+ public static class ExperimentOrderBy implements Specification<ExperimentDAO> {
+
+ private String orderBy;
+ private Boolean descending ;
+ public ExperimentOrderBy(String orderBy, Boolean descending){
+ if (properColumnToBeOrderedBy(orderBy))
+ this.orderBy = orderBy;
+ else
+ throw new BadRequestException("Please provide proper column to order by.");
+ if(descending == null)
+ this.descending = true;
+ else
+ this.descending = descending;
+ }
+ public Predicate toPredicate(Root<ExperimentDAO> root, CriteriaQuery<?> criteriaQuery, CriteriaBuilder cb) {
+ if (descending) {
+ criteriaQuery.orderBy(cb.desc(root.get(orderBy)));
+ } else {
+ criteriaQuery.orderBy(cb.asc(root.get(orderBy)));
+ }
+ return cb.isTrue(cb.literal(true));
+ }
+
+ }
+
+ public static boolean properColumnToBeOrderedBy(String column){
+ {
+ List<String> properColumns = new ArrayList<>();
+ properColumns.add("uuid");
+ properColumns.add("name");
+ properColumns.add("created_by_username");
+ properColumns.add("algorithm");
+ properColumns.add("created");
+ properColumns.add("status");
+ properColumns.add("shared");
+ properColumns.add("viewed");
+ return properColumns.contains(column);
+ }
}
}
diff --git a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
index 5872819bc883efd98a453e363a46ad0a1cb537cd..dea4cd0b5e898f385562a044749970108c592cfc 100644
--- a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
+++ b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
@@ -2,6 +2,7 @@ package eu.hbp.mip.utils;
import com.google.gson.Gson;
import eu.hbp.mip.model.DTOs.PathologyDTO;
+import eu.hbp.mip.utils.Exceptions.BadRequestException;
import org.springframework.security.core.GrantedAuthority;
import java.util.ArrayList;
@@ -22,7 +23,7 @@ public class ClaimUtils {
return "dataset_" + datasetCode.toLowerCase();
}
- public static boolean userHasDatasetsAuthorization(String username, Collection<? extends GrantedAuthority> authorities,
+ public static void validateAccessRightsOnDatasets(String username, Collection<? extends GrantedAuthority> authorities,
String experimentDatasets) {
List<String> userClaims = Arrays.asList(authorities.toString().toLowerCase()
@@ -37,13 +38,12 @@ public class ClaimUtils {
if (!userClaims.contains(datasetRole.toLowerCase())) {
Logging.LogUserAction(username, "(POST) /experiments/runAlgorithm",
"You are not allowed to use dataset: " + dataset);
- return false;
+ throw new BadRequestException("You are not authorized to use these datasets.");
}
}
Logging.LogUserAction(username, "(POST) /experiments/runAlgorithm",
"User is authorized to use the datasets: " + experimentDatasets);
}
- return true;
}
public static String getAuthorizedPathologies(String username, Collection<? extends GrantedAuthority> authorities,
diff --git a/src/main/java/eu/hbp/mip/utils/JsonConverters.java b/src/main/java/eu/hbp/mip/utils/JsonConverters.java
index 52305124aff3c2078d6c87ba95c1b4235782da5a..74d01b851f44877fffe0e146d8f678ee3fb95dfb 100644
--- a/src/main/java/eu/hbp/mip/utils/JsonConverters.java
+++ b/src/main/java/eu/hbp/mip/utils/JsonConverters.java
@@ -7,7 +7,7 @@ import com.google.gson.Gson;
import java.lang.reflect.Type;
public class JsonConverters {
- Gson gson = new Gson();
+ private static final Gson gson = new Gson();
public static String convertObjectToJsonString(Object object) {
ObjectMapper mapper = new ObjectMapper();
@@ -22,6 +22,6 @@ public class JsonConverters {
public static <T> T convertJsonStringToObject(String jsonString, Type typeOfT) {
if(jsonString == null || jsonString.isEmpty())
return null;
- return new Gson().fromJson(jsonString, typeOfT);
+ return gson.fromJson(jsonString, typeOfT);
}
}
diff --git a/src/main/resources/db/migration/V7_0__NewDatabaseStructure.sql b/src/main/resources/db/migration/V7_0__NewDatabaseStructure.sql
index 73a15addd8f1a7cd34594b9708595f7a4447bfb8..5e1bcc6fb1e7ef9931db031241ff39097306069c 100644
--- a/src/main/resources/db/migration/V7_0__NewDatabaseStructure.sql
+++ b/src/main/resources/db/migration/V7_0__NewDatabaseStructure.sql
@@ -15,6 +15,9 @@ RENAME resultsviewed TO viewed;
ALTER TABLE experiment
RENAME workflowstatus TO status;
+ALTER TABLE experiment
+ADD COLUMN updated timestamp without time zone;
+
ALTER TABLE experiment
ADD COLUMN algorithm text;