diff --git a/src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java b/src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java
index 2b2e549d46dc7f8a71fc981f6c8d000f606630c9..9f583da4ef31205007e7467c63cfaf95645a5f28 100644
--- a/src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java
@@ -56,7 +56,7 @@ public class SecurityConfiguration extends KeycloakWebSecurityConfigurerAdapter
"/sso/login",
"/v2/api-docs", "/swagger-ui/**", "/swagger-resources/**" // Swagger URLs
).permitAll()
- .antMatchers("/galaxy*", "/galaxy/*").hasRole("DATA MANAGER")
+ .antMatchers("/galaxy*", "/galaxy/*").hasRole("WORKFLOW_ADMIN")
.antMatchers("/**").authenticated()
.and().csrf().ignoringAntMatchers("/logout").csrfTokenRepository(csrfTokenRepository())
.and().addFilterAfter(csrfHeaderFilter(), CsrfFilter.class);
diff --git a/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java b/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java
index e369e5cf6eff7b2641a4c9815e269eada28b37d9..a696ab52d7c6ff48bd2c1406369d6f7191724d01 100644
--- a/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java
+++ b/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java
@@ -52,7 +52,7 @@ public class ExperimentDAO {
@Expose
@Column(columnDefinition = "TEXT")
- private String result;
+ private String results;
@Expose
@Column(columnDefinition = "TIMESTAMP WITHOUT TIME ZONE")
@@ -95,6 +95,28 @@ public class ExperimentDAO {
*/
}
+
+ public String getResults() {
+ return results;
+ }
+
+ public void setResults(String result) {
+ this.results = result;
+ }
+
+ public class ResultObjectDTO {
+
+ ArrayList<Object> result;
+
+ public ArrayList<Object> getResult() {
+ return this.result;
+ }
+
+ public void setResult(ArrayList<Object> results) {
+ this.result = results;
+ }
+ }
+
public ExperimentDTO convertToDTO(boolean includeResult)
{
ExperimentDTO experimentDTO = new ExperimentDTO();
@@ -105,7 +127,7 @@ public class ExperimentDAO {
experimentDTO.setCreatedBy(this.createdBy.getUsername());
experimentDTO.setName(this.name);
if(includeResult){
- experimentDTO.setResult(JsonConverters.convertJsonStringToObject(String.valueOf(this.result), new ArrayList<ExperimentDTO.ResultDTO>().getClass()));
+ experimentDTO.setResults(JsonConverters.convertJsonStringToObject(this.results, new ArrayList<ArrayList<Object>>().getClass()));
}
experimentDTO.setStatus(this.status);
experimentDTO.setShared(this.shared);
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
index 1a6d8b99d41b4129c85b2b3591cc6ea3f89c950f..52db979d5ddd7b043572be8fc9255c45fa0e9c98 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
@@ -1,51 +1,15 @@
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
+import lombok.Getter;
+import lombok.Setter;
import java.util.List;
+@Getter
+@Setter
public class AlgorithmDTO {
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getDesc() {
- return desc;
- }
-
- public void setDesc(String desc) {
- this.desc = desc;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
- public String getType() {
- return type;
- }
-
- public void setType(String type) {
- this.type = type;
- }
-
- public List<AlgorithmParamDTO> getParameters() {
- return parameters;
- }
-
- public void setParameters(List<AlgorithmParamDTO> parameters) {
- this.parameters = parameters;
- }
-
@SerializedName("name")
private String name;
@@ -61,6 +25,8 @@ public class AlgorithmDTO {
@SerializedName("parameters")
private List<AlgorithmParamDTO> parameters;
+ @Getter
+ @Setter
public static class AlgorithmParamDTO {
@SerializedName("name")
private String name;
@@ -103,118 +69,5 @@ public class AlgorithmDTO {
@SerializedName("valueEnumerations")
private List<String> valueEnumerations;
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getDesc() {
- return desc;
- }
-
- public void setDesc(String desc) {
- this.desc = desc;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
- public String getType() {
- return type;
- }
-
- public void setType(String type) {
- this.type = type;
- }
-
- public String getColumnValuesSQLType() {
- return columnValuesSQLType;
- }
-
- public void setColumnValuesSQLType(String columnValuesSQLType) {
- this.columnValuesSQLType = columnValuesSQLType;
- }
-
- public String getColumnValuesIsCategorical() {
- return columnValuesIsCategorical;
- }
-
- public void setColumnValuesIsCategorical(String columnValuesIsCategorical) {
- this.columnValuesIsCategorical = columnValuesIsCategorical;
- }
-
- public String getValue() {
- return value;
- }
-
- public void setValue(String value) {
- this.value = value;
- }
-
- public String getDefaultValue() {
- return defaultValue;
- }
-
- public void setDefaultValue(String defaultValue) {
- this.defaultValue = defaultValue;
- }
-
- public String getValueType() {
- return valueType;
- }
-
- public void setValueType(String valueType) {
- this.valueType = valueType;
- }
-
- public String getValueNotBlank() {
- return valueNotBlank;
- }
-
- public void setValueNotBlank(String valueNotBlank) {
- this.valueNotBlank = valueNotBlank;
- }
-
- public String getValueMultiple() {
- return valueMultiple;
- }
-
- public void setValueMultiple(String valueMultiple) {
- this.valueMultiple = valueMultiple;
- }
-
- public String getValueMin() {
- return valueMin;
- }
-
- public void setValueMin(String valueMin) {
- this.valueMin = valueMin;
- }
-
- public String getValueMax() {
- return valueMax;
- }
-
- public void setValueMax(String valueMax) {
- this.valueMax = valueMax;
- }
-
- public List<String> getValueEnumerations() {
- return valueEnumerations;
- }
-
- public void setValueEnumerations(List<String> valueEnumerations) {
- this.valueEnumerations = valueEnumerations;
- }
}
-
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
index 2840f669fcb507bf7b91b0f604b54ba7440cafc9..34a1bee9c8fda145bbeba5f5413bb19e711fe575 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
@@ -2,11 +2,15 @@ package eu.hbp.mip.models.DTOs;
import com.fasterxml.jackson.annotation.JsonInclude;
import eu.hbp.mip.models.DAOs.ExperimentDAO;
+import lombok.Getter;
+import lombok.Setter;
import java.util.Date;
import java.util.List;
import java.util.UUID;
+@Getter
+@Setter
@JsonInclude(JsonInclude.Include.NON_NULL)
public class ExperimentDTO {
@@ -18,121 +22,11 @@ public class ExperimentDTO {
private Date finished;
private Boolean shared;
private Boolean viewed;
- private List<ExperimentDTO.ResultDTO> result;
+ private List<List<Object>> results;
private ExperimentDAO.Status status;
-
private AlgorithmDTO algorithm;
public ExperimentDTO() {
- }
-
- public AlgorithmDTO getAlgorithm() {
- return algorithm;
- }
-
- public void setAlgorithm(AlgorithmDTO algorithm) {
- this.algorithm = algorithm;
- }
-
- public UUID getUuid() {
- return uuid;
- }
-
- public void setUuid(UUID uuid) {
- this.uuid = uuid;
- }
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getCreatedBy() {
- return createdBy;
- }
-
- public void setCreatedBy(String createdBy) {
- this.createdBy = createdBy;
- }
-
- public Date getCreated() {
- return created;
- }
-
- 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;
- }
-
- public void setShared(Boolean shared) {
- this.shared = shared;
- }
-
- public Boolean getViewed() {
- return viewed;
- }
-
- public void setViewed(Boolean viewed) {
- this.viewed = viewed;
- }
-
- public List<ExperimentDTO.ResultDTO> getResult() {
- return result;
- }
-
- public void setResult(List<ExperimentDTO.ResultDTO> result) {
- this.result = result;
- }
-
- public ExperimentDAO.Status getStatus() {
- return status;
- }
-
- public void setStatus(ExperimentDAO.Status status) {
- this.status = status;
- }
-
- public static class ResultDTO {
-
- private Object data;
- private String type;
-
- public Object getData() {
- return this.data;
- }
-
- public void setData(Object data) {
- this.data = data;
- }
-
- public String getType() {
- return type;
- }
- public void setType(String type) {
- this.type = type;
- }
}
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
index 2a8887b5f22a309ecf2befcc69e1191a7c00576c..aa78ef8b0e315a2f71261dc1fed480cb8617ccb2 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
@@ -1,43 +1,15 @@
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
+import lombok.Getter;
+import lombok.Setter;
import java.util.List;
+@Getter
+@Setter
public class PathologyDTO {
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
- public Object getMetadataHierarchy() {
- return metadataHierarchy;
- }
-
- public void setMetadataHierarchy(Object metadataHierarchy) {
- this.metadataHierarchy = metadataHierarchy;
- }
-
- public List<PathologyDatasetDTO> getDatasets() {
- return datasets;
- }
-
- public void setDatasets(List<PathologyDatasetDTO> datasets) {
- this.datasets = datasets;
- }
-
@SerializedName("code")
private String code;
@@ -50,6 +22,8 @@ public class PathologyDTO {
@SerializedName("datasets")
private List<PathologyDatasetDTO> datasets;
+ @Getter
+ @Setter
public static class PathologyDatasetDTO {
@SerializedName("code")
private String code;
@@ -57,22 +31,6 @@ public class PathologyDTO {
@SerializedName("label")
private String label;
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
public String toString() {
return code;
}
@@ -81,5 +39,4 @@ public class PathologyDTO {
public String toString() {
return code;
}
-
}
diff --git a/src/main/java/eu/hbp/mip/services/ActiveUserService.java b/src/main/java/eu/hbp/mip/services/ActiveUserService.java
index ee65c170ad2b09ebe6d0e602b5af2316cbf82c48..bc3c8ced7fc3a573a8fe67bd87abaf1dcf19246c 100644
--- a/src/main/java/eu/hbp/mip/services/ActiveUserService.java
+++ b/src/main/java/eu/hbp/mip/services/ActiveUserService.java
@@ -4,15 +4,14 @@ import eu.hbp.mip.models.DAOs.UserDAO;
import eu.hbp.mip.repositories.UserRepository;
import org.keycloak.KeycloakPrincipal;
import org.keycloak.representations.IDToken;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Scope;
import org.springframework.context.annotation.ScopedProxyMode;
-import org.springframework.security.core.Authentication;
import org.springframework.security.core.context.SecurityContextHolder;
import org.springframework.stereotype.Component;
import javax.inject.Named;
+import java.util.Objects;
@Component
@Named("ActiveUserService")
@@ -44,7 +43,7 @@ public class ActiveUserService {
// If Authentication is OFF, create anonymous user with accepted NDA
if (!authenticationIsEnabled) {
- user = new UserDAO("anonymous", "anonymous", "anonymous@anonymous.com","anonymousId");
+ user = new UserDAO("anonymous", "anonymous", "anonymous@anonymous.com", "anonymousId");
user.setAgreeNDA(true);
userRepository.save(user);
return user;
@@ -57,9 +56,20 @@ public class ActiveUserService {
user = new UserDAO(idToken.getPreferredUsername(), idToken.getName(), idToken.getEmail(), idToken.getId());
UserDAO userInDatabase = userRepository.findByUsername(user.getUsername());
- if (userInDatabase == null || !userInDatabase.equals(user)) {
+ if (userInDatabase == null) {
userRepository.save(user);
+ return user;
+ }
+
+ if (!Objects.equals(user.getEmail(),userInDatabase.getEmail())
+ || !Objects.equals(user.getFullname(),userInDatabase.getFullname())
+ ) {
+ userInDatabase.setFullname(user.getFullname());
+ userInDatabase.setEmail(user.getEmail());
}
+
+ user = userInDatabase;
+ userRepository.save(user);
return user;
}
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index 2bc16b0f9939df9c015e25fde52c562d496c1c03..1ef7c09d77e864c5199b60743d49a32a64887f32 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -10,6 +10,7 @@ import com.google.gson.Gson;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
+import com.google.gson.internal.LinkedTreeMap;
import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
import eu.hbp.mip.models.DAOs.ExperimentDAO;
@@ -19,6 +20,7 @@ import eu.hbp.mip.models.DTOs.ExperimentDTO;
import eu.hbp.mip.models.galaxy.GalaxyWorkflowResult;
import eu.hbp.mip.models.galaxy.PostWorkflowToGalaxyDtoResponse;
import eu.hbp.mip.repositories.ExperimentRepository;
+import eu.hbp.mip.services.Specifications.ExperimentSpecifications;
import eu.hbp.mip.utils.ClaimUtils;
import eu.hbp.mip.utils.Exceptions.*;
import eu.hbp.mip.utils.HTTPUtil;
@@ -211,6 +213,14 @@ public class ExperimentService {
//Checking if check (POST) /experiments has proper input.
checkPostExperimentProperInput(experimentDTO, logger);
+ // Get the type and name of algorithm
+ String algorithmType = experimentDTO.getAlgorithm().getType();
+
+ if(algorithmType == "workflow"){
+ logger.LogUserAction("You can not run workflow algorithms transiently.");
+ throw new BadRequestException("You can not run workflow algorithms transiently.");
+ }
+
// Get the parameters
List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
= experimentDTO.getAlgorithm().getParameters();
@@ -236,7 +246,7 @@ public class ExperimentService {
logger.LogUserAction("Experiment with uuid: " + experimentDTO.getUuid() + "gave response code: " + exaremeResult.getCode() + " and result: " + exaremeResult.getResults());
- experimentDTO.setResult((exaremeResult.getCode() >= 400) ? null : exaremeResult.getResults());
+ experimentDTO.setResults((exaremeResult.getCode() >= 400) ? null : JsonConverters.convertJsonStringToObject(exaremeResult.getResults(), new ArrayList<ArrayList<Object>>().getClass()));
experimentDTO.setStatus((exaremeResult.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
return experimentDTO;
@@ -244,10 +254,10 @@ public class ExperimentService {
/**
* The updateExperiment will update the experiment's properties
- *
* @param uuid is the id of the experiment to be updated
* @param experimentDTO is the experiment information to be updated
* @param logger contains username and the endpoint.
+ * @return
*/
public ExperimentDTO updateExperiment(String uuid, ExperimentDTO experimentDTO, Logger logger) {
ExperimentDAO experimentDAO;
@@ -321,7 +331,7 @@ public class ExperimentService {
&& experimentDTO.getViewed() == null
&& experimentDTO.getCreated() == null
&& experimentDTO.getCreatedBy() == null
- && experimentDTO.getResult() == null
+ && experimentDTO.getResults() == null
&& experimentDTO.getStatus() == null
&& experimentDTO.getUuid() == null;
@@ -362,7 +372,7 @@ public class ExperimentService {
throw new BadRequestException("Finished is not editable.");
}
- if (experimentDTO.getResult() != null) {
+ if (experimentDTO.getResults() != null) {
logger.LogUserAction( "Result is not editable.");
throw new BadRequestException("Result is not editable.");
}
@@ -497,6 +507,50 @@ public class ExperimentService {
}
}
+ private String formattingExaremeResult(String result) {
+ List<LinkedTreeMap<String,Object>> jsonObject = JsonConverters.convertJsonStringToObject(result, new ArrayList<ExperimentDAO.ResultObjectDTO>().getClass());
+ LinkedTreeMap<String,Object> firstResult = jsonObject.get(0);
+ return "[" + JsonConverters.convertObjectToJsonString(firstResult.get("result")) + "]";
+ }
+
+ private String formattingGalaxyResult(String result) {
+ List<LinkedTreeMap<String,Object>> jsonObjects = JsonConverters.convertJsonStringToObject(result, new ArrayList<ExperimentDAO.ResultObjectDTO>().getClass());
+ List<Object> objects = new ArrayList<>();
+ for (int i = 0; i < jsonObjects.size(); i++) {
+ LinkedTreeMap<String,Object> k = jsonObjects.get(i);
+ objects.add(k.get("result"));
+ }
+ return JsonConverters.convertObjectToJsonString(objects);
+ }
+
+
+ /**
+ * The runExaremeExperiment will run to exareme the experiment
+ *
+ * @param url is the url that contain the results of the experiment
+ * @param body is the parameters of the algorithm
+ * @param experimentDTO is the experiment information to be executed in the exareme
+ * @return the result of exareme as well as the http status that was retrieved
+ */
+ private ExaremeResult runExaremeExperiment(String url, String body, ExperimentDTO experimentDTO) {
+
+ StringBuilder results = new StringBuilder();
+ int code;
+ try {
+ code = HTTPUtil.sendPost(url, body, results);
+ } catch (Exception e) {
+ throw new InternalServerError("Error occurred : " + e.getMessage());
+ }
+
+ String resultToMatchGalaxy = "[" + results + "]";
+ String formattedResult = formattingExaremeResult(resultToMatchGalaxy);
+ Logger.LogExperimentAction(experimentDTO.getName(), experimentDTO.getUuid(), "Algorithm finished with code: " + code + "and result :" + formattedResult);
+
+ return new ExaremeResult(code, formattedResult);
+ }
+
+
+
/* -------------------------------------- EXAREME CALLS ---------------------------------------------------------*/
/**
@@ -539,7 +593,7 @@ public class ExperimentService {
Logger.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.setResults((exaremeResult.getCode() >= 400) ? null : exaremeResult.getResults());
experimentDAO.setStatus((exaremeResult.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
} catch (Exception e) {
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "There was an exception: " + e.getMessage());
@@ -554,32 +608,6 @@ public class ExperimentService {
return experimentDTO;
}
- /**
- * The runExaremeExperiment will run to exareme the experiment
- *
- * @param url is the url that contain the results of the experiment
- * @param body is the parameters of the algorithm
- * @param experimentDTO is the experiment information to be executed in the exareme
- * @return the result of exareme as well as the http status that was retrieved
- */
- public ExaremeResult runExaremeExperiment(String url, String body, ExperimentDTO experimentDTO) {
-
- StringBuilder results = new StringBuilder();
- int code;
- try {
- code = HTTPUtil.sendPost(url, body, results);
- } catch (Exception e) {
- throw new InternalServerError("Error occurred : " + e.getMessage());
- }
- Logger.LogExperimentAction(experimentDTO.getName(), experimentDTO.getUuid(), "Algorithm finished with code: " + code);
-
- // Results are stored in the experiment object
- ExperimentDTO experimentDTOWithOnlyResult = JsonConverters.convertJsonStringToObject(String.valueOf(results), ExperimentDTO.class);
- List<ExperimentDTO.ResultDTO> resultDTOS = experimentDTOWithOnlyResult.getResult();
- return new ExaremeResult(code, resultDTOS);
- }
-
-
/* --------------------------------------- GALAXY CALLS ---------------------------------------------------------*/
@@ -718,12 +746,12 @@ public class ExperimentService {
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "State is: " + state);
switch (state) {
- case "running":
+ case "pending":
// Do nothing, when the experiment is created the status is set to running
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Workflow is still running.");
break;
- case "completed":
+ case "success":
// Get only the job result that is visible
List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experimentDAO);
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Results are: " + workflowJobsResults.toString());
@@ -739,7 +767,7 @@ public class ExperimentService {
if (result == null) {
experimentDAO.setStatus(ExperimentDAO.Status.error);
} else {
- experimentDAO.setResult(result);
+ experimentDAO.setResults(result);
experimentDAO.setStatus(ExperimentDAO.Status.success);
resultFound = true;
}
@@ -790,8 +818,8 @@ public class ExperimentService {
}
// If result exists return
- if (experimentDAO.getResult() != null) {
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "ResultDTO exists: " + experimentDAO.getResult());
+ if (experimentDAO.getResults() != null) {
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "ResultDTO exists: " + experimentDAO.getResults());
return;
}
}
@@ -801,10 +829,10 @@ public class ExperimentService {
/**
* @param experimentDAO The experiment of the workflow
- * @return "running" -> When the workflow is still running
+ * @return "pending" -> When the workflow is still running
* "internalError" -> When an exception or a bad request occurred
* "error" -> When the workflow produced an error
- * "completed" -> When the workflow completed successfully
+ * "success" -> When the workflow completed successfully
*/
public String getWorkflowStatus(ExperimentDAO experimentDAO) {
String historyId = experimentDAO.getWorkflowHistoryId();
@@ -846,14 +874,14 @@ public class ExperimentService {
Logger.LogExperimentAction(experimentName, experimentId, " Completed!");
switch (state) {
case "ok":
- return "completed";
+ return "success";
case "error":
return "error";
- case "running":
+ case "pending":
case "new":
case "waiting":
case "queued":
- return "running";
+ return "pending";
default:
return "internalError";
}
@@ -919,7 +947,8 @@ public class ExperimentService {
+ response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return null;
}
- resultJson = new Gson().toJson(response.body());
+
+ resultJson = gson.toJson(response.body());
Logger.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + resultJson);
} catch (IOException e) {
@@ -928,8 +957,8 @@ public class ExperimentService {
return null;
}
- Logger.LogExperimentAction(experimentName, experimentId, " Completed!");
- return resultJson;
+
+ return formattingGalaxyResult(resultJson);
}
@@ -979,9 +1008,9 @@ public class ExperimentService {
static class ExaremeResult {
private int code;
- private List<ExperimentDTO.ResultDTO> results;
+ private String results;
- public ExaremeResult(int code, List<ExperimentDTO.ResultDTO> results) {
+ public ExaremeResult(int code, String results) {
this.code = code;
this.results = results;
}
@@ -990,7 +1019,7 @@ public class ExperimentService {
return code;
}
- public List<ExperimentDTO.ResultDTO> getResults() {
+ public String getResults() {
return results;
}
}
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java b/src/main/java/eu/hbp/mip/services/Specifications/ExperimentSpecifications.java
similarity index 99%
rename from src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java
rename to src/main/java/eu/hbp/mip/services/Specifications/ExperimentSpecifications.java
index e5b51a692e286be347901f7d50d9ab39e248ca8b..c1e6a13acae08d9ac2c516884773b5bf9b4c71b2 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java
+++ b/src/main/java/eu/hbp/mip/services/Specifications/ExperimentSpecifications.java
@@ -1,4 +1,4 @@
-package eu.hbp.mip.services;
+package eu.hbp.mip.services.Specifications;
import eu.hbp.mip.models.DAOs.ExperimentDAO;
import eu.hbp.mip.models.DAOs.UserDAO;
diff --git a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
index 902bf9f9fe677e39760e94553b27ff27a57c1c96..f5676b52c130f0b4be1c79d939567f74b752c0db 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.models.DTOs.PathologyDTO;
+import eu.hbp.mip.utils.Exceptions.InternalServerError;
import eu.hbp.mip.utils.Exceptions.UnauthorizedException;
import org.keycloak.KeycloakPrincipal;
import org.keycloak.adapters.springsecurity.token.KeycloakAuthenticationToken;
@@ -29,7 +30,7 @@ public class ClaimUtils {
public static void validateAccessRightsOnDatasets(Authentication authentication,
String experimentDatasets, Logger logger) {
- ArrayList<String> authorities = getKeycloakAuthorities(authentication);
+ ArrayList<String> authorities = getKeycloakAuthorities(authentication, logger);
// Don't check for dataset claims if "super" claim exists allowing everything
if (!hasRoleAccess(authorities, ClaimUtils.allDatasetsAllowedClaim(), logger)) {
@@ -47,7 +48,7 @@ public class ClaimUtils {
public static boolean validateAccessRightsOnExperiments(Authentication authentication, Logger logger) {
- ArrayList<String> authorities = getKeycloakAuthorities(authentication);
+ ArrayList<String> authorities = getKeycloakAuthorities(authentication, logger);
// Check for experiment_all claims
return hasRoleAccess(authorities, ClaimUtils.allExperimentsAllowedClaim(), logger);
@@ -58,7 +59,7 @@ public class ClaimUtils {
// --- Providing only the allowed pathologies/datasets to the user ---
logger.LogUserAction("Filter out the unauthorised datasets.");
- ArrayList<String> authorities = getKeycloakAuthorities(authentication);
+ ArrayList<String> authorities = getKeycloakAuthorities(authentication, logger);
// If the "dataset_all" claim exists then return everything
if (hasRoleAccess(authorities, ClaimUtils.allDatasetsAllowedClaim(), logger)) {
@@ -100,9 +101,15 @@ public class ClaimUtils {
return userClaims.contains(role.toLowerCase());
}
- private static ArrayList<String> getKeycloakAuthorities(Authentication authentication){
+ private static ArrayList<String> getKeycloakAuthorities(Authentication authentication, Logger logger){
KeycloakAuthenticationToken token = (KeycloakAuthenticationToken) authentication;
KeycloakPrincipal keycloakPrincipal = (KeycloakPrincipal) token.getPrincipal();
- return (ArrayList<String>)keycloakPrincipal.getKeycloakSecurityContext().getIdToken().getOtherClaims().get("authorities");
+ if(keycloakPrincipal.getKeycloakSecurityContext().getIdToken().getOtherClaims().get("authorities") == null)
+ {
+ logger.LogUserAction("Your user has no roles.");
+ throw new InternalServerError("Your user has no roles.");
+ }
+
+ return (ArrayList<String>)keycloakPrincipal.getKeycloakSecurityContext().getIdToken().getOtherClaims().get("authorities");
}
}
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index e77b803581f635159456a423b177b91a4ba2bcf0..58ecf45e12c926af36b3019a8e5d457cbf98f077 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -11,7 +11,7 @@ logging:
### AUTHENTICATION ###
authentication:
- enabled: true
+ enabled: false
### DATABASE CONFIGURATION ###
@@ -48,14 +48,13 @@ services:
### KEYCLOAK ###
keycloak:
enabled: true
- auth-server-url: "http://127.0.0.1/auth"
+ auth-server-url: "https://iam.humanbrainproject.eu/auth"
realm: "MIP"
- resource: "MIP"
+ resource: "mipfedqa"
enable-basic-auth: true
credentials:
- secret: "dae83a6b-c769-4186-8383-f0984c6edf05"
+ secret: "492ddb7d-a7c6-4143-89ae-dbfa6f970aca"
principal-attribute: "preferred_username"
- ssl-required: none
### EXTERNAL FILES ###
diff --git a/src/main/resources/db/migration/V7_0__NewDatabaseStructure.sql b/src/main/resources/db/migration/V7_0__NewDatabaseStructure.sql
index c39158269bd59362cfd010913c33f17a03e1a4ce..6a3b0c364b2fed6a6456d7eae8a971b9cab7add2 100644
--- a/src/main/resources/db/migration/V7_0__NewDatabaseStructure.sql
+++ b/src/main/resources/db/migration/V7_0__NewDatabaseStructure.sql
@@ -26,8 +26,8 @@ DROP COLUMN hasservererror,
DROP COLUMN validations,
DROP COLUMN model_slug;
-UPDATE experiment
-SET algorithms = REPLACE(algorithms, '"name"', '"id"');
+ALTER TABLE experiment
+RENAME result TO results;
ALTER TABLE experiment
RENAME algorithms TO algorithm;
ALTER TABLE experiment
@@ -45,7 +45,7 @@ ALTER TABLE experiment
ADD COLUMN algorithmId text;
UPDATE experiment
-SET algorithmId = (algorithm ->> 'id');
+SET algorithmId = (algorithm ->> 'name');
ALTER TABLE experiment
ALTER COLUMN algorithm TYPE text;