diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index 08132000d15bd1f033f9adf625aa24af01c2c542..aea67b056981111fceede22ce964adab2ae7f57d 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -28,7 +28,6 @@ import retrofit2.Response;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.LinkedList;
import java.util.List;
import static eu.hbp.mip.utils.InputStreamConverter.convertInputStreamToString;
@@ -69,25 +68,25 @@ public class AlgorithmsAPI {
Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /algorithms");
logger.LogUserAction("Executing...");
- LinkedList<ExaremeAlgorithmDTO> mipengineAlgorithms = getMIPEngineAlgorithms(logger);
+ ArrayList<ExaremeAlgorithmDTO> mipengineAlgorithms = getMIPEngineAlgorithms(logger);
logger.LogUserAction("Loaded " + mipengineAlgorithms.size() + " mipengine algorithms");
- LinkedList<ExaremeAlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms(logger);
+ ArrayList<ExaremeAlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms(logger);
logger.LogUserAction("Loaded " + exaremeAlgorithms.size() + " exareme algorithms");
- LinkedList<ExaremeAlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows(logger);
+ ArrayList<ExaremeAlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows(logger);
logger.LogUserAction("Loaded " + galaxyAlgorithms.size() + " galaxy algorithms");
- LinkedList<ExaremeAlgorithmDTO> algorithms = new LinkedList<>();
- if (exaremeAlgorithms != null) {
+ ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>();
+ if (!exaremeAlgorithms.isEmpty()) {
algorithms.addAll(exaremeAlgorithms);
} else {
logger.LogUserAction("Getting exareme algorithms failed and returned null");
}
- if (mipengineAlgorithms != null) {
+ if (!mipengineAlgorithms.isEmpty()) {
algorithms.addAll(mipengineAlgorithms);
} else {
logger.LogUserAction("Getting mipengine algorithms failed and returned null");
}
- if (galaxyAlgorithms != null) {
+ if (!galaxyAlgorithms.isEmpty()) {
algorithms.addAll(galaxyAlgorithms);
} else {
logger.LogUserAction("Getting galaxy workflows failed and returned null");
@@ -101,7 +100,7 @@ public class AlgorithmsAPI {
}
// Remove any disabled algorithm
- LinkedList<ExaremeAlgorithmDTO> allowedAlgorithms = new LinkedList<>();
+ ArrayList<ExaremeAlgorithmDTO> allowedAlgorithms = new ArrayList<>();
for (ExaremeAlgorithmDTO algorithm : algorithms) {
if (!disabledAlgorithms.contains(algorithm.getName())) {
allowedAlgorithms.add(algorithm);
@@ -116,15 +115,15 @@ public class AlgorithmsAPI {
*
* @return a list of AlgorithmDTOs or null if something fails
*/
- public LinkedList<ExaremeAlgorithmDTO> getExaremeAlgorithms(Logger logger) {
- LinkedList<ExaremeAlgorithmDTO> algorithms;
+ public ArrayList<ExaremeAlgorithmDTO> getExaremeAlgorithms(Logger logger) {
+ ArrayList<ExaremeAlgorithmDTO> algorithms;
// Get exareme algorithms
try {
StringBuilder response = new StringBuilder();
HTTPUtil.sendGet(exaremeAlgorithmsUrl, response);
algorithms = gson.fromJson(
response.toString(),
- new TypeToken<LinkedList<ExaremeAlgorithmDTO>>() {
+ new TypeToken<ArrayList<ExaremeAlgorithmDTO>>() {
}.getType()
);
} catch (IOException e) {
@@ -141,8 +140,8 @@ public class AlgorithmsAPI {
*
* @return a list of AlgorithmDTOs or null if something fails
*/
- public LinkedList<ExaremeAlgorithmDTO> getMIPEngineAlgorithms(Logger logger) {
- LinkedList<MIPEngineAlgorithmDTO> mipEngineAlgorithms;
+ public ArrayList<ExaremeAlgorithmDTO> getMIPEngineAlgorithms(Logger logger) {
+ ArrayList<MIPEngineAlgorithmDTO> mipEngineAlgorithms;
// Get MIPEngine algorithms
try {
StringBuilder response = new StringBuilder();
@@ -151,7 +150,7 @@ public class AlgorithmsAPI {
mipEngineAlgorithms = gson.fromJson(
response.toString(),
- new TypeToken<LinkedList<MIPEngineAlgorithmDTO>>() {
+ new TypeToken<ArrayList<MIPEngineAlgorithmDTO>>() {
}.getType()
);
} catch (IOException e) {
@@ -159,7 +158,7 @@ public class AlgorithmsAPI {
return null;
}
- LinkedList<ExaremeAlgorithmDTO> algorithms = new LinkedList<>();
+ ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>();
mipEngineAlgorithms.forEach(mipEngineAlgorithm -> algorithms.add(mipEngineAlgorithm.convertToAlgorithmDTO()));
logger.LogUserAction("Completed, returned " + algorithms.size() + " algorithms.");
@@ -171,7 +170,7 @@ public class AlgorithmsAPI {
*
* @return a list of AlgorithmDTOs or null if something fails
*/
- public LinkedList<ExaremeAlgorithmDTO> getGalaxyWorkflows(Logger logger) {
+ public ArrayList<ExaremeAlgorithmDTO> getGalaxyWorkflows(Logger logger) {
List<Workflow> workflowList;
try {
// Get all the workflows with the galaxy client
@@ -185,7 +184,7 @@ public class AlgorithmsAPI {
}
// Get the workflow details with the custom client to receive them as a WorkflowDTO
- List<WorkflowDTO> workflows = new LinkedList<>();
+ List<WorkflowDTO> workflows = new ArrayList<>();
// Create the request client
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
for (Workflow workflow : workflowList) {
@@ -210,7 +209,7 @@ public class AlgorithmsAPI {
logger.LogUserAction("Workflows fetched: " + workflows.size());
// Convert the workflows to algorithms
- LinkedList<ExaremeAlgorithmDTO> algorithms = new LinkedList<>();
+ ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>();
for (WorkflowDTO workflow : workflows) {
logger.LogUserAction("Converting workflow: " + workflow);
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
index b56e16bc7130ad30bc4c3e5739af17908419a4a5..887733de88a395d9c5f7a31b5c55c32024b56312 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
@@ -25,13 +25,13 @@ public class ExaremeAlgorithmDTO {
private String type;
@SerializedName("parameters")
- private List<ExaremeAlgorithmRequestDTO> parameters;
+ private List<ExaremeAlgorithmRequestParamDTO> parameters;
@Getter
@Setter
@AllArgsConstructor
- class Rule
+ static class Rule
{
@SerializedName("id")
private String id;
@@ -45,45 +45,47 @@ public class ExaremeAlgorithmDTO {
@SerializedName("value")
private Object value;
}
- public MIPEngineExperimentDTO convertToMIPEngineBody()
+ public MIPEngineAlgorithmRequestDTO convertToMIPEngineBody()
{
- MIPEngineExperimentDTO mipEngineExperimentDTO = new MIPEngineExperimentDTO();
- MIPEngineExperimentDTO.InputData inputData = new MIPEngineExperimentDTO.InputData();
- Hashtable<String, Object> mipEngineParameters = new Hashtable<>();
+ MIPEngineAlgorithmRequestDTO mipEngineAlgorithmRequestDTO = new MIPEngineAlgorithmRequestDTO();
+ MIPEngineAlgorithmRequestDTO.InputData inputData = new MIPEngineAlgorithmRequestDTO.InputData();
+ HashMap<String, Object> mipEngineParameters = new HashMap<>();
List<Object> rules = new ArrayList<>();
this.parameters.forEach(parameter -> {
- if(parameter.getName().equals("x")) {
- List<String> x = Arrays.asList(parameter.getValue().split(","));
- x.forEach(column -> rules.add(new Rule(column, parameter.getColumnValuesSQLType(), "is_not_null", null)));
- inputData.setX(x);
- }
- else if(parameter.getName().equals("y")) {
- List<String> y = Arrays.asList(parameter.getValue().split(","));
- y.forEach(column -> rules.add(new Rule(column, parameter.getColumnValuesSQLType(), "is_not_null", null)));
- inputData.setY(y);
- }
- else if(parameter.getName().equals("dataset")){
- List<String> datasets = Arrays.asList(parameter.getValue().split(","));
- rules.add(new Rule("dataset","string", "in", datasets));
- inputData.setDatasets(datasets);
- }
- else if(parameter.getName().equals("pathology"))
- inputData.setPathology(parameter.getValue());
-
- else if(parameter.getName().equals("filter")){
- if (parameter.getValue() != "")
- rules.add(JsonConverters.convertJsonStringToObject(parameter.getValue(), MIPEngineExperimentDTO.Filter.class));
- }
- else{
- mipEngineParameters.put(parameter.getName(), Arrays.asList(parameter.getValue().split(",")));
+ switch (parameter.getName()) {
+ case "x":
+ List<String> x = Arrays.asList(parameter.getValue().split(","));
+ x.forEach(column -> rules.add(new Rule(column, parameter.getColumnValuesSQLType(), "is_not_null", null)));
+ inputData.setX(x);
+ break;
+ case "y":
+ List<String> y = Arrays.asList(parameter.getValue().split(","));
+ y.forEach(column -> rules.add(new Rule(column, parameter.getColumnValuesSQLType(), "is_not_null", null)));
+ inputData.setY(y);
+ break;
+ case "dataset":
+ List<String> datasets = Arrays.asList(parameter.getValue().split(","));
+ rules.add(new Rule("dataset", "string", "in", datasets));
+ inputData.setDatasets(datasets);
+ break;
+ case "pathology":
+ inputData.setPathology(parameter.getValue());
+ break;
+ case "filter":
+ if (!parameter.getValue().equals(""))
+ rules.add(JsonConverters.convertJsonStringToObject(parameter.getValue(), MIPEngineAlgorithmRequestDTO.Filter.class));
+ break;
+ default:
+ mipEngineParameters.put(parameter.getName(), Arrays.asList(parameter.getValue().split(",")));
+ break;
}
});
- MIPEngineExperimentDTO.Filter filter = new MIPEngineExperimentDTO.Filter("AND", rules, true);
+ MIPEngineAlgorithmRequestDTO.Filter filter = new MIPEngineAlgorithmRequestDTO.Filter("AND", rules, true);
inputData.setFilters(filter);
- mipEngineExperimentDTO.setInputdata(inputData);
- mipEngineExperimentDTO.setParameters(mipEngineParameters);
- return mipEngineExperimentDTO;
+ mipEngineAlgorithmRequestDTO.setInputdata(inputData);
+ mipEngineAlgorithmRequestDTO.setParameters(mipEngineParameters);
+ return mipEngineAlgorithmRequestDTO;
}
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java
similarity index 89%
rename from src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestDTO.java
rename to src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java
index 84e275ec8663d7e90e6420f77a33ff899fe5773d..6f7d21655c0e5fb7cb8eea1f5bcded5183de55b8 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java
@@ -6,9 +6,10 @@ import lombok.Setter;
import java.util.List;
+//The request of an exareme algorithm is a list of ExaremeAlgorithmRequestParamDTOs.
@Getter
@Setter
-public class ExaremeAlgorithmRequestDTO {
+public class ExaremeAlgorithmRequestParamDTO {
@SerializedName("name")
private String name;
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
index ada09db3bc611bd273b59109a64a450db404d567..98677991e486e2fca38b8c7688a0d77e6eec084c 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
@@ -1,7 +1,7 @@
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
-import eu.hbp.mip.utils.JsonConverters;
+import eu.hbp.mip.utils.Exceptions.InternalServerError;
import lombok.Getter;
import lombok.Setter;
@@ -66,20 +66,20 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("enums")
private List<String> enums;
- public ExaremeAlgorithmRequestDTO convertToexaremeAlgorithmRequestDTO(String name) throws Exception {
- ExaremeAlgorithmRequestDTO exaremeAlgorithmRequestDTO = new ExaremeAlgorithmRequestDTO();
- exaremeAlgorithmRequestDTO.setName(name);
- exaremeAlgorithmRequestDTO.setDesc(this.desc);
- exaremeAlgorithmRequestDTO.setValueType(this.type);
- exaremeAlgorithmRequestDTO.setType("other");
- exaremeAlgorithmRequestDTO.setDefaultValue(this.default_value);
- exaremeAlgorithmRequestDTO.setValueNotBlank(this.notblank);
- exaremeAlgorithmRequestDTO.setLabel(this.label);
- exaremeAlgorithmRequestDTO.setValueEnumerations(this.enums);
- exaremeAlgorithmRequestDTO.setValueMultiple(this.multiple);
- exaremeAlgorithmRequestDTO.setValueMin(this.min);
- exaremeAlgorithmRequestDTO.setValueMax(this.max);
- return exaremeAlgorithmRequestDTO;
+ public ExaremeAlgorithmRequestParamDTO convertToexaremeAlgorithmRequestDTO(String name){
+ ExaremeAlgorithmRequestParamDTO exaremeAlgorithmRequestParamDTO = new ExaremeAlgorithmRequestParamDTO();
+ exaremeAlgorithmRequestParamDTO.setName(name);
+ exaremeAlgorithmRequestParamDTO.setDesc(this.desc);
+ exaremeAlgorithmRequestParamDTO.setValueType(this.type);
+ exaremeAlgorithmRequestParamDTO.setType("other");
+ exaremeAlgorithmRequestParamDTO.setDefaultValue(this.default_value);
+ exaremeAlgorithmRequestParamDTO.setValueNotBlank(this.notblank);
+ exaremeAlgorithmRequestParamDTO.setLabel(this.label);
+ exaremeAlgorithmRequestParamDTO.setValueEnumerations(this.enums);
+ exaremeAlgorithmRequestParamDTO.setValueMultiple(this.multiple);
+ exaremeAlgorithmRequestParamDTO.setValueMin(this.min);
+ exaremeAlgorithmRequestParamDTO.setValueMax(this.max);
+ return exaremeAlgorithmRequestParamDTO;
}
}
@@ -101,14 +101,14 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("filter")
private InputDataDetailDTO filter;
- public List<ExaremeAlgorithmRequestDTO> convertToAlgorithmRequestDTOs() throws Exception {
- List<ExaremeAlgorithmRequestDTO> exaremeAlgorithmRequestDTOS = new ArrayList<>();
- exaremeAlgorithmRequestDTOS.add(this.x.convertToExaremeAlgorithmRequestDTO("x"));
- exaremeAlgorithmRequestDTOS.add(this.y.convertToExaremeAlgorithmRequestDTO("y"));
- exaremeAlgorithmRequestDTOS.add(this.x.convertToExaremeAlgorithmRequestDTO("pathology"));
- exaremeAlgorithmRequestDTOS.add(this.datasets.convertToExaremeAlgorithmRequestDTO("dataset"));
- exaremeAlgorithmRequestDTOS.add(this.filter.convertToExaremeAlgorithmRequestDTO("filter"));
- return exaremeAlgorithmRequestDTOS;
+ public List<ExaremeAlgorithmRequestParamDTO> convertToAlgorithmRequestParamDTOs(){
+ List<ExaremeAlgorithmRequestParamDTO> exaremeAlgorithmRequestParamDTOS = new ArrayList<>();
+ exaremeAlgorithmRequestParamDTOS.add(this.x.convertToExaremeAlgorithmRequestDTO("x"));
+ exaremeAlgorithmRequestParamDTOS.add(this.y.convertToExaremeAlgorithmRequestDTO("y"));
+ exaremeAlgorithmRequestParamDTOS.add(this.pathology.convertToExaremeAlgorithmRequestDTO("pathology"));
+ exaremeAlgorithmRequestParamDTOS.add(this.datasets.convertToExaremeAlgorithmRequestDTO("dataset"));
+ exaremeAlgorithmRequestParamDTOS.add(this.filter.convertToExaremeAlgorithmRequestDTO("filter"));
+ return exaremeAlgorithmRequestParamDTOS;
}
}
@@ -137,28 +137,28 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("desc")
private String desc;
- public ExaremeAlgorithmRequestDTO convertToExaremeAlgorithmRequestDTO(String name) throws Exception {
- ExaremeAlgorithmRequestDTO exaremeAlgorithmRequestDTO = new ExaremeAlgorithmRequestDTO();
- exaremeAlgorithmRequestDTO.setName(name);
- exaremeAlgorithmRequestDTO.setDesc(this.desc);
- exaremeAlgorithmRequestDTO.setValue("");
- exaremeAlgorithmRequestDTO.setValueNotBlank(this.notblank);
- exaremeAlgorithmRequestDTO.setValueMultiple(this.multiple);
+ public ExaremeAlgorithmRequestParamDTO convertToExaremeAlgorithmRequestDTO(String name){
+ ExaremeAlgorithmRequestParamDTO exaremeAlgorithmRequestParamDTO = new ExaremeAlgorithmRequestParamDTO();
+ exaremeAlgorithmRequestParamDTO.setName(name);
+ exaremeAlgorithmRequestParamDTO.setDesc(this.desc);
+ exaremeAlgorithmRequestParamDTO.setValue("");
+ exaremeAlgorithmRequestParamDTO.setValueNotBlank(this.notblank);
+ exaremeAlgorithmRequestParamDTO.setValueMultiple(this.multiple);
String[] hidden = {"x","y","dataset", "filter","pathology","centers","formula"};
- exaremeAlgorithmRequestDTO.setLabel(Arrays.asList(hidden).contains(exaremeAlgorithmRequestDTO.getName()) ? exaremeAlgorithmRequestDTO.getName():this.label);
+ exaremeAlgorithmRequestParamDTO.setLabel(Arrays.asList(hidden).contains(exaremeAlgorithmRequestParamDTO.getName()) ? exaremeAlgorithmRequestParamDTO.getName():this.label);
if(name.equals("dataset") || name.equals("filter") || name.equals("pathology")){
- exaremeAlgorithmRequestDTO.setValueType(this.types.get(0));
- exaremeAlgorithmRequestDTO.setType(exaremeAlgorithmRequestDTO.getName());
+ exaremeAlgorithmRequestParamDTO.setValueType(this.types.get(0));
+ exaremeAlgorithmRequestParamDTO.setType(exaremeAlgorithmRequestParamDTO.getName());
}
else{
- exaremeAlgorithmRequestDTO.setType("column");
- exaremeAlgorithmRequestDTO.setColumnValuesSQLType(String.join(", ", this.types));
- exaremeAlgorithmRequestDTO.setColumnValuesIsCategorical(getColumnValuesIsCategorical(this.stattypes));
+ exaremeAlgorithmRequestParamDTO.setType("column");
+ exaremeAlgorithmRequestParamDTO.setColumnValuesSQLType(String.join(", ", this.types));
+ exaremeAlgorithmRequestParamDTO.setColumnValuesIsCategorical(getColumnValuesIsCategorical(this.stattypes));
}
- return exaremeAlgorithmRequestDTO;
+ return exaremeAlgorithmRequestParamDTO;
}
- private String getColumnValuesIsCategorical(List<String> stattypes) throws Exception {
+ private String getColumnValuesIsCategorical(List<String> stattypes){
if (stattypes.contains("nominal") && stattypes.contains("numerical")){
return "";
@@ -170,7 +170,7 @@ public class MIPEngineAlgorithmDTO {
return "false";
}
else{
- throw new Exception("Invalid stattypes");
+ throw new InternalServerError("Invalid stattypes");
}
}
}
@@ -182,19 +182,10 @@ public class MIPEngineAlgorithmDTO {
exaremeAlgorithmDTO.setLabel(this.label);
exaremeAlgorithmDTO.setDesc(this.desc);
exaremeAlgorithmDTO.setType("mipengine");
- List<ExaremeAlgorithmRequestDTO> parameters = new ArrayList<>();
- try {
- parameters.addAll(this.inputdata.convertToAlgorithmRequestDTOs());
- } catch (Exception e) {
- e.printStackTrace();
- }
+ List<ExaremeAlgorithmRequestParamDTO> parameters = new ArrayList<>(this.inputdata.convertToAlgorithmRequestParamDTOs());
this.parameters.forEach((name, parameterDTO) -> {
- try {
- ExaremeAlgorithmRequestDTO parameter = parameterDTO.convertToexaremeAlgorithmRequestDTO(name);
- parameters.add(parameter);
- } catch (Exception e) {
- e.printStackTrace();
- }
+ ExaremeAlgorithmRequestParamDTO parameter = parameterDTO.convertToexaremeAlgorithmRequestDTO(name);
+ parameters.add(parameter);
});
exaremeAlgorithmDTO.setParameters(parameters);
return exaremeAlgorithmDTO;
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineExperimentDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java
similarity index 96%
rename from src/main/java/eu/hbp/mip/models/DTOs/MIPEngineExperimentDTO.java
rename to src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java
index 46b7df8982f1e8d3f50ac31517489acdf22a8a54..ff8229e372ddd480d58aee2a5c3af36b9536a41f 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineExperimentDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java
@@ -10,7 +10,7 @@ import java.util.List;
@Getter
@Setter
-public class MIPEngineExperimentDTO {
+public class MIPEngineAlgorithmRequestDTO {
@SerializedName("inputdata")
private InputData inputdata;
@SerializedName("parameters")
diff --git a/src/main/java/eu/hbp/mip/models/galaxy/WorkflowDTO.java b/src/main/java/eu/hbp/mip/models/galaxy/WorkflowDTO.java
index edc18117d6660b490a2681cd54b671692ef140e3..eae07531e6f126aa69465a9fcdf6c6cf44c1d267 100644
--- a/src/main/java/eu/hbp/mip/models/galaxy/WorkflowDTO.java
+++ b/src/main/java/eu/hbp/mip/models/galaxy/WorkflowDTO.java
@@ -3,7 +3,7 @@ package eu.hbp.mip.models.galaxy;
import com.google.gson.Gson;
import com.google.gson.annotations.SerializedName;
import eu.hbp.mip.models.DTOs.ExaremeAlgorithmDTO;
-import eu.hbp.mip.models.DTOs.ExaremeAlgorithmRequestDTO;
+import eu.hbp.mip.models.DTOs.ExaremeAlgorithmRequestParamDTO;
import java.util.*;
@@ -115,18 +115,18 @@ public class WorkflowDTO {
exaremeAlgorithmDTO.setType("workflow");
// Transfer workflow parameters information
- List<ExaremeAlgorithmRequestDTO> algorithmParams = new LinkedList<>();
+ List<ExaremeAlgorithmRequestParamDTO> algorithmParams = new LinkedList<>();
Gson gson = new Gson();
for (Map.Entry<String, WorkflowInputDTO> workflowInput : getInputs().entrySet()) {
// Convert the annotation to algorithm Parameter
- ExaremeAlgorithmRequestDTO algorithmParam;
+ ExaremeAlgorithmRequestParamDTO algorithmParam;
if (steps.get(workflowInput.getKey()).getAnnotation() != null) {
algorithmParam = gson.fromJson(steps.get(workflowInput.getKey()).getAnnotation(),
- ExaremeAlgorithmRequestDTO.class);
+ ExaremeAlgorithmRequestParamDTO.class);
} else {
// If annotation is not provided, auto-fill some information
- algorithmParam = new ExaremeAlgorithmRequestDTO();
+ algorithmParam = new ExaremeAlgorithmRequestParamDTO();
// When the constraints are not known, set the most relaxed constraints
algorithmParam.setDesc("");
algorithmParam.setValue("");
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index 587fc7e63adc0a23a182e740028e4b31a1e66e02..3c52503c23ac6976495e3e006e8b765fbb8c9794 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -395,7 +395,7 @@ public class ExperimentService {
private String getDatasetFromExperimentParameters(ExperimentDTO experimentDTO, Logger logger) {
String experimentDatasets = null;
- for (ExaremeAlgorithmRequestDTO parameter : experimentDTO.getAlgorithm().getParameters()) {
+ for (ExaremeAlgorithmRequestParamDTO parameter : experimentDTO.getAlgorithm().getParameters()) {
if (parameter.getLabel().equals("dataset")) {
experimentDatasets = parameter.getValue();
break;
@@ -531,14 +531,14 @@ public class ExperimentService {
// Run with the appropriate engine
if (algorithmType.equals("mipengine")) {
- MIPEngineExperimentDTO mipEngineExperimentDTO = experimentDTO.getAlgorithm().convertToMIPEngineBody();
- String body = JsonConverters.convertObjectToJsonString(mipEngineExperimentDTO);
+ MIPEngineAlgorithmRequestDTO mipEngineAlgorithmRequestDTO = experimentDTO.getAlgorithm().convertToMIPEngineBody();
+ String body = JsonConverters.convertObjectToJsonString(mipEngineAlgorithmRequestDTO);
String url = mipengineAlgorithmsUrl + "/" + algorithmName.toLowerCase();
logger.LogUserAction("url: " + url + ", body: " + body);
logger.LogUserAction("Algorithm runs on MIPEngine.");
return runMIPEngineExperiment(url, body);
} else {
- List<ExaremeAlgorithmRequestDTO> algorithmParameters
+ List<ExaremeAlgorithmRequestParamDTO> algorithmParameters
= experimentDTO.getAlgorithm().getParameters();
String body = gson.toJson(algorithmParameters);
String url = queryExaremeUrl + "/" + algorithmName;
@@ -636,7 +636,7 @@ public class ExperimentService {
}
finishExperiment(experimentDAO, logger);
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Finished the experiment: " + experimentDAO.toString());
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Finished the experiment: " + experimentDAO);
}).start();
experimentDTO = experimentDAO.convertToDTO(true);
return experimentDTO;
@@ -662,13 +662,13 @@ public class ExperimentService {
String workflowId = experimentDTO.getAlgorithm().getName();
// Get the parameters
- List<ExaremeAlgorithmRequestDTO> algorithmParameters
+ List<ExaremeAlgorithmRequestParamDTO> algorithmParameters
= experimentDTO.getAlgorithm().getParameters();
// Convert the parameters to workflow parameters
HashMap<String, String> algorithmParamsIncludingEmpty = new HashMap<>();
if (algorithmParameters != null) {
- for (ExaremeAlgorithmRequestDTO param : algorithmParameters) {
+ for (ExaremeAlgorithmRequestParamDTO param : algorithmParameters) {
algorithmParamsIncludingEmpty.put(param.getName(), param.getValue());
}
}