From 30c06d2e0d526257f70ee9e8bcde3c1da2e3db6f Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Fri, 4 Jun 2021 03:28:08 -0700
Subject: [PATCH 01/12] Mip engine integration first touce
---
docker/README.md | 2 +
docker/config/application.tmpl | 3 +
.../eu/hbp/mip/controllers/AlgorithmsAPI.java | 50 ++++++-
.../models/DTOs/MIPEngineAlgorithmDTO.java | 119 +++++++++++++++++
.../hbp/mip/services/ExperimentService.java | 123 ++++++++++++------
src/main/resources/application.yml | 2 +
6 files changed, 254 insertions(+), 45 deletions(-)
create mode 100644 src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
diff --git a/docker/README.md b/docker/README.md
index 9636ff324..8693aad09 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -24,6 +24,8 @@ To use this image, you need a running instance of PostgreSQL and to configure th
### EXTERNAL SERVICES ###
+* MIPENGINE_URL: URL to MIPENGINE server. Default is "http://localhost:5000" .
+
* EXAREME_URL: URL to Exareme server. Default is "http://localhost:9090" .
* GALAXY_URL: URL to Workflow server. Default is "http://localhost:8090/" .
diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index ae10744aa..0913c99e7 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -34,6 +34,9 @@ spring:
### EXTERNAL SERVICES ###
services:
+ mipengine:
+ algorithmsUrl: {{ default .Env.MIPENGINE_URL "http://localhost:5000" }}/algorithms
+
exareme:
queryExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query
algorithmsUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/algorithms.json
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index 48500bb10..1ca68f13b 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -9,6 +9,7 @@ import com.google.gson.reflect.TypeToken;
import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
import eu.hbp.mip.models.DTOs.AlgorithmDTO;
+import eu.hbp.mip.models.DTOs.MIPEngineAlgorithmDTO;
import eu.hbp.mip.models.galaxy.WorkflowDTO;
import eu.hbp.mip.services.ActiveUserService;
import eu.hbp.mip.utils.CustomResourceLoader;
@@ -42,6 +43,9 @@ public class AlgorithmsAPI {
private final ActiveUserService activeUserService;
+ @Value("#{'${services.mipengine.algorithmsUrl}'}")
+ private String mipengineAlgorithmsUrl;
+
@Value("#{'${services.exareme.algorithmsUrl}'}")
private String exaremeAlgorithmsUrl;
@@ -64,8 +68,9 @@ public class AlgorithmsAPI {
public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /algorithms");
- logger.LogUserAction("Executing...");
-
+// logger.LogUserAction("Executing...");
+ LinkedList<AlgorithmDTO> mipengineAlgorithms = getMIPEngineAlgorithms(logger);
+ logger.LogUserAction("Loaded " + mipengineAlgorithms.size() + " mipengine algorithms");
LinkedList<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms(logger);
logger.LogUserAction("Loaded " + exaremeAlgorithms.size() + " exareme algorithms");
LinkedList<AlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows(logger);
@@ -73,12 +78,17 @@ public class AlgorithmsAPI {
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
if (exaremeAlgorithms != null) {
- algorithms.addAll(exaremeAlgorithms);
+// algorithms.addAll(exaremeAlgorithms);
} else {
logger.LogUserAction("Getting exareme algorithms failed and returned null");
}
+ if (mipengineAlgorithms != null) {
+ algorithms.addAll(mipengineAlgorithms);
+ } else {
+ logger.LogUserAction("Getting mipengine algorithms failed and returned null");
+ }
if (galaxyAlgorithms != null) {
- algorithms.addAll(galaxyAlgorithms);
+// algorithms.addAll(galaxyAlgorithms);
} else {
logger.LogUserAction("Getting galaxy workflows failed and returned null");
}
@@ -112,7 +122,6 @@ public class AlgorithmsAPI {
try {
StringBuilder response = new StringBuilder();
HTTPUtil.sendGet(exaremeAlgorithmsUrl, response);
-
algorithms = gson.fromJson(
response.toString(),
new TypeToken<LinkedList<AlgorithmDTO>>() {
@@ -127,6 +136,37 @@ public class AlgorithmsAPI {
return algorithms;
}
+ /**
+ * This method gets all the available mipengine algorithms and
+ *
+ * @return a list of AlgorithmDTOs or null if something fails
+ */
+ public LinkedList<AlgorithmDTO> getMIPEngineAlgorithms(Logger logger) {
+ LinkedList<MIPEngineAlgorithmDTO> mipEngineAlgorithms;
+ // Get MIPEngine algorithms
+ try {
+ StringBuilder response = new StringBuilder();
+ HTTPUtil.sendGet(mipengineAlgorithmsUrl, response);
+ logger.LogUserAction(response.toString());
+
+ mipEngineAlgorithms = gson.fromJson(
+ response.toString(),
+ new TypeToken<LinkedList<MIPEngineAlgorithmDTO>>() {
+ }.getType()
+ );
+ } catch (IOException e) {
+ logger.LogUserAction("An exception occurred: " + e.getMessage());
+ return null;
+ }
+
+
+ LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
+ mipEngineAlgorithms.forEach(mipEngineAlgorithm -> algorithms.add(mipEngineAlgorithm.convertToAlgorithmDTO()));
+
+ logger.LogUserAction("Completed, returned " + algorithms.size() + " algorithms.");
+ return algorithms;
+ }
+
/**
* This method gets all the available galaxy workflows, converts them into algorithms and
*
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
new file mode 100644
index 000000000..a250e4249
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
@@ -0,0 +1,119 @@
+package eu.hbp.mip.models.DTOs;
+
+import com.google.gson.annotations.SerializedName;
+import lombok.Getter;
+import lombok.Setter;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
+@Getter
+@Setter
+public class MIPEngineAlgorithmDTO {
+
+ @SerializedName("name")
+ private String name;
+
+ @SerializedName("desc")
+ private String desc;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("parameters")
+ private Object parameters;
+
+ @SerializedName("crossvalidation")
+ private String crossvalidation;
+
+ @SerializedName("inputdata")
+ private Hashtable<String, InputDataParamDTO> inputdata;
+
+ @Getter
+ @Setter
+ public static class InputDataParamDTO {
+
+ @SerializedName("stattypes")
+ private List<String> stattypes;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("notblank")
+ private String notblank;
+
+ @SerializedName("enumslen")
+ private Integer enumslen;
+
+ @SerializedName("multiple")
+ private String multiple;
+
+ @SerializedName("types")
+ private List<String> types;
+
+ @SerializedName("desc")
+ private String desc;
+ public AlgorithmDTO.AlgorithmParamDTO convertToAlgorithmParamDTO(String name) throws Exception {
+ AlgorithmDTO.AlgorithmParamDTO algorithmParamDTO = new AlgorithmDTO.AlgorithmParamDTO();
+ algorithmParamDTO.setName(name);
+ algorithmParamDTO.setDesc(this.desc);
+ algorithmParamDTO.setLabel(this.label);
+ if(name.equals("datasets") || name.equals("filter") || name.equals("pathology")){
+ algorithmParamDTO.setType(name.equals("datasets")? "dataset":name);
+ algorithmParamDTO.setValueType(this.types.get(0));
+ }
+ else{
+ if(stattypes == null){
+ System.out.println("Dsafasfads------------------------->>>>>>>>>>>>>>>");
+ System.out.println(name);
+ }
+ algorithmParamDTO.setType("column");
+ algorithmParamDTO.setColumnValuesSQLType(String.join(", ", this.types));
+ algorithmParamDTO.setColumnValuesIsCategorical(getColumnValuesIsCategorical(this.stattypes));
+ }
+ algorithmParamDTO.setValue("");
+ algorithmParamDTO.setValueNotBlank(this.notblank);
+ algorithmParamDTO.setValueMultiple(this.multiple);
+ return algorithmParamDTO;
+ }
+ private String getColumnValuesIsCategorical(List<String> stattypes) throws Exception {
+
+ if (stattypes.contains("nominal") && stattypes.contains("numerical")){
+ return "";
+ }
+ else if (stattypes.contains("nominal")){
+ return "true";
+ }
+ else if (stattypes.contains("numerical")){
+ return "false";
+ }
+ else{
+ throw new Exception("Invalid stattypes");
+ }
+ }
+ }
+
+ public AlgorithmDTO convertToAlgorithmDTO()
+ {
+ AlgorithmDTO algorithmDTO = new AlgorithmDTO();
+ algorithmDTO.setName(this.name);
+ algorithmDTO.setLabel(this.label);
+ algorithmDTO.setDesc(this.desc);
+ algorithmDTO.setType("mipengine");
+ List<AlgorithmDTO.AlgorithmParamDTO> parameters = new ArrayList<>();
+ this.inputdata.forEach((name, inputDataParamDTO) -> {
+ try {
+ AlgorithmDTO.AlgorithmParamDTO parameter = inputDataParamDTO.convertToAlgorithmParamDTO(name);
+ parameters.add(parameter);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ });
+ algorithmDTO.setParameters(parameters);
+ return algorithmDTO;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index 45345c8a5..a8b176d76 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -50,6 +50,9 @@ public class ExperimentService {
@Value("#{'${services.exareme.queryExaremeUrl}'}")
private String queryExaremeUrl;
+ @Value("#{'${services.mipengine.algorithmsUrl}'}")
+ private String mipengineAlgorithmsUrl;
+
@Value("#{'${services.galaxy.galaxyUrl}'}")
private String galaxyUrl;
@@ -194,7 +197,7 @@ public class ExperimentService {
return runGalaxyWorkflow(experimentDTO, logger);
} else {
logger.LogUserAction("Algorithm runs on Exareme.");
- return createExaremeExperiment(experimentDTO, logger);
+ return createExperiment(experimentDTO, logger);
}
}
@@ -219,13 +222,6 @@ public class ExperimentService {
throw new BadRequestException("You can not run workflow algorithms transiently.");
}
- // Get the parameters
- List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
- = experimentDTO.getAlgorithm().getParameters();
-
- // Get the type and name of algorithm
- String algorithmName = experimentDTO.getAlgorithm().getName();
-
algorithmParametersLogging(experimentDTO, logger);
if (authenticationIsEnabled) {
@@ -233,19 +229,15 @@ public class ExperimentService {
ClaimUtils.validateAccessRightsOnDatasets(authentication, experimentDatasets, logger);
}
- String body = gson.toJson(algorithmParameters);
- String url = queryExaremeUrl + "/" + algorithmName;
- logger.LogUserAction("url: " + url + ", body: " + body);
-
- logger.LogUserAction("Completed, returning: " + experimentDTO.toString());
+ logger.LogUserAction("Completed, returning: " + experimentDTO);
// Results are stored in the experiment object
- ExaremeResult exaremeResult = runExaremeExperiment(url, body, experimentDTO);
+ ExperimentResult experimentResult = runExperiment(experimentDTO, logger);
- logger.LogUserAction("Experiment with uuid: " + experimentDTO.getUuid() + "gave response code: " + exaremeResult.getCode() + " and result: " + exaremeResult.getResults());
+ logger.LogUserAction("Experiment with uuid: " + experimentDTO.getUuid() + "gave response code: " + experimentResult.getCode() + " and result: " + experimentResult.getResults());
- experimentDTO.setResult((exaremeResult.getCode() >= 400) ? null : exaremeResult.getResults());
- experimentDTO.setStatus((exaremeResult.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
+ experimentDTO.setResult((experimentResult.getCode() >= 400) ? null : experimentResult.getResults());
+ experimentDTO.setStatus((experimentResult.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
return experimentDTO;
}
@@ -514,15 +506,52 @@ public class ExperimentService {
return JsonConverters.convertObjectToJsonString(finalJsonObject);
}
+ /**
+ * The runExperiment will run the experiment to exareme or MIPEngine.
+ *
+ * @param experimentDTO is the request with the experiment information
+ * @return the result of experiment as well as the http status that was retrieved
+ */
+ public ExperimentResult runExperiment(ExperimentDTO experimentDTO, Logger logger) {
+
+ // Algorithm type
+ String algorithmType = experimentDTO.getAlgorithm().getType();
+
+ // Run the 1st algorithm from the list
+ String algorithmName = experimentDTO.getAlgorithm().getName();
+
+ // Get the parameters
+ List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
+ = experimentDTO.getAlgorithm().getParameters();
+
+ String body = gson.toJson(algorithmParameters);
+
+ logger.LogUserAction("Completed, returning: " + experimentDTO);
+
+
+ // Run with the appropriate engine
+ if (algorithmType.equals("mipengine")) {
+ String url = mipengineAlgorithmsUrl + "/" + algorithmName;
+ logger.LogUserAction("url: " + url + ", body: " + body);
+ logger.LogUserAction("Algorithm runs on MIPEngine.");
+ return runMIPEngineExperiment(url, body);
+ } else {
+ String url = queryExaremeUrl + "/" + algorithmName;
+ logger.LogUserAction("url: " + url + ", body: " + body);
+ logger.LogUserAction("Algorithm runs on Exareme.");
+ return runExaremeExperiment(url, body);
+ }
+ }
+
+
/**
* 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) {
+ public ExperimentResult runExaremeExperiment(String url, String body) {
StringBuilder results = new StringBuilder();
int code;
@@ -536,7 +565,32 @@ public class ExperimentService {
ExperimentDTO experimentDTOWithOnlyResult = JsonConverters.convertJsonStringToObject(String.valueOf(results), ExperimentDTO.class);
List<Object> resultDTOS = experimentDTOWithOnlyResult.getResult();
- return new ExaremeResult(code, resultDTOS);
+ return new ExperimentResult(code, resultDTOS);
+ }
+
+ /**
+ * 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
+ * @return the result of exareme as well as the http status that was retrieved
+ */
+ public ExperimentResult runMIPEngineExperiment(String url, String body) {
+
+ StringBuilder results = new StringBuilder();
+ int code;
+ try {
+ code = HTTPUtil.sendPost(url, body, results);
+ } catch (Exception e) {
+ throw new InternalServerError("Error occurred : " + e.getMessage());
+ }
+ System.out.println("----------------------------------->>>>>>>>>>>>>>>>>>>>>>");
+ System.out.println(results);
+ // Results are stored in the experiment object
+ ExperimentDTO experimentDTOWithOnlyResult = JsonConverters.convertJsonStringToObject(String.valueOf(results), ExperimentDTO.class);
+ List<Object> resultDTOS = experimentDTOWithOnlyResult.getResult();
+
+ return new ExperimentResult(code, resultDTOS);
}
/* -------------------------------------- EXAREME CALLS ---------------------------------------------------------*/
@@ -548,27 +602,15 @@ public class ExperimentService {
* @param logger contains username and the endpoint.
* @return the experiment information that was retrieved from exareme
*/
- public ExperimentDTO createExaremeExperiment(ExperimentDTO experimentDTO, Logger logger) {
+ public ExperimentDTO createExperiment(ExperimentDTO experimentDTO, Logger logger) {
logger.LogUserAction("Running the algorithm...");
ExperimentDAO experimentDAO = createExperimentInTheDatabase(experimentDTO, logger);
logger.LogUserAction("Created experiment with uuid :" + experimentDAO.getUuid());
- // Run the 1st algorithm from the list
- String algorithmName = experimentDTO.getAlgorithm().getName();
-
- // Get the parameters
- List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
- = experimentDTO.getAlgorithm().getParameters();
-
- String body = gson.toJson(algorithmParameters);
- String url = queryExaremeUrl + "/" + algorithmName;
- logger.LogUserAction("url: " + url + ", body: " + body);
-
- logger.LogUserAction("Completed, returning: " + experimentDTO.toString());
- logger.LogUserAction("Starting exareme execution thread");
+ logger.LogUserAction("Starting execution in thread");
ExperimentDTO finalExperimentDTO = experimentDTO;
new Thread(() -> {
@@ -576,13 +618,14 @@ public class ExperimentService {
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Thread named :" + Thread.currentThread().getName() + " with id :" + Thread.currentThread().getId() + " started!");
try {
+
// Results are stored in the experiment object
- ExaremeResult exaremeResult = runExaremeExperiment(url, body, finalExperimentDTO);
+ ExperimentResult experimentResult = runExperiment(finalExperimentDTO, logger);
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Experiment with uuid: " + experimentDAO.getUuid() + "gave response code: " + exaremeResult.getCode() + " and result: " + exaremeResult.getResults());
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Experiment with uuid: " + experimentDAO.getUuid() + "gave response code: " + experimentResult.getCode() + " and result: " + experimentResult.getResults());
- experimentDAO.setResult((exaremeResult.getCode() >= 400) ? null : JsonConverters.convertObjectToJsonString(exaremeResult.getResults()));
- experimentDAO.setStatus((exaremeResult.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
+ experimentDAO.setResult((experimentResult.getCode() >= 400) ? null : JsonConverters.convertObjectToJsonString(experimentResult.getResults()));
+ experimentDAO.setStatus((experimentResult.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
} catch (Exception e) {
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "There was an exception: " + e.getMessage());
@@ -988,11 +1031,11 @@ public class ExperimentService {
return returnError;
}
- static class ExaremeResult {
+ static class ExperimentResult {
private final int code;
private final List<Object> results;
- public ExaremeResult(int code, List<Object> results) {
+ public ExperimentResult(int code, List<Object> results) {
this.code = code;
this.results = results;
}
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index 345fc4bfa..d8d542b6b 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -34,6 +34,8 @@ spring:
### EXTERNAL SERVICES ###
services:
+ mipengine:
+ algorithmsUrl: "http://127.0.0.1:5000/algorithms"
exareme:
queryExaremeUrl: "http://127.0.0.1:9090/mining/query"
algorithmsUrl: "http://127.0.0.1:9090/mining/algorithms.json"
--
GitLab
From af5828b2e6fd108996c4c966aef9d0a25a2990f8 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Wed, 16 Jun 2021 03:25:12 -0700
Subject: [PATCH 02/12] Implemented adaptor for get /algorithms from MIPEngine
and post /algorithms/{alogrithm_name}
---
.../eu/hbp/mip/models/DTOs/AlgorithmDTO.java | 24 ++++++++++++++
.../models/DTOs/MIPEngineAlgorithmDTO.java | 7 ++---
.../eu/hbp/mip/models/DTOs/MIPEngineBody.java | 31 +++++++++++++++++++
.../hbp/mip/services/ExperimentService.java | 31 +++++++++++--------
4 files changed, 75 insertions(+), 18 deletions(-)
create mode 100644 src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
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 52db979d5..47e6f3ddf 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
@@ -1,9 +1,12 @@
package eu.hbp.mip.models.DTOs;
+import com.google.gson.Gson;
import com.google.gson.annotations.SerializedName;
import lombok.Getter;
import lombok.Setter;
+import java.util.Arrays;
+import java.util.Hashtable;
import java.util.List;
@Getter
@@ -70,4 +73,25 @@ public class AlgorithmDTO {
@SerializedName("valueEnumerations")
private List<String> valueEnumerations;
}
+
+ public MIPEngineBody convertToMIPEngineBody()
+ {
+ MIPEngineBody mipEngineBody = new MIPEngineBody();
+ MIPEngineBody.InputData inputData = new MIPEngineBody.InputData();
+
+ this.parameters.forEach(parameter -> {
+ if(parameter.getName().equals("x"))
+ inputData.setX(Arrays.asList(parameter.getValue().split(",")));
+ if(parameter.getName().equals("y"))
+ inputData.setY(Arrays.asList(parameter.getValue().split(",")));
+ if(parameter.getName().equals("dataset"))
+ inputData.setDatasets(Arrays.asList(parameter.getValue().split(",")));
+ if(parameter.getName().equals("pathology"))
+ inputData.setPathology(parameter.getValue());
+ if(parameter.getName().equals("filter"))
+ inputData.setFilters(null);
+ });
+ mipEngineBody.setInputdata(inputData);
+ return mipEngineBody;
+ }
}
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 a250e4249..386195dab 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
@@ -25,7 +25,7 @@ public class MIPEngineAlgorithmDTO {
private String type;
@SerializedName("parameters")
- private Object parameters;
+ private InputDataParamDTO parameters;
@SerializedName("crossvalidation")
private String crossvalidation;
@@ -57,6 +57,7 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("desc")
private String desc;
+
public AlgorithmDTO.AlgorithmParamDTO convertToAlgorithmParamDTO(String name) throws Exception {
AlgorithmDTO.AlgorithmParamDTO algorithmParamDTO = new AlgorithmDTO.AlgorithmParamDTO();
algorithmParamDTO.setName(name);
@@ -67,10 +68,6 @@ public class MIPEngineAlgorithmDTO {
algorithmParamDTO.setValueType(this.types.get(0));
}
else{
- if(stattypes == null){
- System.out.println("Dsafasfads------------------------->>>>>>>>>>>>>>>");
- System.out.println(name);
- }
algorithmParamDTO.setType("column");
algorithmParamDTO.setColumnValuesSQLType(String.join(", ", this.types));
algorithmParamDTO.setColumnValuesIsCategorical(getColumnValuesIsCategorical(this.stattypes));
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
new file mode 100644
index 000000000..bbae5f4a0
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
@@ -0,0 +1,31 @@
+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 MIPEngineBody {
+ @SerializedName("inputdata")
+ private InputData inputdata;
+ @SerializedName("parameters")
+ private Object parameters;
+
+ @Getter
+ @Setter
+ public static class InputData {
+ @SerializedName("pathology")
+ private String pathology;
+ @SerializedName("datasets")
+ private List<String> datasets;
+ @SerializedName("filters")
+ private String filters;
+ @SerializedName("x")
+ private List<String> x;
+ @SerializedName("y")
+ private List<String> y;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index a8b176d76..0179d824e 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -17,6 +17,7 @@ import eu.hbp.mip.models.DAOs.ExperimentDAO;
import eu.hbp.mip.models.DAOs.UserDAO;
import eu.hbp.mip.models.DTOs.AlgorithmDTO;
import eu.hbp.mip.models.DTOs.ExperimentDTO;
+import eu.hbp.mip.models.DTOs.MIPEngineBody;
import eu.hbp.mip.models.galaxy.GalaxyWorkflowResult;
import eu.hbp.mip.models.galaxy.PostWorkflowToGalaxyDtoResponse;
import eu.hbp.mip.repositories.ExperimentRepository;
@@ -506,6 +507,17 @@ public class ExperimentService {
return JsonConverters.convertObjectToJsonString(finalJsonObject);
}
+ private List<Object> formattingMIPEngienResult(String result) {
+ List<List<String>> resultJson = JsonConverters.convertJsonStringToObject(result, new ArrayList<ArrayList<String>>().getClass());
+ List<Object> finalObject = new ArrayList<>();
+ LinkedTreeMap<String,Object> data = new LinkedTreeMap<>();
+ data.put("data", resultJson);
+ data.put("type", "application/json");
+ finalObject.add(data);
+ List<Object> result_kappa = finalObject;
+ return result_kappa;
+ }
+
/**
* The runExperiment will run the experiment to exareme or MIPEngine.
*
@@ -520,22 +532,18 @@ public class ExperimentService {
// Run the 1st algorithm from the list
String algorithmName = experimentDTO.getAlgorithm().getName();
- // Get the parameters
- List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
- = experimentDTO.getAlgorithm().getParameters();
-
- String body = gson.toJson(algorithmParameters);
-
- logger.LogUserAction("Completed, returning: " + experimentDTO);
-
-
// Run with the appropriate engine
if (algorithmType.equals("mipengine")) {
+ MIPEngineBody mipEngineBody = experimentDTO.getAlgorithm().convertToMIPEngineBody();
+ String body = gson.toJson(mipEngineBody);
String url = mipengineAlgorithmsUrl + "/" + algorithmName;
logger.LogUserAction("url: " + url + ", body: " + body);
logger.LogUserAction("Algorithm runs on MIPEngine.");
return runMIPEngineExperiment(url, body);
} else {
+ List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
+ = experimentDTO.getAlgorithm().getParameters();
+ String body = gson.toJson(algorithmParameters);
String url = queryExaremeUrl + "/" + algorithmName;
logger.LogUserAction("url: " + url + ", body: " + body);
logger.LogUserAction("Algorithm runs on Exareme.");
@@ -584,11 +592,8 @@ public class ExperimentService {
} catch (Exception e) {
throw new InternalServerError("Error occurred : " + e.getMessage());
}
- System.out.println("----------------------------------->>>>>>>>>>>>>>>>>>>>>>");
- System.out.println(results);
// Results are stored in the experiment object
- ExperimentDTO experimentDTOWithOnlyResult = JsonConverters.convertJsonStringToObject(String.valueOf(results), ExperimentDTO.class);
- List<Object> resultDTOS = experimentDTOWithOnlyResult.getResult();
+ List<Object> resultDTOS = formattingMIPEngienResult(String.valueOf(results));
return new ExperimentResult(code, resultDTOS);
}
--
GitLab
From 89c85f06535616f9582b487ced1dcea129827865 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Wed, 16 Jun 2021 11:38:48 -0700
Subject: [PATCH 03/12] Added visualzation
---
.../eu/hbp/mip/models/DTOs/AlgorithmDTO.java | 4 +---
.../hbp/mip/services/ExperimentService.java | 20 ++++++++++++++-----
src/main/resources/application.yml | 2 +-
3 files changed, 17 insertions(+), 9 deletions(-)
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 47e6f3ddf..2297ae9be 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
@@ -84,12 +84,10 @@ public class AlgorithmDTO {
inputData.setX(Arrays.asList(parameter.getValue().split(",")));
if(parameter.getName().equals("y"))
inputData.setY(Arrays.asList(parameter.getValue().split(",")));
- if(parameter.getName().equals("dataset"))
+ if(parameter.getName().equals("datasets"))
inputData.setDatasets(Arrays.asList(parameter.getValue().split(",")));
if(parameter.getName().equals("pathology"))
inputData.setPathology(parameter.getValue());
- if(parameter.getName().equals("filter"))
- inputData.setFilters(null);
});
mipEngineBody.setInputdata(inputData);
return mipEngineBody;
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index 0179d824e..bafa71d01 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -509,13 +509,22 @@ public class ExperimentService {
private List<Object> formattingMIPEngienResult(String result) {
List<List<String>> resultJson = JsonConverters.convertJsonStringToObject(result, new ArrayList<ArrayList<String>>().getClass());
- List<Object> finalObject = new ArrayList<>();
+ String schema_json = "{\"fields\":[{\"type\":\"string\",\"name\":\"node\"},{\"type\":\"number\",\"name\":\"row-id\"},{\"type\":\"number\",\"name\":\"alzheimerbroadcategory_bin\"}]}";
+ LinkedTreeMap<String,List<Object>> schema = JsonConverters.convertJsonStringToObject(schema_json, new LinkedTreeMap<String,ArrayList<Object>>().getClass());
+
+
+ LinkedTreeMap<String,Object> data_data = new LinkedTreeMap<>();
+ data_data.put("data", resultJson);
+ data_data.put("profile", "tabular-data-resource");
+ data_data.put("schema", schema);
+ data_data.put("name","Logistic Regression Stuff");
+
LinkedTreeMap<String,Object> data = new LinkedTreeMap<>();
- data.put("data", resultJson);
- data.put("type", "application/json");
+ data.put("data", data_data);
+ data.put("type", "application/vnd.dataresource+json");
+ List<Object> finalObject = new ArrayList<>();
finalObject.add(data);
- List<Object> result_kappa = finalObject;
- return result_kappa;
+ return finalObject;
}
/**
@@ -592,6 +601,7 @@ public class ExperimentService {
} catch (Exception e) {
throw new InternalServerError("Error occurred : " + e.getMessage());
}
+ System.out.println(results);
// Results are stored in the experiment object
List<Object> resultDTOS = formattingMIPEngienResult(String.valueOf(results));
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index d8d542b6b..660671108 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -11,7 +11,7 @@ logging:
### AUTHENTICATION ###
authentication:
- enabled: false
+ enabled: true
### DATABASE CONFIGURATION ###
--
GitLab
From e4ee5adea5b51c7d9ad54198f55d85df592cddf8 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Tue, 29 Jun 2021 03:41:24 -0700
Subject: [PATCH 04/12] Added the filtering on rows which have null values
---
.../eu/hbp/mip/models/DTOs/AlgorithmDTO.java | 81 ++++++++++++++++---
.../models/DTOs/MIPEngineAlgorithmDTO.java | 2 +-
.../eu/hbp/mip/models/DTOs/MIPEngineBody.java | 2 +-
.../hbp/mip/services/ExperimentService.java | 5 +-
4 files changed, 75 insertions(+), 15 deletions(-)
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 2297ae9be..216140ba2 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
@@ -1,13 +1,11 @@
package eu.hbp.mip.models.DTOs;
-import com.google.gson.Gson;
import com.google.gson.annotations.SerializedName;
+import eu.hbp.mip.utils.JsonConverters;
import lombok.Getter;
import lombok.Setter;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
+import java.util.*;
@Getter
@Setter
@@ -74,21 +72,84 @@ public class AlgorithmDTO {
private List<String> valueEnumerations;
}
+ @Getter
+ @Setter
+ public static class Rule
+ {
+ @SerializedName("id")
+ private String id;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("operator")
+ private String operator;
+
+ @SerializedName("value")
+ private Object value;
+
+ public Rule(String id, String type, String operator, Object value) {
+ this.id = id;
+ this.type = type;
+ this.operator = operator;
+ this.value = value;
+ }
+ }
+
+ @Getter
+ @Setter
+ public static class Filters
+ {
+ @SerializedName("condition")
+ private String condition;
+
+ @SerializedName("rules")
+ private List<Object> rules;
+
+ @SerializedName("valid")
+ private boolean valid;
+
+ public Filters(String condition, List<Object> rules, boolean valid) {
+ this.condition = condition;
+ this.rules = rules;
+ this.valid = valid;
+ }
+ }
+
+
public MIPEngineBody convertToMIPEngineBody()
{
MIPEngineBody mipEngineBody = new MIPEngineBody();
MIPEngineBody.InputData inputData = new MIPEngineBody.InputData();
+ List<Object> rules = new ArrayList<>();
this.parameters.forEach(parameter -> {
- if(parameter.getName().equals("x"))
- inputData.setX(Arrays.asList(parameter.getValue().split(",")));
- if(parameter.getName().equals("y"))
- inputData.setY(Arrays.asList(parameter.getValue().split(",")));
- if(parameter.getName().equals("datasets"))
- inputData.setDatasets(Arrays.asList(parameter.getValue().split(",")));
+ 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);
+ }
+ 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);
+ }
+ if(parameter.getName().equals("dataset")){
+ List<String> datasets = Arrays.asList(parameter.getValue().split(","));
+ rules.add(new Rule("dataset","string", "in", datasets));
+ inputData.setDatasets(datasets);
+ }
+ String pathology;
if(parameter.getName().equals("pathology"))
inputData.setPathology(parameter.getValue());
+
+ if(parameter.getName().equals("filter")){
+ if (parameter.getValue() != "")
+ rules.add(JsonConverters.convertJsonStringToObject(parameter.getValue(), Filters.class));
+ }
});
+ Filters filters = new Filters("AND", rules, true);
+ inputData.setFilters(filters);
mipEngineBody.setInputdata(inputData);
return mipEngineBody;
}
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 386195dab..4400ff9e7 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
@@ -97,7 +97,7 @@ public class MIPEngineAlgorithmDTO {
public AlgorithmDTO convertToAlgorithmDTO()
{
AlgorithmDTO algorithmDTO = new AlgorithmDTO();
- algorithmDTO.setName(this.name);
+ algorithmDTO.setName(this.name.toUpperCase());
algorithmDTO.setLabel(this.label);
algorithmDTO.setDesc(this.desc);
algorithmDTO.setType("mipengine");
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
index bbae5f4a0..b8b2f957a 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
@@ -22,7 +22,7 @@ public class MIPEngineBody {
@SerializedName("datasets")
private List<String> datasets;
@SerializedName("filters")
- private String filters;
+ private AlgorithmDTO.Filters filters;
@SerializedName("x")
private List<String> x;
@SerializedName("y")
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index bafa71d01..bc7f4dd11 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -544,8 +544,8 @@ public class ExperimentService {
// Run with the appropriate engine
if (algorithmType.equals("mipengine")) {
MIPEngineBody mipEngineBody = experimentDTO.getAlgorithm().convertToMIPEngineBody();
- String body = gson.toJson(mipEngineBody);
- String url = mipengineAlgorithmsUrl + "/" + algorithmName;
+ String body = JsonConverters.convertObjectToJsonString(mipEngineBody);
+ String url = mipengineAlgorithmsUrl + "/" + algorithmName.toLowerCase();
logger.LogUserAction("url: " + url + ", body: " + body);
logger.LogUserAction("Algorithm runs on MIPEngine.");
return runMIPEngineExperiment(url, body);
@@ -601,7 +601,6 @@ public class ExperimentService {
} catch (Exception e) {
throw new InternalServerError("Error occurred : " + e.getMessage());
}
- System.out.println(results);
// Results are stored in the experiment object
List<Object> resultDTOS = formattingMIPEngienResult(String.valueOf(results));
--
GitLab
From 9606ee4d91404b5cfa33b9e15bf11737ebcdcbd9 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Thu, 1 Jul 2021 04:00:05 -0700
Subject: [PATCH 05/12] Proper url for mip engine
---
docker/README.md | 2 +-
docker/config/application.tmpl | 2 +-
.../eu/hbp/mip/controllers/AlgorithmsAPI.java | 6 +++---
.../mip/models/DTOs/MIPEngineAlgorithmDTO.java | 16 +++++++++++++---
src/main/resources/application.yml | 4 ++--
5 files changed, 20 insertions(+), 10 deletions(-)
diff --git a/docker/README.md b/docker/README.md
index 8693aad09..36a3e1245 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -24,7 +24,7 @@ To use this image, you need a running instance of PostgreSQL and to configure th
### EXTERNAL SERVICES ###
-* MIPENGINE_URL: URL to MIPENGINE server. Default is "http://localhost:5000" .
+* MIPENGINE_URL: URL to MIPENGINE server. Default is "http://192.168.124.129:5000" .
* EXAREME_URL: URL to Exareme server. Default is "http://localhost:9090" .
diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 0913c99e7..6059a902b 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -35,7 +35,7 @@ spring:
### EXTERNAL SERVICES ###
services:
mipengine:
- algorithmsUrl: {{ default .Env.MIPENGINE_URL "http://localhost:5000" }}/algorithms
+ algorithmsUrl: {{ default .Env.MIPENGINE_URL "http://192.168.124.129:5000" }}/algorithms
exareme:
queryExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index 1ca68f13b..68eb31340 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -68,7 +68,7 @@ public class AlgorithmsAPI {
public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /algorithms");
-// logger.LogUserAction("Executing...");
+ logger.LogUserAction("Executing...");
LinkedList<AlgorithmDTO> mipengineAlgorithms = getMIPEngineAlgorithms(logger);
logger.LogUserAction("Loaded " + mipengineAlgorithms.size() + " mipengine algorithms");
LinkedList<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms(logger);
@@ -78,7 +78,7 @@ public class AlgorithmsAPI {
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
if (exaremeAlgorithms != null) {
-// algorithms.addAll(exaremeAlgorithms);
+ algorithms.addAll(exaremeAlgorithms);
} else {
logger.LogUserAction("Getting exareme algorithms failed and returned null");
}
@@ -242,4 +242,4 @@ public class AlgorithmsAPI {
}.getType()
);
}
-}
+}
\ No newline at end of file
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 4400ff9e7..f253bab6d 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
@@ -5,6 +5,7 @@ import lombok.Getter;
import lombok.Setter;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Hashtable;
import java.util.List;
@@ -62,10 +63,16 @@ public class MIPEngineAlgorithmDTO {
AlgorithmDTO.AlgorithmParamDTO algorithmParamDTO = new AlgorithmDTO.AlgorithmParamDTO();
algorithmParamDTO.setName(name);
algorithmParamDTO.setDesc(this.desc);
- algorithmParamDTO.setLabel(this.label);
- if(name.equals("datasets") || name.equals("filter") || name.equals("pathology")){
- algorithmParamDTO.setType(name.equals("datasets")? "dataset":name);
+ if(name.equals("datasets") || name.equals("filters") || name.equals("pathology")){
algorithmParamDTO.setValueType(this.types.get(0));
+ if(name.equals("filters")){
+ algorithmParamDTO.setName("filter");
+ algorithmParamDTO.setType("filter");
+ }
+ if(name.equals("datasets")){
+ algorithmParamDTO.setName("dataset");
+ algorithmParamDTO.setType("dataset");
+ }
}
else{
algorithmParamDTO.setType("column");
@@ -75,6 +82,9 @@ public class MIPEngineAlgorithmDTO {
algorithmParamDTO.setValue("");
algorithmParamDTO.setValueNotBlank(this.notblank);
algorithmParamDTO.setValueMultiple(this.multiple);
+ String[] hidden = {"x","y","dataset", "filter","pathology","centers","formula"};
+ algorithmParamDTO.setLabel(Arrays.asList(hidden).contains(algorithmParamDTO.getName()) ? algorithmParamDTO.getName():this.label);
+
return algorithmParamDTO;
}
private String getColumnValuesIsCategorical(List<String> stattypes) throws Exception {
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index 660671108..8aadac388 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 ###
@@ -35,7 +35,7 @@ spring:
### EXTERNAL SERVICES ###
services:
mipengine:
- algorithmsUrl: "http://127.0.0.1:5000/algorithms"
+ algorithmsUrl: "http://192.168.124.129:5000/algorithms"
exareme:
queryExaremeUrl: "http://127.0.0.1:9090/mining/query"
algorithmsUrl: "http://127.0.0.1:9090/mining/algorithms.json"
--
GitLab
From 1e1b70d32546e46c58485fb2d66028b8ee9e9c01 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Mon, 5 Jul 2021 02:12:41 -0700
Subject: [PATCH 06/12] Visualization is no longer hardcoded
---
.../eu/hbp/mip/controllers/AlgorithmsAPI.java | 6 +-
.../eu/hbp/mip/models/DTOs/AlgorithmDTO.java | 26 ++++---
.../models/DTOs/MIPEngineAlgorithmDTO.java | 73 ++++++++++++++++---
.../eu/hbp/mip/models/DTOs/MIPEngineBody.java | 5 +-
.../hbp/mip/services/ExperimentService.java | 60 ++++++++++-----
5 files changed, 131 insertions(+), 39 deletions(-)
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index 68eb31340..6385d89d5 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -78,7 +78,11 @@ public class AlgorithmsAPI {
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
if (exaremeAlgorithms != null) {
- algorithms.addAll(exaremeAlgorithms);
+ //algorithms.addAll(exaremeAlgorithms);
+ exaremeAlgorithms.forEach(algorithmDTO -> {
+ if(algorithmDTO.getName().equals("LOGISTIC_REGRESSION"))
+ algorithms.add(algorithmDTO);
+ });
} else {
logger.LogUserAction("Getting exareme algorithms failed and returned null");
}
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 216140ba2..6d70c0215 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
@@ -98,7 +98,7 @@ public class AlgorithmDTO {
@Getter
@Setter
- public static class Filters
+ public static class Filter
{
@SerializedName("condition")
private String condition;
@@ -109,7 +109,7 @@ public class AlgorithmDTO {
@SerializedName("valid")
private boolean valid;
- public Filters(String condition, List<Object> rules, boolean valid) {
+ public Filter(String condition, List<Object> rules, boolean valid) {
this.condition = condition;
this.rules = rules;
this.valid = valid;
@@ -121,36 +121,42 @@ public class AlgorithmDTO {
{
MIPEngineBody mipEngineBody = new MIPEngineBody();
MIPEngineBody.InputData inputData = new MIPEngineBody.InputData();
+ Hashtable<String, Object> mipEngineParameters = new Hashtable<>();
List<Object> rules = new ArrayList<>();
this.parameters.forEach(parameter -> {
+
if(parameter.getName().equals("x")) {
+ System.out.println("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);
}
- if(parameter.getName().equals("y")) {
+ 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);
}
- if(parameter.getName().equals("dataset")){
+ 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);
}
- String pathology;
- if(parameter.getName().equals("pathology"))
+ else if(parameter.getName().equals("pathology"))
inputData.setPathology(parameter.getValue());
- if(parameter.getName().equals("filter")){
+ else if(parameter.getName().equals("filter")){
if (parameter.getValue() != "")
- rules.add(JsonConverters.convertJsonStringToObject(parameter.getValue(), Filters.class));
+ rules.add(JsonConverters.convertJsonStringToObject(parameter.getValue(), Filter.class));
+ }
+ else{
+ mipEngineParameters.put(parameter.getName(), Arrays.asList(parameter.getValue().split(",")));
}
});
- Filters filters = new Filters("AND", rules, true);
- inputData.setFilters(filters);
+ Filter filter = new Filter("AND", rules, true);
+ inputData.setFilters(filter);
mipEngineBody.setInputdata(inputData);
+ mipEngineBody.setParameters(mipEngineParameters);
return mipEngineBody;
}
}
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 f253bab6d..d391492d7 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
@@ -1,6 +1,7 @@
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
+import eu.hbp.mip.utils.JsonConverters;
import lombok.Getter;
import lombok.Setter;
@@ -26,7 +27,7 @@ public class MIPEngineAlgorithmDTO {
private String type;
@SerializedName("parameters")
- private InputDataParamDTO parameters;
+ private Hashtable<String, ParameterDTO> parameters;
@SerializedName("crossvalidation")
private String crossvalidation;
@@ -34,6 +35,54 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("inputdata")
private Hashtable<String, InputDataParamDTO> inputdata;
+ @Getter
+ @Setter
+ public static class ParameterDTO {
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("notblank")
+ private String notblank;
+
+ @SerializedName("multiple")
+ private String multiple;
+
+ @SerializedName("types")
+ private String type;
+
+ @SerializedName("desc")
+ private String desc;
+
+ @SerializedName("min")
+ private String min;
+
+ @SerializedName("max")
+ private String max;
+
+ @SerializedName("default_value")
+ private String default_value;
+
+ @SerializedName("enums")
+ private List<String> enums;
+
+ public AlgorithmDTO.AlgorithmParamDTO convertToAlgorithmParamDTO(String name) throws Exception {
+ AlgorithmDTO.AlgorithmParamDTO algorithmParamDTO = new AlgorithmDTO.AlgorithmParamDTO();
+ algorithmParamDTO.setName(name);
+ algorithmParamDTO.setDesc(this.desc);
+ algorithmParamDTO.setValueType(this.type);
+ algorithmParamDTO.setType("other");
+ algorithmParamDTO.setDefaultValue(this.default_value);
+ algorithmParamDTO.setValueNotBlank(this.notblank);
+ algorithmParamDTO.setLabel(this.label);
+ algorithmParamDTO.setValueEnumerations(this.enums);
+ algorithmParamDTO.setValueMultiple(this.multiple);
+ algorithmParamDTO.setValueMin(this.min);
+ algorithmParamDTO.setValueMax(this.max);
+ return algorithmParamDTO;
+ }
+ }
+
@Getter
@Setter
public static class InputDataParamDTO {
@@ -63,16 +112,13 @@ public class MIPEngineAlgorithmDTO {
AlgorithmDTO.AlgorithmParamDTO algorithmParamDTO = new AlgorithmDTO.AlgorithmParamDTO();
algorithmParamDTO.setName(name);
algorithmParamDTO.setDesc(this.desc);
- if(name.equals("datasets") || name.equals("filters") || name.equals("pathology")){
- algorithmParamDTO.setValueType(this.types.get(0));
- if(name.equals("filters")){
- algorithmParamDTO.setName("filter");
- algorithmParamDTO.setType("filter");
- }
+
+ if(name.equals("datasets") || name.equals("filter") || name.equals("pathology")){
if(name.equals("datasets")){
algorithmParamDTO.setName("dataset");
- algorithmParamDTO.setType("dataset");
}
+ algorithmParamDTO.setValueType(this.types.get(0));
+ algorithmParamDTO.setType(algorithmParamDTO.getName());
}
else{
algorithmParamDTO.setType("column");
@@ -84,7 +130,8 @@ public class MIPEngineAlgorithmDTO {
algorithmParamDTO.setValueMultiple(this.multiple);
String[] hidden = {"x","y","dataset", "filter","pathology","centers","formula"};
algorithmParamDTO.setLabel(Arrays.asList(hidden).contains(algorithmParamDTO.getName()) ? algorithmParamDTO.getName():this.label);
-
+ System.out.println("-------------------------------------------------------->");
+ System.out.println(JsonConverters.convertObjectToJsonString(algorithmParamDTO));
return algorithmParamDTO;
}
private String getColumnValuesIsCategorical(List<String> stattypes) throws Exception {
@@ -120,6 +167,14 @@ public class MIPEngineAlgorithmDTO {
e.printStackTrace();
}
});
+ this.parameters.forEach((name, parameterDTO) -> {
+ try {
+ AlgorithmDTO.AlgorithmParamDTO parameter = parameterDTO.convertToAlgorithmParamDTO(name);
+ parameters.add(parameter);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ });
algorithmDTO.setParameters(parameters);
return algorithmDTO;
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
index b8b2f957a..1572eb7da 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
@@ -4,6 +4,7 @@ import com.google.gson.annotations.SerializedName;
import lombok.Getter;
import lombok.Setter;
+import java.util.Hashtable;
import java.util.List;
@Getter
@@ -12,7 +13,7 @@ public class MIPEngineBody {
@SerializedName("inputdata")
private InputData inputdata;
@SerializedName("parameters")
- private Object parameters;
+ private Hashtable<String, Object> parameters;
@Getter
@Setter
@@ -22,7 +23,7 @@ public class MIPEngineBody {
@SerializedName("datasets")
private List<String> datasets;
@SerializedName("filters")
- private AlgorithmDTO.Filters filters;
+ private AlgorithmDTO.Filter filters;
@SerializedName("x")
private List<String> x;
@SerializedName("y")
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index bc7f4dd11..a48beb3aa 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -27,6 +27,9 @@ import eu.hbp.mip.utils.Exceptions.*;
import eu.hbp.mip.utils.HTTPUtil;
import eu.hbp.mip.utils.JsonConverters;
import eu.hbp.mip.utils.Logger;
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+import lombok.Setter;
import org.codehaus.jettison.json.JSONException;
import org.codehaus.jettison.json.JSONObject;
import org.springframework.beans.factory.annotation.Value;
@@ -386,7 +389,7 @@ public class ExperimentService {
.append("\n"));
logger.LogUserAction("Executing " + algorithmName + parametersLogMessage);
}
-
+
/**
* The getDatasetFromExperimentParameters will retrieve the dataset from the experiment parameters
*
@@ -508,19 +511,9 @@ public class ExperimentService {
}
private List<Object> formattingMIPEngienResult(String result) {
- List<List<String>> resultJson = JsonConverters.convertJsonStringToObject(result, new ArrayList<ArrayList<String>>().getClass());
- String schema_json = "{\"fields\":[{\"type\":\"string\",\"name\":\"node\"},{\"type\":\"number\",\"name\":\"row-id\"},{\"type\":\"number\",\"name\":\"alzheimerbroadcategory_bin\"}]}";
- LinkedTreeMap<String,List<Object>> schema = JsonConverters.convertJsonStringToObject(schema_json, new LinkedTreeMap<String,ArrayList<Object>>().getClass());
-
-
- LinkedTreeMap<String,Object> data_data = new LinkedTreeMap<>();
- data_data.put("data", resultJson);
- data_data.put("profile", "tabular-data-resource");
- data_data.put("schema", schema);
- data_data.put("name","Logistic Regression Stuff");
-
+ MIPVisualization mipVisualization = JsonConverters.convertJsonStringToObject(result, MIPVisualization.class);
LinkedTreeMap<String,Object> data = new LinkedTreeMap<>();
- data.put("data", data_data);
+ data.put("data", mipVisualization.convertToVisualization());
data.put("type", "application/vnd.dataresource+json");
List<Object> finalObject = new ArrayList<>();
finalObject.add(data);
@@ -601,6 +594,7 @@ public class ExperimentService {
} catch (Exception e) {
throw new InternalServerError("Error occurred : " + e.getMessage());
}
+ System.out.println(results);
// Results are stored in the experiment object
List<Object> resultDTOS = formattingMIPEngienResult(String.valueOf(results));
@@ -1045,6 +1039,8 @@ public class ExperimentService {
return returnError;
}
+ @Getter
+ @Setter
static class ExperimentResult {
private final int code;
private final List<Object> results;
@@ -1053,13 +1049,43 @@ public class ExperimentService {
this.code = code;
this.results = results;
}
+ }
- public int getCode() {
- return code;
+ @Getter
+ @Setter
+ @AllArgsConstructor
+ static class Visualization {
+ private final String title;
+ private final String profile;
+ private final List<Field> columns;
+ private final List<List<Object>> data;
+ }
+
+ @Getter
+ @Setter
+ @AllArgsConstructor
+ static class MIPVisualization {
+ private final String title;
+ private final List<String> columns;
+ private final List<List<Object>> data;
+
+ public Visualization convertToVisualization() {
+ ArrayList<Field> fields = new ArrayList<>();
+ this.columns.forEach(header_name -> fields.add(new Field(header_name, "number")));
+ return new Visualization(this.title, "tabular-data-resource", fields, this.data);
}
- public List<Object> getResults() {
- return results;
+ }
+
+ @Getter
+ @Setter
+ static class Field {
+ private final String name;
+ private final String type;
+
+ Field(String name, String type) {
+ this.name = name;
+ this.type = type;
}
}
}
--
GitLab
From ea916dbc8c3b0cd03de4e721eb69d5b7da4ff1a8 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Mon, 5 Jul 2021 07:44:59 -0700
Subject: [PATCH 07/12] Visualization is now dynamic in a tabular data form
---
.../eu/hbp/mip/controllers/AlgorithmsAPI.java | 39 ++---
.../eu/hbp/mip/models/DAOs/ExperimentDAO.java | 4 +-
.../eu/hbp/mip/models/DTOs/AlgorithmDTO.java | 162 ------------------
.../mip/models/DTOs/ExaremeAlgorithmDTO.java | 89 ++++++++++
.../DTOs/ExaremeAlgorithmRequestDTO.java | 53 ++++++
.../DTOs/ExaremeAlgorithmResultDTO.java | 17 ++
.../eu/hbp/mip/models/DTOs/ExperimentDTO.java | 8 +-
.../models/DTOs/MIPEngineAlgorithmDTO.java | 133 ++++++++------
.../DTOs/MIPEngineAlgorithmResultDTO.java | 23 +++
...eBody.java => MIPEngineExperimentDTO.java} | 20 ++-
.../MIPEngineTabularVisualizationDTO.java | 27 +++
.../eu/hbp/mip/models/galaxy/WorkflowDTO.java | 27 +--
.../hbp/mip/services/ExperimentService.java | 109 +++---------
13 files changed, 369 insertions(+), 342 deletions(-)
delete mode 100644 src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
create mode 100644 src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
create mode 100644 src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestDTO.java
create mode 100644 src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java
create mode 100644 src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java
rename src/main/java/eu/hbp/mip/models/DTOs/{MIPEngineBody.java => MIPEngineExperimentDTO.java} (64%)
create mode 100644 src/main/java/eu/hbp/mip/models/DTOs/MIPEngineTabularVisualizationDTO.java
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index 6385d89d5..08132000d 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -8,7 +8,7 @@ import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
-import eu.hbp.mip.models.DTOs.AlgorithmDTO;
+import eu.hbp.mip.models.DTOs.ExaremeAlgorithmDTO;
import eu.hbp.mip.models.DTOs.MIPEngineAlgorithmDTO;
import eu.hbp.mip.models.galaxy.WorkflowDTO;
import eu.hbp.mip.services.ActiveUserService;
@@ -65,24 +65,20 @@ public class AlgorithmsAPI {
@ApiOperation(value = "List all algorithms", response = String.class)
@RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
+ public ResponseEntity<List<ExaremeAlgorithmDTO>> getAlgorithms() {
Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /algorithms");
logger.LogUserAction("Executing...");
- LinkedList<AlgorithmDTO> mipengineAlgorithms = getMIPEngineAlgorithms(logger);
+ LinkedList<ExaremeAlgorithmDTO> mipengineAlgorithms = getMIPEngineAlgorithms(logger);
logger.LogUserAction("Loaded " + mipengineAlgorithms.size() + " mipengine algorithms");
- LinkedList<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms(logger);
+ LinkedList<ExaremeAlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms(logger);
logger.LogUserAction("Loaded " + exaremeAlgorithms.size() + " exareme algorithms");
- LinkedList<AlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows(logger);
+ LinkedList<ExaremeAlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows(logger);
logger.LogUserAction("Loaded " + galaxyAlgorithms.size() + " galaxy algorithms");
- LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
+ LinkedList<ExaremeAlgorithmDTO> algorithms = new LinkedList<>();
if (exaremeAlgorithms != null) {
- //algorithms.addAll(exaremeAlgorithms);
- exaremeAlgorithms.forEach(algorithmDTO -> {
- if(algorithmDTO.getName().equals("LOGISTIC_REGRESSION"))
- algorithms.add(algorithmDTO);
- });
+ algorithms.addAll(exaremeAlgorithms);
} else {
logger.LogUserAction("Getting exareme algorithms failed and returned null");
}
@@ -92,7 +88,7 @@ public class AlgorithmsAPI {
logger.LogUserAction("Getting mipengine algorithms failed and returned null");
}
if (galaxyAlgorithms != null) {
-// algorithms.addAll(galaxyAlgorithms);
+ algorithms.addAll(galaxyAlgorithms);
} else {
logger.LogUserAction("Getting galaxy workflows failed and returned null");
}
@@ -105,8 +101,8 @@ public class AlgorithmsAPI {
}
// Remove any disabled algorithm
- LinkedList<AlgorithmDTO> allowedAlgorithms = new LinkedList<>();
- for (AlgorithmDTO algorithm : algorithms) {
+ LinkedList<ExaremeAlgorithmDTO> allowedAlgorithms = new LinkedList<>();
+ for (ExaremeAlgorithmDTO algorithm : algorithms) {
if (!disabledAlgorithms.contains(algorithm.getName())) {
allowedAlgorithms.add(algorithm);
}
@@ -120,15 +116,15 @@ public class AlgorithmsAPI {
*
* @return a list of AlgorithmDTOs or null if something fails
*/
- public LinkedList<AlgorithmDTO> getExaremeAlgorithms(Logger logger) {
- LinkedList<AlgorithmDTO> algorithms;
+ public LinkedList<ExaremeAlgorithmDTO> getExaremeAlgorithms(Logger logger) {
+ LinkedList<ExaremeAlgorithmDTO> algorithms;
// Get exareme algorithms
try {
StringBuilder response = new StringBuilder();
HTTPUtil.sendGet(exaremeAlgorithmsUrl, response);
algorithms = gson.fromJson(
response.toString(),
- new TypeToken<LinkedList<AlgorithmDTO>>() {
+ new TypeToken<LinkedList<ExaremeAlgorithmDTO>>() {
}.getType()
);
} catch (IOException e) {
@@ -145,7 +141,7 @@ public class AlgorithmsAPI {
*
* @return a list of AlgorithmDTOs or null if something fails
*/
- public LinkedList<AlgorithmDTO> getMIPEngineAlgorithms(Logger logger) {
+ public LinkedList<ExaremeAlgorithmDTO> getMIPEngineAlgorithms(Logger logger) {
LinkedList<MIPEngineAlgorithmDTO> mipEngineAlgorithms;
// Get MIPEngine algorithms
try {
@@ -163,8 +159,7 @@ public class AlgorithmsAPI {
return null;
}
-
- LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
+ LinkedList<ExaremeAlgorithmDTO> algorithms = new LinkedList<>();
mipEngineAlgorithms.forEach(mipEngineAlgorithm -> algorithms.add(mipEngineAlgorithm.convertToAlgorithmDTO()));
logger.LogUserAction("Completed, returned " + algorithms.size() + " algorithms.");
@@ -176,7 +171,7 @@ public class AlgorithmsAPI {
*
* @return a list of AlgorithmDTOs or null if something fails
*/
- public LinkedList<AlgorithmDTO> getGalaxyWorkflows(Logger logger) {
+ public LinkedList<ExaremeAlgorithmDTO> getGalaxyWorkflows(Logger logger) {
List<Workflow> workflowList;
try {
// Get all the workflows with the galaxy client
@@ -215,7 +210,7 @@ public class AlgorithmsAPI {
logger.LogUserAction("Workflows fetched: " + workflows.size());
// Convert the workflows to algorithms
- LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
+ LinkedList<ExaremeAlgorithmDTO> algorithms = new LinkedList<>();
for (WorkflowDTO workflow : workflows) {
logger.LogUserAction("Converting workflow: " + workflow);
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 585bd8bd6..4e206fae0 100644
--- a/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java
+++ b/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java
@@ -3,7 +3,7 @@ package eu.hbp.mip.models.DAOs;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.google.gson.Gson;
import com.google.gson.annotations.Expose;
-import eu.hbp.mip.models.DTOs.AlgorithmDTO;
+import eu.hbp.mip.models.DTOs.ExaremeAlgorithmDTO;
import eu.hbp.mip.models.DTOs.ExperimentDTO;
import eu.hbp.mip.utils.JsonConverters;
import io.swagger.annotations.ApiModel;
@@ -98,7 +98,7 @@ public class ExperimentDAO {
public ExperimentDTO convertToDTO(boolean includeResult)
{
ExperimentDTO experimentDTO = new ExperimentDTO();
- experimentDTO.setAlgorithm(JsonConverters.convertJsonStringToObject(this.algorithm, AlgorithmDTO.class));
+ experimentDTO.setAlgorithm(JsonConverters.convertJsonStringToObject(this.algorithm, ExaremeAlgorithmDTO.class));
experimentDTO.setCreated(this.created);
experimentDTO.setUpdated(this.updated);
experimentDTO.setFinished(this.finished);
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
deleted file mode 100644
index 6d70c0215..000000000
--- a/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
+++ /dev/null
@@ -1,162 +0,0 @@
-package eu.hbp.mip.models.DTOs;
-
-import com.google.gson.annotations.SerializedName;
-import eu.hbp.mip.utils.JsonConverters;
-import lombok.Getter;
-import lombok.Setter;
-
-import java.util.*;
-
-@Getter
-@Setter
-public class AlgorithmDTO {
-
- @SerializedName("name")
- private String name;
-
- @SerializedName("desc")
- private String desc;
-
- @SerializedName("label")
- private String label;
-
- @SerializedName("type")
- private String type;
-
- @SerializedName("parameters")
- private List<AlgorithmParamDTO> parameters;
-
- @Getter
- @Setter
- public static class AlgorithmParamDTO {
- @SerializedName("name")
- private String name;
-
- @SerializedName("desc")
- private String desc;
-
- @SerializedName("label")
- private String label;
-
- @SerializedName("type")
- private String type;
-
- @SerializedName("columnValuesSQLType")
- private String columnValuesSQLType;
-
- @SerializedName("columnValuesIsCategorical")
- private String columnValuesIsCategorical;
-
- @SerializedName("value")
- private String value;
-
- @SerializedName("defaultValue")
- private String defaultValue;
-
- @SerializedName("valueType")
- private String valueType;
-
- @SerializedName("valueNotBlank")
- private String valueNotBlank;
-
- @SerializedName("valueMultiple")
- private String valueMultiple;
-
- @SerializedName("valueMin")
- private String valueMin;
-
- @SerializedName("valueMax")
- private String valueMax;
-
- @SerializedName("valueEnumerations")
- private List<String> valueEnumerations;
- }
-
- @Getter
- @Setter
- public static class Rule
- {
- @SerializedName("id")
- private String id;
-
- @SerializedName("type")
- private String type;
-
- @SerializedName("operator")
- private String operator;
-
- @SerializedName("value")
- private Object value;
-
- public Rule(String id, String type, String operator, Object value) {
- this.id = id;
- this.type = type;
- this.operator = operator;
- this.value = value;
- }
- }
-
- @Getter
- @Setter
- public static class Filter
- {
- @SerializedName("condition")
- private String condition;
-
- @SerializedName("rules")
- private List<Object> rules;
-
- @SerializedName("valid")
- private boolean valid;
-
- public Filter(String condition, List<Object> rules, boolean valid) {
- this.condition = condition;
- this.rules = rules;
- this.valid = valid;
- }
- }
-
-
- public MIPEngineBody convertToMIPEngineBody()
- {
- MIPEngineBody mipEngineBody = new MIPEngineBody();
- MIPEngineBody.InputData inputData = new MIPEngineBody.InputData();
- Hashtable<String, Object> mipEngineParameters = new Hashtable<>();
-
- List<Object> rules = new ArrayList<>();
- this.parameters.forEach(parameter -> {
-
- if(parameter.getName().equals("x")) {
- System.out.println("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(), Filter.class));
- }
- else{
- mipEngineParameters.put(parameter.getName(), Arrays.asList(parameter.getValue().split(",")));
- }
- });
- Filter filter = new Filter("AND", rules, true);
- inputData.setFilters(filter);
- mipEngineBody.setInputdata(inputData);
- mipEngineBody.setParameters(mipEngineParameters);
- return mipEngineBody;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
new file mode 100644
index 000000000..b56e16bc7
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
@@ -0,0 +1,89 @@
+package eu.hbp.mip.models.DTOs;
+
+import com.google.gson.annotations.SerializedName;
+import eu.hbp.mip.utils.JsonConverters;
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+import lombok.Setter;
+
+import java.util.*;
+
+@Getter
+@Setter
+public class ExaremeAlgorithmDTO {
+
+ @SerializedName("name")
+ private String name;
+
+ @SerializedName("desc")
+ private String desc;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("parameters")
+ private List<ExaremeAlgorithmRequestDTO> parameters;
+
+
+ @Getter
+ @Setter
+ @AllArgsConstructor
+ class Rule
+ {
+ @SerializedName("id")
+ private String id;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("operator")
+ private String operator;
+
+ @SerializedName("value")
+ private Object value;
+ }
+ public MIPEngineExperimentDTO convertToMIPEngineBody()
+ {
+ MIPEngineExperimentDTO mipEngineExperimentDTO = new MIPEngineExperimentDTO();
+ MIPEngineExperimentDTO.InputData inputData = new MIPEngineExperimentDTO.InputData();
+ Hashtable<String, Object> mipEngineParameters = new Hashtable<>();
+
+ 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(",")));
+ }
+ });
+ MIPEngineExperimentDTO.Filter filter = new MIPEngineExperimentDTO.Filter("AND", rules, true);
+ inputData.setFilters(filter);
+ mipEngineExperimentDTO.setInputdata(inputData);
+ mipEngineExperimentDTO.setParameters(mipEngineParameters);
+ return mipEngineExperimentDTO;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestDTO.java
new file mode 100644
index 000000000..84e275ec8
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestDTO.java
@@ -0,0 +1,53 @@
+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 ExaremeAlgorithmRequestDTO {
+ @SerializedName("name")
+ private String name;
+
+ @SerializedName("desc")
+ private String desc;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("columnValuesSQLType")
+ private String columnValuesSQLType;
+
+ @SerializedName("columnValuesIsCategorical")
+ private String columnValuesIsCategorical;
+
+ @SerializedName("value")
+ private String value;
+
+ @SerializedName("defaultValue")
+ private String defaultValue;
+
+ @SerializedName("valueType")
+ private String valueType;
+
+ @SerializedName("valueNotBlank")
+ private String valueNotBlank;
+
+ @SerializedName("valueMultiple")
+ private String valueMultiple;
+
+ @SerializedName("valueMin")
+ private String valueMin;
+
+ @SerializedName("valueMax")
+ private String valueMax;
+
+ @SerializedName("valueEnumerations")
+ private List<String> valueEnumerations;
+}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java
new file mode 100644
index 000000000..ca556bb73
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java
@@ -0,0 +1,17 @@
+package eu.hbp.mip.models.DTOs;
+
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+import lombok.Setter;
+
+import java.util.List;
+
+@Getter
+@Setter
+@AllArgsConstructor
+public class ExaremeAlgorithmResultDTO {
+ private int code;
+ private List<Object> results;
+}
+
+
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 e64c6f75e..765c20144 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
@@ -22,10 +22,12 @@ public class ExperimentDTO {
private Date finished;
private Boolean shared;
private Boolean viewed;
+ // Result is a list of objects because there is a limitation that java has in types.
+ // Exareme has result in the type of a List<HashMap<String, Object>>
+ // Galaxy has result in the type of a List<HashMap<String, List<Object>>>
+ //And there is no generic type that describes either an object or a list of objects
private List<Object> result;
private ExperimentDAO.Status status;
- private AlgorithmDTO algorithm;
+ private ExaremeAlgorithmDTO algorithm;
- public ExperimentDTO() {
- }
}
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 d391492d7..ada09db3b 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
@@ -33,7 +33,7 @@ public class MIPEngineAlgorithmDTO {
private String crossvalidation;
@SerializedName("inputdata")
- private Hashtable<String, InputDataParamDTO> inputdata;
+ private InputdataDTO inputdata;
@Getter
@Setter
@@ -66,26 +66,55 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("enums")
private List<String> enums;
- public AlgorithmDTO.AlgorithmParamDTO convertToAlgorithmParamDTO(String name) throws Exception {
- AlgorithmDTO.AlgorithmParamDTO algorithmParamDTO = new AlgorithmDTO.AlgorithmParamDTO();
- algorithmParamDTO.setName(name);
- algorithmParamDTO.setDesc(this.desc);
- algorithmParamDTO.setValueType(this.type);
- algorithmParamDTO.setType("other");
- algorithmParamDTO.setDefaultValue(this.default_value);
- algorithmParamDTO.setValueNotBlank(this.notblank);
- algorithmParamDTO.setLabel(this.label);
- algorithmParamDTO.setValueEnumerations(this.enums);
- algorithmParamDTO.setValueMultiple(this.multiple);
- algorithmParamDTO.setValueMin(this.min);
- algorithmParamDTO.setValueMax(this.max);
- return algorithmParamDTO;
+ 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;
}
}
@Getter
@Setter
- public static class InputDataParamDTO {
+ public static class InputdataDTO {
+ @SerializedName("x")
+ private InputDataDetailDTO x;
+
+ @SerializedName("y")
+ private InputDataDetailDTO y;
+
+ @SerializedName("pathology")
+ private InputDataDetailDTO pathology;
+
+ @SerializedName("datasets")
+ private InputDataDetailDTO datasets;
+
+ @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;
+ }
+ }
+
+ @Getter
+ @Setter
+ public static class InputDataDetailDTO {
@SerializedName("stattypes")
private List<String> stattypes;
@@ -108,32 +137,27 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("desc")
private String desc;
- public AlgorithmDTO.AlgorithmParamDTO convertToAlgorithmParamDTO(String name) throws Exception {
- AlgorithmDTO.AlgorithmParamDTO algorithmParamDTO = new AlgorithmDTO.AlgorithmParamDTO();
- algorithmParamDTO.setName(name);
- algorithmParamDTO.setDesc(this.desc);
-
- if(name.equals("datasets") || name.equals("filter") || name.equals("pathology")){
- if(name.equals("datasets")){
- algorithmParamDTO.setName("dataset");
- }
- algorithmParamDTO.setValueType(this.types.get(0));
- algorithmParamDTO.setType(algorithmParamDTO.getName());
+ 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);
+ String[] hidden = {"x","y","dataset", "filter","pathology","centers","formula"};
+ exaremeAlgorithmRequestDTO.setLabel(Arrays.asList(hidden).contains(exaremeAlgorithmRequestDTO.getName()) ? exaremeAlgorithmRequestDTO.getName():this.label);
+ if(name.equals("dataset") || name.equals("filter") || name.equals("pathology")){
+ exaremeAlgorithmRequestDTO.setValueType(this.types.get(0));
+ exaremeAlgorithmRequestDTO.setType(exaremeAlgorithmRequestDTO.getName());
}
else{
- algorithmParamDTO.setType("column");
- algorithmParamDTO.setColumnValuesSQLType(String.join(", ", this.types));
- algorithmParamDTO.setColumnValuesIsCategorical(getColumnValuesIsCategorical(this.stattypes));
+ exaremeAlgorithmRequestDTO.setType("column");
+ exaremeAlgorithmRequestDTO.setColumnValuesSQLType(String.join(", ", this.types));
+ exaremeAlgorithmRequestDTO.setColumnValuesIsCategorical(getColumnValuesIsCategorical(this.stattypes));
}
- algorithmParamDTO.setValue("");
- algorithmParamDTO.setValueNotBlank(this.notblank);
- algorithmParamDTO.setValueMultiple(this.multiple);
- String[] hidden = {"x","y","dataset", "filter","pathology","centers","formula"};
- algorithmParamDTO.setLabel(Arrays.asList(hidden).contains(algorithmParamDTO.getName()) ? algorithmParamDTO.getName():this.label);
- System.out.println("-------------------------------------------------------->");
- System.out.println(JsonConverters.convertObjectToJsonString(algorithmParamDTO));
- return algorithmParamDTO;
+ return exaremeAlgorithmRequestDTO;
}
+
private String getColumnValuesIsCategorical(List<String> stattypes) throws Exception {
if (stattypes.contains("nominal") && stattypes.contains("numerical")){
@@ -151,31 +175,28 @@ public class MIPEngineAlgorithmDTO {
}
}
- public AlgorithmDTO convertToAlgorithmDTO()
+ public ExaremeAlgorithmDTO convertToAlgorithmDTO()
{
- AlgorithmDTO algorithmDTO = new AlgorithmDTO();
- algorithmDTO.setName(this.name.toUpperCase());
- algorithmDTO.setLabel(this.label);
- algorithmDTO.setDesc(this.desc);
- algorithmDTO.setType("mipengine");
- List<AlgorithmDTO.AlgorithmParamDTO> parameters = new ArrayList<>();
- this.inputdata.forEach((name, inputDataParamDTO) -> {
- try {
- AlgorithmDTO.AlgorithmParamDTO parameter = inputDataParamDTO.convertToAlgorithmParamDTO(name);
- parameters.add(parameter);
- } catch (Exception e) {
- e.printStackTrace();
- }
- });
+ ExaremeAlgorithmDTO exaremeAlgorithmDTO = new ExaremeAlgorithmDTO();
+ exaremeAlgorithmDTO.setName(this.name.toUpperCase());
+ 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();
+ }
this.parameters.forEach((name, parameterDTO) -> {
try {
- AlgorithmDTO.AlgorithmParamDTO parameter = parameterDTO.convertToAlgorithmParamDTO(name);
+ ExaremeAlgorithmRequestDTO parameter = parameterDTO.convertToexaremeAlgorithmRequestDTO(name);
parameters.add(parameter);
} catch (Exception e) {
e.printStackTrace();
}
});
- algorithmDTO.setParameters(parameters);
- return algorithmDTO;
+ exaremeAlgorithmDTO.setParameters(parameters);
+ return exaremeAlgorithmDTO;
}
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java
new file mode 100644
index 000000000..087adb1f8
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java
@@ -0,0 +1,23 @@
+package eu.hbp.mip.models.DTOs;
+
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+import lombok.Setter;
+
+import java.util.HashMap;
+import java.util.List;
+
+@Getter
+@Setter
+@AllArgsConstructor
+public class MIPEngineAlgorithmResultDTO {
+ private final String title;
+ private final List<MIPEngineTabularVisualizationDTO.Field> columns;
+ private final List<List<Object>> data;
+
+ public MIPEngineTabularVisualizationDTO convertToVisualization() {
+ HashMap<String, List<MIPEngineTabularVisualizationDTO.Field>> schema = new HashMap<>();
+ schema.put("fields", columns);
+ return new MIPEngineTabularVisualizationDTO(this.title, "tabular-data-resource", schema, this.data);
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineExperimentDTO.java
similarity index 64%
rename from src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
rename to src/main/java/eu/hbp/mip/models/DTOs/MIPEngineExperimentDTO.java
index 1572eb7da..46b7df898 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineExperimentDTO.java
@@ -1,6 +1,7 @@
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
+import lombok.AllArgsConstructor;
import lombok.Getter;
import lombok.Setter;
@@ -9,7 +10,7 @@ import java.util.List;
@Getter
@Setter
-public class MIPEngineBody {
+public class MIPEngineExperimentDTO {
@SerializedName("inputdata")
private InputData inputdata;
@SerializedName("parameters")
@@ -23,10 +24,25 @@ public class MIPEngineBody {
@SerializedName("datasets")
private List<String> datasets;
@SerializedName("filters")
- private AlgorithmDTO.Filter filters;
+ private Filter filters;
@SerializedName("x")
private List<String> x;
@SerializedName("y")
private List<String> y;
}
+
+ @Getter
+ @Setter
+ @AllArgsConstructor
+ public static class Filter
+ {
+ @SerializedName("condition")
+ private String condition;
+
+ @SerializedName("rules")
+ private List<Object> rules;
+
+ @SerializedName("valid")
+ private boolean valid;
+ }
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineTabularVisualizationDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineTabularVisualizationDTO.java
new file mode 100644
index 000000000..7be3fad33
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineTabularVisualizationDTO.java
@@ -0,0 +1,27 @@
+package eu.hbp.mip.models.DTOs;
+
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+import lombok.Setter;
+
+import java.util.HashMap;
+import java.util.List;
+
+@Getter
+@Setter
+@AllArgsConstructor
+public class MIPEngineTabularVisualizationDTO {
+ private final String name;
+ private final String profile;
+ private final HashMap<String, List<Field>> schema;
+ private final List<List<Object>> data;
+
+ @Getter
+ @Setter
+ @AllArgsConstructor
+ public static class Field {
+ private final String name;
+ private final String type;
+ }
+}
+
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 496ee2dfe..edc18117d 100644
--- a/src/main/java/eu/hbp/mip/models/galaxy/WorkflowDTO.java
+++ b/src/main/java/eu/hbp/mip/models/galaxy/WorkflowDTO.java
@@ -2,7 +2,8 @@ package eu.hbp.mip.models.galaxy;
import com.google.gson.Gson;
import com.google.gson.annotations.SerializedName;
-import eu.hbp.mip.models.DTOs.AlgorithmDTO;
+import eu.hbp.mip.models.DTOs.ExaremeAlgorithmDTO;
+import eu.hbp.mip.models.DTOs.ExaremeAlgorithmRequestDTO;
import java.util.*;
@@ -103,29 +104,29 @@ public class WorkflowDTO {
}
}
- public AlgorithmDTO convertToAlgorithmDTO() {
+ public ExaremeAlgorithmDTO convertToAlgorithmDTO() {
- AlgorithmDTO algorithmDTO = new AlgorithmDTO();
+ ExaremeAlgorithmDTO exaremeAlgorithmDTO = new ExaremeAlgorithmDTO();
// Transfer workflow information
- algorithmDTO.setName(id);
- algorithmDTO.setDesc("");
- algorithmDTO.setLabel(name);
- algorithmDTO.setType("workflow");
+ exaremeAlgorithmDTO.setName(id);
+ exaremeAlgorithmDTO.setDesc("");
+ exaremeAlgorithmDTO.setLabel(name);
+ exaremeAlgorithmDTO.setType("workflow");
// Transfer workflow parameters information
- List<AlgorithmDTO.AlgorithmParamDTO> algorithmParams = new LinkedList<>();
+ List<ExaremeAlgorithmRequestDTO> algorithmParams = new LinkedList<>();
Gson gson = new Gson();
for (Map.Entry<String, WorkflowInputDTO> workflowInput : getInputs().entrySet()) {
// Convert the annotation to algorithm Parameter
- AlgorithmDTO.AlgorithmParamDTO algorithmParam;
+ ExaremeAlgorithmRequestDTO algorithmParam;
if (steps.get(workflowInput.getKey()).getAnnotation() != null) {
algorithmParam = gson.fromJson(steps.get(workflowInput.getKey()).getAnnotation(),
- AlgorithmDTO.AlgorithmParamDTO.class);
+ ExaremeAlgorithmRequestDTO.class);
} else {
// If annotation is not provided, auto-fill some information
- algorithmParam = new AlgorithmDTO.AlgorithmParamDTO();
+ algorithmParam = new ExaremeAlgorithmRequestDTO();
// When the constraints are not known, set the most relaxed constraints
algorithmParam.setDesc("");
algorithmParam.setValue("");
@@ -154,9 +155,9 @@ public class WorkflowDTO {
algorithmParams.add(algorithmParam);
}
- algorithmDTO.setParameters(algorithmParams);
+ exaremeAlgorithmDTO.setParameters(algorithmParams);
- return algorithmDTO;
+ return exaremeAlgorithmDTO;
}
}
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index a48beb3aa..587fc7e63 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -15,9 +15,7 @@ import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
import eu.hbp.mip.models.DAOs.ExperimentDAO;
import eu.hbp.mip.models.DAOs.UserDAO;
-import eu.hbp.mip.models.DTOs.AlgorithmDTO;
-import eu.hbp.mip.models.DTOs.ExperimentDTO;
-import eu.hbp.mip.models.DTOs.MIPEngineBody;
+import eu.hbp.mip.models.DTOs.*;
import eu.hbp.mip.models.galaxy.GalaxyWorkflowResult;
import eu.hbp.mip.models.galaxy.PostWorkflowToGalaxyDtoResponse;
import eu.hbp.mip.repositories.ExperimentRepository;
@@ -27,9 +25,6 @@ import eu.hbp.mip.utils.Exceptions.*;
import eu.hbp.mip.utils.HTTPUtil;
import eu.hbp.mip.utils.JsonConverters;
import eu.hbp.mip.utils.Logger;
-import lombok.AllArgsConstructor;
-import lombok.Getter;
-import lombok.Setter;
import org.codehaus.jettison.json.JSONException;
import org.codehaus.jettison.json.JSONObject;
import org.springframework.beans.factory.annotation.Value;
@@ -236,12 +231,12 @@ public class ExperimentService {
logger.LogUserAction("Completed, returning: " + experimentDTO);
// Results are stored in the experiment object
- ExperimentResult experimentResult = runExperiment(experimentDTO, logger);
+ ExaremeAlgorithmResultDTO exaremeAlgorithmResultDTO = runExperiment(experimentDTO, logger);
- logger.LogUserAction("Experiment with uuid: " + experimentDTO.getUuid() + "gave response code: " + experimentResult.getCode() + " and result: " + experimentResult.getResults());
+ logger.LogUserAction("Experiment with uuid: " + experimentDTO.getUuid() + "gave response code: " + exaremeAlgorithmResultDTO.getCode() + " and result: " + exaremeAlgorithmResultDTO.getResults());
- experimentDTO.setResult((experimentResult.getCode() >= 400) ? null : experimentResult.getResults());
- experimentDTO.setStatus((experimentResult.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
+ experimentDTO.setResult((exaremeAlgorithmResultDTO.getCode() >= 400) ? null : exaremeAlgorithmResultDTO.getResults());
+ experimentDTO.setStatus((exaremeAlgorithmResultDTO.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
return experimentDTO;
}
@@ -400,7 +395,7 @@ public class ExperimentService {
private String getDatasetFromExperimentParameters(ExperimentDTO experimentDTO, Logger logger) {
String experimentDatasets = null;
- for (AlgorithmDTO.AlgorithmParamDTO parameter : experimentDTO.getAlgorithm().getParameters()) {
+ for (ExaremeAlgorithmRequestDTO parameter : experimentDTO.getAlgorithm().getParameters()) {
if (parameter.getLabel().equals("dataset")) {
experimentDatasets = parameter.getValue();
break;
@@ -510,14 +505,14 @@ public class ExperimentService {
return JsonConverters.convertObjectToJsonString(finalJsonObject);
}
- private List<Object> formattingMIPEngienResult(String result) {
- MIPVisualization mipVisualization = JsonConverters.convertJsonStringToObject(result, MIPVisualization.class);
+ private ExaremeAlgorithmResultDTO convertMIPEngineResultToExaremeAlgorithmResult(int code, String result) {
+ MIPEngineAlgorithmResultDTO mipVisualization = JsonConverters.convertJsonStringToObject(result, MIPEngineAlgorithmResultDTO.class);
LinkedTreeMap<String,Object> data = new LinkedTreeMap<>();
data.put("data", mipVisualization.convertToVisualization());
data.put("type", "application/vnd.dataresource+json");
List<Object> finalObject = new ArrayList<>();
finalObject.add(data);
- return finalObject;
+ return new ExaremeAlgorithmResultDTO(code, finalObject);
}
/**
@@ -526,7 +521,7 @@ public class ExperimentService {
* @param experimentDTO is the request with the experiment information
* @return the result of experiment as well as the http status that was retrieved
*/
- public ExperimentResult runExperiment(ExperimentDTO experimentDTO, Logger logger) {
+ public ExaremeAlgorithmResultDTO runExperiment(ExperimentDTO experimentDTO, Logger logger) {
// Algorithm type
String algorithmType = experimentDTO.getAlgorithm().getType();
@@ -536,14 +531,14 @@ public class ExperimentService {
// Run with the appropriate engine
if (algorithmType.equals("mipengine")) {
- MIPEngineBody mipEngineBody = experimentDTO.getAlgorithm().convertToMIPEngineBody();
- String body = JsonConverters.convertObjectToJsonString(mipEngineBody);
+ MIPEngineExperimentDTO mipEngineExperimentDTO = experimentDTO.getAlgorithm().convertToMIPEngineBody();
+ String body = JsonConverters.convertObjectToJsonString(mipEngineExperimentDTO);
String url = mipengineAlgorithmsUrl + "/" + algorithmName.toLowerCase();
logger.LogUserAction("url: " + url + ", body: " + body);
logger.LogUserAction("Algorithm runs on MIPEngine.");
return runMIPEngineExperiment(url, body);
} else {
- List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
+ List<ExaremeAlgorithmRequestDTO> algorithmParameters
= experimentDTO.getAlgorithm().getParameters();
String body = gson.toJson(algorithmParameters);
String url = queryExaremeUrl + "/" + algorithmName;
@@ -561,7 +556,7 @@ public class ExperimentService {
* @param body is the parameters of the algorithm
* @return the result of exareme as well as the http status that was retrieved
*/
- public ExperimentResult runExaremeExperiment(String url, String body) {
+ public ExaremeAlgorithmResultDTO runExaremeExperiment(String url, String body) {
StringBuilder results = new StringBuilder();
int code;
@@ -572,10 +567,12 @@ public class ExperimentService {
}
// Results are stored in the experiment object
- ExperimentDTO experimentDTOWithOnlyResult = JsonConverters.convertJsonStringToObject(String.valueOf(results), ExperimentDTO.class);
- List<Object> resultDTOS = experimentDTOWithOnlyResult.getResult();
+ ExaremeAlgorithmResultDTO exaremeResult = JsonConverters.convertJsonStringToObject(
+ String.valueOf(results), ExaremeAlgorithmResultDTO.class
+ );
+ exaremeResult.setCode(code);
- return new ExperimentResult(code, resultDTOS);
+ return exaremeResult;
}
/**
@@ -585,7 +582,7 @@ public class ExperimentService {
* @param body is the parameters of the algorithm
* @return the result of exareme as well as the http status that was retrieved
*/
- public ExperimentResult runMIPEngineExperiment(String url, String body) {
+ public ExaremeAlgorithmResultDTO runMIPEngineExperiment(String url, String body) {
StringBuilder results = new StringBuilder();
int code;
@@ -596,9 +593,7 @@ public class ExperimentService {
}
System.out.println(results);
// Results are stored in the experiment object
- List<Object> resultDTOS = formattingMIPEngienResult(String.valueOf(results));
-
- return new ExperimentResult(code, resultDTOS);
+ return convertMIPEngineResultToExaremeAlgorithmResult(code, String.valueOf(results));
}
/* -------------------------------------- EXAREME CALLS ---------------------------------------------------------*/
@@ -628,12 +623,12 @@ public class ExperimentService {
try {
// Results are stored in the experiment object
- ExperimentResult experimentResult = runExperiment(finalExperimentDTO, logger);
+ ExaremeAlgorithmResultDTO exaremeAlgorithmResultDTO = runExperiment(finalExperimentDTO, logger);
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Experiment with uuid: " + experimentDAO.getUuid() + "gave response code: " + experimentResult.getCode() + " and result: " + experimentResult.getResults());
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Experiment with uuid: " + experimentDAO.getUuid() + "gave response code: " + exaremeAlgorithmResultDTO.getCode() + " and result: " + exaremeAlgorithmResultDTO.getResults());
- experimentDAO.setResult((experimentResult.getCode() >= 400) ? null : JsonConverters.convertObjectToJsonString(experimentResult.getResults()));
- experimentDAO.setStatus((experimentResult.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
+ experimentDAO.setResult((exaremeAlgorithmResultDTO.getCode() >= 400) ? null : JsonConverters.convertObjectToJsonString(exaremeAlgorithmResultDTO.getResults()));
+ experimentDAO.setStatus((exaremeAlgorithmResultDTO.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
} catch (Exception e) {
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "There was an exception: " + e.getMessage());
@@ -667,13 +662,13 @@ public class ExperimentService {
String workflowId = experimentDTO.getAlgorithm().getName();
// Get the parameters
- List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
+ List<ExaremeAlgorithmRequestDTO> algorithmParameters
= experimentDTO.getAlgorithm().getParameters();
// Convert the parameters to workflow parameters
HashMap<String, String> algorithmParamsIncludingEmpty = new HashMap<>();
if (algorithmParameters != null) {
- for (AlgorithmDTO.AlgorithmParamDTO param : algorithmParameters) {
+ for (ExaremeAlgorithmRequestDTO param : algorithmParameters) {
algorithmParamsIncludingEmpty.put(param.getName(), param.getValue());
}
}
@@ -1038,54 +1033,4 @@ public class ExperimentService {
return returnError;
}
-
- @Getter
- @Setter
- static class ExperimentResult {
- private final int code;
- private final List<Object> results;
-
- public ExperimentResult(int code, List<Object> results) {
- this.code = code;
- this.results = results;
- }
- }
-
- @Getter
- @Setter
- @AllArgsConstructor
- static class Visualization {
- private final String title;
- private final String profile;
- private final List<Field> columns;
- private final List<List<Object>> data;
- }
-
- @Getter
- @Setter
- @AllArgsConstructor
- static class MIPVisualization {
- private final String title;
- private final List<String> columns;
- private final List<List<Object>> data;
-
- public Visualization convertToVisualization() {
- ArrayList<Field> fields = new ArrayList<>();
- this.columns.forEach(header_name -> fields.add(new Field(header_name, "number")));
- return new Visualization(this.title, "tabular-data-resource", fields, this.data);
- }
-
- }
-
- @Getter
- @Setter
- static class Field {
- private final String name;
- private final String type;
-
- Field(String name, String type) {
- this.name = name;
- this.type = type;
- }
- }
}
--
GitLab
From b5fba832cb44954763e05a52aca28870027301ec Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Tue, 6 Jul 2021 07:10:06 -0700
Subject: [PATCH 08/12] Fixed warnings from DeepCode
---
.../eu/hbp/mip/controllers/AlgorithmsAPI.java | 37 ++++----
.../mip/models/DTOs/ExaremeAlgorithmDTO.java | 70 +++++++-------
...a => ExaremeAlgorithmRequestParamDTO.java} | 3 +-
.../models/DTOs/MIPEngineAlgorithmDTO.java | 93 +++++++++----------
...java => MIPEngineAlgorithmRequestDTO.java} | 2 +-
.../eu/hbp/mip/models/galaxy/WorkflowDTO.java | 10 +-
.../hbp/mip/services/ExperimentService.java | 14 +--
7 files changed, 111 insertions(+), 118 deletions(-)
rename src/main/java/eu/hbp/mip/models/DTOs/{ExaremeAlgorithmRequestDTO.java => ExaremeAlgorithmRequestParamDTO.java} (89%)
rename src/main/java/eu/hbp/mip/models/DTOs/{MIPEngineExperimentDTO.java => MIPEngineAlgorithmRequestDTO.java} (96%)
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index 08132000d..aea67b056 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 b56e16bc7..887733de8 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 84e275ec8..6f7d21655 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 ada09db3b..98677991e 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 46b7df898..ff8229e37 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 edc18117d..eae07531e 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 587fc7e63..3c52503c2 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());
}
}
--
GitLab
From 192daf69f3d4bd55f787f9e7f31697ae70f08ef9 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Fri, 9 Jul 2021 06:57:33 -0700
Subject: [PATCH 09/12] Accordingly named classes with proper prefix, seperated
GalaxyService from main service, replaced @Setter @Getter with @Data,
instead of converters created constructors for each class so its better
organized, functions that were accessing database were moved to the according
repository
---
docker/README.md | 2 +-
docker/config/application.tmpl | 2 +-
.../eu/hbp/mip/controllers/AlgorithmsAPI.java | 8 +-
.../eu/hbp/mip/controllers/ExperimentAPI.java | 2 +
.../eu/hbp/mip/models/DAOs/ExperimentDAO.java | 29 +-
.../java/eu/hbp/mip/models/DAOs/UserDAO.java | 8 +-
.../mip/models/DTOs/ExaremeAlgorithmDTO.java | 76 +--
.../DTOs/ExaremeAlgorithmRequestParamDTO.java | 60 +-
.../DTOs/ExaremeAlgorithmResultDTO.java | 6 +-
.../eu/hbp/mip/models/DTOs/ExperimentDTO.java | 29 +-
.../models/DTOs/MIPEngineAlgorithmDTO.java | 122 +---
.../DTOs/MIPEngineAlgorithmRequestDTO.java | 70 ++-
.../DTOs/MIPEngineAlgorithmResultDTO.java | 15 +-
.../MIPEngineTabularVisualizationDTO.java | 27 -
.../eu/hbp/mip/models/DTOs/PathologyDTO.java | 15 +-
.../repositories/ExperimentRepository.java | 95 +++
.../hbp/mip/services/ExperimentService.java | 540 +-----------------
.../eu/hbp/mip/services/GalaxyService.java | 454 +++++++++++++++
src/main/resources/application.yml | 2 +-
19 files changed, 779 insertions(+), 783 deletions(-)
delete mode 100644 src/main/java/eu/hbp/mip/models/DTOs/MIPEngineTabularVisualizationDTO.java
create mode 100644 src/main/java/eu/hbp/mip/services/GalaxyService.java
diff --git a/docker/README.md b/docker/README.md
index 36a3e1245..8693aad09 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -24,7 +24,7 @@ To use this image, you need a running instance of PostgreSQL and to configure th
### EXTERNAL SERVICES ###
-* MIPENGINE_URL: URL to MIPENGINE server. Default is "http://192.168.124.129:5000" .
+* MIPENGINE_URL: URL to MIPENGINE server. Default is "http://localhost:5000" .
* EXAREME_URL: URL to Exareme server. Default is "http://localhost:9090" .
diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 6059a902b..a8bfdf9ff 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -35,7 +35,7 @@ spring:
### EXTERNAL SERVICES ###
services:
mipengine:
- algorithmsUrl: {{ default .Env.MIPENGINE_URL "http://192.168.124.129:5000" }}/algorithms
+ algorithmsUrl: {{ .Env.MIPENGINE_URL}}/algorithms
exareme:
queryExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index aea67b056..5ac49a402 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -76,17 +76,17 @@ public class AlgorithmsAPI {
logger.LogUserAction("Loaded " + galaxyAlgorithms.size() + " galaxy algorithms");
ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>();
- if (!exaremeAlgorithms.isEmpty()) {
+ if (exaremeAlgorithms != null) {
algorithms.addAll(exaremeAlgorithms);
} else {
logger.LogUserAction("Getting exareme algorithms failed and returned null");
}
- if (!mipengineAlgorithms.isEmpty()) {
+ if (mipengineAlgorithms != null) {
algorithms.addAll(mipengineAlgorithms);
} else {
logger.LogUserAction("Getting mipengine algorithms failed and returned null");
}
- if (!galaxyAlgorithms.isEmpty()) {
+ if (galaxyAlgorithms != null) {
algorithms.addAll(galaxyAlgorithms);
} else {
logger.LogUserAction("Getting galaxy workflows failed and returned null");
@@ -159,7 +159,7 @@ public class AlgorithmsAPI {
}
ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>();
- mipEngineAlgorithms.forEach(mipEngineAlgorithm -> algorithms.add(mipEngineAlgorithm.convertToAlgorithmDTO()));
+ mipEngineAlgorithms.forEach(mipEngineAlgorithm -> algorithms.add(new ExaremeAlgorithmDTO(mipEngineAlgorithm)));
logger.LogUserAction("Completed, returned " + algorithms.size() + " algorithms.");
return algorithms;
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java b/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java
index e5d0b04c5..449765fc9 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java
@@ -78,6 +78,7 @@ public class ExperimentAPI {
@ApiOperation(value = "Create an experiment", response = ExperimentDTO.class)
@RequestMapping(method = RequestMethod.POST)
public ResponseEntity<String> createExperiment(Authentication authentication, @RequestBody ExperimentDTO experimentDTO) {
+ new Logger(activeUserService.getActiveUser().getUsername(),"(POST) /experiments").LogUserAction("TEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEST");
experimentDTO = experimentService.createExperiment(authentication, experimentDTO, new Logger(activeUserService.getActiveUser().getUsername(),"(POST) /experiments"));
return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.CREATED);
}
@@ -103,6 +104,7 @@ public class ExperimentAPI {
@ApiOperation(value = "Create a transient experiment", response = ExperimentDTO.class)
@RequestMapping(value = "/transient", method = RequestMethod.POST)
public ResponseEntity<String> createTransientExperiment(Authentication authentication, @RequestBody ExperimentDTO experimentDTO) {
+ new Logger(activeUserService.getActiveUser().getUsername(),"(POST) /experiments").LogUserAction("TEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEST");
experimentDTO = experimentService.createTransientExperiment(authentication, experimentDTO, new Logger(activeUserService.getActiveUser().getUsername(), "(POST) /experiments/transient"));
return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.OK);
}
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 4e206fae0..8eb343c9c 100644
--- a/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java
+++ b/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java
@@ -3,12 +3,9 @@ package eu.hbp.mip.models.DAOs;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.google.gson.Gson;
import com.google.gson.annotations.Expose;
-import eu.hbp.mip.models.DTOs.ExaremeAlgorithmDTO;
-import eu.hbp.mip.models.DTOs.ExperimentDTO;
-import eu.hbp.mip.utils.JsonConverters;
import io.swagger.annotations.ApiModel;
-import lombok.Getter;
-import lombok.Setter;
+import lombok.AllArgsConstructor;
+import lombok.Data;
import javax.persistence.*;
import java.util.*;
@@ -17,8 +14,8 @@ import java.util.*;
* Created by habfast on 21/04/16.
*/
@Entity
-@Getter
-@Setter
+@Data
+@AllArgsConstructor
@Table(name = "`experiment`")
@ApiModel
@JsonInclude(JsonInclude.Include.NON_NULL)
@@ -95,22 +92,4 @@ public class ExperimentDAO {
*/
}
- public ExperimentDTO convertToDTO(boolean includeResult)
- {
- ExperimentDTO experimentDTO = new ExperimentDTO();
- experimentDTO.setAlgorithm(JsonConverters.convertJsonStringToObject(this.algorithm, ExaremeAlgorithmDTO.class));
- experimentDTO.setCreated(this.created);
- experimentDTO.setUpdated(this.updated);
- experimentDTO.setFinished(this.finished);
- experimentDTO.setCreatedBy(this.createdBy.getUsername());
- experimentDTO.setName(this.name);
- if(includeResult){
- experimentDTO.setResult(JsonConverters.convertJsonStringToObject(String.valueOf(this.result), new ArrayList<>().getClass()));
- }
- experimentDTO.setStatus(this.status);
- experimentDTO.setShared(this.shared);
- experimentDTO.setUuid(this.uuid);
- experimentDTO.setViewed(this.viewed);
- return experimentDTO;
- }
}
diff --git a/src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java b/src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java
index 9279b3793..3bb43f3ee 100644
--- a/src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java
+++ b/src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java
@@ -7,16 +7,16 @@ package eu.hbp.mip.models.DAOs;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.google.gson.annotations.Expose;
import io.swagger.annotations.ApiModel;
-import lombok.Getter;
-import lombok.Setter;
+import lombok.AllArgsConstructor;
+import lombok.Data;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
@Entity
-@Getter
-@Setter
+@Data
+@AllArgsConstructor
@Table(name = "`user`")
@ApiModel
@JsonInclude(JsonInclude.Include.NON_NULL)
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 887733de8..584ffd424 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
@@ -1,15 +1,13 @@
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
-import eu.hbp.mip.utils.JsonConverters;
import lombok.AllArgsConstructor;
-import lombok.Getter;
-import lombok.Setter;
+import lombok.Data;
import java.util.*;
-@Getter
-@Setter
+@Data
+@AllArgsConstructor
public class ExaremeAlgorithmDTO {
@SerializedName("name")
@@ -27,9 +25,30 @@ public class ExaremeAlgorithmDTO {
@SerializedName("parameters")
private List<ExaremeAlgorithmRequestParamDTO> parameters;
+ public ExaremeAlgorithmDTO()
+ {
+
+ }
- @Getter
- @Setter
+ public ExaremeAlgorithmDTO(MIPEngineAlgorithmDTO mipEngineAlgorithm )
+ {
+ this.name = mipEngineAlgorithm.getName().toUpperCase();
+ this.label = mipEngineAlgorithm.getLabel();
+ this.desc = mipEngineAlgorithm.getDesc();
+ this.type = "mipengine";
+ List<ExaremeAlgorithmRequestParamDTO> parameters = new ArrayList<>();
+ parameters.add(new ExaremeAlgorithmRequestParamDTO("x", mipEngineAlgorithm.getInputdata().getX()));
+ parameters.add(new ExaremeAlgorithmRequestParamDTO("y", mipEngineAlgorithm.getInputdata().getY()));
+ parameters.add(new ExaremeAlgorithmRequestParamDTO("pathology", mipEngineAlgorithm.getInputdata().getPathology()));
+ parameters.add(new ExaremeAlgorithmRequestParamDTO("dataset", mipEngineAlgorithm.getInputdata().getDatasets()));
+ parameters.add(new ExaremeAlgorithmRequestParamDTO("filter", mipEngineAlgorithm.getInputdata().getFilter()));
+ mipEngineAlgorithm.getParameters().forEach((name, parameterDTO) -> {
+ ExaremeAlgorithmRequestParamDTO parameter = new ExaremeAlgorithmRequestParamDTO(name, parameterDTO);
+ parameters.add(parameter);
+ });
+ this.setParameters(parameters);
+ }
+ @Data
@AllArgsConstructor
static class Rule
{
@@ -45,47 +64,4 @@ public class ExaremeAlgorithmDTO {
@SerializedName("value")
private Object value;
}
- public MIPEngineAlgorithmRequestDTO convertToMIPEngineBody()
- {
- 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 -> {
-
- 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;
- }
- });
- MIPEngineAlgorithmRequestDTO.Filter filter = new MIPEngineAlgorithmRequestDTO.Filter("AND", rules, true);
- inputData.setFilters(filter);
- mipEngineAlgorithmRequestDTO.setInputdata(inputData);
- mipEngineAlgorithmRequestDTO.setParameters(mipEngineParameters);
- return mipEngineAlgorithmRequestDTO;
- }
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java
index 6f7d21655..4109c5e59 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java
@@ -1,14 +1,16 @@
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
-import lombok.Getter;
-import lombok.Setter;
+import eu.hbp.mip.utils.Exceptions.InternalServerError;
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import java.util.Arrays;
import java.util.List;
//The request of an exareme algorithm is a list of ExaremeAlgorithmRequestParamDTOs.
-@Getter
-@Setter
+@Data
+@AllArgsConstructor
public class ExaremeAlgorithmRequestParamDTO {
@SerializedName("name")
private String name;
@@ -51,4 +53,54 @@ public class ExaremeAlgorithmRequestParamDTO {
@SerializedName("valueEnumerations")
private List<String> valueEnumerations;
+ public ExaremeAlgorithmRequestParamDTO (){}
+
+ public ExaremeAlgorithmRequestParamDTO (String name, MIPEngineAlgorithmDTO.MIPEngineAlgorithmParameterDTO parameter){
+ this.name = name;
+ this.desc = parameter.getDesc();
+ this.valueType = parameter.getType();
+ this.type = "other";
+ this.defaultValue = parameter.getDefault_value();
+ this.valueNotBlank = parameter.getNotblank();
+ this.label = parameter.getLabel();
+ this.valueEnumerations = parameter.getEnums();
+ this.valueMultiple = parameter.getMultiple();
+ this.valueMax = parameter.getMin();
+ this.valueMin = parameter.getMax();
+ }
+
+ public ExaremeAlgorithmRequestParamDTO (String name, MIPEngineAlgorithmDTO.MIPEngineAlgorithmInputDataDetailDTO inputDataDetail){
+ this.name = name;
+ this.desc = inputDataDetail.getDesc();
+ this.value = "";
+ this.valueNotBlank = inputDataDetail.getNotblank();
+ this.valueMultiple = inputDataDetail.getMultiple();
+ String[] hidden = {"x","y","dataset", "filter","pathology","centers","formula"};
+ this.label = (Arrays.asList(hidden).contains(this.name) ? this.name : inputDataDetail.getLabel());
+ if(name.equals("dataset") || name.equals("filter") || name.equals("pathology")){
+ this.valueType = inputDataDetail.getTypes().get(0);
+ this.type = this.name;
+ }
+ else{
+ this.type = "column";
+ this.columnValuesSQLType = String.join(", ", inputDataDetail.getTypes());
+ this.columnValuesIsCategorical = getColumnValuesIsCategorical(inputDataDetail.getStattypes());
+ }
+ }
+
+ private String getColumnValuesIsCategorical(List<String> stattypes){
+
+ if (stattypes.contains("nominal") && stattypes.contains("numerical")){
+ return "";
+ }
+ else if (stattypes.contains("nominal")){
+ return "true";
+ }
+ else if (stattypes.contains("numerical")){
+ return "false";
+ }
+ else{
+ throw new InternalServerError("Invalid stattypes");
+ }
+ }
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java
index ca556bb73..d1f5947c8 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java
@@ -1,13 +1,11 @@
package eu.hbp.mip.models.DTOs;
import lombok.AllArgsConstructor;
-import lombok.Getter;
-import lombok.Setter;
+import lombok.Data;
import java.util.List;
-@Getter
-@Setter
+@Data
@AllArgsConstructor
public class ExaremeAlgorithmResultDTO {
private int code;
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 765c20144..0dd28c1d6 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
@@ -2,15 +2,17 @@ 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 eu.hbp.mip.utils.JsonConverters;
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.UUID;
-@Getter
-@Setter
+@Data
+@AllArgsConstructor
@JsonInclude(JsonInclude.Include.NON_NULL)
public class ExperimentDTO {
@@ -30,4 +32,23 @@ public class ExperimentDTO {
private ExperimentDAO.Status status;
private ExaremeAlgorithmDTO algorithm;
+ public ExperimentDTO(){
+
+ }
+ public ExperimentDTO(boolean includeResult, ExperimentDAO experimentDAO)
+ {
+ this.algorithm = JsonConverters.convertJsonStringToObject(experimentDAO.getAlgorithm(), ExaremeAlgorithmDTO.class);
+ this.created = experimentDAO.getCreated();
+ this.updated = experimentDAO.getUpdated();
+ this.finished = experimentDAO.getFinished();
+ this.createdBy = experimentDAO.getCreatedBy().getUsername();
+ this.name = experimentDAO.getName();
+ if(includeResult){
+ this.result = JsonConverters.convertJsonStringToObject(String.valueOf(experimentDAO.getResult()), new ArrayList<>().getClass());
+ }
+ this.status = experimentDAO.getStatus();
+ this.uuid = experimentDAO.getUuid();
+ this.shared = experimentDAO.isShared();
+ this.viewed = experimentDAO.isViewed();
+ }
}
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 98677991e..5edfbfe77 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
@@ -1,17 +1,14 @@
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
-import eu.hbp.mip.utils.Exceptions.InternalServerError;
-import lombok.Getter;
-import lombok.Setter;
+import lombok.AllArgsConstructor;
+import lombok.Data;
-import java.util.ArrayList;
-import java.util.Arrays;
import java.util.Hashtable;
import java.util.List;
-@Getter
-@Setter
+@Data
+@AllArgsConstructor
public class MIPEngineAlgorithmDTO {
@SerializedName("name")
@@ -27,17 +24,17 @@ public class MIPEngineAlgorithmDTO {
private String type;
@SerializedName("parameters")
- private Hashtable<String, ParameterDTO> parameters;
+ private Hashtable<String, MIPEngineAlgorithmParameterDTO> parameters;
@SerializedName("crossvalidation")
private String crossvalidation;
@SerializedName("inputdata")
- private InputdataDTO inputdata;
+ private MIPEngineAlgorithmInputdataDTO inputdata;
- @Getter
- @Setter
- public static class ParameterDTO {
+ @Data
+ @AllArgsConstructor
+ public static class MIPEngineAlgorithmParameterDTO {
@SerializedName("label")
private String label;
@@ -65,56 +62,30 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("enums")
private List<String> enums;
-
- 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;
- }
}
- @Getter
- @Setter
- public static class InputdataDTO {
+ @Data
+ @AllArgsConstructor
+ public static class MIPEngineAlgorithmInputdataDTO {
@SerializedName("x")
- private InputDataDetailDTO x;
+ private MIPEngineAlgorithmInputDataDetailDTO x;
@SerializedName("y")
- private InputDataDetailDTO y;
+ private MIPEngineAlgorithmInputDataDetailDTO y;
@SerializedName("pathology")
- private InputDataDetailDTO pathology;
+ private MIPEngineAlgorithmInputDataDetailDTO pathology;
@SerializedName("datasets")
- private InputDataDetailDTO datasets;
+ private MIPEngineAlgorithmInputDataDetailDTO datasets;
@SerializedName("filter")
- private InputDataDetailDTO filter;
-
- 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;
- }
+ private MIPEngineAlgorithmInputDataDetailDTO filter;
}
- @Getter
- @Setter
- public static class InputDataDetailDTO {
+ @Data
+ @AllArgsConstructor
+ public static class MIPEngineAlgorithmInputDataDetailDTO {
@SerializedName("stattypes")
private List<String> stattypes;
@@ -136,58 +107,5 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("desc")
private String desc;
-
- 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"};
- exaremeAlgorithmRequestParamDTO.setLabel(Arrays.asList(hidden).contains(exaremeAlgorithmRequestParamDTO.getName()) ? exaremeAlgorithmRequestParamDTO.getName():this.label);
- if(name.equals("dataset") || name.equals("filter") || name.equals("pathology")){
- exaremeAlgorithmRequestParamDTO.setValueType(this.types.get(0));
- exaremeAlgorithmRequestParamDTO.setType(exaremeAlgorithmRequestParamDTO.getName());
- }
- else{
- exaremeAlgorithmRequestParamDTO.setType("column");
- exaremeAlgorithmRequestParamDTO.setColumnValuesSQLType(String.join(", ", this.types));
- exaremeAlgorithmRequestParamDTO.setColumnValuesIsCategorical(getColumnValuesIsCategorical(this.stattypes));
- }
- return exaremeAlgorithmRequestParamDTO;
- }
-
- private String getColumnValuesIsCategorical(List<String> stattypes){
-
- if (stattypes.contains("nominal") && stattypes.contains("numerical")){
- return "";
- }
- else if (stattypes.contains("nominal")){
- return "true";
- }
- else if (stattypes.contains("numerical")){
- return "false";
- }
- else{
- throw new InternalServerError("Invalid stattypes");
- }
- }
- }
-
- public ExaremeAlgorithmDTO convertToAlgorithmDTO()
- {
- ExaremeAlgorithmDTO exaremeAlgorithmDTO = new ExaremeAlgorithmDTO();
- exaremeAlgorithmDTO.setName(this.name.toUpperCase());
- exaremeAlgorithmDTO.setLabel(this.label);
- exaremeAlgorithmDTO.setDesc(this.desc);
- exaremeAlgorithmDTO.setType("mipengine");
- List<ExaremeAlgorithmRequestParamDTO> parameters = new ArrayList<>(this.inputdata.convertToAlgorithmRequestParamDTOs());
- this.parameters.forEach((name, parameterDTO) -> {
- ExaremeAlgorithmRequestParamDTO parameter = parameterDTO.convertToexaremeAlgorithmRequestDTO(name);
- parameters.add(parameter);
- });
- exaremeAlgorithmDTO.setParameters(parameters);
- return exaremeAlgorithmDTO;
}
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java
index ff8229e37..a5604f2e7 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java
@@ -1,23 +1,68 @@
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
+import eu.hbp.mip.utils.JsonConverters;
import lombok.AllArgsConstructor;
-import lombok.Getter;
-import lombok.Setter;
+import lombok.Data;
-import java.util.Hashtable;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
import java.util.List;
-@Getter
-@Setter
+@Data
+@AllArgsConstructor
public class MIPEngineAlgorithmRequestDTO {
@SerializedName("inputdata")
private InputData inputdata;
@SerializedName("parameters")
- private Hashtable<String, Object> parameters;
+ private HashMap<String, Object> parameters;
- @Getter
- @Setter
+ public MIPEngineAlgorithmRequestDTO(List<ExaremeAlgorithmRequestParamDTO> exaremeAlgorithmRequestParamDTOs)
+ {
+ MIPEngineAlgorithmRequestDTO.InputData inputData = new MIPEngineAlgorithmRequestDTO.InputData();
+ HashMap<String, Object> mipEngineParameters = new HashMap<>();
+
+ List<Object> rules = new ArrayList<>();
+ exaremeAlgorithmRequestParamDTOs.forEach(parameter -> {
+
+ switch (parameter.getName()) {
+ case "x":
+ List<String> x = Arrays.asList(parameter.getValue().split(","));
+ x.forEach(column -> rules.add(new ExaremeAlgorithmDTO.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 ExaremeAlgorithmDTO.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 ExaremeAlgorithmDTO.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;
+ }
+ });
+ MIPEngineAlgorithmRequestDTO.Filter filter = new MIPEngineAlgorithmRequestDTO.Filter("AND", rules);
+ inputData.setFilters(filter);
+ this.inputdata = inputData;
+ this.parameters = mipEngineParameters;
+ }
+
+
+ @Data
+ @AllArgsConstructor
public static class InputData {
@SerializedName("pathology")
private String pathology;
@@ -29,10 +74,12 @@ public class MIPEngineAlgorithmRequestDTO {
private List<String> x;
@SerializedName("y")
private List<String> y;
+ public InputData(){
+
+ }
}
- @Getter
- @Setter
+ @Data
@AllArgsConstructor
public static class Filter
{
@@ -41,8 +88,5 @@ public class MIPEngineAlgorithmRequestDTO {
@SerializedName("rules")
private List<Object> rules;
-
- @SerializedName("valid")
- private boolean valid;
}
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java
index 087adb1f8..4491ddb44 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmResultDTO.java
@@ -1,23 +1,14 @@
package eu.hbp.mip.models.DTOs;
import lombok.AllArgsConstructor;
-import lombok.Getter;
-import lombok.Setter;
+import lombok.Data;
-import java.util.HashMap;
import java.util.List;
-@Getter
-@Setter
+@Data
@AllArgsConstructor
public class MIPEngineAlgorithmResultDTO {
private final String title;
- private final List<MIPEngineTabularVisualizationDTO.Field> columns;
+ private final List<TabularVisualizationDTO.Field> columns;
private final List<List<Object>> data;
-
- public MIPEngineTabularVisualizationDTO convertToVisualization() {
- HashMap<String, List<MIPEngineTabularVisualizationDTO.Field>> schema = new HashMap<>();
- schema.put("fields", columns);
- return new MIPEngineTabularVisualizationDTO(this.title, "tabular-data-resource", schema, this.data);
- }
}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineTabularVisualizationDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineTabularVisualizationDTO.java
deleted file mode 100644
index 7be3fad33..000000000
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineTabularVisualizationDTO.java
+++ /dev/null
@@ -1,27 +0,0 @@
-package eu.hbp.mip.models.DTOs;
-
-import lombok.AllArgsConstructor;
-import lombok.Getter;
-import lombok.Setter;
-
-import java.util.HashMap;
-import java.util.List;
-
-@Getter
-@Setter
-@AllArgsConstructor
-public class MIPEngineTabularVisualizationDTO {
- private final String name;
- private final String profile;
- private final HashMap<String, List<Field>> schema;
- private final List<List<Object>> data;
-
- @Getter
- @Setter
- @AllArgsConstructor
- public static class Field {
- private final String name;
- private final String 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 aa78ef8b0..ecc5b723b 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
@@ -1,13 +1,13 @@
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
-import lombok.Getter;
-import lombok.Setter;
+import lombok.AllArgsConstructor;
+import lombok.Data;
import java.util.List;
-@Getter
-@Setter
+@Data
+@AllArgsConstructor
public class PathologyDTO {
@SerializedName("code")
@@ -22,8 +22,11 @@ public class PathologyDTO {
@SerializedName("datasets")
private List<PathologyDatasetDTO> datasets;
- @Getter
- @Setter
+ public PathologyDTO(){
+
+ }
+ @Data
+ @AllArgsConstructor
public static class PathologyDatasetDTO {
@SerializedName("code")
private String code;
diff --git a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
index 9ac54cada..b776b6c46 100644
--- a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
@@ -1,9 +1,17 @@
package eu.hbp.mip.repositories;
import eu.hbp.mip.models.DAOs.ExperimentDAO;
+import eu.hbp.mip.models.DAOs.UserDAO;
+import eu.hbp.mip.models.DTOs.ExperimentDTO;
+import eu.hbp.mip.utils.Exceptions.BadRequestException;
+import eu.hbp.mip.utils.Exceptions.ExperimentNotFoundException;
+import eu.hbp.mip.utils.Exceptions.InternalServerError;
+import eu.hbp.mip.utils.JsonConverters;
+import eu.hbp.mip.utils.Logger;
import org.springframework.data.jpa.repository.JpaSpecificationExecutor;
import org.springframework.data.repository.CrudRepository;
+import java.util.Date;
import java.util.Optional;
import java.util.UUID;
@@ -14,4 +22,91 @@ import java.util.UUID;
public interface ExperimentRepository extends CrudRepository<ExperimentDAO, UUID>, JpaSpecificationExecutor<ExperimentDAO>
{
ExperimentDAO findByUuid(UUID experimentUuid);
+
+ /**
+ * The loadExperiment access the database and load the information of a specific experiment
+ *
+ * @param uuid is the id of the experiment to be retrieved
+ * @return the experiment information that was retrieved from database
+ */
+ default ExperimentDAO loadExperiment(String uuid, Logger logger) {
+ UUID experimentUuid;
+ ExperimentDAO experimentDAO;
+
+ try {
+ experimentUuid = UUID.fromString(uuid);
+ } catch (Exception e) {
+ logger.LogUserAction( e.getMessage());
+ throw new BadRequestException(e.getMessage());
+ }
+
+ experimentDAO = findByUuid(experimentUuid);
+ if (experimentDAO == null) {
+ logger.LogUserAction( "Experiment with uuid : " + uuid + "was not found.");
+ throw new ExperimentNotFoundException("Experiment with uuid : " + uuid + " was not found.");
+ }
+
+ return experimentDAO;
+ }
+
+ /**
+ * The createExperimentInTheDatabase will insert a new experiment in the database according to the given experiment information
+ *
+ * @param experimentDTO is the experiment information to inserted in the database
+ * @return the experiment information that was inserted into the database
+ * @Note In the database there will be stored Algorithm Details that is the whole information about the algorithm
+ * and an Algorithm column that is required for the filtering with algorithm name in the GET /experiments.
+ */
+ default ExperimentDAO createExperimentInTheDatabase(ExperimentDTO experimentDTO, UserDAO user, Logger logger) {
+
+ ExperimentDAO experimentDAO = new ExperimentDAO();
+ experimentDAO.setUuid(UUID.randomUUID());
+ experimentDAO.setCreatedBy(user);
+ experimentDAO.setAlgorithm(JsonConverters.convertObjectToJsonString(experimentDTO.getAlgorithm()));
+ experimentDAO.setAlgorithmId(experimentDTO.getAlgorithm().getName());
+ experimentDAO.setName(experimentDTO.getName());
+ experimentDAO.setStatus(ExperimentDAO.Status.pending);
+
+ try {
+ save(experimentDAO);
+ } catch (Exception e) {
+ logger.LogUserAction("Attempted to save changes to database but an error ocurred : " + e.getMessage() + ".");
+ throw new InternalServerError(e.getMessage());
+ }
+
+ logger.LogUserAction(" id : " + experimentDAO.getUuid());
+ logger.LogUserAction(" algorithm : " + experimentDAO.getAlgorithm());
+ logger.LogUserAction(" name : " + experimentDAO.getName());
+ return experimentDAO;
+ }
+
+ default void saveExperiment(ExperimentDAO experimentDAO, Logger logger) {
+
+ logger.LogUserAction(" id : " + experimentDAO.getUuid());
+ logger.LogUserAction(" algorithm : " + experimentDAO.getAlgorithm());
+ logger.LogUserAction(" name : " + experimentDAO.getName());
+ logger.LogUserAction(" historyId : " + experimentDAO.getWorkflowHistoryId());
+ logger.LogUserAction(" status : " + experimentDAO.getStatus());
+
+ try {
+ save(experimentDAO);
+ } catch (Exception e) {
+ logger.LogUserAction("Attempted to save changes to database but an error ocurred : " + e.getMessage() + ".");
+ throw new InternalServerError(e.getMessage());
+ }
+
+ logger.LogUserAction("Saved experiment");
+ }
+
+ default void finishExperiment(ExperimentDAO experimentDAO, Logger logger) {
+ experimentDAO.setFinished(new Date());
+
+ try {
+ save(experimentDAO);
+ } catch (Exception e) {
+ logger.LogUserAction( "Attempted to save changes to database but an error ocurred : " + e.getMessage() + ".");
+ throw new InternalServerError(e.getMessage());
+ }
+ }
+
}
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index 3c52503c2..c421fd471 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -1,23 +1,10 @@
package eu.hbp.mip.services;
-import com.github.jmchilton.blend4j.galaxy.GalaxyInstance;
-import com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory;
-import com.github.jmchilton.blend4j.galaxy.WorkflowsClient;
-import com.github.jmchilton.blend4j.galaxy.beans.Workflow;
-import com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails;
-import com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition;
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;
import eu.hbp.mip.models.DAOs.UserDAO;
import eu.hbp.mip.models.DTOs.*;
-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;
@@ -25,8 +12,6 @@ import eu.hbp.mip.utils.Exceptions.*;
import eu.hbp.mip.utils.HTTPUtil;
import eu.hbp.mip.utils.JsonConverters;
import eu.hbp.mip.utils.Logger;
-import org.codehaus.jettison.json.JSONException;
-import org.codehaus.jettison.json.JSONObject;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
@@ -34,13 +19,8 @@ import org.springframework.data.domain.Pageable;
import org.springframework.data.jpa.domain.Specification;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Service;
-import retrofit2.Call;
-import retrofit2.Response;
-
-import java.io.IOException;
import java.util.*;
-import static java.lang.Thread.sleep;
@Service
public class ExperimentService {
@@ -52,22 +32,18 @@ public class ExperimentService {
@Value("#{'${services.mipengine.algorithmsUrl}'}")
private String mipengineAlgorithmsUrl;
- @Value("#{'${services.galaxy.galaxyUrl}'}")
- private String galaxyUrl;
-
- @Value("#{'${services.galaxy.galaxyApiKey}'}")
- private String galaxyApiKey;
-
@Value("#{'${authentication.enabled}'}")
private boolean authenticationIsEnabled;
private static final Gson gson = new Gson();
private final ActiveUserService activeUserService;
+ private final GalaxyService galaxyService;
private final ExperimentRepository experimentRepository;
- public ExperimentService(ActiveUserService activeUserService, ExperimentRepository experimentRepository) {
+ public ExperimentService(ActiveUserService activeUserService, GalaxyService galaxyService, ExperimentRepository experimentRepository) {
this.activeUserService = activeUserService;
+ this.galaxyService = galaxyService;
this.experimentRepository = experimentRepository;
}
@@ -121,7 +97,7 @@ public class ExperimentService {
throw new NoContent("No experiment found with the filters provided.");
List<ExperimentDTO> experimentDTOs = new ArrayList<>();
- experimentDAOs.forEach(experimentDAO -> experimentDTOs.add(experimentDAO.convertToDTO(false)));
+ experimentDAOs.forEach(experimentDAO -> experimentDTOs.add(new ExperimentDTO(false, experimentDAO)));
Map<String, Object> response = new HashMap<>();
response.put("experiments", experimentDTOs);
@@ -146,7 +122,7 @@ public class ExperimentService {
logger.LogUserAction("Loading Experiment with uuid : " + uuid);
- experimentDAO = loadExperiment(uuid, logger);
+ experimentDAO = experimentRepository.loadExperiment(uuid, logger);
if (
!experimentDAO.isShared()
&& !experimentDAO.getCreatedBy().getUsername().equals(user.getUsername())
@@ -156,7 +132,7 @@ public class ExperimentService {
logger.LogUserAction("Accessing Experiment is unauthorized.");
throw new UnauthorizedException("You don't have access to the experiment.");
}
- ExperimentDTO experimentDTO = experimentDAO.convertToDTO(true);
+ ExperimentDTO experimentDTO = new ExperimentDTO(true, experimentDAO);
logger.LogUserAction("Experiment was Loaded with uuid : " + uuid + ".");
return experimentDTO;
@@ -193,7 +169,7 @@ public class ExperimentService {
// Run with the appropriate engine
if (algorithmType.equals("workflow")) {
logger.LogUserAction("Algorithm runs on Galaxy.");
- return runGalaxyWorkflow(experimentDTO, logger);
+ return galaxyService.runGalaxyWorkflow(experimentDTO, logger);
} else {
logger.LogUserAction("Algorithm runs on Exareme.");
return createExperiment(experimentDTO, logger);
@@ -253,7 +229,7 @@ public class ExperimentService {
UserDAO user = activeUserService.getActiveUser();
logger.LogUserAction("Updating experiment with uuid : " + uuid + ".");
- experimentDAO = loadExperiment(uuid, logger);
+ experimentDAO = experimentRepository.loadExperiment(uuid, logger);
//Verify (PATCH) /experiments non editable fields.
verifyPatchExperimentNonEditableFields(experimentDTO, logger);
@@ -281,7 +257,7 @@ public class ExperimentService {
logger.LogUserAction("Updated experiment with uuid : " + uuid + ".");
- experimentDTO = experimentDAO.convertToDTO(true);
+ experimentDTO = new ExperimentDTO(true, experimentDAO);
return experimentDTO;
}
@@ -296,7 +272,7 @@ public class ExperimentService {
UserDAO user = activeUserService.getActiveUser();
logger.LogUserAction("Deleting experiment with uuid : " + uuid + ".");
- experimentDAO = loadExperiment(uuid, logger);
+ experimentDAO = experimentRepository.loadExperiment(uuid, logger);
if (!experimentDAO.getCreatedBy().getUsername().equals(user.getUsername()))
throw new UnauthorizedException("You don't have access to the experiment.");
@@ -409,106 +385,10 @@ public class ExperimentService {
return experimentDatasets;
}
- /**
- * The loadExperiment access the database and load the information of a specific experiment
- *
- * @param uuid is the id of the experiment to be retrieved
- * @return the experiment information that was retrieved from database
- */
- private ExperimentDAO loadExperiment(String uuid, Logger logger) {
- UUID experimentUuid;
- ExperimentDAO experimentDAO;
-
- try {
- experimentUuid = UUID.fromString(uuid);
- } catch (Exception e) {
- logger.LogUserAction( e.getMessage());
- throw new BadRequestException(e.getMessage());
- }
-
- experimentDAO = experimentRepository.findByUuid(experimentUuid);
- if (experimentDAO == null) {
- logger.LogUserAction( "Experiment with uuid : " + uuid + "was not found.");
- throw new ExperimentNotFoundException("Experiment with uuid : " + uuid + " was not found.");
- }
-
- return experimentDAO;
- }
-
- /**
- * The createExperimentInTheDatabase will insert a new experiment in the database according to the given experiment information
- *
- * @param experimentDTO is the experiment information to inserted in the database
- * @return the experiment information that was inserted into the database
- * @Note In the database there will be stored Algorithm Details that is the whole information about the algorithm
- * and an Algorithm column that is required for the filtering with algorithm name in the GET /experiments.
- */
- private ExperimentDAO createExperimentInTheDatabase(ExperimentDTO experimentDTO, Logger logger) {
- UserDAO user = activeUserService.getActiveUser();
-
- ExperimentDAO experimentDAO = new ExperimentDAO();
- experimentDAO.setUuid(UUID.randomUUID());
- experimentDAO.setCreatedBy(user);
- experimentDAO.setAlgorithm(JsonConverters.convertObjectToJsonString(experimentDTO.getAlgorithm()));
- experimentDAO.setAlgorithmId(experimentDTO.getAlgorithm().getName());
- experimentDAO.setName(experimentDTO.getName());
- experimentDAO.setStatus(ExperimentDAO.Status.pending);
-
- try {
- experimentRepository.save(experimentDAO);
- } catch (Exception e) {
- logger.LogUserAction("Attempted to save changes to database but an error ocurred : " + e.getMessage() + ".");
- throw new InternalServerError(e.getMessage());
- }
-
- logger.LogUserAction(" id : " + experimentDAO.getUuid());
- logger.LogUserAction(" algorithm : " + experimentDAO.getAlgorithm());
- logger.LogUserAction(" name : " + experimentDAO.getName());
- return experimentDAO;
- }
-
- private void saveExperiment(ExperimentDAO experimentDAO, Logger logger) {
-
- logger.LogUserAction(" id : " + experimentDAO.getUuid());
- logger.LogUserAction(" algorithm : " + experimentDAO.getAlgorithm());
- logger.LogUserAction(" name : " + experimentDAO.getName());
- logger.LogUserAction(" historyId : " + experimentDAO.getWorkflowHistoryId());
- logger.LogUserAction(" status : " + experimentDAO.getStatus());
-
- try {
- experimentRepository.save(experimentDAO);
- } catch (Exception e) {
- logger.LogUserAction("Attempted to save changes to database but an error ocurred : " + e.getMessage() + ".");
- throw new InternalServerError(e.getMessage());
- }
-
- logger.LogUserAction("Saved experiment");
- }
-
- private void finishExperiment(ExperimentDAO experimentDAO, Logger logger) {
- experimentDAO.setFinished(new Date());
-
- try {
- experimentRepository.save(experimentDAO);
- } catch (Exception e) {
- logger.LogUserAction( "Attempted to save changes to database but an error ocurred : " + e.getMessage() + ".");
- throw new InternalServerError(e.getMessage());
- }
- }
-
- private String formattingGalaxyResult(String result) {
- List<LinkedTreeMap<String,Object>> jsonObject = JsonConverters.convertJsonStringToObject(result, new ArrayList<ArrayList<Object>>().getClass());
- LinkedTreeMap<String,Object> firstResult = jsonObject.get(0);
- jsonObject = (List<LinkedTreeMap<String, Object>>) firstResult.get("result");
- List<LinkedTreeMap<String,Object>> finalJsonObject = new ArrayList<>();
- finalJsonObject.add(jsonObject.get(0));
- return JsonConverters.convertObjectToJsonString(finalJsonObject);
- }
-
private ExaremeAlgorithmResultDTO convertMIPEngineResultToExaremeAlgorithmResult(int code, String result) {
MIPEngineAlgorithmResultDTO mipVisualization = JsonConverters.convertJsonStringToObject(result, MIPEngineAlgorithmResultDTO.class);
LinkedTreeMap<String,Object> data = new LinkedTreeMap<>();
- data.put("data", mipVisualization.convertToVisualization());
+ data.put("data", new TabularVisualizationDTO(mipVisualization));
data.put("type", "application/vnd.dataresource+json");
List<Object> finalObject = new ArrayList<>();
finalObject.add(data);
@@ -531,7 +411,7 @@ public class ExperimentService {
// Run with the appropriate engine
if (algorithmType.equals("mipengine")) {
- MIPEngineAlgorithmRequestDTO mipEngineAlgorithmRequestDTO = experimentDTO.getAlgorithm().convertToMIPEngineBody();
+ MIPEngineAlgorithmRequestDTO mipEngineAlgorithmRequestDTO = new MIPEngineAlgorithmRequestDTO(experimentDTO.getAlgorithm().getParameters());
String body = JsonConverters.convertObjectToJsonString(mipEngineAlgorithmRequestDTO);
String url = mipengineAlgorithmsUrl + "/" + algorithmName.toLowerCase();
logger.LogUserAction("url: " + url + ", body: " + body);
@@ -609,10 +489,9 @@ public class ExperimentService {
logger.LogUserAction("Running the algorithm...");
- ExperimentDAO experimentDAO = createExperimentInTheDatabase(experimentDTO, logger);
+ ExperimentDAO experimentDAO = experimentRepository.createExperimentInTheDatabase(experimentDTO, activeUserService.getActiveUser(), logger);
logger.LogUserAction("Created experiment with uuid :" + experimentDAO.getUuid());
-
logger.LogUserAction("Starting execution in thread");
ExperimentDTO finalExperimentDTO = experimentDTO;
new Thread(() -> {
@@ -635,402 +514,13 @@ public class ExperimentService {
experimentDAO.setStatus(ExperimentDAO.Status.error);
}
- finishExperiment(experimentDAO, logger);
+ experimentRepository.finishExperiment(experimentDAO, logger);
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Finished the experiment: " + experimentDAO);
}).start();
- experimentDTO = experimentDAO.convertToDTO(true);
+ experimentDTO = new ExperimentDTO(true, experimentDAO);
return experimentDTO;
}
/* --------------------------------------- GALAXY CALLS ---------------------------------------------------------*/
-
- /**
- * The runWorkflow will POST the algorithm to the galaxy client
- *
- * @param experimentDTO is the request with the experiment information
- * @return the response to be returned
- */
- public ExperimentDTO runGalaxyWorkflow(ExperimentDTO experimentDTO, Logger logger) {
- logger.LogUserAction("Running a workflow...");
-
- ExperimentDAO experimentDAO = createExperimentInTheDatabase(experimentDTO, logger);
- logger.LogUserAction("Created experiment with uuid :" + experimentDAO.getUuid());
-
-
- // Run the 1st algorithm from the list
- String workflowId = experimentDTO.getAlgorithm().getName();
-
- // Get the parameters
- List<ExaremeAlgorithmRequestParamDTO> algorithmParameters
- = experimentDTO.getAlgorithm().getParameters();
-
- // Convert the parameters to workflow parameters
- HashMap<String, String> algorithmParamsIncludingEmpty = new HashMap<>();
- if (algorithmParameters != null) {
- for (ExaremeAlgorithmRequestParamDTO param : algorithmParameters) {
- algorithmParamsIncludingEmpty.put(param.getName(), param.getValue());
- }
- }
-
- // Get all the algorithm parameters because the frontend provides only the non-null
- final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
- final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
- Workflow workflow = null;
- for (Workflow curWorkflow : workflowsClient.getWorkflows()) {
- if (curWorkflow.getId().equals(workflowId)) {
- workflow = curWorkflow;
- break;
- }
- }
- if (workflow == null) {
- logger.LogUserAction("Could not find algorithm code: " + workflowId);
- throw new BadRequestException("Could not find galaxy algorithm.");
- }
- final WorkflowDetails workflowDetails = workflowsClient.showWorkflow(workflow.getId());
- for (Map.Entry<String, WorkflowInputDefinition> workflowParameter : workflowDetails.getInputs().entrySet()) {
- if (!(algorithmParamsIncludingEmpty.containsKey(workflowParameter.getValue().getUuid()))) {
- algorithmParamsIncludingEmpty.put(workflowParameter.getValue().getUuid(), "");
- }
- }
-
- // Create the body of the request
- HashMap<String, HashMap<String, String>> requestBody = new HashMap<>();
- requestBody.put("inputs", algorithmParamsIncludingEmpty);
- JsonObject requestBodyJson = new JsonParser().parse(gson.toJson(requestBody)).getAsJsonObject();
-
- // Create the request client
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- logger.LogUserAction("Running Galaxy workflow with id: " + workflow.getId());
-
- // Call Galaxy to run the workflow
- Call<PostWorkflowToGalaxyDtoResponse> call = service.postWorkflowToGalaxy(workflow.getId(), galaxyApiKey, requestBodyJson);
- try {
- Response<PostWorkflowToGalaxyDtoResponse> response = call.execute();
-
- if (response.code() == 200) { // Call succeeded
- String responseBody = gson.toJson(response.body());
- logger.LogUserAction("Response: " + responseBody);
-
- String historyId = (String) new JSONObject(responseBody).get("history_id");
- experimentDAO.setWorkflowHistoryId(historyId);
- experimentDAO.setStatus(ExperimentDAO.Status.success);
-
- } else { // Something unexpected happened
- String msgErr = gson.toJson(response.errorBody());
- logger.LogUserAction("Error Response: " + msgErr);
- experimentDTO.setStatus((response.code() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
- }
-
- } catch (Exception e) {
- logger.LogUserAction("An exception occurred: " + e.getMessage());
- experimentDAO.setStatus(ExperimentDAO.Status.error);
- }
- saveExperiment(experimentDAO, logger);
-
- // Start the process of fetching the status
- updateWorkflowExperiment(experimentDAO, logger);
-
- logger.LogUserAction("Run workflow completed!");
-
- experimentDTO = experimentDAO.convertToDTO(true);
- return experimentDTO;
- }
-
-
- /**
- * This method creates a thread that will fetch the workflow result when it is ready
- *
- * @param experimentDAO will be used to fetch it's workflow status, it should have the workflowHistoryId initialized
- * and the result should not already be fetched
- */
- public void updateWorkflowExperiment(ExperimentDAO experimentDAO, Logger logger) {
-
- if (experimentDAO == null) {
- logger.LogUserAction("The experiment does not exist.");
- return;
- }
-
- logger.LogUserAction(" Experiment id : " + experimentDAO.getUuid());
- if (experimentDAO.getWorkflowHistoryId() == null) {
- logger.LogUserAction("History Id does not exist.");
- return;
- }
-
- logger.LogUserAction("Starting Thread...");
- new Thread(() -> {
- while (true) {
- // ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogExperimentAction!
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Thread is running...");
-
- try {
- sleep(2000);
- } catch (InterruptedException e) {
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Sleep was disrupted: " + e.getMessage());
- }
-
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Fetching status for experiment Id: " + experimentDAO.getUuid());
-
- String state = getWorkflowStatus(experimentDAO);
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "State is: " + state);
-
- switch (state) {
- 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 "success":
- // Get only the job result that is visible
- List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experimentDAO);
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Results are: " + workflowJobsResults.toString());
-
- boolean resultFound = false;
- for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
- if (jobResult.getVisible()) {
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Visible result are: " + jobResult.getId());
-
- String result = getWorkflowResultBody(experimentDAO, jobResult.getId());
-
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "ResultDTO: " + result);
- if (result == null) {
- experimentDAO.setStatus(ExperimentDAO.Status.error);
- } else {
- experimentDAO.setResult(result);
- experimentDAO.setStatus(ExperimentDAO.Status.success);
- resultFound = true;
- }
- }
- }
-
- if (!resultFound) { // If there is no visible result
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "No visible result");
- experimentDAO.setStatus(ExperimentDAO.Status.error);
- }
-
- finishExperiment(experimentDAO, logger);
- break;
-
- case "error":
- // Get the job result that failed
- workflowJobsResults = getWorkflowResults(experimentDAO);
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Error results are: " + workflowJobsResults.toString());
-
- boolean failedJobFound = false;
- for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
- if (jobResult.getState().equals("error")) {
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Failed job is: " + jobResult.getId());
-
- String result = getWorkflowJobError(jobResult.getId(), experimentDAO);
-
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Job result: " + result);
- if (result == null) {
- experimentDAO.setStatus(ExperimentDAO.Status.error);
- }
- experimentDAO.setStatus(ExperimentDAO.Status.error);
- failedJobFound = true;
- }
- }
-
- if (!failedJobFound) { // If there is no visible failed job
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "No failed result");
- experimentDAO.setStatus(ExperimentDAO.Status.error);
- }
- finishExperiment(experimentDAO, logger);
- break;
-
- default: // InternalError or unexpected result
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "An unexpected error occurred.");
- experimentDAO.setStatus(ExperimentDAO.Status.error);
- finishExperiment(experimentDAO, logger);
- break;
- }
-
- // If result exists return
- if (experimentDAO.getResult() != null) {
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "ResultDTO exists: " + experimentDAO.getResult());
- return;
- }
- }
- }).start();
- }
-
-
- /**
- * @param experimentDAO The experiment of the workflow
- * @return "pending" -> When the workflow is still running
- * "internalError" -> When an exception or a bad request occurred
- * "error" -> When the workflow produced an error
- * "success" -> When the workflow completed successfully
- */
- public String getWorkflowStatus(ExperimentDAO experimentDAO) {
- String historyId = experimentDAO.getWorkflowHistoryId();
- String experimentName = experimentDAO.getName();
- UUID experimentId = experimentDAO.getUuid();
-
- // ATTENTION: This function is used from a Thread. Only LogExperimentAction should be used, not LogUserAction!
- Logger.LogExperimentAction(experimentName, experimentId, " History Id : " + historyId);
-
- // Create the request client
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<Object> call = service.getWorkflowStatusFromGalaxy(historyId, galaxyApiKey);
-
- String result;
- try {
- Response<Object> response = call.execute();
- if (response.code() >= 400) {
- Logger.LogExperimentAction(experimentName, experimentId, " Response code: "
- + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return "internalError";
- }
- result = new Gson().toJson(response.body());
- Logger.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + result);
-
- } catch (IOException e) {
- Logger.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
- return "internalError";
- }
-
- String state;
- try {
- JSONObject resultJson = new JSONObject(result);
- state = resultJson.getString("state");
- } catch (JSONException e) {
- Logger.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
- return "internalError";
- }
-
- Logger.LogExperimentAction(experimentName, experimentId, " Completed!");
- switch (state) {
- case "ok":
- return "success";
- case "error":
- return "error";
- case "pending":
- case "new":
- case "waiting":
- case "queued":
- return "pending";
- default:
- return "internalError";
- }
- }
-
- /**
- * @param experimentDAO The experiment of the workflow
- * @return a List<GalaxyWorkflowResult> or null when an error occurred
- */
- public List<GalaxyWorkflowResult> getWorkflowResults(ExperimentDAO experimentDAO) {
-
- String historyId = experimentDAO.getWorkflowHistoryId();
- String experimentName = experimentDAO.getName();
- UUID experimentId = experimentDAO.getUuid();
- Logger.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
-
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<List<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(historyId, galaxyApiKey);
-
- List<GalaxyWorkflowResult> getGalaxyWorkflowResultList;
- try {
- Response<List<GalaxyWorkflowResult>> response = call.execute();
- if (response.code() >= 400) {
- Logger.LogExperimentAction(experimentName, experimentId, " Response code: "
- + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return null;
- }
- getGalaxyWorkflowResultList = response.body();
- Logger.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + response.body());
-
- } catch (IOException e) {
- Logger.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
- return null;
- }
-
- Logger.LogExperimentAction(experimentName, experimentId, " Completed!");
- return getGalaxyWorkflowResultList;
-
- }
-
- /**
- * @param experimentDAO The experiment of the workflow
- * @param contentId the id of the job result that we want
- * @return the result of the specific workflow job, null if there was an error
- */
- public String getWorkflowResultBody(ExperimentDAO experimentDAO, String contentId) {
-
- String historyId = experimentDAO.getWorkflowHistoryId();
- String experimentName = experimentDAO.getName();
- UUID experimentId = experimentDAO.getUuid();
-
- Logger.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
-
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<Object> call =
- service.getWorkflowResultsBodyFromGalaxy(historyId, contentId, galaxyApiKey);
-
- String resultJson;
- try {
- Response<Object> response = call.execute();
- if (response.code() >= 400) {
- Logger.LogExperimentAction(experimentName, experimentId, " Response code: "
- + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return null;
- }
- resultJson = new Gson().toJson(response.body());
- Logger.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + resultJson);
-
- } catch (IOException e) {
- Logger.LogExperimentAction(experimentName, experimentId,
- " An exception happened: " + e.getMessage());
- return null;
- }
-
- Logger.LogExperimentAction(experimentName, experimentId, " Completed!");
- return formattingGalaxyResult(resultJson);
- }
-
-
- /**
- * @param jobId the id of the workflow job that failed
- * @return the error that was produced or null if an error occurred
- */
- public String getWorkflowJobError(String jobId, ExperimentDAO experimentDAO) {
- String experimentName = experimentDAO.getName();
- UUID experimentId = experimentDAO.getUuid();
-
- Logger.LogExperimentAction(experimentName, experimentId, " jobId : " + jobId);
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId, galaxyApiKey);
-
- String fullError;
- String returnError;
- try {
- Response<Object> response = callError.execute();
- if (response.code() >= 400) {
- Logger.LogExperimentAction(experimentName, experimentId, "Response code: "
- + response.code() + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return null;
- }
-
- // Parsing the stderr of the job that failed
- String jsonString = new Gson().toJson(response.body());
- JsonElement jsonElement = new JsonParser().parse(jsonString);
- JsonObject rootObject = jsonElement.getAsJsonObject();
- fullError = rootObject.get("stderr").getAsString();
- Logger.LogExperimentAction(experimentName, experimentId, "Error: " + fullError);
-
- String[] arrOfStr = fullError.split("ValueError", 0);
- String specError = arrOfStr[arrOfStr.length - 1];
- returnError = specError.substring(1);
- Logger.LogExperimentAction(experimentName, experimentId, "Parsed Error: " + returnError);
-
- } catch (IOException e) {
- Logger.LogExperimentAction(experimentName, experimentId, "Exception: " + e.getMessage());
- return null;
- }
-
- Logger.LogExperimentAction(experimentName, experimentId, "Completed successfully!");
-
- return returnError;
- }
}
diff --git a/src/main/java/eu/hbp/mip/services/GalaxyService.java b/src/main/java/eu/hbp/mip/services/GalaxyService.java
new file mode 100644
index 000000000..80590c7be
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/services/GalaxyService.java
@@ -0,0 +1,454 @@
+package eu.hbp.mip.services;
+
+import com.github.jmchilton.blend4j.galaxy.GalaxyInstance;
+import com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory;
+import com.github.jmchilton.blend4j.galaxy.WorkflowsClient;
+import com.github.jmchilton.blend4j.galaxy.beans.Workflow;
+import com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails;
+import com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition;
+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;
+import eu.hbp.mip.models.DTOs.ExaremeAlgorithmRequestParamDTO;
+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.utils.Exceptions.BadRequestException;
+import eu.hbp.mip.utils.JsonConverters;
+import eu.hbp.mip.utils.Logger;
+import org.codehaus.jettison.json.JSONException;
+import org.codehaus.jettison.json.JSONObject;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.stereotype.Service;
+import retrofit2.Call;
+import retrofit2.Response;
+
+import java.io.IOException;
+import java.util.*;
+
+import static java.lang.Thread.sleep;
+
+@Service
+public class GalaxyService {
+
+ private final ActiveUserService activeUserService;
+ private final ExperimentRepository experimentRepository;
+ public GalaxyService(
+ ActiveUserService activeUserService,
+ ExperimentRepository experimentRepository
+ ) {
+ this.activeUserService = activeUserService;
+ this.experimentRepository = experimentRepository;
+ }
+ @Value("#{'${services.galaxy.galaxyUrl}'}")
+ private String galaxyUrl;
+
+ @Value("#{'${services.galaxy.galaxyApiKey}'}")
+ private String galaxyApiKey;
+
+ private static final Gson gson = new Gson();
+
+ /**
+ * The runWorkflow will POST the algorithm to the galaxy client
+ *
+ * @param experimentDTO is the request with the experiment information
+ * @return the response to be returned
+ */
+ public ExperimentDTO runGalaxyWorkflow(ExperimentDTO experimentDTO, Logger logger) {
+ logger.LogUserAction("Running a workflow...");
+
+ ExperimentDAO experimentDAO = experimentRepository.createExperimentInTheDatabase(experimentDTO, activeUserService.getActiveUser(), logger);
+ logger.LogUserAction("Created experiment with uuid :" + experimentDAO.getUuid());
+
+
+ // Run the 1st algorithm from the list
+ String workflowId = experimentDTO.getAlgorithm().getName();
+
+ // Get the parameters
+ List<ExaremeAlgorithmRequestParamDTO> algorithmParameters
+ = experimentDTO.getAlgorithm().getParameters();
+
+ // Convert the parameters to workflow parameters
+ HashMap<String, String> algorithmParamsIncludingEmpty = new HashMap<>();
+ if (algorithmParameters != null) {
+ for (ExaremeAlgorithmRequestParamDTO param : algorithmParameters) {
+ algorithmParamsIncludingEmpty.put(param.getName(), param.getValue());
+ }
+ }
+
+ // Get all the algorithm parameters because the frontend provides only the non-null
+ final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
+ final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
+ Workflow workflow = null;
+ for (Workflow curWorkflow : workflowsClient.getWorkflows()) {
+ if (curWorkflow.getId().equals(workflowId)) {
+ workflow = curWorkflow;
+ break;
+ }
+ }
+ if (workflow == null) {
+ logger.LogUserAction("Could not find algorithm code: " + workflowId);
+ throw new BadRequestException("Could not find galaxy algorithm.");
+ }
+ final WorkflowDetails workflowDetails = workflowsClient.showWorkflow(workflow.getId());
+ for (Map.Entry<String, WorkflowInputDefinition> workflowParameter : workflowDetails.getInputs().entrySet()) {
+ if (!(algorithmParamsIncludingEmpty.containsKey(workflowParameter.getValue().getUuid()))) {
+ algorithmParamsIncludingEmpty.put(workflowParameter.getValue().getUuid(), "");
+ }
+ }
+
+ // Create the body of the request
+ HashMap<String, HashMap<String, String>> requestBody = new HashMap<>();
+ requestBody.put("inputs", algorithmParamsIncludingEmpty);
+ JsonObject requestBodyJson = new JsonParser().parse(gson.toJson(requestBody)).getAsJsonObject();
+
+ // Create the request client
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ logger.LogUserAction("Running Galaxy workflow with id: " + workflow.getId());
+
+ // Call Galaxy to run the workflow
+ Call<PostWorkflowToGalaxyDtoResponse> call = service.postWorkflowToGalaxy(workflow.getId(), galaxyApiKey, requestBodyJson);
+ try {
+ Response<PostWorkflowToGalaxyDtoResponse> response = call.execute();
+
+ if (response.code() == 200) { // Call succeeded
+ String responseBody = gson.toJson(response.body());
+ logger.LogUserAction("Response: " + responseBody);
+
+ String historyId = (String) new JSONObject(responseBody).get("history_id");
+ experimentDAO.setWorkflowHistoryId(historyId);
+ experimentDAO.setStatus(ExperimentDAO.Status.success);
+
+ } else { // Something unexpected happened
+ String msgErr = gson.toJson(response.errorBody());
+ logger.LogUserAction("Error Response: " + msgErr);
+ experimentDTO.setStatus((response.code() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
+ }
+
+ } catch (Exception e) {
+ logger.LogUserAction("An exception occurred: " + e.getMessage());
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+ experimentRepository.saveExperiment(experimentDAO, logger);
+
+ // Start the process of fetching the status
+ updateWorkflowExperiment(experimentDAO, logger);
+
+ logger.LogUserAction("Run workflow completed!");
+
+ experimentDTO = new ExperimentDTO(true, experimentDAO);
+ return experimentDTO;
+ }
+
+
+
+ /**
+ * @param experimentDAO The experiment of the workflow
+ * @return "pending" -> When the workflow is still running
+ * "internalError" -> When an exception or a bad request occurred
+ * "error" -> When the workflow produced an error
+ * "success" -> When the workflow completed successfully
+ */
+ public String getWorkflowStatus(ExperimentDAO experimentDAO) {
+ String historyId = experimentDAO.getWorkflowHistoryId();
+ String experimentName = experimentDAO.getName();
+ UUID experimentId = experimentDAO.getUuid();
+
+ // ATTENTION: This function is used from a Thread. Only LogExperimentAction should be used, not LogUserAction!
+ Logger.LogExperimentAction(experimentName, experimentId, " History Id : " + historyId);
+
+ // Create the request client
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> call = service.getWorkflowStatusFromGalaxy(historyId, galaxyApiKey);
+
+ String result;
+ try {
+ Response<Object> response = call.execute();
+ if (response.code() >= 400) {
+ Logger.LogExperimentAction(experimentName, experimentId, " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return "internalError";
+ }
+ result = new Gson().toJson(response.body());
+ Logger.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + result);
+
+ } catch (IOException e) {
+ Logger.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
+ return "internalError";
+ }
+
+ String state;
+ try {
+ JSONObject resultJson = new JSONObject(result);
+ state = resultJson.getString("state");
+ } catch (JSONException e) {
+ Logger.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
+ return "internalError";
+ }
+
+ Logger.LogExperimentAction(experimentName, experimentId, " Completed!");
+ switch (state) {
+ case "ok":
+ return "success";
+ case "error":
+ return "error";
+ case "pending":
+ case "new":
+ case "waiting":
+ case "queued":
+ return "pending";
+ default:
+ return "internalError";
+ }
+ }
+
+ /**
+ * @param experimentDAO The experiment of the workflow
+ * @return a List<GalaxyWorkflowResult> or null when an error occurred
+ */
+ public List<GalaxyWorkflowResult> getWorkflowResults(ExperimentDAO experimentDAO) {
+
+ String historyId = experimentDAO.getWorkflowHistoryId();
+ String experimentName = experimentDAO.getName();
+ UUID experimentId = experimentDAO.getUuid();
+ Logger.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
+
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<List<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(historyId, galaxyApiKey);
+
+ List<GalaxyWorkflowResult> getGalaxyWorkflowResultList;
+ try {
+ Response<List<GalaxyWorkflowResult>> response = call.execute();
+ if (response.code() >= 400) {
+ Logger.LogExperimentAction(experimentName, experimentId, " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+ getGalaxyWorkflowResultList = response.body();
+ Logger.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + response.body());
+
+ } catch (IOException e) {
+ Logger.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
+ return null;
+ }
+
+ Logger.LogExperimentAction(experimentName, experimentId, " Completed!");
+ return getGalaxyWorkflowResultList;
+
+ }
+
+ /**
+ * @param experimentDAO The experiment of the workflow
+ * @param contentId the id of the job result that we want
+ * @return the result of the specific workflow job, null if there was an error
+ */
+ public String getWorkflowResultBody(ExperimentDAO experimentDAO, String contentId) {
+
+ String historyId = experimentDAO.getWorkflowHistoryId();
+ String experimentName = experimentDAO.getName();
+ UUID experimentId = experimentDAO.getUuid();
+
+ Logger.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
+
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> call =
+ service.getWorkflowResultsBodyFromGalaxy(historyId, contentId, galaxyApiKey);
+
+ String resultJson;
+ try {
+ Response<Object> response = call.execute();
+ if (response.code() >= 400) {
+ Logger.LogExperimentAction(experimentName, experimentId, " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+ resultJson = new Gson().toJson(response.body());
+ Logger.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + resultJson);
+
+ } catch (IOException e) {
+ Logger.LogExperimentAction(experimentName, experimentId,
+ " An exception happened: " + e.getMessage());
+ return null;
+ }
+
+ Logger.LogExperimentAction(experimentName, experimentId, " Completed!");
+ return formattingGalaxyResult(resultJson);
+ }
+
+ private String formattingGalaxyResult(String result) {
+ List<LinkedTreeMap<String,Object>> jsonObject = JsonConverters.convertJsonStringToObject(result, new ArrayList<ArrayList<Object>>().getClass());
+ LinkedTreeMap<String,Object> firstResult = jsonObject.get(0);
+ jsonObject = (List<LinkedTreeMap<String, Object>>) firstResult.get("result");
+ List<LinkedTreeMap<String,Object>> finalJsonObject = new ArrayList<>();
+ finalJsonObject.add(jsonObject.get(0));
+ return JsonConverters.convertObjectToJsonString(finalJsonObject);
+ }
+
+
+ /**
+ * @param jobId the id of the workflow job that failed
+ * @return the error that was produced or null if an error occurred
+ */
+ public String getWorkflowJobError(String jobId, ExperimentDAO experimentDAO) {
+ String experimentName = experimentDAO.getName();
+ UUID experimentId = experimentDAO.getUuid();
+
+ Logger.LogExperimentAction(experimentName, experimentId, " jobId : " + jobId);
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId, galaxyApiKey);
+
+ String fullError;
+ String returnError;
+ try {
+ Response<Object> response = callError.execute();
+ if (response.code() >= 400) {
+ Logger.LogExperimentAction(experimentName, experimentId, "Response code: "
+ + response.code() + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+
+ // Parsing the stderr of the job that failed
+ String jsonString = new Gson().toJson(response.body());
+ JsonElement jsonElement = new JsonParser().parse(jsonString);
+ JsonObject rootObject = jsonElement.getAsJsonObject();
+ fullError = rootObject.get("stderr").getAsString();
+ Logger.LogExperimentAction(experimentName, experimentId, "Error: " + fullError);
+
+ String[] arrOfStr = fullError.split("ValueError", 0);
+ String specError = arrOfStr[arrOfStr.length - 1];
+ returnError = specError.substring(1);
+ Logger.LogExperimentAction(experimentName, experimentId, "Parsed Error: " + returnError);
+
+ } catch (IOException e) {
+ Logger.LogExperimentAction(experimentName, experimentId, "Exception: " + e.getMessage());
+ return null;
+ }
+
+ Logger.LogExperimentAction(experimentName, experimentId, "Completed successfully!");
+
+ return returnError;
+ }
+
+ /**
+ * This method creates a thread that will fetch the workflow result when it is ready
+ *
+ * @param experimentDAO will be used to fetch it's workflow status, it should have the workflowHistoryId initialized
+ * and the result should not already be fetched
+ */
+ public void updateWorkflowExperiment(ExperimentDAO experimentDAO, Logger logger) {
+
+ if (experimentDAO == null) {
+ logger.LogUserAction("The experiment does not exist.");
+ return;
+ }
+
+ logger.LogUserAction(" Experiment id : " + experimentDAO.getUuid());
+ if (experimentDAO.getWorkflowHistoryId() == null) {
+ logger.LogUserAction("History Id does not exist.");
+ return;
+ }
+
+ logger.LogUserAction("Starting Thread...");
+ new Thread(() -> {
+ while (true) {
+ // ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogExperimentAction!
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Thread is running...");
+
+ try {
+ sleep(2000);
+ } catch (InterruptedException e) {
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Sleep was disrupted: " + e.getMessage());
+ }
+
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Fetching status for experiment Id: " + experimentDAO.getUuid());
+
+ String state = getWorkflowStatus(experimentDAO);
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "State is: " + state);
+
+ switch (state) {
+ 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 "success":
+ // Get only the job result that is visible
+ List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experimentDAO);
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Results are: " + workflowJobsResults.toString());
+
+ boolean resultFound = false;
+ for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
+ if (jobResult.getVisible()) {
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Visible result are: " + jobResult.getId());
+
+ String result = getWorkflowResultBody(experimentDAO, jobResult.getId());
+
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "ResultDTO: " + result);
+ if (result == null) {
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ } else {
+ experimentDAO.setResult(result);
+ experimentDAO.setStatus(ExperimentDAO.Status.success);
+ resultFound = true;
+ }
+ }
+ }
+
+ if (!resultFound) { // If there is no visible result
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "No visible result");
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+
+ experimentRepository.finishExperiment(experimentDAO, logger);
+ break;
+
+ case "error":
+ // Get the job result that failed
+ workflowJobsResults = getWorkflowResults(experimentDAO);
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Error results are: " + workflowJobsResults.toString());
+
+ boolean failedJobFound = false;
+ for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
+ if (jobResult.getState().equals("error")) {
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Failed job is: " + jobResult.getId());
+
+ String result = getWorkflowJobError(jobResult.getId(), experimentDAO);
+
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Job result: " + result);
+ if (result == null) {
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ failedJobFound = true;
+ }
+ }
+
+ if (!failedJobFound) { // If there is no visible failed job
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "No failed result");
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+ experimentRepository.finishExperiment(experimentDAO, logger);
+ break;
+
+ default: // InternalError or unexpected result
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "An unexpected error occurred.");
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ experimentRepository.finishExperiment(experimentDAO, logger);
+ break;
+ }
+
+ // If result exists return
+ if (experimentDAO.getResult() != null) {
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "ResultDTO exists: " + experimentDAO.getResult());
+ return;
+ }
+ }
+ }).start();
+ }
+}
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index 8aadac388..d8d542b6b 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -35,7 +35,7 @@ spring:
### EXTERNAL SERVICES ###
services:
mipengine:
- algorithmsUrl: "http://192.168.124.129:5000/algorithms"
+ algorithmsUrl: "http://127.0.0.1:5000/algorithms"
exareme:
queryExaremeUrl: "http://127.0.0.1:9090/mining/query"
algorithmsUrl: "http://127.0.0.1:9090/mining/algorithms.json"
--
GitLab
From 82c131267c4de8e4e6eb4dd7e94225dfc70a01c5 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Fri, 9 Jul 2021 07:07:13 -0700
Subject: [PATCH 10/12] Add the TabularVisualizationDTO class
---
.../models/DTOs/TabularVisualizationDTO.java | 33 +++++++++++++++++++
.../eu/hbp/mip/services/GalaxyService.java | 2 ++
2 files changed, 35 insertions(+)
create mode 100644 src/main/java/eu/hbp/mip/models/DTOs/TabularVisualizationDTO.java
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/TabularVisualizationDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/TabularVisualizationDTO.java
new file mode 100644
index 000000000..3e17932f7
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/TabularVisualizationDTO.java
@@ -0,0 +1,33 @@
+package eu.hbp.mip.models.DTOs;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+
+import java.util.HashMap;
+import java.util.List;
+
+@Data
+@AllArgsConstructor
+public class TabularVisualizationDTO {
+ private final String name;
+ private final String profile;
+ private final HashMap<String, List<Field>> schema;
+ private final List<List<Object>> data;
+
+
+ public TabularVisualizationDTO(MIPEngineAlgorithmResultDTO mipEngineAlgorithmResultDTO) {
+ HashMap<String, List<TabularVisualizationDTO.Field>> schema = new HashMap<>();
+ schema.put("fields", mipEngineAlgorithmResultDTO.getColumns());
+ this.name = mipEngineAlgorithmResultDTO.getTitle();
+ this.profile = "tabular-data-resource";
+ this.schema = schema;
+ this.data = mipEngineAlgorithmResultDTO.getData();
+ }
+ @Data
+ @AllArgsConstructor
+ public static class Field {
+ private final String name;
+ private final String type;
+ }
+}
+
diff --git a/src/main/java/eu/hbp/mip/services/GalaxyService.java b/src/main/java/eu/hbp/mip/services/GalaxyService.java
index 80590c7be..cc10afebd 100644
--- a/src/main/java/eu/hbp/mip/services/GalaxyService.java
+++ b/src/main/java/eu/hbp/mip/services/GalaxyService.java
@@ -20,6 +20,7 @@ import eu.hbp.mip.models.galaxy.GalaxyWorkflowResult;
import eu.hbp.mip.models.galaxy.PostWorkflowToGalaxyDtoResponse;
import eu.hbp.mip.repositories.ExperimentRepository;
import eu.hbp.mip.utils.Exceptions.BadRequestException;
+import eu.hbp.mip.utils.Exceptions.InternalServerError;
import eu.hbp.mip.utils.JsonConverters;
import eu.hbp.mip.utils.Logger;
import org.codehaus.jettison.json.JSONException;
@@ -364,6 +365,7 @@ public class GalaxyService {
sleep(2000);
} catch (InterruptedException e) {
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Sleep was disrupted: " + e.getMessage());
+ throw new InternalServerError(e.getMessage());
}
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Fetching status for experiment Id: " + experimentDAO.getUuid());
--
GitLab
From 5e48e460c7571092c0d57f642e4d8d91edd95a32 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Fri, 16 Jul 2021 07:30:07 -0700
Subject: [PATCH 11/12] Updated Exareme algorithm results to result
---
.../eu/hbp/mip/controllers/AlgorithmsAPI.java | 19 +++++++++++++------
.../DTOs/ExaremeAlgorithmResultDTO.java | 2 +-
.../hbp/mip/services/ExperimentService.java | 8 ++++----
3 files changed, 18 insertions(+), 11 deletions(-)
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index 5ac49a402..a15fd37cd 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -27,6 +27,7 @@ import retrofit2.Call;
import retrofit2.Response;
import java.io.IOException;
+import java.net.ConnectException;
import java.util.ArrayList;
import java.util.List;
@@ -69,27 +70,27 @@ public class AlgorithmsAPI {
logger.LogUserAction("Executing...");
ArrayList<ExaremeAlgorithmDTO> mipengineAlgorithms = getMIPEngineAlgorithms(logger);
- logger.LogUserAction("Loaded " + mipengineAlgorithms.size() + " mipengine algorithms");
ArrayList<ExaremeAlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms(logger);
- logger.LogUserAction("Loaded " + exaremeAlgorithms.size() + " exareme algorithms");
ArrayList<ExaremeAlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows(logger);
- logger.LogUserAction("Loaded " + galaxyAlgorithms.size() + " galaxy algorithms");
ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>();
if (exaremeAlgorithms != null) {
algorithms.addAll(exaremeAlgorithms);
+ logger.LogUserAction("Loaded " + exaremeAlgorithms.size() + " exareme algorithms");
} else {
- logger.LogUserAction("Getting exareme algorithms failed and returned null");
+ logger.LogUserAction("Fetching exareme algorithms failed");
}
if (mipengineAlgorithms != null) {
algorithms.addAll(mipengineAlgorithms);
+ logger.LogUserAction("Loaded " + mipengineAlgorithms.size() + " mipengine algorithms");
} else {
- logger.LogUserAction("Getting mipengine algorithms failed and returned null");
+ logger.LogUserAction("Fetching mipengine algorithms failed");
}
if (galaxyAlgorithms != null) {
algorithms.addAll(galaxyAlgorithms);
+ logger.LogUserAction("Loaded " + galaxyAlgorithms.size() + " galaxy algorithms");
} else {
- logger.LogUserAction("Getting galaxy workflows failed and returned null");
+ logger.LogUserAction("Fetching galaxy workflows failed");
}
List<String> disabledAlgorithms = new ArrayList<>();
@@ -126,6 +127,9 @@ public class AlgorithmsAPI {
new TypeToken<ArrayList<ExaremeAlgorithmDTO>>() {
}.getType()
);
+ } catch (ConnectException e) {
+ logger.LogUserAction("An exception occurred: " + e.getMessage());
+ return null;
} catch (IOException e) {
logger.LogUserAction("An exception occurred: " + e.getMessage());
return null;
@@ -153,6 +157,9 @@ public class AlgorithmsAPI {
new TypeToken<ArrayList<MIPEngineAlgorithmDTO>>() {
}.getType()
);
+ } catch (ConnectException e) {
+ logger.LogUserAction("An exception occurred: " + e.getMessage());
+ return null;
} catch (IOException e) {
logger.LogUserAction("An exception occurred: " + e.getMessage());
return null;
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java
index d1f5947c8..88b5fb627 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java
@@ -9,7 +9,7 @@ import java.util.List;
@AllArgsConstructor
public class ExaremeAlgorithmResultDTO {
private int code;
- private List<Object> results;
+ private List<Object> result;
}
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index c421fd471..1bd848ed6 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -209,9 +209,9 @@ public class ExperimentService {
// Results are stored in the experiment object
ExaremeAlgorithmResultDTO exaremeAlgorithmResultDTO = runExperiment(experimentDTO, logger);
- logger.LogUserAction("Experiment with uuid: " + experimentDTO.getUuid() + "gave response code: " + exaremeAlgorithmResultDTO.getCode() + " and result: " + exaremeAlgorithmResultDTO.getResults());
+ logger.LogUserAction("Experiment with uuid: " + experimentDTO.getUuid() + "gave response code: " + exaremeAlgorithmResultDTO.getCode() + " and result: " + exaremeAlgorithmResultDTO.getResult());
- experimentDTO.setResult((exaremeAlgorithmResultDTO.getCode() >= 400) ? null : exaremeAlgorithmResultDTO.getResults());
+ experimentDTO.setResult((exaremeAlgorithmResultDTO.getCode() >= 400) ? null : exaremeAlgorithmResultDTO.getResult());
experimentDTO.setStatus((exaremeAlgorithmResultDTO.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
return experimentDTO;
@@ -504,9 +504,9 @@ public class ExperimentService {
// Results are stored in the experiment object
ExaremeAlgorithmResultDTO exaremeAlgorithmResultDTO = runExperiment(finalExperimentDTO, logger);
- Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Experiment with uuid: " + experimentDAO.getUuid() + "gave response code: " + exaremeAlgorithmResultDTO.getCode() + " and result: " + exaremeAlgorithmResultDTO.getResults());
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Experiment with uuid: " + experimentDAO.getUuid() + "gave response code: " + exaremeAlgorithmResultDTO.getCode() + " and result: " + exaremeAlgorithmResultDTO.getResult());
- experimentDAO.setResult((exaremeAlgorithmResultDTO.getCode() >= 400) ? null : JsonConverters.convertObjectToJsonString(exaremeAlgorithmResultDTO.getResults()));
+ experimentDAO.setResult((exaremeAlgorithmResultDTO.getCode() >= 400) ? null : JsonConverters.convertObjectToJsonString(exaremeAlgorithmResultDTO.getResult()));
experimentDAO.setStatus((exaremeAlgorithmResultDTO.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
} catch (Exception e) {
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "There was an exception: " + e.getMessage());
--
GitLab
From 3abaf92884ff6e1797b5a268821f0e0af4ed236e Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Mon, 19 Jul 2021 01:23:53 -0700
Subject: [PATCH 12/12] Remove debugging comments.
---
src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java | 2 --
1 file changed, 2 deletions(-)
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java b/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java
index 449765fc9..e5d0b04c5 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java
@@ -78,7 +78,6 @@ public class ExperimentAPI {
@ApiOperation(value = "Create an experiment", response = ExperimentDTO.class)
@RequestMapping(method = RequestMethod.POST)
public ResponseEntity<String> createExperiment(Authentication authentication, @RequestBody ExperimentDTO experimentDTO) {
- new Logger(activeUserService.getActiveUser().getUsername(),"(POST) /experiments").LogUserAction("TEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEST");
experimentDTO = experimentService.createExperiment(authentication, experimentDTO, new Logger(activeUserService.getActiveUser().getUsername(),"(POST) /experiments"));
return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.CREATED);
}
@@ -104,7 +103,6 @@ public class ExperimentAPI {
@ApiOperation(value = "Create a transient experiment", response = ExperimentDTO.class)
@RequestMapping(value = "/transient", method = RequestMethod.POST)
public ResponseEntity<String> createTransientExperiment(Authentication authentication, @RequestBody ExperimentDTO experimentDTO) {
- new Logger(activeUserService.getActiveUser().getUsername(),"(POST) /experiments").LogUserAction("TEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEST");
experimentDTO = experimentService.createTransientExperiment(authentication, experimentDTO, new Logger(activeUserService.getActiveUser().getUsername(), "(POST) /experiments/transient"));
return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.OK);
}
--
GitLab