diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
new file mode 100644
index 0000000000000000000000000000000000000000..492358c59c14801df01548032d0722a1c929a5bb
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
@@ -0,0 +1,157 @@
+package eu.hbp.mip.controllers;
+
+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.google.gson.Gson;
+import eu.hbp.mip.controllers.retrofit.RetroFitGalaxyClients;
+import eu.hbp.mip.controllers.retrofit.RetrofitClientInstance;
+import eu.hbp.mip.model.AlgorithmDTO;
+import eu.hbp.mip.model.galaxy.WorkflowDTO;
+import eu.hbp.mip.utils.HTTPUtil;
+import eu.hbp.mip.utils.UserActionLogging;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+import retrofit2.Call;
+import retrofit2.Response;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
+
+import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
+
+@RestController
+@RequestMapping(value = "/algorithms", produces = {APPLICATION_JSON_VALUE})
+@Api(value = "/algorithms")
+public class AlgorithmsApi {
+
+ private static final Gson gson = new Gson();
+
+ @Value("#{'${services.exareme.algorithmsUrl}'}")
+ private String exaremeAlgorithmsUrl;
+
+ @Value("#{'${services.galaxy.galaxyUrl}'}")
+ private String galaxyUrl;
+
+ @Value("#{'${services.galaxy.galaxyApiKey}'}")
+ private String galaxyApiKey;
+
+ @ApiOperation(value = "List all algorithms", response = String.class)
+ @RequestMapping(value = "/", method = RequestMethod.GET)
+ public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
+ UserActionLogging.LogAction("List all algorithms", "");
+
+ List<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms();
+ List<AlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows();
+
+ List<AlgorithmDTO> algorithms = new LinkedList<>();
+ if (exaremeAlgorithms != null) {
+ algorithms.addAll(exaremeAlgorithms);
+ } else {
+ UserActionLogging.LogAction("List all algorithms",
+ "Getting exareme algorithms failed and returned null");
+ }
+ if (galaxyAlgorithms != null) {
+ algorithms.addAll(galaxyAlgorithms);
+ } else {
+ UserActionLogging.LogAction("List all algorithms",
+ "Getting galaxy workflows failed and returned null");
+ }
+
+ return ResponseEntity.ok(algorithms);
+ }
+
+ /**
+ * This method gets all the available exareme algorithms and
+ *
+ * @return a list of AlgorithmDTOs or null if something fails
+ */
+ public List<AlgorithmDTO> getExaremeAlgorithms() {
+ UserActionLogging.LogAction("List exareme algorithms", "");
+
+ List<AlgorithmDTO> algorithms = new LinkedList<>();
+ // Get exareme algorithms
+ try {
+ StringBuilder response = new StringBuilder();
+ HTTPUtil.sendGet(exaremeAlgorithmsUrl, response);
+
+ algorithms = gson.fromJson(response.toString(), algorithms.getClass());
+ } catch (IOException e) {
+ UserActionLogging.LogAction("List exareme algorithms", "An exception occurred: " + e.getMessage());
+ return null;
+ }
+
+ UserActionLogging.LogAction("List exareme algorithms",
+ "Completed, returned " + algorithms.size() + " algorithms.");
+ return algorithms;
+ }
+
+ /**
+ * This method gets all the available galaxy workflows, converts them into algorithms and
+ *
+ * @return a list of AlgorithmDTOs or null if something fails
+ */
+ public List<AlgorithmDTO> getGalaxyWorkflows() {
+ UserActionLogging.LogAction("List Galaxy workflows", "");
+
+ List<Workflow> workflowList = null;
+ try {
+ // Get all the workflows with the galaxy client
+ final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
+ final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
+
+ workflowList = new ArrayList<>(workflowsClient.getWorkflows());
+ } catch (Exception e) {
+ UserActionLogging.LogAction("List Galaxy workflows", "Error when calling list galaxy workflows: " + e.getMessage());
+
+ return null;
+ }
+
+ // Get the workflow details with the custom client to receive them as a WorkflowDTO
+ List<WorkflowDTO> workflows = new LinkedList<>();
+ // Create the request client
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ for (Workflow workflow : workflowList) {
+ // Call Galaxy to run the workflow
+ Call<WorkflowDTO> call = service.getWorkflowFromGalaxy(workflow.getId(), galaxyApiKey);
+ try {
+ Response<WorkflowDTO> response = call.execute();
+
+ if (response.code() == 200) { // Call succeeded
+ workflows.add(response.body());
+
+ } else { // Something unexpected happened
+ String msgErr = gson.toJson(response.errorBody());
+ UserActionLogging.LogAction("List Galaxy workflows", "Error Response: " + msgErr);
+ return null;
+ }
+ } catch (Exception e) {
+ UserActionLogging.LogAction("List Galaxy workflows", "An exception occurred: " + e.getMessage());
+ return null;
+ }
+ }
+ UserActionLogging.LogAction("List Galaxy workflows", "Workflows fetched: " + workflows.size());
+
+ // Convert the workflows to algorithms
+ List<AlgorithmDTO> algorithms = new LinkedList<>();
+ for (WorkflowDTO workflow : workflows) {
+ UserActionLogging.LogAction("List Galaxy workflows", "Converting workflow: " + workflow);
+
+ algorithms.add(workflow.convertToAlgorithmDTO());
+
+ UserActionLogging.LogAction("List Galaxy workflows",
+ "Converted algorithm: " + algorithms.get(algorithms.size() - 1));
+ }
+
+ UserActionLogging.LogAction("List Galaxy workflows", "Completed!");
+ 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 b936cdd35a7dadb97ca7d1d95a2a0167d00527b8..927bcf8f13a23a87f816c602077bf3570277120e 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -10,10 +10,11 @@ import com.google.common.collect.Lists;
import com.google.gson.*;
import eu.hbp.mip.controllers.retrofit.RetroFitGalaxyClients;
import eu.hbp.mip.controllers.retrofit.RetrofitClientInstance;
-import eu.hbp.mip.dto.ErrorResponse;
-import eu.hbp.mip.dto.GalaxyWorkflowResult;
-import eu.hbp.mip.dto.PostWorkflowToGalaxyDtoResponse;
import eu.hbp.mip.model.*;
+import eu.hbp.mip.model.ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO;
+import eu.hbp.mip.model.galaxy.ErrorResponse;
+import eu.hbp.mip.model.galaxy.GalaxyWorkflowResult;
+import eu.hbp.mip.model.galaxy.PostWorkflowToGalaxyDtoResponse;
import eu.hbp.mip.repositories.ExperimentRepository;
import eu.hbp.mip.repositories.ModelRepository;
import eu.hbp.mip.utils.HTTPUtil;
@@ -41,15 +42,13 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/experiments")
public class ExperimentApi {
- //private static final Logger LOGGER = LoggerFactory.getLogger(ExperimentApi.class);
-
private static final Gson gson = new Gson();
private static final Gson gsonOnlyExposed = new GsonBuilder().serializeNulls()
.setDateFormat("yyyy-MM-dd'T'HH:mm:ssZ").excludeFieldsWithoutExposeAnnotation().create();
- @Value("#{'${services.exareme.miningExaremeUrl:http://localhost:9090/mining/query}'}")
- public String miningExaremeQueryUrl;
+ @Value("#{'${services.exareme.miningExaremeUrl}'}")
+ public String exaremeUrl;
@Value("#{'${services.workflows.workflowUrl}'}")
private String workflowUrl;
@@ -57,6 +56,12 @@ public class ExperimentApi {
@Value("#{'${services.workflows.jwtSecret}'}")
private String jwtSecret;
+ @Value("#{'${services.galaxy.galaxyUrl}'}")
+ private String galaxyUrl;
+
+ @Value("#{'${services.galaxy.galaxyApiKey}'}")
+ private String galaxyApiKey;
+
@Autowired
private UserInfo userInfo;
@@ -66,69 +71,110 @@ public class ExperimentApi {
@Autowired
private ExperimentRepository experimentRepository;
- @Value("#{'${services.galaxy.galaxyUrl}'}")
- private String galaxyUrl;
+ @ApiOperation(value = "Create an experiment", response = Experiment.class)
+ @RequestMapping(value = "/runAlgorithm", method = RequestMethod.POST)
+ public ResponseEntity<String> runExperiment(@RequestBody ExperimentExecutionDTO experimentExecutionDTO) {
+ UserActionLogging.LogAction("Run algorithm", "Running the algorithm...");
- @Value("#{'${services.galaxy.galaxyApiKey}'}")
- private String galaxyApiKey;
+ // Get the type of algorithm
+ String algorithmType = experimentExecutionDTO.getAlgorithms().get(0).getType();
- @ApiOperation(value = "Create an experiment on Exareme", response = Experiment.class)
- @RequestMapping(value = "/exareme", method = RequestMethod.POST)
- public ResponseEntity<String> runExaremeExperiment(@RequestBody ExperimentQuery expQuery) {
- //LOGGER.info("send ExaremeExperiment");
+ if (algorithmType.equals("workflow")) {
+ return runGalaxyWorkflow(experimentExecutionDTO);
+ } else {
+ return runExaremeAlgorithm(experimentExecutionDTO);
+ }
- Experiment experiment = saveExperiment(expQuery);
+ }
- String algoCode = expQuery.getAlgorithms().get(0).getCode();
- List<AlgorithmParam> params = expQuery.getAlgorithms().get(0).getParameters();
- new Thread(() -> {
- List<HashMap<String, String>> queryList = new ArrayList<HashMap<String, String>>();
+ /**
+ * The runExaremeExperiment will POST the algorithm to the exareme client
+ *
+ * @param experimentExecutionDTO is the request with the experiment information
+ * @return the response to be returned
+ */
+ public ResponseEntity<String> runExaremeAlgorithm(ExperimentExecutionDTO experimentExecutionDTO) {
+ UserActionLogging.LogAction("Run exareme algorithm", "Running the algorithm...");
- if (params != null) {
- for (AlgorithmParam p : params) {
- queryList.add(makeObject(p.getName(), p.getValue()));
- }
- }
+ Experiment experiment = createExperiment(experimentExecutionDTO);
+
+ // Run the 1st algorithm from the list
+ String algorithmName = experimentExecutionDTO.getAlgorithms().get(0).getName();
+
+ // Get the parameters
+ List<AlgorithmExecutionParamDTO> algorithmParameters
+ = experimentExecutionDTO.getAlgorithms().get(0).getParameters();
+
+ String body = gson.toJson(algorithmParameters);
+ String url = exaremeUrl + "/" + algorithmName;
+ UserActionLogging.LogAction("Run exareme algorithm", "url: " + url + ", body: " + body);
+
+ ResponseEntity<String> response = new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
+ UserActionLogging.LogAction("Run exareme algorithm",
+ "Completed, returning: " + experiment.toString());
- String query = gson.toJson(queryList);
- String url = miningExaremeQueryUrl + "/" + algoCode;
+ UserActionLogging.LogAction("Run exareme algorithm",
+ "Starting exareme execution thread");
+ new Thread(() -> {
+ // ATTENTION: Inside the Thread only LogThreadAction should be used, not LogAction!
+ UserActionLogging.LogThreadAction("Thread, Run exareme algorithm",
+ "Thread started!");
- // Results are stored in the experiment object
try {
+ UserActionLogging.LogThreadAction("Thread, Run exareme algorithm",
+ "Thread started!");
StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, query, results);
+ int code = HTTPUtil.sendPost(url, body, results);
+
+ UserActionLogging.LogThreadAction("Thread, Run exareme algorithm",
+ "Algorithm finished with code: " + code);
+
+ // Results are stored in the experiment object
experiment.setResult("[" + results.toString() + "]");
experiment.setHasError(code >= 400);
experiment.setHasServerError(code >= 500);
- } catch (IOException e) {
- //LOGGER.trace("Invalid UUID", e);
- //LOGGER.warn("Exareme experiment failed to run properly !");
+ } catch (Exception e) {
+ UserActionLogging.LogThreadAction("Thread, Run exareme algorithm",
+ "There was an exception: " + e.getMessage());
+
experiment.setHasError(true);
experiment.setHasServerError(true);
experiment.setResult(e.getMessage());
}
+ UserActionLogging.LogThreadAction("Thread, Run exareme algorithm",
+ "Finished the experiment: " + experiment.toString());
finishExperiment(experiment);
- }).start();
- UserActionLogging.LogAction("create ExaremeExperiment", "no info");
+ UserActionLogging.LogThreadAction("Thread, Run exareme algorithm",
+ "Finished!");
+ }).start();
- return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
+ return response;
}
- @ApiOperation(value = "Create a workflow", response = Experiment.class)
- @RequestMapping(value = "/workflow", method = RequestMethod.POST)
- public ResponseEntity runWorkflow(@RequestBody ExperimentQuery expQuery) {
+ /**
+ * The runWorkflow will POST the algorithm to the galaxy client
+ *
+ * @param experimentExecutionDTO is the request with the experiment information
+ * @return the response to be returned
+ */
+ public ResponseEntity<String> runGalaxyWorkflow(ExperimentExecutionDTO experimentExecutionDTO) {
UserActionLogging.LogAction("Run workflow", "Running a workflow...");
- Experiment experiment = saveExperiment(expQuery);
+ Experiment experiment = createExperiment(experimentExecutionDTO);
+
+ // Run the 1st algorithm from the list
+ String workflowId = experimentExecutionDTO.getAlgorithms().get(0).getName();
+
+ // Get the parameters
+ List<AlgorithmExecutionParamDTO> algorithmParameters
+ = experimentExecutionDTO.getAlgorithms().get(0).getParameters();
- // Get the algorithm parameters provided
- String algorithmName = expQuery.getAlgorithms().get(0).getName();
- List<AlgorithmParam> algorithmParams = expQuery.getAlgorithms().get(0).getParameters();
+ // Convert the parameters to workflow parameters
HashMap<String, String> algorithmParamsIncludingEmpty = new HashMap<>();
- if (algorithmParams != null) {
- for (AlgorithmParam p : algorithmParams) {
- algorithmParamsIncludingEmpty.put(p.getName(), p.getValue());
+ if (algorithmParameters != null) {
+ for (AlgorithmExecutionParamDTO param : algorithmParameters) {
+ algorithmParamsIncludingEmpty.put(param.getName(), param.getValue());
}
}
@@ -137,14 +183,16 @@ public class ExperimentApi {
final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
Workflow workflow = null;
for (Workflow curWorkflow : workflowsClient.getWorkflows()) {
- if (curWorkflow.getName().equals(algorithmName)) {
+ if (curWorkflow.getId().equals(workflowId)) {
workflow = curWorkflow;
break;
}
}
if (workflow == null) {
- UserActionLogging.LogAction("Run workflow", "Could not find algorithm code");
- return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ErrorResponse("Could not find galaxy algorithm.", "99"));
+ UserActionLogging.LogAction("Run workflow",
+ "Could not find algorithm code: " + workflowId);
+ return ResponseEntity.status(HttpStatus.BAD_REQUEST)
+ .body(new ErrorResponse("Could not find galaxy algorithm.", "99").toString());
}
final WorkflowDetails workflowDetails = workflowsClient.showWorkflow(workflow.getId());
for (Map.Entry<String, WorkflowInputDefinition> workflowParameter : workflowDetails.getInputs().entrySet()) {
@@ -197,7 +245,8 @@ public class ExperimentApi {
experiment.setHasServerError(true);
experiment.setResult(e.getMessage());
}
- finishExperiment(experiment);
+ saveExperiment(experiment);
+
UserActionLogging.LogAction("Run workflow", "Run workflow completed!");
return new ResponseEntity(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
@@ -304,6 +353,8 @@ public class ExperimentApi {
experiment.setHasError(true);
experiment.setHasServerError(true);
}
+
+ finishExperiment(experiment);
break;
case "error":
@@ -337,12 +388,14 @@ public class ExperimentApi {
experiment.setHasError(true);
experiment.setHasServerError(true);
}
+ finishExperiment(experiment);
break;
default: // InternalError or unexpected result
experiment.setResult(new ErrorResponse("An unexpected error occurred.", "500").toString());
experiment.setHasError(true);
experiment.setHasServerError(true);
+ finishExperiment(experiment);
break;
}
@@ -647,37 +700,43 @@ public class ExperimentApi {
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
- private void finishExperiment(Experiment experiment) {
- experiment.setFinished(new Date());
+ private Experiment createExperiment(ExperimentExecutionDTO experimentExecutionDTO) throws NullPointerException{
+ User user = userInfo.getUser();
+
+ Experiment experiment = new Experiment();
+ experiment.setUuid(UUID.randomUUID());
+ experiment.setCreatedBy(user);
+ experiment.setAlgorithms(gson.toJson(experimentExecutionDTO.getAlgorithms()));
+ Model model = modelRepository.findOne(experimentExecutionDTO.getModel());
+ experiment.setModel(model);
+ experiment.setName(experimentExecutionDTO.getName());
experimentRepository.save(experiment);
- UserActionLogging.LogAction("Experiment updated (finished)", "");
+ UserActionLogging.LogAction("Created an experiment", " id : " + experiment.getUuid());
+ UserActionLogging.LogAction("Created an experiment", " algorithms : " + experiment.getAlgorithms());
+ UserActionLogging.LogAction("Created an experiment", " model : " + experiment.getModel().getSlug());
+ UserActionLogging.LogAction("Created an experiment", " name : " + experiment.getName());
+ return experiment;
}
- private HashMap<String, String> makeObject(String name, String value) {
- HashMap<String, String> o = new HashMap<String, String>();
- o.put("name", name);
- o.put("value", value);
-
- return o;
- }
+ private void saveExperiment(Experiment experiment) {
+ UserActionLogging.LogAction("Saved an experiment", " id : " + experiment.getUuid());
+ UserActionLogging.LogAction("Saved an experiment", " algorithms : " + experiment.getAlgorithms());
+ UserActionLogging.LogAction("Saved an experiment", " model : " + experiment.getModel().getSlug());
+ UserActionLogging.LogAction("Saved an experiment", " name : " + experiment.getName());
+ UserActionLogging.LogAction("Saved an experiment", " historyId : " + experiment.getWorkflowHistoryId());
+ UserActionLogging.LogAction("Saved an experiment", " status : " + experiment.getWorkflowStatus());
- private Experiment saveExperiment(ExperimentQuery expQuery) {
+ experimentRepository.save(experiment);
- Experiment experiment = new Experiment();
- experiment.setUuid(UUID.randomUUID());
- User user = userInfo.getUser();
+ UserActionLogging.LogAction("Experiment saved", "");
+ }
- experiment.setAlgorithms(gson.toJson(expQuery.getAlgorithms()));
- experiment.setValidations(gson.toJson(expQuery.getValidations()));
- experiment.setName(expQuery.getName());
- experiment.setCreatedBy(user);
- experiment.setModel(modelRepository.findOne(expQuery.getModel()));
+ private void finishExperiment(Experiment experiment) {
+ experiment.setFinished(new Date());
experimentRepository.save(experiment);
- UserActionLogging.LogAction("Saved an experiment", " id : " + experiment.getUuid());
-
- return experiment;
+ UserActionLogging.LogThreadAction("Experiment finished!", "");
}
}
diff --git a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
deleted file mode 100644
index bbae570a584151e1c2cfbfe16df074bac6a30342..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
+++ /dev/null
@@ -1,83 +0,0 @@
-package eu.hbp.mip.controllers;
-
-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.google.gson.*;
-import com.sun.jersey.api.client.ClientHandlerException;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.*;
-import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.utils.HTTPUtil;
-import org.springframework.beans.factory.annotation.Value;
-import java.io.IOException;
-import java.net.SocketException;
-import java.util.ArrayList;
-import java.util.List;
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-import org.springframework.beans.factory.annotation.Autowired;
-import eu.hbp.mip.utils.UserActionLogging;
-
-@RestController
-@RequestMapping(value = "/methods", produces = { APPLICATION_JSON_VALUE })
-@Api(value = "/methods")
-public class MethodsApi {
-
- private static final Gson gson = new Gson();
-
- @Value("#{'${services.exareme.algorithmsUrl:http://localhost:9090/mining/algorithms.json}'}")
- private String exaremeAlgorithmsUrl;
-
- @Value("#{'${services.galaxy.galaxyUrl}'}")
- private String galaxyUrl;
-
- @Value("#{'${services.galaxy.galaxyApiKey}'}")
- private String galaxyApiKey;
-
- @ApiOperation(value = "List Exareme algorithms and validations", response = String.class)
- @RequestMapping(value = "/exareme", method = RequestMethod.GET)
- public ResponseEntity<Object> getExaremeAlgorithms() {
- UserActionLogging.LogAction("List Exareme algorithms and validations", "");
-
- try {
- StringBuilder response = new StringBuilder();
- HTTPUtil.sendGet(exaremeAlgorithmsUrl, response);
- JsonElement element = new JsonParser().parse(response.toString());
-
- return ResponseEntity.ok(gson.toJson(element));
- } catch (IOException e) {
- return ResponseEntity.status(500).body(e.getMessage());
- }
- }
-
- @ApiOperation(value = "List Galaxy workflows", response = String.class)
- @RequestMapping(value = "/workflows", method = RequestMethod.GET)
- public ResponseEntity<Object> getWorkflows() {
- UserActionLogging.LogAction("List Galaxy workflows", "");
-
- try {
- final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
- final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
-
- List<Workflow> workflowList = new ArrayList<>(workflowsClient.getWorkflows());
-
- List<WorkflowDetails> workflowDetailsList = new ArrayList<>();
- for(Workflow workflow : workflowList){
- workflowDetailsList.add(workflowsClient.showWorkflow(workflow.getId()));
- }
-
- return ResponseEntity.ok(workflowDetailsList);
- } catch (Exception e) {
- UserActionLogging.LogAction("List Galaxy workflows", "Error when calling list galaxy workflows: " + e.getMessage());
-
- return ResponseEntity.ok(new ArrayList<>());
- }
-
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java b/src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java
index 43f22af2b830639ea7c0897273184bf30a9ad7be..6acd92f0aeff3dde2a40ece432a6dc10ef86ed7c 100644
--- a/src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java
+++ b/src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java
@@ -1,8 +1,9 @@
package eu.hbp.mip.controllers.retrofit;
import com.google.gson.JsonObject;
-import eu.hbp.mip.dto.GalaxyWorkflowResult;
-import eu.hbp.mip.dto.PostWorkflowToGalaxyDtoResponse;
+import eu.hbp.mip.model.galaxy.GalaxyWorkflowResult;
+import eu.hbp.mip.model.galaxy.PostWorkflowToGalaxyDtoResponse;
+import eu.hbp.mip.model.galaxy.WorkflowDTO;
import retrofit2.Call;
import retrofit2.http.*;
@@ -10,6 +11,9 @@ import java.util.List;
public interface RetroFitGalaxyClients {
+ @GET("workflows/{workflowId}")
+ Call<WorkflowDTO> getWorkflowFromGalaxy(@Path("workflowId") String workflowId, @Query("key") String key);
+
@POST("workflows/{workflowId}/invocations")
Call<PostWorkflowToGalaxyDtoResponse> postWorkflowToGalaxy(@Path("workflowId") String workflowId, @Query("key") String key, @Body JsonObject body);
diff --git a/src/main/java/eu/hbp/mip/model/Algorithm.java b/src/main/java/eu/hbp/mip/model/Algorithm.java
deleted file mode 100644
index bd08093a82e0cc7823fdc6c33c193a3feff774ba..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Algorithm.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package eu.hbp.mip.model;
-
-import java.util.LinkedList;
-
-/**
- * Created by mirco on 09.11.16.
- */
-
-public class Algorithm extends ExperimentValidator {
-
- private boolean validation;
-
- public Algorithm() {
-
- }
-
- public Algorithm(String code, String name, boolean validation) {
- this.validation = validation;
- setCode(code);
- setName(name);
- setParameters(new LinkedList<>());
- }
-
- public boolean isValidation() {
- return validation;
- }
-
- public void setValidation(boolean validation) {
- this.validation = validation;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/AlgorithmDTO.java b/src/main/java/eu/hbp/mip/model/AlgorithmDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..ed0ef2a15606ef09f139bad65c90c3cf436c2474
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/model/AlgorithmDTO.java
@@ -0,0 +1,220 @@
+package eu.hbp.mip.model;
+
+import com.google.gson.annotations.SerializedName;
+
+import java.util.List;
+
+public class AlgorithmDTO {
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getDesc() {
+ return desc;
+ }
+
+ public void setDesc(String desc) {
+ this.desc = desc;
+ }
+
+ public String getLabel() {
+ return label;
+ }
+
+ public void setLabel(String label) {
+ this.label = label;
+ }
+
+ public String getType() {
+ return type;
+ }
+
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ public List<AlgorithmParamDTO> getParameters() {
+ return parameters;
+ }
+
+ public void setParameters(List<AlgorithmParamDTO> parameters) {
+ this.parameters = parameters;
+ }
+
+ @SerializedName("name")
+ private String name;
+
+ @SerializedName("desc")
+ private String desc;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("parameters")
+ private List<AlgorithmParamDTO> parameters;
+
+ 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;
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getDesc() {
+ return desc;
+ }
+
+ public void setDesc(String desc) {
+ this.desc = desc;
+ }
+
+ public String getLabel() {
+ return label;
+ }
+
+ public void setLabel(String label) {
+ this.label = label;
+ }
+
+ public String getType() {
+ return type;
+ }
+
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ public String getColumnValuesSQLType() {
+ return columnValuesSQLType;
+ }
+
+ public void setColumnValuesSQLType(String columnValuesSQLType) {
+ this.columnValuesSQLType = columnValuesSQLType;
+ }
+
+ public String getColumnValuesIsCategorical() {
+ return columnValuesIsCategorical;
+ }
+
+ public void setColumnValuesIsCategorical(String columnValuesIsCategorical) {
+ this.columnValuesIsCategorical = columnValuesIsCategorical;
+ }
+
+ public String getValue() {
+ return value;
+ }
+
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ public String getDefaultValue() {
+ return defaultValue;
+ }
+
+ public void setDefaultValue(String defaultValue) {
+ this.defaultValue = defaultValue;
+ }
+
+ public String getValueType() {
+ return valueType;
+ }
+
+ public void setValueType(String valueType) {
+ this.valueType = valueType;
+ }
+
+ public String getValueNotBlank() {
+ return valueNotBlank;
+ }
+
+ public void setValueNotBlank(String valueNotBlank) {
+ this.valueNotBlank = valueNotBlank;
+ }
+
+ public String getValueMultiple() {
+ return valueMultiple;
+ }
+
+ public void setValueMultiple(String valueMultiple) {
+ this.valueMultiple = valueMultiple;
+ }
+
+ public String getValueMin() {
+ return valueMin;
+ }
+
+ public void setValueMin(String valueMin) {
+ this.valueMin = valueMin;
+ }
+
+ public String getValueMax() {
+ return valueMax;
+ }
+
+ public void setValueMax(String valueMax) {
+ this.valueMax = valueMax;
+ }
+
+ public List<String> getValueEnumerations() {
+ return valueEnumerations;
+ }
+
+ public void setValueEnumerations(List<String> valueEnumerations) {
+ this.valueEnumerations = valueEnumerations;
+ }
+ }
+
+}
diff --git a/src/main/java/eu/hbp/mip/model/AlgorithmParam.java b/src/main/java/eu/hbp/mip/model/AlgorithmParam.java
deleted file mode 100644
index 62c48ba13b4cffcf647d4da97a0509735f18cac4..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/AlgorithmParam.java
+++ /dev/null
@@ -1,36 +0,0 @@
-package eu.hbp.mip.model;
-
-/**
- * Created by mirco on 09.11.16.
- */
-
-public class AlgorithmParam {
-
- private String code;
- private String value;
-
- public String getCode() {
- return code;
-
- }
-
- public void setName(String name) {
- this.code = name;
- }
-
- public String getName() {
- return this.code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
- public String getValue() {
- return value;
- }
-
- public void setValue(String value) {
- this.value = value;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/Experiment.java b/src/main/java/eu/hbp/mip/model/Experiment.java
index 3cb3a85ee74126f8da14f02f0c186f22debe06f2..25a851f0f6e32d5828ffdce68faeadefb57b2cfe 100644
--- a/src/main/java/eu/hbp/mip/model/Experiment.java
+++ b/src/main/java/eu/hbp/mip/model/Experiment.java
@@ -16,8 +16,6 @@ import java.util.*;
@Table(name = "`experiment`")
public class Experiment {
- private static final Logger LOGGER = LoggerFactory.getLogger(Experiment.class);
-
private static final Gson gson = new Gson();
@Id
diff --git a/src/main/java/eu/hbp/mip/model/ExperimentExecutionDTO.java b/src/main/java/eu/hbp/mip/model/ExperimentExecutionDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..a68cd9121d852503bc01eb6b2f0d23dd8af525dd
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/model/ExperimentExecutionDTO.java
@@ -0,0 +1,106 @@
+package eu.hbp.mip.model;
+
+import java.util.List;
+
+public class ExperimentExecutionDTO {
+
+ private String name;
+ private String model;
+ private List<AlgorithmExecutionDTO> algorithms;
+
+ public String getModel() {
+ return model;
+ }
+
+ public void setModel(String model) {
+ this.model = model;
+ }
+
+ public List<AlgorithmExecutionDTO> getAlgorithms() {
+ return algorithms;
+ }
+
+ public void setAlgorithms(List<AlgorithmExecutionDTO> algorithms) {
+ this.algorithms = algorithms;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public static class AlgorithmExecutionDTO {
+
+ private String name;
+ private String label;
+ private String type;
+
+ private List<AlgorithmExecutionParamDTO> parameters;
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getType() {
+ return type;
+ }
+
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ public List<AlgorithmExecutionDTO.AlgorithmExecutionParamDTO> getParameters() {
+ return parameters;
+ }
+
+ public void setParameters(List<AlgorithmExecutionDTO.AlgorithmExecutionParamDTO> parameters) {
+ this.parameters = parameters;
+ }
+
+ public String getLabel() {
+ return label;
+ }
+
+ public void setLabel(String label) {
+ this.label = label;
+ }
+
+ public static class AlgorithmExecutionParamDTO {
+
+ private String name;
+ private String label;
+ private String value;
+
+ public String getName() {
+ return this.name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getValue() {
+ return value;
+ }
+
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ public String getLabel() {
+ return label;
+ }
+
+ public void setLabel(String label) {
+ this.label = label;
+ }
+ }
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/model/ExperimentQuery.java b/src/main/java/eu/hbp/mip/model/ExperimentQuery.java
deleted file mode 100644
index 333751c438099de62942918e17f019505a800de7..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/ExperimentQuery.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package eu.hbp.mip.model;
-
-import java.util.List;
-
-/**
- * Created by mirco on 09.11.16.
- */
-public class ExperimentQuery {
-
- private String name;
- private String model;
- private List<ExperimentValidator> validations;
- private List<Algorithm> algorithms;
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getModel() {
- return model;
- }
-
- public void setModel(String model) {
- this.model = model;
- }
-
- public List<ExperimentValidator> getValidations() {
- return validations;
- }
-
- public void setValidations(List<ExperimentValidator> validations) {
- this.validations = validations;
- }
-
- public List<Algorithm> getAlgorithms() {
- return algorithms;
- }
-
- public void setAlgorithms(List<Algorithm> algorithms) {
- this.algorithms = algorithms;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/ExperimentValidator.java b/src/main/java/eu/hbp/mip/model/ExperimentValidator.java
deleted file mode 100644
index 208fc90fa7272779bf51e09ca7fa0b6f409c66d3..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/ExperimentValidator.java
+++ /dev/null
@@ -1,40 +0,0 @@
-package eu.hbp.mip.model;
-
-import java.util.List;
-
-/**
- * Created by mirco on 09.11.16.
- */
-
-public class ExperimentValidator {
-
- private String code;
- private String name;
-
- private List<AlgorithmParam> parameters;
-
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public List<AlgorithmParam> getParameters() {
- return parameters;
- }
-
- public void setParameters(List<AlgorithmParam> parameters) {
- this.parameters = parameters;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/MiningQuery.java b/src/main/java/eu/hbp/mip/model/MiningQuery.java
index 6ced265037ba4148d4f18e6ba06d9434e4610317..171c55032eee4b3c5f63d636c137d6ae41bfe051 100644
--- a/src/main/java/eu/hbp/mip/model/MiningQuery.java
+++ b/src/main/java/eu/hbp/mip/model/MiningQuery.java
@@ -1,6 +1,7 @@
package eu.hbp.mip.model;
import com.google.gson.Gson;
+
import java.util.LinkedList;
import java.util.List;
@@ -14,7 +15,7 @@ public class MiningQuery {
private List<Variable> grouping;
private List<Variable> datasets;
private String filters;
- private Algorithm algorithm;
+ private ExperimentExecutionDTO.AlgorithmExecutionDTO algorithm;
public MiningQuery() {
this.variables = new LinkedList<>();
@@ -32,7 +33,9 @@ public class MiningQuery {
this.variables = variables;
}
- public void addVariable(Variable variable) { this.variables.add(variable); }
+ public void addVariable(Variable variable) {
+ this.variables.add(variable);
+ }
public List<Variable> getCovariables() {
return covariables;
@@ -42,7 +45,9 @@ public class MiningQuery {
this.covariables = covariables;
}
- public void addCovariable(Variable variable) { this.covariables.add(variable); }
+ public void addCovariable(Variable variable) {
+ this.covariables.add(variable);
+ }
public List<Variable> getGrouping() {
return grouping;
@@ -52,15 +57,21 @@ public class MiningQuery {
this.grouping = grouping;
}
- public List<Variable> getDatasets() { return datasets; }
+ public List<Variable> getDatasets() {
+ return datasets;
+ }
public void setDataset(List<Variable> datasets) {
this.datasets = datasets;
}
- public void addDataset(Variable variable) { this.datasets.add(variable); }
+ public void addDataset(Variable variable) {
+ this.datasets.add(variable);
+ }
- public void addGrouping(Variable variable) { this.grouping.add(variable); }
+ public void addGrouping(Variable variable) {
+ this.grouping.add(variable);
+ }
public String getFilters() {
return filters;
@@ -70,11 +81,11 @@ public class MiningQuery {
this.filters = filters;
}
- public Algorithm getAlgorithm() {
+ public ExperimentExecutionDTO.AlgorithmExecutionDTO getAlgorithm() {
return algorithm;
}
- public void setAlgorithm(Algorithm algorithm) {
+ public void setAlgorithm(ExperimentExecutionDTO.AlgorithmExecutionDTO algorithm) {
this.algorithm = algorithm;
}
diff --git a/src/main/java/eu/hbp/mip/dto/ErrorResponse.java b/src/main/java/eu/hbp/mip/model/galaxy/ErrorResponse.java
similarity index 95%
rename from src/main/java/eu/hbp/mip/dto/ErrorResponse.java
rename to src/main/java/eu/hbp/mip/model/galaxy/ErrorResponse.java
index 1051340acbb3db553173d8e5ff4a7818d2f4df7e..e4144da6502ca26cf0f2032ace1d5d19d6c65746 100644
--- a/src/main/java/eu/hbp/mip/dto/ErrorResponse.java
+++ b/src/main/java/eu/hbp/mip/model/galaxy/ErrorResponse.java
@@ -3,7 +3,7 @@
* Copyright (c) 2019. MIT License
*/
-package eu.hbp.mip.dto;
+package eu.hbp.mip.model.galaxy;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/dto/GalaxyWorkflowResult.java b/src/main/java/eu/hbp/mip/model/galaxy/GalaxyWorkflowResult.java
similarity index 99%
rename from src/main/java/eu/hbp/mip/dto/GalaxyWorkflowResult.java
rename to src/main/java/eu/hbp/mip/model/galaxy/GalaxyWorkflowResult.java
index 566910c6fda59d9acd30e06a48ccdfe1efe17f63..089a6a626ed1e0d38306c911b515edd3fa8fa5f0 100644
--- a/src/main/java/eu/hbp/mip/dto/GalaxyWorkflowResult.java
+++ b/src/main/java/eu/hbp/mip/model/galaxy/GalaxyWorkflowResult.java
@@ -3,7 +3,7 @@
* Copyright (c) 2019. MIT License
*/
-package eu.hbp.mip.dto;
+package eu.hbp.mip.model.galaxy;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/dto/PostWorkflowToGalaxyDtoResponse.java b/src/main/java/eu/hbp/mip/model/galaxy/PostWorkflowToGalaxyDtoResponse.java
similarity index 98%
rename from src/main/java/eu/hbp/mip/dto/PostWorkflowToGalaxyDtoResponse.java
rename to src/main/java/eu/hbp/mip/model/galaxy/PostWorkflowToGalaxyDtoResponse.java
index bc504c5f5a2894b4fb2a4a75acac56bf4f949a12..edefd63266a8d1678bf82d057882e4eccab112cc 100644
--- a/src/main/java/eu/hbp/mip/dto/PostWorkflowToGalaxyDtoResponse.java
+++ b/src/main/java/eu/hbp/mip/model/galaxy/PostWorkflowToGalaxyDtoResponse.java
@@ -3,7 +3,7 @@
* Copyright (c) 2019. MIT License
*/
-package eu.hbp.mip.dto;
+package eu.hbp.mip.model.galaxy;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java b/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..de537a1dcc4649e0ea6b28ff967567b599c77251
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
@@ -0,0 +1,162 @@
+package eu.hbp.mip.model.galaxy;
+
+import com.google.gson.Gson;
+import com.google.gson.annotations.SerializedName;
+import eu.hbp.mip.model.AlgorithmDTO;
+
+import java.util.*;
+
+public class WorkflowDTO {
+
+ @SerializedName("id")
+ private String id;
+
+ @SerializedName("name")
+ private String name;
+
+ @SerializedName("inputs")
+ private HashMap<String, WorkflowInputDTO> inputs;
+
+ @SerializedName("steps")
+ private HashMap<String, WorkflowStepDTO> steps;
+
+ public String getId() {
+ return id;
+ }
+
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public HashMap<String, WorkflowInputDTO> getInputs() {
+ return inputs;
+ }
+
+ public void setInputs(HashMap<String, WorkflowInputDTO> inputs) {
+ this.inputs = inputs;
+ }
+
+ public HashMap<String, WorkflowStepDTO> getSteps() {
+ return steps;
+ }
+
+ public void setSteps(HashMap<String, WorkflowStepDTO> steps) {
+ this.steps = steps;
+ }
+
+ public class WorkflowInputDTO {
+ @SerializedName("uuid")
+ private String uuid;
+
+ @SerializedName("label")
+ private String label;
+
+ public String getLabel() {
+ return label;
+ }
+
+ public void setLabel(String label) {
+ this.label = label;
+ }
+
+ public String getUuid() {
+ return uuid;
+ }
+
+ public void setUuid(String uuid) {
+ this.uuid = uuid;
+ }
+ }
+
+ public class WorkflowStepDTO {
+ @SerializedName("id")
+ private int id;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("annotation")
+ private String annotation;
+
+ public int getId() {
+ return id;
+ }
+
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ public String getAnnotation() {
+ return annotation;
+ }
+
+ public void setAnnotation(String annotation) {
+ this.annotation = annotation;
+ }
+ }
+
+ public AlgorithmDTO convertToAlgorithmDTO(){
+
+ AlgorithmDTO algorithmDTO = new AlgorithmDTO();
+
+ // Transfer workflow information
+ algorithmDTO.setName(id);
+ algorithmDTO.setDesc("");
+ algorithmDTO.setLabel(name);
+ algorithmDTO.setType("workflow");
+
+ // Transfer workflow parameters information
+ List<AlgorithmDTO.AlgorithmParamDTO> algorithmParams = new LinkedList<>();
+ Gson gson = new Gson();
+ for (Map.Entry<String, WorkflowInputDTO> workflowInput : getInputs().entrySet()) {
+
+ // Convert the annotation to algorithm Parameter
+ AlgorithmDTO.AlgorithmParamDTO algorithmParam;
+ if(steps.get(workflowInput.getKey()).getAnnotation() != null) {
+ algorithmParam = gson.fromJson(steps.get(workflowInput.getKey()).getAnnotation(),
+ AlgorithmDTO.AlgorithmParamDTO.class);
+ }else{
+ // If annotation is not provided, auto-fill some information
+ algorithmParam = new AlgorithmDTO.AlgorithmParamDTO();
+ // When the constraints are not known, set the most relaxed constraints
+ algorithmParam.setDesc("");
+ algorithmParam.setValue("");
+ algorithmParam.setValueType("string");
+ algorithmParam.setValueNotBlank("false");
+ algorithmParam.setDefaultValue("");
+ algorithmParam.setDefaultValue("true");
+ // If label is dataset/pathology/filter/formula the type should be the same
+ if(workflowInput.getValue().getLabel().equals("dataset") ||
+ workflowInput.getValue().getLabel().equals("pathology")||
+ workflowInput.getValue().getLabel().equals("filter")||
+ workflowInput.getValue().getLabel().equals("formula")){
+ algorithmParam.setType(workflowInput.getValue().getLabel());
+ }else if(workflowInput.getValue().getLabel().equals("x") ||
+ workflowInput.getValue().getLabel().equals("y")){
+ algorithmParam.setType("column");
+ algorithmParam.setColumnValuesSQLType("text,real,integer");
+ algorithmParam.setColumnValuesIsCategorical("");
+ }else{
+ algorithmParam.setType("other");
+ }
+ }
+ // Set the name to the workflow id
+ algorithmParam.setName(workflowInput.getValue().getUuid());
+ algorithmParam.setLabel(workflowInput.getValue().getLabel());
+
+ algorithmParams.add(algorithmParam);
+ }
+ algorithmDTO.setParameters(algorithmParams);
+
+ return algorithmDTO;
+ }
+
+}
diff --git a/src/main/java/eu/hbp/mip/utils/UserActionLogging.java b/src/main/java/eu/hbp/mip/utils/UserActionLogging.java
index c1257fa537c714e34bdf989960174f97bbe39a35..2c37ccb31cfbb7922da969c7062327c65cfe8912 100644
--- a/src/main/java/eu/hbp/mip/utils/UserActionLogging.java
+++ b/src/main/java/eu/hbp/mip/utils/UserActionLogging.java
@@ -4,8 +4,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.security.core.context.SecurityContextHolder;
-import java.time.LocalTime;
-
public class UserActionLogging {
@@ -19,4 +17,8 @@ public class UserActionLogging {
+ " info: " + actionIdInfo);
}
+ public static void LogThreadAction(String actionName, String actionIdInfo)
+ {
+ LOGGER.info( "Called endpoint: " + actionName + " info: " + actionIdInfo);
+ }
}