Merge Galaxy_Middleware_API with back end.KK

 On branch dev_merge_middleware
 Changes to be committed:
	modified:   build.sh
	modified:   pom.xml
	new file:   src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
	new file:   src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java
	new file:   src/main/java/eu/hbp/mip/controllers/retrofit/RetrofitClientInstance.java
	new file:   src/main/java/eu/hbp/mip/dto/ErrorResponse.java
	new file:   src/main/java/eu/hbp/mip/dto/GetWorkflowResultsFromGalaxyDtoResponse.java
	new file:   src/main/java/eu/hbp/mip/dto/JwtResponse.java
	new file:   src/main/java/eu/hbp/mip/dto/LoginDto.java
	new file:   src/main/java/eu/hbp/mip/dto/PostWorkflowToGalaxyDtoResponse.java
	new file:   src/main/java/eu/hbp/mip/dto/SignUpDto.java
	new file:   src/main/java/eu/hbp/mip/dto/StringDtoResponse.java
	new file:   src/main/java/eu/hbp/mip/helpers/GenParameters.java
	new file:   src/main/java/eu/hbp/mip/helpers/LogHelper.java

build.sh

@@ -26,7 +26,7 @@ else
   DOCKER="sudo docker"
 fi
 
-IMAGE="hbpmip/portal-backend"
+IMAGE="kkech/portal_backend"
 VCS_REF=$(git describe --tags --dirty)
 VERSION=$(git describe --tags --dirty)
 
@@ -37,6 +37,9 @@ docker build --build-arg BUILD_DATE=$(date -Iseconds) \
     --tag "$IMAGE:$VERSION" \
     .
 
+docker push kkech/portal_backend:latest
+
+
 BUGSNAG_KEY=""
 eval $(grep -e "^\\s*BUGSNAG_KEY" Dockerfile | tr '\\' ' ')
 

pom.xml

@@ -249,6 +249,35 @@
             <artifactId>java-jwt</artifactId>
             <version>3.8.3</version>
         </dependency>
+
+        <!-- https://mvnrepository.com/artifact/com.github.jmchilton.blend4j/blend4j -->
+        <dependency>
+            <groupId>com.github.jmchilton.blend4j</groupId>
+            <artifactId>blend4j</artifactId>
+            <version>0.2.0</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.squareup.retrofit2</groupId>
+            <artifactId>retrofit</artifactId>
+            <version>2.5.0</version>
+        </dependency>
+
+        <!-- https://mvnrepository.com/artifact/com.squareup.retrofit2/converter-gson -->
+        <dependency>
+            <groupId>com.squareup.retrofit2</groupId>
+            <artifactId>converter-gson</artifactId>
+            <version>2.4.0</version>
+        </dependency>
+
+
+        <!-- https://mvnrepository.com/artifact/com.squareup.okhttp3/logging-interceptor -->
+        <dependency>
+            <groupId>com.squareup.okhttp3</groupId>
+            <artifactId>logging-interceptor</artifactId>
+            <version>3.12.1</version>
+        </dependency>
+
     </dependencies>
 
     <build>

src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java

+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.Gson;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParser;
+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.GetWorkflowResultsFromGalaxyDtoResponse;
+import eu.hbp.mip.dto.PostWorkflowToGalaxyDtoResponse;
+import eu.hbp.mip.dto.StringDtoResponse;
+import eu.hbp.mip.helpers.GenParameters;
+import eu.hbp.mip.helpers.LogHelper;
+import org.codehaus.jettison.json.JSONException;
+import org.codehaus.jettison.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.security.core.annotation.AuthenticationPrincipal;
+import org.springframework.security.core.userdetails.UserDetails;
+import org.springframework.web.bind.annotation.*;
+import retrofit2.Call;
+import retrofit2.Response;
+
+import java.io.IOException;
+import java.util.*;
+
+@RestController
+@RequestMapping("/galaxyApi/")
+class GalaxyAPI {
+
+    private static final Logger logger = LoggerFactory.getLogger(GalaxyAPI.class);
+
+    //The galaxy URL
+    private final String url = GenParameters.getGenParamInstance().getGalaxyURL();
+
+    //The galaxy ApiKey
+    private final String apiKey = GenParameters.getGenParamInstance().getGalaxyApiKey();
+
+    /**
+     * Test if integration works.
+     *
+     * @return Return a @{@link ResponseEntity}.
+     */
+    @RequestMapping(method = RequestMethod.GET, value = "getTestIntegration", produces = "application/json")
+    @ResponseStatus(value = HttpStatus.OK)
+    public ResponseEntity getTestIntegration(@AuthenticationPrincipal UserDetails userDetails){
+        logger.info(LogHelper.logUser(userDetails) + "Get Test Integration called");
+        return ResponseEntity.ok(new StringDtoResponse("success"));
+    }
+
+    /**
+     * Get Galaxy Reverse Proxy basic access token.
+     *
+     * @return Return a @{@link ResponseEntity} with the token.
+     */
+    @RequestMapping(method = RequestMethod.GET, value = "getGalaxyBasicAccessToken", produces = "application/json")
+    @ResponseStatus(value = HttpStatus.OK)
+    public ResponseEntity getGalaxyBasicAccessToken(@AuthenticationPrincipal UserDetails userDetails){
+        logger.info(LogHelper.logUser(userDetails) + "Get Galaxy Basic Access Token called");
+        String username = GenParameters.getGenParamInstance().getGalaxyReverseProxyUsername();
+        String password = GenParameters.getGenParamInstance().getGalaxyReverseProxyPassword();
+
+        String stringEncoded = Base64.getEncoder().encodeToString((username + ":" + password).getBytes());
+        logger.info(LogHelper.logUser(userDetails) + "Get Galaxy Basic Access Token completed");
+        return ResponseEntity.ok(username + ":" + password);
+        //        return ResponseEntity.ok(new StringDtoResponse(stringEncoded));
+    }
+
+    /**
+     * Get all the workflows with few details.
+     *
+     * @return Return a @{@link ResponseEntity}.
+     */
+    @RequestMapping(method = RequestMethod.GET, value = "getWorkflows", produces = "application/json")
+    @ResponseStatus(value = HttpStatus.OK)
+    public ResponseEntity getWorkflows(@AuthenticationPrincipal UserDetails userDetails) {
+        logger.info(LogHelper.logUser(userDetails) + "Get workflows called");
+
+        final GalaxyInstance instance = GalaxyInstanceFactory.get(url, apiKey);
+        final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
+
+        ArrayList<Workflow> workflowArrayList = new ArrayList<>();
+        workflowArrayList.addAll(workflowsClient.getWorkflows());
+        logger.info(LogHelper.logUser(userDetails) + "Get workflows completed");
+
+        return ResponseEntity.ok(workflowArrayList);
+    }
+
+    /**
+     * Get details for a specific workflow.
+     *
+     * @param id : The id as @{@link String} for the specific workflow.
+     * @return Return a @{@link ResponseEntity}.
+     */
+    @RequestMapping(method = RequestMethod.GET, value = "/getDetailWorkflow/{id}", produces = "application/json")
+    @ResponseStatus(value = HttpStatus.OK)
+    public ResponseEntity getDetailWorkflow(@AuthenticationPrincipal UserDetails userDetails, @PathVariable String id) {
+        logger.info(LogHelper.logUser(userDetails) + "Get detail workflow called");
+
+        final GalaxyInstance instance = GalaxyInstanceFactory.get(url, apiKey);
+        final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
+
+        Workflow matchingWorkflow = null;
+        for(Workflow workflow : workflowsClient.getWorkflows()) {
+            if(workflow.getId().equals(id)) {
+                matchingWorkflow = workflow;
+            }
+        }
+        if(matchingWorkflow == null){
+            logger.error(LogHelper.logUser(userDetails) + "Get detail workflow could not find workflow with id : " + id);
+            return ResponseEntity.notFound().build();
+        }
+        final WorkflowDetails workflowDetails = workflowsClient.showWorkflow(matchingWorkflow.getId());
+        logger.info(LogHelper.logUser(userDetails) + "Get detail workflow completed");
+
+        return ResponseEntity.ok(workflowDetails);
+    }
+
+    /**
+     * Get all the workflows with details.
+     *
+     * @return Return a @{@link ResponseEntity}.
+     */
+    @RequestMapping(method = RequestMethod.GET, value = "getAllWorkflowWithDetails", produces = "application/json")
+    @ResponseStatus(value = HttpStatus.OK)
+    public ResponseEntity getAllWorkflowWithDetails(@AuthenticationPrincipal UserDetails userDetails) {
+        logger.info(LogHelper.logUser(userDetails) + "Get all workflow with details called");
+
+        final GalaxyInstance instance = GalaxyInstanceFactory.get(url, apiKey);
+        final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
+
+        List<Workflow> workflowList = new ArrayList<Workflow>();
+        for(Workflow workflow : workflowsClient.getWorkflows()) {
+            workflowList.add(workflow);
+        }
+
+        List<WorkflowDetails> workflowDetailsList = new ArrayList<>();
+        for(Workflow workflow : workflowList){
+            workflowDetailsList.add(workflowsClient.showWorkflow(workflow.getId()));
+        }
+        logger.info(LogHelper.logUser(userDetails) + "Get all workflow with details completed");
+
+        return ResponseEntity.ok(workflowDetailsList);
+    }
+
+    /**
+     * Invoke a workflow.
+     *
+     * @param id : The id as @{@link String} of the workflow.
+     * @param httpEntity : The @{@link HttpEntity} to get the body of the request which is the parameter of the workflow.
+     * @return Return a @{@link ResponseEntity}.
+     */
+    @RequestMapping(method = RequestMethod.POST, value = "/runWorkflow/{id}", produces = "application/json")
+    @ResponseStatus(value = HttpStatus.OK)
+    public ResponseEntity runWorkflow(@AuthenticationPrincipal UserDetails userDetails, @PathVariable String id, HttpEntity<String> httpEntity) {
+        logger.info(LogHelper.logUser(userDetails) + "Run workflow called");
+
+        //In order to parse Json with undefined number of value/key
+        String json = httpEntity.getBody();
+        JSONObject jObject  = null;
+        try {
+            jObject = new JSONObject(json);
+        } catch (JSONException e) {
+            logger.error(LogHelper.logUser(userDetails) + "Cannot parse JSON", e);
+        }
+        Map<String,String> allJsonParams = new HashMap<String,String>();
+        Iterator iter = jObject.keys();
+        while(iter.hasNext()){
+            String key = (String)iter.next();
+            String value = null;
+            try {
+                value = jObject.getString(key);
+            } catch (JSONException e) {
+                logger.error(LogHelper.logUser(userDetails) + "Cannot parse JSON", e);
+            }
+            logger.info(LogHelper.logUser(userDetails) + "Put to map: " + key + " : " + value);
+            allJsonParams.put(key,value);
+        }
+
+        StringBuffer stringBuffer = new StringBuffer("{\n" +
+                "\t\"inputs\": {\n");
+        for (Map.Entry<String, String> entry : allJsonParams.entrySet()) {
+            stringBuffer.append("\t\t\"" + entry.getKey() + "\" " + " : \"" + entry.getValue() + "\",\n");
+            logger.debug(LogHelper.logUser(userDetails) + entry.getKey() + "/" + entry.getValue());
+        }
+        //Remove Last Comma
+        stringBuffer.deleteCharAt(stringBuffer.length() - 2);
+        stringBuffer.append("\t}\n");
+        stringBuffer.append("}");
+        logger.info(LogHelper.logUser(userDetails) + stringBuffer.toString());
+
+        JsonObject jsonObject = new JsonParser().parse(stringBuffer.toString()).getAsJsonObject();
+
+        RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+        Call<PostWorkflowToGalaxyDtoResponse> call = service.postWorkflowToGalaxy(id, apiKey, jsonObject);
+
+        PostWorkflowToGalaxyDtoResponse postWorkflowToGalaxyDtoResponse = null;
+        try {
+            Response<PostWorkflowToGalaxyDtoResponse> response = call.execute();
+            if(response.code() >= 400){
+                //Value are read it from streams.
+                Integer codeErr = response.code();
+                String msgErr = response.errorBody().string();
+                logger.error(LogHelper.logUser(userDetails) + "Resonse code: " + codeErr + "" + " with body: " + msgErr);
+                logger.info("---" + msgErr);
+                JSONObject jObjectError  = null;
+                try {
+                    jObjectError = new JSONObject(msgErr);
+                } catch (JSONException e) {
+                    logger.error(LogHelper.logUser(userDetails) + "Cannot parse Error JSON", e);
+                }
+                logger.info(jObjectError.toString());
+                String errMsg = jObjectError.get("err_msg").toString();
+                String errCode = jObjectError.get("err_code").toString();
+
+                response.errorBody();
+                return ResponseEntity
+                        .status(HttpStatus.BAD_REQUEST)
+                        .body(new ErrorResponse(errMsg,errCode));
+            }
+            postWorkflowToGalaxyDtoResponse = response.body();
+            logger.info(LogHelper.logUser(userDetails) + "----" + response.body() + "----" + response.code());
+        } catch (IOException e) {
+            logger.error(LogHelper.logUser(userDetails) + "Cannot make the call to Galaxy API", e);
+            return ResponseEntity
+                    .status(HttpStatus.BAD_REQUEST)
+                    .body(new ErrorResponse("An error has been occurred","99"));
+        } catch (JSONException e) {
+            logger.error(LogHelper.logUser(userDetails) + "Cannot find field in Error Json", e);
+            return ResponseEntity
+                    .status(HttpStatus.BAD_REQUEST)
+                    .body(new ErrorResponse("An error has been occurred","99"));
+        }
+        logger.info(LogHelper.logUser(userDetails) + "Run workflow completed");
+
+        return ResponseEntity.ok(postWorkflowToGalaxyDtoResponse);
+    }
+
+    /**
+     * Get the status of a specific workflow.
+     *
+     * @param id : The id as @{@link String} of the workflow.
+     * @return Return a @{@link ResponseEntity}.
+     */
+    @RequestMapping(method = RequestMethod.GET, value = "/getWorkflowStatus/{id}", produces = "application/json")
+    @ResponseStatus(value = HttpStatus.OK)
+    public ResponseEntity getWorkflowStatus(@AuthenticationPrincipal UserDetails userDetails, @PathVariable String id) {
+        logger.info(LogHelper.logUser(userDetails) + "Get workflow status called");
+
+        RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+        Call<Object> call = service.getWorkflowStatusFromGalaxy(id,apiKey);
+
+        String jsonString = null;
+        try {
+            Response<Object> response = call.execute();
+            if(response.code() >= 400){
+                logger.error(LogHelper.logUser(userDetails) + "Resonse code: " + response.code() + "" + " with body: " + response.errorBody().string());
+                return ResponseEntity.badRequest().build();
+            }
+            jsonString = new Gson().toJson(response.body());
+            logger.info(LogHelper.logUser(userDetails) + jsonString);
+
+            logger.info(LogHelper.logUser(userDetails) + "----" + response.body() + "----" + response.code());
+        } catch (IOException e) {
+            logger.error(LogHelper.logUser(userDetails) + "Cannot make the call to Galaxy API", e);
+        }
+        logger.info(LogHelper.logUser(userDetails) + "Get workflow status completed");
+
+        return ResponseEntity.ok(jsonString);
+    }
+
+    /**
+     * Get the status of a multiple workflows.
+     * @param httpEntity : The @{@link HttpEntity} to get the body of the request which is the workflow ID.
+     * @return Return a @{@link ResponseEntity}.
+     */
+    @RequestMapping(method = RequestMethod.GET, value = "/getMultipleWorkflowStatus", produces = "application/json")
+    @ResponseStatus(value = HttpStatus.OK)
+    public ResponseEntity getMultipleWorkflowStatus(@AuthenticationPrincipal UserDetails userDetails, HttpEntity<String> httpEntity) {
+        logger.info(LogHelper.logUser(userDetails) + "Get Multiple workflow status called");
+
+        //In order to parse Json with undefined number of value/key
+        String json = httpEntity.getBody();
+        JSONObject jObject  = null;
+        try {
+            jObject = new JSONObject(json);
+        } catch (JSONException e) {
+            logger.error(LogHelper.logUser(userDetails) + "Cannot parse JSON", e);
+        }
+        Map<String,String> allJsonParams = new HashMap<String,String>();
+        Iterator iter = jObject.keys();
+
+        while(iter.hasNext()){
+            String key = (String)iter.next();
+            String value = null;
+            try {
+                value = jObject.getString(key);
+                System.out.println(key + ":" + value);
+            } catch (JSONException e) {
+                logger.error(LogHelper.logUser(userDetails) + "Cannot parse JSON", e);
+            }
+            logger.info(LogHelper.logUser(userDetails) + "Put to map: " + key + " : " + value);
+            allJsonParams.put(key,value);
+        }
+
+        StringBuffer stringBuffer = new StringBuffer();
+        for (Map.Entry<String, String> entry : allJsonParams.entrySet()) {
+            RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+            Call<Object> call = service.getWorkflowStatusFromGalaxy(entry.getValue(),apiKey);
+
+            String jsonString = null;
+            try {
+                Response<Object> response = call.execute();
+                if(response.code() >= 400){
+                    logger.error(LogHelper.logUser(userDetails) + "Resonse code: " + response.code() + "" + " with body: " + response.errorBody().string());
+                    return ResponseEntity.badRequest().build();
+                }
+                jsonString = new Gson().toJson(response.body());
+                logger.info(LogHelper.logUser(userDetails) + jsonString);
+                stringBuffer.append(jsonString + ",");
+                logger.info(LogHelper.logUser(userDetails) + "----" + response.body() + "----" + response.code());
+            } catch (IOException e) {
+                logger.error(LogHelper.logUser(userDetails) + "Cannot make the call to Galaxy API", e);
+            }
+        }
+        stringBuffer.deleteCharAt(stringBuffer.length() - 1);
+        logger.info(LogHelper.logUser(userDetails) + "Get Multiple workflow status completed");
+        return ResponseEntity.ok(stringBuffer.toString());
+    }
+
+    /**
+     * Get the result of a specific workflow.
+     *
+     * @param id : The id as @{@link String} of the workflow.
+     * @return Return a @{@link ResponseEntity}.
+     */
+    @RequestMapping(method = RequestMethod.GET, value = "/getWorkflowResults/{id}", produces = "application/json")
+    @ResponseStatus(value = HttpStatus.OK)
+    public ResponseEntity getWorkflowResults(@AuthenticationPrincipal UserDetails userDetails, @PathVariable String id) {
+        logger.info(LogHelper.logUser(userDetails) + "Get workflow results called");
+
+        RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+        Call<List<GetWorkflowResultsFromGalaxyDtoResponse>> call = service.getWorkflowResultsFromGalaxy(id,apiKey);
+
+        List<GetWorkflowResultsFromGalaxyDtoResponse> getWorkflowResultsFromGalaxyDtoResponsesList = null;
+        try {
+            Response<List<GetWorkflowResultsFromGalaxyDtoResponse>> response = call.execute();
+            if(response.code() >= 400){
+                logger.error(LogHelper.logUser(userDetails) + "Resonse code: " + response.code() + "" + " with body: " + response.errorBody().string());
+                return ResponseEntity.badRequest().build();
+            }
+            getWorkflowResultsFromGalaxyDtoResponsesList = response.body();
+        } catch (IOException e) {
+            logger.error(LogHelper.logUser(userDetails) + "Cannot make the call to Galaxy API", e);
+        }
+        logger.info(LogHelper.logUser(userDetails) + "Get workflow results completed");
+
+        return ResponseEntity.ok(getWorkflowResultsFromGalaxyDtoResponsesList);
+    }
+
+    /**
+     * Get the result body of a specific workflow.
+     *
+     * @param id : The id as @{@link String} of the workflow.
+     * @param contentId : The content id as @{@link String}.
+     * @return Return a @{@link ResponseEntity}.
+     */
+    @RequestMapping(method = RequestMethod.GET, value = "/getWorkflowResultsBody/{id}/contents/{contentId}", produces = "application/json")
+    @ResponseStatus(value = HttpStatus.OK)
+    public ResponseEntity getWorkflowResultsBody(@AuthenticationPrincipal UserDetails userDetails, @PathVariable String id, @PathVariable String contentId) {
+        logger.info(LogHelper.logUser(userDetails) + "Get workflow results body called");
+
+        RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+        Call<Object> call = service.getWorkflowResultsBodyFromGalaxy(id,contentId,apiKey);
+
+        String jsonString = null;
+        try {
+            Response<Object> response = call.execute();
+            if(response.code() >= 400){
+                logger.error(LogHelper.logUser(userDetails) + "Resonse code: " + response.code() + "" + " with body: " + response.errorBody().string());
+                return ResponseEntity.badRequest().build();
+            }
+            jsonString = new Gson().toJson(response.body());
+            logger.info(LogHelper.logUser(userDetails) + "----" + response.body() + "----" + response.code());
+        } catch (IOException e) {
+            logger.error(LogHelper.logUser(userDetails) + "Cannot make the call to Galaxy API", e);
+        }
+        logger.info(LogHelper.logUser(userDetails) + "Get workflow results body completed");
+
+        return ResponseEntity.ok(jsonString);
+    }
+
+    /**
+     * Get the result body of a specific workflow with details.
+     *
+     * @param id : The id as @{@link String} of the workflow.
+     * @param contentId : The content id as @{@link String}.
+     * @return Return a @{@link ResponseEntity}.
+     */
+    @RequestMapping(method = RequestMethod.GET, value = "/getWorkflowResultsDetails/{id}/contents/{contentId}", produces = "application/json")
+    @ResponseStatus(value = HttpStatus.OK)
+    public ResponseEntity getWorkflowResultsDetails(@AuthenticationPrincipal UserDetails userDetails, @PathVariable String id, @PathVariable String contentId) {
+        logger.info(LogHelper.logUser(userDetails) + "Get workflow results details called");
+
+        RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+        Call<Object> call = service.getWorkflowResultsDetailsFromGalaxy(id,contentId,apiKey);
+
+        String jsonString = null;
+        try {
+            Response<Object> response = call.execute();
+            if(response.code() >= 400){
+                logger.error(LogHelper.logUser(userDetails) + "Resonse code: " + response.code() + "" + " with body: " + response.errorBody().string());
+                return ResponseEntity.badRequest().build();
+            }
+            jsonString = new Gson().toJson(response.body());
+            System.out.println(jsonString);
+            logger.info(LogHelper.logUser(userDetails) + "----" + response.body() + "----" + response.code());
+        } catch (IOException e) {
+            logger.error(LogHelper.logUser(userDetails) + "Cannot make the call to Galaxy API", e);
+        }
+        logger.info(LogHelper.logUser(userDetails) + "Get workflow results details completed");
+
+        return ResponseEntity.ok(jsonString);
+    }
+
+    @RequestMapping(method = RequestMethod.GET, value = "getErrorMessageOfWorkflow/{id}", produces = "application/json")
+    @ResponseStatus(value = HttpStatus.OK)
+    public ResponseEntity getErrorMessageOfWorkflow(@AuthenticationPrincipal UserDetails userDetails, @PathVariable String id) {
+        logger.info(LogHelper.logUser(userDetails) + "Get error message of workflow called");
+
+        RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+        Call<Object> call = service.getErrorMessageOfWorkflowFromGalaxy(id,apiKey);
+
+        String fullError = null;
+        String returnError = null;
+        try {
+            Response<Object> response = call.execute();
+            if(response.code() >= 400){
+                logger.error(LogHelper.logUser(userDetails) + "Resonse code: " + response.code() + "" + " with body: " + response.errorBody().string());
+                return ResponseEntity.badRequest().build();
+            }
+            JsonParser parser = new JsonParser();
+            String jsonString = new Gson().toJson(response.body());
+            System.out.println(jsonString);
+            JsonElement jsonElement = parser.parse(jsonString);
+            JsonObject rootObject = jsonElement.getAsJsonObject();
+            fullError = rootObject.get("stderr").getAsString();
+            String[] arrOfStr = fullError.split("ValueError", 0);
+            String specError = arrOfStr[arrOfStr.length-1];
+            returnError = specError.substring(1);
+
+            logger.info(LogHelper.logUser(userDetails) + "----" + response.body() + "----" + response.code());
+        } catch (IOException e) {
+            logger.error(LogHelper.logUser(userDetails) + "Cannot make the call to Galaxy API", e);
+        }
+
+        logger.info(LogHelper.logUser(userDetails) + "Get error message of workflow completed");
+
+        return ResponseEntity.ok(returnError);
+    }
+}
\ No newline at end of file

src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java

+package eu.hbp.mip.controllers.retrofit;
+
+import com.google.gson.JsonObject;
+import eu.hbp.mip.dto.GetWorkflowResultsFromGalaxyDtoResponse;
+import eu.hbp.mip.dto.PostWorkflowToGalaxyDtoResponse;
+import retrofit2.Call;
+import retrofit2.http.*;
+
+import java.util.List;
+
+public interface RetroFitGalaxyClients {
+
+    @POST("workflows/{workflowId}/invocations")
+    Call<PostWorkflowToGalaxyDtoResponse> postWorkflowToGalaxy(@Path("workflowId") String workflowId, @Query("key") String key, @Body JsonObject body);
+
+    @GET("histories/{historyId}")
+    Call<Object> getWorkflowStatusFromGalaxy(@Path("historyId") String historyId, @Query("key") String key);
+
+    @GET("histories/{historyId}/contents")
+    Call<List<GetWorkflowResultsFromGalaxyDtoResponse>> getWorkflowResultsFromGalaxy(@Path("historyId") String historyId, @Query("key") String key);
+
+    @GET("histories/{historyId}/contents/{contentId}/display")
+    Call<Object> getWorkflowResultsBodyFromGalaxy(@Path("historyId") String historyId, @Path("contentId") String contentId, @Query("key") String key);
+
+    @GET("histories/{historyId}/contents/{contentId}")
+    Call<Object> getWorkflowResultsDetailsFromGalaxy(@Path("historyId") String historyId, @Path("contentId") String contentId, @Query("key") String key);
+
+    @GET("jobs/{jobId}?full=true")
+    Call<Object> getErrorMessageOfWorkflowFromGalaxy(@Path("jobId") String historyId, @Query("key") String key);
+}
\ No newline at end of file

src/main/java/eu/hbp/mip/controllers/retrofit/RetrofitClientInstance.java

+package eu.hbp.mip.controllers.retrofit;
+
+import eu.hbp.mip.helpers.GenParameters;
+import okhttp3.OkHttpClient;
+import okhttp3.logging.HttpLoggingInterceptor;
+import retrofit2.Retrofit;
+import retrofit2.converter.gson.GsonConverterFactory;
+
+public class RetrofitClientInstance {
+
+    private static Retrofit retrofit;
+
+    private static final String BASE_URL = GenParameters.getGenParamInstance().getGalaxyURL() + "/api/";
+
+    public static Retrofit getRetrofitInstance() {
+        if (retrofit == null) {
+
+            HttpLoggingInterceptor interceptor = new HttpLoggingInterceptor();
+            interceptor.setLevel(HttpLoggingInterceptor.Level.BODY);
+            OkHttpClient client = new OkHttpClient.Builder().addInterceptor(interceptor).build();
+
+            retrofit = new retrofit2.Retrofit.Builder()
+                    .baseUrl(BASE_URL)
+                    .client(client)
+                    .addConverterFactory(GsonConverterFactory.create())
+                    .build();
+        }
+        return retrofit;
+    }
+}
\ No newline at end of file

src/main/java/eu/hbp/mip/dto/ErrorResponse.java

+/*
+ * Developed by Kechagias Konstantinos.
+ * Copyright (c) 2019. MIT License
+ */
+
+package eu.hbp.mip.dto;
+
+import com.google.gson.annotations.SerializedName;
+
+public class ErrorResponse {
+
+    @SerializedName("err_msg")
+    String errMsg;
+
+    @SerializedName("err_code")
+    String errCode;
+
+    public ErrorResponse() {
+    }
+
+    public ErrorResponse(String errMsg, String errCode) {
+        this.errMsg = errMsg;
+        this.errCode = errCode;
+    }
+
+    public String getErrMsg() {
+        return errMsg;
+    }
+
+    public void setErrMsg(String errMsg) {
+        this.errMsg = errMsg;
+    }
+
+    public String getErrCode() {
+        return errCode;
+    }
+
+    public void setErrCode(String errCode) {
+        this.errCode = errCode;
+    }
+}

src/main/java/eu/hbp/mip/dto/GetWorkflowResultsFromGalaxyDtoResponse.java

+/*
+ * Developed by Kechagias Konstantinos.
+ * Copyright (c) 2019. MIT License
+ */
+
+package eu.hbp.mip.dto;
+
+import com.google.gson.annotations.SerializedName;
+
+import java.util.List;
+
+public class GetWorkflowResultsFromGalaxyDtoResponse {
+
+    @SerializedName("history_content_type")
+    private String historyContentType;
+    @SerializedName("update_time")
+    private String updateTime;
+    @SerializedName("name")
+    private String name;
+    @SerializedName("extension")
+    private String extension;
+    @SerializedName("type_id")
+    private String typeId;
+    @SerializedName("deleted")
+    private Boolean deleted;
+    @SerializedName("history_id")
+    private String historyId;
+    @SerializedName("tags")
+    private List<Object> tags = null;
+    @SerializedName("id")
+    private String id;
+    @SerializedName("visible")
+    private Boolean visible;
+    @SerializedName("state")
+    private String state;
+    @SerializedName("create_time")
+    private String createTime;
+    @SerializedName("hid")
+    private Integer hid;
+    @SerializedName("url")
+    private String url;
+    @SerializedName("dataset_id")
+    private String datasetId;
+    @SerializedName("type")
+    private String type;
+    @SerializedName("purged")
+    private Boolean purged;
+
+    public GetWorkflowResultsFromGalaxyDtoResponse() {
+    }
+
+    public GetWorkflowResultsFromGalaxyDtoResponse(String historyContentType, String updateTime, String name, String extension, String typeId, Boolean deleted, String historyId, List<Object> tags, String id, Boolean visible, String state, String createTime, Integer hid, String url, String datasetId, String type, Boolean purged) {
+        this.historyContentType = historyContentType;
+        this.updateTime = updateTime;
+        this.name = name;
+        this.extension = extension;
+        this.typeId = typeId;
+        this.deleted = deleted;
+        this.historyId = historyId;
+        this.tags = tags;
+        this.id = id;
+        this.visible = visible;
+        this.state = state;
+        this.createTime = createTime;
+        this.hid = hid;
+        this.url = url;
+        this.datasetId = datasetId;
+        this.type = type;
+        this.purged = purged;
+    }
+
+    public String getHistoryContentType() {
+        return historyContentType;
+    }
+
+    public void setHistoryContentType(String historyContentType) {
+        this.historyContentType = historyContentType;
+    }
+
+    public String getUpdateTime() {
+        return updateTime;
+    }
+
+    public void setUpdateTime(String updateTime) {
+        this.updateTime = updateTime;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getExtension() {
+        return extension;
+    }
+
+    public void setExtension(String extension) {
+        this.extension = extension;
+    }
+
+    public String getTypeId() {
+        return typeId;
+    }
+
+    public void setTypeId(String typeId) {
+        this.typeId = typeId;
+    }
+
+    public Boolean getDeleted() {
+        return deleted;
+    }
+
+    public void setDeleted(Boolean deleted) {
+        this.deleted = deleted;
+    }
+
+    public String getHistoryId() {
+        return historyId;
+    }
+
+    public void setHistoryId(String historyId) {
+        this.historyId = historyId;
+    }
+
+    public List<Object> getTags() {
+        return tags;
+    }
+
+    public void setTags(List<Object> tags) {
+        this.tags = tags;
+    }
+
+    public String getId() {
+        return id;
+    }
+
+    public void setId(String id) {
+        this.id = id;
+    }
+
+    public Boolean getVisible() {
+        return visible;
+    }
+
+    public void setVisible(Boolean visible) {
+        this.visible = visible;
+    }
+
+    public String getState() {
+        return state;
+    }
+
+    public void setState(String state) {
+        this.state = state;
+    }
+
+    public String getCreateTime() {
+        return createTime;
+    }
+
+    public void setCreateTime(String createTime) {
+        this.createTime = createTime;
+    }
+
+    public Integer getHid() {
+        return hid;
+    }
+
+    public void setHid(Integer hid) {
+        this.hid = hid;
+    }
+
+    public String getUrl() {
+        return url;
+    }
+
+    public void setUrl(String url) {
+        this.url = url;
+    }
+
+    public String getDatasetId() {
+        return datasetId;
+    }
+
+    public void setDatasetId(String datasetId) {
+        this.datasetId = datasetId;
+    }
+
+    public String getType() {
+        return type;
+    }
+
+    public void setType(String type) {
+        this.type = type;
+    }
+
+    public Boolean getPurged() {
+        return purged;
+    }
+
+    public void setPurged(Boolean purged) {
+        this.purged = purged;
+    }
+}
+

src/main/java/eu/hbp/mip/dto/JwtResponse.java

+/*
+ * Developed by Kechagias Konstantinos.
+ * Copyright (c) 2019. MIT License
+ */
+
+package eu.hbp.mip.dto;
+
+public class JwtResponse {
+    private String token;
+    private String type = "Bearer";
+
+    public JwtResponse(String accessToken) {
+        this.token = accessToken;
+    }
+
+    public String getAccessToken() {
+        return token;
+    }
+
+    public void setAccessToken(String accessToken) {
+        this.token = accessToken;
+    }
+
+    public String getTokenType() {
+        return type;
+    }
+
+    public void setTokenType(String tokenType) {
+        this.type = tokenType;
+    }
+}
\ No newline at end of file

src/main/java/eu/hbp/mip/dto/LoginDto.java

+/*
+ * Developed by Kechagias Konstantinos.
+ * Copyright (c) 2019. MIT License
+ */
+
+package eu.hbp.mip.dto;
+
+import org.hibernate.validator.constraints.NotBlank;
+
+import javax.validation.constraints.Size;
+
+public class LoginDto {
+    @NotBlank
+    @Size(min=3, max = 60)
+    private String username;
+
+    @NotBlank
+    @Size(min = 6, max = 40)
+    private String password;
+
+    public String getUsername() {
+        return username;
+    }
+
+    public void setUsername(String username) {
+        this.username = username;
+    }
+
+    public String getPassword() {
+        return password;
+    }
+
+    public void setPassword(String password) {
+        this.password = password;
+    }
+}

src/main/java/eu/hbp/mip/dto/PostWorkflowToGalaxyDtoResponse.java

+/*
+ * Developed by Kechagias Konstantinos.
+ * Copyright (c) 2019. MIT License
+ */
+
+package eu.hbp.mip.dto;
+
+import com.google.gson.annotations.SerializedName;
+
+public class PostWorkflowToGalaxyDtoResponse {
+
+
+    @SerializedName("update_time")
+    String updateTime;
+    String uuid;
+    @SerializedName("history_id")
+    String historyId;
+    String stake;
+    @SerializedName("workflow_id")
+    String workflowId;
+    @SerializedName("model_class")
+    String modelClass;
+    String id;
+
+    public PostWorkflowToGalaxyDtoResponse() {
+    }
+
+    public PostWorkflowToGalaxyDtoResponse(String updateTime, String uuid, String historyId, String stake, String workflowId, String modelClass, String id) {
+        this.updateTime = updateTime;
+        this.uuid = uuid;
+        this.historyId = historyId;
+        this.stake = stake;
+        this.workflowId = workflowId;
+        this.modelClass = modelClass;
+        this.id = id;
+    }
+
+    public String getUpdateTime() {
+        return updateTime;
+    }
+
+    public void setUpdateTime(String updateTime) {
+        this.updateTime = updateTime;
+    }
+
+    public String getUuid() {
+        return uuid;
+    }
+
+    public void setUuid(String uuid) {
+        this.uuid = uuid;
+    }
+
+    public String getHistoryId() {
+        return historyId;
+    }
+
+    public void setHistoryId(String historyId) {
+        this.historyId = historyId;
+    }
+
+    public String getStake() {
+        return stake;
+    }
+
+    public void setStake(String stake) {
+        this.stake = stake;
+    }
+
+    public String getWorkflowId() {
+        return workflowId;
+    }
+
+    public void setWorkflowId(String workflowId) {
+        this.workflowId = workflowId;
+    }
+
+    public String getModelClass() {
+        return modelClass;
+    }
+
+    public void setModelClass(String modelClass) {
+        this.modelClass = modelClass;
+    }
+
+    public String getId() {
+        return id;
+    }
+
+    public void setId(String id) {
+        this.id = id;
+    }
+}

src/main/java/eu/hbp/mip/dto/SignUpDto.java

+/*
+ * Developed by Kechagias Konstantinos.
+ * Copyright (c) 2019. MIT License
+ */
+
+package eu.hbp.mip.dto;
+
+import org.hibernate.validator.constraints.Email;
+import org.hibernate.validator.constraints.NotBlank;
+
+import javax.validation.constraints.Size;
+import java.util.Set;
+
+public class SignUpDto {
+    @NotBlank
+    @Size(min = 3, max = 50)
+    private String name;
+
+    @NotBlank
+    @Size(min = 3, max = 50)
+    private String username;
+
+    @NotBlank
+    @Size(max = 60)
+    @Email
+    private String email;
+
+    private Set<String> role;
+
+    @NotBlank
+    @Size(min = 6, max = 40)
+    private String password;
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getUsername() {
+        return username;
+    }
+
+    public void setUsername(String username) {
+        this.username = username;
+    }
+
+    public String getEmail() {
+        return email;
+    }
+
+    public void setEmail(String email) {
+        this.email = email;
+    }
+
+    public String getPassword() {
+        return password;
+    }
+
+    public void setPassword(String password) {
+        this.password = password;
+    }
+
+    public Set<String> getRole() {
+        return this.role;
+    }
+
+    public void setRole(Set<String> role) {
+        this.role = role;
+    }
+}

src/main/java/eu/hbp/mip/dto/StringDtoResponse.java

+/*
+ * Developed by Kechagias Konstantinos.
+ * Copyright (c) 2019. MIT License
+ */
+
+package eu.hbp.mip.dto;
+
+public class StringDtoResponse {
+
+    private String response;
+
+    public StringDtoResponse() {
+    }
+
+    public StringDtoResponse(String response) {
+        this.response = response;
+    }
+
+    public String getResponse() {
+        return response;
+    }
+
+    public void setResponse(String response) {
+        this.response = response;
+    }
+}

src/main/java/eu/hbp/mip/helpers/GenParameters.java

+/*
+ * Developed by Kechagias Konstantinos.
+ * Copyright (c) 2019. MIT License
+ */
+
+package eu.hbp.mip.helpers;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.core.io.ClassPathResource;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Properties;
+
+public class GenParameters {
+
+    private static final Logger logger = LoggerFactory.getLogger(GenParameters.class);
+
+    private static GenParameters genParams;
+
+    private String jwtSecret;
+
+    private String jwtIssuer;
+
+    private String galaxyURL;
+
+    private String galaxyApiKey;
+
+    private String galaxyReverseProxyUsername;
+
+    private String galaxyReverseProxyPassword;
+
+    private GenParameters(){
+
+    }
+
+    public static GenParameters getGenParamInstance() {
+        if (genParams == null) {
+            logger.info("->>>>>>>Reading Enviroment variables");
+            genParams = new GenParameters();
+
+            genParams.setJwtSecret(System.getenv("JWT_SECRET"));
+            genParams.setJwtIssuer(System.getenv("JWT_ISSUER"));
+            genParams.setGalaxyURL(System.getenv("GALAXY_URL"));
+            genParams.setGalaxyApiKey(System.getenv("GALAXY_API_KEY"));
+            genParams.setGalaxyReverseProxyUsername(System.getenv("GALAXY_REVERSE_PROXY_USERNAME"));
+            genParams.setGalaxyReverseProxyPassword(System.getenv("GALAXY_REVERSE_PROXY_PASSWORD"));
+
+
+            //If environment variable not exists read from file.
+            if (genParams.getJwtSecret() == null){
+                throw new RuntimeException("Cannot find Enviroment Variables");
+//                logger.info("->>>>>>>Reading from file");
+//
+//                File file = null;
+//                try {
+//                    file = new ClassPathResource("config.properties").getFile();
+//                    InputStream input = new FileInputStream(file);
+//                    Properties prop = new Properties();
+//
+//                    // load a properties file
+//                    prop.load(input);
+//
+//                    // get the property value and print it out
+//                    genParams.setJwtSecret(prop.getProperty("jwtSecret"));
+//                    genParams.setJwtIssuer(prop.getProperty("jwtIssuer"));
+//                    genParams.setGalaxyURL(prop.getProperty("galaxyURL"));
+//                    genParams.setGalaxyApiKey(prop.getProperty("galaxyApiKey"));
+//                    genParams.setGalaxyReverseProxyUsername(prop.getProperty("galaxyReverseProxyUsername"));
+//                    genParams.setGalaxyReverseProxyPassword(prop.getProperty("galaxyReverseProxyPassword"));
+//                } catch (IOException e) {
+//                    logger.error("Cannot initialize GenParameters from config file", e);
+//                }
+            }
+        }
+        return genParams;
+    }
+
+    public String getJwtSecret() {
+        return jwtSecret;
+    }
+
+    private void setJwtSecret(String jwtSecret) {
+        this.jwtSecret = jwtSecret;
+    }
+
+    public String getJwtIssuer() {
+        return  jwtIssuer;
+    }
+
+    private void setJwtIssuer(String jwtIssuer) {
+        this.jwtIssuer = jwtIssuer;
+    }
+
+    public String getGalaxyURL() {
+        return galaxyURL;
+    }
+
+    private void setGalaxyURL(String galaxyURL) {
+        this.galaxyURL = galaxyURL;
+    }
+
+    public String getGalaxyApiKey() {
+        return galaxyApiKey;
+    }
+
+    private void setGalaxyApiKey(String galaxyApiKey) {
+        this.galaxyApiKey = galaxyApiKey;
+    }
+
+    public String getGalaxyReverseProxyUsername() {
+        return galaxyReverseProxyUsername;
+    }
+
+    public void setGalaxyReverseProxyUsername(String galaxyReverseProxyUsername) {
+        this.galaxyReverseProxyUsername = galaxyReverseProxyUsername;
+    }
+
+    public String getGalaxyReverseProxyPassword() {
+        return galaxyReverseProxyPassword;
+    }
+
+    public void setGalaxyReverseProxyPassword(String galaxyReverseProxyPassword) {
+        this.galaxyReverseProxyPassword = galaxyReverseProxyPassword;
+    }
+}
\ No newline at end of file

src/main/java/eu/hbp/mip/helpers/LogHelper.java

+package eu.hbp.mip.helpers;
+
+
+import org.springframework.security.core.userdetails.UserDetails;
+
+public class LogHelper {
+    public static String logUser(UserDetails userDetails){
+        return ("User(subject)->User(" + userDetails.getUsername() + ") : ");
+    }
+}
\ No newline at end of file