diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index 873dba34923825c3aacdbb90759a5fc3fabae3a2..b936cdd35a7dadb97ca7d1d95a2a0167d00527b8 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -13,12 +13,10 @@ 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.helpers.LogHelper;
import eu.hbp.mip.model.*;
import eu.hbp.mip.repositories.ExperimentRepository;
import eu.hbp.mip.repositories.ModelRepository;
import eu.hbp.mip.utils.HTTPUtil;
-import eu.hbp.mip.utils.JWTUtil;
import eu.hbp.mip.utils.UserActionLogging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
@@ -300,7 +298,7 @@ public class ExperimentApi {
}
}
- if(!resultFound) { // If there is no visible result
+ if (!resultFound) { // If there is no visible result
UserActionLogging.LogAction("Get workflow experiment", "No visible result");
experiment.setResult(new ErrorResponse("The workflow has no visible result.", "500").toString());
experiment.setHasError(true);
@@ -333,7 +331,7 @@ public class ExperimentApi {
}
}
- if(!failedJobFound) { // If there is no visible failed job
+ if (!failedJobFound) { // If there is no visible failed job
UserActionLogging.LogAction("Get workflow experiment", "No failed result");
experiment.setResult(new ErrorResponse("The workflow has no failed result.", "500").toString());
experiment.setHasError(true);
@@ -477,20 +475,20 @@ public class ExperimentApi {
/**
* @param jobId the id of the workflow job that failed
- * @return the error that was produced or null if an error occurred
+ * @return the error that was produced or null if an error occurred
*/
- public String getWorkflowJobError(String jobId){
+ public String getWorkflowJobError(String jobId) {
UserActionLogging.LogAction("Get workflow job error", " jobId : " + jobId);
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId,galaxyApiKey);
+ Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId, galaxyApiKey);
String fullError = null;
String returnError = null;
try {
Response<Object> response = callError.execute();
- if(response.code() >= 400){
- UserActionLogging.LogAction("Get workflow job error","Response code: "
+ if (response.code() >= 400) {
+ UserActionLogging.LogAction("Get workflow job error", "Response code: "
+ response.code() + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return null;
}
@@ -500,19 +498,19 @@ public class ExperimentApi {
JsonElement jsonElement = new JsonParser().parse(jsonString);
JsonObject rootObject = jsonElement.getAsJsonObject();
fullError = rootObject.get("stderr").getAsString();
- UserActionLogging.LogAction("Get workflow job error","Error: " + fullError);
+ UserActionLogging.LogAction("Get workflow job error", "Error: " + fullError);
String[] arrOfStr = fullError.split("ValueError", 0);
- String specError = arrOfStr[arrOfStr.length-1];
+ String specError = arrOfStr[arrOfStr.length - 1];
returnError = specError.substring(1);
- UserActionLogging.LogAction("Get workflow job error","Parsed Error: " + returnError);
+ UserActionLogging.LogAction("Get workflow job error", "Parsed Error: " + returnError);
} catch (IOException e) {
- UserActionLogging.LogAction("Get workflow job error","Exception: " + e.getMessage());
+ UserActionLogging.LogAction("Get workflow job error", "Exception: " + e.getMessage());
return null;
}
- UserActionLogging.LogAction("Get workflow job error","Completed successfully!");
+ UserActionLogging.LogAction("Get workflow job error", "Completed successfully!");
return returnError;
}
diff --git a/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java b/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
deleted file mode 100644
index 41c8a6576b4277658c58ec4e4d2b5afcc0f66359..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
+++ /dev/null
@@ -1,485 +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.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition;
-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.dto.StringDtoResponse;
-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 = "123";
-
- //The galaxy ApiKey
- private final String apiKey = "123;";
-
- /**
- * 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 = "admin";
- String password = "passwrod";
-
- 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);
- }
- 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) + "Run workflow could not find workflow with id : " + id + " ,in order to get missing input parameters");
- return ResponseEntity.notFound().build();
- }
- final WorkflowDetails workflowDetails = workflowsClient.showWorkflow(matchingWorkflow.getId());
- for (Map.Entry<String, WorkflowInputDefinition> entry : workflowDetails.getInputs().entrySet()) {
- if(!(allJsonParams.containsKey(entry.getValue().getUuid()))) {
- logger.warn("Find extra value with label:" + entry.getValue().getLabel() + ", and uuid:" + entry.getValue().getUuid() + ", that is mandatory to run the workflow. The uuid will be automate add it with empty value in the parameters to run the workflow.");
- allJsonParams.put(entry.getValue().getUuid(), "");
- }
- }
-
- ////
-
- 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<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(id,apiKey);
-
- List<GalaxyWorkflowResult> workflowGalaxyDtoResponsesList = null;
- try {
- Response<List<GalaxyWorkflowResult>> 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();
- }
- workflowGalaxyDtoResponsesList = 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(workflowGalaxyDtoResponsesList);
- }
-
- /**
- * 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);
- }
-
- @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.getWorkflowStatusFromGalaxy(id,apiKey);
- String errorState = 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());
- JsonElement jsonElement = parser.parse(jsonString);
- JsonObject rootObject = jsonElement.getAsJsonObject();
- String state = rootObject.get("state").getAsString();
- if(state.equals("error")){
- JsonArray arrayOfErrors = rootObject.get("state_ids").getAsJsonObject().get("error").getAsJsonArray();
- errorState = arrayOfErrors.get(0).getAsString();
- }else{
- logger.warn("Unknown state of the workflow.");
- return ResponseEntity.status(HttpStatus.NO_CONTENT).build();
- }
-
- 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);
- }
-
- Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(errorState,apiKey);
-
- String fullError = null;
- String returnError = null;
- try {
- Response<Object> response = callError.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);
-
- System.out.println(fullError);
- 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
diff --git a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
index f8995bf7ba319c2b38e1d84ee79cd1ff04db84c6..bbae570a584151e1c2cfbfe16df074bac6a30342 100644
--- a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
@@ -64,10 +64,7 @@ public class MethodsApi {
final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
- List<Workflow> workflowList = new ArrayList<>();
- for(Workflow workflow : workflowsClient.getWorkflows()) {
- workflowList.add(workflow);
- }
+ List<Workflow> workflowList = new ArrayList<>(workflowsClient.getWorkflows());
List<WorkflowDetails> workflowDetailsList = new ArrayList<>();
for(Workflow workflow : workflowList){
diff --git a/src/main/java/eu/hbp/mip/dto/JwtResponse.java b/src/main/java/eu/hbp/mip/dto/JwtResponse.java
deleted file mode 100644
index 2007a8f60bd08331860138bbe178b6b5a4cc7a4b..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/dto/JwtResponse.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * 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
diff --git a/src/main/java/eu/hbp/mip/dto/LoginDto.java b/src/main/java/eu/hbp/mip/dto/LoginDto.java
deleted file mode 100644
index 5fada1e1f0118bd940e8f58d286dd74cdf3b3762..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/dto/LoginDto.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * 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;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/dto/SignUpDto.java b/src/main/java/eu/hbp/mip/dto/SignUpDto.java
deleted file mode 100644
index c7129853cea70e5fd8cec23b6c8a77b2438c43c8..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/dto/SignUpDto.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * 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;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/dto/StringDtoResponse.java b/src/main/java/eu/hbp/mip/dto/StringDtoResponse.java
deleted file mode 100644
index ce5eb9700eccf31807d9a5884e1b9d39d8578602..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/dto/StringDtoResponse.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * 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;
- }
-}