From 115cde1e09aff157c0848b60c0be410a9ee82371 Mon Sep 17 00:00:00 2001
From: Konstantinos <kostas24061992@yahoo.com>
Date: Wed, 4 Dec 2019 11:52:10 +0200
Subject: [PATCH] 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 | 5 +-
pom.xml | 29 ++
.../eu/hbp/mip/controllers/GalaxyAPI.java | 470 ++++++++++++++++++
.../retrofit/RetroFitGalaxyClients.java | 30 ++
.../retrofit/RetrofitClientInstance.java | 30 ++
.../java/eu/hbp/mip/dto/ErrorResponse.java | 41 ++
...tWorkflowResultsFromGalaxyDtoResponse.java | 208 ++++++++
src/main/java/eu/hbp/mip/dto/JwtResponse.java | 31 ++
src/main/java/eu/hbp/mip/dto/LoginDto.java | 36 ++
.../dto/PostWorkflowToGalaxyDtoResponse.java | 93 ++++
src/main/java/eu/hbp/mip/dto/SignUpDto.java | 73 +++
.../eu/hbp/mip/dto/StringDtoResponse.java | 26 +
.../eu/hbp/mip/helpers/GenParameters.java | 129 +++++
.../java/eu/hbp/mip/helpers/LogHelper.java | 10 +
14 files changed, 1210 insertions(+), 1 deletion(-)
create mode 100644 src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
create mode 100644 src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java
create mode 100644 src/main/java/eu/hbp/mip/controllers/retrofit/RetrofitClientInstance.java
create mode 100644 src/main/java/eu/hbp/mip/dto/ErrorResponse.java
create mode 100644 src/main/java/eu/hbp/mip/dto/GetWorkflowResultsFromGalaxyDtoResponse.java
create mode 100644 src/main/java/eu/hbp/mip/dto/JwtResponse.java
create mode 100644 src/main/java/eu/hbp/mip/dto/LoginDto.java
create mode 100644 src/main/java/eu/hbp/mip/dto/PostWorkflowToGalaxyDtoResponse.java
create mode 100644 src/main/java/eu/hbp/mip/dto/SignUpDto.java
create mode 100644 src/main/java/eu/hbp/mip/dto/StringDtoResponse.java
create mode 100644 src/main/java/eu/hbp/mip/helpers/GenParameters.java
create mode 100644 src/main/java/eu/hbp/mip/helpers/LogHelper.java
diff --git a/build.sh b/build.sh
index 5df0e1ce8..796a240e3 100755
--- a/build.sh
+++ b/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 '\\' ' ')
diff --git a/pom.xml b/pom.xml
index 33287a67e..aa37b02bc 100644
--- a/pom.xml
+++ b/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>
diff --git a/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java b/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
new file mode 100644
index 000000000..b78b60d34
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
@@ -0,0 +1,470 @@
+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
diff --git a/src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java b/src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java
new file mode 100644
index 000000000..23143bf89
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java
@@ -0,0 +1,30 @@
+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
diff --git a/src/main/java/eu/hbp/mip/controllers/retrofit/RetrofitClientInstance.java b/src/main/java/eu/hbp/mip/controllers/retrofit/RetrofitClientInstance.java
new file mode 100644
index 000000000..46328df33
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/controllers/retrofit/RetrofitClientInstance.java
@@ -0,0 +1,30 @@
+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
diff --git a/src/main/java/eu/hbp/mip/dto/ErrorResponse.java b/src/main/java/eu/hbp/mip/dto/ErrorResponse.java
new file mode 100644
index 000000000..1051340ac
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/dto/ErrorResponse.java
@@ -0,0 +1,41 @@
+/*
+ * 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;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/dto/GetWorkflowResultsFromGalaxyDtoResponse.java b/src/main/java/eu/hbp/mip/dto/GetWorkflowResultsFromGalaxyDtoResponse.java
new file mode 100644
index 000000000..a81660ac4
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/dto/GetWorkflowResultsFromGalaxyDtoResponse.java
@@ -0,0 +1,208 @@
+/*
+ * 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;
+ }
+}
+
diff --git a/src/main/java/eu/hbp/mip/dto/JwtResponse.java b/src/main/java/eu/hbp/mip/dto/JwtResponse.java
new file mode 100644
index 000000000..2007a8f60
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/dto/JwtResponse.java
@@ -0,0 +1,31 @@
+/*
+ * 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
new file mode 100644
index 000000000..5fada1e1f
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/dto/LoginDto.java
@@ -0,0 +1,36 @@
+/*
+ * 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/PostWorkflowToGalaxyDtoResponse.java b/src/main/java/eu/hbp/mip/dto/PostWorkflowToGalaxyDtoResponse.java
new file mode 100644
index 000000000..bc504c5f5
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/dto/PostWorkflowToGalaxyDtoResponse.java
@@ -0,0 +1,93 @@
+/*
+ * 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;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/dto/SignUpDto.java b/src/main/java/eu/hbp/mip/dto/SignUpDto.java
new file mode 100644
index 000000000..c7129853c
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/dto/SignUpDto.java
@@ -0,0 +1,73 @@
+/*
+ * 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
new file mode 100644
index 000000000..ce5eb9700
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/dto/StringDtoResponse.java
@@ -0,0 +1,26 @@
+/*
+ * 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;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/helpers/GenParameters.java b/src/main/java/eu/hbp/mip/helpers/GenParameters.java
new file mode 100644
index 000000000..92de05524
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/helpers/GenParameters.java
@@ -0,0 +1,129 @@
+/*
+ * 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
diff --git a/src/main/java/eu/hbp/mip/helpers/LogHelper.java b/src/main/java/eu/hbp/mip/helpers/LogHelper.java
new file mode 100644
index 000000000..9fa950c2d
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/helpers/LogHelper.java
@@ -0,0 +1,10 @@
+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
--
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