From a37f8670e836a83fb9105791c45437646dd583d0 Mon Sep 17 00:00:00 2001
From: ThanKarab <tkarabatsis@hotmail.com>
Date: Thu, 6 Feb 2020 14:55:09 +0200
Subject: [PATCH] Get workflow refactored.
---
.../eu/hbp/mip/controllers/ExperimentApi.java | 308 ++++++++++++++----
.../eu/hbp/mip/controllers/GalaxyAPI.java | 45 +--
.../retrofit/RetroFitGalaxyClients.java | 9 +-
...esponse.java => GalaxyWorkflowResult.java} | 6 +-
4 files changed, 250 insertions(+), 118 deletions(-)
rename src/main/java/eu/hbp/mip/dto/{GetWorkflowResultsFromGalaxyDtoResponse.java => GalaxyWorkflowResult.java} (90%)
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index b5e43338b..873dba349 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -11,6 +11,7 @@ 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.helpers.LogHelper;
import eu.hbp.mip.model.*;
@@ -22,6 +23,7 @@ import eu.hbp.mip.utils.UserActionLogging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
+import org.codehaus.jettison.json.JSONException;
import org.codehaus.jettison.json.JSONObject;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
@@ -36,9 +38,6 @@ import java.util.*;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-/**
- * Created by habfast on 21/04/16.
- */
@RestController
@RequestMapping(value = "/experiments", produces = {APPLICATION_JSON_VALUE})
@Api(value = "/experiments")
@@ -177,11 +176,10 @@ public class ExperimentApi {
String historyId = (String) new JSONObject(responseBody).get("history_id");
experiment.setWorkflowHistoryId(historyId);
experiment.setWorkflowStatus("running");
- experiment.setResult("");
experiment.setHasError(false);
experiment.setHasServerError(response.code() >= 500);
- }else { // Something unexpected happened
+ } else { // Something unexpected happened
String msgErr = gson.toJson(response.errorBody());
UserActionLogging.LogAction("Run workflow", "Error Response: " + msgErr);
@@ -217,8 +215,7 @@ public class ExperimentApi {
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
- //LOGGER.trace("Invalid UUID", iae);
- //LOGGER.warn("An invalid Experiment UUID was received ! " + uuid);
+ UserActionLogging.LogAction("Get Experiment", "Invalid Experiment UUID.");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
@@ -233,120 +230,291 @@ public class ExperimentApi {
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
- @ApiOperation(value = "get workflow status", response = String.class)
- @RequestMapping(value = "/workflow/status/{experimentId}", method = RequestMethod.GET)
- public ResponseEntity<String> getWorkflowStatus(
- @ApiParam(value = "historyId", required = true) @PathVariable("experimentId") String experimentId) {
-
- UserActionLogging.LogAction("Get a workflow status", " Experiment Id : " + experimentId);
+ @ApiOperation(value = "get a workflow", response = Experiment.class)
+ @RequestMapping(value = "/workflow/{experimentId}", method = RequestMethod.GET)
+ public ResponseEntity<String> getWorkflowExperiment(
+ @ApiParam(value = "experimentId", required = true) @PathVariable("experimentId") String experimentId) {
+ UserActionLogging.LogAction("Get workflow experiment", " Experiment Id : " + experimentId);
Experiment experiment;
UUID experimentUuid;
try {
experimentUuid = UUID.fromString(experimentId);
} catch (IllegalArgumentException iae) {
- UserActionLogging.LogAction("Get a workflow status", " Invalid Experiment Id");
+ UserActionLogging.LogAction("Get workflow experiment", " Invalid Experiment Id");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
experiment = experimentRepository.findOne(experimentUuid);
- if(experiment == null){
- UserActionLogging.LogAction("Get a workflow status", "The experiment does not exist.");
+ if (experiment == null) {
+ UserActionLogging.LogAction("Get workflow experiment", "The experiment does not exist.");
return ResponseEntity.badRequest().body("The experiment does not exist.");
}
- if(experiment.getWorkflowHistoryId() == null){
- UserActionLogging.LogAction("Get a workflow status", "History Id does not exist.");
+ if (experiment.getWorkflowHistoryId() == null) {
+ UserActionLogging.LogAction("Get workflow experiment", "History Id does not exist.");
return ResponseEntity.badRequest().body("The experiment is not a workflow.");
}
+ // If result already exists return
+ if (experiment.getResult() != null) {
+ UserActionLogging.LogAction("Get workflow experiment",
+ "Result exists: " + experiment.getResult());
+ return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
+ }
+
+ // If result doesn't exist, fetch it
+ UserActionLogging.LogAction("Get workflow experiment", "Result is null.");
+
+ String state = getWorkflowStatus(experiment.getWorkflowHistoryId());
+ UserActionLogging.LogAction("Get workflow experiment", "State is: " + state);
+
+ switch (state) {
+ case "running":
+ // Do nothing, when the experiment is created the status is set to running
+ UserActionLogging.LogAction("Get workflow experiment", "Result is still running.");
+ break;
+
+ case "completed":
+ // Get only the job result that is visible
+ List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experiment.getWorkflowHistoryId());
+ UserActionLogging.LogAction("Get workflow experiment",
+ "Results are: " + workflowJobsResults.toString());
+
+ boolean resultFound = false;
+ for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
+ if (jobResult.getVisible()) {
+ UserActionLogging.LogAction("Get workflow experiment",
+ "Visible result are: " + jobResult.getId());
+
+ String result = getWorkflowResultBody(experiment.getWorkflowHistoryId(), jobResult.getId());
+
+ UserActionLogging.LogAction("Get workflow experiment", "Result: " + result);
+ if (result == null) {
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ }
+ experiment.setResult(result);
+ experiment.setWorkflowStatus("completed");
+ resultFound = true;
+ }
+ }
+
+ 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);
+ experiment.setHasServerError(true);
+ }
+ break;
+
+ case "error":
+ // Get the job result that failed
+ workflowJobsResults = getWorkflowResults(experiment.getWorkflowHistoryId());
+ UserActionLogging.LogAction("Get workflow experiment",
+ "Error results are: " + workflowJobsResults.toString());
+
+ boolean failedJobFound = false;
+ for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
+ if (jobResult.getState().equals("error")) {
+ UserActionLogging.LogAction("Get workflow experiment",
+ "Failed job is: " + jobResult.getId());
+
+ String result = getWorkflowJobError(jobResult.getId());
+
+ UserActionLogging.LogAction("Get workflow experiment", "Job result: " + result);
+ if (result == null) {
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ }
+ experiment.setResult(result);
+ experiment.setWorkflowStatus("error");
+ failedJobFound = true;
+ }
+ }
+
+ 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);
+ experiment.setHasServerError(true);
+ }
+ break;
+
+ default: // InternalError or unexpected result
+ experiment.setResult(new ErrorResponse("An unexpected error occurred.", "500").toString());
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ break;
+ }
+
+ return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
+ }
+
+
+ /**
+ * @param historyId The historyId of the workflow
+ * @return "running" -> When the workflow is still running
+ * "internalError" -> When an exception or a bad request occurred
+ * "error" -> When the workflow produced an error
+ * "completed" -> When the workflow completed successfully
+ */
+ public String getWorkflowStatus(String historyId) {
+ UserActionLogging.LogAction("Get workflow status", " History Id : " + historyId);
+
// Create the request client
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<Object> call = service.getWorkflowStatusFromGalaxy(experiment.getWorkflowHistoryId(), galaxyApiKey);
+ Call<Object> call = service.getWorkflowStatusFromGalaxy(historyId, galaxyApiKey);
- String resultJson = null;
+ String result = null;
try {
Response<Object> response = call.execute();
if (response.code() >= 400) {
- UserActionLogging.LogAction("Get a workflow status", " Response code: "
+ UserActionLogging.LogAction("Get workflow status", " Response code: "
+ response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return ResponseEntity.status(response.code()).body((response.errorBody() != null ? response.errorBody().string() : " "));
+ return "internalError";
}
- resultJson = new Gson().toJson(response.body());
- UserActionLogging.LogAction("Get a workflow status", " Result: " + resultJson);
+ result = new Gson().toJson(response.body());
+ UserActionLogging.LogAction("Get workflow status", " Result: " + result);
} catch (IOException e) {
- UserActionLogging.LogAction("Get a workflow status"
- , " An exception happend: " + e.getMessage());
- return ResponseEntity.status(500).body(e.getMessage());
+ UserActionLogging.LogAction("Get workflow status"
+ , " An exception happened: " + e.getMessage());
+ return "internalError";
+ }
+
+ String state = null;
+ try {
+ JSONObject resultJson = new JSONObject(result);
+ state = resultJson.getString("state");
+ } catch (JSONException e) {
+ UserActionLogging.LogAction("Get workflow status"
+ , " An exception happened: " + e.getMessage());
+ return "internalError";
}
- UserActionLogging.LogAction("Get a workflow status", " Completed!");
- return ResponseEntity.ok(resultJson);
+ UserActionLogging.LogAction("Get workflow status", " Completed!");
+ switch (state) {
+ case "ok":
+ return "completed";
+ case "error":
+ return "error";
+ case "running":
+ case "new":
+ case "waiting":
+ case "queued":
+ return "running";
+ default:
+ return "internalError";
+ }
}
- // TODO: factorize workflow results
- @ApiOperation(value = "get workflow results", response = String.class)
- @RequestMapping(value = "/workflow/results/{historyId}", method = RequestMethod.GET)
- public ResponseEntity<String> getWorkflowResults(
- @ApiParam(value = "historyId", required = true) @PathVariable("historyId") String historyId) {
+ /**
+ * @param historyId The historyId of the workflow
+ * @return a List<GalaxyWorkflowResult> or null when an error occurred
+ */
+ public List<GalaxyWorkflowResult> getWorkflowResults(String historyId) {
UserActionLogging.LogAction("Get workflow results", " historyId : " + historyId);
- String url = workflowUrl + "/getWorkflowResults/" + historyId;
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<List<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(historyId, galaxyApiKey);
+
+ List<GalaxyWorkflowResult> getGalaxyWorkflowResultList = null;
try {
- StringBuilder response = new StringBuilder();
- User user = userInfo.getUser();
- String token = JWTUtil.getJWT(jwtSecret, user.getEmail());
- HTTPUtil.sendAuthorizedHTTP(url, "", response, "GET", "Bearer " + token);
- JsonElement element = new JsonParser().parse(response.toString());
+ Response<List<GalaxyWorkflowResult>> response = call.execute();
+ if (response.code() >= 400) {
+ UserActionLogging.LogAction("Get workflow results", " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+ getGalaxyWorkflowResultList = response.body();
+ UserActionLogging.LogAction("Get workflow results", " Result: " + response.body());
- return ResponseEntity.ok(gson.toJson(element));
} catch (IOException e) {
- return ResponseEntity.status(500).body(e.getMessage());
+ UserActionLogging.LogAction("Get workflow results"
+ , " An exception happened: " + e.getMessage());
+ return null;
}
+
+ UserActionLogging.LogAction("Get workflow results", " Completed!");
+ return getGalaxyWorkflowResultList;
+
}
- @ApiOperation(value = "get workflow result body", response = String.class)
- @RequestMapping(value = "/workflow/resultsbody/{historyId}/content/{resultId}", method = RequestMethod.GET)
- public ResponseEntity<String> getWorkflowResultBody(
- @ApiParam(value = "historyId", required = true) @PathVariable("historyId") String historyId,
- @ApiParam(value = "resultId", required = true) @PathVariable("resultId") String resultId) {
+ /**
+ * @param historyId the historyId of the workflow
+ * @param contentId the id of the job result that we want
+ * @return the result of the specific workflow job, null if there was an error
+ */
+ public String getWorkflowResultBody(String historyId, String contentId) {
+ UserActionLogging.LogAction("Get workflow results Body", " historyId : " + historyId);
- UserActionLogging.LogAction("Get workflow result content", " historyId : " + historyId + " resultId : " + resultId);
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> call =
+ service.getWorkflowResultsBodyFromGalaxy(historyId, contentId, galaxyApiKey);
- String url = workflowUrl + "/getWorkflowResultsBody/" + historyId + "/contents/" + resultId;
+ String resultJson = null;
try {
- StringBuilder response = new StringBuilder();
- User user = userInfo.getUser();
- String token = JWTUtil.getJWT(jwtSecret, user.getEmail());
- HTTPUtil.sendAuthorizedHTTP(url, "", response, "GET", "Bearer " + token);
- JsonElement element = new JsonParser().parse(response.toString());
+ Response<Object> response = call.execute();
+ if (response.code() >= 400) {
+ UserActionLogging.LogAction("Get workflow results Body", " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+ resultJson = new Gson().toJson(response.body());
+ UserActionLogging.LogAction("Get workflow results Body", " Result: " + resultJson);
- return ResponseEntity.ok(gson.toJson(element));
} catch (IOException e) {
- return ResponseEntity.status(500).body(e.getMessage());
+ UserActionLogging.LogAction("Get workflow results Body",
+ " An exception happened: " + e.getMessage());
+ return null;
}
+
+ UserActionLogging.LogAction("Get workflow results Body", " Completed!");
+ return resultJson;
}
- @ApiOperation(value = "get workflow result details", response = String.class)
- @RequestMapping(value = "/workflow/resultsdetails/{historyId}/content/{resultId}", method = RequestMethod.GET)
- public ResponseEntity<String> getWorkflowResultsDetails(
- @ApiParam(value = "historyId", required = true) @PathVariable("historyId") String historyId,
- @ApiParam(value = "resultId", required = true) @PathVariable("resultId") String resultId) {
- UserActionLogging.LogAction("Get workflow result details", " historyId : " + historyId + " resultId : " + resultId);
- String url = workflowUrl + "/getWorkflowResultsDetails/" + historyId + "/contents/" + resultId;
+ /**
+ * @param jobId the id of the workflow job that failed
+ * @return the error that was produced or null if an error occurred
+ */
+ public String getWorkflowJobError(String jobId){
+ UserActionLogging.LogAction("Get workflow job error", " jobId : " + jobId);
+
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId,galaxyApiKey);
+
+ String fullError = null;
+ String returnError = null;
try {
- StringBuilder response = new StringBuilder();
- User user = userInfo.getUser();
- String token = JWTUtil.getJWT(jwtSecret, user.getEmail());
- HTTPUtil.sendAuthorizedHTTP(url, "", response, "GET", "Bearer " + token);
- JsonElement element = new JsonParser().parse(response.toString());
+ Response<Object> response = callError.execute();
+ if(response.code() >= 400){
+ UserActionLogging.LogAction("Get workflow job error","Response code: "
+ + response.code() + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+
+ // Parsing the stderr of the job that failed
+ String jsonString = new Gson().toJson(response.body());
+ JsonElement jsonElement = new JsonParser().parse(jsonString);
+ JsonObject rootObject = jsonElement.getAsJsonObject();
+ fullError = rootObject.get("stderr").getAsString();
+ UserActionLogging.LogAction("Get workflow job error","Error: " + fullError);
+
+ String[] arrOfStr = fullError.split("ValueError", 0);
+ String specError = arrOfStr[arrOfStr.length-1];
+ returnError = specError.substring(1);
+ UserActionLogging.LogAction("Get workflow job error","Parsed Error: " + returnError);
- return ResponseEntity.ok(gson.toJson(element));
} catch (IOException e) {
- return ResponseEntity.status(500).body(e.getMessage());
+ UserActionLogging.LogAction("Get workflow job error","Exception: " + e.getMessage());
+ return null;
}
+
+ UserActionLogging.LogAction("Get workflow job error","Completed successfully!");
+
+ return returnError;
}
@ApiOperation(value = "Mark an experiment as viewed", response = Experiment.class)
diff --git a/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java b/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
index 52ccdc665..41c8a6576 100644
--- a/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
@@ -10,7 +10,7 @@ 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.GetWorkflowResultsFromGalaxyDtoResponse;
+import eu.hbp.mip.dto.GalaxyWorkflowResult;
import eu.hbp.mip.dto.PostWorkflowToGalaxyDtoResponse;
import eu.hbp.mip.dto.StringDtoResponse;
import eu.hbp.mip.helpers.LogHelper;
@@ -368,22 +368,22 @@ class GalaxyAPI {
logger.info(LogHelper.logUser(userDetails) + "Get workflow results called");
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<List<GetWorkflowResultsFromGalaxyDtoResponse>> call = service.getWorkflowResultsFromGalaxy(id,apiKey);
+ Call<List<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(id,apiKey);
- List<GetWorkflowResultsFromGalaxyDtoResponse> getWorkflowResultsFromGalaxyDtoResponsesList = null;
+ List<GalaxyWorkflowResult> workflowGalaxyDtoResponsesList = null;
try {
- Response<List<GetWorkflowResultsFromGalaxyDtoResponse>> response = call.execute();
+ 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();
}
- getWorkflowResultsFromGalaxyDtoResponsesList = response.body();
+ 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(getWorkflowResultsFromGalaxyDtoResponsesList);
+ return ResponseEntity.ok(workflowGalaxyDtoResponsesList);
}
/**
@@ -418,39 +418,6 @@ class GalaxyAPI {
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) {
diff --git a/src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java b/src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java
index 23143bf89..43f22af2b 100644
--- a/src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java
+++ b/src/main/java/eu/hbp/mip/controllers/retrofit/RetroFitGalaxyClients.java
@@ -1,7 +1,7 @@
package eu.hbp.mip.controllers.retrofit;
import com.google.gson.JsonObject;
-import eu.hbp.mip.dto.GetWorkflowResultsFromGalaxyDtoResponse;
+import eu.hbp.mip.dto.GalaxyWorkflowResult;
import eu.hbp.mip.dto.PostWorkflowToGalaxyDtoResponse;
import retrofit2.Call;
import retrofit2.http.*;
@@ -17,14 +17,11 @@ public interface RetroFitGalaxyClients {
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);
+ Call<List<GalaxyWorkflowResult>> 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);
+ Call<Object> getErrorMessageOfWorkflowFromGalaxy(@Path("jobId") String jobId, @Query("key") String key);
}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/dto/GetWorkflowResultsFromGalaxyDtoResponse.java b/src/main/java/eu/hbp/mip/dto/GalaxyWorkflowResult.java
similarity index 90%
rename from src/main/java/eu/hbp/mip/dto/GetWorkflowResultsFromGalaxyDtoResponse.java
rename to src/main/java/eu/hbp/mip/dto/GalaxyWorkflowResult.java
index a81660ac4..566910c6f 100644
--- a/src/main/java/eu/hbp/mip/dto/GetWorkflowResultsFromGalaxyDtoResponse.java
+++ b/src/main/java/eu/hbp/mip/dto/GalaxyWorkflowResult.java
@@ -9,7 +9,7 @@ import com.google.gson.annotations.SerializedName;
import java.util.List;
-public class GetWorkflowResultsFromGalaxyDtoResponse {
+public class GalaxyWorkflowResult {
@SerializedName("history_content_type")
private String historyContentType;
@@ -46,10 +46,10 @@ public class GetWorkflowResultsFromGalaxyDtoResponse {
@SerializedName("purged")
private Boolean purged;
- public GetWorkflowResultsFromGalaxyDtoResponse() {
+ public GalaxyWorkflowResult() {
}
- 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) {
+ public GalaxyWorkflowResult(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;
--
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