diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index deef20f755c0fd961e09a238eb662a671a9532e2..649fdab22f5152d30deeaf17cce5a95f07064de6 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -25,7 +25,38 @@ import eu.hbp.mip.utils.UserActionLogging;
import java.io.IOException;
import java.util.*;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
+//galaxyapi copy paste
+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.GetWorkflowResultsFromGalaxyDtoResponse;
+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.*;
+
+//galaxyapi copy paste
/**
* Created by habfast on 21/04/16.
*/
@@ -58,7 +89,13 @@ public class ExperimentApi {
@Autowired
private ExperimentRepository experimentRepository;
+
+ @Value("#{'${services.galaxy.galaxyUrl}'}")
+ private String galaxyUrl;
+ @Value("#{'${services.galaxy.galaxyApiKey}'}")
+ private String galaxyApiKey;
+
@ApiOperation(value = "Create an experiment on Exareme", response = Experiment.class)
@RequestMapping(value = "/exareme", method = RequestMethod.POST)
public ResponseEntity<String> runExaremeExperiment(@RequestBody ExperimentQuery expQuery) {
@@ -114,37 +151,115 @@ public class ExperimentApi {
User user = userInfo.getUser();
String token = JWTUtil.getJWT(jwtSecret, user.getEmail());
- HashMap<String, String> queryMap = new HashMap<String, String>();
+ HashMap<String, String> allJsonParams = new HashMap<String, String>();
if (params != null) {
for (AlgorithmParam p : params) {
- queryMap.put(p.getName(), p.getValue());
+ allJsonParams.put(p.getName(), p.getValue());
}
}
- String query = gson.toJson(queryMap);
- String url = workflowUrl + "/runWorkflow/" + algoCode;
+ //String query = gson.toJson(queryMap);
+ //String url = workflowUrl + "/runWorkflow/" + algoCode;
// Results are stored in the experiment object
- new Thread(() -> {
- try {
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendAuthorizedHTTP(url, query, results, "POST", "Bearer " + token);
- experiment.setResult("[" + results.toString() + "]");
- experiment.setHasError(code >= 400);
- experiment.setHasServerError(code >= 500);
- } catch (IOException e) {
+ // new Thread(() -> {
+ // try {
+ // StringBuilder results = new StringBuilder();
+ // int code = HTTPUtil.sendAuthorizedHTTP(url, query, results, "POST", "Bearer " + token);
+ // experiment.setResult("[" + results.toString() + "]");
+ // experiment.setHasError(code >= 400);
+ // experiment.setHasServerError(code >= 500);
+ // } catch (IOException e) {
//LOGGER.trace("Invalid UUID", e);
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- experiment.setResult(e.getMessage());
+ // experiment.setHasError(true);
+ // experiment.setHasServerError(true);
+ // experiment.setResult(e.getMessage());
+ // }
+ // finishExperiment(experiment);
+ // }).start();
+
+ // UserActionLogging.LogAction("create workflow", "no info");
+
+ // return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
+ final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
+ final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
+
+ Workflow matchingWorkflow = null;
+ for(Workflow workflow : workflowsClient.getWorkflows()) {
+ if(workflow.getId().equals(algoCode)) {
+ matchingWorkflow = workflow;
}
- finishExperiment(experiment);
- }).start();
+ }
+ if(matchingWorkflow == null){
+ //logger.error(LogHelper.logUser(userDetails) + "Run workflow could not find workflow with id : " + algoCode + " ,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());
- UserActionLogging.LogAction("create workflow", "no info");
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
+ JsonObject jsonObject = new JsonParser().parse(stringBuffer.toString()).getAsJsonObject();
+
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<PostWorkflowToGalaxyDtoResponse> call = service.postWorkflowToGalaxy(algoCode, galaxyApiKey, 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);
+ return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
@ApiOperation(value = "get an experiment", response = Experiment.class)