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Commit 854b1853 authored by kostas's avatar kostas
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Reverting results to result and accessing only the first result from galaxy.

parent 36ca121d
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1 merge request!19Feat/186 experiment refactor
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src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java
+ 2
− 24
View file @ 854b1853
......@@ -52,7 +52,7 @@ public class ExperimentDAO {
@Expose
@Column(columnDefinition = "TEXT")
private String results;
private String result;
@Expose
@Column(columnDefinition = "TIMESTAMP WITHOUT TIME ZONE")
......@@ -95,28 +95,6 @@ public class ExperimentDAO {
*/
}
public String getResults() {
return results;
}
public void setResults(String result) {
this.results = result;
}
public class ResultObjectDTO {
ArrayList<Object> result;
public ArrayList<Object> getResult() {
return this.result;
}
public void setResult(ArrayList<Object> results) {
this.result = results;
}
}
public ExperimentDTO convertToDTO(boolean includeResult)
{
ExperimentDTO experimentDTO = new ExperimentDTO();
......@@ -127,7 +105,7 @@ public class ExperimentDAO {
experimentDTO.setCreatedBy(this.createdBy.getUsername());
experimentDTO.setName(this.name);
if(includeResult){
experimentDTO.setResults(JsonConverters.convertJsonStringToObject(this.results, new ArrayList<ArrayList<Object>>().getClass()));
experimentDTO.setResult(JsonConverters.convertJsonStringToObject(String.valueOf(this.result), new ArrayList<>().getClass()));
}
experimentDTO.setStatus(this.status);
experimentDTO.setShared(this.shared);
......
src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
+ 1
− 2
View file @ 854b1853
......@@ -22,11 +22,10 @@ public class ExperimentDTO {
private Date finished;
private Boolean shared;
private Boolean viewed;
private List<List<Object>> results;
private List<Object> result;
private ExperimentDAO.Status status;
private AlgorithmDTO algorithm;
public ExperimentDTO() {
}
}
src/main/java/eu/hbp/mip/services/ExperimentService.java
+ 27
− 44
View file @ 854b1853
......@@ -169,7 +169,6 @@ public class ExperimentService {
* @return the experiment information which was created
*/
public ExperimentDTO createExperiment(Authentication authentication, ExperimentDTO experimentDTO, Logger logger) {
UserDAO user = activeUserService.getActiveUser();
//Checking if check (POST) /experiments has proper input.
checkPostExperimentProperInput(experimentDTO, logger);
......@@ -208,7 +207,6 @@ public class ExperimentService {
* @return the experiment information which was created
*/
public ExperimentDTO createTransientExperiment(Authentication authentication, ExperimentDTO experimentDTO, Logger logger) {
UserDAO user = activeUserService.getActiveUser();
//Checking if check (POST) /experiments has proper input.
checkPostExperimentProperInput(experimentDTO, logger);
......@@ -216,7 +214,7 @@ public class ExperimentService {
// Get the type and name of algorithm
String algorithmType = experimentDTO.getAlgorithm().getType();
if(algorithmType == "workflow"){
if(algorithmType.equals("workflow")){
logger.LogUserAction("You can not run workflow algorithms transiently.");
throw new BadRequestException("You can not run workflow algorithms transiently.");
}
......@@ -246,7 +244,7 @@ public class ExperimentService {
logger.LogUserAction("Experiment with uuid: " + experimentDTO.getUuid() + "gave response code: " + exaremeResult.getCode() + " and result: " + exaremeResult.getResults());
experimentDTO.setResults((exaremeResult.getCode() >= 400) ? null : JsonConverters.convertJsonStringToObject(exaremeResult.getResults(), new ArrayList<ArrayList<Object>>().getClass()));
experimentDTO.setResult((exaremeResult.getCode() >= 400) ? null : exaremeResult.getResults());
experimentDTO.setStatus((exaremeResult.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
return experimentDTO;
......@@ -254,10 +252,10 @@ public class ExperimentService {
/**
* The updateExperiment will update the experiment's properties
*
* @param uuid is the id of the experiment to be updated
* @param experimentDTO is the experiment information to be updated
* @param logger contains username and the endpoint.
* @return
*/
public ExperimentDTO updateExperiment(String uuid, ExperimentDTO experimentDTO, Logger logger) {
ExperimentDAO experimentDAO;
......@@ -331,7 +329,7 @@ public class ExperimentService {
&& experimentDTO.getViewed() == null
&& experimentDTO.getCreated() == null
&& experimentDTO.getCreatedBy() == null
&& experimentDTO.getResults() == null
&& experimentDTO.getResult() == null
&& experimentDTO.getStatus() == null
&& experimentDTO.getUuid() == null;
......@@ -372,7 +370,7 @@ public class ExperimentService {
throw new BadRequestException("Finished is not editable.");
}
if (experimentDTO.getResults() != null) {
if (experimentDTO.getResult() != null) {
logger.LogUserAction( "Result is not editable.");
throw new BadRequestException("Result is not editable.");
}
......@@ -507,23 +505,15 @@ public class ExperimentService {
}
}
private String formattingExaremeResult(String result) {
List<LinkedTreeMap<String,Object>> jsonObject = JsonConverters.convertJsonStringToObject(result, new ArrayList<ExperimentDAO.ResultObjectDTO>().getClass());
LinkedTreeMap<String,Object> firstResult = jsonObject.get(0);
return "[" + JsonConverters.convertObjectToJsonString(firstResult.get("result")) + "]";
}
private String formattingGalaxyResult(String result) {
List<LinkedTreeMap<String,Object>> jsonObjects = JsonConverters.convertJsonStringToObject(result, new ArrayList<ExperimentDAO.ResultObjectDTO>().getClass());
List<Object> objects = new ArrayList<>();
for (int i = 0; i < jsonObjects.size(); i++) {
LinkedTreeMap<String,Object> k = jsonObjects.get(i);
objects.add(k.get("result"));
}
return JsonConverters.convertObjectToJsonString(objects);
List<LinkedTreeMap<String,Object>> jsonObject = JsonConverters.convertJsonStringToObject(result, new ArrayList<ArrayList<Object>>().getClass());
LinkedTreeMap<String,Object> firstResult = jsonObject.get(0);
jsonObject = (List<LinkedTreeMap<String, Object>>) firstResult.get("result");
List<LinkedTreeMap<String,Object>> finalJsonObject = new ArrayList<>();
finalJsonObject.add(jsonObject.get(0));
return JsonConverters.convertObjectToJsonString(finalJsonObject);
}
/**
* The runExaremeExperiment will run to exareme the experiment
*
......@@ -532,7 +522,7 @@ public class ExperimentService {
* @param experimentDTO is the experiment information to be executed in the exareme
* @return the result of exareme as well as the http status that was retrieved
*/
private ExaremeResult runExaremeExperiment(String url, String body, ExperimentDTO experimentDTO) {
public ExaremeResult runExaremeExperiment(String url, String body, ExperimentDTO experimentDTO) {
StringBuilder results = new StringBuilder();
int code;
......@@ -542,15 +532,14 @@ public class ExperimentService {
throw new InternalServerError("Error occurred : " + e.getMessage());
}
String resultToMatchGalaxy = "[" + results + "]";
String formattedResult = formattingExaremeResult(resultToMatchGalaxy);
Logger.LogExperimentAction(experimentDTO.getName(), experimentDTO.getUuid(), "Algorithm finished with code: " + code + "and result :" + formattedResult);
// Results are stored in the experiment object
ExperimentDTO experimentDTOWithOnlyResult = JsonConverters.convertJsonStringToObject(String.valueOf(results), ExperimentDTO.class);
List<Object> resultDTOS = experimentDTOWithOnlyResult.getResult();
Logger.LogExperimentAction(experimentDTO.getName(), experimentDTO.getUuid(), "Thread named :" + Thread.currentThread().getName() + " with id :" + Thread.currentThread().getId() + " started!");
return new ExaremeResult(code, formattedResult);
return new ExaremeResult(code, resultDTOS);
}
/* -------------------------------------- EXAREME CALLS ---------------------------------------------------------*/
/**
......@@ -593,7 +582,7 @@ public class ExperimentService {
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Experiment with uuid: " + experimentDAO.getUuid() + "gave response code: " + exaremeResult.getCode() + " and result: " + exaremeResult.getResults());
experimentDAO.setResults((exaremeResult.getCode() >= 400) ? null : exaremeResult.getResults());
experimentDAO.setResult((exaremeResult.getCode() >= 400) ? null : JsonConverters.convertObjectToJsonString(exaremeResult.getResults()));
experimentDAO.setStatus((exaremeResult.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
} catch (Exception e) {
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "There was an exception: " + e.getMessage());
......@@ -685,11 +674,6 @@ public class ExperimentService {
} else { // Something unexpected happened
String msgErr = gson.toJson(response.errorBody());
logger.LogUserAction("Error Response: " + msgErr);
// Values are read from streams.
JSONObject jObjectError = new JSONObject(msgErr);
String errMsg = jObjectError.get("err_msg").toString();
experimentDTO.setStatus((response.code() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
}
......@@ -767,7 +751,7 @@ public class ExperimentService {
if (result == null) {
experimentDAO.setStatus(ExperimentDAO.Status.error);
} else {
experimentDAO.setResults(result);
experimentDAO.setResult(result);
experimentDAO.setStatus(ExperimentDAO.Status.success);
resultFound = true;
}
......@@ -818,8 +802,8 @@ public class ExperimentService {
}
// If result exists return
if (experimentDAO.getResults() != null) {
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "ResultDTO exists: " + experimentDAO.getResults());
if (experimentDAO.getResult() != null) {
Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "ResultDTO exists: " + experimentDAO.getResult());
return;
}
}
......@@ -947,8 +931,7 @@ public class ExperimentService {
+ response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return null;
}
resultJson = gson.toJson(response.body());
resultJson = new Gson().toJson(response.body());
Logger.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + resultJson);
} catch (IOException e) {
......@@ -957,7 +940,7 @@ public class ExperimentService {
return null;
}
Logger.LogExperimentAction(experimentName, experimentId, " Completed!");
return formattingGalaxyResult(resultJson);
}
......@@ -1007,10 +990,10 @@ public class ExperimentService {
}
static class ExaremeResult {
private int code;
private String results;
private final int code;
private final List<Object> results;
public ExaremeResult(int code, String results) {
public ExaremeResult(int code, List<Object> results) {
this.code = code;
this.results = results;
}
......@@ -1019,7 +1002,7 @@ public class ExperimentService {
return code;
}
public String getResults() {
public List<Object> getResults() {
return results;
}
}
......
src/main/resources/db/migration/V7_0__NewDatabaseStructure.sql
+ 0
− 2
View file @ 854b1853
......@@ -26,8 +26,6 @@ DROP COLUMN hasservererror,
DROP COLUMN validations,
DROP COLUMN model_slug;
ALTER TABLE experiment
RENAME result TO results;
ALTER TABLE experiment
RENAME algorithms TO algorithm;
ALTER TABLE experiment
......
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