diff --git a/build.sh b/build.sh
index 6a18d98ecec05885651675049490ca44c990ec7f..ef4f10565705b3eb3d0fae54b60de23671f356bf 100755
--- a/build.sh
+++ b/build.sh
@@ -26,7 +26,7 @@ else
DOCKER="sudo docker"
fi
-IMAGE="kfilippopolitis/portal-backend"
+IMAGE="hbpmip/portal-backend"
VCS_REF=$(git describe --tags --dirty)
VERSION=$(git describe --tags --dirty)
diff --git a/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java b/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
index 90d05b9d3254d1f36989a533923a6d5961d56549..7836edf941914247a7a86d41d63108bfb33d3316 100644
--- a/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
@@ -274,7 +274,7 @@ public class SecurityConfiguration extends WebSecurityConfigurerAdapter {
public void logout() {
// POSTã™ã‚‹ãƒªã‚¯ã‚¨ã‚¹ãƒˆãƒ‘ラメーターを作æˆ
- ActionLogging.LogAction("refresh token ", this.oauth2ClientContext.getAccessToken().getRefreshToken().getValue());
+ Logging.LogAction("refresh token ", this.oauth2ClientContext.getAccessToken().getRefreshToken().getValue());
RestTemplate restTemplate = new RestTemplate();
MultiValueMap<String, String> formParams = new LinkedMultiValueMap<>();
formParams.add("client_id", hbp().getClientId());
@@ -284,7 +284,7 @@ public class SecurityConfiguration extends WebSecurityConfigurerAdapter {
HttpHeaders httpHeaders = new HttpHeaders();
httpHeaders.add(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_FORM_URLENCODED_VALUE);
// リクエストを作æˆ
- ActionLogging.LogAction("logoutUri is ", logoutUri);
+ Logging.LogAction("logoutUri is ", logoutUri);
RequestEntity<MultiValueMap<String, String>> requestEntity =
new RequestEntity<>(formParams, httpHeaders, HttpMethod.POST,
URI.create(logoutUri));
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
index db9b7d124bf76e3cec71c9c99399a48b6544868d..8310973a308ec810853519552dc48855f494e4d7 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
@@ -13,7 +13,7 @@ import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.model.galaxy.WorkflowDTO;
import eu.hbp.mip.utils.CustomResourceLoader;
import eu.hbp.mip.utils.HTTPUtil;
-import eu.hbp.mip.utils.ActionLogging;
+import eu.hbp.mip.utils.Logging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
@@ -57,24 +57,24 @@ public class AlgorithmsApi {
@ApiOperation(value = "List all algorithms", response = String.class)
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Executing...");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Executing...");
LinkedList<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms();
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Loaded " + exaremeAlgorithms.size() + " exareme algorithms");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Loaded " + exaremeAlgorithms.size() + " exareme algorithms");
LinkedList<AlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows();
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Loaded " + galaxyAlgorithms.size() + " galaxy algorithms");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Loaded " + galaxyAlgorithms.size() + " galaxy algorithms");
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
if (exaremeAlgorithms != null) {
algorithms.addAll(exaremeAlgorithms);
} else {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
"Getting exareme algorithms failed and returned null");
}
if (galaxyAlgorithms != null) {
algorithms.addAll(galaxyAlgorithms);
} else {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
"Getting galaxy workflows failed and returned null");
}
@@ -82,7 +82,7 @@ public class AlgorithmsApi {
try {
disabledAlgorithms = getDisabledAlgorithms();
} catch (IOException e) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
disabledAlgorithmsCouldNotBeLoaded);
}
@@ -93,7 +93,7 @@ public class AlgorithmsApi {
allowedAlgorithms.add(algorithm);
}
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
"Successfully listed " + allowedAlgorithms.size() + " algorithms");
return ResponseEntity.ok(allowedAlgorithms);
}
@@ -116,11 +116,11 @@ public class AlgorithmsApi {
}.getType()
);
} catch (IOException e) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "An exception occurred: " + e.getMessage());
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "An exception occurred: " + e.getMessage());
return null;
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
"Completed, returned " + algorithms.size() + " algorithms.");
return algorithms;
}
@@ -140,7 +140,7 @@ public class AlgorithmsApi {
workflowList = new ArrayList<>(workflowsClient.getWorkflows());
} catch (Exception e) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Error when calling list galaxy workflows: " + e.getMessage());
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Error when calling list galaxy workflows: " + e.getMessage());
return null;
}
@@ -160,28 +160,28 @@ public class AlgorithmsApi {
} else { // Something unexpected happened
String msgErr = gson.toJson(response.errorBody());
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Error Response: " + msgErr);
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Error Response: " + msgErr);
return null;
}
} catch (Exception e) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "An exception occurred: " + e.getMessage());
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "An exception occurred: " + e.getMessage());
return null;
}
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Workflows fetched: " + workflows.size());
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Workflows fetched: " + workflows.size());
// Convert the workflows to algorithms
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
for (WorkflowDTO workflow : workflows) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Converting workflow: " + workflow);
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Converting workflow: " + workflow);
algorithms.add(workflow.convertToAlgorithmDTO());
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
"Converted algorithm: " + algorithms.get(algorithms.size() - 1));
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Completed!");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Completed!");
return algorithms;
}
diff --git a/src/main/java/eu/hbp/mip/controllers/ArticlesApi.java b/src/main/java/eu/hbp/mip/controllers/ArticlesApi.java
index e73b2d061d45329a064e725492186a73fe7a2074..d4eb46e9f3d072255e23be8a37a4e956add16873 100644
--- a/src/main/java/eu/hbp/mip/controllers/ArticlesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ArticlesApi.java
@@ -10,7 +10,7 @@ import eu.hbp.mip.model.Article;
import eu.hbp.mip.model.User;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.repositories.ArticleRepository;
-import eu.hbp.mip.utils.ActionLogging;
+import eu.hbp.mip.utils.Logging;
import io.swagger.annotations.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
@@ -43,7 +43,7 @@ public class ArticlesApi {
) {
User user = userInfo.getUser();
Iterable<Article> articles;
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /articles", "Loading articles...");
+ Logging.LogUserAction(user.getUsername(), "(GET) /articles", "Loading articles...");
if (own != null && own) {
articles = articleRepository.findByCreatedBy(user);
@@ -60,7 +60,7 @@ public class ArticlesApi {
articlesSize++;
}
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles", "Successfully Loaded " + articlesSize + " articles");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles", "Successfully Loaded " + articlesSize + " articles");
return ResponseEntity.ok(articles);
}
@@ -74,7 +74,7 @@ public class ArticlesApi {
) {
User user = userInfo.getUser();
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /articles", "Creating article...");
+ Logging.LogUserAction(user.getUsername(), "(POST) /articles", "Creating article...");
article.setCreatedAt(new Date());
if ("published".equals(article.getStatus())) {
@@ -116,7 +116,7 @@ public class ArticlesApi {
}
articleRepository.save(article);
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /articles", "Successfully created article with id : " + article.getSlug());
+ Logging.LogUserAction(user.getUsername(), "(POST) /articles", "Successfully created article with id : " + article.getSlug());
return new ResponseEntity<>(HttpStatus.CREATED);
}
@@ -126,7 +126,7 @@ public class ArticlesApi {
public ResponseEntity<Article> getAnArticle(
@ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles/{slug}", "Loading article with id : " + slug);
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles/{slug}", "Loading article with id : " + slug);
User user = userInfo.getUser();
Article article;
@@ -134,7 +134,7 @@ public class ArticlesApi {
if (article == null) {
//LOGGER.warn("Cannot find article : " + slug);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles/{slug}", "Article not found");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles/{slug}", "Article not found");
return ResponseEntity.badRequest().body(null);
}
@@ -142,7 +142,7 @@ public class ArticlesApi {
return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /articles/{slug}", "Successfully Loaded article with id : " + slug);
+ Logging.LogUserAction(user.getUsername(), "(GET) /articles/{slug}", "Successfully Loaded article with id : " + slug);
return ResponseEntity.ok(article);
}
@@ -155,7 +155,7 @@ public class ArticlesApi {
@ApiParam(value = "slug", required = true) @PathVariable("slug") String slug,
@RequestBody @ApiParam(value = "Article to update", required = true) @Valid Article article
) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(PUT) /articles/{slug}", "Updating article with id : " + slug);
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(PUT) /articles/{slug}", "Updating article with id : " + slug);
User user = userInfo.getUser();
@@ -185,7 +185,7 @@ public class ArticlesApi {
articleRepository.save(article);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(PUT) /articles/{slug}", "Successfully pdated article with id : " + slug);
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(PUT) /articles/{slug}", "Successfully pdated article with id : " + slug);
return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index b4a7d2bbd63def24b4e48d3a08e417a0252a4749..e81d2ee5ba782718e2db98b5a4e40f35b853ef8d 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -19,7 +19,7 @@ import eu.hbp.mip.repositories.ExperimentRepository;
import eu.hbp.mip.repositories.ModelRepository;
import eu.hbp.mip.utils.ClaimUtils;
import eu.hbp.mip.utils.HTTPUtil;
-import eu.hbp.mip.utils.ActionLogging;
+import eu.hbp.mip.utils.Logging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
@@ -92,28 +92,28 @@ public class ExperimentApi {
UUID experimentUuid;
User user = userInfo.getUser();
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Loading Experiment with uuid : " + uuid);
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Loading Experiment with uuid : " + uuid);
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Invalid Experiment UUID.");
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Invalid Experiment UUID.");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
experiment = experimentRepository.findOne(experimentUuid);
if (experiment == null) {
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Experiment Not found.");
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Experiment Not found.");
return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
}
if (!experiment.isShared() && !experiment.getCreatedBy().getUsername().equals(user.getUsername())) {
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Accessing Experiment is unauthorized.");
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Accessing Experiment is unauthorized.");
return new ResponseEntity<>("You don't have access to the experiment.", HttpStatus.UNAUTHORIZED);
}
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Experiment was Loaded with uuid : " + uuid + ".");
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Experiment was Loaded with uuid : " + uuid + ".");
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
@@ -127,7 +127,7 @@ public class ExperimentApi {
String algorithmType = experimentExecutionDTO.getAlgorithms().get(0).getType();
String algorithmName = experimentExecutionDTO.getAlgorithms().get(0).getName();
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Executing " + algorithmName + " with algorithmType : " + algorithmType + ".");
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Executing " + algorithmName + " with algorithmType : " + algorithmType + ".");
if (authenticationIsEnabled) {
// Getting the dataset from the experiment parameters
@@ -140,7 +140,7 @@ public class ExperimentApi {
}
if (experimentDatasets == null || experimentDatasets.equals("")) {
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
"A dataset should be specified to run an algorithm.");
return ResponseEntity.badRequest().body("Please provide at least one dataset to run the algorithm.");
}
@@ -153,10 +153,10 @@ public class ExperimentApi {
// Run with the appropriate engine
if (algorithmType.equals("workflow")) {
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Algorithm runs on Galaxy.");
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Algorithm runs on Galaxy.");
return runGalaxyWorkflow(experimentExecutionDTO);
} else {
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Algorithm runs on Exareme.");
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Algorithm runs on Exareme.");
return runExaremeAlgorithm(experimentExecutionDTO);
}
}
@@ -170,24 +170,24 @@ public class ExperimentApi {
UUID experimentUuid;
User user = userInfo.getUser();
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Marking as viewed the experiment with uuid : " + uuid + ".");
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Marking as viewed the experiment with uuid : " + uuid + ".");
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Invalid Experiment UUID" + uuid + ".");
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Invalid Experiment UUID" + uuid + ".");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
experiment = experimentRepository.findOne(experimentUuid);
if (!experiment.getCreatedBy().getUsername().equals(user.getUsername())) {
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "You're not the owner of this experiment");
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "You're not the owner of this experiment");
return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.UNAUTHORIZED);
}
experiment.setResultsViewed(true);
experimentRepository.save(experiment);
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Experiment with uuid: " + uuid + " was marked as viewed.");
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Experiment with uuid: " + uuid + " was marked as viewed.");
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
@@ -197,7 +197,7 @@ public class ExperimentApi {
public ResponseEntity<String> markExperimentAsShared(
@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{uuid}/markAsShared", "Marking as shared the experiment with uuid : " + uuid + ".");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{uuid}/markAsShared", "Marking as shared the experiment with uuid : " + uuid + ".");
return doMarkExperimentAsShared(uuid, true);
}
@@ -206,7 +206,7 @@ public class ExperimentApi {
@RequestMapping(value = "/{uuid}/markAsUnshared", method = RequestMethod.GET)
public ResponseEntity<String> markExperimentAsUnshared(
@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{uuid}/markAs/Unshared", "Marking as unshared the experiment with uuid : " + uuid + ".");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{uuid}/markAs/Unshared", "Marking as unshared the experiment with uuid : " + uuid + ".");
return doMarkExperimentAsShared(uuid, false);
}
@@ -216,10 +216,10 @@ public class ExperimentApi {
public ResponseEntity<String> listExperiments(
@ApiParam(value = "maxResultCount") @RequestParam int maxResultCount) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{maxResultCount}", "Listing experiments with a maximum amount of : " + maxResultCount + ".");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{maxResultCount}", "Listing experiments with a maximum amount of : " + maxResultCount + ".");
List<Experiment> expList = doListExperiments(false, null);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{maxResultCount}", "Successfully listed experiments.");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{maxResultCount}", "Successfully listed experiments.");
return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
}
@@ -229,7 +229,7 @@ public class ExperimentApi {
public ResponseEntity<String> listExperiments(@ApiParam(value = "slug") @RequestParam("slug") String modelSlug,
@ApiParam(value = "maxResultCount") @RequestParam("maxResultCount") int maxResultCount) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{slug}/{maxResultCount}", "Listing experiments with a maximum amount of :" + maxResultCount + "with modelSlug : " + modelSlug + ".");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{slug}/{maxResultCount}", "Listing experiments with a maximum amount of :" + maxResultCount + "with modelSlug : " + modelSlug + ".");
if (maxResultCount <= 0 || modelSlug == null || "".equals(modelSlug)) {
return new ResponseEntity<>("You must provide at least a slug or a limit of result",
@@ -237,16 +237,16 @@ public class ExperimentApi {
}
List<Experiment> expList = doListExperiments(false, null);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{slug}/{maxResultCount}", "Successfully listed my experiments.");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{slug}/{maxResultCount}", "Successfully listed my experiments.");
return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
}
@ApiOperation(value = "list my experiments", response = Experiment.class, responseContainer = "List")
@RequestMapping(method = RequestMethod.GET, params = {"mine"})
public ResponseEntity<String> listMyExperiments(Authentication authentication, @ApiParam(value = "mine") @RequestParam("mine") boolean mine) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{mine}", "Listing my experiments.");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{mine}", "Listing my experiments.");
List<Experiment> expList = doListExperiments(true, null);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{mine}", "Successfully listed my experiments.");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{mine}", "Successfully listed my experiments.");
return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
}
@@ -285,7 +285,7 @@ public class ExperimentApi {
} catch (IllegalArgumentException iae) {
//LOGGER.trace("Invalid UUID", iae);
//LOGGER.warn("An invalid Experiment UUID was received !");
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List my experiments", "Listing my experiments.");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "List my experiments", "Listing my experiments.");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
@@ -297,7 +297,7 @@ public class ExperimentApi {
experiment.setShared(shared);
experimentRepository.save(experiment);
- ActionLogging.LogUserAction(user.getUsername(), "Experiment updated (marked as shared)", "");
+ Logging.LogUserAction(user.getUsername(), "Experiment updated (marked as shared)", "");
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
@@ -316,26 +316,26 @@ public class ExperimentApi {
experiment.setName(experimentExecutionDTO.getName());
experimentRepository.save(experiment);
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " id : " + experiment.getUuid());
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " algorithms : " + experiment.getAlgorithms());
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " model : " + experiment.getModel().getSlug());
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " name : " + experiment.getName());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " id : " + experiment.getUuid());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " algorithms : " + experiment.getAlgorithms());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " model : " + experiment.getModel().getSlug());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " name : " + experiment.getName());
return experiment;
}
private void saveExperiment(Experiment experiment) {
User user = userInfo.getUser();
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " id : " + experiment.getUuid());
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " algorithms : " + experiment.getAlgorithms());
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " model : " + experiment.getModel().getSlug());
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " name : " + experiment.getName());
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " historyId : " + experiment.getWorkflowHistoryId());
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " status : " + experiment.getWorkflowStatus());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " id : " + experiment.getUuid());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " algorithms : " + experiment.getAlgorithms());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " model : " + experiment.getModel().getSlug());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " name : " + experiment.getName());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " historyId : " + experiment.getWorkflowHistoryId());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " status : " + experiment.getWorkflowStatus());
experimentRepository.save(experiment);
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Saved experiment");
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Saved experiment");
}
private void finishExperiment(Experiment experiment) {
@@ -352,11 +352,11 @@ public class ExperimentApi {
* @return the response to be returned
*/
public ResponseEntity<String> runExaremeAlgorithm(ExperimentExecutionDTO experimentExecutionDTO) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Running the algorithm...");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Running the algorithm...");
Experiment experiment = createExperiment(experimentExecutionDTO);
User user = userInfo.getUser();
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
// Run the 1st algorithm from the list
String algorithmName = experimentExecutionDTO.getAlgorithms().get(0).getName();
@@ -367,30 +367,30 @@ public class ExperimentApi {
String body = gson.toJson(algorithmParameters);
String url = queryExaremeUrl + "/" + algorithmName;
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "url: " + url + ", body: " + body);
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "url: " + url + ", body: " + body);
ResponseEntity<String> response = new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
"Completed, returning: " + experiment.toString());
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
"Starting exareme execution thread");
new Thread(() -> {
// ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogUserAction!
- ActionLogging.LogExperimentAction(experiment.getName(), "Thread named :" + Thread.currentThread().getName() + " with id :" + Thread.currentThread().getId() + " started!");
+ Logging.LogExperimentAction(experiment.getName(), "Thread named :" + Thread.currentThread().getName() + " with id :" + Thread.currentThread().getId() + " started!");
try {
StringBuilder results = new StringBuilder();
int code = HTTPUtil.sendPost(url, body, results);
- ActionLogging.LogExperimentAction(experiment.getName(), "Algorithm finished with code: " + code);
+ Logging.LogExperimentAction(experiment.getName(), "Algorithm finished with code: " + code);
// Results are stored in the experiment object
experiment.setResult("[" + results.toString() + "]");
experiment.setHasError(code >= 400);
experiment.setHasServerError(code >= 500);
} catch (Exception e) {
- ActionLogging.LogExperimentAction(experiment.getName(), "There was an exception: " + e.getMessage());
+ Logging.LogExperimentAction(experiment.getName(), "There was an exception: " + e.getMessage());
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -398,7 +398,7 @@ public class ExperimentApi {
}
finishExperiment(experiment);
- ActionLogging.LogExperimentAction(experiment.getName(), "Finished the experiment: " + experiment.toString());
+ Logging.LogExperimentAction(experiment.getName(), "Finished the experiment: " + experiment.toString());
}).start();
return response;
@@ -414,10 +414,10 @@ public class ExperimentApi {
* @return the response to be returned
*/
public ResponseEntity<String> runGalaxyWorkflow(ExperimentExecutionDTO experimentExecutionDTO) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Running a workflow...");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Running a workflow...");
Experiment experiment = createExperiment(experimentExecutionDTO);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
User user = userInfo.getUser();
@@ -447,7 +447,7 @@ public class ExperimentApi {
}
}
if (workflow == null) {
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
"Could not find algorithm code: " + workflowId);
return ResponseEntity.status(HttpStatus.BAD_REQUEST)
.body(new ErrorResponse("Could not find galaxy algorithm.").toString());
@@ -466,7 +466,7 @@ public class ExperimentApi {
// Create the request client
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Running Galaxy workflow with id: " + workflow.getId());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Running Galaxy workflow with id: " + workflow.getId());
// Call Galaxy to run the workflow
Call<PostWorkflowToGalaxyDtoResponse> call = service.postWorkflowToGalaxy(workflow.getId(), galaxyApiKey, requestBodyJson);
@@ -475,7 +475,7 @@ public class ExperimentApi {
if (response.code() == 200) { // Call succeeded
String responseBody = gson.toJson(response.body());
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Response: " + responseBody);
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Response: " + responseBody);
String historyId = (String) new JSONObject(responseBody).get("history_id");
experiment.setWorkflowHistoryId(historyId);
@@ -485,7 +485,7 @@ public class ExperimentApi {
} else { // Something unexpected happened
String msgErr = gson.toJson(response.errorBody());
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Error Response: " + msgErr);
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Error Response: " + msgErr);
// Values are read from streams.
JSONObject jObjectError = new JSONObject(msgErr);
@@ -497,7 +497,7 @@ public class ExperimentApi {
}
} catch (Exception e) {
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "An exception occurred: " + e.getMessage());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "An exception occurred: " + e.getMessage());
experiment.setHasError(true);
experiment.setHasServerError(true);
experiment.setResult(e.getMessage());
@@ -507,7 +507,7 @@ public class ExperimentApi {
// Start the process of fetching the status
updateWorkflowExperiment(experiment);
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Run workflow completed!");
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Run workflow completed!");
return new ResponseEntity(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
@@ -524,53 +524,53 @@ public class ExperimentApi {
User user = userInfo.getUser();
if (experiment == null) {
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "The experiment does not exist.");
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "The experiment does not exist.");
return;
}
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
" Experiment id : " + experiment.getUuid());
if (experiment.getWorkflowHistoryId() == null) {
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "History Id does not exist.");
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "History Id does not exist.");
return;
}
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Starting Thread...");
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Starting Thread...");
new Thread(() -> {
while (true) {
// ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogExperimentAction!
- ActionLogging.LogExperimentAction(experiment.getName(), "Thread is running...");
+ Logging.LogExperimentAction(experiment.getName(), "Thread is running...");
try {
sleep(2000);
} catch (InterruptedException e) {
- ActionLogging.LogExperimentAction(experiment.getName(), "Sleep was disrupted: " + e.getMessage());
+ Logging.LogExperimentAction(experiment.getName(), "Sleep was disrupted: " + e.getMessage());
}
- ActionLogging.LogExperimentAction(experiment.getName(), "Fetching status for experiment Id: " + experiment.getUuid());
+ Logging.LogExperimentAction(experiment.getName(), "Fetching status for experiment Id: " + experiment.getUuid());
String state = getWorkflowStatus(experiment.getWorkflowHistoryId(), experiment.getName());
- ActionLogging.LogExperimentAction(experiment.getName(), "State is: " + state);
+ Logging.LogExperimentAction(experiment.getName(), "State is: " + state);
switch (state) {
case "running":
// Do nothing, when the experiment is created the status is set to running
- ActionLogging.LogExperimentAction(experiment.getName(), "Workflow is still running.");
+ Logging.LogExperimentAction(experiment.getName(), "Workflow is still running.");
break;
case "completed":
// Get only the job result that is visible
List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experiment);
- ActionLogging.LogExperimentAction(experiment.getName(), "Results are: " + workflowJobsResults.toString());
+ Logging.LogExperimentAction(experiment.getName(), "Results are: " + workflowJobsResults.toString());
boolean resultFound = false;
for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
if (jobResult.getVisible()) {
- ActionLogging.LogExperimentAction(experiment.getName(), "Visible result are: " + jobResult.getId());
+ Logging.LogExperimentAction(experiment.getName(), "Visible result are: " + jobResult.getId());
String result = getWorkflowResultBody(experiment, jobResult.getId());
- ActionLogging.LogExperimentAction(experiment.getName(), "Result: " + result);
+ Logging.LogExperimentAction(experiment.getName(), "Result: " + result);
if (result == null) {
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -582,7 +582,7 @@ public class ExperimentApi {
}
if (!resultFound) { // If there is no visible result
- ActionLogging.LogExperimentAction(experiment.getName(), "No visible result");
+ Logging.LogExperimentAction(experiment.getName(), "No visible result");
experiment.setResult("[" + new ErrorResponse("The workflow has no visible result.").toString() + "]");
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -594,16 +594,16 @@ public class ExperimentApi {
case "error":
// Get the job result that failed
workflowJobsResults = getWorkflowResults(experiment);
- ActionLogging.LogExperimentAction(experiment.getName(), "Error results are: " + workflowJobsResults.toString());
+ Logging.LogExperimentAction(experiment.getName(), "Error results are: " + workflowJobsResults.toString());
boolean failedJobFound = false;
for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
if (jobResult.getState().equals("error")) {
- ActionLogging.LogExperimentAction(experiment.getName(), "Failed job is: " + jobResult.getId());
+ Logging.LogExperimentAction(experiment.getName(), "Failed job is: " + jobResult.getId());
String result = getWorkflowJobError(jobResult.getId(), experiment.getName());
- ActionLogging.LogExperimentAction(experiment.getName(), "Job result: " + result);
+ Logging.LogExperimentAction(experiment.getName(), "Job result: " + result);
if (result == null) {
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -615,7 +615,7 @@ public class ExperimentApi {
}
if (!failedJobFound) { // If there is no visible failed job
- ActionLogging.LogExperimentAction(experiment.getName(), "No failed result");
+ Logging.LogExperimentAction(experiment.getName(), "No failed result");
experiment.setResult("[" + new ErrorResponse("The workflow has no failed result.").toString() + "]");
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -633,7 +633,7 @@ public class ExperimentApi {
// If result exists return
if (experiment.getResult() != null) {
- ActionLogging.LogExperimentAction(experiment.getName(), "Result exists: " + experiment.getResult());
+ Logging.LogExperimentAction(experiment.getName(), "Result exists: " + experiment.getResult());
return;
}
}
@@ -650,7 +650,7 @@ public class ExperimentApi {
*/
public String getWorkflowStatus(String historyId, String experimentName) {
// ATTENTION: This function is used from a Thread. Only LogExperimentAction should be used, not LogUserAction!
- ActionLogging.LogExperimentAction(experimentName, " History Id : " + historyId);
+ Logging.LogExperimentAction(experimentName, " History Id : " + historyId);
// Create the request client
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
@@ -660,15 +660,15 @@ public class ExperimentApi {
try {
Response<Object> response = call.execute();
if (response.code() >= 400) {
- ActionLogging.LogExperimentAction(experimentName, " Response code: "
+ Logging.LogExperimentAction(experimentName, " Response code: "
+ response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return "internalError";
}
result = new Gson().toJson(response.body());
- ActionLogging.LogExperimentAction(experimentName, " Result: " + result);
+ Logging.LogExperimentAction(experimentName, " Result: " + result);
} catch (IOException e) {
- ActionLogging.LogExperimentAction(experimentName
+ Logging.LogExperimentAction(experimentName
, " An exception happened: " + e.getMessage());
return "internalError";
}
@@ -678,12 +678,12 @@ public class ExperimentApi {
JSONObject resultJson = new JSONObject(result);
state = resultJson.getString("state");
} catch (JSONException e) {
- ActionLogging.LogExperimentAction(experimentName
+ Logging.LogExperimentAction(experimentName
, " An exception happened: " + e.getMessage());
return "internalError";
}
- ActionLogging.LogExperimentAction(experimentName, " Completed!");
+ Logging.LogExperimentAction(experimentName, " Completed!");
switch (state) {
case "ok":
return "completed";
@@ -707,7 +707,7 @@ public class ExperimentApi {
String historyId = experiment.getWorkflowHistoryId();
String experimentName = experiment.getName();
- ActionLogging.LogExperimentAction(experimentName, " historyId : " + historyId);
+ Logging.LogExperimentAction(experimentName, " historyId : " + historyId);
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
Call<List<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(historyId, galaxyApiKey);
@@ -716,20 +716,20 @@ public class ExperimentApi {
try {
Response<List<GalaxyWorkflowResult>> response = call.execute();
if (response.code() >= 400) {
- ActionLogging.LogExperimentAction(experimentName, " Response code: "
+ Logging.LogExperimentAction(experimentName, " Response code: "
+ response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return null;
}
getGalaxyWorkflowResultList = response.body();
- ActionLogging.LogExperimentAction(experimentName, " Result: " + response.body());
+ Logging.LogExperimentAction(experimentName, " Result: " + response.body());
} catch (IOException e) {
- ActionLogging.LogExperimentAction(experimentName
+ Logging.LogExperimentAction(experimentName
, " An exception happened: " + e.getMessage());
return null;
}
- ActionLogging.LogExperimentAction(experimentName, " Completed!");
+ Logging.LogExperimentAction(experimentName, " Completed!");
return getGalaxyWorkflowResultList;
}
@@ -744,7 +744,7 @@ public class ExperimentApi {
String historyId = experiment.getWorkflowHistoryId();
String experimentName = experiment.getName();
- ActionLogging.LogExperimentAction(experimentName, " historyId : " + historyId);
+ Logging.LogExperimentAction(experimentName, " historyId : " + historyId);
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
Call<Object> call =
@@ -754,20 +754,20 @@ public class ExperimentApi {
try {
Response<Object> response = call.execute();
if (response.code() >= 400) {
- ActionLogging.LogExperimentAction(experimentName, " Response code: "
+ Logging.LogExperimentAction(experimentName, " Response code: "
+ response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return null;
}
resultJson = new Gson().toJson(response.body());
- ActionLogging.LogExperimentAction(experimentName, " Result: " + resultJson);
+ Logging.LogExperimentAction(experimentName, " Result: " + resultJson);
} catch (IOException e) {
- ActionLogging.LogExperimentAction(experimentName,
+ Logging.LogExperimentAction(experimentName,
" An exception happened: " + e.getMessage());
return null;
}
- ActionLogging.LogExperimentAction(experimentName, " Completed!");
+ Logging.LogExperimentAction(experimentName, " Completed!");
return resultJson;
}
@@ -777,7 +777,7 @@ public class ExperimentApi {
* @return the error that was produced or null if an error occurred
*/
public String getWorkflowJobError(String jobId, String experimentName) {
- ActionLogging.LogExperimentAction(experimentName, " jobId : " + jobId);
+ Logging.LogExperimentAction(experimentName, " jobId : " + jobId);
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId, galaxyApiKey);
@@ -786,7 +786,7 @@ public class ExperimentApi {
try {
Response<Object> response = callError.execute();
if (response.code() >= 400) {
- ActionLogging.LogExperimentAction(experimentName, "Response code: "
+ Logging.LogExperimentAction(experimentName, "Response code: "
+ response.code() + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return null;
}
@@ -796,19 +796,19 @@ public class ExperimentApi {
JsonElement jsonElement = new JsonParser().parse(jsonString);
JsonObject rootObject = jsonElement.getAsJsonObject();
fullError = rootObject.get("stderr").getAsString();
- ActionLogging.LogExperimentAction(experimentName, "Error: " + fullError);
+ Logging.LogExperimentAction(experimentName, "Error: " + fullError);
String[] arrOfStr = fullError.split("ValueError", 0);
String specError = arrOfStr[arrOfStr.length - 1];
returnError = specError.substring(1);
- ActionLogging.LogExperimentAction(experimentName, "Parsed Error: " + returnError);
+ Logging.LogExperimentAction(experimentName, "Parsed Error: " + returnError);
} catch (IOException e) {
- ActionLogging.LogExperimentAction(experimentName, "Exception: " + e.getMessage());
+ Logging.LogExperimentAction(experimentName, "Exception: " + e.getMessage());
return null;
}
- ActionLogging.LogExperimentAction(experimentName, "Completed successfully!");
+ Logging.LogExperimentAction(experimentName, "Completed successfully!");
return returnError;
}
diff --git a/src/main/java/eu/hbp/mip/controllers/FilesAPI.java b/src/main/java/eu/hbp/mip/controllers/FilesAPI.java
index 34f64984c96ab584f08e354abd1d519c10cfdbb2..69e7f3ba94702ee9b5465920d3234ca4dcac0248 100644
--- a/src/main/java/eu/hbp/mip/controllers/FilesAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/FilesAPI.java
@@ -5,8 +5,6 @@ import eu.hbp.mip.model.UserInfo;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
@@ -15,9 +13,7 @@ import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
-import eu.hbp.mip.utils.ActionLogging;
-
-import java.time.LocalDateTime;
+import eu.hbp.mip.utils.Logging;
/**
* Created by mirco on 08.05.17.
@@ -38,10 +34,10 @@ public class FilesAPI {
@ApiParam(value = "filename", required = true) @PathVariable("filename") String filename
) {
User user = userInfo.getUser();
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /protected/{filename:.+}", "Loading protected file with filename : " + filename);
+ Logging.LogUserAction(user.getUsername(), "(GET) /protected/{filename:.+}", "Loading protected file with filename : " + filename);
String filepath = "/protected/" + filename;
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /protected/{filename:.+}" + filepath, "Downloaded protected file");
+ Logging.LogUserAction(user.getUsername(), "(GET) /protected/{filename:.+}" + filepath, "Downloaded protected file");
HttpHeaders headers = new HttpHeaders();
headers.add("X-Accel-Redirect", filepath);
diff --git a/src/main/java/eu/hbp/mip/controllers/MiningApi.java b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
index a5fc94b78f729aaaa69186f333191c04561dbcff..6a198cc0d4571c58b1ff424e590bc418893a39f1 100644
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
@@ -4,18 +4,12 @@ import eu.hbp.mip.utils.HTTPUtil;
import com.google.gson.Gson;
-import eu.hbp.mip.model.Mining;
-import eu.hbp.mip.model.User;
import eu.hbp.mip.model.UserInfo;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
-import io.swagger.annotations.ApiParam;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
-import org.springframework.cache.annotation.Cacheable;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.RequestBody;
@@ -23,9 +17,7 @@ import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
-import eu.hbp.mip.utils.ActionLogging;
-
-import org.springframework.web.bind.annotation.*;
+import eu.hbp.mip.utils.Logging;
import java.util.*;
@@ -52,7 +44,7 @@ public class MiningApi {
@ApiOperation(value = "Create a histogram on Exareme", response = String.class)
@RequestMapping(value = "/histograms", method = RequestMethod.POST)
public ResponseEntity runExaremeHistograms(@RequestBody List<HashMap<String, String>> queryList) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Executing histogram...");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Executing histogram...");
String query = gson.toJson(queryList);
String url = queryExaremeUrl + "/" + "MULTIPLE_HISTOGRAMS";
@@ -61,10 +53,10 @@ public class MiningApi {
StringBuilder results = new StringBuilder();
int code = HTTPUtil.sendPost(url, query, results);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Executed histogram with result :" + results.toString());
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Executed histogram with result :" + results.toString());
return ResponseEntity.ok(gson.toJson(results.toString()));
} catch (IOException e) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Histogram algorithm was not found");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Histogram algorithm was not found");
return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
}
}
@@ -72,7 +64,7 @@ public class MiningApi {
@ApiOperation(value = "Create a descriptive statistic on Exareme", response = String.class)
@RequestMapping(value = "/descriptive_stats", method = RequestMethod.POST)
public ResponseEntity runExaremeDescriptiveStats(@RequestBody List<HashMap<String, String>> queryList) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Executing Exareme descriptive stats...");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Executing Exareme descriptive stats...");
String query = gson.toJson(queryList);
String url = queryExaremeUrl + "/" + "DESCRIPTIVE_STATS";
@@ -80,10 +72,10 @@ public class MiningApi {
try {
StringBuilder results = new StringBuilder();
int code = HTTPUtil.sendPost(url, query, results);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Executed descriptive stats with result : " + results.toString());
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Executed descriptive stats with result : " + results.toString());
return ResponseEntity.ok(gson.toJson(results.toString()));
} catch (IOException e) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Descriptive stats algorithm was not found");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Descriptive stats algorithm was not found");
return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
}
}
@@ -91,7 +83,7 @@ public class MiningApi {
@ApiOperation(value = "Create a descriptive statistic on Exareme", response = String.class)
@RequestMapping(value = "/descriptive_stats_v2", method = RequestMethod.POST)
public ResponseEntity runExaremeDescriptiveStatsV2(@RequestBody List<HashMap<String, String>> queryList) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Executing an Exareme descriptive stats v2");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Executing an Exareme descriptive stats v2");
String query = gson.toJson(queryList);
String url = queryExaremeUrl + "/" + "DESCRIPTIVE_STATS_v2";
@@ -100,10 +92,10 @@ public class MiningApi {
StringBuilder results = new StringBuilder();
int code = HTTPUtil.sendPost(url, query, results);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Successfully executed descriptive stats v2 with results : " + results.toString());
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Successfully executed descriptive stats v2 with results : " + results.toString());
return ResponseEntity.ok(gson.toJson(results.toString()));
} catch (IOException e) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Descriptive stats v2 algorithm was not found");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Descriptive stats v2 algorithm was not found");
return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
}
}
@@ -111,7 +103,7 @@ public class MiningApi {
@ApiOperation(value = "Check if a formula is valid", response = String.class)
@RequestMapping(value = "/checkFormula", method = RequestMethod.POST)
public ResponseEntity checkFormulaValidity(String formula) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/checkFormula", "Executing checkFormula ...");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/checkFormula", "Executing checkFormula ...");
return ResponseEntity.ok("");
}
diff --git a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
index 08f5199eada383a5a3553d14a4ead3a6954ef880..6f013ee336815bbb25514b37cdb764fe7710e8fd 100644
--- a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
@@ -11,13 +11,11 @@ import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.model.Variable;
import eu.hbp.mip.repositories.*;
import io.swagger.annotations.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
-import eu.hbp.mip.utils.ActionLogging;
+import eu.hbp.mip.utils.Logging;
import java.io.IOException;
import java.util.*;
@@ -54,7 +52,7 @@ public class ModelsApi {
@ApiParam(value = "Only ask own models") @RequestParam(value = "own", required = false) Boolean own,
@ApiParam(value = "Only ask published models") @RequestParam(value = "valid", required = false) Boolean valid
) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /models", "Loading models ...");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /models", "Loading models ...");
User user = userInfo.getUser();
@@ -81,7 +79,7 @@ public class ModelsApi {
modelsList.add(m);
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /models", "Successfully loaded " + modelsList.size() + " models.");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /models", "Successfully loaded " + modelsList.size() + " models.");
return ResponseEntity.ok(modelsList);
}
@@ -94,7 +92,7 @@ public class ModelsApi {
@RequestBody @ApiParam(value = "Model to create", required = true) Model model
) {
User user = userInfo.getUser();
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /models", "Creating a model");
+ Logging.LogUserAction(user.getUsername(), "(POST) /models", "Creating a model");
model.setTitle(model.getConfig().getTitle().get("text"));
model.setCreatedBy(user);
@@ -122,7 +120,7 @@ public class ModelsApi {
}
modelRepository.save(model);
- ActionLogging.LogUserAction(user.getUsername(), "(POST) /models", "Created model with id : " + model.getSlug() + ", model.config and model.query");
+ Logging.LogUserAction(user.getUsername(), "(POST) /models", "Created model with id : " + model.getSlug() + ", model.config and model.query");
return ResponseEntity.status(HttpStatus.CREATED).body(model);
}
@@ -181,17 +179,17 @@ public class ModelsApi {
User user = userInfo.getUser();
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Loading model with id : " + slug);
+ Logging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Loading model with id : " + slug);
Model model = modelRepository.findOne(slug);
if (model == null) {
//LOGGER.warn("Cannot find model : " + slug);
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Model was not found");
+ Logging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Model was not found");
return ResponseEntity.badRequest().body(null);
}
if (!model.getValid() && !model.getCreatedBy().getUsername().equals(user.getUsername())) {
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "You are not authorized to retrieve models. ");
+ Logging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "You are not authorized to retrieve models. ");
return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
@@ -199,7 +197,7 @@ public class ModelsApi {
Collection<String> yAxisVarsColl = new LinkedHashSet<>(yAxisVars);
model.getConfig().setyAxisVariables(new LinkedList<>(yAxisVarsColl));
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Loaded model with id : " + slug);
+ Logging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Loaded model with id : " + slug);
return ResponseEntity.ok(model);
}
@@ -212,7 +210,7 @@ public class ModelsApi {
@RequestBody @ApiParam(value = "Model to update", required = true) Model model
) {
User user = userInfo.getUser();
- ActionLogging.LogUserAction(user.getUsername(), "(PUT) /models/{slug}", "Updating model with id : " + slug);
+ Logging.LogUserAction(user.getUsername(), "(PUT) /models/{slug}", "Updating model with id : " + slug);
Model oldModel = modelRepository.findOne(slug);
if (!user.getUsername().equals(oldModel.getCreatedBy().getUsername())) {
@@ -253,7 +251,7 @@ public class ModelsApi {
datasetRepository.save(model.getDataset());
modelRepository.save(model);
- ActionLogging.LogUserAction(user.getUsername(), "(PUT) /models/{slug}", "Updated model and saved/updated model.config and model.query");
+ Logging.LogUserAction(user.getUsername(), "(PUT) /models/{slug}", "Updated model and saved/updated model.config and model.query");
return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
index 0469056a81622d8a83fb60ef5afe76449fe35e5d..77916981465827ae4e0806366663a16c7ad1e70b 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
@@ -11,10 +11,9 @@ import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.utils.ClaimUtils;
import eu.hbp.mip.utils.CustomResourceLoader;
import eu.hbp.mip.utils.InputStreamConverter;
-import eu.hbp.mip.utils.ActionLogging;
+import eu.hbp.mip.utils.Logging;
import io.swagger.annotations.Api;
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.Resource;
import org.springframework.http.ResponseEntity;
@@ -48,7 +47,7 @@ public class PathologiesApi {
@RequestMapping(name = "/pathologies", method = RequestMethod.GET)
public ResponseEntity<String> getPathologies(Authentication authentication) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Loading pathologies ...");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Loading pathologies ...");
// Load pathologies from file
Resource resource = resourceLoader.getResource("file:/opt/portal/api/pathologies.json");
@@ -57,17 +56,17 @@ public class PathologiesApi {
allPathologies = gson.fromJson(InputStreamConverter.convertInputStreamToString(resource.getInputStream()), new TypeToken<List<PathologyDTO>>() {
}.getType());
} catch (IOException e) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Unable to load pathologies");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Unable to load pathologies");
return ResponseEntity.badRequest().body(pathologiesCouldNotBeLoaded);
}
// If authentication is disabled return everything
if (!authenticationIsEnabled) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Successfully loaded " + allPathologies.size() + " pathologies");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Successfully loaded " + allPathologies.size() + " pathologies");
return ResponseEntity.ok().body(gson.toJson(allPathologies));
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Successfully loaded all authorized pathologies");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Successfully loaded all authorized pathologies");
return ResponseEntity.ok().body(ClaimUtils.getAuthorizedPathologies(
userInfo.getUser().getUsername(), authentication.getAuthorities(), allPathologies));
}
diff --git a/src/main/java/eu/hbp/mip/controllers/SecurityApi.java b/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
index a1eb3e8b77c27ed01933b8061400cb63b47f92db..4e412aea08da5612f47d60baafd4bac791f2fc6e 100644
--- a/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
@@ -8,14 +8,13 @@ import eu.hbp.mip.configuration.SecurityConfiguration;
import eu.hbp.mip.model.User;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.repositories.UserRepository;
-import eu.hbp.mip.utils.ActionLogging;
+import eu.hbp.mip.utils.Logging;
import io.swagger.annotations.ApiParam;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
-import org.springframework.security.access.AccessDeniedException;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.web.bind.annotation.*;
@@ -45,7 +44,7 @@ public class SecurityApi {
public Object user(Principal principal, HttpServletResponse response) {
ObjectMapper mapper = new ObjectMapper();
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /user", "Loading user : " + userInfo.getUser().getUsername());
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /user", "Loading user : " + userInfo.getUser().getUsername());
try {
String userJSON = mapper.writeValueAsString(userInfo.getUser());
Cookie cookie = new Cookie("user", URLEncoder.encode(userJSON, "UTF-8"));
@@ -77,7 +76,7 @@ public class SecurityApi {
userRepository.save(user);
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /user", "User has agreed on the NDA");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /user", "User has agreed on the NDA");
return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
@@ -86,7 +85,7 @@ public class SecurityApi {
@ConditionalOnExpression("${hbp.authentication.enabled:0}")
public void noLogin(HttpServletResponse httpServletResponse) throws IOException {
userInfo.setFakeAuth(true);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /user/login/hbp", "Unathorized login.");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /user/login/hbp", "Unathorized login.");
httpServletResponse.sendRedirect(securityConfiguration.getFrontendRedirectAfterLogin());
}
@@ -114,7 +113,7 @@ public class SecurityApi {
JsonObject object = new JsonObject();
object.addProperty("authorization", stringEncoded);
object.addProperty("context", galaxyContext);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /user/galaxy", "Successfully Loaded galaxy information.");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /user/galaxy", "Successfully Loaded galaxy information.");
return ResponseEntity.ok(gson.toJson(object));
}
diff --git a/src/main/java/eu/hbp/mip/controllers/StatsApi.java b/src/main/java/eu/hbp/mip/controllers/StatsApi.java
index 77ef125dbfe55f201d35c5a2f67fb703b1e67ac6..8bd109e535b7c29b5dac96b68b2ba59329ca6a59 100644
--- a/src/main/java/eu/hbp/mip/controllers/StatsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/StatsApi.java
@@ -8,7 +8,7 @@ import eu.hbp.mip.model.GeneralStats;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.repositories.ArticleRepository;
import eu.hbp.mip.repositories.UserRepository;
-import eu.hbp.mip.utils.ActionLogging;
+import eu.hbp.mip.utils.Logging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
@@ -36,14 +36,14 @@ public class StatsApi {
@ApiOperation(value = "Get general statistics", response = GeneralStats.class)
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<GeneralStats> getGeneralStatistics() {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /stats", "Loading general statistics");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /stats", "Loading general statistics");
GeneralStats stats = new GeneralStats();
stats.setUsers(userRepository.count());
stats.setArticles(articleRepository.count());
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /stats", "Loaded " + userRepository.count() + " user statistics and " + articleRepository.count() + " artcle statistics.");
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /stats", "Loaded " + userRepository.count() + " user statistics and " + articleRepository.count() + " artcle statistics.");
return ResponseEntity.ok(stats);
}
diff --git a/src/main/java/eu/hbp/mip/controllers/UsersApi.java b/src/main/java/eu/hbp/mip/controllers/UsersApi.java
index 4dc7de343b810ebf5965498b15de447ef276f982..b791a7858e216d8ce0f8cd36610763c5c123e66a 100644
--- a/src/main/java/eu/hbp/mip/controllers/UsersApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/UsersApi.java
@@ -7,7 +7,7 @@ package eu.hbp.mip.controllers;
import eu.hbp.mip.model.User;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.repositories.UserRepository;
-import eu.hbp.mip.utils.ActionLogging;
+import eu.hbp.mip.utils.Logging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
@@ -36,7 +36,7 @@ public class UsersApi {
public ResponseEntity<User> getAUser(
@ApiParam(value = "username", required = true) @PathVariable("username") String username
) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /users/{username}", "Loaded a user with username : " + userInfo.getUser().getUsername());
+ Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /users/{username}", "Loaded a user with username : " + userInfo.getUser().getUsername());
return ResponseEntity.ok(userRepository.findOne(username));
}
diff --git a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
index 2749a96d60f7a5a1a90ec355cc481b148de5cf67..e71d3f19083d03ae0067176b2fccfe4f06175915 100644
--- a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
+++ b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
@@ -27,7 +27,7 @@ public class ClaimUtils {
List<String> userClaims = Arrays.asList(authorities.toString().toLowerCase()
.replaceAll("[\\s+\\]\\[]", "").split(","));
- ActionLogging.LogUserAction(username, "(POST) /experiments/runAlgorithm", userClaims.toString());
+ Logging.LogUserAction(username, "(POST) /experiments/runAlgorithm", userClaims.toString());
// Don't check for dataset claims if "super" claim exists allowing everything
if (!userClaims.contains(ClaimUtils.allDatasetsAllowedClaim())) {
@@ -35,12 +35,12 @@ public class ClaimUtils {
for (String dataset : experimentDatasets.split(",")) {
String datasetRole = ClaimUtils.getDatasetClaim(dataset);
if (!userClaims.contains(datasetRole.toLowerCase())) {
- ActionLogging.LogUserAction(username, "(POST) /experiments/runAlgorithm",
+ Logging.LogUserAction(username, "(POST) /experiments/runAlgorithm",
"You are not allowed to use dataset: " + dataset);
return false;
}
}
- ActionLogging.LogUserAction(username, "(POST) /experiments/runAlgorithm",
+ Logging.LogUserAction(username, "(POST) /experiments/runAlgorithm",
"User is authorized to use the datasets: " + experimentDatasets);
}
return true;
@@ -49,13 +49,13 @@ public class ClaimUtils {
public static String getAuthorizedPathologies(String username, Collection<? extends GrantedAuthority> authorities,
List<PathologyDTO> allPathologies) {
// --- Providing only the allowed pathologies/datasets to the user ---
- ActionLogging.LogUserAction(username,
+ Logging.LogUserAction(username,
"(GET) /pathologies", "Filter out the unauthorised datasets.");
List<String> userClaims = Arrays.asList(authorities.toString().toLowerCase()
.replaceAll("[\\s+\\]\\[]", "").split(","));
- ActionLogging.LogUserAction(username,
+ Logging.LogUserAction(username,
"(GET) /pathologies", "User Claims: " + userClaims);
// If the "dataset_all" claim exists then return everything
@@ -68,14 +68,14 @@ public class ClaimUtils {
List<PathologyDTO.PathologyDatasetDTO> userPathologyDatasets = new ArrayList<PathologyDTO.PathologyDatasetDTO>();
for (PathologyDTO.PathologyDatasetDTO dataset : curPathology.getDatasets()) {
if (userClaims.contains(ClaimUtils.getDatasetClaim(dataset.getCode()))) {
- ActionLogging.LogUserAction(username, "(GET) /pathologies",
+ Logging.LogUserAction(username, "(GET) /pathologies",
"Added dataset: " + dataset.getCode());
userPathologyDatasets.add(dataset);
}
}
if (userPathologyDatasets.size() > 0) {
- ActionLogging.LogUserAction(username, "(GET) /pathologies",
+ Logging.LogUserAction(username, "(GET) /pathologies",
"Added pathology '" + curPathology.getLabel()
+ "' with datasets: '" + userPathologyDatasets + "'");
diff --git a/src/main/java/eu/hbp/mip/utils/ActionLogging.java b/src/main/java/eu/hbp/mip/utils/Logging.java
similarity index 92%
rename from src/main/java/eu/hbp/mip/utils/ActionLogging.java
rename to src/main/java/eu/hbp/mip/utils/Logging.java
index 7004fb89e7d829324381954a0230acf0eda97a6c..89218110811d089c5b54b79ed5ded4bf72492a3e 100644
--- a/src/main/java/eu/hbp/mip/utils/ActionLogging.java
+++ b/src/main/java/eu/hbp/mip/utils/Logging.java
@@ -3,11 +3,9 @@ package eu.hbp.mip.utils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import java.util.UUID;
+public class Logging {
-public class ActionLogging {
-
- private static final Logger LOGGER = LoggerFactory.getLogger(ActionLogging.class);
+ private static final Logger LOGGER = LoggerFactory.getLogger(Logging.class);
private static Integer maxEndpointLen = 5;
private static Integer maxInfoLen = 5;