From 1a0a5fce954f91304159f4e27e4d3dd5056b79bb Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Tue, 13 Oct 2020 08:34:15 -0700
Subject: [PATCH 1/4] Refactored all logs.
1) Disabled spring boot framework logs.
2) Added 2 logs at every endpoint, when entering and returning, with useful information.
3) Unified the logs output.
---
build.sh | 2 +-
.../configuration/SecurityConfiguration.java | 4 +-
.../eu/hbp/mip/controllers/AlgorithmsApi.java | 36 +--
.../eu/hbp/mip/controllers/ArticlesApi.java | 22 +-
.../eu/hbp/mip/controllers/ExperimentApi.java | 284 +++++++++---------
.../java/eu/hbp/mip/controllers/FilesAPI.java | 10 +-
.../eu/hbp/mip/controllers/MiningApi.java | 25 +-
.../eu/hbp/mip/controllers/ModelsApi.java | 26 +-
.../hbp/mip/controllers/PathologiesApi.java | 7 +-
.../eu/hbp/mip/controllers/SecurityApi.java | 10 +-
.../java/eu/hbp/mip/controllers/StatsApi.java | 5 +-
.../java/eu/hbp/mip/controllers/UsersApi.java | 4 +-
.../java/eu/hbp/mip/utils/ActionLogging.java | 38 +++
.../java/eu/hbp/mip/utils/ClaimUtils.java | 18 +-
.../eu/hbp/mip/utils/UserActionLogging.java | 22 --
src/main/resources/logback.xml | 3 +-
16 files changed, 281 insertions(+), 235 deletions(-)
create mode 100644 src/main/java/eu/hbp/mip/utils/ActionLogging.java
delete mode 100644 src/main/java/eu/hbp/mip/utils/UserActionLogging.java
diff --git a/build.sh b/build.sh
index ef4f10565..6a18d98ec 100755
--- a/build.sh
+++ b/build.sh
@@ -26,7 +26,7 @@ else
DOCKER="sudo docker"
fi
-IMAGE="hbpmip/portal-backend"
+IMAGE="kfilippopolitis/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 adc3df815..90d05b9d3 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
- UserActionLogging.LogAction("refresh token ", this.oauth2ClientContext.getAccessToken().getRefreshToken().getValue());
+ ActionLogging.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
- UserActionLogging.LogAction("logoutUri is ", logoutUri);
+ ActionLogging.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 27e9b8e5d..f495c5d8f 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.UserActionLogging;
+import eu.hbp.mip.utils.ActionLogging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
@@ -57,22 +57,24 @@ public class AlgorithmsApi {
@ApiOperation(value = "List all algorithms", response = String.class)
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List all algorithms", "");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms", "Executing...");
LinkedList<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms();
+ ActionLogging.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");
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
if (exaremeAlgorithms != null) {
algorithms.addAll(exaremeAlgorithms);
} else {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List all algorithms",
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms",
"Getting exareme algorithms failed and returned null");
}
if (galaxyAlgorithms != null) {
algorithms.addAll(galaxyAlgorithms);
} else {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List all algorithms",
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms",
"Getting galaxy workflows failed and returned null");
}
@@ -80,7 +82,7 @@ public class AlgorithmsApi {
try {
disabledAlgorithms = getDisabledAlgorithms();
} catch (IOException e) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List all algorithms",
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms",
disabledAlgorithmsCouldNotBeLoaded);
}
@@ -91,7 +93,8 @@ public class AlgorithmsApi {
allowedAlgorithms.add(algorithm);
}
}
-
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms",
+ "Successfully listed "+ allowedAlgorithms.size() +" algorithms");
return ResponseEntity.ok(allowedAlgorithms);
}
@@ -101,8 +104,6 @@ public class AlgorithmsApi {
* @return a list of AlgorithmDTOs or null if something fails
*/
public LinkedList<AlgorithmDTO> getExaremeAlgorithms() {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List exareme algorithms", "");
-
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
// Get exareme algorithms
try {
@@ -115,11 +116,11 @@ public class AlgorithmsApi {
}.getType()
);
} catch (IOException e) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List exareme algorithms", "An exception occurred: " + e.getMessage());
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms", "An exception occurred: " + e.getMessage());
return null;
}
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List exareme algorithms",
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms",
"Completed, returned " + algorithms.size() + " algorithms.");
return algorithms;
}
@@ -130,7 +131,6 @@ public class AlgorithmsApi {
* @return a list of AlgorithmDTOs or null if something fails
*/
public LinkedList<AlgorithmDTO> getGalaxyWorkflows() {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List Galaxy workflows", "");
List<Workflow> workflowList;
try {
@@ -140,7 +140,7 @@ public class AlgorithmsApi {
workflowList = new ArrayList<>(workflowsClient.getWorkflows());
} catch (Exception e) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List Galaxy workflows", "Error when calling list galaxy workflows: " + e.getMessage());
+ ActionLogging.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());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List Galaxy workflows", "Error Response: " + msgErr);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms", "Error Response: " + msgErr);
return null;
}
} catch (Exception e) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List Galaxy workflows", "An exception occurred: " + e.getMessage());
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms", "An exception occurred: " + e.getMessage());
return null;
}
}
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List Galaxy workflows", "Workflows fetched: " + workflows.size());
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms", "Workflows fetched: " + workflows.size());
// Convert the workflows to algorithms
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
for (WorkflowDTO workflow : workflows) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List Galaxy workflows", "Converting workflow: " + workflow);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms", "Converting workflow: " + workflow);
algorithms.add(workflow.convertToAlgorithmDTO());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List Galaxy workflows",
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms",
"Converted algorithm: " + algorithms.get(algorithms.size() - 1));
}
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List Galaxy workflows", "Completed!");
+ ActionLogging.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 2e5fb3dc5..467e558d2 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.UserActionLogging;
+import eu.hbp.mip.utils.ActionLogging;
import io.swagger.annotations.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -45,6 +45,7 @@ public class ArticlesApi {
) {
User user = userInfo.getUser();
Iterable<Article> articles;
+ ActionLogging.LogUserAction(user.getUsername() , "(GET) /articles", "Loading articles...");
if(own != null && own)
{
@@ -54,7 +55,7 @@ public class ArticlesApi {
{
articles = articleRepository.findByStatusOrCreatedBy("published", user);
}
-
+ int articlesSize = 0;
if(status != null)
{
for(Iterator<Article> i = articles.iterator(); i.hasNext();)
@@ -64,9 +65,10 @@ public class ArticlesApi {
{
i.remove();
}
+ articlesSize++;
}
}
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Get articles", "id : Get All articles");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /articles", "Successfully Loaded "+ articlesSize +" articles");
return ResponseEntity.ok(articles);
}
@@ -78,8 +80,8 @@ public class ArticlesApi {
public ResponseEntity<Void> addAnArticle(
@RequestBody @ApiParam(value = "Article to create", required = true) @Valid Article article
) {
-
User user = userInfo.getUser();
+ ActionLogging.LogUserAction(user.getUsername() , "(POST) /articles", "Creating article...");
article.setCreatedAt(new Date());
if ("published".equals(article.getStatus())) {
@@ -127,7 +129,7 @@ public class ArticlesApi {
}
articleRepository.save(article);
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Created article", "id : " + article.getSlug());
+ ActionLogging.LogUserAction(user.getUsername() , "(POST) /articles", "Successfully created article with id : " + article.getSlug());
return new ResponseEntity<>(HttpStatus.CREATED);
}
@@ -137,7 +139,7 @@ public class ArticlesApi {
public ResponseEntity<Article> getAnArticle(
@ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Getting an article", "id : " + slug);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /articles/{slug}", "Loading article with id : " + slug);
User user = userInfo.getUser();
Article article;
@@ -146,6 +148,7 @@ public class ArticlesApi {
if(article == null)
{
//LOGGER.warn("Cannot find article : " + slug);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /articles/{slug}", "Article not found");
return ResponseEntity.badRequest().body(null);
}
@@ -154,6 +157,8 @@ public class ArticlesApi {
return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
+ ActionLogging.LogUserAction(user.getUsername() , "(GET) /articles/{slug}", "Successfully Loaded article with id : " + slug);
+
return ResponseEntity.ok(article);
}
@@ -165,7 +170,7 @@ public class ArticlesApi {
@ApiParam(value = "slug", required = true) @PathVariable("slug") String slug,
@RequestBody @ApiParam(value = "Article to update", required = true) @Valid Article article
) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Update an article", "id : " + slug);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(PUT) /articles/{slug}", "Updating article with id : " + slug);
User user = userInfo.getUser();
@@ -197,7 +202,8 @@ public class ArticlesApi {
articleRepository.save(article);
-
+ ActionLogging.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 a800711b5..9d1635122 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.UserActionLogging;
+import eu.hbp.mip.utils.ActionLogging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
@@ -90,26 +90,30 @@ public class ExperimentApi {
Experiment experiment;
UUID experimentUuid;
+ User user = userInfo.getUser();
+
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Loading Experiment with uuid : "+uuid);
+
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Get Experiment", "Invalid Experiment UUID.");
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Invalid Experiment UUID.");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
experiment = experimentRepository.findOne(experimentUuid);
if (experiment == null) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Get Experiment", "Experiment Not found.");
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Experiment Not found.");
return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
}
- if (!experiment.isShared() && experiment.getCreatedBy().getUsername().compareTo(userInfo.getUser().getUsername()) != 0) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Get Experiment", "Accessing Experiment is unauthorized.");
+ if (!experiment.isShared() && !experiment.getCreatedBy().getUsername().equals(user.getUsername())) {
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Accessing Experiment is unauthorized.");
return new ResponseEntity<>("You don't have access to the experiment.", HttpStatus.UNAUTHORIZED);
}
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Get an experiment ", " uuid : " + uuid);
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Experiment was Loaded with uuid : " + uuid +".");
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
@@ -118,7 +122,12 @@ public class ExperimentApi {
@ApiOperation(value = "Create an experiment", response = Experiment.class)
@RequestMapping(value = "/runAlgorithm", method = RequestMethod.POST)
public ResponseEntity<String> runExperiment(Authentication authentication, @RequestBody ExperimentExecutionDTO experimentExecutionDTO) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run algorithm", "Running the algorithm...");
+ User user = userInfo.getUser();
+ // Get the type and name of algorithm
+ 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 + ".");
if (authenticationIsEnabled) {
// Getting the dataset from the experiment parameters
@@ -126,32 +135,28 @@ public class ExperimentApi {
for (ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO parameter : experimentExecutionDTO.getAlgorithms().get(0).getParameters()) {
if (parameter.getLabel().equals("dataset")) {
experimentDatasets = parameter.getValue();
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run algorithm", "Got the dataset parameter!");
break;
}
}
if (experimentDatasets == null || experimentDatasets.equals("")) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run algorithm",
+ ActionLogging.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.");
}
// --- Validating proper access rights on the datasets ---
- if (!ClaimUtils.userHasDatasetsAuthorization(userInfo.getUser().getUsername(), authentication.getAuthorities(), experimentDatasets)) {
+ if (!ClaimUtils.userHasDatasetsAuthorization(user.getUsername(), authentication.getAuthorities(), experimentDatasets)) {
return ResponseEntity.badRequest().body("You are not authorized to use these datasets.");
}
}
- // --- Run the experiment ---
-
- // Get the type of algorithm
- String algorithmType = experimentExecutionDTO.getAlgorithms().get(0).getType();
-
// Run with the appropriate engine
if (algorithmType.equals("workflow")) {
+ ActionLogging.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.");
return runExaremeAlgorithm(experimentExecutionDTO);
}
}
@@ -161,25 +166,28 @@ public class ExperimentApi {
public ResponseEntity<String> markExperimentAsViewed(
@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Mark an experiment as viewed", " uuid : " + uuid);
-
Experiment experiment;
UUID experimentUuid;
User user = userInfo.getUser();
+
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Marking as viewed the experiment with uuid : " + uuid + ".");
+
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Mark an experiment as viewed", "Invalid Experiment UUID" + uuid);
+ ActionLogging.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()))
- return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
+ if (!experiment.getCreatedBy().getUsername().equals(user.getUsername())){
+ ActionLogging.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);
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Experiment updated (marked as viewed)", " ");
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Experiment with uuid: " + uuid + " was marked as viewed.");
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
@@ -189,7 +197,7 @@ public class ExperimentApi {
public ResponseEntity<String> markExperimentAsShared(
@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Mark an experiment as shared", " uuid : " + uuid);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{uuid}/markAsShared", "Marking as shared the experiment with uuid : " + uuid + ".");
return doMarkExperimentAsShared(uuid, true);
}
@@ -198,7 +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) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Mark an experiment as unshared", " uuid : " + uuid);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{uuid}/markAs/Unshared", "Marking as unshared the experiment with uuid : " + uuid + ".");
return doMarkExperimentAsShared(uuid, false);
}
@@ -208,9 +216,12 @@ public class ExperimentApi {
public ResponseEntity<String> listExperiments(
@ApiParam(value = "maxResultCount") @RequestParam int maxResultCount) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List experiments", " maxResultCount : " + maxResultCount);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{maxResultCount}", "Listing experiments with a maximum amount of : " + maxResultCount + ".");
- return doListExperiments(false, null);
+ List<Experiment> expList = doListExperiments(false, null);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{maxResultCount}", "Successfully listed experiments.");
+
+ return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
}
@ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
@@ -218,25 +229,28 @@ public class ExperimentApi {
public ResponseEntity<String> listExperiments(@ApiParam(value = "slug") @RequestParam("slug") String modelSlug,
@ApiParam(value = "maxResultCount") @RequestParam("maxResultCount") int maxResultCount) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List experiments", " modelSlug : " + modelSlug);
+ ActionLogging.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))) {
+ if (maxResultCount <= 0 || modelSlug == null || "".equals(modelSlug)) {
return new ResponseEntity<>("You must provide at least a slug or a limit of result",
HttpStatus.BAD_REQUEST);
}
- return doListExperiments(false, modelSlug);
+ List<Experiment> expList = doListExperiments(false, null);
+ ActionLogging.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) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List my experiments", " mine : " + mine);
-
- return doListExperiments(true, null);
+ ActionLogging.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.");
+ return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
}
- private ResponseEntity<String> doListExperiments(boolean mine, String modelSlug) {
+ private List<Experiment> doListExperiments(boolean mine, String modelSlug) {
User user = userInfo.getUser();
Iterable<Experiment> myExperiments = experimentRepository.findByCreatedBy(user);
@@ -258,31 +272,32 @@ public class ExperimentApi {
}
}
}
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
+ return expList;
}
private ResponseEntity<String> doMarkExperimentAsShared(String uuid, boolean shared) {
Experiment experiment;
UUID experimentUuid;
User user = userInfo.getUser();
+
try {
experimentUuid = UUID.fromString(uuid);
} 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.");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
experiment = experimentRepository.findOne(experimentUuid);
if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
- return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
+ return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.UNAUTHORIZED);
experiment.setShared(shared);
experimentRepository.save(experiment);
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Experiment updated (marked as shared)", "");
+ ActionLogging.LogUserAction(user.getUsername(), "Experiment updated (marked as shared)", "");
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
@@ -301,31 +316,31 @@ public class ExperimentApi {
experiment.setName(experimentExecutionDTO.getName());
experimentRepository.save(experiment);
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Created an experiment", " id : " + experiment.getUuid());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Created an experiment", " algorithms : " + experiment.getAlgorithms());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Created an experiment", " model : " + experiment.getModel().getSlug());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Created an experiment", " name : " + experiment.getName());
+ 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());
return experiment;
}
private void saveExperiment(Experiment experiment) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Saved an experiment", " id : " + experiment.getUuid());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Saved an experiment", " algorithms : " + experiment.getAlgorithms());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Saved an experiment", " model : " + experiment.getModel().getSlug());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Saved an experiment", " name : " + experiment.getName());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Saved an experiment", " historyId : " + experiment.getWorkflowHistoryId());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Saved an experiment", " status : " + experiment.getWorkflowStatus());
+ 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());
experimentRepository.save(experiment);
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Experiment saved", "");
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Saved experiment");
}
private void finishExperiment(Experiment experiment) {
experiment.setFinished(new Date());
experimentRepository.save(experiment);
-
- UserActionLogging.LogAction("Experiment finished!", "");
}
/* -------------------------------------- EXAREME CALLS ---------------------------------------------------------*/
@@ -337,9 +352,11 @@ public class ExperimentApi {
* @return the response to be returned
*/
public ResponseEntity<String> runExaremeAlgorithm(ExperimentExecutionDTO experimentExecutionDTO) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run exareme algorithm", "Running the algorithm...");
+ ActionLogging.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());
// Run the 1st algorithm from the list
String algorithmName = experimentExecutionDTO.getAlgorithms().get(0).getName();
@@ -350,46 +367,38 @@ public class ExperimentApi {
String body = gson.toJson(algorithmParameters);
String url = queryExaremeUrl + "/" + algorithmName;
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run exareme algorithm", "url: " + url + ", body: " + body);
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "url: " + url + ", body: " + body);
ResponseEntity<String> response = new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run exareme algorithm",
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
"Completed, returning: " + experiment.toString());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run exareme algorithm",
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
"Starting exareme execution thread");
new Thread(() -> {
- // ATTENTION: Inside the Thread only LogAction should be used, not LogAction!
- UserActionLogging.LogAction("Run exareme algorithm",
- "Thread started!");
+ // 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!");
try {
- UserActionLogging.LogAction("Run exareme algorithm",
- "Thread started!");
StringBuilder results = new StringBuilder();
int code = HTTPUtil.sendPost(url, body, results);
- UserActionLogging.LogAction("Run exareme algorithm",
- "Algorithm finished with code: " + code);
+ ActionLogging.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) {
- UserActionLogging.LogAction("Run exareme algorithm",
- "There was an exception: " + e.getMessage());
+ ActionLogging.LogExperimentAction(experiment.getName(),"There was an exception: " + e.getMessage());
experiment.setHasError(true);
experiment.setHasServerError(true);
experiment.setResult(e.getMessage());
}
- UserActionLogging.LogAction("Run exareme algorithm",
- "Finished the experiment: " + experiment.toString());
- finishExperiment(experiment);
- UserActionLogging.LogAction("Run exareme algorithm",
- "Finished!");
+ finishExperiment(experiment);
+ ActionLogging.LogExperimentAction(experiment.getName(),"Finished the experiment: " + experiment.toString());
}).start();
return response;
@@ -405,9 +414,12 @@ public class ExperimentApi {
* @return the response to be returned
*/
public ResponseEntity<String> runGalaxyWorkflow(ExperimentExecutionDTO experimentExecutionDTO) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run workflow", "Running a workflow...");
+ ActionLogging.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());
+ User user = userInfo.getUser();
+
// Run the 1st algorithm from the list
String workflowId = experimentExecutionDTO.getAlgorithms().get(0).getName();
@@ -435,7 +447,7 @@ public class ExperimentApi {
}
}
if (workflow == null) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run workflow",
+ ActionLogging.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());
@@ -454,7 +466,7 @@ public class ExperimentApi {
// Create the request client
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run workflow", "Running Galaxy workflow with id: " + workflow.getId());
+ ActionLogging.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);
@@ -463,7 +475,7 @@ public class ExperimentApi {
if (response.code() == 200) { // Call succeeded
String responseBody = gson.toJson(response.body());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run workflow", "Response: " + responseBody);
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Response: " + responseBody);
String historyId = (String) new JSONObject(responseBody).get("history_id");
experiment.setWorkflowHistoryId(historyId);
@@ -473,7 +485,7 @@ public class ExperimentApi {
} else { // Something unexpected happened
String msgErr = gson.toJson(response.errorBody());
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run workflow", "Error Response: " + msgErr);
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Error Response: " + msgErr);
// Values are read from streams.
JSONObject jObjectError = new JSONObject(msgErr);
@@ -485,7 +497,7 @@ public class ExperimentApi {
}
} catch (Exception e) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run workflow", "An exception occurred: " + e.getMessage());
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "An exception occurred: " + e.getMessage());
experiment.setHasError(true);
experiment.setHasServerError(true);
experiment.setResult(e.getMessage());
@@ -495,7 +507,7 @@ public class ExperimentApi {
// Start the process of fetching the status
updateWorkflowExperiment(experiment);
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run workflow", "Run workflow completed!");
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Run workflow completed!");
return new ResponseEntity(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
@@ -509,61 +521,56 @@ public class ExperimentApi {
* @return nothing, just updates the experiment
*/
public void updateWorkflowExperiment(Experiment experiment) {
+ User user = userInfo.getUser();
if (experiment == null) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Update workflow experiment", "The experiment does not exist.");
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "The experiment does not exist.");
return;
}
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Update workflow experiment",
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
" Experiment id : " + experiment.getUuid());
-
if (experiment.getWorkflowHistoryId() == null) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Update workflow experiment", "History Id does not exist.");
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "History Id does not exist.");
return;
}
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Update workflow experiment", "Starting Thread...");
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Starting Thread...");
new Thread(() -> {
while (true) {
- // ATTENTION: Inside the Thread only LogAction should be used, not LogAction!
- UserActionLogging.LogAction("Update workflow experiment", "Thread is running...");
+ // ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogExperimentAction!
+ ActionLogging.LogExperimentAction(experiment.getName(), "Thread is running...");
try {
sleep(2000);
} catch (InterruptedException e) {
- UserActionLogging.LogAction("Update workflow experiment",
- "Sleep was disrupted: " + e.getMessage());
+ ActionLogging.LogExperimentAction(experiment.getName(),"Sleep was disrupted: " + e.getMessage());
}
- UserActionLogging.LogAction("Update workflow experiment",
- "Fetching status for experiment Id: " + experiment.getUuid());
+ ActionLogging.LogExperimentAction(experiment.getName(),"Fetching status for experiment Id: " + experiment.getUuid());
- String state = getWorkflowStatus(experiment.getWorkflowHistoryId());
- UserActionLogging.LogAction("Update workflow experiment", "State is: " + state);
+ String state = getWorkflowStatus(experiment.getWorkflowHistoryId(), experiment.getName());
+ ActionLogging.LogExperimentAction(experiment.getName(), "State is: " + state);
switch (state) {
case "running":
// Do nothing, when the experiment is created the status is set to running
- UserActionLogging.LogAction("Update workflow experiment",
- "Workflow is still running.");
+ ActionLogging.LogExperimentAction(experiment.getName(),"Workflow is still running.");
break;
case "completed":
// Get only the job result that is visible
- List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experiment.getWorkflowHistoryId());
- UserActionLogging.LogAction("Update workflow experiment",
- "Results are: " + workflowJobsResults.toString());
+ List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experiment);
+ ActionLogging.LogExperimentAction(experiment.getName(),"Results are: " + workflowJobsResults.toString());
boolean resultFound = false;
for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
if (jobResult.getVisible()) {
- UserActionLogging.LogAction("Update workflow experiment",
- "Visible result are: " + jobResult.getId());
+ ActionLogging.LogExperimentAction(experiment.getName(),"Visible result are: " + jobResult.getId());
- String result = getWorkflowResultBody(experiment.getWorkflowHistoryId(), jobResult.getId());
+ String result = getWorkflowResultBody(experiment, jobResult.getId());
- UserActionLogging.LogAction("Update workflow experiment", "Result: " + result);
+ ActionLogging.LogExperimentAction(experiment.getName(),"Result: " + result);
if (result == null) {
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -575,7 +582,7 @@ public class ExperimentApi {
}
if (!resultFound) { // If there is no visible result
- UserActionLogging.LogAction("Update workflow experiment", "No visible result");
+ ActionLogging.LogExperimentAction(experiment.getName(),"No visible result");
experiment.setResult("[" + new ErrorResponse("The workflow has no visible result.").toString() + "]");
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -586,19 +593,17 @@ public class ExperimentApi {
case "error":
// Get the job result that failed
- workflowJobsResults = getWorkflowResults(experiment.getWorkflowHistoryId());
- UserActionLogging.LogAction("Update workflow experiment",
- "Error results are: " + workflowJobsResults.toString());
+ workflowJobsResults = getWorkflowResults(experiment);
+ ActionLogging.LogExperimentAction(experiment.getName(),"Error results are: " + workflowJobsResults.toString());
boolean failedJobFound = false;
for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
if (jobResult.getState().equals("error")) {
- UserActionLogging.LogAction("Update workflow experiment",
- "Failed job is: " + jobResult.getId());
+ ActionLogging.LogExperimentAction(experiment.getName(),"Failed job is: " + jobResult.getId());
- String result = getWorkflowJobError(jobResult.getId());
+ String result = getWorkflowJobError(jobResult.getId(), experiment.getName());
- UserActionLogging.LogAction("Update workflow experiment", "Job result: " + result);
+ ActionLogging.LogExperimentAction(experiment.getName(),"Job result: " + result);
if (result == null) {
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -610,7 +615,7 @@ public class ExperimentApi {
}
if (!failedJobFound) { // If there is no visible failed job
- UserActionLogging.LogAction("Update workflow experiment", "No failed result");
+ ActionLogging.LogExperimentAction(experiment.getName(),"No failed result");
experiment.setResult("[" + new ErrorResponse("The workflow has no failed result.").toString() + "]");
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -628,8 +633,7 @@ public class ExperimentApi {
// If result exists return
if (experiment.getResult() != null) {
- UserActionLogging.LogAction("Update workflow experiment",
- "Result exists: " + experiment.getResult());
+ ActionLogging.LogExperimentAction(experiment.getName(),"Result exists: " + experiment.getResult());
return;
}
}
@@ -644,9 +648,9 @@ public class ExperimentApi {
* "error" -> When the workflow produced an error
* "completed" -> When the workflow completed successfully
*/
- public String getWorkflowStatus(String historyId) {
- // ATTENTION: This function is used from a Thread. Only LogAction should be used, not LogAction!
- UserActionLogging.LogAction("Get workflow status", " History Id : " + historyId);
+ 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);
// Create the request client
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
@@ -656,15 +660,15 @@ public class ExperimentApi {
try {
Response<Object> response = call.execute();
if (response.code() >= 400) {
- UserActionLogging.LogAction("Get workflow status", " Response code: "
+ ActionLogging.LogExperimentAction(experimentName, " Response code: "
+ response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return "internalError";
}
result = new Gson().toJson(response.body());
- UserActionLogging.LogAction("Get workflow status", " Result: " + result);
+ ActionLogging.LogExperimentAction(experimentName, " Result: " + result);
} catch (IOException e) {
- UserActionLogging.LogAction("Get workflow status"
+ ActionLogging.LogExperimentAction(experimentName
, " An exception happened: " + e.getMessage());
return "internalError";
}
@@ -674,12 +678,12 @@ public class ExperimentApi {
JSONObject resultJson = new JSONObject(result);
state = resultJson.getString("state");
} catch (JSONException e) {
- UserActionLogging.LogAction("Get workflow status"
+ ActionLogging.LogExperimentAction(experimentName
, " An exception happened: " + e.getMessage());
return "internalError";
}
- UserActionLogging.LogAction("Get workflow status", " Completed!");
+ ActionLogging.LogExperimentAction(experimentName, " Completed!");
switch (state) {
case "ok":
return "completed";
@@ -696,11 +700,14 @@ public class ExperimentApi {
}
/**
- * @param historyId The historyId of the workflow
+ * @param experiment The experiment of the workflow
* @return a List<GalaxyWorkflowResult> or null when an error occurred
*/
- public List<GalaxyWorkflowResult> getWorkflowResults(String historyId) {
- UserActionLogging.LogAction("Get workflow results", " historyId : " + historyId);
+ public List<GalaxyWorkflowResult> getWorkflowResults(Experiment experiment) {
+
+ String historyId = experiment.getWorkflowHistoryId();
+ String experimentName = experiment.getName();
+ ActionLogging.LogExperimentAction(experimentName, " historyId : " + historyId);
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
Call<List<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(historyId, galaxyApiKey);
@@ -709,31 +716,35 @@ public class ExperimentApi {
try {
Response<List<GalaxyWorkflowResult>> response = call.execute();
if (response.code() >= 400) {
- UserActionLogging.LogAction("Get workflow results", " Response code: "
+ ActionLogging.LogExperimentAction(experimentName, " Response code: "
+ response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return null;
}
getGalaxyWorkflowResultList = response.body();
- UserActionLogging.LogAction("Get workflow results", " Result: " + response.body());
+ ActionLogging.LogExperimentAction(experimentName, " Result: " + response.body());
} catch (IOException e) {
- UserActionLogging.LogAction("Get workflow results"
+ ActionLogging.LogExperimentAction(experimentName
, " An exception happened: " + e.getMessage());
return null;
}
- UserActionLogging.LogAction("Get workflow results", " Completed!");
+ ActionLogging.LogExperimentAction(experimentName, " Completed!");
return getGalaxyWorkflowResultList;
}
/**
- * @param historyId the historyId of the workflow
+ * @param experiment The experiment of the workflow
* @param contentId the id of the job result that we want
* @return the result of the specific workflow job, null if there was an error
*/
- public String getWorkflowResultBody(String historyId, String contentId) {
- UserActionLogging.LogAction("Get workflow results Body", " historyId : " + historyId);
+ public String getWorkflowResultBody(Experiment experiment, String contentId) {
+
+ String historyId = experiment.getWorkflowHistoryId();
+ String experimentName = experiment.getName();
+
+ ActionLogging.LogExperimentAction(experimentName, " historyId : " + historyId);
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
Call<Object> call =
@@ -743,20 +754,20 @@ public class ExperimentApi {
try {
Response<Object> response = call.execute();
if (response.code() >= 400) {
- UserActionLogging.LogAction("Get workflow results Body", " Response code: "
+ ActionLogging.LogExperimentAction(experimentName, " Response code: "
+ response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return null;
}
resultJson = new Gson().toJson(response.body());
- UserActionLogging.LogAction("Get workflow results Body", " Result: " + resultJson);
+ ActionLogging.LogExperimentAction(experimentName, " Result: " + resultJson);
} catch (IOException e) {
- UserActionLogging.LogAction("Get workflow results Body",
+ ActionLogging.LogExperimentAction(experimentName,
" An exception happened: " + e.getMessage());
return null;
}
- UserActionLogging.LogAction("Get workflow results Body", " Completed!");
+ ActionLogging.LogExperimentAction(experimentName, " Completed!");
return resultJson;
}
@@ -765,9 +776,8 @@ public class ExperimentApi {
* @param jobId the id of the workflow job that failed
* @return the error that was produced or null if an error occurred
*/
- public String getWorkflowJobError(String jobId) {
- UserActionLogging.LogAction("Get workflow job error", " jobId : " + jobId);
-
+ public String getWorkflowJobError(String jobId, String experimentName) {
+ ActionLogging.LogExperimentAction(experimentName, " jobId : " + jobId);
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId, galaxyApiKey);
@@ -776,7 +786,7 @@ public class ExperimentApi {
try {
Response<Object> response = callError.execute();
if (response.code() >= 400) {
- UserActionLogging.LogAction("Get workflow job error", "Response code: "
+ ActionLogging.LogExperimentAction(experimentName, "Response code: "
+ response.code() + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return null;
}
@@ -786,19 +796,19 @@ public class ExperimentApi {
JsonElement jsonElement = new JsonParser().parse(jsonString);
JsonObject rootObject = jsonElement.getAsJsonObject();
fullError = rootObject.get("stderr").getAsString();
- UserActionLogging.LogAction("Get workflow job error", "Error: " + fullError);
+ ActionLogging.LogExperimentAction(experimentName, "Error: " + fullError);
String[] arrOfStr = fullError.split("ValueError", 0);
String specError = arrOfStr[arrOfStr.length - 1];
returnError = specError.substring(1);
- UserActionLogging.LogAction("Get workflow job error", "Parsed Error: " + returnError);
+ ActionLogging.LogExperimentAction(experimentName, "Parsed Error: " + returnError);
} catch (IOException e) {
- UserActionLogging.LogAction("Get workflow job error", "Exception: " + e.getMessage());
+ ActionLogging.LogExperimentAction(experimentName, "Exception: " + e.getMessage());
return null;
}
- UserActionLogging.LogAction("Get workflow job error", "Completed successfully!");
+ ActionLogging.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 3b4ec96ab..74d8c8093 100644
--- a/src/main/java/eu/hbp/mip/controllers/FilesAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/FilesAPI.java
@@ -1,5 +1,6 @@
package eu.hbp.mip.controllers;
+import eu.hbp.mip.model.User;
import eu.hbp.mip.model.UserInfo;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
@@ -14,7 +15,7 @@ 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.UserActionLogging;
+import eu.hbp.mip.utils.ActionLogging;
import java.time.LocalDateTime;
@@ -36,12 +37,11 @@ public class FilesAPI {
public ResponseEntity<Void> getProtectedFile(
@ApiParam(value = "filename", required = true) @PathVariable("filename") String filename
) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Get protected file", " filename : " + filename);
+ User user = userInfo.getUser();
+ ActionLogging.LogUserAction(user.getUsername() , "(GET) /protected/{filename:.+}", "Loading protected file with filename : " + filename);
String filepath = "/protected/" + filename;
- String user = userInfo.getUser().getUsername();
- String time = LocalDateTime.now().toString();
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Downloaded " + filepath, "");
+ ActionLogging.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 75369d0b4..e05b4ca94 100644
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
@@ -22,7 +22,7 @@ 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.UserActionLogging;
+import eu.hbp.mip.utils.ActionLogging;
import org.springframework.web.bind.annotation.*;
@@ -51,7 +51,7 @@ 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) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run an histogram", "");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(POST) /mining/histogram", "Executing histogram...");
String query = gson.toJson(queryList);
String url = queryExaremeUrl + "/" + "MULTIPLE_HISTOGRAMS";
@@ -60,16 +60,18 @@ 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());
return ResponseEntity.ok(gson.toJson(results.toString()));
- } catch (IOException e) {
- return new ResponseEntity<>("Not found", HttpStatus.BAD_REQUEST);
+ } catch (IOException e) {
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(POST) /mining/histogram", "Histogram algorithm was not found");
+ return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
}
}
@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) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run descriptive stats", "");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Executing Exareme descriptive stats...");
String query = gson.toJson(queryList);
String url = queryExaremeUrl + "/" + "DESCRIPTIVE_STATS";
@@ -77,17 +79,18 @@ 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());
return ResponseEntity.ok(gson.toJson(results.toString()));
} catch (IOException e) {
- return new ResponseEntity<>("Not found", HttpStatus.BAD_REQUEST);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Descriptive stats algorithm was not found");
+ return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
}
}
@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) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Run descriptive stats v2", "");
+ ActionLogging.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";
@@ -96,16 +99,18 @@ 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());
return ResponseEntity.ok(gson.toJson(results.toString()));
} catch (IOException e) {
- return new ResponseEntity<>("Not found", HttpStatus.BAD_REQUEST);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Descriptive stats v2 algorithm was not found");
+ return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
}
}
@ApiOperation(value = "Check if a formula is valid", response = String.class)
@RequestMapping(value = "/checkFormula", method = RequestMethod.POST)
public ResponseEntity checkFormulaValidity(String formula) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Check Formula Validity", "");
+ ActionLogging.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 633c01783..de5c7f5d4 100644
--- a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
@@ -17,7 +17,7 @@ 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.UserActionLogging;
+import eu.hbp.mip.utils.ActionLogging;
import java.io.IOException;
import java.util.*;
@@ -48,13 +48,13 @@ public class ModelsApi {
@Autowired
private VariableRepository variableRepository;
- @ApiOperation(value = "Get models", response = Model.class, responseContainer = "List")
+ @ApiOperation(value = "get models", response = Model.class, responseContainer = "List")
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<List> getModels(
@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
) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Get models","");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /models","Loading models ...");
User user = userInfo.getUser();
@@ -86,6 +86,8 @@ public class ModelsApi {
m.setDataset(datasetRepository.findOne(m.getDataset().getCode()));
modelsList.add(m);
}
+
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /models","Successfully loaded " + modelsList.size() + " models.");
return ResponseEntity.ok(modelsList);
}
@@ -97,10 +99,8 @@ public class ModelsApi {
public ResponseEntity<Model> addAModel(
@RequestBody @ApiParam(value = "Model to create", required = true) Model model
) {
-
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Create a model","");
-
User user = userInfo.getUser();
+ ActionLogging.LogUserAction(user.getUsername() , "(POST) /models","Creating a model");
model.setTitle(model.getConfig().getTitle().get("text"));
model.setCreatedBy(user);
@@ -129,7 +129,7 @@ public class ModelsApi {
}
modelRepository.save(model);
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Model saved (also saved model.config and model.query)"," id : " + model.getSlug());
+ ActionLogging.LogUserAction(user.getUsername() , "(POST) /models","Created model with id : " + model.getSlug()+ ", model.config and model.query");
return ResponseEntity.status(HttpStatus.CREATED).body(model);
}
@@ -192,20 +192,22 @@ public class ModelsApi {
public ResponseEntity<Model> getAModel(
@ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Get a model", " id : " + slug);
User user = userInfo.getUser();
- Model model = modelRepository.findOne(slug);
+ ActionLogging.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");
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. ");
return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
@@ -213,6 +215,7 @@ 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);
return ResponseEntity.ok(model);
}
@@ -224,9 +227,8 @@ public class ModelsApi {
@ApiParam(value = "slug", required = true) @PathVariable("slug") String slug,
@RequestBody @ApiParam(value = "Model to update", required = true) Model model
) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Update a model", " id : "+ slug);
-
User user = userInfo.getUser();
+ ActionLogging.LogUserAction(user.getUsername() , "(PUT) /models/{slug}", "Updating model with id : "+ slug);
Model oldModel = modelRepository.findOne(slug);
if(!user.getUsername().equals(oldModel.getCreatedBy().getUsername()))
@@ -269,7 +271,7 @@ public class ModelsApi {
datasetRepository.save(model.getDataset());
modelRepository.save(model);
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Model updated (also saved/updated model.config and model.query)", " id : "+ slug);
+ ActionLogging.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 7b6b3e650..41518bd11 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
@@ -11,7 +11,7 @@ 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.UserActionLogging;
+import eu.hbp.mip.utils.ActionLogging;
import io.swagger.annotations.Api;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
@@ -48,7 +48,7 @@ public class PathologiesApi {
@RequestMapping(name = "/pathologies", method = RequestMethod.GET)
public ResponseEntity<String> getPathologies(Authentication authentication) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Load pathologies", "Running ...");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /pathologies", "Loading pathologies ...");
// Load pathologies from file
Resource resource = resourceLoader.getResource("file:/opt/portal/api/pathologies.json");
@@ -57,14 +57,17 @@ 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");
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");
return ResponseEntity.ok().body(gson.toJson(allPathologies));
}
+ ActionLogging.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 397f1ae6c..852e7e12c 100644
--- a/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
@@ -8,7 +8,7 @@ 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.UserActionLogging;
+import eu.hbp.mip.utils.ActionLogging;
import io.swagger.annotations.ApiParam;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
@@ -45,7 +45,7 @@ public class SecurityApi {
public Object user(Principal principal, HttpServletResponse response) {
ObjectMapper mapper = new ObjectMapper();
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "get user from /user", "");
+ ActionLogging.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 +77,7 @@ public class SecurityApi {
userRepository.save(user);
}
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "user agreeNDA", "");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(POST) /user", "User has agreed on the NDA");
return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
@@ -86,6 +86,8 @@ 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.");
+
httpServletResponse.sendRedirect(securityConfiguration.getFrontendRedirectAfterLogin());
}
@@ -112,7 +114,7 @@ public class SecurityApi {
JsonObject object = new JsonObject();
object.addProperty("authorization", stringEncoded);
object.addProperty("context", galaxyContext);
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "get galaxy information", "");
+ ActionLogging.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 56d256793..7fb491ee8 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.UserActionLogging;
+import eu.hbp.mip.utils.ActionLogging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
@@ -36,13 +36,14 @@ public class StatsApi {
@ApiOperation(value = "Get general statistics", response = GeneralStats.class)
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<GeneralStats> getGeneralStatistics() {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Get statistics (count on users, articles and variables)", "");
+ ActionLogging.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.");
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 0620c34e4..9485f99fe 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.UserActionLogging;
+import eu.hbp.mip.utils.ActionLogging;
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
) {
- UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "Get a user", "");
+ ActionLogging.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/ActionLogging.java b/src/main/java/eu/hbp/mip/utils/ActionLogging.java
new file mode 100644
index 000000000..8e9757276
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/utils/ActionLogging.java
@@ -0,0 +1,38 @@
+package eu.hbp.mip.utils;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.UUID;
+
+public class ActionLogging {
+
+ private static final Logger LOGGER = LoggerFactory.getLogger(ActionLogging.class);
+ private static Integer maxEndpointLen = 5;
+ private static Integer maxInfoLen = 5;
+
+ public static void LogUserAction(String userName, String endpoint, String actionInfo) {
+ maxEndpointLen = (maxEndpointLen < userName.length() ? userName.length() : maxEndpointLen);
+ maxInfoLen = (maxInfoLen < endpoint.length() ? endpoint.length() : maxInfoLen);
+ String endpointSpacing = String.format("%" + (maxEndpointLen - userName.length() + 2) + "s", "");
+ String infoSpacing = String.format("%" + (maxInfoLen - endpoint.length() + 2) + "s", "");
+ LOGGER.info(" User -> " + userName
+ + endpointSpacing
+ + ", Endpoint -> " + endpoint
+ + infoSpacing
+ + ", Info -> " + actionInfo);
+ }
+
+ // Used from Threads because threads can't get userName.
+ public static void LogExperimentAction(String experimentName, String actionInfo) {
+ LOGGER.info(" Experiment -> "+ experimentName
+ + " , Info -> " + actionInfo);
+ }
+
+ // Used when a user is not authorised yet
+ public static void LogAction(String actionName, String actionIdInfo) {
+ LOGGER.info(" Action -> " + actionName
+ + " , Info -> " + actionIdInfo);
+ }
+
+}
diff --git a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
index eeceb5d21..bad70279e 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(","));
- UserActionLogging.LogUserAction(username, "User Claims", userClaims.toString());
+ ActionLogging.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())) {
- UserActionLogging.LogUserAction(username, "Run algorithm",
+ ActionLogging.LogUserAction(username, "(POST) /experiments/runAlgorithm",
"You are not allowed to use dataset: " + dataset);
return false;
}
}
- UserActionLogging.LogUserAction(username, "Run algorithm",
+ ActionLogging.LogUserAction(username, "(POST) /experiments/runAlgorithm",
"User is authorized to use the datasets: " + experimentDatasets);
}
return true;
@@ -49,14 +49,14 @@ 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 ---
- UserActionLogging.LogUserAction(username,
- "Load pathologies", "Filter out the unauthorised datasets.");
+ ActionLogging.LogUserAction(username,
+ "(GET) /pathologies", "Filter out the unauthorised datasets.");
List<String> userClaims = Arrays.asList(authorities.toString().toLowerCase()
.replaceAll("[\\s+\\]\\[]", "").split(","));
- UserActionLogging.LogUserAction(username,
- "Load pathologies", "User Claims: " + userClaims);
+ ActionLogging.LogUserAction(username,
+ "(GET) /pathologies", "User Claims: " + userClaims);
// If the "dataset_all" claim exists then return everything
if (userClaims.contains(ClaimUtils.allDatasetsAllowedClaim())) {
@@ -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()))) {
- UserActionLogging.LogUserAction(username, "Load pathologies",
+ ActionLogging.LogUserAction(username , "(GET) /pathologies",
"Added dataset: " + dataset.getCode());
userPathologyDatasets.add(dataset);
}
}
if (userPathologyDatasets.size() > 0) {
- UserActionLogging.LogUserAction(username, "Load pathologies",
+ ActionLogging.LogUserAction(username , "(GET) /pathologies",
"Added pathology '" + curPathology.getLabel()
+ "' with datasets: '" + userPathologyDatasets + "'");
diff --git a/src/main/java/eu/hbp/mip/utils/UserActionLogging.java b/src/main/java/eu/hbp/mip/utils/UserActionLogging.java
deleted file mode 100644
index 18e27317a..000000000
--- a/src/main/java/eu/hbp/mip/utils/UserActionLogging.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package eu.hbp.mip.utils;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class UserActionLogging {
-
- private static final Logger LOGGER = LoggerFactory.getLogger(UserActionLogging.class);
-
- public static void LogUserAction(String userName, String actionName, String actionInfo) {
- LOGGER.info(" User : "
- + userName
- + " called endpoint: " + actionName
- + ", info: " + actionInfo);
- }
-
- // Usually, used from Threads because threads can't get userName.
- // Also used when a user is not authorised yet
- public static void LogAction(String actionName, String actionIdInfo) {
- LOGGER.info("Action -->" + actionName + " info: " + actionIdInfo);
- }
-}
diff --git a/src/main/resources/logback.xml b/src/main/resources/logback.xml
index d4a1e4765..0726d82f4 100644
--- a/src/main/resources/logback.xml
+++ b/src/main/resources/logback.xml
@@ -10,7 +10,8 @@
<logger name="eu.hbp.mip">
<appender-ref ref="FILE1" />
</logger>
- <logger name="org.springframework">
+ <include resource="org/springframework/boot/logging/logback/base.xml"/>
+ <logger name="org.springframework.web" level="ERROR">
<appender-ref ref="FILE1" />
</logger>
<logger name="eu.hbp.mip.utils" level="INFO" additivity="false">
--
GitLab
From 32658797bfc2cfac53ffb10119954eb6a8379f78 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Tue, 13 Oct 2020 08:43:35 -0700
Subject: [PATCH 2/4] Identation fixes on the whole solution.
---
src/main/java/eu/hbp/mip/MIPApplication.java | 6 +-
.../PersistenceConfiguration.java | 2 +-
.../configuration/PortalErrorAttributes.java | 2 +-
.../eu/hbp/mip/controllers/AlgorithmsApi.java | 34 +++----
.../eu/hbp/mip/controllers/ArticlesApi.java | 83 +++++++---------
.../eu/hbp/mip/controllers/ExperimentApi.java | 50 +++++-----
.../java/eu/hbp/mip/controllers/FilesAPI.java | 8 +-
.../eu/hbp/mip/controllers/MiningApi.java | 11 ++-
.../eu/hbp/mip/controllers/ModelsApi.java | 96 ++++++++-----------
.../hbp/mip/controllers/PathologiesApi.java | 8 +-
.../eu/hbp/mip/controllers/SecurityApi.java | 8 +-
.../java/eu/hbp/mip/controllers/StatsApi.java | 4 +-
.../java/eu/hbp/mip/controllers/UsersApi.java | 2 +-
src/main/java/eu/hbp/mip/model/Article.java | 4 +-
src/main/java/eu/hbp/mip/model/Config.java | 6 +-
src/main/java/eu/hbp/mip/model/Dataset.java | 4 +-
.../java/eu/hbp/mip/model/Experiment.java | 24 +++--
.../java/eu/hbp/mip/model/GeneralStats.java | 4 +-
src/main/java/eu/hbp/mip/model/Group.java | 6 +-
src/main/java/eu/hbp/mip/model/Model.java | 4 +-
.../java/eu/hbp/mip/model/PathologyDTO.java | 6 +-
src/main/java/eu/hbp/mip/model/Query.java | 42 ++++----
src/main/java/eu/hbp/mip/model/Tag.java | 4 +-
src/main/java/eu/hbp/mip/model/User.java | 7 +-
src/main/java/eu/hbp/mip/model/Variable.java | 4 +-
.../eu/hbp/mip/model/galaxy/WorkflowDTO.java | 22 ++---
.../mip/repositories/ArticleRepository.java | 2 +
.../repositories/ExperimentRepository.java | 1 +
.../hbp/mip/repositories/ModelRepository.java | 2 +
.../java/eu/hbp/mip/utils/ActionLogging.java | 6 +-
.../java/eu/hbp/mip/utils/ClaimUtils.java | 4 +-
src/main/java/eu/hbp/mip/utils/HTTPUtil.java | 2 +-
32 files changed, 219 insertions(+), 249 deletions(-)
diff --git a/src/main/java/eu/hbp/mip/MIPApplication.java b/src/main/java/eu/hbp/mip/MIPApplication.java
index e6ccd8e1e..9af69bdd9 100644
--- a/src/main/java/eu/hbp/mip/MIPApplication.java
+++ b/src/main/java/eu/hbp/mip/MIPApplication.java
@@ -13,13 +13,11 @@ import org.slf4j.LoggerFactory;
@SpringBootApplication
public class MIPApplication {
- private static final Logger LOGGER = LoggerFactory.getLogger(MIPApplication.class);
-
+ private static final Logger LOGGER = LoggerFactory.getLogger(MIPApplication.class);
+
public static void main(String[] args) {
SpringApplication.run(MIPApplication.class, args);
}
-
-
}
diff --git a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
index 6b973dc65..c8024e1bf 100644
--- a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
@@ -23,7 +23,7 @@ public class PersistenceConfiguration {
@Primary
@Bean(name = "portalDatasource")
- @ConfigurationProperties(prefix="spring.portalDatasource")
+ @ConfigurationProperties(prefix = "spring.portalDatasource")
public DataSource portalDataSource() {
return DataSourceBuilder.create().build();
}
diff --git a/src/main/java/eu/hbp/mip/configuration/PortalErrorAttributes.java b/src/main/java/eu/hbp/mip/configuration/PortalErrorAttributes.java
index aba509034..352b1d156 100644
--- a/src/main/java/eu/hbp/mip/configuration/PortalErrorAttributes.java
+++ b/src/main/java/eu/hbp/mip/configuration/PortalErrorAttributes.java
@@ -20,7 +20,7 @@ public class PortalErrorAttributes extends DefaultErrorAttributes {
Throwable throwable = getError(requestAttributes);
StringBuilder sb = new StringBuilder("[");
- for (String attr: requestAttributes.getAttributeNames(RequestAttributes.SCOPE_REQUEST)) {
+ for (String attr : requestAttributes.getAttributeNames(RequestAttributes.SCOPE_REQUEST)) {
Object v = requestAttributes.getAttribute(attr, RequestAttributes.SCOPE_REQUEST);
sb.append(attr).append(" = ").append(v).append('\n');
}
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
index f495c5d8f..db9b7d124 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
@@ -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...");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Executing...");
LinkedList<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms();
- ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms", "Loaded "+ exaremeAlgorithms.size() +" exareme algorithms");
+ ActionLogging.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");
+ ActionLogging.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",
+ ActionLogging.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",
+ ActionLogging.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",
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
disabledAlgorithmsCouldNotBeLoaded);
}
@@ -93,8 +93,8 @@ public class AlgorithmsApi {
allowedAlgorithms.add(algorithm);
}
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms",
- "Successfully listed "+ allowedAlgorithms.size() +" algorithms");
+ ActionLogging.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());
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "An exception occurred: " + e.getMessage());
return null;
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms",
+ ActionLogging.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());
+ ActionLogging.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);
+ ActionLogging.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());
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "An exception occurred: " + e.getMessage());
return null;
}
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms", "Workflows fetched: " + workflows.size());
+ ActionLogging.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);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Converting workflow: " + workflow);
algorithms.add(workflow.convertToAlgorithmDTO());
- ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms",
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
"Converted algorithm: " + algorithms.get(algorithms.size() - 1));
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /algorithms", "Completed!");
+ ActionLogging.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 467e558d2..e73b2d061 100644
--- a/src/main/java/eu/hbp/mip/controllers/ArticlesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ArticlesApi.java
@@ -12,8 +12,6 @@ import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.repositories.ArticleRepository;
import eu.hbp.mip.utils.ActionLogging;
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;
@@ -45,43 +43,38 @@ public class ArticlesApi {
) {
User user = userInfo.getUser();
Iterable<Article> articles;
- ActionLogging.LogUserAction(user.getUsername() , "(GET) /articles", "Loading articles...");
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /articles", "Loading articles...");
- if(own != null && own)
- {
- articles = articleRepository.findByCreatedBy(user);
- }
- else
- {
+ if (own != null && own) {
+ articles = articleRepository.findByCreatedBy(user);
+ } else {
articles = articleRepository.findByStatusOrCreatedBy("published", user);
}
int articlesSize = 0;
- if(status != null)
- {
- for(Iterator<Article> i = articles.iterator(); i.hasNext();)
- {
+ if (status != null) {
+ for (Iterator<Article> i = articles.iterator(); i.hasNext(); ) {
Article a = i.next();
- if(!status.equals(a.getStatus()))
- {
+ if (!status.equals(a.getStatus())) {
i.remove();
}
articlesSize++;
}
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /articles", "Successfully Loaded "+ articlesSize +" articles");
-
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles", "Successfully Loaded " + articlesSize + " articles");
+
return ResponseEntity.ok(articles);
}
@ApiOperation(value = "Create an article")
- @ApiResponses(value = { @ApiResponse(code = 201, message = "Article created") })
+ @ApiResponses(value = {@ApiResponse(code = 201, message = "Article created")})
@RequestMapping(method = RequestMethod.POST)
public ResponseEntity<Void> addAnArticle(
@RequestBody @ApiParam(value = "Article to create", required = true) @Valid Article article
) {
+
User user = userInfo.getUser();
- ActionLogging.LogUserAction(user.getUsername() , "(POST) /articles", "Creating article...");
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /articles", "Creating article...");
article.setCreatedAt(new Date());
if ("published".equals(article.getStatus())) {
@@ -90,16 +83,13 @@ public class ArticlesApi {
article.setCreatedBy(user);
long count = 1;
- for(int i = 1; count > 0; i++)
- {
+ for (int i = 1; count > 0; i++) {
count = articleRepository.countByTitle(article.getTitle());
- if(count > 0)
- {
+ if (count > 0) {
String title = article.getTitle();
- if(i > 1)
- {
- title = title.substring(0, title.length()-4);
+ if (i > 1) {
+ title = title.substring(0, title.length() - 4);
}
article.setTitle(title + " (" + i + ")");
}
@@ -114,22 +104,19 @@ public class ArticlesApi {
}
boolean alreadyExists = true;
- for(int i = 1; alreadyExists; i++)
- {
+ for (int i = 1; alreadyExists; i++) {
alreadyExists = articleRepository.exists(slug);
- if(alreadyExists)
- {
- if(i > 1)
- {
- slug = slug.substring(0, slug.length()-2);
+ if (alreadyExists) {
+ if (i > 1) {
+ slug = slug.substring(0, slug.length() - 2);
}
- slug += "-"+i;
+ slug += "-" + i;
}
article.setSlug(slug);
}
articleRepository.save(article);
- ActionLogging.LogUserAction(user.getUsername() , "(POST) /articles", "Successfully created article with id : " + article.getSlug());
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /articles", "Successfully created article with id : " + article.getSlug());
return new ResponseEntity<>(HttpStatus.CREATED);
}
@@ -139,45 +126,42 @@ 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);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles/{slug}", "Loading article with id : " + slug);
User user = userInfo.getUser();
Article article;
article = articleRepository.findOne(slug);
- if(article == null)
- {
+ if (article == null) {
//LOGGER.warn("Cannot find article : " + slug);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /articles/{slug}", "Article not found");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles/{slug}", "Article not found");
return ResponseEntity.badRequest().body(null);
}
- if (!"published".equals(article.getStatus()) && !article.getCreatedBy().getUsername().equals(user.getUsername()))
- {
+ if (!"published".equals(article.getStatus()) && !article.getCreatedBy().getUsername().equals(user.getUsername())) {
return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
- ActionLogging.LogUserAction(user.getUsername() , "(GET) /articles/{slug}", "Successfully Loaded article with id : " + slug);
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /articles/{slug}", "Successfully Loaded article with id : " + slug);
return ResponseEntity.ok(article);
}
@ApiOperation(value = "Update an article")
- @ApiResponses(value = { @ApiResponse(code = 204, message = "Article updated") })
+ @ApiResponses(value = {@ApiResponse(code = 204, message = "Article updated")})
@RequestMapping(value = "/{slug}", method = RequestMethod.PUT)
public ResponseEntity<Void> updateAnArticle(
@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);
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(PUT) /articles/{slug}", "Updating article with id : " + slug);
User user = userInfo.getUser();
String author = articleRepository.findOne(slug).getCreatedBy().getUsername();
- if(!user.getUsername().equals(author))
- {
+ if (!user.getUsername().equals(author)) {
return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
@@ -185,10 +169,9 @@ public class ArticlesApi {
String newTitle = article.getTitle();
- if(!newTitle.equals(oldTitle)) {
+ if (!newTitle.equals(oldTitle)) {
long count = 1;
- for(int i = 1; count > 0 && !newTitle.equals(oldTitle); i++)
- {
+ for (int i = 1; count > 0 && !newTitle.equals(oldTitle); i++) {
newTitle = article.getTitle();
count = articleRepository.countByTitle(newTitle);
if (count > 0 && !newTitle.equals(oldTitle)) {
@@ -202,7 +185,7 @@ public class ArticlesApi {
articleRepository.save(article);
- ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(PUT) /articles/{slug}", "Successfully pdated article with id : " + slug);
+ ActionLogging.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 9d1635122..b4a7d2bbd 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -92,7 +92,7 @@ public class ExperimentApi {
UUID experimentUuid;
User user = userInfo.getUser();
- ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Loading Experiment with uuid : "+uuid);
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Loading Experiment with uuid : " + uuid);
try {
experimentUuid = UUID.fromString(uuid);
@@ -113,7 +113,7 @@ public class ExperimentApi {
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 +".");
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Experiment was Loaded with uuid : " + uuid + ".");
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
@@ -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.");
+ ActionLogging.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.");
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Algorithm runs on Exareme.");
return runExaremeAlgorithm(experimentExecutionDTO);
}
}
@@ -180,7 +180,7 @@ public class ExperimentApi {
}
experiment = experimentRepository.findOne(experimentUuid);
- if (!experiment.getCreatedBy().getUsername().equals(user.getUsername())){
+ if (!experiment.getCreatedBy().getUsername().equals(user.getUsername())) {
ActionLogging.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);
}
@@ -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 + ".");
+ ActionLogging.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",
@@ -356,7 +356,7 @@ public class ExperimentApi {
Experiment experiment = createExperiment(experimentExecutionDTO);
User user = userInfo.getUser();
- ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :"+ experiment.getUuid());
+ ActionLogging.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();
@@ -377,20 +377,20 @@ public class ExperimentApi {
"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!");
+ ActionLogging.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);
+ ActionLogging.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());
+ ActionLogging.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());
+ ActionLogging.LogExperimentAction(experiment.getName(), "Finished the experiment: " + experiment.toString());
}).start();
return response;
@@ -417,7 +417,7 @@ public class ExperimentApi {
ActionLogging.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());
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
User user = userInfo.getUser();
@@ -544,10 +544,10 @@ public class ExperimentApi {
try {
sleep(2000);
} catch (InterruptedException e) {
- ActionLogging.LogExperimentAction(experiment.getName(),"Sleep was disrupted: " + e.getMessage());
+ ActionLogging.LogExperimentAction(experiment.getName(), "Sleep was disrupted: " + e.getMessage());
}
- ActionLogging.LogExperimentAction(experiment.getName(),"Fetching status for experiment Id: " + experiment.getUuid());
+ ActionLogging.LogExperimentAction(experiment.getName(), "Fetching status for experiment Id: " + experiment.getUuid());
String state = getWorkflowStatus(experiment.getWorkflowHistoryId(), experiment.getName());
ActionLogging.LogExperimentAction(experiment.getName(), "State is: " + state);
@@ -555,22 +555,22 @@ public class ExperimentApi {
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.");
+ ActionLogging.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());
+ ActionLogging.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());
+ ActionLogging.LogExperimentAction(experiment.getName(), "Visible result are: " + jobResult.getId());
String result = getWorkflowResultBody(experiment, jobResult.getId());
- ActionLogging.LogExperimentAction(experiment.getName(),"Result: " + result);
+ ActionLogging.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");
+ ActionLogging.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());
+ ActionLogging.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());
+ ActionLogging.LogExperimentAction(experiment.getName(), "Failed job is: " + jobResult.getId());
String result = getWorkflowJobError(jobResult.getId(), experiment.getName());
- ActionLogging.LogExperimentAction(experiment.getName(),"Job result: " + result);
+ ActionLogging.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");
+ ActionLogging.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());
+ ActionLogging.LogExperimentAction(experiment.getName(), "Result exists: " + experiment.getResult());
return;
}
}
@@ -736,7 +736,7 @@ public class ExperimentApi {
/**
* @param experiment The experiment of the workflow
- * @param contentId the id of the job result that we want
+ * @param contentId the id of the job result that we want
* @return the result of the specific workflow job, null if there was an error
*/
public String getWorkflowResultBody(Experiment experiment, String contentId) {
diff --git a/src/main/java/eu/hbp/mip/controllers/FilesAPI.java b/src/main/java/eu/hbp/mip/controllers/FilesAPI.java
index 74d8c8093..34f64984c 100644
--- a/src/main/java/eu/hbp/mip/controllers/FilesAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/FilesAPI.java
@@ -28,20 +28,20 @@ import java.time.LocalDateTime;
@Api(value = "/protected", description = "the protected files API")
public class FilesAPI {
-
+
@Autowired
private UserInfo userInfo;
@ApiOperation(value = "Get protected files")
- @RequestMapping(value = "/{filename:.+}" , method = RequestMethod.GET)
+ @RequestMapping(value = "/{filename:.+}", method = RequestMethod.GET)
public ResponseEntity<Void> getProtectedFile(
@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);
+ ActionLogging.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");
+ ActionLogging.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 e05b4ca94..a5fc94b78 100644
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
@@ -1,4 +1,5 @@
package eu.hbp.mip.controllers;
+
import eu.hbp.mip.utils.HTTPUtil;
import com.google.gson.Gson;
@@ -36,7 +37,7 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
* Created by mirco on 06.01.17.
*/
@RestController
-@RequestMapping(value = "/mining", produces = { APPLICATION_JSON_VALUE })
+@RequestMapping(value = "/mining", produces = {APPLICATION_JSON_VALUE})
@Api(value = "/mining", description = "the mining API")
public class MiningApi {
@@ -51,7 +52,7 @@ 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...");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Executing histogram...");
String query = gson.toJson(queryList);
String url = queryExaremeUrl + "/" + "MULTIPLE_HISTOGRAMS";
@@ -60,10 +61,10 @@ 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());
+ ActionLogging.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");
+ } catch (IOException e) {
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Histogram algorithm was not found");
return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
}
}
diff --git a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
index de5c7f5d4..08f5199ea 100644
--- a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
@@ -53,28 +53,22 @@ public class ModelsApi {
public ResponseEntity<List> getModels(
@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 ...");
+ ) {
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /models", "Loading models ...");
User user = userInfo.getUser();
Iterable<Model> models;
- if(own != null && own)
- {
+ if (own != null && own) {
models = modelRepository.findByCreatedByOrderByCreatedAt(user);
- }
- else
- {
+ } else {
models = modelRepository.findByValidOrCreatedByOrderByCreatedAt(true, user);
}
- if(valid != null && models != null)
- {
- for (Iterator<Model> i = models.iterator(); i.hasNext(); )
- {
+ if (valid != null && models != null) {
+ for (Iterator<Model> i = models.iterator(); i.hasNext(); ) {
Model m = i.next();
- if(valid != m.getValid())
- {
+ if (valid != m.getValid()) {
i.remove();
}
}
@@ -86,27 +80,26 @@ public class ModelsApi {
m.setDataset(datasetRepository.findOne(m.getDataset().getCode()));
modelsList.add(m);
}
-
- ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /models","Successfully loaded " + modelsList.size() + " models.");
+
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /models", "Successfully loaded " + modelsList.size() + " models.");
return ResponseEntity.ok(modelsList);
}
@ApiOperation(value = "Create a model", response = Model.class)
- @ApiResponses(value = { @ApiResponse(code = 201, message = "Model created") })
+ @ApiResponses(value = {@ApiResponse(code = 201, message = "Model created")})
@RequestMapping(method = RequestMethod.POST)
public ResponseEntity<Model> addAModel(
@RequestBody @ApiParam(value = "Model to create", required = true) Model model
- ) {
+ ) {
User user = userInfo.getUser();
- ActionLogging.LogUserAction(user.getUsername() , "(POST) /models","Creating a model");
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /models", "Creating a model");
model.setTitle(model.getConfig().getTitle().get("text"));
model.setCreatedBy(user);
model.setCreatedAt(new Date());
- if(model.getValid() == null)
- {
+ if (model.getValid() == null) {
model.setValid(false);
}
@@ -120,7 +113,7 @@ public class ModelsApi {
saveVariables(model.getQuery().getVariables());
saveVariables(model.getQuery().getCovariables());
saveVariables(model.getQuery().getGrouping());
- saveVariables(model.getQuery().getTrainingDatasets());
+ saveVariables(model.getQuery().getTrainingDatasets());
configRepository.save(model.getConfig());
queryRepository.save(model.getQuery());
@@ -129,14 +122,13 @@ public class ModelsApi {
}
modelRepository.save(model);
- ActionLogging.LogUserAction(user.getUsername() , "(POST) /models","Created model with id : " + model.getSlug()+ ", model.config and model.query");
+ ActionLogging.LogUserAction(user.getUsername(), "(POST) /models", "Created model with id : " + model.getSlug() + ", model.config and model.query");
return ResponseEntity.status(HttpStatus.CREATED).body(model);
}
private void saveVariables(@RequestBody @ApiParam(value = "Model to create", required = true) List<Variable> variables) {
- for (Variable var : variables)
- {
+ for (Variable var : variables) {
variableRepository.save(var);
}
}
@@ -144,16 +136,13 @@ public class ModelsApi {
private void ensureSlugUniqueness(@RequestBody @ApiParam(value = "Model to create", required = true) Model model) {
String slug = createSlug(model.getTitle());
boolean slugExists = true;
- for(int i = 1; slugExists; i++)
- {
+ for (int i = 1; slugExists; i++) {
slugExists = modelRepository.exists(slug);
- if(slugExists)
- {
- if(i > 1)
- {
- slug = slug.substring(0, slug.length()-2);
+ if (slugExists) {
+ if (i > 1) {
+ slug = slug.substring(0, slug.length() - 2);
}
- slug += "-"+i;
+ slug += "-" + i;
}
model.setSlug(slug);
}
@@ -172,15 +161,12 @@ public class ModelsApi {
private void ensureTitleUniqueness(@RequestBody @ApiParam(value = "Model to create", required = true) Model model) {
boolean titleExists = true;
- for(int i = 1; titleExists; i++)
- {
+ for (int i = 1; titleExists; i++) {
String title = model.getTitle();
titleExists = modelRepository.countByTitle(title) > 0;
- if(titleExists)
- {
- if(i > 1)
- {
- title = title.substring(0, title.length()-4);
+ if (titleExists) {
+ if (i > 1) {
+ title = title.substring(0, title.length() - 4);
}
model.setTitle(title + " (" + i + ")");
}
@@ -191,23 +177,21 @@ public class ModelsApi {
@RequestMapping(value = "/{slug}", method = RequestMethod.GET)
public ResponseEntity<Model> getAModel(
@ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
- ) {
+ ) {
User user = userInfo.getUser();
- ActionLogging.LogUserAction(user.getUsername() , "(GET) /models/{slug}", "Loading model with id : " + slug);
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Loading model with id : " + slug);
Model model = modelRepository.findOne(slug);
- if(model == null)
- {
+ if (model == null) {
//LOGGER.warn("Cannot find model : " + slug);
- ActionLogging.LogUserAction(user.getUsername() , "(GET) /models/{slug}", "Model was not found");
+ ActionLogging.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. ");
+ if (!model.getValid() && !model.getCreatedBy().getUsername().equals(user.getUsername())) {
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "You are not authorized to retrieve models. ");
return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
@@ -215,24 +199,23 @@ 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);
+ ActionLogging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Loaded model with id : " + slug);
return ResponseEntity.ok(model);
}
@ApiOperation(value = "Update a model", response = Void.class)
- @ApiResponses(value = { @ApiResponse(code = 204, message = "Model updated") })
+ @ApiResponses(value = {@ApiResponse(code = 204, message = "Model updated")})
@RequestMapping(value = "/{slug}", method = RequestMethod.PUT)
public ResponseEntity<Void> updateAModel(
@ApiParam(value = "slug", required = true) @PathVariable("slug") String slug,
@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);
+ ActionLogging.LogUserAction(user.getUsername(), "(PUT) /models/{slug}", "Updating model with id : " + slug);
Model oldModel = modelRepository.findOne(slug);
- if(!user.getUsername().equals(oldModel.getCreatedBy().getUsername()))
- {
+ if (!user.getUsername().equals(oldModel.getCreatedBy().getUsername())) {
return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
@@ -242,10 +225,9 @@ public class ModelsApi {
String newTitle = model.getTitle();
// If title has been updated, ensure it is unique
- if(!newTitle.equals(oldTitle)) {
+ if (!newTitle.equals(oldTitle)) {
boolean newTitleExists = true;
- for(int i = 1; newTitleExists && !newTitle.equals(oldTitle); i++)
- {
+ for (int i = 1; newTitleExists && !newTitle.equals(oldTitle); i++) {
newTitle = model.getTitle();
newTitleExists = modelRepository.countByTitle(newTitle) > 0;
if (newTitleExists && !newTitle.equals(oldTitle)) {
@@ -271,7 +253,7 @@ 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");
+ ActionLogging.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 41518bd11..0469056a8 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
@@ -48,7 +48,7 @@ public class PathologiesApi {
@RequestMapping(name = "/pathologies", method = RequestMethod.GET)
public ResponseEntity<String> getPathologies(Authentication authentication) {
- ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(GET) /pathologies", "Loading pathologies ...");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Loading pathologies ...");
// Load pathologies from file
Resource resource = resourceLoader.getResource("file:/opt/portal/api/pathologies.json");
@@ -57,17 +57,17 @@ 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");
+ ActionLogging.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");
+ ActionLogging.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");
+ ActionLogging.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 852e7e12c..a1eb3e8b7 100644
--- a/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
@@ -45,7 +45,7 @@ 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());
+ ActionLogging.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 +77,7 @@ public class SecurityApi {
userRepository.save(user);
}
- ActionLogging.LogUserAction(userInfo.getUser().getUsername() , "(POST) /user", "User has agreed on the NDA");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /user", "User has agreed on the NDA");
return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
@@ -86,7 +86,7 @@ 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.");
+ ActionLogging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /user/login/hbp", "Unathorized login.");
httpServletResponse.sendRedirect(securityConfiguration.getFrontendRedirectAfterLogin());
}
@@ -114,7 +114,7 @@ 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.");
+ ActionLogging.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 7fb491ee8..77ef125db 100644
--- a/src/main/java/eu/hbp/mip/controllers/StatsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/StatsApi.java
@@ -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");
+ ActionLogging.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.");
+ ActionLogging.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 9485f99fe..4dc7de343 100644
--- a/src/main/java/eu/hbp/mip/controllers/UsersApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/UsersApi.java
@@ -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());
+ ActionLogging.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/model/Article.java b/src/main/java/eu/hbp/mip/model/Article.java
index 4fdfc40b8..95c7cbbae 100644
--- a/src/main/java/eu/hbp/mip/model/Article.java
+++ b/src/main/java/eu/hbp/mip/model/Article.java
@@ -58,8 +58,8 @@ public class Article {
public Article() {
/*
- * Empty constructor is needed by Hibernate
- */
+ * Empty constructor is needed by Hibernate
+ */
title = "";
}
diff --git a/src/main/java/eu/hbp/mip/model/Config.java b/src/main/java/eu/hbp/mip/model/Config.java
index d950d5074..2362194b2 100644
--- a/src/main/java/eu/hbp/mip/model/Config.java
+++ b/src/main/java/eu/hbp/mip/model/Config.java
@@ -16,7 +16,7 @@ import java.util.Map;
@Entity
@Table(name = "`config`")
@ApiModel
-@JsonIgnoreProperties(value = { "id" })
+@JsonIgnoreProperties(value = {"id"})
public class Config {
@Id
@@ -42,8 +42,8 @@ public class Config {
public Config() {
/*
- * Empty constructor is needed by Hibernate
- */
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/eu/hbp/mip/model/Dataset.java b/src/main/java/eu/hbp/mip/model/Dataset.java
index d7d1e486a..d920571d9 100644
--- a/src/main/java/eu/hbp/mip/model/Dataset.java
+++ b/src/main/java/eu/hbp/mip/model/Dataset.java
@@ -47,8 +47,8 @@ public class Dataset {
public Dataset() {
/*
- * Empty constructor is needed by Hibernate
- */
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/eu/hbp/mip/model/Experiment.java b/src/main/java/eu/hbp/mip/model/Experiment.java
index 902cf37da..c40d91d34 100644
--- a/src/main/java/eu/hbp/mip/model/Experiment.java
+++ b/src/main/java/eu/hbp/mip/model/Experiment.java
@@ -20,11 +20,11 @@ public class Experiment {
@Id
@Column(columnDefinition = "uuid")
- @org.hibernate.annotations.Type(type="pg-uuid")
+ @org.hibernate.annotations.Type(type = "pg-uuid")
@Expose
private UUID uuid;
- @Column(columnDefinition="TEXT")
+ @Column(columnDefinition = "TEXT")
@Expose
private String name;
@@ -38,22 +38,22 @@ public class Experiment {
@Expose
private Model model;
- @Column(columnDefinition="TEXT")
+ @Column(columnDefinition = "TEXT")
@Expose
private String algorithms;
- @Column(columnDefinition="TEXT")
+ @Column(columnDefinition = "TEXT")
private String validations;
- @Column(columnDefinition="TEXT")
+ @Column(columnDefinition = "TEXT")
@Expose
private String workflowHistoryId;
- @Column(columnDefinition="TEXT")
+ @Column(columnDefinition = "TEXT")
@Expose
private String workflowStatus;
- @Column(columnDefinition="TEXT")
+ @Column(columnDefinition = "TEXT")
@Expose
private String result;
@@ -78,8 +78,8 @@ public class Experiment {
public Experiment() {
/*
- * Empty constructor is needed by Hibernate
- */
+ * Empty constructor is needed by Hibernate
+ */
}
@@ -87,15 +87,13 @@ public class Experiment {
JsonObject exp = gson.toJsonTree(this).getAsJsonObject();
JsonParser parser = new JsonParser();
- if (this.algorithms != null)
- {
+ if (this.algorithms != null) {
exp.remove("algorithms");
JsonArray jsonAlgorithms = parser.parse(this.algorithms).getAsJsonArray();
exp.add("algorithms", jsonAlgorithms);
}
- if (this.validations != null)
- {
+ if (this.validations != null) {
exp.remove("validations");
JsonArray jsonValidations = parser.parse(this.validations).getAsJsonArray();
exp.add("validations", jsonValidations);
diff --git a/src/main/java/eu/hbp/mip/model/GeneralStats.java b/src/main/java/eu/hbp/mip/model/GeneralStats.java
index 302cf8edd..4253ae7dd 100644
--- a/src/main/java/eu/hbp/mip/model/GeneralStats.java
+++ b/src/main/java/eu/hbp/mip/model/GeneralStats.java
@@ -17,8 +17,8 @@ public class GeneralStats {
public GeneralStats() {
/*
- * Empty constructor is needed by Hibernate
- */
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/eu/hbp/mip/model/Group.java b/src/main/java/eu/hbp/mip/model/Group.java
index 3cf2a0706..abb195a93 100644
--- a/src/main/java/eu/hbp/mip/model/Group.java
+++ b/src/main/java/eu/hbp/mip/model/Group.java
@@ -15,7 +15,7 @@ import javax.persistence.Table;
@Entity
@Table(name = "`group`")
@ApiModel
-@JsonIgnoreProperties(value = { "parent" })
+@JsonIgnoreProperties(value = {"parent"})
@JsonInclude(JsonInclude.Include.NON_NULL)
public class Group {
@@ -25,8 +25,8 @@ public class Group {
public Group() {
/*
- * Empty constructor is needed by Hibernate
- */
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/eu/hbp/mip/model/Model.java b/src/main/java/eu/hbp/mip/model/Model.java
index 8b25b7410..b15908037 100644
--- a/src/main/java/eu/hbp/mip/model/Model.java
+++ b/src/main/java/eu/hbp/mip/model/Model.java
@@ -57,8 +57,8 @@ public class Model {
public Model() {
/*
- * Empty constructor is needed by Hibernate
- */
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/eu/hbp/mip/model/PathologyDTO.java b/src/main/java/eu/hbp/mip/model/PathologyDTO.java
index cc407e7f2..c58238b62 100644
--- a/src/main/java/eu/hbp/mip/model/PathologyDTO.java
+++ b/src/main/java/eu/hbp/mip/model/PathologyDTO.java
@@ -73,10 +73,12 @@ public class PathologyDTO {
this.label = label;
}
- public String toString(){ return code;}
+ public String toString() {
+ return code;
+ }
}
- public String toString(){
+ public String toString() {
return code;
}
diff --git a/src/main/java/eu/hbp/mip/model/Query.java b/src/main/java/eu/hbp/mip/model/Query.java
index 0e4a59850..8e4d78dcb 100644
--- a/src/main/java/eu/hbp/mip/model/Query.java
+++ b/src/main/java/eu/hbp/mip/model/Query.java
@@ -16,7 +16,7 @@ import java.util.List;
@Entity
@ApiModel
@Table(name = "`query`")
-@JsonIgnoreProperties(value = { "id" })
+@JsonIgnoreProperties(value = {"id"})
@JsonInclude(JsonInclude.Include.NON_NULL)
public class Query {
@@ -26,44 +26,44 @@ public class Query {
@ManyToMany
@JoinTable(name = "query_variable", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false) },
- inverseJoinColumns = { @JoinColumn(name = "code",
- nullable = false, updatable = false) })
+ @JoinColumn(name = "id", nullable = false, updatable = false)},
+ inverseJoinColumns = {@JoinColumn(name = "code",
+ nullable = false, updatable = false)})
private List<Variable> variables = new LinkedList<>();
@ManyToMany
@JoinTable(name = "query_covariable", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false) },
- inverseJoinColumns = { @JoinColumn(name = "code",
- nullable = false, updatable = false) })
+ @JoinColumn(name = "id", nullable = false, updatable = false)},
+ inverseJoinColumns = {@JoinColumn(name = "code",
+ nullable = false, updatable = false)})
private List<Variable> covariables = new LinkedList<>();
@ManyToMany
@JoinTable(name = "query_grouping", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false) },
- inverseJoinColumns = { @JoinColumn(name = "code",
- nullable = false, updatable = false) })
+ @JoinColumn(name = "id", nullable = false, updatable = false)},
+ inverseJoinColumns = {@JoinColumn(name = "code",
+ nullable = false, updatable = false)})
private List<Variable> grouping = new LinkedList<>();
@ManyToMany
@JoinTable(name = "query_training_datasets", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false) },
- inverseJoinColumns = { @JoinColumn(name = "code",
- nullable = false, updatable = false) })
+ @JoinColumn(name = "id", nullable = false, updatable = false)},
+ inverseJoinColumns = {@JoinColumn(name = "code",
+ nullable = false, updatable = false)})
private List<Variable> trainingDatasets = new LinkedList<>();
@ManyToMany
@JoinTable(name = "query_testing_datasets", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false) },
- inverseJoinColumns = { @JoinColumn(name = "code",
- nullable = false, updatable = false) })
+ @JoinColumn(name = "id", nullable = false, updatable = false)},
+ inverseJoinColumns = {@JoinColumn(name = "code",
+ nullable = false, updatable = false)})
private List<Variable> testingDatasets = new LinkedList<>();
@ManyToMany
@JoinTable(name = "query_validation_datasets", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false) },
- inverseJoinColumns = { @JoinColumn(name = "code",
- nullable = false, updatable = false) })
+ @JoinColumn(name = "id", nullable = false, updatable = false)},
+ inverseJoinColumns = {@JoinColumn(name = "code",
+ nullable = false, updatable = false)})
private List<Variable> validationDatasets = new LinkedList<>();
@Column(columnDefinition = "text")
@@ -75,8 +75,8 @@ public class Query {
public Query() {
/*
- * Empty constructor is needed by Hibernate
- */
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/eu/hbp/mip/model/Tag.java b/src/main/java/eu/hbp/mip/model/Tag.java
index 3e1fbccbc..693c98656 100644
--- a/src/main/java/eu/hbp/mip/model/Tag.java
+++ b/src/main/java/eu/hbp/mip/model/Tag.java
@@ -23,8 +23,8 @@ public class Tag {
public Tag() {
/*
- * Empty constructor is needed by Hibernate
- */
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/eu/hbp/mip/model/User.java b/src/main/java/eu/hbp/mip/model/User.java
index d95be07d0..64fee4b67 100644
--- a/src/main/java/eu/hbp/mip/model/User.java
+++ b/src/main/java/eu/hbp/mip/model/User.java
@@ -19,7 +19,7 @@ import java.util.stream.Collectors;
@Table(name = "`user`")
@ApiModel
@JsonInclude(JsonInclude.Include.NON_NULL)
-@JsonIgnoreProperties(value = { "appsVotes" })
+@JsonIgnoreProperties(value = {"appsVotes"})
public class User {
@Id
@@ -86,13 +86,14 @@ public class User {
public User() {
/*
- * Empty constructor is needed by Hibernate
- */
+ * Empty constructor is needed by Hibernate
+ */
}
/**
* Create a user using OpenID user profile
+ *
* @param userInfo info from OpenID UserInfo endpoint
*/
public User(String userInfo) {
diff --git a/src/main/java/eu/hbp/mip/model/Variable.java b/src/main/java/eu/hbp/mip/model/Variable.java
index 1fcce2e48..596be8d77 100644
--- a/src/main/java/eu/hbp/mip/model/Variable.java
+++ b/src/main/java/eu/hbp/mip/model/Variable.java
@@ -17,7 +17,7 @@ import java.util.List;
@Entity
@Table(name = "`variable`")
@ApiModel
-@JsonIgnoreProperties(value = { "queries" })
+@JsonIgnoreProperties(value = {"queries"})
@JsonInclude(JsonInclude.Include.NON_NULL)
public class Variable {
@@ -26,7 +26,7 @@ public class Variable {
private String code = null;
/**
- * Empty constructor is needed by Hibernate
+ * Empty constructor is needed by Hibernate
*/
public Variable() {
}
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java b/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
index de537a1dc..fa0cb4b33 100644
--- a/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
+++ b/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
@@ -103,7 +103,7 @@ public class WorkflowDTO {
}
}
- public AlgorithmDTO convertToAlgorithmDTO(){
+ public AlgorithmDTO convertToAlgorithmDTO() {
AlgorithmDTO algorithmDTO = new AlgorithmDTO();
@@ -120,10 +120,10 @@ public class WorkflowDTO {
// Convert the annotation to algorithm Parameter
AlgorithmDTO.AlgorithmParamDTO algorithmParam;
- if(steps.get(workflowInput.getKey()).getAnnotation() != null) {
+ if (steps.get(workflowInput.getKey()).getAnnotation() != null) {
algorithmParam = gson.fromJson(steps.get(workflowInput.getKey()).getAnnotation(),
- AlgorithmDTO.AlgorithmParamDTO.class);
- }else{
+ AlgorithmDTO.AlgorithmParamDTO.class);
+ } else {
// If annotation is not provided, auto-fill some information
algorithmParam = new AlgorithmDTO.AlgorithmParamDTO();
// When the constraints are not known, set the most relaxed constraints
@@ -134,17 +134,17 @@ public class WorkflowDTO {
algorithmParam.setDefaultValue("");
algorithmParam.setDefaultValue("true");
// If label is dataset/pathology/filter/formula the type should be the same
- if(workflowInput.getValue().getLabel().equals("dataset") ||
- workflowInput.getValue().getLabel().equals("pathology")||
- workflowInput.getValue().getLabel().equals("filter")||
- workflowInput.getValue().getLabel().equals("formula")){
+ if (workflowInput.getValue().getLabel().equals("dataset") ||
+ workflowInput.getValue().getLabel().equals("pathology") ||
+ workflowInput.getValue().getLabel().equals("filter") ||
+ workflowInput.getValue().getLabel().equals("formula")) {
algorithmParam.setType(workflowInput.getValue().getLabel());
- }else if(workflowInput.getValue().getLabel().equals("x") ||
- workflowInput.getValue().getLabel().equals("y")){
+ } else if (workflowInput.getValue().getLabel().equals("x") ||
+ workflowInput.getValue().getLabel().equals("y")) {
algorithmParam.setType("column");
algorithmParam.setColumnValuesSQLType("text,real,integer");
algorithmParam.setColumnValuesIsCategorical("");
- }else{
+ } else {
algorithmParam.setType("other");
}
}
diff --git a/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java b/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java
index 4ad0e3942..1a93186ff 100644
--- a/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java
@@ -10,6 +10,8 @@ import org.springframework.data.repository.CrudRepository;
public interface ArticleRepository extends CrudRepository<Article, String> {
Long countByTitle(String title);
+
Iterable<Article> findByCreatedBy(User user);
+
Iterable<Article> findByStatusOrCreatedBy(String status, User user);
}
diff --git a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
index 6609d6450..2f6ae857d 100644
--- a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
@@ -12,5 +12,6 @@ import java.util.UUID;
public interface ExperimentRepository extends CrudRepository<Experiment, UUID> {
Iterable<Experiment> findByCreatedBy(User user);
+
Iterable<Experiment> findByShared(Boolean shared);
}
diff --git a/src/main/java/eu/hbp/mip/repositories/ModelRepository.java b/src/main/java/eu/hbp/mip/repositories/ModelRepository.java
index de44afc6c..c25b1e5bb 100644
--- a/src/main/java/eu/hbp/mip/repositories/ModelRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/ModelRepository.java
@@ -10,6 +10,8 @@ import org.springframework.data.repository.CrudRepository;
public interface ModelRepository extends CrudRepository<Model, String> {
Long countByTitle(String Title);
+
Iterable<Model> findByCreatedByOrderByCreatedAt(User user);
+
Iterable<Model> findByValidOrCreatedByOrderByCreatedAt(Boolean valid, User user);
}
diff --git a/src/main/java/eu/hbp/mip/utils/ActionLogging.java b/src/main/java/eu/hbp/mip/utils/ActionLogging.java
index 8e9757276..7004fb89e 100644
--- a/src/main/java/eu/hbp/mip/utils/ActionLogging.java
+++ b/src/main/java/eu/hbp/mip/utils/ActionLogging.java
@@ -12,8 +12,8 @@ public class ActionLogging {
private static Integer maxInfoLen = 5;
public static void LogUserAction(String userName, String endpoint, String actionInfo) {
- maxEndpointLen = (maxEndpointLen < userName.length() ? userName.length() : maxEndpointLen);
- maxInfoLen = (maxInfoLen < endpoint.length() ? endpoint.length() : maxInfoLen);
+ maxEndpointLen = (maxEndpointLen < userName.length() ? userName.length() : maxEndpointLen);
+ maxInfoLen = (maxInfoLen < endpoint.length() ? endpoint.length() : maxInfoLen);
String endpointSpacing = String.format("%" + (maxEndpointLen - userName.length() + 2) + "s", "");
String infoSpacing = String.format("%" + (maxInfoLen - endpoint.length() + 2) + "s", "");
LOGGER.info(" User -> " + userName
@@ -25,7 +25,7 @@ public class ActionLogging {
// Used from Threads because threads can't get userName.
public static void LogExperimentAction(String experimentName, String actionInfo) {
- LOGGER.info(" Experiment -> "+ experimentName
+ LOGGER.info(" Experiment -> " + experimentName
+ " , Info -> " + actionInfo);
}
diff --git a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
index bad70279e..2749a96d6 100644
--- a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
+++ b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
@@ -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",
+ ActionLogging.LogUserAction(username, "(GET) /pathologies",
"Added dataset: " + dataset.getCode());
userPathologyDatasets.add(dataset);
}
}
if (userPathologyDatasets.size() > 0) {
- ActionLogging.LogUserAction(username , "(GET) /pathologies",
+ ActionLogging.LogUserAction(username, "(GET) /pathologies",
"Added pathology '" + curPathology.getLabel()
+ "' with datasets: '" + userPathologyDatasets + "'");
diff --git a/src/main/java/eu/hbp/mip/utils/HTTPUtil.java b/src/main/java/eu/hbp/mip/utils/HTTPUtil.java
index 5c5043463..cd3778a00 100644
--- a/src/main/java/eu/hbp/mip/utils/HTTPUtil.java
+++ b/src/main/java/eu/hbp/mip/utils/HTTPUtil.java
@@ -27,7 +27,7 @@ public class HTTPUtil {
}
public static int sendAuthorizedHTTP(String url, String query, StringBuilder resp, String httpVerb,
- String authorization) throws IOException {
+ String authorization) throws IOException {
return sendHTTP(url, query, resp, httpVerb, authorization);
}
--
GitLab
From 2a8732d7f49810f2db1a47f73ade22d2d8dcccfa Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Tue, 13 Oct 2020 09:05:56 -0700
Subject: [PATCH 3/4] Renamed ActionLogging to Logging.
---
build.sh | 2 +-
.../configuration/SecurityConfiguration.java | 4 +-
.../eu/hbp/mip/controllers/AlgorithmsApi.java | 34 ++--
.../eu/hbp/mip/controllers/ArticlesApi.java | 20 +-
.../eu/hbp/mip/controllers/ExperimentApi.java | 184 +++++++++---------
.../java/eu/hbp/mip/controllers/FilesAPI.java | 10 +-
.../eu/hbp/mip/controllers/MiningApi.java | 30 ++-
.../eu/hbp/mip/controllers/ModelsApi.java | 24 ++-
.../hbp/mip/controllers/PathologiesApi.java | 11 +-
.../eu/hbp/mip/controllers/SecurityApi.java | 11 +-
.../java/eu/hbp/mip/controllers/StatsApi.java | 6 +-
.../java/eu/hbp/mip/controllers/UsersApi.java | 4 +-
.../java/eu/hbp/mip/utils/ClaimUtils.java | 14 +-
.../{ActionLogging.java => Logging.java} | 6 +-
14 files changed, 171 insertions(+), 189 deletions(-)
rename src/main/java/eu/hbp/mip/utils/{ActionLogging.java => Logging.java} (92%)
diff --git a/build.sh b/build.sh
index 6a18d98ec..ef4f10565 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 90d05b9d3..7836edf94 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 db9b7d124..8310973a3 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 e73b2d061..d4eb46e9f 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 b4a7d2bbd..e81d2ee5b 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 34f64984c..69e7f3ba9 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 a5fc94b78..6a198cc0d 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 08f5199ea..6f013ee33 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 0469056a8..779169814 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 a1eb3e8b7..4e412aea0 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 77ef125db..8bd109e53 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 4dc7de343..b791a7858 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 2749a96d6..e71d3f190 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 7004fb89e..892181108 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;
--
GitLab
From ac9030d2cbd8609d3ba2f47a9f314d8e649362b0 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Wed, 14 Oct 2020 11:11:45 -0700
Subject: [PATCH 4/4] Update logs on /experiments/runAlgorithm to output the
parameters of the algorithm
---
.../eu/hbp/mip/controllers/ExperimentApi.java | 144 ++++++++++--------
src/main/java/eu/hbp/mip/utils/Logging.java | 34 +++--
2 files changed, 99 insertions(+), 79 deletions(-)
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index e81d2ee5b..f05151474 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -127,7 +127,16 @@ public class ExperimentApi {
String algorithmType = experimentExecutionDTO.getAlgorithms().get(0).getType();
String algorithmName = experimentExecutionDTO.getAlgorithms().get(0).getName();
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Executing " + algorithmName + " with algorithmType : " + algorithmType + ".");
+ StringBuilder parametersLogMessage = new StringBuilder(", Parameters:\n");
+ for (ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO params : experimentExecutionDTO.getAlgorithms().get(0).getParameters()) {
+ parametersLogMessage
+ .append(" ")
+ .append(params.getLabel())
+ .append(" -> ")
+ .append(params.getValue())
+ .append("\n");
+ }
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Executing " + algorithmName + parametersLogMessage);
if (authenticationIsEnabled) {
// Getting the dataset from the experiment parameters
@@ -215,11 +224,11 @@ public class ExperimentApi {
@RequestMapping(method = RequestMethod.GET, params = {"maxResultCount"})
public ResponseEntity<String> listExperiments(
@ApiParam(value = "maxResultCount") @RequestParam int maxResultCount) {
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{maxResultCount}", "Listing experiments with a maximum amount of : " + maxResultCount + ".");
+ User user = userInfo.getUser();
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{maxResultCount}", "Listing experiments with a maximum amount of : " + maxResultCount + ".");
List<Experiment> expList = doListExperiments(false, null);
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{maxResultCount}", "Successfully listed experiments.");
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{maxResultCount}", "Successfully listed experiments.");
return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
}
@@ -228,8 +237,8 @@ public class ExperimentApi {
@RequestMapping(method = RequestMethod.GET, params = {"slug", "maxResultCount"})
public ResponseEntity<String> listExperiments(@ApiParam(value = "slug") @RequestParam("slug") String modelSlug,
@ApiParam(value = "maxResultCount") @RequestParam("maxResultCount") int maxResultCount) {
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{slug}/{maxResultCount}", "Listing experiments with a maximum amount of :" + maxResultCount + "with modelSlug : " + modelSlug + ".");
+ User user = userInfo.getUser();
+ Logging.LogUserAction(user.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 +246,17 @@ public class ExperimentApi {
}
List<Experiment> expList = doListExperiments(false, null);
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{slug}/{maxResultCount}", "Successfully listed my experiments.");
+ Logging.LogUserAction(user.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) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{mine}", "Listing my experiments.");
+ User user = userInfo.getUser();
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{mine}", "Listing my experiments.");
List<Experiment> expList = doListExperiments(true, null);
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{mine}", "Successfully listed my experiments.");
+ Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{mine}", "Successfully listed my experiments.");
return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
}
@@ -285,7 +295,7 @@ public class ExperimentApi {
} catch (IllegalArgumentException iae) {
//LOGGER.trace("Invalid UUID", iae);
//LOGGER.warn("An invalid Experiment UUID was received !");
- Logging.LogUserAction(userInfo.getUser().getUsername(), "List my experiments", "Listing my experiments.");
+ Logging.LogUserAction(user.getUsername(), "List my experiments", "Listing my experiments.");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
@@ -352,11 +362,11 @@ public class ExperimentApi {
* @return the response to be returned
*/
public ResponseEntity<String> runExaremeAlgorithm(ExperimentExecutionDTO experimentExecutionDTO) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Running the algorithm...");
+ User user = userInfo.getUser();
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Running the algorithm...");
Experiment experiment = createExperiment(experimentExecutionDTO);
- User user = userInfo.getUser();
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
// Run the 1st algorithm from the list
String algorithmName = experimentExecutionDTO.getAlgorithms().get(0).getName();
@@ -377,20 +387,20 @@ public class ExperimentApi {
"Starting exareme execution thread");
new Thread(() -> {
// ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogUserAction!
- Logging.LogExperimentAction(experiment.getName(), "Thread named :" + Thread.currentThread().getName() + " with id :" + Thread.currentThread().getId() + " started!");
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Thread named :" + Thread.currentThread().getName() + " with id :" + Thread.currentThread().getId() + " started!");
try {
StringBuilder results = new StringBuilder();
int code = HTTPUtil.sendPost(url, body, results);
- Logging.LogExperimentAction(experiment.getName(), "Algorithm finished with code: " + code);
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "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) {
- Logging.LogExperimentAction(experiment.getName(), "There was an exception: " + e.getMessage());
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "There was an exception: " + e.getMessage());
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -398,7 +408,7 @@ public class ExperimentApi {
}
finishExperiment(experiment);
- Logging.LogExperimentAction(experiment.getName(), "Finished the experiment: " + experiment.toString());
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Finished the experiment: " + experiment.toString());
}).start();
return response;
@@ -414,11 +424,11 @@ public class ExperimentApi {
* @return the response to be returned
*/
public ResponseEntity<String> runGalaxyWorkflow(ExperimentExecutionDTO experimentExecutionDTO) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Running a workflow...");
+ User user = userInfo.getUser();
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Running a workflow...");
Experiment experiment = createExperiment(experimentExecutionDTO);
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
- User user = userInfo.getUser();
+ Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
// Run the 1st algorithm from the list
@@ -539,38 +549,38 @@ public class ExperimentApi {
new Thread(() -> {
while (true) {
// ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogExperimentAction!
- Logging.LogExperimentAction(experiment.getName(), "Thread is running...");
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Thread is running...");
try {
sleep(2000);
} catch (InterruptedException e) {
- Logging.LogExperimentAction(experiment.getName(), "Sleep was disrupted: " + e.getMessage());
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Sleep was disrupted: " + e.getMessage());
}
- Logging.LogExperimentAction(experiment.getName(), "Fetching status for experiment Id: " + experiment.getUuid());
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Fetching status for experiment Id: " + experiment.getUuid());
- String state = getWorkflowStatus(experiment.getWorkflowHistoryId(), experiment.getName());
- Logging.LogExperimentAction(experiment.getName(), "State is: " + state);
+ String state = getWorkflowStatus(experiment);
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "State is: " + state);
switch (state) {
case "running":
// Do nothing, when the experiment is created the status is set to running
- Logging.LogExperimentAction(experiment.getName(), "Workflow is still running.");
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Workflow is still running.");
break;
case "completed":
// Get only the job result that is visible
List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experiment);
- Logging.LogExperimentAction(experiment.getName(), "Results are: " + workflowJobsResults.toString());
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Results are: " + workflowJobsResults.toString());
boolean resultFound = false;
for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
if (jobResult.getVisible()) {
- Logging.LogExperimentAction(experiment.getName(), "Visible result are: " + jobResult.getId());
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Visible result are: " + jobResult.getId());
String result = getWorkflowResultBody(experiment, jobResult.getId());
- Logging.LogExperimentAction(experiment.getName(), "Result: " + result);
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Result: " + result);
if (result == null) {
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -582,7 +592,7 @@ public class ExperimentApi {
}
if (!resultFound) { // If there is no visible result
- Logging.LogExperimentAction(experiment.getName(), "No visible result");
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "No visible result");
experiment.setResult("[" + new ErrorResponse("The workflow has no visible result.").toString() + "]");
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -594,16 +604,16 @@ public class ExperimentApi {
case "error":
// Get the job result that failed
workflowJobsResults = getWorkflowResults(experiment);
- Logging.LogExperimentAction(experiment.getName(), "Error results are: " + workflowJobsResults.toString());
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Error results are: " + workflowJobsResults.toString());
boolean failedJobFound = false;
for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
if (jobResult.getState().equals("error")) {
- Logging.LogExperimentAction(experiment.getName(), "Failed job is: " + jobResult.getId());
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Failed job is: " + jobResult.getId());
- String result = getWorkflowJobError(jobResult.getId(), experiment.getName());
+ String result = getWorkflowJobError(jobResult.getId(), experiment);
- Logging.LogExperimentAction(experiment.getName(), "Job result: " + result);
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Job result: " + result);
if (result == null) {
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -615,7 +625,7 @@ public class ExperimentApi {
}
if (!failedJobFound) { // If there is no visible failed job
- Logging.LogExperimentAction(experiment.getName(), "No failed result");
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "No failed result");
experiment.setResult("[" + new ErrorResponse("The workflow has no failed result.").toString() + "]");
experiment.setHasError(true);
experiment.setHasServerError(true);
@@ -633,7 +643,7 @@ public class ExperimentApi {
// If result exists return
if (experiment.getResult() != null) {
- Logging.LogExperimentAction(experiment.getName(), "Result exists: " + experiment.getResult());
+ Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Result exists: " + experiment.getResult());
return;
}
}
@@ -642,15 +652,19 @@ public class ExperimentApi {
/**
- * @param historyId The historyId of the workflow
+ * @param experiment The experiment of the workflow
* @return "running" -> When the workflow is still running
* "internalError" -> When an exception or a bad request occurred
* "error" -> When the workflow produced an error
* "completed" -> When the workflow completed successfully
*/
- public String getWorkflowStatus(String historyId, String experimentName) {
+ public String getWorkflowStatus(Experiment experiment) {
+ String historyId = experiment.getWorkflowHistoryId();
+ String experimentName = experiment.getName();
+ UUID experimentId = experiment.getUuid();
+
// ATTENTION: This function is used from a Thread. Only LogExperimentAction should be used, not LogUserAction!
- Logging.LogExperimentAction(experimentName, " History Id : " + historyId);
+ Logging.LogExperimentAction(experimentName, experimentId, " History Id : " + historyId);
// Create the request client
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
@@ -660,16 +674,15 @@ public class ExperimentApi {
try {
Response<Object> response = call.execute();
if (response.code() >= 400) {
- Logging.LogExperimentAction(experimentName, " Response code: "
+ Logging.LogExperimentAction(experimentName, experimentId, " Response code: "
+ response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return "internalError";
}
result = new Gson().toJson(response.body());
- Logging.LogExperimentAction(experimentName, " Result: " + result);
+ Logging.LogExperimentAction(experimentName, experimentId, " Result: " + result);
} catch (IOException e) {
- Logging.LogExperimentAction(experimentName
- , " An exception happened: " + e.getMessage());
+ Logging.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
return "internalError";
}
@@ -678,12 +691,11 @@ public class ExperimentApi {
JSONObject resultJson = new JSONObject(result);
state = resultJson.getString("state");
} catch (JSONException e) {
- Logging.LogExperimentAction(experimentName
- , " An exception happened: " + e.getMessage());
+ Logging.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
return "internalError";
}
- Logging.LogExperimentAction(experimentName, " Completed!");
+ Logging.LogExperimentAction(experimentName, experimentId, " Completed!");
switch (state) {
case "ok":
return "completed";
@@ -707,7 +719,8 @@ public class ExperimentApi {
String historyId = experiment.getWorkflowHistoryId();
String experimentName = experiment.getName();
- Logging.LogExperimentAction(experimentName, " historyId : " + historyId);
+ UUID experimentId = experiment.getUuid();
+ Logging.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
Call<List<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(historyId, galaxyApiKey);
@@ -716,20 +729,19 @@ public class ExperimentApi {
try {
Response<List<GalaxyWorkflowResult>> response = call.execute();
if (response.code() >= 400) {
- Logging.LogExperimentAction(experimentName, " Response code: "
+ Logging.LogExperimentAction(experimentName, experimentId, " Response code: "
+ response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return null;
}
getGalaxyWorkflowResultList = response.body();
- Logging.LogExperimentAction(experimentName, " Result: " + response.body());
+ Logging.LogExperimentAction(experimentName, experimentId, " Result: " + response.body());
} catch (IOException e) {
- Logging.LogExperimentAction(experimentName
- , " An exception happened: " + e.getMessage());
+ Logging.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
return null;
}
- Logging.LogExperimentAction(experimentName, " Completed!");
+ Logging.LogExperimentAction(experimentName, experimentId, " Completed!");
return getGalaxyWorkflowResultList;
}
@@ -743,8 +755,9 @@ public class ExperimentApi {
String historyId = experiment.getWorkflowHistoryId();
String experimentName = experiment.getName();
+ UUID experimentId = experiment.getUuid();
- Logging.LogExperimentAction(experimentName, " historyId : " + historyId);
+ Logging.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
Call<Object> call =
@@ -754,20 +767,20 @@ public class ExperimentApi {
try {
Response<Object> response = call.execute();
if (response.code() >= 400) {
- Logging.LogExperimentAction(experimentName, " Response code: "
+ Logging.LogExperimentAction(experimentName, experimentId, " Response code: "
+ response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return null;
}
resultJson = new Gson().toJson(response.body());
- Logging.LogExperimentAction(experimentName, " Result: " + resultJson);
+ Logging.LogExperimentAction(experimentName, experimentId, " Result: " + resultJson);
} catch (IOException e) {
- Logging.LogExperimentAction(experimentName,
+ Logging.LogExperimentAction(experimentName, experimentId,
" An exception happened: " + e.getMessage());
return null;
}
- Logging.LogExperimentAction(experimentName, " Completed!");
+ Logging.LogExperimentAction(experimentName, experimentId, " Completed!");
return resultJson;
}
@@ -776,8 +789,11 @@ public class ExperimentApi {
* @param jobId the id of the workflow job that failed
* @return the error that was produced or null if an error occurred
*/
- public String getWorkflowJobError(String jobId, String experimentName) {
- Logging.LogExperimentAction(experimentName, " jobId : " + jobId);
+ public String getWorkflowJobError(String jobId, Experiment experiment) {
+ String experimentName = experiment.getName();
+ UUID experimentId = experiment.getUuid();
+
+ Logging.LogExperimentAction(experimentName, experimentId, " jobId : " + jobId);
RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId, galaxyApiKey);
@@ -786,7 +802,7 @@ public class ExperimentApi {
try {
Response<Object> response = callError.execute();
if (response.code() >= 400) {
- Logging.LogExperimentAction(experimentName, "Response code: "
+ Logging.LogExperimentAction(experimentName, experimentId, "Response code: "
+ response.code() + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
return null;
}
@@ -796,19 +812,19 @@ public class ExperimentApi {
JsonElement jsonElement = new JsonParser().parse(jsonString);
JsonObject rootObject = jsonElement.getAsJsonObject();
fullError = rootObject.get("stderr").getAsString();
- Logging.LogExperimentAction(experimentName, "Error: " + fullError);
+ Logging.LogExperimentAction(experimentName, experimentId, "Error: " + fullError);
String[] arrOfStr = fullError.split("ValueError", 0);
String specError = arrOfStr[arrOfStr.length - 1];
returnError = specError.substring(1);
- Logging.LogExperimentAction(experimentName, "Parsed Error: " + returnError);
+ Logging.LogExperimentAction(experimentName, experimentId, "Parsed Error: " + returnError);
} catch (IOException e) {
- Logging.LogExperimentAction(experimentName, "Exception: " + e.getMessage());
+ Logging.LogExperimentAction(experimentName, experimentId, "Exception: " + e.getMessage());
return null;
}
- Logging.LogExperimentAction(experimentName, "Completed successfully!");
+ Logging.LogExperimentAction(experimentName, experimentId, "Completed successfully!");
return returnError;
}
diff --git a/src/main/java/eu/hbp/mip/utils/Logging.java b/src/main/java/eu/hbp/mip/utils/Logging.java
index 892181108..f3ed45e83 100644
--- a/src/main/java/eu/hbp/mip/utils/Logging.java
+++ b/src/main/java/eu/hbp/mip/utils/Logging.java
@@ -3,34 +3,38 @@ package eu.hbp.mip.utils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import java.util.UUID;
+
public class Logging {
private static final Logger LOGGER = LoggerFactory.getLogger(Logging.class);
- private static Integer maxEndpointLen = 5;
- private static Integer maxInfoLen = 5;
public static void LogUserAction(String userName, String endpoint, String actionInfo) {
- maxEndpointLen = (maxEndpointLen < userName.length() ? userName.length() : maxEndpointLen);
- maxInfoLen = (maxInfoLen < endpoint.length() ? endpoint.length() : maxInfoLen);
- String endpointSpacing = String.format("%" + (maxEndpointLen - userName.length() + 2) + "s", "");
- String infoSpacing = String.format("%" + (maxInfoLen - endpoint.length() + 2) + "s", "");
- LOGGER.info(" User -> " + userName
- + endpointSpacing
- + ", Endpoint -> " + endpoint
- + infoSpacing
- + ", Info -> " + actionInfo);
+ LOGGER.info(" User -> " + userName + " ,"
+ + calculateAdditionalSpacing(userName.length(), 8)
+ + "Endpoint -> " + endpoint + " ,"
+ + calculateAdditionalSpacing(endpoint.length(), 32)
+ + "Info -> " + actionInfo);
}
// Used from Threads because threads can't get userName.
- public static void LogExperimentAction(String experimentName, String actionInfo) {
+ public static void LogExperimentAction(String experimentName, UUID experimentId, String actionInfo) {
LOGGER.info(" Experiment -> " + experimentName
- + " , Info -> " + actionInfo);
+ + "(" + experimentId + ") ,"
+ + calculateAdditionalSpacing(experimentName.length() + experimentId.toString().length() + 2, 20)
+ + "Info -> " + actionInfo);
}
// Used when a user is not authorised yet
public static void LogAction(String actionName, String actionIdInfo) {
- LOGGER.info(" Action -> " + actionName
- + " , Info -> " + actionIdInfo);
+ LOGGER.info(" Action -> " + actionName + " ,"
+ + calculateAdditionalSpacing(actionName.length() + 2, 20)
+ + "Info -> " + actionIdInfo);
}
+ // Calculates the spacing that is needed to create consistent logs.
+ private static String calculateAdditionalSpacing(Integer currentLen, Integer maxLen) {
+ int additionalSpacing = (maxLen > currentLen ? maxLen - currentLen + 2 : 2);
+ return String.format("%" + additionalSpacing + "s", "");
+ }
}
--
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