diff --git a/build.sh b/build.sh
index ef4f10565705b3eb3d0fae54b60de23671f356bf..6a18d98ecec05885651675049490ca44c990ec7f 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 adc3df815fbc74d27f78e8bbf661ff31fc168a89..90d05b9d3254d1f36989a533923a6d5961d56549 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 27e9b8e5db7cf2339bfea34fee0d17893ee97336..f495c5d8f8dc58651ff72deb0d49dcaf9b96e6bf 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 2e5fb3dc551a96cf0fd34b89cd4d159d7fcbb67f..467e558d2626d54fcf9705445eded95786ddd01f 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 a800711b544db852553de1ed7938781ffa14f995..9d16351226a59a11e099af55740644b462a09adb 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 3b4ec96ab88749ea8cfb64777c8bd79f090fa12d..74d8c80930bb7b7b77f2a727f4d0f13f25192dc9 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 75369d0b4b02faf2a755a3b42ad31b12d61f9674..e05b4ca9495d39f3a915e46bdbc9216d45a29808 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 633c01783d340a9b76bd71723fc62dd16db16fb1..de5c7f5d4d121c6f4134069f72a72230ac4745f6 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 7b6b3e65017204ea3e52897e15a2345a82deeda4..41518bd11da72009e1cc65e58da24ff8af50036f 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 397f1ae6c149a3693632a0b7817709d6cb2318f3..852e7e12c68ca3d8560d4503eb061ffd77422835 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 56d25679321043aec77613e0d028c0332ef49604..7fb491ee8e0fd1c90fd122529f454c742e7bde56 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 0620c34e444315dc6c472c304539f9c6b5d8d28d..9485f99fedc2aff53d636a656b731b7260e22960 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 0000000000000000000000000000000000000000..8e97572769643ae236eed2bc2cc0dd16d597c551
--- /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 eeceb5d21d41463e7b8412d649fad80454fdc675..bad70279e61372a828d80977075981ce61c42a88 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 18e27317a455cb8b87a605ef8495720a32bca889..0000000000000000000000000000000000000000
--- 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 d4a1e4765b7d25b98ccaf68141e28784a6ff09cb..0726d82f41564d850f92eaa301010d39ea89b068 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">