Merge branch 'add_logs' into 'master'

add logs for each API call and each time something is saved in the DB



See merge request !26

src/main/java/eu/hbp/mip/controllers/AppsApi.java

@@ -49,6 +49,8 @@ public class AppsApi {
     @RequestMapping(method = RequestMethod.GET)
     public ResponseEntity<Iterable> getApps(
     ) {
+        LOGGER.info("Get apps");
+
         return ResponseEntity.ok(appRepository.findAll());
     }
 
@@ -59,6 +61,8 @@ public class AppsApi {
             @ApiParam(value = "id", required = true) @PathVariable("id") Integer id,
             @ApiParam(value = "value", required = true) @PathVariable("value") Integer value
     ) {
+        LOGGER.info("Post a vote");
+
         User user = userRepository.findOne(securityConfiguration.getUser().getUsername());
         App app = appRepository.findOne(id);
         Vote vote;
@@ -78,6 +82,8 @@ public class AppsApi {
         vote.setValue(value);
         voteRepository.save(vote);
 
+        LOGGER.info("Vote saved");
+
         return new ResponseEntity<>(HttpStatus.CREATED);
 
     }

src/main/java/eu/hbp/mip/controllers/ArticlesApi.java

@@ -45,6 +45,7 @@ public class ArticlesApi {
             @ApiParam(value = "Only ask results matching status", allowableValues = "{values=[draft, published, closed]}") @RequestParam(value = "status", required = false) String status,
             @ApiParam(value = "Only ask articles from own team") @RequestParam(value = "team", required = false) Boolean team
     ) {
+        LOGGER.info("Get articles");
 
         User user = securityConfiguration.getUser();
         Iterable<Article> articles;
@@ -80,6 +81,7 @@ public class ArticlesApi {
     public ResponseEntity<Void> addAnArticle(
             @RequestBody @ApiParam(value = "Article to create", required = true) @Valid Article article
     ) {
+        LOGGER.info("Create an article");
 
         User user = securityConfiguration.getUser();
 
@@ -129,6 +131,8 @@ public class ArticlesApi {
         }
         articleRepository.save(article);
 
+        LOGGER.info("Article saved");
+
         return new ResponseEntity<>(HttpStatus.CREATED);
     }
 
@@ -139,6 +143,7 @@ public class ArticlesApi {
     public ResponseEntity<Article> getAnArticle(
             @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
     ) {
+        LOGGER.info("Get an article");
 
         User user = securityConfiguration.getUser();
         Article article;
@@ -147,6 +152,7 @@ public class ArticlesApi {
         {
             return new ResponseEntity<>(HttpStatus.FORBIDDEN);
         }
+
         return ResponseEntity.ok(article);
     }
 
@@ -158,6 +164,7 @@ public class ArticlesApi {
             @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug,
             @RequestBody @ApiParam(value = "Article to update", required = true) @Valid Article article
     ) {
+        LOGGER.info("Update an article");
 
         User user = securityConfiguration.getUser();
 
@@ -189,6 +196,8 @@ public class ArticlesApi {
 
         articleRepository.save(article);
 
+        LOGGER.info("Article updated");
+
         return new ResponseEntity<>(HttpStatus.NO_CONTENT);
     }
 

src/main/java/eu/hbp/mip/controllers/DatasetsApi.java

@@ -8,6 +8,7 @@ package eu.hbp.mip.controllers;
 import io.swagger.annotations.*;
 import eu.hbp.mip.model.Dataset;
 import eu.hbp.mip.repositories.DatasetRepository;
+import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.PathVariable;
@@ -22,6 +23,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 @Api(value = "/datasets", description = "the datasets API")
 public class DatasetsApi {
 
+    private static final Logger LOGGER = Logger.getLogger(DatasetsApi.class);
+
     @Autowired
     DatasetRepository datasetRepository;
 
@@ -31,6 +34,8 @@ public class DatasetsApi {
     public ResponseEntity<Dataset> getADataset(
             @ApiParam(value = "code", required = true) @PathVariable("code") String code
     )  {
+        LOGGER.info("Get a dataset");
+
         return ResponseEntity.ok(datasetRepository.findOne(code));
     }
 

src/main/java/eu/hbp/mip/controllers/ExperimentApi.java

@@ -72,6 +72,8 @@ public class ExperimentApi {
     @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(method = RequestMethod.POST)
     public ResponseEntity<String> runExperiment(@RequestBody String incomingQueryString) {
+        LOGGER.info("Run an experiment");
+
         JsonObject incomingQuery = gson.fromJson(incomingQueryString, JsonObject.class);
 
         Experiment experiment = new Experiment();
@@ -85,6 +87,8 @@ public class ExperimentApi {
         experiment.setModel(modelRepository.findOne(incomingQuery.get("model").getAsString()));
         experimentRepository.save(experiment);
 
+        LOGGER.info("Experiment saved");
+
         try {
             if(isExaremeAlgo(experiment))
             {
@@ -103,6 +107,8 @@ public class ExperimentApi {
     @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(value = "/{uuid}", method = RequestMethod.GET)
     public ResponseEntity<String> getExperiment(@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
+        LOGGER.info("Get an experiment");
+
         Experiment experiment;
         UUID experimentUuid;
         try {
@@ -121,10 +127,11 @@ public class ExperimentApi {
         return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
     }
 
-    @ApiOperation(value = "get an experiment", response = Experiment.class)
+    @ApiOperation(value = "Mark an experiment as viewed", response = Experiment.class)
     @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(value = "/{uuid}/markAsViewed", method = RequestMethod.GET)
     public ResponseEntity<String> markExperimentAsViewed(@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
+        LOGGER.info("Mark an experiment as viewed");
 
         Experiment experiment;
         UUID experimentUuid;
@@ -142,20 +149,27 @@ public class ExperimentApi {
             return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
         experiment.setResultsViewed(true);
         experimentRepository.save(experiment);
+
+        LOGGER.info("Experiment updated (marked as viewed)");
+
         return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
     }
 
-    @ApiOperation(value = "get an experiment", response = Experiment.class)
+    @ApiOperation(value = "Mark an experiment as shared", response = Experiment.class)
     @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(value = "/{uuid}/markAsShared", method = RequestMethod.GET)
     public ResponseEntity<String> markExperimentAsShared(@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
+        LOGGER.info("Mark an experiment as shared");
+
         return doMarkExperimentAsShared(uuid, true);
     }
 
-    @ApiOperation(value = "get an experiment", response = Experiment.class)
+    @ApiOperation(value = "Mark an experiment as unshared", response = Experiment.class)
     @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(value = "/{uuid}/markAsUnshared", method = RequestMethod.GET)
     public ResponseEntity<String> markExperimentAsUnshared(@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
+        LOGGER.info("Mark an experiment as unshared");
+
         return doMarkExperimentAsShared(uuid, false);
     }
 
@@ -165,6 +179,8 @@ public class ExperimentApi {
     public ResponseEntity<String> listExperiments(
             @ApiParam(value = "maxResultCount", required = false) @RequestParam int maxResultCount
     ) {
+        LOGGER.info("List experiments");
+
         return doListExperiments(true, maxResultCount, null);
     }
 
@@ -175,6 +191,7 @@ public class ExperimentApi {
             @ApiParam(value = "slug", required = false) @RequestParam("slug") String modelSlug,
             @ApiParam(value = "maxResultCount", required = false) @RequestParam("maxResultCount") int maxResultCount
     ) {
+        LOGGER.info("List experiments");
 
         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);
@@ -187,6 +204,7 @@ public class ExperimentApi {
     @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(path = "/methods", method = RequestMethod.GET)
     public ResponseEntity<String> listAvailableMethodsAndValidations() throws IOException {
+        LOGGER.info("List available methods and validations");
 
         StringBuilder response = new StringBuilder();
 
@@ -260,6 +278,8 @@ public class ExperimentApi {
         experiment.setShared(shared);
         experimentRepository.save(experiment);
 
+        LOGGER.info("Experiment updated (marked as shared)");
+
         return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
     }
 
@@ -314,6 +334,8 @@ public class ExperimentApi {
     {
         experiment.setFinished(new Date());
         experimentRepository.save(experiment);
+
+        LOGGER.info("Experiment updated (finished)");
     }
 
     private static void executeExperiment(String url, String query, Experiment experiment) throws IOException {

src/main/java/eu/hbp/mip/controllers/GroupsApi.java

@@ -10,6 +10,7 @@ import io.swagger.annotations.ApiResponse;
 import io.swagger.annotations.ApiResponses;
 import eu.hbp.mip.model.Group;
 import eu.hbp.mip.repositories.GroupRepository;
+import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.RequestMapping;
@@ -23,6 +24,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 @Api(value = "/groups", description = "the groups API")
 public class GroupsApi {
 
+    private static final Logger LOGGER = Logger.getLogger(GroupsApi.class);
+
     private static final String ROOT_CODE = "root";
 
     @Autowired
@@ -32,6 +35,8 @@ public class GroupsApi {
     @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(method = RequestMethod.GET)
     public ResponseEntity<Group> getTheRootGroup()  {
+        LOGGER.info("Get root group and its whole sub-groups tree");
+
         return ResponseEntity.ok(groupRepository.findOne(ROOT_CODE));
     }
 

src/main/java/eu/hbp/mip/controllers/ModelsApi.java

@@ -64,6 +64,7 @@ public class ModelsApi {
             @ApiParam(value = "Only ask models from own team") @RequestParam(value = "team", required = false) Boolean team,
             @ApiParam(value = "Only ask published models") @RequestParam(value = "valid", required = false) Boolean valid
     )  {
+        LOGGER.info("Get models");
 
         User user = securityConfiguration.getUser();
         Iterable<Model> models = null;
@@ -102,6 +103,8 @@ public class ModelsApi {
             @RequestBody @ApiParam(value = "Model to create", required = true) Model model
     )  {
 
+        LOGGER.info("Create a model");
+
         User user = securityConfiguration.getUser();
 
         model.setTitle(model.getConfig().getTitle().get("text"));
@@ -160,6 +163,8 @@ public class ModelsApi {
         datasetRepository.save(model.getDataset());
         modelRepository.save(model);
 
+        LOGGER.info("Model saved (also saved model.config, model.query and model.dataset)");
+
         return new ResponseEntity<Model>(HttpStatus.CREATED).ok(model);
     }
 
@@ -169,6 +174,7 @@ public class ModelsApi {
     public ResponseEntity<Model> getAModel(
             @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
     )  {
+        LOGGER.info("Get a model");
 
         User user = securityConfiguration.getUser();
 
@@ -226,6 +232,7 @@ public class ModelsApi {
             @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug,
             @RequestBody @ApiParam(value = "Model to update", required = true) Model model
     )  {
+        LOGGER.info("Update a model");
 
         User user = securityConfiguration.getUser();
 
@@ -267,6 +274,8 @@ public class ModelsApi {
         datasetRepository.save(model.getDataset());
         modelRepository.save(model);
 
+        LOGGER.info("Model updated (also saved/updated model.config, model.query and model.dataset)");
+
         return new ResponseEntity<>(HttpStatus.NO_CONTENT);
     }
 

src/main/java/eu/hbp/mip/controllers/RequestsApi.java

@@ -8,6 +8,7 @@ import io.swagger.annotations.*;
 import eu.hbp.mip.model.Dataset;
 import eu.hbp.mip.model.Query;
 import eu.hbp.mip.utils.CSVUtil;
+import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.RequestBody;
@@ -22,17 +23,21 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 @Api(value = "/queries/requests", description = "the requests API")
 public class RequestsApi {
 
+    private static final Logger LOGGER = Logger.getLogger(RequestsApi.class);
+
     private static final String DATA_FILE = "data/values.csv";
 
     @Autowired
     CSVUtil csvUtil;
 
-    @ApiOperation(value = "Send a request", response = Dataset.class)
+    @ApiOperation(value = "Post a request", response = Dataset.class)
     @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(method = RequestMethod.POST)
     public ResponseEntity<Dataset> postRequests(
             @RequestBody @ApiParam(value = "Query to process", required = true) Query query
     )  {
+        LOGGER.info("Post a request");
+
         return ResponseEntity.ok(csvUtil.parseValues(DATA_FILE, query));
     }
 

src/main/java/eu/hbp/mip/controllers/StatsApi.java

@@ -12,6 +12,7 @@ import io.swagger.annotations.ApiResponses;
 import eu.hbp.mip.model.GeneralStats;
 import eu.hbp.mip.repositories.ArticleRepository;
 import eu.hbp.mip.repositories.UserRepository;
+import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.RequestMapping;
@@ -25,6 +26,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 @Api(value = "/stats", description = "the stats API")
 public class StatsApi {
 
+    private static final Logger LOGGER = Logger.getLogger(StatsApi.class);
+
     @Autowired
     UserRepository userRepository;
 
@@ -38,6 +41,7 @@ public class StatsApi {
     @ApiResponses(value = {@ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
     @RequestMapping(method = RequestMethod.GET)
     public ResponseEntity<GeneralStats> getGeneralStatistics()  {
+        LOGGER.info("Get statistics (count on users, articles and variables)");
 
         GeneralStats stats = new GeneralStats();
 

src/main/java/eu/hbp/mip/controllers/UsersApi.java

@@ -7,6 +7,7 @@ package eu.hbp.mip.controllers;
 import io.swagger.annotations.*;
 import eu.hbp.mip.model.User;
 import eu.hbp.mip.repositories.UserRepository;
+import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.PathVariable;
@@ -21,6 +22,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 @Api(value = "/users", description = "the users API")
 public class UsersApi {
 
+    private static final Logger LOGGER = Logger.getLogger(UsersApi.class);
+
     @Autowired
     UserRepository userRepository;
 
@@ -30,6 +33,8 @@ public class UsersApi {
     public ResponseEntity<User> getAUser(
             @ApiParam(value = "username", required = true) @PathVariable("username") String username
     )  {
+        LOGGER.info("Get a user");
+
         return ResponseEntity.ok(userRepository.findOne(username));
     }
 }

src/main/java/eu/hbp/mip/controllers/VariablesApi.java

@@ -9,6 +9,7 @@ import eu.hbp.mip.repositories.VariableRepository;
 import io.swagger.annotations.*;
 import eu.hbp.mip.model.Value;
 import eu.hbp.mip.model.Variable;
+import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;
@@ -22,6 +23,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 @Api(value = "/variables", description = "the variables API")
 public class VariablesApi {
 
+    private static final Logger LOGGER = Logger.getLogger(VariablesApi.class);
+
     @Autowired
     VariableRepository variableRepository;
 
@@ -36,6 +39,8 @@ public class VariablesApi {
             @ApiParam(value = "Boolean value formatted like : (\"0\") or (\"1\") or (\"false\") or (\"true\")") @RequestParam(value = "isCovariable", required = false) String isCovariable,
             @ApiParam(value = "Boolean value formatted like : (\"0\") or (\"1\") or (\"false\") or (\"true\")") @RequestParam(value = "isFilter", required = false) String isFilter
     )  {
+        LOGGER.info("Get variables");
+
         return ResponseEntity.ok(variableRepository.findAll());
     }
 
@@ -45,6 +50,8 @@ public class VariablesApi {
     public ResponseEntity<Variable> getAVariable(
             @ApiParam(value = "code of the variable ( multiple codes are allowed, separated by \",\" )", required = true) @PathVariable("code") String code
     )  {
+        LOGGER.info("Get a variable");
+
         return ResponseEntity.ok(variableRepository.findOne(code));
     }
 
@@ -56,6 +63,8 @@ public class VariablesApi {
             @ApiParam(value = "code", required = true) @PathVariable("code") String code,
             @ApiParam(value = "Pattern to match") @RequestParam(value = "q", required = false) String q
     )  {
+        LOGGER.info("Get values from a variable");
+
         return ResponseEntity.ok(variableRepository.findOne(code).getValues());
     }