clean Swagger annotations and add ExperimentQuery model

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

@@ -45,7 +45,6 @@ public class AppsApi {
     private UserRepository userRepository;
 
     @ApiOperation(value = "Get apps", response = App.class, responseContainer = "List")
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(method = RequestMethod.GET)
     public ResponseEntity<Iterable> getApps(
     ) {
@@ -55,7 +54,6 @@ public class AppsApi {
     }
 
     @ApiOperation(value = "Post a vote")
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(value = "/{id}/vote/{value}", method = RequestMethod.POST)
     public ResponseEntity<Void> vote(
             @ApiParam(value = "id", required = true) @PathVariable("id") Integer id,

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

@@ -38,12 +38,10 @@ public class ArticlesApi {
     private ArticleRepository articleRepository;
 
     @ApiOperation(value = "Get articles", response = Article.class, responseContainer = "List")
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(method = RequestMethod.GET)
     public ResponseEntity<Iterable> getArticles(
             @ApiParam(value = "Only ask own articles") @RequestParam(value = "own", required = false) Boolean own,
-            @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
+            @ApiParam(value = "Only ask results matching status", allowableValues = "{values=[draft, published, closed]}") @RequestParam(value = "status", required = false) String status
     ) {
         LOGGER.info("Get articles");
 
@@ -75,7 +73,7 @@ public class ArticlesApi {
     }
 
 
-    @ApiOperation(value = "Create an article", response = Void.class)
+    @ApiOperation(value = "Create an article")
     @ApiResponses(value = { @ApiResponse(code = 201, message = "Article created") })
     @RequestMapping(method = RequestMethod.POST)
     public ResponseEntity<Void> addAnArticle(
@@ -138,7 +136,6 @@ public class ArticlesApi {
 
 
     @ApiOperation(value = "Get an article", response = Article.class)
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
     @RequestMapping(value = "/{slug}", method = RequestMethod.GET)
     public ResponseEntity<Article> getAnArticle(
             @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
@@ -164,7 +161,7 @@ public class ArticlesApi {
     }
 
 
-    @ApiOperation(value = "Update an article", response = Void.class)
+    @ApiOperation(value = "Update an article")
     @ApiResponses(value = { @ApiResponse(code = 204, message = "Article updated") })
     @RequestMapping(value = "/{slug}", method = RequestMethod.PUT)
     public ResponseEntity<Void> updateAnArticle(

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

@@ -29,7 +29,6 @@ public class DatasetsApi {
     private DatasetRepository datasetRepository;
 
     @ApiOperation(value = "Get a dataset", response = Dataset.class)
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(value = "/{code}", method = RequestMethod.GET)
     public ResponseEntity<Dataset> getADataset(
             @ApiParam(value = "code", required = true) @PathVariable("code") String code

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

@@ -35,7 +35,6 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 @RestController
 @RequestMapping(value = "/experiments", produces = {APPLICATION_JSON_VALUE})
 @Api(value = "/experiments", description = "the experiments API")
-@javax.annotation.Generated(value = "class io.swagger.codegen.languages.SpringMVCServerCodegen", date = "2016-01-07T07:38:20.227Z")
 public class ExperimentApi {
 
     private static final Logger LOGGER = Logger.getLogger(ExperimentApi.class);
@@ -70,7 +69,6 @@ public class ExperimentApi {
 
 
     @ApiOperation(value = "Send a request to the workflow to run an experiment", response = Experiment.class)
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(method = RequestMethod.POST)
     public ResponseEntity<String> runExperiment(@RequestBody String incomingQueryString) {
         LOGGER.info("Run an experiment");
@@ -105,7 +103,6 @@ public class ExperimentApi {
     }
 
     @ApiOperation(value = "get an experiment", response = Experiment.class)
-    @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");
@@ -130,7 +127,6 @@ public class ExperimentApi {
     }
 
     @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");
@@ -158,7 +154,6 @@ public class ExperimentApi {
     }
 
     @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");
@@ -167,7 +162,6 @@ public class ExperimentApi {
     }
 
     @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");
@@ -176,7 +170,6 @@ public class ExperimentApi {
     }
 
     @ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(value = "/mine", method = RequestMethod.GET, params = {"maxResultCount"})
     public ResponseEntity<String> listExperiments(
             @ApiParam(value = "maxResultCount", required = false) @RequestParam int maxResultCount
@@ -187,7 +180,6 @@ public class ExperimentApi {
     }
 
     @ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(method = RequestMethod.GET, params = {"slug", "maxResultCount"})
     public ResponseEntity<String> listExperiments(
             @ApiParam(value = "slug", required = false) @RequestParam("slug") String modelSlug,
@@ -203,7 +195,6 @@ public class ExperimentApi {
     }
 
     @ApiOperation(value = "List available methods and validations", response = String.class)
-    @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");

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

@@ -11,8 +11,6 @@ import com.google.gson.JsonObject;
 import eu.hbp.mip.model.Group;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiOperation;
-import io.swagger.annotations.ApiResponse;
-import io.swagger.annotations.ApiResponses;
 import org.apache.log4j.Logger;
 import org.postgresql.util.PGobject;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -41,7 +39,6 @@ public class GroupsApi {
 
 
     @ApiOperation(value = "Get the root group (containing all subgroups)", response = Group.class)
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(method = RequestMethod.GET)
     public ResponseEntity<Object> getTheRootGroup()  {
         LOGGER.info("Get root group and its whole sub-groups tree");

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

@@ -29,7 +29,6 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 @RestController
 @RequestMapping(value = "/models", produces = {APPLICATION_JSON_VALUE})
 @Api(value = "/models", description = "the models API")
-@javax.annotation.Generated(value = "class io.swagger.codegen.languages.SpringMVCServerCodegen", date = "2016-01-07T07:38:20.227Z")
 public class ModelsApi {
 
     private static final Logger LOGGER = Logger.getLogger(ModelsApi.class);
@@ -54,16 +53,13 @@ public class ModelsApi {
 
     @Autowired
     @Qualifier("dataUtil")
-    public DataUtil dataUtil;
+    private DataUtil dataUtil;
 
 
     @ApiOperation(value = "Get models", response = Model.class, responseContainer = "List")
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(method = RequestMethod.GET)
     public ResponseEntity<List> getModels(
-            @ApiParam(value = "Max number of results") @RequestParam(value = "limit", required = false) Integer limit,
             @ApiParam(value = "Only ask own models") @RequestParam(value = "own", required = false) Boolean own,
-            @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");
@@ -193,7 +189,6 @@ public class ModelsApi {
     }
 
     @ApiOperation(value = "Get a model", response = Model.class)
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
     @RequestMapping(value = "/{slug}", method = RequestMethod.GET)
     public ResponseEntity<Model> getAModel(
             @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug

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

@@ -38,7 +38,7 @@ public class RequestsApi {
 
     @Autowired
     @Qualifier("dataUtil")
-    public DataUtil dataUtil;
+    private DataUtil dataUtil;
 
 
     @ApiOperation(value = "Post a request", response = Dataset.class)

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

@@ -10,8 +10,6 @@ import eu.hbp.mip.repositories.UserRepository;
 import eu.hbp.mip.utils.DataUtil;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiOperation;
-import io.swagger.annotations.ApiResponse;
-import io.swagger.annotations.ApiResponses;
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
@@ -37,11 +35,10 @@ public class StatsApi {
 
     @Autowired
     @Qualifier("dataUtil")
-    public DataUtil dataUtil;
+    private DataUtil dataUtil;
 
 
     @ApiOperation(value = "Get general statistics", response = GeneralStats.class)
-    @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)");

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

@@ -28,7 +28,6 @@ public class UsersApi {
     private UserRepository userRepository;
 
     @ApiOperation(value = "Get a user", response = User.class)
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
     @RequestMapping(value = "/{username}", method = RequestMethod.GET)
     public ResponseEntity<User> getAUser(
             @ApiParam(value = "username", required = true) @PathVariable("username") String username

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

@@ -39,7 +39,6 @@ public class VariablesApi {
 
 
     @ApiOperation(value = "Get variables", response = List.class, responseContainer = "List")
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
     @RequestMapping(method = RequestMethod.GET)
     public ResponseEntity<Iterable> getVariables(
             @ApiParam(value = "List of groups formatted like : (\"val1\", \"val2\", ...)") @RequestParam(value = "group", required = false) String group,
@@ -64,7 +63,6 @@ public class VariablesApi {
     }
 
     @ApiOperation(value = "Get a variable", response = Object.class)
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
     @RequestMapping(value = "/{code}", method = RequestMethod.GET)
     public ResponseEntity<Object> getAVariable(
             @ApiParam(value = "code of the variable ( multiple codes are allowed, separated by \",\" )", required = true) @PathVariable("code") String code
@@ -89,7 +87,6 @@ public class VariablesApi {
 
 
     @ApiOperation(value = "Get values from a variable", response = List.class, responseContainer = "List")
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
     @RequestMapping(value = "/{code}/values", method = RequestMethod.GET)
     public ResponseEntity<Iterable> getValuesFromAVariable(
             @ApiParam(value = "code", required = true) @PathVariable("code") String code,
@@ -119,7 +116,6 @@ public class VariablesApi {
     }
 
     @ApiOperation(value = "Get groups and variables hierarchy", response = Object.class)
-    @ApiResponses(value = { @ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
     @RequestMapping(value = "/hierarchy", method = RequestMethod.GET)
     public ResponseEntity<Object> getVariablesHierarchy(
     )  {

src/main/java/eu/hbp/mip/model/Algorithm.java

+package eu.hbp.mip.model;
+
+/**
+ * Created by mirco on 09.11.16.
+ */
+
+public class Algorithm extends ExperimentValidator {
+
+    private boolean validation;
+
+    public boolean isValidation() {
+        return validation;
+    }
+
+    public void setValidation(boolean validation) {
+        this.validation = validation;
+    }
+
+}

src/main/java/eu/hbp/mip/model/AlgorithmParam.java

+package eu.hbp.mip.model;
+
+/**
+ * Created by mirco on 09.11.16.
+ */
+
+public class AlgorithmParam {
+
+    private String code;
+    private String value;
+
+    public String getCode() {
+        return code;
+    }
+
+    public void setCode(String code) {
+        this.code = code;
+    }
+
+    public String getValue() {
+        return value;
+    }
+
+    public void setValue(String value) {
+        this.value = value;
+    }
+}

src/main/java/eu/hbp/mip/model/ExperimentQuery.java

+package eu.hbp.mip.model;
+
+import java.util.List;
+
+/**
+ * Created by mirco on 09.11.16.
+ */
+public class ExperimentQuery {
+
+    private String name;
+    private String model;
+    private List<ExperimentValidator> validations;
+    private List<Algorithm> algorithms;
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getModel() {
+        return model;
+    }
+
+    public void setModel(String model) {
+        this.model = model;
+    }
+
+    public List<ExperimentValidator> getValidations() {
+        return validations;
+    }
+
+    public void setValidations(List<ExperimentValidator> validations) {
+        this.validations = validations;
+    }
+
+    public List<Algorithm> getAlgorithms() {
+        return algorithms;
+    }
+
+    public void setAlgorithms(List<Algorithm> algorithms) {
+        this.algorithms = algorithms;
+    }
+}

src/main/java/eu/hbp/mip/model/ExperimentValidator.java

+package eu.hbp.mip.model;
+
+import java.util.List;
+
+/**
+ * Created by mirco on 09.11.16.
+ */
+
+public class ExperimentValidator {
+
+    private String code;
+    private String name;
+
+    private List<AlgorithmParam> parameters;
+
+    public String getCode() {
+        return code;
+    }
+
+    public void setCode(String code) {
+        this.code = code;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public List<AlgorithmParam> getParameters() {
+        return parameters;
+    }
+
+    public void setParameters(List<AlgorithmParam> parameters) {
+        this.parameters = parameters;
+    }
+
+}