Merge pull request #3 from openminted/version/3.0.2

Version/3.0.2

pom.xml

@@ -2,8 +2,8 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>eu.openminted</groupId>
     <artifactId>omtd-registry-rest</artifactId>
-    <version>2.0.3-SNAPSHOT</version>
-
+    <version>2.1.1-SNAPSHOT</version>
+    <packaging>jar</packaging>
 
     <parent>
         <groupId>eu.openminted</groupId>
@@ -90,7 +90,7 @@
         <dependency>
             <groupId>org.elasticsearch</groupId>
             <artifactId>elasticsearch</artifactId>
-            <version>5.0.0</version>
+            <version>5.6.0</version>
         </dependency>
         <dependency>
             <groupId>javax.servlet</groupId>
@@ -128,6 +128,11 @@
             <artifactId>tika-core</artifactId>
             <version>RELEASE</version>
         </dependency>
+        <dependency>
+            <groupId>io.springfox</groupId>
+            <artifactId>springfox-swagger2</artifactId>
+            <version>2.7.0</version>
+        </dependency>
     </dependencies>
 
     <distributionManagement>

src/main/java/eu/openminted/registry/service/GenericRestController.java → src/main/java/eu/openminted/registry/controllers/GenericRestController.java

@@ -1,4 +1,4 @@
-package eu.openminted.registry.service;
+package eu.openminted.registry.controllers;
 
 import eu.openminted.registry.core.domain.Browsing;
 import eu.openminted.registry.core.domain.FacetFilter;
@@ -9,7 +9,6 @@
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
-import org.springframework.security.access.prepost.PostAuthorize;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.web.bind.annotation.*;
 

src/main/java/eu/openminted/registry/service/omtd/ApplicationController.java → src/main/java/eu/openminted/registry/controllers/omtd/ApplicationController.java

@@ -1,14 +1,16 @@
-package eu.openminted.registry.service.omtd;
+package eu.openminted.registry.controllers.omtd;
 
 import eu.openminted.registry.domain.Component;
 import eu.openminted.registry.service.ValidateInterface;
+import io.swagger.annotations.Api;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RestController;
 
 @RestController
 @RequestMapping("/request/application")
+@Api(value = "/request/application", description = "Operations about OMTD Applications.", tags="Applications")
 public class ApplicationController extends OmtdRestController<Component>{
 
     @Autowired

src/main/java/eu/openminted/registry/service/omtd/ComponentController.java → src/main/java/eu/openminted/registry/controllers/omtd/ComponentController.java

@@ -1,14 +1,16 @@
-package eu.openminted.registry.service.omtd;
+package eu.openminted.registry.controllers.omtd;
 
 import eu.openminted.registry.domain.Component;
 import eu.openminted.registry.service.ValidateInterface;
+import io.swagger.annotations.Api;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RestController;
 
 @RestController
 @RequestMapping("/request/component")
+@Api(value = "/request/component", description = "Operations about OMTD Components.", tags="Components")
 public class ComponentController extends OmtdRestController<Component>{
 
     private ValidateInterface<Component> validateInterface;

src/main/java/eu/openminted/registry/service/omtd/CorpusController.java → src/main/java/eu/openminted/registry/controllers/omtd/CorpusController.java

@@ -1,4 +1,4 @@
-package eu.openminted.registry.service.omtd;
+package eu.openminted.registry.controllers.omtd;
 
 import eu.openminted.registry.core.domain.Browsing;
 import eu.openminted.registry.domain.Corpus;
@@ -9,6 +9,7 @@
 import eu.openminted.registry.service.CorpusService;
 import eu.openminted.registry.service.StoreService;
 import eu.openminted.registry.service.ValidateInterface;
+import io.swagger.annotations.Api;
 import org.apache.commons.io.IOUtils;
 import org.apache.tika.exception.TikaException;
 import org.apache.tika.parser.ParseContext;
@@ -29,13 +30,13 @@
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
-import javax.xml.ws.Response;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.Optional;
 
 @RestController
 @RequestMapping("/request/corpus")
+@Api(value = "/request/corpus", description = "Operations about OMTD Corpora.",tags="Corpora")
 public class CorpusController extends OmtdRestController<Corpus> {
 
     @Autowired

src/main/java/eu/openminted/registry/service/omtd/IncompleteCorpusController.java → src/main/java/eu/openminted/registry/controllers/omtd/IncompleteCorpusController.java

@@ -1,16 +1,20 @@
-package eu.openminted.registry.service.omtd;
+package eu.openminted.registry.controllers.omtd;
 
 import eu.openminted.registry.domain.Corpus;
-import eu.openminted.registry.service.GenericRestController;
+import eu.openminted.registry.controllers.GenericRestController;
 import eu.openminted.registry.service.IncompleteCorpusService;
+import io.swagger.annotations.Api;
 import org.springframework.beans.factory.annotation.Autowired;
 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 springfox.documentation.annotations.ApiIgnore;
 
 @RestController
 @RequestMapping("/request/incompleteCorpus")
+@Api(value = "/request/incompleteCorpus", description = "Operations about OMTD Incomplete corpora.", hidden = true)
+@ApiIgnore
 public class IncompleteCorpusController extends GenericRestController<Corpus> {
 
     final private IncompleteCorpusService corpusService;

src/main/java/eu/openminted/registry/service/omtd/LanguageController.java → src/main/java/eu/openminted/registry/controllers/omtd/LanguageController.java

@@ -1,10 +1,11 @@
-package eu.openminted.registry.service.omtd;
+package eu.openminted.registry.controllers.omtd;
 
 import eu.openminted.registry.domain.LanguageDescription;
 import eu.openminted.registry.service.AncillaryService;
-import eu.openminted.registry.service.GenericRestController;
+import eu.openminted.registry.controllers.GenericRestController;
 import eu.openminted.registry.service.StoreService;
 import eu.openminted.registry.service.ValidateInterface;
+import io.swagger.annotations.Api;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
@@ -21,6 +22,7 @@
  */
 @RestController
 @RequestMapping("/request/language")
+@Api(value = "/request/language", description = "Operations about OMTD Models and Grammars.",tags="Models and Grammars")
 public class LanguageController extends GenericRestController<LanguageDescription> {
 
     @Autowired

src/main/java/eu/openminted/registry/service/omtd/LexicalController.java → src/main/java/eu/openminted/registry/controllers/omtd/LexicalController.java

@@ -1,9 +1,10 @@
-package eu.openminted.registry.service.omtd;
+package eu.openminted.registry.controllers.omtd;
 
 import eu.openminted.registry.domain.Lexical;
 import eu.openminted.registry.service.AncillaryService;
 import eu.openminted.registry.service.StoreService;
 import eu.openminted.registry.service.ValidateInterface;
+import io.swagger.annotations.Api;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
@@ -20,6 +21,7 @@
  */
 @RestController
 @RequestMapping("/request/lexical")
+@Api(value = "/request/lexical", description = "Operations about OMTD Annotation Resources.", tags="Annotation Resources")
 public class LexicalController extends OmtdRestController<Lexical> {
 
     @Autowired

src/main/java/eu/openminted/registry/service/omtd/OmtdControllerAdvice.java → src/main/java/eu/openminted/registry/controllers/omtd/OmtdControllerAdvice.java

@@ -1,4 +1,4 @@
-package eu.openminted.registry.service.omtd;
+package eu.openminted.registry.controllers.omtd;
 
 import eu.openminted.registry.core.exception.ServerError;
 import org.apache.logging.log4j.Logger;

src/main/java/eu/openminted/registry/service/omtd/OmtdRestController.java → src/main/java/eu/openminted/registry/controllers/omtd/OmtdRestController.java

@@ -1,13 +1,11 @@
-package eu.openminted.registry.service.omtd;
+package eu.openminted.registry.controllers.omtd;
 
 import eu.openminted.registry.core.exception.ResourceNotFoundException;
 import eu.openminted.registry.core.service.ServiceException;
 import eu.openminted.registry.domain.*;
-import eu.openminted.registry.service.GenericRestController;
+import eu.openminted.registry.controllers.GenericRestController;
 import eu.openminted.registry.service.ValidateInterface;
-import eu.openminted.registry.service.policy.PolicyInterface;
 import org.apache.commons.io.IOUtils;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
 import org.springframework.security.access.prepost.PostAuthorize;

src/main/java/eu/openminted/registry/service/other/CorpusBuildingStateController.java → src/main/java/eu/openminted/registry/controllers/other/CorpusBuildingStateController.java

@@ -1,11 +1,12 @@
-package eu.openminted.registry.service.other;
+package eu.openminted.registry.controllers.other;
 
 import eu.openminted.corpus.CorpusBuildingState;
 import eu.openminted.registry.core.exception.ResourceNotFoundException;
 import eu.openminted.registry.core.service.ResourceCRUDService;
 import eu.openminted.registry.service.CorpusBuildingStatusService;
-import eu.openminted.registry.service.GenericRestController;
+import io.swagger.annotations.Api;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.PathVariable;
@@ -17,10 +18,11 @@
 
 @RestController
 @RequestMapping("/request/corpusbuildingstate")
+@Api(value = "/request/corpusbuildingstate", description = "Operations about OMTD corpus building states.", tags="Corpus Building State")
 public class CorpusBuildingStateController extends OtherRestController<CorpusBuildingState> {
 
     @Autowired
-    CorpusBuildingStateController(ResourceCRUDService<CorpusBuildingState> service) {
+    CorpusBuildingStateController(@Qualifier("corpusBuildingStateService") ResourceCRUDService<CorpusBuildingState> service) {
         super(service);
     }
 

src/main/java/eu/openminted/registry/service/other/OperationController.java → src/main/java/eu/openminted/registry/controllers/other/OperationController.java

@@ -1,9 +1,9 @@
-package eu.openminted.registry.service.other;
+package eu.openminted.registry.controllers.other;
 
 import eu.openminted.registry.core.service.ResourceCRUDService;
 import eu.openminted.registry.domain.operation.Operation;
-import eu.openminted.registry.service.GenericRestController;
 import eu.openminted.registry.service.OperationService;
+import io.swagger.annotations.Api;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.ResponseEntity;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -17,7 +17,8 @@
  */
 
 @RestController
-@RequestMapping({"operation", "/request/operation"})
+@RequestMapping({"/request/operation"})
+@Api(value = "/request/operation", description = "Creates and controls the operations executed on Galaxy", tags="Operations")
 public class OperationController extends OtherRestController<Operation> {
 
     @Autowired

src/main/java/eu/openminted/registry/service/other/OtherRestController.java → src/main/java/eu/openminted/registry/controllers/other/OtherRestController.java

@@ -1,12 +1,13 @@
-package eu.openminted.registry.service.other;
+package eu.openminted.registry.controllers.other;
 
 import eu.openminted.registry.core.exception.ResourceNotFoundException;
 import eu.openminted.registry.core.service.ResourceCRUDService;
-import eu.openminted.registry.service.GenericRestController;
+import eu.openminted.registry.controllers.GenericRestController;
 import org.springframework.http.ResponseEntity;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestBody;
+import springfox.documentation.annotations.ApiIgnore;
 
 public class OtherRestController<T> extends GenericRestController<T> {
 
@@ -20,18 +21,21 @@ public ResponseEntity<T> get(@PathVariable("id") String id) throws ResourceNotFo
     }
 
     @Override
+    @ApiIgnore
     @PreAuthorize("hasRole('ROLE_ADMIN') or denyAll()")
     public ResponseEntity<T> update(@RequestBody T component) throws ResourceNotFoundException {
         return super.update(component);
     }
 
     @Override
+    @ApiIgnore
     @PreAuthorize("hasRole('ROLE_ADMIN') or denyAll()")
     public ResponseEntity<String> delete(@RequestBody T component) throws ResourceNotFoundException {
         return super.delete(component);
     }
 
     @Override
+    @ApiIgnore
     @PreAuthorize("hasRole('ROLE_ADMIN') or denyAll()")
     public ResponseEntity<T> add(@RequestBody T component) {
         return super.add(component);

src/main/java/eu/openminted/registry/service/other/WorkflowDefinitionController.java → src/main/java/eu/openminted/registry/controllers/other/WorkflowDefinitionController.java

@@ -1,13 +1,15 @@
-package eu.openminted.registry.service.other;
+package eu.openminted.registry.controllers.other;
 
 import eu.openminted.registry.core.exception.ResourceNotFoundException;
 import eu.openminted.registry.core.service.ResourceCRUDService;
 import eu.openminted.registry.domain.workflow.WorkflowDefinition;
-import eu.openminted.registry.service.GenericRestController;
 import eu.openminted.registry.service.WorkflowService;
+import io.swagger.annotations.Api;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.ResponseEntity;
+import org.springframework.security.access.prepost.PostAuthorize;
 import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.security.core.Authentication;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
@@ -20,7 +22,8 @@
  */
 
 @RestController
-@RequestMapping({"workflow", "/request/workflow"})
+@RequestMapping({"/request/workflow"})
+@Api(value = "/request/workflow", description = "Operations about Galaxy workflows.", tags="Galaxy Workflows")
 public class WorkflowDefinitionController extends OtherRestController<WorkflowDefinition> {
 
     WorkflowService workflowService;
@@ -33,18 +36,21 @@ public class WorkflowDefinitionController extends OtherRestController<WorkflowDe
 
     @RequestMapping(value = "create", method = RequestMethod.GET)
     @PreAuthorize("hasRole('ROLE_USER')")
-    public ResponseEntity<WorkflowDefinition> createWorkflow() {
+    public ResponseEntity<WorkflowDefinition> createWorkflow(Authentication authentication) {
+        System.out.println(authentication);
         return ResponseEntity.ok(workflowService.createWorkflow());
     }
 
     @RequestMapping(value = "update/{workflowId}", method = {RequestMethod.GET, RequestMethod.POST})
     @PreAuthorize("hasRole('ROLE_USER')")
+    @PostAuthorize("hasRole('ROLE_ADMIN') or returnObject.body.personIdentifier==principal['sub']")
     public ResponseEntity<WorkflowDefinition> updateWorkflow(@PathVariable("workflowId") String workflowID) throws ResourceNotFoundException {
         return ResponseEntity.ok(workflowService.updateWorkflow(workflowID));
     }
 
     @RequestMapping(value = "restore/{workflowId}", method = {RequestMethod.GET, RequestMethod.POST})
     @PreAuthorize("hasRole('ROLE_USER')")
+    @PostAuthorize("hasRole('ROLE_ADMIN') or returnObject.body.personIdentifier==principal['sub']")
     public ResponseEntity<WorkflowDefinition> restoreWorkflow(@PathVariable("workflowId") String workflowID) throws ResourceNotFoundException {
         return ResponseEntity.ok(workflowService.restoreWorkflow(workflowID));
     }

src/main/java/eu/openminted/registry/service/requests/AnnotationStateChangeMessage.java → src/main/java/eu/openminted/registry/controllers/requests/AnnotationStateChangeMessage.java

@@ -1,4 +1,4 @@
-package eu.openminted.registry.service.requests;
+package eu.openminted.registry.controllers.requests;
 
 public class AnnotationStateChangeMessage {
 

src/main/java/eu/openminted/registry/service/requests/DocumentStateChangeMessage.java → src/main/java/eu/openminted/registry/controllers/requests/DocumentStateChangeMessage.java

@@ -1,4 +1,4 @@
-package eu.openminted.registry.service.requests;
+package eu.openminted.registry.controllers.requests;
 
 public class DocumentStateChangeMessage {
 

src/main/java/eu/openminted/registry/service/requests/ProjectStateChangeMessage.java → src/main/java/eu/openminted/registry/controllers/requests/ProjectStateChangeMessage.java

@@ -1,4 +1,4 @@
-package eu.openminted.registry.service.requests;
+package eu.openminted.registry.controllers.requests;
 
 public class ProjectStateChangeMessage {
 

src/main/java/eu/openminted/registry/service/tools/MavenResolverController.java → src/main/java/eu/openminted/registry/controllers/tools/MavenResolverController.java

@@ -1,7 +1,8 @@
-package eu.openminted.registry.service.tools;
+package eu.openminted.registry.controllers.tools;
 
 import eu.openminted.registry.domain.MavenComponent;
 import eu.openminted.registry.service.MavenResolverService;
+import io.swagger.annotations.Api;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
@@ -13,6 +14,7 @@
 import java.util.List;
 
 @RestController
+@Api(description = "Resolve mvn coordinates.", tags="Maven Resolver")
 public class MavenResolverController {
 
     @Autowired

src/main/java/eu/openminted/registry/service/tools/RequestController.java → src/main/java/eu/openminted/registry/controllers/tools/RequestController.java

@@ -1,9 +1,10 @@
-package eu.openminted.registry.service.tools;
+package eu.openminted.registry.controllers.tools;
 
 import eu.openminted.registry.core.domain.Browsing;
 import eu.openminted.registry.core.domain.FacetFilter;
 import eu.openminted.registry.core.service.ResourceService;
 import eu.openminted.registry.service.RequestService;
+import io.swagger.annotations.Api;
 import org.mitre.openid.connect.model.OIDCAuthenticationToken;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
@@ -20,6 +21,7 @@
 import java.util.Map;
 
 @RestController
+@Api(description = "Search all OMTD resources", tags="Search")
 public class RequestController {
 
     @Autowired

src/main/java/eu/openminted/registry/service/tools/StatsController.java → src/main/java/eu/openminted/registry/controllers/tools/StatsController.java

@@ -1,4 +1,4 @@
-package eu.openminted.registry.service.tools;
+package eu.openminted.registry.controllers.tools;
 
 import eu.openminted.registry.service.DockerService;
 import eu.openminted.registry.service.StatsService;