Swagger fixes and additions

backend/web/src/main/java/org/opencdmp/controllers/PrincipalController.java

@@ -14,7 +14,7 @@ import io.swagger.v3.oas.annotations.tags.Tag;
 import org.opencdmp.audit.AuditableAction;
 import org.opencdmp.controllers.swagger.SwaggerHelpers;
 import org.opencdmp.controllers.swagger.annotation.OperationWithTenantHeader;
-import org.opencdmp.model.Lock;
+import org.opencdmp.controllers.swagger.annotation.SwaggerCommonErrorResponses;
 import org.opencdmp.model.Tenant;
 import org.opencdmp.models.Account;
 import org.opencdmp.models.AccountBuilder;
@@ -32,84 +32,89 @@ import java.util.List;
 @RestController
 @RequestMapping("/api/principal/")
 @Tag(name = "Principal", description = "Get user account information")
+@SwaggerCommonErrorResponses
 public class PrincipalController {
-	private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(PrincipalController.class));
-	private final AuditService auditService;
 
-	private final CurrentPrincipalResolver currentPrincipalResolver;
+    private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(PrincipalController.class));
-	private final AccountBuilder accountBuilder;
-	private final TenantService tenantService;
 
-	@Autowired
+    private final AuditService auditService;
-	public PrincipalController(
-			CurrentPrincipalResolver currentPrincipalResolver,
-			AccountBuilder accountBuilder,
-			AuditService auditService, TenantService tenantService) {
-		this.currentPrincipalResolver = currentPrincipalResolver;
-		this.accountBuilder = accountBuilder;
-		this.auditService = auditService;
-		this.tenantService = tenantService;
-	}
 
-	@RequestMapping(path = "me", method = RequestMethod.GET )
+    private final CurrentPrincipalResolver currentPrincipalResolver;
-	@OperationWithTenantHeader(summary = "Fetch auth information of the logged in user", description = "",
-			responses = @ApiResponse(description = "OK", responseCode = "200", content = @Content(
-					schema = @Schema(
-							implementation = Account.class
-					))
-			))
-	public Account me(
-			@Parameter(name = "fieldSet", description = SwaggerHelpers.Commons.fieldset_description, required = true) FieldSet fieldSet
-	) throws InvalidApplicationException {
-		logger.debug("me");
 
-		if (fieldSet == null || fieldSet.isEmpty()) {
+    private final AccountBuilder accountBuilder;
-			fieldSet = new BaseFieldSet(
-					Account._isAuthenticated,
-					BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._subject),
-					BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._userId),
-					BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._name),
-					BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._scope),
-					BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._client),
-					BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._issuedAt),
-					BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._notBefore),
-					BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._authenticatedAt),
-					BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._expiresAt),
-					BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._more),
-					BaseFieldSet.asIndexer(Account._profile, Account.UserProfileInfo._avatarUrl),
-					BaseFieldSet.asIndexer(Account._profile, Account.UserProfileInfo._language),
-					BaseFieldSet.asIndexer(Account._profile, Account.UserProfileInfo._culture),
-					BaseFieldSet.asIndexer(Account._profile, Account.UserProfileInfo._timezone),
-					Account._permissions,
-					BaseFieldSet.asIndexer(Account._selectedTenant, Tenant._id),
-					BaseFieldSet.asIndexer(Account._selectedTenant, Tenant._name),
-					BaseFieldSet.asIndexer(Account._selectedTenant, Tenant._code));
-		}
 
-		MyPrincipal principal = this.currentPrincipalResolver.currentPrincipal();
+    private final TenantService tenantService;
 
-		Account me = this.accountBuilder.build(fieldSet, principal);
+    @Autowired
+    public PrincipalController(
+            CurrentPrincipalResolver currentPrincipalResolver,
+            AccountBuilder accountBuilder,
+            AuditService auditService, TenantService tenantService) {
+        this.currentPrincipalResolver = currentPrincipalResolver;
+        this.accountBuilder = accountBuilder;
+        this.auditService = auditService;
+        this.tenantService = tenantService;
+    }
 
-		this.auditService.track(AuditableAction.Principal_Lookup);
+    @RequestMapping(path = "me", method = RequestMethod.GET)
-		//auditService.trackIdentity(AuditableAction.IdentityTracking_Action);
+    @OperationWithTenantHeader(summary = "Fetch auth information of the logged in user", description = "",
+            responses = @ApiResponse(description = "OK", responseCode = "200", content = @Content(
+                    schema = @Schema(
+                            implementation = Account.class
+                    ))
+            ))
+    public Account me(
+            @Parameter(name = "fieldSet", description = SwaggerHelpers.Commons.fieldset_description, required = true) FieldSet fieldSet
+    ) throws InvalidApplicationException {
+        logger.debug("me");
 
-		return me;
+        if (fieldSet == null || fieldSet.isEmpty()) {
-	}
+            fieldSet = new BaseFieldSet(
+                    Account._isAuthenticated,
+                    BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._subject),
+                    BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._userId),
+                    BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._name),
+                    BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._scope),
+                    BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._client),
+                    BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._issuedAt),
+                    BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._notBefore),
+                    BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._authenticatedAt),
+                    BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._expiresAt),
+                    BaseFieldSet.asIndexer(Account._principal, Account.PrincipalInfo._more),
+                    BaseFieldSet.asIndexer(Account._profile, Account.UserProfileInfo._avatarUrl),
+                    BaseFieldSet.asIndexer(Account._profile, Account.UserProfileInfo._language),
+                    BaseFieldSet.asIndexer(Account._profile, Account.UserProfileInfo._culture),
+                    BaseFieldSet.asIndexer(Account._profile, Account.UserProfileInfo._timezone),
+                    Account._permissions,
+                    BaseFieldSet.asIndexer(Account._selectedTenant, Tenant._id),
+                    BaseFieldSet.asIndexer(Account._selectedTenant, Tenant._name),
+                    BaseFieldSet.asIndexer(Account._selectedTenant, Tenant._code));
+        }
 
-	@GetMapping("my-tenants")
+        MyPrincipal principal = this.currentPrincipalResolver.currentPrincipal();
-	@OperationWithTenantHeader(summary = "Fetch a list with the tenants the user belongs to", description = "",
-			responses = @ApiResponse(description = "OK", responseCode = "200"))
-	public List<Tenant> myTenants(
-			@Parameter(name = "fieldSet", description = SwaggerHelpers.Commons.fieldset_description, required = true) FieldSet fieldSet
-	) {
-		logger.debug("my-tenants");
 
-		List<Tenant> models = this.tenantService.myTenants(fieldSet);
+        Account me = this.accountBuilder.build(fieldSet, principal);
 
-		this.auditService.track(AuditableAction.Principal_MyTenants);
+        this.auditService.track(AuditableAction.Principal_Lookup);
-		//auditService.trackIdentity(AuditableAction.IdentityTracking_Action);
+        //auditService.trackIdentity(AuditableAction.IdentityTracking_Action);
-		
+
-		return models;
+        return me;
-	}
+    }
+
+    @GetMapping("my-tenants")
+    @OperationWithTenantHeader(summary = "Fetch a list with the tenants the user belongs to", description = "",
+            responses = @ApiResponse(description = "OK", responseCode = "200"))
+    public List<Tenant> myTenants(
+            @Parameter(name = "fieldSet", description = SwaggerHelpers.Commons.fieldset_description, required = true) FieldSet fieldSet
+    ) {
+        logger.debug("my-tenants");
+
+        List<Tenant> models = this.tenantService.myTenants(fieldSet);
+
+        this.auditService.track(AuditableAction.Principal_MyTenants);
+        //auditService.trackIdentity(AuditableAction.IdentityTracking_Action);
+
+        return models;
+    }
 
 }

backend/web/src/main/java/org/opencdmp/controllers/ReferenceController.java

@@ -12,7 +12,6 @@ import gr.cite.tools.fieldset.FieldSet;
 import gr.cite.tools.logging.LoggerService;
 import gr.cite.tools.logging.MapLogEntry;
 import gr.cite.tools.validation.ValidationFilterAnnotation;
-import io.swagger.v3.oas.annotations.Hidden;
 import io.swagger.v3.oas.annotations.Parameter;
 import io.swagger.v3.oas.annotations.media.ArraySchema;
 import io.swagger.v3.oas.annotations.media.Content;
@@ -33,7 +32,6 @@ import org.opencdmp.data.ReferenceEntity;
 import org.opencdmp.model.builder.reference.ReferenceBuilder;
 import org.opencdmp.model.censorship.reference.ReferenceCensor;
 import org.opencdmp.model.persist.ReferencePersist;
-import org.opencdmp.model.planblueprint.PlanBlueprint;
 import org.opencdmp.model.reference.Reference;
 import org.opencdmp.model.result.QueryResult;
 import org.opencdmp.query.ReferenceQuery;
@@ -74,7 +72,6 @@ public class ReferenceController {
 
     private final MessageSource messageSource;
 
-
     @Autowired
     public ReferenceController(
             BuilderFactory builderFactory,
@@ -126,10 +123,27 @@ public class ReferenceController {
         return new QueryResult<>(models, count);
     }
 
-
     @PostMapping("search")
-    @Hidden
+    @OperationWithTenantHeader(summary = "Query all references including results from external APIs", description = SwaggerHelpers.Reference.endpoint_search, requestBody = @io.swagger.v3.oas.annotations.parameters.RequestBody(description = SwaggerHelpers.Reference.endpoint_search_request_body, content = @Content(
-    //TODO thgiannos add swagger docs
+            examples = {
+                    @ExampleObject(
+                            name = "Pagination and projection",
+                            description = "Simple paginated request using a property projection list and pagination info",
+                            value = SwaggerHelpers.Reference.endpoint_search_request_body_example
+                    )
+            }
+    )), responses = @ApiResponse(description = "OK", responseCode = "200", content = @Content(
+            array = @ArraySchema(
+                    schema = @Schema(
+                            implementation = Reference.class
+                    )
+            ),
+            examples = @ExampleObject(
+                    name = "First page",
+                    description = "Example with the first page of paginated results",
+                    value = SwaggerHelpers.Reference.endpoint_search_response_example
+            ))))
+    @Swagger404
     public List<Reference> searchReferenceWithDefinition(@RequestBody ReferenceSearchLookup lookup) throws MyNotFoundException, InvalidApplicationException {
         logger.debug("search with db definition {}", Reference.class.getSimpleName());
 
@@ -138,7 +152,7 @@ public class ReferenceController {
         List<Reference> references = this.referenceService.searchReferenceData(lookup);
 
         this.auditService.track(AuditableAction.Reference_Search, "lookup", lookup);
-        
+
         return references;
     }
 

backend/web/src/main/java/org/opencdmp/controllers/UserController.java

@@ -12,7 +12,6 @@ import gr.cite.tools.fieldset.FieldSet;
 import gr.cite.tools.logging.LoggerService;
 import gr.cite.tools.logging.MapLogEntry;
 import gr.cite.tools.validation.ValidationFilterAnnotation;
-import io.swagger.v3.oas.annotations.Hidden;
 import io.swagger.v3.oas.annotations.Parameter;
 import io.swagger.v3.oas.annotations.media.ArraySchema;
 import io.swagger.v3.oas.annotations.media.Content;
@@ -37,9 +36,11 @@ import org.opencdmp.model.builder.PlanAssociatedUserBuilder;
 import org.opencdmp.model.builder.UserBuilder;
 import org.opencdmp.model.censorship.PlanAssociatedUserCensor;
 import org.opencdmp.model.censorship.UserCensor;
-import org.opencdmp.model.persist.*;
+import org.opencdmp.model.persist.UserMergeRequestPersist;
+import org.opencdmp.model.persist.UserPersist;
+import org.opencdmp.model.persist.UserRolePatchPersist;
+import org.opencdmp.model.persist.UserTenantUsersInviteRequest;
 import org.opencdmp.model.persist.actionconfirmation.RemoveCredentialRequestPersist;
-import org.opencdmp.model.plan.Plan;
 import org.opencdmp.model.result.QueryResult;
 import org.opencdmp.model.user.User;
 import org.opencdmp.query.UserQuery;
@@ -143,7 +144,25 @@ public class UserController {
     }
 
     @PostMapping("plan-associated/query")
-    @Hidden
+    @OperationWithTenantHeader(summary = "Query all plan associated users", description = SwaggerHelpers.User.endpoint_query_plan_associated, requestBody = @io.swagger.v3.oas.annotations.parameters.RequestBody(description = SwaggerHelpers.User.endpoint_query_request_body, content = @Content(
+            examples = {
+                    @ExampleObject(
+                            name = "Pagination and projection",
+                            description = "Simple paginated request using a property projection list and pagination info",
+                            value = SwaggerHelpers.User.endpoint_query_plan_associated_request_body_example
+                    )
+            }
+    )), responses = @ApiResponse(description = "OK", responseCode = "200", content = @Content(
+            array = @ArraySchema(
+                    schema = @Schema(
+                            implementation = PlanAssociatedUser.class
+                    )
+            ),
+            examples = @ExampleObject(
+                    name = "First page",
+                    description = "Example with the first page of paginated results",
+                    value = SwaggerHelpers.User.endpoint_query_plan_associated_response_example
+            ))))
     public QueryResult<PlanAssociatedUser> queryPlanAssociated(@RequestBody UserLookup lookup) throws MyApplicationException, MyForbiddenException {
         logger.debug("querying {}", User.class.getSimpleName());
 
@@ -219,8 +238,11 @@ public class UserController {
     }
 
     @GetMapping("/export/csv/{hasTenantAdminMode}")
-    @Hidden
+    @OperationWithTenantHeader(summary = "Export users in a .csv file", description = "",
-    public ResponseEntity<byte[]> exportCsv(@PathVariable("hasTenantAdminMode") Boolean hasTenantAdminMode) throws MyApplicationException, MyForbiddenException, MyNotFoundException, IOException, InvalidApplicationException {
+            responses = @ApiResponse(description = "OK", responseCode = "200"))
+    public ResponseEntity<byte[]> exportCsv(
+            @Parameter(name = "hasTenantAdminMode", description = "Controls whether to fetch users as a tenant admin or not", example = "false", required = true) @PathVariable("hasTenantAdminMode") Boolean hasTenantAdminMode
+    ) throws MyApplicationException, MyForbiddenException, MyNotFoundException, IOException, InvalidApplicationException {
         logger.debug(new MapLogEntry("export" + User.class.getSimpleName()).And("hasTenantAdminMode", hasTenantAdminMode));
 
 //        this.censorFactory.censor(UserCensor.class).censor(fieldSet, null);

backend/web/src/main/java/org/opencdmp/controllers/swagger/SwaggerHelpers.java

@@ -3346,6 +3346,190 @@ public final class SwaggerHelpers {
                         }
                         """;
 
+        public static final String endpoint_search =
+                """
+                        This endpoint is used to fetch all the available references.<br/>
+                        It also allows to restrict the results using a query object passed in the request body.<br/>
+                        """;
+
+        public static final String endpoint_search_request_body =
+                """
+                        Let's explore the options this object gives us.
+                        
+                        ### <u>General query parameters:</u>
+                        
+                        <ul>
+                            <li><b>page:</b>
+                            This is an object controlling the pagination of the results. It contains two properties.
+                            </li>
+                            <ul>
+                                <li><b>offset:</b>
+                                How many records to omit.
+                                </li>
+                                <li><b>size:</b>
+                                How many records to include in each page.
+                                </li>
+                            </ul>
+                        </ul>
+                        
+                        For example, if we want the third page, and our pages to contain 15 elements, we would pass the following object:
+                        
+                        ```JSON
+                        {
+                            "offset": 30,
+                            "size": 15
+                        }
+                        ```
+                        
+                        <ul>
+                            <li><b>order:</b>
+                            This is an object controlling the ordering of the results.
+                            It contains a list of strings called <i>items</i> with the names of the properties to use.
+                            <br/>If the name of the property is prefixed with a <b>'-'</b>, the ordering direction is <b>DESC</b>. Otherwise, it is <b>ASC</b>.
+                            </li>
+                        </ul>
+                        
+                        For example, if we wanted to order based on the field 'createdAt' in descending order, we would pass the following object:
+                        
+                        ```JSON
+                        {
+                            "items": [
+                                "-createdAt"
+                            ],
+                        }
+                        ```
+                        
+                        <ul>
+                            <li><b>metadata:</b>
+                            This is an object containing metadata for the request. There is only one available option.
+                            <ul>
+                                <li><b>countAll:</b>
+                                If this is set to true, the count property included in the response will account for all the records regardless the pagination,
+                                with all the rest of filtering options applied of course.
+                                Otherwise, if it is set to false or not present, only the returned results will be counted.
+                                <br/>The first option is useful for the UI clients to calculate how many result pages are available.
+                                </li>
+                            </ul>
+                            </li>
+                            <li><b>project:</b>
+                            This is an object controlling the data projection of the results.
+                            It contains a list of strings called <i>fields</i> with the names of the properties to project.
+                            <br/>You can also include properties that are deeper in the object tree by prefixing them with dots.
+                            </li>
+                        </ul>
+                        
+                        ### <u>Reference specific query parameters:</u>
+                        
+                        <ul>
+                            <li><b>like:</b>
+                            If there is a like parameter present in the query, only the reference entities that include the contents of the parameter either in their labels, descriptions or the references will be in the response.
+                            </li>
+                            <li><b>typeId:</b>
+                            This is the type id of the references we want in the response. <br/>If empty, every record is included.
+                            </li>
+                            <li><b>key:</b>
+                            This is the id of the external source (API) we want results from.
+                            <br/>If not present, no external reference is included.
+                            </li>
+                            <li><b>dependencyReferences:</b>
+                            This is a list and determines which records we want to include in the response, based on the references they depend on.
+                            <br/>If not present, every record is included.
+                            </li>
+                        </ul>
+                        """;
+
+        public static final String endpoint_search_request_body_example =
+                """
+                        {
+                           "project":{
+                              "fields":[
+                                 "id",
+                                 "hash",
+                                 "label",
+                                 "type",
+                                 "type.id",
+                                 "description",
+                                 "definition.fields.code",
+                                 "definition.fields.dataType",
+                                 "definition.fields.value",
+                                 "reference",
+                                 "abbreviation",
+                                 "source",
+                                 "sourceType"
+                              ]
+                           },
+                           "page":{
+                              "size":100,
+                              "offset":0
+                           },
+                           "typeId":"5b9c284f-f041-4995-96cc-fad7ad13289c",
+                           "dependencyReferences":[
+                             \s
+                           ],
+                           "order":{
+                              "items":[
+                                 "label"
+                              ]
+                           }
+                        }
+                        """;
+
+        public static final String endpoint_search_response_example =
+                """
+                        [
+                             {
+                                 "label": "A Randomized, Double-Blind, Placebo-Controlled, Multi-Center Study to Evaluate the Efficacy of ManNAc in Subjects with GNE Myopathy (nih_________::5U01AR070498-04)",
+                                 "type": {
+                                     "id": "5b9c284f-f041-4995-96cc-fad7ad13289c"
+                                 },
+                                 "description": "A Randomized, Double-Blind, Placebo-Controlled, Multi-Center Study to Evaluate the Efficacy of ManNAc in Subjects with GNE Myopathy",
+                                 "definition": {
+                                     "fields": [
+                                         {
+                                             "code": "referenceType",
+                                             "dataType": 0,
+                                             "value": "Grants"
+                                         },
+                                         {
+                                             "code": "key",
+                                             "dataType": 0,
+                                             "value": "openaire"
+                                         }
+                                     ]
+                                 },
+                                 "reference": "nih_________::5U01AR070498-04",
+                                 "source": "openaire",
+                                 "sourceType": 1,
+                                 "hash": ""
+                             },
+                             {
+                                 "label": "A genome scale census of virulence factors in the major mould pathogen of human lungs, Aspergillus fumigatus (ukri________::1640253)",
+                                 "type": {
+                                     "id": "5b9c284f-f041-4995-96cc-fad7ad13289c"
+                                 },
+                                 "description": "A genome scale census of virulence factors in the major mould pathogen of human lungs, Aspergillus fumigatus",
+                                 "definition": {
+                                     "fields": [
+                                         {
+                                             "code": "referenceType",
+                                             "dataType": 0,
+                                             "value": "Grants"
+                                         },
+                                         {
+                                             "code": "key",
+                                             "dataType": 0,
+                                             "value": "openaire"
+                                         }
+                                     ]
+                                 },
+                                 "reference": "ukri________::1640253",
+                                 "source": "openaire",
+                                 "sourceType": 1,
+                                 "hash": ""
+                             }
+                        ]
+                        """;
+
     }
 
     public static final class ReferenceType {
@@ -3779,6 +3963,12 @@ public final class SwaggerHelpers {
                         It also allows to restrict the results using a query object passed in the request body.<br/>
                         """;
 
+        public static final String endpoint_query_plan_associated =
+                """
+                        This endpoint is used to fetch all the available users.<br/>
+                        It also allows to restrict the results using a query object passed in the request body.<br/>
+                        """;
+
         public static final String endpoint_query_request_body =
                 """
                         Let's explore the options this object gives us.
@@ -3908,6 +4098,32 @@ public final class SwaggerHelpers {
                              }
                         """;
 
+        public static final String endpoint_query_plan_associated_request_body_example =
+                """
+                        {
+                           "project":{
+                              "fields":[
+                                 "id",
+                                 "name",
+                                 "email"
+                              ]
+                           },
+                           "page":{
+                              "size":100,
+                              "offset":0
+                           },
+                           "isActive":[
+                              1
+                           ],
+                           "order":{
+                              "items":[
+                                 "name"
+                              ]
+                           },
+                           "like":"user%"
+                        }
+                        """;
+
         public static final String endpoint_query_response_example =
                 """
                         {
@@ -4241,6 +4457,25 @@ public final class SwaggerHelpers {
                         }
                         """;
 
+        public static final String endpoint_query_plan_associated_response_example =
+                """
+                        {
+                           "items":[
+                              {
+                                 "id":"d26916c6-8763-450e-9048-b06e1114d0b4",
+                                 "name":"user3 user3",
+                                 "email":"user3@dmp.gr"
+                              },
+                              {
+                                 "id":"02832fb6-0b12-469f-a886-7685406959d4",
+                                 "name":"user4",
+                                 "email":"user4@dmp.gr"
+                              }
+                           ],
+                           "count":2
+                        }
+                        """;
+
     }
 
     public static final class Principal {