Changes related to error status 400 and updates to deletion of visa

pom.xml

@@ -93,7 +93,16 @@
             <artifactId>spring-boot-starter-test</artifactId>
             <scope>test</scope>
         </dependency>
-
+        <dependency>
+            <groupId>com.auth0</groupId>
+            <artifactId>java-jwt</artifactId>
+            <version>4.4.0</version>
+        </dependency>
+        <dependency>
+            <groupId>com.auth0</groupId>
+            <artifactId>jwks-rsa</artifactId>
+            <version>0.22.0</version>
+        </dependency>
         <dependency>
             <groupId>org.springframework.security</groupId>
             <artifactId>spring-security-test</artifactId>

src/main/java/bio/overture/ego/controller/VisaController.java

@@ -1,11 +1,17 @@
 package bio.overture.ego.controller;
 
+import static java.lang.String.format;
 import static org.springframework.web.bind.annotation.RequestMethod.*;
 
-import bio.overture.ego.model.dto.*;
-import bio.overture.ego.model.entity.*;
+import bio.overture.ego.model.dto.PageDTO;
+import bio.overture.ego.model.dto.VisaPermissionRequest;
+import bio.overture.ego.model.dto.VisaRequest;
+import bio.overture.ego.model.entity.Visa;
+import bio.overture.ego.model.entity.VisaPermission;
+import bio.overture.ego.model.exceptions.NotFoundException;
 import bio.overture.ego.security.AdminScoped;
-import bio.overture.ego.service.*;
+import bio.overture.ego.service.VisaPermissionService;
+import bio.overture.ego.service.VisaService;
 import bio.overture.ego.view.Views;
 import com.fasterxml.jackson.annotation.JsonView;
 import io.swagger.v3.oas.annotations.Parameter;
@@ -33,22 +39,11 @@ public class VisaController {
 
   private final VisaPermissionService visaPermissionService;
 
-  private final UserPermissionService userPermissionService;
-  private final GroupPermissionService groupPermissionService;
-  private final ApplicationPermissionService applicationPermissionService;
-
   @Autowired
   public VisaController(
-      @NonNull VisaService visaService,
-      @NotNull VisaPermissionService visaPermissionService,
-      @NonNull UserPermissionService userPermissionService,
-      @NonNull GroupPermissionService groupPermissionService,
-      @NonNull ApplicationPermissionService applicationPermissionService) {
+      @NonNull VisaService visaService, @NotNull VisaPermissionService visaPermissionService) {
     this.visaService = visaService;
     this.visaPermissionService = visaPermissionService;
-    this.groupPermissionService = groupPermissionService;
-    this.userPermissionService = userPermissionService;
-    this.applicationPermissionService = applicationPermissionService;
   }
 
   /*
@@ -67,7 +62,13 @@ public VisaController(
           final String authorization,
       @PathVariable(value = "type", required = true) String type,
       @PathVariable(value = "value", required = true) String value) {
-    return visaService.getByTypeAndValue(type, value);
+    List<Visa> visas = visaService.getByTypeAndValue(type, value);
+    if (visas != null && !visas.isEmpty()) {
+      return visas;
+    } else {
+      throw new NotFoundException(
+          format("No Visa exists with type '%s' and value '%s'", type, value));
+    }
   }
 
   /*
@@ -110,28 +111,28 @@ public VisaController(
    * @return Visa visa
    */
   @AdminScoped
-  @RequestMapping(method = PUT, value = "/{id}")
+  @RequestMapping(method = PUT, value = "/{type}/{value}")
   @ApiResponses(value = {@ApiResponse(responseCode = "200", description = "Update Visa")})
-  public @ResponseBody Visa updateVisa(
+  public @ResponseBody List<Visa> updateVisa(
       @Parameter(hidden = true) @RequestHeader(value = "Authorization", required = true)
           final String authorization,
-      @PathVariable(value = "id", required = true) UUID id,
       @RequestBody(required = true) VisaRequest visaRequest) {
-    return visaService.partialUpdate(id, visaRequest);
+    return visaService.partialUpdate(visaRequest);
   }
 
   /*
    * This method is used to delete visa using visa id
    * @param visaId UUID
    */
   @AdminScoped
-  @RequestMapping(method = DELETE, value = "/{id}")
+  @RequestMapping(method = DELETE, value = "/{type}/{value}")
   @ResponseStatus(value = HttpStatus.OK)
   public void deleteVisa(
       @Parameter(hidden = true) @RequestHeader(value = "Authorization", required = true)
           final String authorization,
-      @PathVariable(value = "id", required = true) UUID id) {
-    visaService.delete(id);
+      @PathVariable(value = "type", required = true) String type,
+      @PathVariable(value = "value", required = true) String value) {
+    visaService.delete(type, value);
   }
 
   /*
@@ -192,7 +193,7 @@ public void deleteVisa(
    * @param visaPermissionRequest VisaPermissionRequest
    */
   @AdminScoped
-  @RequestMapping(method = DELETE, value = "/permissions/{policyId}/{visaId}")
+  @RequestMapping(method = DELETE, value = "/permissions/{policyId}/{type}/{value}")
   @ApiResponses(value = {@ApiResponse(responseCode = "200", description = "Remove VisaPermission")})
   @JsonView(Views.REST.class)
   public @ResponseBody void removePermissions(

src/main/java/bio/overture/ego/model/exceptions/ExceptionHandlers.java

@@ -1,8 +1,7 @@
 package bio.overture.ego.model.exceptions;
 
 import static java.lang.String.format;
-import static org.springframework.http.HttpStatus.BAD_REQUEST;
-import static org.springframework.http.HttpStatus.NOT_FOUND;
+import static org.springframework.http.HttpStatus.*;
 
 import bio.overture.ego.utils.Joiners;
 import jakarta.servlet.http.HttpServletRequest;
@@ -13,6 +12,7 @@
 import lombok.val;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.MissingRequestHeaderException;
 import org.springframework.web.bind.annotation.ControllerAdvice;
 import org.springframework.web.bind.annotation.ExceptionHandler;
 
@@ -35,6 +35,21 @@ public ResponseEntity<Object> handleConstraintViolationException(
         NOT_FOUND);
   }
 
+  @ExceptionHandler(MissingRequestHeaderException.class)
+  public ResponseEntity<Object> handleMissingRequestHeaderException(
+      HttpServletRequest req, MissingRequestHeaderException ex) {
+    val message = ex.getMessage();
+    log.error(message);
+    return new ResponseEntity<Object>(
+        Map.of(
+            "message", ex.getMessage(),
+            "timestamp", new Date(),
+            "path", req.getServletPath(),
+            "error", UNAUTHORIZED.getReasonPhrase()),
+        new HttpHeaders(),
+        UNAUTHORIZED);
+  }
+
   @ExceptionHandler(ConstraintViolationException.class)
   public ResponseEntity<Object> handleConstraintViolationException(
       HttpServletRequest req, ConstraintViolationException ex) {

src/main/java/bio/overture/ego/service/PassportService.java

@@ -4,12 +4,16 @@
 import bio.overture.ego.model.dto.PassportVisa;
 import bio.overture.ego.model.entity.Visa;
 import bio.overture.ego.model.entity.VisaPermission;
-import bio.overture.ego.model.exceptions.InvalidTokenException;
 import bio.overture.ego.utils.CacheUtil;
+import com.auth0.jwk.Jwk;
+import com.auth0.jwk.JwkException;
+import com.auth0.jwt.JWT;
+import com.auth0.jwt.algorithms.Algorithm;
+import com.auth0.jwt.interfaces.DecodedJWT;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import io.jsonwebtoken.Claims;
-import io.jsonwebtoken.Jwts;
+import java.security.interfaces.RSAPublicKey;
+import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -41,11 +45,10 @@ public PassportService(
     this.visaPermissionService = visaPermissionService;
   }
 
-  public List<VisaPermission> getPermissions(String authToken) throws JsonProcessingException {
+  public List<VisaPermission> getPermissions(String authToken)
+      throws JsonProcessingException, ParseException, JwkException {
     // Validates passport auth token
-    if (!isValidPassport(authToken)) {
-      throw new InvalidTokenException("The passport token received from broker is invalid");
-    }
+    isValidPassport(authToken);
     // Parses passport JWT token
     Passport parsedPassport = parsePassport(authToken);
     // Fetches visas for parsed passport
@@ -58,21 +61,12 @@ public List<VisaPermission> getPermissions(String authToken) throws JsonProcessi
   }
 
   // Validates passport token based on public key
-  private boolean isValidPassport(@NonNull String authToken) {
-    Claims claims;
-    try {
-      claims =
-          Jwts.parser()
-              .setSigningKey(cacheUtil.getPassportBrokerPublicKey())
-              .parseClaimsJws(authToken)
-              .getBody();
-      if (claims != null) {
-        return true;
-      }
-    } catch (Exception exception) {
-      throw new InvalidTokenException("The passport token received from broker is invalid");
-    }
-    return false;
+  private void isValidPassport(@NonNull String authToken)
+      throws ParseException, JwkException, JsonProcessingException {
+    DecodedJWT jwt = JWT.decode(authToken);
+    Jwk jwk = cacheUtil.getPassportBrokerPublicKey().get(jwt.getKeyId());
+    Algorithm algorithm = Algorithm.RSA256((RSAPublicKey) jwk.getPublicKey(), null);
+    algorithm.verify(jwt);
   }
 
   // Extracts Visas from parsed passport object
@@ -82,13 +76,12 @@ private List<PassportVisa> getVisas(Passport passport) {
         .forEach(
             visaJwt -> {
               try {
-                if (visaService.isValidVisa(visaJwt)) {
-                  PassportVisa visa = visaService.parseVisa(visaJwt);
-                  if (visa != null) {
-                    visas.add(visa);
-                  }
+                visaService.isValidVisa(visaJwt);
+                PassportVisa visa = visaService.parseVisa(visaJwt);
+                if (visa != null) {
+                  visas.add(visa);
                 }
-              } catch (JsonProcessingException e) {
+              } catch (JsonProcessingException | JwkException e) {
                 e.printStackTrace();
               }
             });
@@ -105,7 +98,9 @@ private List<VisaPermission> getVisaPermissions(List<PassportVisa> visas) {
               List<Visa> visaEntities =
                   visaService.getByTypeAndValue(
                       visa.getGa4ghVisaV1().getType(), visa.getGa4ghVisaV1().getValue());
-              visaPermissions.addAll(visaPermissionService.getPermissionsForVisa(visaEntities));
+              if (visaEntities != null && !visaEntities.isEmpty()) {
+                visaPermissions.addAll(visaPermissionService.getPermissionsForVisa(visaEntities));
+              }
             });
     return visaPermissions;
   }

src/main/java/bio/overture/ego/service/VisaService.java

@@ -9,15 +9,19 @@
 import bio.overture.ego.model.dto.PassportVisa;
 import bio.overture.ego.model.dto.VisaRequest;
 import bio.overture.ego.model.entity.Visa;
-import bio.overture.ego.model.exceptions.InvalidTokenException;
 import bio.overture.ego.model.exceptions.NotFoundException;
 import bio.overture.ego.repository.VisaRepository;
 import bio.overture.ego.utils.CacheUtil;
+import com.auth0.jwk.Jwk;
+import com.auth0.jwk.JwkException;
+import com.auth0.jwt.JWT;
+import com.auth0.jwt.algorithms.Algorithm;
+import com.auth0.jwt.interfaces.DecodedJWT;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import io.jsonwebtoken.Claims;
-import io.jsonwebtoken.Jwts;
 import jakarta.validation.constraints.NotNull;
+import java.security.interfaces.RSAPublicKey;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 import java.util.UUID;
@@ -75,17 +79,20 @@ public List<Visa> getByTypeAndValue(@NonNull String type, @NotNull String value)
     val result = visaRepository.getByTypeAndValue(type, value);
     if (!result.isEmpty()) {
       return result;
+    }
+    return null;
+  }
+
+  public void delete(@NonNull String type, @NotNull String value) {
+    List<Visa> visas = getByTypeAndValue(type, value);
+    if (visas != null && !visas.isEmpty()) {
+      visas.stream().forEach(visa -> visaRepository.delete(visa));
     } else {
       throw new NotFoundException(
           format("No Visa exists with type '%s' and value '%s'", type, value));
     }
   }
 
-  public void delete(@NonNull UUID id) {
-    checkExistence(id);
-    super.delete(id);
-  }
-
   // Parses Visa JWT token to convert into Visa Object
   public PassportVisa parseVisa(@NonNull String visaJwtToken) throws JsonProcessingException {
     String[] split_string = visaJwtToken.split("\\.");
@@ -99,31 +106,33 @@ public PassportVisa parseVisa(@NonNull String visaJwtToken) throws JsonProcessin
   }
 
   // Checks if the visa is a valid visa
-  public boolean isValidVisa(@NonNull String authToken) {
-    Claims claims;
-    try {
-      claims =
-          Jwts.parser()
-              .setSigningKey(cacheUtil.getPassportBrokerPublicKey())
-              .parseClaimsJws(authToken)
-              .getBody();
-      if (claims != null) {
-        return true;
-      }
-    } catch (Exception exception) {
-      throw new InvalidTokenException("The visa token received from broker is invalid");
-    }
-    return false;
+  public void isValidVisa(@NonNull String authToken) throws JwkException, JsonProcessingException {
+    DecodedJWT jwt = JWT.decode(authToken);
+    Jwk jwk = cacheUtil.getPassportBrokerPublicKey().get(jwt.getKeyId());
+    Algorithm algorithm = Algorithm.RSA256((RSAPublicKey) jwk.getPublicKey(), null);
+    algorithm.verify(jwt);
   }
 
   public Page<Visa> listVisa(@NonNull Pageable pageable) {
     return visaRepository.findAll(pageable);
   }
 
-  public Visa partialUpdate(@NotNull UUID id, @NonNull VisaRequest updateRequest) {
-    val visa = getById(id);
-    VISA_CONVERTER.updateVisa(updateRequest, visa);
-    return getRepository().save(visa);
+  public List<Visa> partialUpdate(@NonNull VisaRequest updateRequest) {
+    List<Visa> updatedVisas = new ArrayList<>();
+    List<Visa> visas = getByTypeAndValue(updateRequest.getType(), updateRequest.getValue());
+    if (visas != null && !visas.isEmpty()) {
+      for (Visa visa : visas) {
+        visa.setBy(updateRequest.getBy());
+        visa.setSource(updateRequest.getSource());
+        updatedVisas.add(getRepository().save(visa));
+      }
+    } else {
+      throw new NotFoundException(
+          format(
+              "No Visa exists with type '%s' and value '%s'",
+              updateRequest.getType(), updateRequest.getValue()));
+    }
+    return updatedVisas;
   }
 
   @Mapper(