moved from no.uio.ifi to no.elixir.fega and updated version to 2.0.0

pom.xml

@@ -8,9 +8,9 @@
         <version>3.1.3</version>
         <relativePath/> <!-- lookup parent from repository -->
     </parent>
-    <groupId>no.uio.ifi</groupId>
+    <groupId>no.elixir.fega</groupId>
     <artifactId>localega-tsd-proxy</artifactId>
-    <version>1.1.7</version>
+    <version>2.0.0</version>
     <name>localega-tsd-proxy</name>
     <description>LocalEGA TSD Proxy</description>
 

src/main/java/no/uio/ifi/ltp/LocalEGATSDProxyApplication.java → src/main/java/no/elixir/fega/ltp/LocalEGATSDProxyApplication.java

@@ -1,4 +1,4 @@
-package no.uio.ifi.ltp;
+package no.elixir.fega.ltp;
 
 import lombok.extern.slf4j.Slf4j;
 import no.uio.ifi.tc.TSDFileAPIClient;

src/main/java/no/uio/ifi/ltp/aspects/AAIAspect.java → src/main/java/no/elixir/fega/ltp/aspects/AAIAspect.java

@@ -1,13 +1,13 @@
-package no.uio.ifi.ltp.aspects;
+package no.elixir.fega.ltp.aspects;
 
 import com.auth0.jwt.JWT;
 import com.auth0.jwt.interfaces.DecodedJWT;
 import lombok.extern.slf4j.Slf4j;
+import no.elixir.fega.ltp.authentication.CEGACredentialsProvider;
 import no.uio.ifi.clearinghouse.Clearinghouse;
 import no.uio.ifi.clearinghouse.model.Visa;
 import no.uio.ifi.clearinghouse.model.VisaType;
-import no.uio.ifi.ltp.authentication.CEGACredentialsProvider;
-import no.uio.ifi.ltp.dto.Credentials;
+import no.elixir.fega.ltp.dto.Credentials;
 import org.apache.commons.codec.digest.Crypt;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.http.auth.AuthenticationException;
@@ -34,9 +34,6 @@
 import java.util.*;
 import java.util.stream.Collectors;
 
-import static no.uio.ifi.ltp.aspects.ProcessArgumentsAspect.EGA_USERNAME;
-import static no.uio.ifi.ltp.aspects.ProcessArgumentsAspect.ELIXIR_ID;
-
 /**
  * AOP aspect that handles authentication and authorization.
  */
@@ -68,7 +65,7 @@ public class AAIAspect {
      * @return Either the object, returned by the proxied method, or HTTP error response.
      * @throws Throwable In case of error.
      */
-    @Around("execution(public * no.uio.ifi.ltp.controllers.rest.ProxyController.*(..))")
+    @Around("execution(public * no.elixir.fega.ltp.controllers.rest.ProxyController.*(..))")
     public Object authenticateElixirAAI(ProceedingJoinPoint joinPoint) throws Throwable {
         Optional<String> optionalBearerAuth = getBearerAuth();
         if (optionalBearerAuth.isEmpty()) {
@@ -80,7 +77,7 @@ public Object authenticateElixirAAI(ProceedingJoinPoint joinPoint) throws Throwa
             DecodedJWT decodedJWT = JWT.decode(jwtToken);
             List<Visa> controlledAccessGrantsVisas = getVisas(jwtToken, decodedJWT);
             log.info("Elixir user {} authenticated and provided following valid GA4GH Visas: {}", decodedJWT.getSubject(), controlledAccessGrantsVisas);
-            request.setAttribute(ELIXIR_ID, decodedJWT.getSubject());
+            request.setAttribute(ProcessArgumentsAspect.ELIXIR_ID, decodedJWT.getSubject());
             return joinPoint.proceed();
         } catch (Exception e) {
             log.info(e.getMessage(), e);
@@ -95,8 +92,8 @@ public Object authenticateElixirAAI(ProceedingJoinPoint joinPoint) throws Throwa
      * @return Either the object, returned by the proxied method, or HTTP error response.
      * @throws Throwable In case of error.
      */
-    @Around("execution(public * no.uio.ifi.ltp.controllers.rest.ProxyController.*(..)) && " +
-            "!execution(public * no.uio.ifi.ltp.controllers.rest.ProxyController.stream(jakarta.servlet.http.HttpServletResponse, String, String))") // we don't need CEGA auth for Data Out endpoints
+    @Around("execution(public * no.elixir.fega.ltp.controllers.rest.ProxyController.*(..)) && " +
+            "!execution(public * no.elixir.fega.ltp.controllers.rest.ProxyController.stream(jakarta.servlet.http.HttpServletResponse, String, String))") // we don't need CEGA auth for Data Out endpoints
     public Object authenticateCEGA(ProceedingJoinPoint joinPoint) throws Throwable {
         if (((MethodSignature) joinPoint.getSignature()).getMethod().getName().equalsIgnoreCase("getFiles")) {
             if (Boolean.FALSE.equals(joinPoint.getArgs()[1])) {
@@ -114,7 +111,7 @@ public Object authenticateCEGA(ProceedingJoinPoint joinPoint) throws Throwable {
                 throw new AuthenticationException("EGA authentication failed");
             }
             log.info("EGA user {} authenticated", usernameAndPassword[0]);
-            request.setAttribute(EGA_USERNAME, usernameAndPassword[0]);
+            request.setAttribute(ProcessArgumentsAspect.EGA_USERNAME, usernameAndPassword[0]);
             return joinPoint.proceed();
         } catch (Exception e) {
             log.info(e.getMessage(), e);

src/main/java/no/uio/ifi/ltp/aspects/CredentialsMappingAspect.java → src/main/java/no/elixir/fega/ltp/aspects/CredentialsMappingAspect.java

@@ -1,4 +1,4 @@
-package no.uio.ifi.ltp.aspects;
+package no.elixir.fega.ltp.aspects;
 
 import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.collections4.CollectionUtils;
@@ -12,8 +12,8 @@
 import jakarta.servlet.http.HttpServletRequest;
 import java.util.List;
 
-import static no.uio.ifi.ltp.aspects.ProcessArgumentsAspect.EGA_USERNAME;
-import static no.uio.ifi.ltp.aspects.ProcessArgumentsAspect.ELIXIR_ID;
+import static no.elixir.fega.ltp.aspects.ProcessArgumentsAspect.EGA_USERNAME;
+import static no.elixir.fega.ltp.aspects.ProcessArgumentsAspect.ELIXIR_ID;
 
 /**
  * AOP aspect that maps EGA username with Elixir ID.
@@ -35,7 +35,7 @@ public class CredentialsMappingAspect {
      *
      * @param result Object returned by the proxied method.
      */
-    @AfterReturning(pointcut = "execution(public * no.uio.ifi.ltp.controllers.rest.ProxyController.stream(..))", returning = "result")
+    @AfterReturning(pointcut = "execution(public * no.elixir.fega.ltp.controllers.rest.ProxyController.stream(..))", returning = "result")
     public void publishMessage(Object result) {
         String egaUsername = request.getAttribute(EGA_USERNAME).toString();
         String elixirId = request.getAttribute(ELIXIR_ID).toString();

src/main/java/no/uio/ifi/ltp/aspects/ProcessArgumentsAspect.java → src/main/java/no/elixir/fega/ltp/aspects/ProcessArgumentsAspect.java

@@ -1,4 +1,4 @@
-package no.uio.ifi.ltp.aspects;
+package no.elixir.fega.ltp.aspects;
 
 import lombok.extern.slf4j.Slf4j;
 import org.aspectj.lang.ProceedingJoinPoint;
@@ -42,7 +42,7 @@ public class ProcessArgumentsAspect {
      * @throws Throwable In case of error.
      */
     @SuppressWarnings("rawtypes")
-    @Around("execution(public * no.uio.ifi.ltp.controllers.rest.ProxyController.stream(..)) || execution(public * no.uio.ifi.ltp.controllers.rest.ProxyController.deleteFile(..))")
+    @Around("execution(public * no.elixir.fega.ltp.controllers.rest.ProxyController.stream(..)) || execution(public * no.elixir.fega.ltp.controllers.rest.ProxyController.deleteFile(..))")
     public Object processArguments(ProceedingJoinPoint joinPoint) throws Throwable {
         try {
             Object[] arguments = joinPoint.getArgs();

src/main/java/no/uio/ifi/ltp/aspects/PublishMQAspect.java → src/main/java/no/elixir/fega/ltp/aspects/PublishMQAspect.java

@@ -1,10 +1,10 @@
-package no.uio.ifi.ltp.aspects;
+package no.elixir.fega.ltp.aspects;
 
 import com.google.gson.Gson;
 import lombok.extern.slf4j.Slf4j;
-import no.uio.ifi.ltp.dto.EncryptedIntegrity;
-import no.uio.ifi.ltp.dto.FileDescriptor;
-import no.uio.ifi.ltp.dto.Operation;
+import no.elixir.fega.ltp.dto.EncryptedIntegrity;
+import no.elixir.fega.ltp.dto.FileDescriptor;
+import no.elixir.fega.ltp.dto.Operation;
 import no.uio.ifi.tc.model.pojo.TSDFileAPIResponse;
 import org.apache.http.entity.ContentType;
 import org.aspectj.lang.annotation.AfterReturning;
@@ -20,7 +20,7 @@
 import java.util.Objects;
 import java.util.UUID;
 
-import static no.uio.ifi.ltp.aspects.ProcessArgumentsAspect.*;
+import static no.elixir.fega.ltp.aspects.ProcessArgumentsAspect.*;
 
 /**
  * AOP aspect that publishes MQ messages.
@@ -58,7 +58,7 @@ public class PublishMQAspect {
      * @param result Object returned by the proxied method.
      */
     @SuppressWarnings({"unchecked", "rawtypes"})
-    @AfterReturning(pointcut = "execution(@org.springframework.web.bind.annotation.PatchMapping public * no.uio.ifi.ltp.controllers.rest.ProxyController.stream(..))", returning = "result")
+    @AfterReturning(pointcut = "execution(@org.springframework.web.bind.annotation.PatchMapping public * no.elixir.fega.ltp.controllers.rest.ProxyController.stream(..))", returning = "result")
     public void publishUpload(Object result) {
         ResponseEntity genericResponseEntity = (ResponseEntity) result;
         if (!String.valueOf(Objects.requireNonNull(genericResponseEntity).getStatusCode()).startsWith("20")) {
@@ -97,7 +97,7 @@ public void publishUpload(Object result) {
      * @param result Object returned by the proxied method.
      */
     @SuppressWarnings({"unchecked", "rawtypes"})
-    @AfterReturning(pointcut = "execution(public * no.uio.ifi.ltp.controllers.rest.ProxyController.deleteFile(..))", returning = "result")
+    @AfterReturning(pointcut = "execution(public * no.elixir.fega.ltp.controllers.rest.ProxyController.deleteFile(..))", returning = "result")
     public void publishRemove(Object result) {
         ResponseEntity genericResponseEntity = (ResponseEntity) result;
         if (!String.valueOf(Objects.requireNonNull(genericResponseEntity).getStatusCode()).startsWith("20")) {

src/main/java/no/uio/ifi/ltp/authentication/CEGACredentialsProvider.java → src/main/java/no/elixir/fega/ltp/authentication/CEGACredentialsProvider.java

@@ -1,6 +1,6 @@
-package no.uio.ifi.ltp.authentication;
+package no.elixir.fega.ltp.authentication;
 
-import no.uio.ifi.ltp.dto.Credentials;
+import no.elixir.fega.ltp.dto.Credentials;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.cache.annotation.Cacheable;

src/main/java/no/uio/ifi/ltp/controllers/rest/AuthController.java → src/main/java/no/elixir/fega/ltp/controllers/rest/AuthController.java

@@ -1,4 +1,4 @@
-package no.uio.ifi.ltp.controllers.rest;
+package no.elixir.fega.ltp.controllers.rest;
 
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;

src/main/java/no/uio/ifi/ltp/controllers/rest/ProxyController.java → src/main/java/no/elixir/fega/ltp/controllers/rest/ProxyController.java

@@ -1,4 +1,4 @@
-package no.uio.ifi.ltp.controllers.rest;
+package no.elixir.fega.ltp.controllers.rest;
 
 import lombok.extern.slf4j.Slf4j;
 import no.uio.ifi.tc.TSDFileAPIClient;

src/main/java/no/uio/ifi/ltp/dto/Credentials.java → src/main/java/no/elixir/fega/ltp/dto/Credentials.java

@@ -1,4 +1,4 @@
-package no.uio.ifi.ltp.dto;
+package no.elixir.fega.ltp.dto;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
 import lombok.Data;

src/main/java/no/uio/ifi/ltp/dto/EncryptedIntegrity.java → src/main/java/no/elixir/fega/ltp/dto/EncryptedIntegrity.java

@@ -1,4 +1,4 @@
-package no.uio.ifi.ltp.dto;
+package no.elixir.fega.ltp.dto;
 
 import com.google.gson.annotations.SerializedName;
 import lombok.Data;

src/main/java/no/uio/ifi/ltp/dto/FileDescriptor.java → src/main/java/no/elixir/fega/ltp/dto/FileDescriptor.java

@@ -1,4 +1,4 @@
-package no.uio.ifi.ltp.dto;
+package no.elixir.fega.ltp.dto;
 
 import com.google.gson.annotations.SerializedName;
 import lombok.Data;

src/main/java/no/uio/ifi/ltp/dto/Operation.java → src/main/java/no/elixir/fega/ltp/dto/Operation.java

@@ -1,4 +1,4 @@
-package no.uio.ifi.ltp.dto;
+package no.elixir.fega.ltp.dto;
 
 /**
  * Type of file event (created, moved, removed, etc.)

src/test/java/no/uio/ifi/ltp/LocalEGATSDProxyApplicationTests.java → src/test/java/no/elixir/fega/ltp/LocalEGATSDProxyApplicationTests.java

@@ -1,4 +1,4 @@
-package no.uio.ifi.ltp;
+package no.elixir.fega.ltp;
 
 import org.junit.jupiter.api.Test;
 import org.springframework.boot.test.context.SpringBootTest;