Fixing bytes length for localEGA profile

.travis.yml

@@ -35,7 +35,7 @@ jobs:
         - sleep 90
         - cd ../ega-data-api-it
       script:
-        - mvn test -Dtest=!DataedgeIntgTest,!MetadataControllerIntgTest
+        - mvn test
     - stage: image build
       script: ./extras/travis_push_docker_hub.sh
 

ega-data-api-dataedge/src/main/java/eu/elixir/ega/ebi/dataedge/service/FileLengthService.java

@@ -0,0 +1,27 @@
+/*
+ * Copyright 2016 ELIXIR EGA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package eu.elixir.ega.ebi.dataedge.service;
+
+import eu.elixir.ega.ebi.shared.dto.File;
+
+/**
+ * @author amohan
+ */
+public interface FileLengthService {
+
+    long getContentLength(File reqFile, String destinationFormat, long startCoordinate, long endCoordinate);
+
+}

ega-data-api-dataedge/src/main/java/eu/elixir/ega/ebi/dataedge/service/internal/FileLengthServiceImpl.java

@@ -0,0 +1,56 @@
+/*
+ * Copyright 2016 ELIXIR EGA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package eu.elixir.ega.ebi.dataedge.service.internal;
+
+import org.springframework.context.annotation.Primary;
+import org.springframework.context.annotation.Profile;
+import org.springframework.stereotype.Service;
+
+import eu.elixir.ega.ebi.dataedge.service.FileLengthService;
+import eu.elixir.ega.ebi.shared.dto.File;
+
+/**
+ * @author amohan
+ */
+@Service
+@Primary
+@Profile("!LocalEGA")
+public class FileLengthServiceImpl implements FileLengthService {
+
+    @Override
+    public long getContentLength(File reqFile, String destinationFormat, long startCoordinate, long endCoordinate) {
+        long length = 0;
+
+        // EncryptionFormat
+        // If destinationFormat is encrypted then we add extra 16 byte to store the IV.
+        int prefix = 16;
+        if (destinationFormat.equalsIgnoreCase("plain"))
+            prefix = 0;
+
+        // Range specified?
+        // The AES encrypted data has a 16 byte random IV at the start, so to
+        // get the correct (raw) file length we need to remove this 16 byte
+        // prefix.
+        if (startCoordinate > 0 || endCoordinate > 0) {
+            length = endCoordinate - startCoordinate;
+        } else {
+            length = reqFile.getFileSize() - 16;
+        }
+
+        return (length + prefix);
+    }
+
+}

ega-data-api-dataedge/src/main/java/eu/elixir/ega/ebi/dataedge/service/internal/LocalEGAFileLengthServiceImpl.java

@@ -0,0 +1,44 @@
+/*
+ * Copyright 2016 ELIXIR EGA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package eu.elixir.ega.ebi.dataedge.service.internal;
+
+import org.springframework.context.annotation.Profile;
+import org.springframework.stereotype.Service;
+
+import eu.elixir.ega.ebi.dataedge.service.FileLengthService;
+import eu.elixir.ega.ebi.shared.dto.File;
+
+/**
+ * @author amohan
+ */
+@Service
+@Profile("LocalEGA")
+public class LocalEGAFileLengthServiceImpl  implements FileLengthService {
+
+    @Override
+    public long getContentLength(File reqFile, String destinationFormat, long startCoordinate, long endCoordinate) {
+        long length = 0;
+
+        if (startCoordinate > 0 || endCoordinate > 0) {
+            length = endCoordinate - startCoordinate;
+        } else {
+            length = reqFile.getFileSize();
+        }
+
+        return length;
+    }
+
+}

ega-data-api-dataedge/src/main/java/eu/elixir/ega/ebi/dataedge/service/internal/RemoteFileServiceImpl.java

@@ -25,6 +25,7 @@
 import eu.elixir.ega.ebi.shared.dto.EventEntry;
 import eu.elixir.ega.ebi.shared.service.DownloaderLogService;
 import eu.elixir.ega.ebi.shared.service.FileInfoService;
+import eu.elixir.ega.ebi.dataedge.service.FileLengthService;
 import eu.elixir.ega.ebi.dataedge.service.FileService;
 import eu.elixir.ega.ebi.shared.dto.File;
 import eu.elixir.ega.ebi.shared.dto.FileIndexFile;
@@ -102,6 +103,9 @@ public class RemoteFileServiceImpl implements FileService {
 
     @Autowired
     private FileInfoService fileInfoService;
+
+    @Autowired
+    private FileLengthService fileLengthService;
 
     @Override
     //@HystrixCommand
@@ -147,12 +151,12 @@ public void getFile(String fileId,
         String headerValue = dlIdentifier.toString();
         response = setHeaders(response, headerValue);
 
+        long fileLength = fileLengthService.getContentLength(reqFile, destinationFormat, startCoordinate, endCoordinate);
+
         // Content Length of response (if available)
-        response.setContentLengthLong(getContentLength(reqFile, destinationFormat, startCoordinate, endCoordinate));
+        response.setContentLengthLong(fileLength);
 
         // If byte range, set response 206
-        long fileLength = reqFile.getFileSize();
-        if (destinationFormat.equalsIgnoreCase("plain")) fileLength -= 16;
         if (startCoordinate > 0 || endCoordinate > 0) {
             response.setStatus(HttpServletResponse.SC_PARTIAL_CONTENT);
             response.addHeader("Content-Range", "bytes " + startCoordinate +
@@ -275,8 +279,8 @@ public void getFileHead(String fileId,
             response = setHeaders(response, headerValue);
 
             // Content Length of response (if available)
-            response.setContentLengthLong(getContentLength(reqFile, destinationFormat, 0, 0));
-            response.addHeader("X-Content-Length", String.valueOf(getContentLength(reqFile, destinationFormat, 0, 0)));
+            response.setContentLengthLong(fileLengthService.getContentLength(reqFile, destinationFormat, 0, 0));
+            response.addHeader("X-Content-Length", String.valueOf(fileLengthService.getContentLength(reqFile, destinationFormat, 0, 0)));
         }
     }
 
@@ -773,22 +777,4 @@ private VariantContext filterMe(VariantContext context, List<String> fields, Lis
         return context;
     }
 
-    private long getContentLength(File reqFile, String destinationFormat, long startCoordinate, long endCoordinate) {
-        long length = 0;
-
-        // EncryptionFormat
-        int prefix = 16;
-        if (destinationFormat.equalsIgnoreCase("plain"))
-            prefix = 0;
-
-        // Range specified?
-        if (startCoordinate > 0 || endCoordinate > 0) {
-            length = endCoordinate - startCoordinate;
-        } else {
-            length = reqFile.getFileSize() - 16;
-        }
-
-        return (length + prefix);
-    }
-
 }

ega-data-api-dataedge/src/test/java/eu/elixir/ega/ebi/dataedge/service/internal/RemoteFileServiceImplTest.java

@@ -17,6 +17,7 @@
 
 import eu.elixir.ega.ebi.dataedge.config.InternalErrorException;
 import eu.elixir.ega.ebi.dataedge.dto.*;
+import eu.elixir.ega.ebi.dataedge.service.FileLengthService;
 import eu.elixir.ega.ebi.shared.service.DownloaderLogService;
 import eu.elixir.ega.ebi.shared.service.FileInfoService;
 import eu.elixir.ega.ebi.shared.dto.File;
@@ -102,6 +103,9 @@ public class RemoteFileServiceImplTest {
 
     @Mock
     private FileInfoService fileInfoService;
+
+    @Mock
+    private FileLengthService fileLengthService;
 
     /**
      * Test class for

extras/docker-compose.yml

@@ -6,7 +6,7 @@ services:
       - "9058:9058"
       - "5059:5059"
     environment:
-      - SPRING_PROFILES_ACTIVE=no-oss
+      - SPRING_PROFILES_ACTIVE=no-oss,LocalEGA
       - server.port=9058
       - JWTKEY=${JWTKEY}
       - FILEDATABASE.listOfServers=filedatabase:9051