Merged in dev (pull request #10)

Merge dev to master
KathiraveluLab · Aug 17, 2017 · 14f4899 · 14f4899
2 parents 59bc248 + c8cdca4
commit 14f4899
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Showing 3 changed files with 39 additions and 32 deletions.
diff --git a/README.md b/README.md
@@ -73,6 +73,7 @@ This project depends on the below major projects.
 * Apache Velocity
 * Apache Log4j2
 * Mashape Unirest
+* SparkJava
 
 
 

diff --git a/modules/repl-server/src/main/java/edu/emory/bmi/datarepl/ds_mgmt/tcia/TCIAClientImpl.java b/modules/repl-server/src/main/java/edu/emory/bmi/datarepl/ds_mgmt/tcia/TCIAClientImpl.java
@@ -1,6 +1,7 @@
 package edu.emory.bmi.datarepl.ds_mgmt.tcia;
 
 
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URI;
@@ -293,6 +294,38 @@ public String getPatient(String collection, OutputFormat format)
         }
     }
 
+    /**
+     * Downloads the images in a given series
+     * @param seriesInstanceUID the inst
+     * @throws TCIAClientException
+     * @throws IOException
+     */
+    public void downloadImagesOfSeries(String seriesInstanceUID) throws TCIAClientException, IOException {
+            ITCIAClient.ImageResult imageResult =  getImage(seriesInstanceUID);
+            saveTo(imageResult.getRawData(), seriesInstanceUID + ".zip", ".");
+    }
+
+
+    private static void saveTo(InputStream in, String name, String directory) throws IOException {
+        FileOutputStream fos = new FileOutputStream(directory + "/" + name);
+        byte[] buffer = new byte[4096];
+        int read = -1;
+        int sum = 0;
+        while ((read = in.read(buffer)) > 0) {
+            fos.write(buffer, 0, read);
+            long mseconds = System.currentTimeMillis();
+            sum += read;
+
+            if (mseconds % 10 == 0) {
+                System.out.println(String.format("Bytes Written %s", sum));
+            }
+        }
+
+        fos.close();
+        in.close();
+    }
+
+
     public ImageResult getImage(String seriesInstanceUID)
             throws edu.emory.bmi.datarepl.ds_mgmt.tcia.TCIAClientException {
         try {
@@ -310,8 +343,6 @@ public ImageResult getImage(String seriesInstanceUID)
 // create a new HttpGet request
             HttpGet request = new HttpGet(uri);
 
-// add api_key to the header
-            request.setHeader(API_KEY_FIELD, apiKey);
             long startTime = System.currentTimeMillis();
             HttpResponse response = httpClient.execute(request);
             long diff = System.currentTimeMillis() - startTime;

diff --git a/modules/repl-server/src/test/java/edu/emory/bmi/datarepl/test/TestTCIAClient.java b/modules/repl-server/src/test/java/edu/emory/bmi/datarepl/test/TestTCIAClient.java
@@ -53,24 +53,17 @@ public void testGetCollectionValues() {
      * Method : GetImage
      * Description : Returns images in a zip file
      */
-
     @Test
     public void testGetImage() {
-
-        // create TCIA Client by passing API-Key and baseUrl in the constructor
-        ITCIAClient client = TCIAClientImpl.getTCIAClientImpl();
+        TCIAClientImpl client = TCIAClientImpl.getTCIAClientImpl();
         String seriesInstanceUID = "1.3.6.1.4.1.14519.5.2.1.7695.4001.306204232344341694648035234440";
         try {
-            // Make the RESTfull call . Response comes back as InputStream.
-            ITCIAClient.ImageResult imageResult = client.getImage(seriesInstanceUID);
-            saveTo(imageResult.getRawData(), seriesInstanceUID + ".zip", ".");
-
+            client.downloadImagesOfSeries(seriesInstanceUID);
         } catch (TCIAClientException e) {
-            fail(e.getMessage()); // request failed
-        } catch (Exception e) {
-            fail(e.getMessage()); // request failed
+            fail("TCIA Client Exception in downloading the images. " + e.getMessage());
+        } catch (IOException e) {
+            fail("IOException in downloading the images. " + e.getMessage());
         }
-
     }
 
 
@@ -238,24 +231,6 @@ public static void saveTo(InputStream in, String name, String directory, int est
         in.close();
     }
 
-    public static void saveTo(InputStream in, String name, String directory) throws IOException {
-        FileOutputStream fos = new FileOutputStream(directory + "/" + name);
-        byte[] buffer = new byte[4096];
-        int read = -1;
-        int sum = 0;
-        while ((read = in.read(buffer)) > 0) {
-            fos.write(buffer, 0, read);
-            long mseconds = System.currentTimeMillis();
-            sum += read;
-
-            if (mseconds % 10 == 0) {
-                System.out.println(String.format("Bytes Written %s", sum));
-            }
-        }
-
-        fos.close();
-        in.close();
-    }
 
     public static String toString(InputStream in) throws IOException {
         ByteArrayOutputStream baos = new ByteArrayOutputStream();