Download files as bytes

Author: hvarg

.gitignore

@@ -1,4 +1,5 @@
 server-local.properties
+public
 !.gitkeep
 *.egg
 *.egg-info

server/src/main/java/org/diskproject/server/adapters/AirFlowAdapter.java

@@ -117,7 +117,7 @@ public WorkflowRun getRunStatus(String runId) {
     }
 
     @Override
-    public String fetchData(String dataId) {
+    public byte[] fetchData(String dataId) {
         // Auto-generated method stub
         return null;
     }

server/src/main/java/org/diskproject/server/api/impl/DiskResource.java

@@ -1,6 +1,7 @@
 package org.diskproject.server.api.impl;
 
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 import java.util.List;
 import java.util.Map;
 
@@ -573,11 +574,13 @@ public Map<String, String> getNarratives(
   @Override
   public String getOutputData(
       @JsonProperty("request") ExternalDataRequest r) {
-    String result = this.repo.getOutputData(r.getSource(), r.getDataId());
+    byte[] result = this.repo.getOutputData(r.getSource(), r.getDataId());
+    String tmp = ""; // FIXME: this should not be an string.
     if (result == null) {
       System.out.println("ERROR: " + r.getDataId() + " not available on " + r.getSource() + ".");
-      result = "";
+    } else {
+      tmp = new String(result, StandardCharsets.UTF_8);
     }
-    return result;
+    return tmp;
   }
 }

server/src/main/java/org/diskproject/server/repository/DiskRepository.java

@@ -1,6 +1,7 @@
 package org.diskproject.server.repository;
 
 import java.io.Serializable;
+import java.nio.charset.StandardCharsets;
 import java.text.DecimalFormat;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
@@ -1929,7 +1930,7 @@ public WorkflowRun getWorkflowRunStatus(String source, String id) {
         return methodAdapter.getRunStatus(id);
     }
 
-    public String getOutputData(String source, String id) {
+    public byte[] getOutputData(String source, String id) {
         MethodAdapter methodAdapter = getMethodAdapterByName(source);
         if (methodAdapter == null)
             return null;
@@ -2067,14 +2068,15 @@ public void run() {
                             for (String outname : outputs.keySet()) {
                                 if (outname.equals("p_value") || outname.equals("pval") || outname.equals("p_val")) {
                                     String dataid = outputs.get(outname);
-                                    String wingsP = methodAdapter.fetchData(dataid);
-                                    Double pval = 0.0;
+                                    byte[] byteConf = methodAdapter.fetchData(dataid);
+                                    String wingsP = byteConf != null ? new String(byteConf, StandardCharsets.UTF_8) : null;
+                                    Double pval = null;
                                     try {
                                         pval = Double.valueOf(wingsP);
                                     } catch (Exception e) {
                                         System.err.println("[M] Error: " + dataid + " is a non valid p-value");
                                     }
-                                    if (pval > 0) {
+                                    if (pval != null) {
                                         System.out.println("[M] Detected p-value: " + pval);
                                         tloi.setConfidenceValue(pval);
                                         tloi.setConfidenceType("P-VALUE");

server/src/main/java/org/diskproject/server/repository/WingsAdapter.java

@@ -663,13 +663,41 @@ public String runWorkflow(String wflowname, List<VariableBinding> vbindings, Map
 		//return null;
 	}
 
-	public String fetchDataFromWings(String dataid) {
-		String getpage = "users/" + getUsername() + "/" + domain + "/data/fetch";
-
-		// Check for data already present on the server
+	public byte[] fetchDataFromWings(String dataid) {
+		String url = this.server + "/users/" + getUsername() + "/" + domain + "/data/fetch";
+		// Download data already present on the server
 		List<NameValuePair> formdata = new ArrayList<NameValuePair>();
 		formdata.add(new BasicNameValuePair("data_id", dataid));
-		return this.get(getpage, formdata);
+		url += "?" + URLEncodedUtils.format(formdata, "UTF-8");
+
+		this.login();
+		CloseableHttpClient client = HttpClientBuilder.create().build();
+		byte[] bytes = null;
+		try {
+			HttpGet securedResource = new HttpGet(url);
+			CloseableHttpResponse httpResponse = client.execute(securedResource);
+			try {
+				HttpEntity responseEntity = httpResponse.getEntity();
+				ByteArrayOutputStream baos = new ByteArrayOutputStream(); 
+    			responseEntity.writeTo(baos);
+				bytes = baos.toByteArray();
+				EntityUtils.consume(responseEntity);
+				httpResponse.close();
+			} catch (Exception e) {
+				throw e;
+			} finally {
+				httpResponse.close();
+			}
+		} catch (Exception e) {
+			e.printStackTrace();
+		} finally {
+			try {
+				client.close();
+			} catch (IOException e) {
+			}
+		}
+
+		return bytes;
 	}
 
 	public String addOrUpdateData(String id, String type, String contents, boolean addServer) {
@@ -1310,7 +1338,7 @@ public WorkflowRun getRunStatus(String runId) {
 	}
 
 	@Override
-	public String fetchData(String dataId) {
+	public byte[] fetchData(String dataId) {
 		return this.fetchDataFromWings(dataId);
 	}
 

shared/src/main/java/org/diskproject/shared/classes/adapters/MethodAdapter.java

@@ -87,7 +87,7 @@ public String toString () {
 
 	public abstract WorkflowRun getRunStatus (String runId);
 
-	public abstract String fetchData (String dataId);
+	public abstract byte[] fetchData (String dataId);
 
 	public abstract Map<String, String> getRunVariableBindings (String runId);