From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Sat, 17 Nov 2012 20:09:15 +0000 (+0000)
Subject: simple HTTP multipart entity poster - may not be useful
X-Git-Tag: Jalview_2_9~265^2~16
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3b94f01f4edf56896ae3b5f0ce6cb4f1996e7bbc;p=jalview.git

simple HTTP multipart entity poster - may not be useful
---

diff --git a/src/jalview/ws/HttpClientUtils.java b/src/jalview/ws/HttpClientUtils.java
index 01892e7..740b669 100644
--- a/src/jalview/ws/HttpClientUtils.java
+++ b/src/jalview/ws/HttpClientUtils.java
@@ -18,7 +18,9 @@
 package jalview.ws;
 
 import java.io.BufferedReader;
+import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.util.List;
 
@@ -29,6 +31,11 @@ import org.apache.http.client.ClientProtocolException;
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.entity.UrlEncodedFormEntity;
 import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.mime.HttpMultipartMode;
+import org.apache.http.entity.mime.MultipartEntity;
+import org.apache.http.entity.mime.content.FileBody;
+import org.apache.http.entity.mime.content.InputStreamBody;
+import org.apache.http.entity.mime.content.StringBody;
 import org.apache.http.impl.client.DefaultHttpClient;
 
 /**
@@ -72,4 +79,64 @@ public class HttpClientUtils
     }
   }
 
+  public static BufferedReader doHttpMpartFilePost(String postUrl,
+          List<NameValuePair> vals, String fparm,File file, String mtype) throws ClientProtocolException,
+          IOException
+  {
+    HttpClient httpclient = new DefaultHttpClient();
+    HttpPost httppost = new HttpPost(postUrl);
+    MultipartEntity mpe = new MultipartEntity(HttpMultipartMode.BROWSER_COMPATIBLE);
+    for (NameValuePair nvp:vals)
+    {
+      mpe.addPart(nvp.getName(), new StringBody(nvp.getValue()));
+    }
+    
+    FileBody fb = new FileBody(file, mtype!=null ? mtype : "application/octet-stream");
+    mpe.addPart(fparm, fb);
+    UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
+    httppost.setEntity(ue);
+    HttpResponse response = httpclient.execute(httppost);
+    HttpEntity resEntity = response.getEntity();
+
+    if (resEntity != null)
+    {
+      BufferedReader r = new BufferedReader(new InputStreamReader(
+              resEntity.getContent()));
+      return r;
+    }
+    else
+    {
+      return null;
+    }
+  }
+  public static BufferedReader doHttpMpartInputstreamPost(String postUrl,
+          List<NameValuePair> vals, String fparm,String fname, InputStream is, String mtype) throws ClientProtocolException,
+          IOException
+  {
+    HttpClient httpclient = new DefaultHttpClient();
+    HttpPost httppost = new HttpPost(postUrl);
+    MultipartEntity mpe = new MultipartEntity(HttpMultipartMode.STRICT);
+    for (NameValuePair nvp:vals)
+    {
+      mpe.addPart(nvp.getName(), new StringBody(nvp.getValue()));
+    }
+    
+    InputStreamBody fb = (mtype!=null) ? new InputStreamBody(is, fname, mtype) : new InputStreamBody(is, fname);
+    mpe.addPart(fparm, fb);
+    UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
+    httppost.setEntity(ue);
+    HttpResponse response = httpclient.execute(httppost);
+    HttpEntity resEntity = response.getEntity();
+
+    if (resEntity != null)
+    {
+      BufferedReader r = new BufferedReader(new InputStreamReader(
+              resEntity.getContent()));
+      return r;
+    }
+    else
+    {
+      return null;
+    }
+  }
 }
diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
new file mode 100644
index 0000000..f5913e6
--- /dev/null
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -0,0 +1,37 @@
+package jalview.ws;
+
+import static org.junit.Assert.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.List;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class PDBSequenceFetcherTest
+{
+
+  @Before
+  public void setUp() throws Exception
+  {
+  }
+
+  @Test
+  public void testRnaSeqRetrieve() throws Exception
+  {
+    List<DbSourceProxy> sps = new SequenceFetcher(false)
+    .getSourceProxy("PDB");
+    AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
+    assertTrue(response!=null);
+    assertTrue(response.getHeight()==1);
+    for (SequenceI sq:response.getSequences())
+    {
+      assertTrue("No annotation transfered to sequence.",sq.getAnnotation().length>0);
+      assertTrue("No PDBEntry on sequence.",sq.getPDBId().size()>0);
+      assertTrue("No RNA annotation on sequence.", sq.getRNA()!=null);
+    }
+  }
+
+}