X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FHttpResultSet.java;h=8414da5d78ac2a17eda45752462f9b06d1c49f3d;hb=7b9f93ca2c7f5e5d9347f00be309522f76e3e778;hp=bfef0cce1efce6125b9bc84a55c9e87f2139caea;hpb=c762d9525db36ffd5d3fca49fb5e7d506d13401a;p=jalview.git

diff --git a/src/jalview/ws/rest/HttpResultSet.java b/src/jalview/ws/rest/HttpResultSet.java
index bfef0cc..8414da5 100644
--- a/src/jalview/ws/rest/HttpResultSet.java
+++ b/src/jalview/ws/rest/HttpResultSet.java
@@ -1,23 +1,48 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.rest;
 
-import java.io.BufferedInputStream;
+import jalview.bin.Cache;
+import jalview.io.FileParse;
+import jalview.io.packed.DataProvider;
+import jalview.io.packed.DataProvider.JvDataType;
+import jalview.io.packed.ParsePackedSet;
+import jalview.io.packed.SimpleDataProvider;
+import jalview.util.MessageManager;
+import jalview.ws.io.mime.JalviewMimeContentHandler;
+
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.apache.http.HttpEntity;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.methods.HttpRequestBase;
 import org.apache.http.entity.mime.MultipartEntity;
+import org.apache.http.util.EntityUtils;
 import org.apache.james.mime4j.MimeException;
-import org.apache.james.mime4j.parser.ContentHandler;
 import org.apache.james.mime4j.parser.MimeStreamParser;
-
-import jalview.bin.Cache;
-import jalview.io.FileParse;
-import jalview.io.mime.JalviewMimeContentHandler;
-
 /**
  * data source instantiated from the response of an httpclient request.
  * 
@@ -25,7 +50,7 @@ import jalview.io.mime.JalviewMimeContentHandler;
  * 
  */
 
-public class HttpResultSet extends FileParse
+public class HttpResultSet extends FileParse implements AutoCloseable
 {
 
   private HttpRequestBase cachedRequest;
@@ -56,38 +81,87 @@ public class HttpResultSet extends FileParse
     initDataSource(con);
   }
 
-  private void initDataSource(HttpResponse con) throws IOException
+  /**
+   * construct a set of dataproviders to parse a result set from this service
+   * 
+   * @param resSet
+   * @return
+   */
+  public List<DataProvider> createResultDataProviders()
   {
-    en = con.getEntity();
-    repeatable = en.isRepeatable();
+    List<DataProvider> dp = new ArrayList<>();
+    for (JvDataType type : restJob.rsd.getResultDataTypes())
+    {
+      dp.add(new SimpleDataProvider(type, this, null));
+    }
+    return dp;
+  }
 
-    if (en instanceof MultipartEntity)
+  /**
+   * parses the results of the service output.
+   * 
+   * @return the result of ParsePackedSet.getAlignment()
+   * @throws Exception
+   * @throws Error
+   */
+  public Object[] parseResultSet() throws Exception, Error
+  {
+    List<DataProvider> dp = new ArrayList<>();
+    Object[] results = null;
+
+    if (en == null)
+    {
+      throw new Error(MessageManager.getString(
+              "error.implementation_error_need_to_have_httpresponse"));
+    }
+    jalview.io.packed.JalviewDataset ds = restJob.newJalviewDataset();
+    // Decide how we deal with content.
+    // TODO : verify we are detecting a multipart response correctly
+    if (en.getContentType().getValue().startsWith("multipart/form-data"))
     {
-      MultipartEntity mpe = (MultipartEntity) en;
-      // multipart
-      jalview.io.packed.JalviewDataset ds = restJob.newJalviewDataset();
-      ContentHandler handler = new JalviewMimeContentHandler(ds);
+      // Multipart messages should be properly typed, so we parse them as we go.
+      JalviewMimeContentHandler handler = new JalviewMimeContentHandler(ds);
       MimeStreamParser parser = new MimeStreamParser();
       parser.setContentHandler(handler);
       try
       {
-        parser.parse(mpe.getContent());
+        parser.parse(en.getContent());
       } catch (MimeException me)
       {
         error = true;
         errormessage = "Couldn't parse message from web service.";
         Cache.log.warn("Failed to parse MIME multipart content", me);
-        en.consumeContent();
+        EntityUtils.consume(en);
       }
+      return new ParsePackedSet().getAlignment(ds,
+              handler.getJalviewDataProviders());
     }
     else
     {
+      // Need to use hints from rest service description.
+      dp = createResultDataProviders();
+      ParsePackedSet pps = new ParsePackedSet();
+      return pps.getAlignment(ds, dp);
+    }
+  }
+
+  private void initDataSource(HttpResponse con) throws IOException
+  {
+    en = con.getEntity();
+    repeatable = en.isRepeatable();
+
+    if (!(en instanceof MultipartEntity))
+    {
       // assume content is simple text stream that can be read from
-      String enc = (en.getContentEncoding()==null) ? null : en.getContentEncoding().getValue();
-      if (en.getContentType()!=null) {
-        Cache.log.info("Result Type: " + en.getContentType().toString());
-      } else {
-        Cache.log.info("No Result Type Specified.");
+      String enc = (en.getContentEncoding() == null) ? null
+              : en.getContentEncoding().getValue();
+      if (en.getContentType() != null)
+      {
+        Cache.log.debug("Result Type: " + en.getContentType().toString());
+      }
+      else
+      {
+        Cache.log.debug("No Result Type Specified.");
       }
       if (enc == null || enc.length() < 1)
       {
@@ -95,7 +169,7 @@ public class HttpResultSet extends FileParse
       }
       else
       {
-        Cache.log.debug("Result Encoded as : "+enc);
+        Cache.log.debug("Result Encoded as : " + enc);
       }
       // attempt to identify file and construct an appropriate DataSource
       // identifier for it.
@@ -111,7 +185,7 @@ public class HttpResultSet extends FileParse
       {
         Cache.log.error("Can't handle encoding '" + enc
                 + "' for response from webservice.", e);
-        en.consumeContent();
+        EntityUtils.consume(en);
         error = true;
         errormessage = "Can't handle encoding for response from webservice";
         return;
@@ -119,13 +193,13 @@ public class HttpResultSet extends FileParse
       if (br != null)
       {
         dataIn = new BufferedReader(br);
-        error=false;
+        error = false;
       }
     }
   }
 
   @Override
-  protected void finalize() throws Throwable
+  public void close()
   {
     dataIn = null;
     cachedRequest = null;
@@ -140,7 +214,24 @@ public class HttpResultSet extends FileParse
     } catch (Error ex)
     {
     }
-    super.finalize();
+    // no finalize for FileParse
+    // super.close();
+  }
+
+  /**
+   * 
+   * @return the URL that this result set read data from.
+   */
+  public String getUrl()
+  {
+    try
+    {
+      return cachedRequest.getURI().toURL().toString();
+    } catch (Exception x)
+    {
+      x.printStackTrace();
+      return null;
+    }
   }
 
 }