2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ws.rest;
23 import jalview.bin.Cache;
24 import jalview.io.FileParse;
25 import jalview.io.packed.DataProvider;
26 import jalview.io.packed.ParsePackedSet;
27 import jalview.io.packed.SimpleDataProvider;
28 import jalview.io.packed.DataProvider.JvDataType;
29 import jalview.util.MessageManager;
30 import jalview.ws.io.mime.JalviewMimeContentHandler;
32 import java.io.BufferedReader;
33 import java.io.IOException;
34 import java.io.InputStreamReader;
35 import java.io.UnsupportedEncodingException;
36 import java.util.ArrayList;
37 import java.util.List;
39 import org.apache.http.HttpEntity;
40 import org.apache.http.HttpResponse;
41 import org.apache.http.client.methods.HttpRequestBase;
42 import org.apache.http.entity.mime.MultipartEntity;
43 import org.apache.james.mime4j.MimeException;
44 import org.apache.james.mime4j.parser.MimeStreamParser;
47 * data source instantiated from the response of an httpclient request.
53 public class HttpResultSet extends FileParse
56 private HttpRequestBase cachedRequest;
59 * when set, indicates that en can be recreated by repeating the HttpRequest
62 boolean repeatable = false;
65 * response that is to be parsed as jalview input data
67 private HttpEntity en = null;
70 * (sub)job that produced this result set.
72 private RestJob restJob;
74 public HttpResultSet(RestJob rj, HttpResponse con, HttpRequestBase req)
78 setDataName(rj.getJobId() + " Part " + rj.getJobnum());
85 * construct a set of dataproviders to parse a result set from this service
90 public List<DataProvider> createResultDataProviders()
92 List<DataProvider> dp = new ArrayList<DataProvider>();
93 for (JvDataType type : restJob.rsd.getResultDataTypes())
95 dp.add(new SimpleDataProvider(type, this, null));
101 * parses the results of the service output.
103 * @return the result of ParsePackedSet.getAlignment()
107 public Object[] parseResultSet() throws Exception, Error
109 List<DataProvider> dp = new ArrayList<DataProvider>();
110 Object[] results = null;
114 throw new Error(MessageManager.getString("error.implementation_error_need_to_have_httpresponse"));
116 jalview.io.packed.JalviewDataset ds = restJob.newJalviewDataset();
117 // Decide how we deal with content.
118 if (en instanceof MultipartEntity)
120 // Multipart messages should be properly typed, so we parse them as we go.
121 MultipartEntity mpe = (MultipartEntity) en;
123 JalviewMimeContentHandler handler = new JalviewMimeContentHandler(ds);
124 MimeStreamParser parser = new MimeStreamParser();
125 parser.setContentHandler(handler);
128 parser.parse(mpe.getContent());
129 } catch (MimeException me)
132 errormessage = "Couldn't parse message from web service.";
133 Cache.log.warn("Failed to parse MIME multipart content", me);
136 return new ParsePackedSet().getAlignment(ds,
137 handler.getJalviewDataProviders());
141 // Need to use hints from rest service description.
142 dp = createResultDataProviders();
143 ParsePackedSet pps = new ParsePackedSet();
144 return pps.getAlignment(ds, dp);
148 private void initDataSource(HttpResponse con) throws IOException
150 en = con.getEntity();
151 repeatable = en.isRepeatable();
153 if (!(en instanceof MultipartEntity))
155 // assume content is simple text stream that can be read from
156 String enc = (en.getContentEncoding() == null) ? null : en
157 .getContentEncoding().getValue();
158 if (en.getContentType() != null)
160 Cache.log.debug("Result Type: " + en.getContentType().toString());
164 Cache.log.debug("No Result Type Specified.");
166 if (enc == null || enc.length() < 1)
168 Cache.log.debug("Assuming 'Default' Result Encoding.");
172 Cache.log.debug("Result Encoded as : " + enc);
174 // attempt to identify file and construct an appropriate DataSource
175 // identifier for it.
177 // Mime-Multipart or single content type will be expected.
178 // if (enc.equals(org.apache.http.client.utils.)))
179 InputStreamReader br = null;
182 br = (enc != null) ? new InputStreamReader(en.getContent(), enc)
183 : new InputStreamReader(en.getContent());
184 } catch (UnsupportedEncodingException e)
186 Cache.log.error("Can't handle encoding '" + enc
187 + "' for response from webservice.", e);
190 errormessage = "Can't handle encoding for response from webservice";
195 dataIn = new BufferedReader(br);
202 protected void finalize() throws Throwable
205 cachedRequest = null;
212 } catch (Exception e)
222 * @return the URL that this result set read data from.
224 public String getUrl()
228 return cachedRequest.getURI().toURL().toString();
229 } catch (Exception x)