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Coverage Report

  1. Project Clover database Wed Nov 13 2024 16:21:17 GMT
  2. Package jalview.ws.rest

File HttpResultSet.java

 

Coverage histogram

../../../img/srcFileCovDistChart0.png
59% of files have more coverage

Code metrics

18
59
6
1
238
155
21
0.36
9.83
6
3.5

Classes

Class Line # Actions
HttpResultSet 53 59 21
0.00%
 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.ws.rest;
22   
23    import jalview.bin.Console;
24    import jalview.io.FileParse;
25    import jalview.io.packed.DataProvider;
26    import jalview.io.packed.DataProvider.JvDataType;
27    import jalview.io.packed.ParsePackedSet;
28    import jalview.io.packed.SimpleDataProvider;
29    import jalview.util.MessageManager;
30    import jalview.ws.io.mime.JalviewMimeContentHandler;
31   
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;
38   
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;
45   
46    /**
47    * data source instantiated from the response of an httpclient request.
48    *
49    * @author JimP
50    *
51    */
52   
 
53    public class HttpResultSet extends FileParse implements AutoCloseable
54    {
55   
56    private HttpRequestBase cachedRequest;
57   
58    /**
59    * when set, indicates that en can be recreated by repeating the HttpRequest
60    * in cachedRequest
61    */
62    boolean repeatable = false;
63   
64    /**
65    * response that is to be parsed as jalview input data
66    */
67    private HttpEntity en = null;
68   
69    /**
70    * (sub)job that produced this result set.
71    */
72    private RestJob restJob;
73   
 
74  0 toggle public HttpResultSet(RestJob rj, HttpResponse con, HttpRequestBase req)
75    throws IOException
76    {
77  0 super();
78  0 setDataName(rj.getJobId() + " Part " + rj.getJobnum());
79  0 restJob = rj;
80  0 cachedRequest = req;
81  0 initDataSource(con);
82    }
83   
84    /**
85    * construct a set of dataproviders to parse a result set from this service
86    *
87    * @param resSet
88    * @return
89    */
 
90  0 toggle public List<DataProvider> createResultDataProviders()
91    {
92  0 List<DataProvider> dp = new ArrayList<>();
93  0 for (JvDataType type : restJob.rsd.getResultDataTypes())
94    {
95  0 dp.add(new SimpleDataProvider(type, this, null));
96    }
97  0 return dp;
98    }
99   
100    /**
101    * parses the results of the service output.
102    *
103    * @return the result of ParsePackedSet.getAlignment()
104    * @throws Exception
105    * @throws Error
106    */
 
107  0 toggle public Object[] parseResultSet() throws Exception, Error
108    {
109  0 List<DataProvider> dp = new ArrayList<>();
110  0 Object[] results = null;
111   
112  0 if (en == null)
113    {
114  0 throw new Error(MessageManager.getString(
115    "error.implementation_error_need_to_have_httpresponse"));
116    }
117  0 jalview.io.packed.JalviewDataset ds = restJob.newJalviewDataset();
118    // Decide how we deal with content.
119  0 if (en instanceof MultipartEntity)
120    {
121    // Multipart messages should be properly typed, so we parse them as we go.
122  0 MultipartEntity mpe = (MultipartEntity) en;
123    // multipart
124  0 JalviewMimeContentHandler handler = new JalviewMimeContentHandler(ds);
125  0 MimeStreamParser parser = new MimeStreamParser();
126  0 parser.setContentHandler(handler);
127  0 try
128    {
129  0 parser.parse(mpe.getContent());
130    } catch (MimeException me)
131    {
132  0 error = true;
133  0 errormessage = "Couldn't parse message from web service.";
134  0 Console.warn("Failed to parse MIME multipart content", me);
135  0 en.consumeContent();
136    }
137  0 return new ParsePackedSet().getAlignment(ds,
138    handler.getJalviewDataProviders());
139    }
140    else
141    {
142    // Need to use hints from rest service description.
143  0 dp = createResultDataProviders();
144  0 ParsePackedSet pps = new ParsePackedSet();
145  0 return pps.getAlignment(ds, dp);
146    }
147    }
148   
 
149  0 toggle private void initDataSource(HttpResponse con) throws IOException
150    {
151  0 en = con.getEntity();
152  0 repeatable = en.isRepeatable();
153   
154  0 if (!(en instanceof MultipartEntity))
155    {
156    // assume content is simple text stream that can be read from
157  0 String enc = (en.getContentEncoding() == null) ? null
158    : en.getContentEncoding().getValue();
159  0 if (en.getContentType() != null)
160    {
161  0 Console.debug("Result Type: " + en.getContentType().toString());
162    }
163    else
164    {
165  0 Console.debug("No Result Type Specified.");
166    }
167  0 if (enc == null || enc.length() < 1)
168    {
169  0 Console.debug("Assuming 'Default' Result Encoding.");
170    }
171    else
172    {
173  0 Console.debug("Result Encoded as : " + enc);
174    }
175    // attempt to identify file and construct an appropriate DataSource
176    // identifier for it.
177    // try to parse
178    // Mime-Multipart or single content type will be expected.
179    // if (enc.equals(org.apache.http.client.utils.)))
180  0 InputStreamReader br = null;
181  0 try
182    {
183  0 br = (enc != null) ? new InputStreamReader(en.getContent(), enc)
184    : new InputStreamReader(en.getContent());
185    } catch (UnsupportedEncodingException e)
186    {
187  0 Console.error("Can't handle encoding '" + enc
188    + "' for response from webservice.", e);
189  0 en.consumeContent();
190  0 error = true;
191  0 errormessage = "Can't handle encoding for response from webservice";
192  0 return;
193    }
194  0 if (br != null)
195    {
196  0 dataIn = new BufferedReader(br);
197  0 error = false;
198    }
199    }
200    }
201   
 
202  0 toggle @Override
203    public void close()
204    {
205  0 dataIn = null;
206  0 cachedRequest = null;
207  0 try
208    {
209  0 if (en != null)
210    {
211  0 en.consumeContent();
212    }
213    } catch (Exception e)
214    {
215    } catch (Error ex)
216    {
217    }
218    // no finalize for FileParse
219    // super.close();
220    }
221   
222    /**
223    *
224    * @return the URL that this result set read data from.
225    */
 
226  0 toggle public String getUrl()
227    {
228  0 try
229    {
230  0 return cachedRequest.getURI().toURL().toString();
231    } catch (Exception x)
232    {
233  0 x.printStackTrace();
234  0 return null;
235    }
236    }
237   
238    }