Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HttpResultSet	53	59	21	0.00%	Show methods

Class HttpResultSet

Class HttpResultSet	Line # 53	Total Statements 59	Complexity 21	TOTAL Coverage 0.00%
HttpResultSet(RestJob,HttpResponse,HttpRequestBase)   HttpResultSet(RestJob,HttpResponse,HttpRequestBase)	7474	5.05	1.01	0.0 0.00%
createResultDataProviders() : List<DataProvider>   createResultDataProviders() : List<DataProvider>	9090	4.04	1.01	0.0 0.00%
parseResultSet() : Object[]   parseResultSet() : Object[]	107107	20.020	4.04	0.0 0.00%
initDataSource(HttpResponse) : void   initDataSource(HttpResponse) : void	149149	21.021	9.09	0.0 0.00%
close() : void   close() : void	202202	5.05	4.04	0.0 0.00%
getUrl() : String   getUrl() : String	226226	4.04	2.02	0.0 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
		0% Uncovered Elements: 83 (83) Complexity: 21 Complexity Density: 0.36
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
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
74	0	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		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
90	0	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		*/
		0% Uncovered Elements: 24 (24) Complexity: 4 Complexity Density: 0.2
107	0	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
		0% Uncovered Elements: 33 (33) Complexity: 9 Complexity Density: 0.43
149	0	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
		0% Uncovered Elements: 7 (7) Complexity: 4 Complexity Density: 0.8
202	0	@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		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
226	0	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		}