Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
Annotate3D | 58 | 30 | 14 | ||
RvalsIterator | 190 | 16 | 10 |
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.ext.paradise; | |
22 | ||
23 | import java.io.BufferedReader; | |
24 | import java.io.IOException; | |
25 | import java.io.InputStreamReader; | |
26 | import java.io.Reader; | |
27 | import java.io.StringReader; | |
28 | import java.net.URL; | |
29 | import java.util.ArrayList; | |
30 | import java.util.Iterator; | |
31 | import java.util.List; | |
32 | import java.util.Map; | |
33 | ||
34 | import org.apache.http.NameValuePair; | |
35 | import org.apache.http.message.BasicNameValuePair; | |
36 | import org.json.simple.parser.ContentHandler; | |
37 | import org.json.simple.parser.ParseException; | |
38 | ||
39 | import jalview.util.HttpUtils; | |
40 | import jalview.util.JSONUtils; | |
41 | import jalview.util.MessageManager; | |
42 | import jalview.ws.HttpClientUtils; | |
43 | ||
44 | /** | |
45 | * simple methods for calling the various paradise RNA tools | |
46 | * | |
47 | * @author jimp | |
48 | * | |
49 | * @version v1.0 revised from original due to refactoring of | |
50 | * paradise-ubmc.u-strasbg.fr/webservices/annotate3d to | |
51 | * http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview <br/> | |
52 | * See also testing URL from fjossinet:<br/> | |
53 | * http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d <br/> | |
54 | * If in doubt, check against the REST client at: | |
55 | * https://github.com/fjossinet/RNA-Science | |
56 | * -Toolbox/blob/master/pyrna/restclient.py | |
57 | */ | |
58 | public class Annotate3D | |
59 | { | |
60 | // also test with | |
61 | // "http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d"; | |
62 | private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview"; | |
63 | ||
64 | 0 | private static ContentHandler createContentHandler() |
65 | { | |
66 | 0 | ContentHandler ch = new ContentHandler() |
67 | { | |
68 | ||
69 | 0 | @Override |
70 | public void startJSON() throws ParseException, IOException | |
71 | { | |
72 | // TODO Auto-generated method stub | |
73 | ||
74 | } | |
75 | ||
76 | 0 | @Override |
77 | public void endJSON() throws ParseException, IOException | |
78 | { | |
79 | // TODO Auto-generated method stub | |
80 | ||
81 | } | |
82 | ||
83 | 0 | @Override |
84 | public boolean startObject() throws ParseException, IOException | |
85 | { | |
86 | // TODO Auto-generated method stub | |
87 | 0 | return false; |
88 | } | |
89 | ||
90 | 0 | @Override |
91 | public boolean endObject() throws ParseException, IOException | |
92 | { | |
93 | // TODO Auto-generated method stub | |
94 | 0 | return false; |
95 | } | |
96 | ||
97 | 0 | @Override |
98 | public boolean startObjectEntry(String key) | |
99 | throws ParseException, IOException | |
100 | { | |
101 | // TODO Auto-generated method stub | |
102 | 0 | return false; |
103 | } | |
104 | ||
105 | 0 | @Override |
106 | public boolean endObjectEntry() throws ParseException, IOException | |
107 | { | |
108 | // TODO Auto-generated method stub | |
109 | 0 | return false; |
110 | } | |
111 | ||
112 | 0 | @Override |
113 | public boolean startArray() throws ParseException, IOException | |
114 | { | |
115 | // TODO Auto-generated method stub | |
116 | 0 | return false; |
117 | } | |
118 | ||
119 | 0 | @Override |
120 | public boolean endArray() throws ParseException, IOException | |
121 | { | |
122 | // TODO Auto-generated method stub | |
123 | 0 | return false; |
124 | } | |
125 | ||
126 | 0 | @Override |
127 | public boolean primitive(Object value) | |
128 | throws ParseException, IOException | |
129 | { | |
130 | // TODO Auto-generated method stub | |
131 | 0 | return false; |
132 | } | |
133 | ||
134 | }; | |
135 | 0 | return ch; |
136 | } | |
137 | ||
138 | 0 | public static Iterator<Reader> getRNAMLForPDBFileAsString(String pdbfile) |
139 | throws Exception | |
140 | { | |
141 | 0 | List<NameValuePair> vals = new ArrayList<>(); |
142 | 0 | vals.add(new BasicNameValuePair("tool", "rnaview")); |
143 | 0 | vals.add(new BasicNameValuePair("data", pdbfile)); |
144 | 0 | vals.add(new BasicNameValuePair("output", "rnaml")); |
145 | // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, | |
146 | // vals)); | |
147 | 0 | ArrayList<Reader> readers = new ArrayList<>(); |
148 | 0 | final BufferedReader postResponse = HttpClientUtils |
149 | .doHttpUrlPost(twoDtoolsURL, vals, 0, 0); | |
150 | 0 | readers.add(postResponse); |
151 | 0 | return readers.iterator(); |
152 | ||
153 | } | |
154 | ||
155 | 0 | public static Iterator<Reader> processJsonResponseFor(Reader respons) |
156 | throws Exception | |
157 | { | |
158 | 0 | org.json.simple.parser.JSONParser jp = new org.json.simple.parser.JSONParser(); |
159 | 0 | try |
160 | { | |
161 | 0 | final RvalsIterator rvals = new RvalsIterator(respons); |
162 | 0 | return rvals; |
163 | } catch (Exception foo) | |
164 | { | |
165 | 0 | throw new Exception(MessageManager.getString( |
166 | "exception.couldnt_parse_responde_from_annotated3d_server"), | |
167 | foo); | |
168 | } | |
169 | ||
170 | } | |
171 | ||
172 | 0 | public static Iterator<Reader> getRNAMLForPDBId(String pdbid) |
173 | throws Exception | |
174 | { | |
175 | 0 | List<NameValuePair> vals = new ArrayList<>(); |
176 | 0 | vals.add(new BasicNameValuePair("tool", "rnaview")); |
177 | 0 | vals.add(new BasicNameValuePair("pdbid", pdbid)); |
178 | 0 | vals.add(new BasicNameValuePair("output", "rnaml")); |
179 | 0 | java.net.URL geturl = new URL(twoDtoolsURL + "?tool=rnaview&pdbid=" |
180 | + pdbid + "&output=rnaml"); | |
181 | // return processJsonResponseFor(new | |
182 | // InputStreamReader(geturl.openStream())); | |
183 | 0 | ArrayList<Reader> readers = new ArrayList<>(); |
184 | 0 | readers.add(new InputStreamReader(HttpUtils.openStream(geturl))); |
185 | 0 | return readers.iterator(); |
186 | } | |
187 | ||
188 | } | |
189 | ||
190 | class RvalsIterator implements Iterator, AutoCloseable | |
191 | { | |
192 | private Iterator<Object> rvals; | |
193 | ||
194 | 0 | @SuppressWarnings("unchecked") |
195 | protected RvalsIterator(Reader respons) throws IOException, ParseException | |
196 | { | |
197 | /* | |
198 | * as in 2.11.1 (pre-JalviewJS) | |
199 | */ | |
200 | // final JSONArray responses = (JSONArray) jp.parse(respons); | |
201 | // this.rvals = responses.iterator(); | |
202 | ||
203 | /* | |
204 | * as in JalviewJS (with comment that this code is never called) | |
205 | */ | |
206 | 0 | this.rvals = ((List<Object>) JSONUtils.parse(respons)).iterator(); |
207 | } | |
208 | ||
209 | 0 | @Override |
210 | public boolean hasNext() | |
211 | { | |
212 | 0 | return rvals.hasNext(); |
213 | } | |
214 | ||
215 | 0 | @Override |
216 | public Reader next() | |
217 | { | |
218 | // JSONObject val = (JSONObject) rvals.next(); // 2.11.1 | |
219 | 0 | @SuppressWarnings("unchecked") |
220 | Map<String, Object> val = (Map<String, Object>) rvals.next(); | |
221 | ||
222 | 0 | Object sval = null; |
223 | 0 | try |
224 | { | |
225 | 0 | sval = val.get("2D"); |
226 | } catch (Exception x) | |
227 | { | |
228 | 0 | x.printStackTrace(); |
229 | } | |
230 | ||
231 | 0 | if (sval == null) |
232 | { | |
233 | 0 | jalview.bin.Console.errPrintln( |
234 | "DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :" | |
235 | + val.toString()); | |
236 | ||
237 | 0 | sval = ""; |
238 | } | |
239 | // 2.11.1: | |
240 | // return new StringReader( | |
241 | // (sval instanceof JSONObject) ? ((JSONObject) sval).toString() | |
242 | // : sval.toString()); | |
243 | 0 | return new StringReader(sval.toString()); |
244 | ||
245 | } | |
246 | ||
247 | 0 | @Override |
248 | public void remove() | |
249 | { | |
250 | 0 | throw new Error( |
251 | MessageManager.getString("error.not_implemented_remove")); | |
252 | ||
253 | } | |
254 | ||
255 | 0 | @Override |
256 | protected Object clone() throws CloneNotSupportedException | |
257 | { | |
258 | 0 | throw new CloneNotSupportedException( |
259 | MessageManager.getString("error.not_implemented_clone")); | |
260 | } | |
261 | ||
262 | 0 | @Override |
263 | public boolean equals(Object obj) | |
264 | { | |
265 | 0 | return super.equals(obj); |
266 | } | |
267 | ||
268 | 0 | @Override |
269 | public void close() | |
270 | { | |
271 | 0 | while (rvals.hasNext()) |
272 | { | |
273 | 0 | rvals.next(); |
274 | } | |
275 | } | |
276 | } |