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comparison smart_toolShed/SMART/Java/Sav/PythonHelperReader.java @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 /**
2 *
3 * Copyright INRA-URGI 2009-2010
4 *
5 * This software is governed by the CeCILL license under French law and
6 * abiding by the rules of distribution of free software. You can use,
7 * modify and/ or redistribute the software under the terms of the CeCILL
8 * license as circulated by CEA, CNRS and INRIA at the following URL
9 * "http://www.cecill.info".
10 *
11 * As a counterpart to the access to the source code and rights to copy,
12 * modify and redistribute granted by the license, users are provided only
13 * with a limited warranty and the software's author, the holder of the
14 * economic rights, and the successive licensors have only limited
15 * liability.
16 *
17 * In this respect, the user's attention is drawn to the risks associated
18 * with loading, using, modifying and/or developing or reproducing the
19 * software by the user in light of its specific status of free software,
20 * that may mean that it is complicated to manipulate, and that also
21 * therefore means that it is reserved for developers and experienced
22 * professionals having in-depth computer knowledge. Users are therefore
23 * encouraged to load and test the software's suitability as regards their
24 * requirements in conditions enabling the security of their systems and/or
25 * data to be ensured and, more generally, to use and operate it in the
26 * same conditions as regards security.
27 *
28 * The fact that you are presently reading this means that you have had
29 * knowledge of the CeCILL license and that you accept its terms.
30 *
31 */
32 import java.util.*;
33 import java.io.File;
34 import java.io.*;
35 import java.util.regex.*;
36
37 public class PythonHelperReader {
38
39 String fileName;
40 Program program;
41 BufferedReader reader;
42 String message;
43
44 public PythonHelperReader(String fileName) {
45 this.fileName = fileName;
46 this.reader = reader;
47 this.message = null;
48 }
49
50 public void setReader(BufferedReader reader) {
51 this.reader = reader;
52 }
53
54 public void run() {
55 this.program = new Program();
56 boolean inBeginning = true;
57 boolean inUsage = false;
58 boolean afterUsage = false;
59 boolean inDescription = false;
60 boolean afterDescription = false;
61 boolean inOptions = false;
62 boolean inOptionBlank = false;
63 boolean inError = false;
64 String usage = null;
65 String description = null;
66 String option = null;
67 Vector <String> options = new Vector < String > ();
68 String[] optionSplitted;
69
70 // Parse file
71 try {
72 String line = null;
73
74 while ((line = reader.readLine()) != null) {
75 line = line.trim();
76 if (line.startsWith("Traceback")) {
77 this.message = "Problem with header of '" + this.fileName + "':\n" + line + "\n";
78 inError = true;
79 inBeginning = false;
80 inUsage = false;
81 afterUsage = false;
82 inDescription = false;
83 afterDescription = false;
84 inOptions = false;
85 inOptionBlank = false;
86 }
87 else if (inError) {
88 this.message += line + "\n";
89 }
90 else if (inBeginning) {
91 if (line.startsWith("Usage:")) {
92 inUsage = true;
93 inBeginning = false;
94 usage = line;
95 }
96 }
97 else if (inUsage) {
98 if ("".equals(line)) {
99 inUsage = false;
100 afterUsage = true;
101 }
102 else {
103 usage += " " + line;
104 }
105 }
106 else if (afterUsage) {
107 if (! "".equals(line)) {
108 description = line;
109 afterUsage = false;
110 inDescription = true;
111 }
112 }
113 else if (inDescription) {
114 if ("".equals(line)) {
115 inDescription = false;
116 afterDescription = true;
117 }
118 else {
119 description += " " + line;
120 }
121 }
122 else if (afterDescription) {
123 if (! "".equals(line)) {
124 afterDescription = false;
125 inOptions = true;
126 }
127 }
128 else if (inOptions) {
129 if ("".equals(line)) {
130 inOptions = false;
131 inOptionBlank = true;
132 }
133 else {
134 if (option == null) {
135 option = line;
136 }
137 else {
138 if (line.charAt(0) == '-') {
139 options.add(option);
140 option = line;
141 }
142 else {
143 option += " " + line;
144 }
145 }
146 }
147 }
148 else if (inOptionBlank) {
149 if (! "".equals(line)) {
150 inOptionBlank = false;
151 inOptions = true;
152 }
153 }
154 else {
155 this.message = "Something is wrong in the file '" + this.fileName + "'.";
156 return;
157 }
158 }
159
160 reader.close();
161 }
162 catch (FileNotFoundException e) {
163 this.message = "File " + this.fileName + " not found";
164 return;
165 }
166 catch (IOException e) {
167 this.message = "IOException while reading file " + this.fileName;
168 return;
169 }
170
171 if (inError) {
172 return;
173 }
174
175 if (option != null) {
176 options.add(option);
177 }
178
179 HashMap < String, ProgramOption > identifierToOptions = new HashMap < String, ProgramOption > ();
180 HashMap < ProgramOption, String > associatedOption = new HashMap < ProgramOption, String > ();
181
182 if (usage == null) {
183 this.message = "Cannot read the usage of file " + this.fileName;
184 return;
185 }
186 program.setShortName(usage.split(" ")[1].trim());
187 program.setName(description.split(":")[0].trim());
188
189 Pattern pattern = Pattern.compile("\\[Category: .*\\]");
190 Matcher matcher = pattern.matcher(description);
191 if (matcher.find()) {
192 program.setSection(description.substring(matcher.start() + "[Category: ".length(), matcher.end() - 1));
193 program.setDescription(description.substring(0, matcher.start() - 1).trim());
194 }
195 else {
196 this.message = "Cannot find category in description '" + description + "' in file " + this.fileName;
197 return;
198 }
199 for (int i = 0; i < options.size(); i++) {
200 option = options.get(i).replace("\t", " ");
201 optionSplitted = option.split(" ");
202 option = "";
203 for (int j = 3; j < optionSplitted.length; j++) {
204 option += optionSplitted[j] + " ";
205 }
206
207 String identifier = optionSplitted[0].replace("-", "").replace(",", "");
208 // Skip -h and -v options
209 if (("h".equals(identifier)) || ("v".equals(identifier)))
210 continue;
211
212 ProgramOption programOption = new ProgramOption();
213 programOption.setIdentifier("-" + identifier);
214 programOption.setComment(option.substring(0, option.indexOf("[")).trim());
215 identifierToOptions.put(identifier, programOption);
216
217 pattern = Pattern.compile("\\[[^\\]]*\\]");
218 matcher = pattern.matcher(option);
219 while (matcher.find()) {
220 String inner = option.substring(matcher.start()+1, matcher.end()-1);
221 if (inner.contains(":")) {
222 String type = inner.substring(0, inner.indexOf(":")).trim();
223 String value = inner.substring(inner.indexOf(":")+1).trim();
224 // Types of the options
225 if ("format".compareToIgnoreCase(type) == 0) {
226 String currentWord = "";
227 String rest = "";
228 if (value.contains(" ")) {
229 int pos = value.indexOf(" ");
230 currentWord = value.substring(0, pos);
231 rest = value.substring(pos+1);
232 }
233 else {
234 currentWord = value;
235 }
236 // Output file type
237 if ("output".compareToIgnoreCase(currentWord) == 0) {
238 programOption.setInput(false);
239 int pos = rest.indexOf(" ");
240 currentWord = rest.substring(0, pos).trim();
241 rest = rest.substring(pos+1).trim();
242 }
243 // File (input or output file)
244 if ("file".compareToIgnoreCase(currentWord) == 0) {
245 programOption.setType("file");
246 // Format given by an associated option (to be found later)
247 if (rest.startsWith("in format given by ")) {
248 associatedOption.put(programOption, rest.substring(rest.indexOf("format given by ") + "format given by ".length() + 1).trim());
249 }
250 else {
251 if (! rest.startsWith("in ")) {
252 this.message = "Descriptor " + option + " does not have a proper format.";
253 return;
254 }
255 rest = rest.substring("in ".length());
256 int pos = rest.indexOf(" format");
257 if (pos == -1) {
258 this.message = "Descriptor " + option + " does not have a proper format.";
259 return;
260 }
261 programOption.setFormat(rest.substring(0, pos).trim().toLowerCase().split(" or "));
262 }
263 }
264 // Format type
265 else if (rest.endsWith("file format")) {
266 programOption.setFormat((currentWord + " " + rest.substring(0, rest.indexOf("file format"))).trim().toLowerCase().split(" or "));
267 programOption.setType("format");
268 }
269 // Choice type
270 else if ("choice".compareToIgnoreCase(currentWord) == 0) {
271 programOption.setChoices(rest.replace("(", "").replace(")", "").split(", "));
272 programOption.setType("choice");
273 }
274 // Boolean type
275 else if ("bool".compareToIgnoreCase(currentWord) == 0) {
276 programOption.setType("boolean");
277 }
278 // Other type
279 else {
280 programOption.setType(currentWord);
281 }
282 }
283 // Default value
284 else if ("default".compareToIgnoreCase(type) == 0) {
285 programOption.setDefault(value);
286 }
287 else {
288 this.message = "Do not understand option descriptor '" + inner + "'.";
289 return;
290 }
291 }
292 else {
293 // Compulsory option
294 if ("compulsory".compareToIgnoreCase(inner) == 0) {
295 programOption.setCompulsory(true);
296 }
297 else {
298 this.message = "Do not understand option descriptor '" + inner + "'.";
299 return;
300 }
301 }
302 }
303 program.addOption(programOption);
304 }
305
306 // Set associated option
307 Iterator it = associatedOption.keySet().iterator();
308 while (it.hasNext()) {
309 ProgramOption programOption = (ProgramOption) it.next();
310 programOption.setAssociatedOption(identifierToOptions.get(associatedOption.get(programOption)));
311 }
312 }
313
314 public String getMessage () {
315 return this.message;
316 }
317
318 public Program getProgram () {
319 return this.program;
320 }
321 }
322
323