Mercurial > repos > yufei-luo > s_mart

comparison commons/core/checker/test/Test_ConfigChecker.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 from commons.core.checker.ConfigChecker import ConfigChecker
2 from commons.core.checker.ConfigChecker import ConfigRules
3 from commons.core.checker.RepetException import RepetException
4 import os
5 import unittest
6
7 class Test_ConfigChecker(unittest.TestCase):
8
9 def setUp(self):
10 self._configFileName = "testConfigChecker.cfg"
11 self._iMock = MockConfig()
12
13 def test_checkIfExistsConfigFile_file_exist(self):
14 f=open(self._configFileName, "w")
15 f.close()
16
17 doesFileExists = True
18 iConfigRules = ConfigRules()
19 try:
20 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
21 iConfigChecker.checkIfExistsConfigFile()
22 except RepetException:
23 doesFileExists = False
24 os.remove(self._configFileName)
25 self.assertTrue(doesFileExists)
26
27 def test_checkIfExistsConfigFile_file_not_exist(self):
28 iConfigRules = ConfigRules()
29 expMsg ="CONFIG FILE not found - '%s'" %self._configFileName
30 doesFileExists = True
31 try:
32 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
33 iConfigChecker.checkIfExistsConfigFile()
34 except RepetException, re:
35 doesFileExists = False
36 self.assertFalse(doesFileExists)
37 self.assertEqual(expMsg, re.getMessage())
38
39 def test_readConfigFile(self):
40 self._iMock.write_config(self._configFileName)
41 iConfigRules = ConfigRules()
42 expDictRawConfigValues = {"dir_name" : {"work_dir":"toto"},
43 "organism" : {"abbreviation":"T.aestivum",
44 "genus":"triticum",
45 "species":"aestivum",
46 "common_name":"wheat",
47 "comment":""},
48 'analysis1': {'description': '',
49 'gff_name': 'BLASTX.gff2',
50 'name': 'BLASTXWheat2',
51 'program': 'BLASTX2',
52 'programversion': '3.32',
53 'sourcename': 'dummyDesc_BLASTX2'}
54 }
55 isNoExceptionRaised = True
56 try:
57 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
58 iConfig = iConfigChecker.readConfigFile()
59 iConfigChecker.setRawConfig(iConfig)
60 obsDictRawConfigValues = iConfigChecker._iRawConfig.dOptionsValues4Sections
61 except RepetException:
62 isNoExceptionRaised = False
63 os.remove(self._configFileName)
64 self.assertTrue(isNoExceptionRaised)
65 self.assertEquals(obsDictRawConfigValues, expDictRawConfigValues)
66
67 def test_readConfigFile_section_define_twice(self):
68 self._iMock.write_case_section_define_twice(self._configFileName)
69 iConfigRules = ConfigRules()
70 expMsg = "Duplicate section exist in config file %s" %self._configFileName
71 expDictRawConfigValues = {"dir_name": {"work_dir":"toto"},
72 "analysis1" : {"name": "BLASTXWheat2",
73 "program" : "BLASTX2",
74 "programversion" : "3.32",
75 "sourcename" :"dummyDesc_BLASTX2",
76 "description" : "",
77 "gff_name" :"BLASTX.gff2"}
78 }
79 doesNoExceptionRaised = True
80 try:
81 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
82 iConfig = iConfigChecker.readConfigFile()
83 iConfigChecker.setRawConfig(iConfig)
84 obsDictRawConfigValues = iConfigChecker._iRawConfig.dOptionsValues4Sections
85 except RepetException, re:
86 doesNoExceptionRaised = False
87 os.remove(self._configFileName)
88 # self.assertFalse(doesNoExceptionRaised)
89 # self.assertEqual(expMsg, re.getMessage())
90 #
91 self.assertTrue(doesNoExceptionRaised)
92 self.assertEquals(obsDictRawConfigValues, expDictRawConfigValues)
93
94 def test_readConfigFile_option_define_twice(self):
95 self._iMock.write_case_option_define_twice(self._configFileName)
96 iConfigRules = ConfigRules()
97 doesNoExceptionRaised = True
98 expDictRawConfigValues = {"dir_name": {"work_dir":"toto"},
99 "analysis1" : {"name": "BLASTXWheat",
100 "program" : "BLASTX2",
101 "programversion" : "3.3",
102 "sourcename" :"dummyDesc_BLASTX",
103 "description" : "",
104 "gff_name" :"BLASTX.gff"}
105 }
106 try:
107 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
108 iConfig = iConfigChecker.readConfigFile()
109 iConfigChecker.setRawConfig(iConfig)
110 obsDictRawConfigValues = iConfigChecker._iRawConfig.dOptionsValues4Sections
111 except RepetException, re:
112 doesNoExceptionRaised = False
113 os.remove(self._configFileName)
114 ## self.assertFalse(doesNoExceptionRaised)
115 ## self.assertEqual(expMsg, re.getMessage())
116
117 self.assertTrue(doesNoExceptionRaised)
118 self.assertEquals(obsDictRawConfigValues, expDictRawConfigValues)
119
120 def test_checkMandatorySections(self):
121 self._iMock.write_config(self._configFileName)
122 iConfigRules = ConfigRules()
123 iConfigRules.addRuleSection(section="dir_name", mandatory=True)
124 iConfigRules.addRuleSection(section="organism", mandatory=True)
125 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
126 iConfig = iConfigChecker.readConfigFile()
127 iConfigChecker.setRawConfig(iConfig)
128 iConfigChecker.extendConfigRulesWithPatternRules()
129 areAllMandatorySectionsFound = True
130 try:
131 iConfigChecker.checkMandatorySections()
132 except RepetException:
133 areAllMandatorySectionsFound = False
134 os.remove(self._configFileName)
135 self.assertTrue(areAllMandatorySectionsFound)
136
137 def test_checkMandatorySections_one_missing (self):
138 self._iMock.write_config(self._configFileName)
139 iConfigRules = ConfigRules()
140 iConfigRules.addRuleSection(section="dir_name", mandatory=True)
141 iConfigRules.addRuleSection(section="target", mandatory=True)
142 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
143 iConfig = iConfigChecker.readConfigFile()
144 iConfigChecker.setRawConfig(iConfig)
145 iConfigChecker.extendConfigRulesWithPatternRules()
146 expMsg = "Error in configuration file %s, following sections are missing:\n - target\n"% self._configFileName
147 areAllMandatorySectionsFound = True
148 try:
149 iConfigChecker.checkMandatorySections()
150 except RepetException, re:
151 areAllMandatorySectionsFound = False
152 os.remove(self._configFileName)
153 self.assertFalse(areAllMandatorySectionsFound)
154 self.assertEquals(expMsg, re.getMessage())
155
156 def test_checkMandatorySections_mandatory_section_with_pattern_section_is_missing (self):
157 self._iMock.write_config(self._configFileName)
158 iConfigRules = ConfigRules()
159 iConfigRules.addRuleSection(section="dir_name", mandatory=True)
160 iConfigRules.addRuleSection(section="mandatorySection", mandatory=True, isPattern = True)
161 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
162 iConfig = iConfigChecker.readConfigFile()
163 iConfigChecker.setRawConfig(iConfig)
164 iConfigChecker.extendConfigRulesWithPatternRules()
165 expMsg = "Error in configuration file %s, following sections are missing:\n - mandatorySection\n"% self._configFileName
166 areAllMandatorySectionsFound = True
167 try:
168 iConfigChecker.checkMandatorySections()
169 except RepetException, re:
170 areAllMandatorySectionsFound = False
171 os.remove(self._configFileName)
172 self.assertFalse(areAllMandatorySectionsFound)
173 self.assertEquals(expMsg, re.getMessage())
174
175 def test_checkMandatorySections_mandatory_section_is_pattern (self):
176 self._iMock.write_case_pattern_rule(self._configFileName)
177 iConfigRules = ConfigRules()
178 iConfigRules.addRuleSection(section="dir_name", mandatory=True)
179 iConfigRules.addRuleSection(section="analysis[0-9]*", mandatory=True, isPattern = True)
180 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
181 iConfig = iConfigChecker.readConfigFile()
182 iConfigChecker.setRawConfig(iConfig)
183 iConfigChecker.extendConfigRulesWithPatternRules()
184 areAllMandatorySectionsFound = True
185 try:
186 iConfigChecker.checkMandatorySections()
187 except RepetException:
188 areAllMandatorySectionsFound = False
189 os.remove(self._configFileName)
190 self.assertTrue(areAllMandatorySectionsFound)
191
192 def test_checkMandatoryOptions_in_mandatory_section (self):
193 self._iMock.write_config(self._configFileName)
194 iConfigRules = ConfigRules()
195 iConfigRules.addRuleSection(section="organism", mandatory=True)
196 iConfigRules.addRuleOption(section="organism", option ="genus", mandatory=True)
197 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
198 iConfig = iConfigChecker.readConfigFile()
199 iConfigChecker.setRawConfig(iConfig)
200 iConfigChecker.extendConfigRulesWithPatternRules()
201 areAllMandatoryOptionsFound = True
202 try:
203 iConfigChecker.checkMandatoryOptions()
204 except RepetException:
205 areAllMandatoryOptionsFound = False
206 os.remove(self._configFileName)
207 self.assertTrue(areAllMandatoryOptionsFound)
208
209 def test_checkMandatoryOptions_in_mandatory_section_option_is_missing (self):
210 self._iMock.write_config(self._configFileName)
211 iConfigRules = ConfigRules()
212 iConfigRules.addRuleSection(section="organism", mandatory=True)
213 iConfigRules.addRuleOption(section="organism", option ="MissingOption", mandatory=True)
214 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
215 iConfig = iConfigChecker.readConfigFile()
216 iConfigChecker.setRawConfig(iConfig)
217 iConfigChecker.extendConfigRulesWithPatternRules()
218 expMsg = "Error in configuration file %s, following options are missing: \n - [organism]: MissingOption\n" % self._configFileName
219 areAllMandatoryOptionsFound = True
220 try:
221 iConfigChecker.checkMandatoryOptions()
222 except RepetException, re:
223 areAllMandatoryOptionsFound = False
224 os.remove(self._configFileName)
225 self.assertFalse(areAllMandatoryOptionsFound)
226 self.assertEquals(expMsg, re.getMessage())
227
228 def test_checkMandatoryOptions_in_non_mandatory_section_and_section_and_option_exist (self):
229 self._iMock.write_config(self._configFileName)
230 iConfigRules = ConfigRules()
231 iConfigRules.addRuleOption(section="organism", option ="genus", mandatory=True)
232 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
233 iConfig = iConfigChecker.readConfigFile()
234 iConfigChecker.setRawConfig(iConfig)
235 iConfigChecker.extendConfigRulesWithPatternRules()
236 areAllMandatoryOptionsFound = True
237 try:
238 iConfigChecker.checkMandatoryOptions()
239 except RepetException:
240 areAllMandatoryOptionsFound = False
241 os.remove(self._configFileName)
242 self.assertTrue(areAllMandatoryOptionsFound)
243
244 def test_checkMandatoryOptions_in_non_mandatory_section_and_section_exist_option_is_missing (self):
245 self._iMock.write_config(self._configFileName)
246 iConfigRules = ConfigRules()
247 iConfigRules.addRuleOption(section="organism", option ="MissingOption", mandatory=True)
248 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
249 iConfig = iConfigChecker.readConfigFile()
250 iConfigChecker.setRawConfig(iConfig)
251 iConfigChecker.extendConfigRulesWithPatternRules()
252 expMsg = "Error in configuration file %s, following options are missing: \n - [organism]: MissingOption\n" % self._configFileName
253 areAllMandatoryOptionsFound = True
254 try:
255 iConfigChecker.checkMandatoryOptions()
256 except RepetException, re:
257 areAllMandatoryOptionsFound = False
258 os.remove(self._configFileName)
259 self.assertFalse(areAllMandatoryOptionsFound)
260 self.assertEquals(expMsg,re.getMessage())
261
262 def test_checkMandatoryOptions_in_non_mandatory_section_and_section_does_not_exist (self):
263 self._iMock.write_config(self._configFileName)
264 iConfigRules = ConfigRules()
265 iConfigRules.addRuleOption(section="NonExistingAndNonMandatorySection", option ="genus", mandatory=True)
266 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
267 iConfig = iConfigChecker.readConfigFile()
268 iConfigChecker.setRawConfig(iConfig)
269 iConfigChecker.extendConfigRulesWithPatternRules()
270 areAllMandatoryOptionsFound = True
271 try:
272 iConfigChecker.checkMandatoryOptions()
273 except RepetException:
274 areAllMandatoryOptionsFound = False
275 os.remove(self._configFileName)
276 self.assertTrue(areAllMandatoryOptionsFound)
277
278 def test_checkMandatoryOptions_with_Pattern_rules_in_section (self):
279 self._iMock.write_case_pattern_rule(self._configFileName)
280 iConfigRules = ConfigRules()
281 iConfigRules.addRuleSection(section="analysis", isPattern=True)
282 iConfigRules.addRuleOption(section="analysis", option ="name", mandatory=True)
283 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
284 iConfig = iConfigChecker.readConfigFile()
285 iConfigChecker.setRawConfig(iConfig)
286 iConfigChecker.extendConfigRulesWithPatternRules()
287 areAllMandatoryOptionsFound = True
288 try:
289 iConfigChecker.checkMandatoryOptions()
290 except RepetException:
291 areAllMandatoryOptionsFound = False
292 os.remove(self._configFileName)
293 self.assertTrue(areAllMandatoryOptionsFound)
294
295 def test_checkMandatoryOptions_with_pattern_rules_in_option_section_is_mandatory (self):
296 self._iMock.write_case_pattern_rule(self._configFileName)
297 iConfigRules = ConfigRules()
298 iConfigRules.addRuleSection(section="section_with_option_pattern", mandatory=True)
299 iConfigRules.addRuleOption(section="section_with_option_pattern", option ="option", isPattern= True, mandatory=True)
300 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
301 iConfig = iConfigChecker.readConfigFile()
302 iConfigChecker.setRawConfig(iConfig)
303 iConfigChecker.extendConfigRulesWithPatternRules()
304 areAllMandatoryOptionsFound = True
305 try:
306 iConfigChecker.checkMandatoryOptions()
307 except RepetException:
308 areAllMandatoryOptionsFound = False
309 os.remove(self._configFileName)
310 self.assertTrue(areAllMandatoryOptionsFound)
311
312 def test_checkMandatoryOptions_with_pattern_rules_in_option_in_mandatory_section_option_is_missing (self):
313 self._iMock.write_case_pattern_rule(self._configFileName)
314 iConfigRules = ConfigRules()
315 iConfigRules.addRuleSection(section="section_with_option_pattern", mandatory=True)
316 iConfigRules.addRuleOption(section="section_with_option_pattern", option ="MissingOption", isPattern= True, mandatory=True)
317 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
318 iConfig = iConfigChecker.readConfigFile()
319 iConfigChecker.setRawConfig(iConfig)
320 iConfigChecker.extendConfigRulesWithPatternRules()
321 expMsg = "Error in configuration file %s, following options are missing: \n - [section_with_option_pattern]: MissingOption\n" % self._configFileName
322 areAllMandatoryOptionsFound = True
323 try:
324 iConfigChecker.checkMandatoryOptions()
325 except RepetException, re:
326 areAllMandatoryOptionsFound = False
327 os.remove(self._configFileName)
328 self.assertFalse(areAllMandatoryOptionsFound)
329 self.assertEquals(expMsg, re.getMessage())
330
331 def test_checkMandatoryOptions_with_pattern_rules_in_non_mandatory_section_and_section_and_option_exist (self):
332 self._iMock.write_case_pattern_rule(self._configFileName)
333 iConfigRules = ConfigRules()
334 iConfigRules.addRuleOption(section="section_with_option_pattern", option ="option", isPattern= True, mandatory=True)
335 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
336 iConfig = iConfigChecker.readConfigFile()
337 iConfigChecker.setRawConfig(iConfig)
338 iConfigChecker.extendConfigRulesWithPatternRules()
339 areAllMandatoryOptionsFound = True
340 try:
341 iConfigChecker.checkMandatoryOptions()
342 except RepetException:
343 areAllMandatoryOptionsFound = False
344 os.remove(self._configFileName)
345 self.assertTrue(areAllMandatoryOptionsFound)
346
347 def test_checkMandatoryOptions_with_pattern_rules_in_non_mandatory_section_and_section_exist_option_is_missing (self):
348 self._iMock.write_case_pattern_rule(self._configFileName)
349 iConfigRules = ConfigRules()
350 iConfigRules.addRuleOption(section="section_with_option_pattern", option ="MissingOption", isPattern= True, mandatory=True)
351 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
352 iConfig = iConfigChecker.readConfigFile()
353 iConfigChecker.setRawConfig(iConfig)
354 iConfigChecker.extendConfigRulesWithPatternRules()
355 expMsg = "Error in configuration file %s, following options are missing: \n - [section_with_option_pattern]: MissingOption\n" % self._configFileName
356 areAllMandatoryOptionsFound = True
357 try:
358 iConfigChecker.checkMandatoryOptions()
359 except RepetException, re:
360 areAllMandatoryOptionsFound = False
361 os.remove(self._configFileName)
362 self.assertFalse(areAllMandatoryOptionsFound)
363 self.assertEquals(expMsg,re.getMessage())
364
365 def test_checkMandatoryOptions_with_pattern_rules_in_non_mandatory_section_and_section_does_not_exist (self):
366 self._iMock.write_case_pattern_rule(self._configFileName)
367 iConfigRules = ConfigRules()
368 iConfigRules.addRuleOption(section="non_mandatory_section", option ="MissingOption", isPattern= True, mandatory=True)
369 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
370 iConfig = iConfigChecker.readConfigFile()
371 iConfigChecker.setRawConfig(iConfig)
372 iConfigChecker.extendConfigRulesWithPatternRules()
373 areAllMandatoryOptionsFound = True
374 try:
375 iConfigChecker.checkMandatoryOptions()
376 except RepetException:
377 areAllMandatoryOptionsFound = False
378 os.remove(self._configFileName)
379 self.assertTrue(areAllMandatoryOptionsFound)
380
381 def test_checkMandatoryOptions_with_pattern_rules_for_both_section_and_option (self):
382 self._iMock.write_case_pattern_rule(self._configFileName)
383 iConfigRules = ConfigRules()
384 iConfigRules.addRuleSection(section="section_with_option_pattern", isPattern=True)
385 iConfigRules.addRuleOption(section="section_with_option_pattern", option ="option", isPattern= True, mandatory=True)
386 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
387 iConfig = iConfigChecker.readConfigFile()
388 iConfigChecker.setRawConfig(iConfig)
389 iConfigChecker.extendConfigRulesWithPatternRules()
390 areAllMandatoryOptionsFound = True
391 try:
392 iConfigChecker.checkMandatoryOptions()
393 except RepetException:
394 areAllMandatoryOptionsFound = False
395 os.remove(self._configFileName)
396 self.assertTrue(areAllMandatoryOptionsFound)
397
398 def test_checkMandatoryOptions_case(self):
399 self._iMock.write_config_case(self._configFileName)
400 iConfigRules = ConfigRules()
401 iConfigRules.addRuleSection("dir_name", True)
402 iConfigRules.addRuleSection("organism", True)
403 iConfigRules.addRuleOption("organism", "min_SSR_coverage", True)
404 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
405 iConfig = iConfigChecker.readConfigFile()
406 iConfigChecker.setRawConfig(iConfig)
407 iConfigChecker.extendConfigRulesWithPatternRules()
408 areAllMandatorySectionsFound = True
409 try:
410 iConfigChecker.checkMandatoryOptions()
411 except RepetException:
412 areAllMandatorySectionsFound = False
413 os.remove(self._configFileName)
414 self.assertTrue(areAllMandatorySectionsFound)
415
416 #TODO Test de extendConfigRulesWithPatternRules et de applyRuleToRawValue
417 # option avec une liste de valeurs possibles dans un ensemble
418 # option type=string type="num" type="date"???.
419 #option define twice and options use in other
420
421 class MockConfig (object):
422
423 def write_config(self, configFileName):
424 configF = open(configFileName, "w" )
425 configF.write( "[dir_name]\n")
426 configF.write( "work_dir : toto \n")
427 configF.write( "\n")
428 configF.write( "[organism]\n")
429 configF.write( "abbreviation: T.aestivum\n")
430 configF.write( "genus: triticum\n")
431 configF.write( "species: aestivum\n")
432 configF.write( "common_name: wheat\n")
433 configF.write( "comment: \n")
434 configF.write( "[analysis1]\n")
435 configF.write( "name: BLASTXWheat2\n")
436 configF.write( "program: BLASTX2\n")
437 configF.write( "programversion: 3.32\n")
438 configF.write( "sourcename: dummyDesc_BLASTX2\n")
439 configF.write( "description: \n")
440 configF.write( "gff_name: BLASTX.gff2\n")
441 configF.write( "\n")
442 configF.close()
443
444 def write_case_section_define_twice(self, configFileName):
445 configF = open(configFileName, "w" )
446 configF.write( "[dir_name]\n")
447 configF.write( "work_dir : toto \n")
448 configF.write( "\n")
449 configF.write( "[analysis1]\n")
450 configF.write( "name: BLASTXWheat\n")
451 configF.write( "program: BLASTX\n")
452 configF.write( "programversion: 3.3\n")
453 configF.write( "sourcename: dummyDesc_BLASTX\n")
454 configF.write( "description: \n")
455 configF.write( "gff_name: BLASTX.gff\n")
456 configF.write( "\n")
457 configF.write( "[analysis1]\n")
458 configF.write( "name: BLASTXWheat2\n")
459 configF.write( "program: BLASTX2\n")
460 configF.write( "programversion: 3.32\n")
461 configF.write( "sourcename: dummyDesc_BLASTX2\n")
462 configF.write( "description: \n")
463 configF.write( "gff_name: BLASTX.gff2\n")
464 configF.write( "\n")
465 configF.close()
466
467 def write_case_option_define_twice(self, configFileName):
468 configF = open(configFileName, "w" )
469 configF.write( "[dir_name]\n")
470 configF.write( "work_dir : toto \n")
471 configF.write( "\n")
472 configF.write( "[analysis1]\n")
473 configF.write( "name: BLASTXWheat\n")
474 configF.write( "program: BLASTX\n")
475 configF.write( "programversion: 3.3\n")
476 configF.write( "sourcename: dummyDesc_BLASTX\n")
477 configF.write( "program: BLASTX2\n")
478 configF.write( "description: \n")
479 configF.write( "gff_name: BLASTX.gff\n")
480 configF.write( "\n")
481 configF.write( "\n")
482 configF.close()
483
484 #configuration file with section with option depends on presence of other options
485 def write_with_one_option_depends_of_an_other_one(self, configFileName ):
486 configF = open(configFileName, "w" )
487 configF.write( "[dir_name]\n")
488 configF.write( "work_dir : toto\n")
489 configF.write( "\n")
490 configF.write( "[organism]\n")
491 configF.write( "abbreviation: T.aestivum\n")
492 configF.write( "genus: Triticum\n")
493 configF.write( "species: aestivum\n")
494 configF.write( "common_name: wheat\n")
495 configF.write( "comment: \n")
496 configF.write( "\n")
497 configF.write( "[analysis1]\n")
498 configF.write( "name: BLASTXWheat\n")
499 configF.write( "program: BLASTX\n")
500 configF.write( "programversion: 3.3\n")
501 configF.write( "sourcename: src_BLASTX\n")
502 configF.write( "description: \n")
503 configF.write( "gff_name: BLASTX.gff\n")
504 configF.write( "\n")
505 configF.write( "[analysis2]\n")
506 configF.write( "name: GMHMMWheat\n")
507 configF.write( "program: GMHMM\n")
508 configF.write( "programversion: 4.3\n")
509 configF.write( "sourcename: src_GMHMM\n")
510 configF.write( "description: \n")
511 configF.write( "gff_name: GMHMM.gff\n")
512 configF.write( "\n")
513 configF.write( "[target]\n")
514 configF.write( "target_used: yes\n")
515 configF.write( "target_used_list: target.lst\n")
516 configF.close()
517
518 def write_case_pattern_rule(self, configFileName ):
519 configF = open(configFileName, "w" )
520 configF.write( "[dir_name]\n")
521 configF.write( "work_dir : toto\n" )
522 configF.write( "\n")
523 configF.write( "[organism]\n")
524 configF.write( "abbreviation: T.aestivum\n")
525 configF.write( "genus: Triticum\n")
526 configF.write( "species: aestivum\n")
527 configF.write( "common_name: wheat\n")
528 configF.write( "comment: \n")
529 configF.write( "\n")
530 configF.write( "[analysis1]\n")
531 configF.write( "name: BLASTXWheat\n")
532 configF.write( "program: BLASTX\n")
533 configF.write( "programversion: 3.3\n")
534 configF.write( "sourcename: src_BLASTX\n")
535 configF.write( "description: \n")
536 configF.write( "gff_name: BLASTX.gff\n")
537 configF.write( "\n")
538 configF.write( "[analysis2]\n")
539 configF.write( "name: GMHMMWheat\n")
540 configF.write( "program: GMHMM\n")
541 configF.write( "programversion: 4.3\n")
542 configF.write( "sourcename: src_GMHMM\n")
543 configF.write( "description: \n")
544 configF.write( "gff_name: GMHMM.gff\n")
545 configF.write( "\n")
546 configF.write( "[target]\n")
547 configF.write( "target_used: yes\n")
548 configF.write( "target_used_list: target.lst\n")
549 configF.write( "\n")
550 configF.write( "[section_with_option_pattern]\n")
551 configF.write( "option1: value1\n")
552 configF.write( "option2: value2\n")
553 configF.write( "[second_section_with_option_pattern]\n")
554 configF.write( "option1: value1\n")
555 configF.write( "option2: value2\n")
556 configF.close()
557
558 def write_config_case(self, configFileName):
559 configF = open(configFileName, "w" )
560 configF.write( "[dir_name]\n")
561 configF.write( "work_dir : toto \n")
562 configF.write( "\n")
563 configF.write( "[organism]\n")
564 configF.write( "min_SSR_coverage: 0.50\n")
565 configF.write( "\n")
566 configF.close()
567
568 if __name__ == "__main__":
569 unittest.main()