6
|
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() |