def test_archive2folder(self):
##############################
print "Running unittests for this project: ", project_name
print "Running this unittest: ", self._testMethodName
##############################
from zipper import zipUtils
zip_archive = r"%s%sInvestigation.blah.zip" % (dir_of_the_current_test, delimiter())
instOfzipUtils = zipUtils(delimiter_value=delimiter())
sub_folder_count = instOfzipUtils.archive2folder(zip_archive)
print "sub_folder_count=", sub_folder_count
assert 0 == sub_folder_count
cwd = os.getcwd()
# os.chdir(r'%s%sdoesNotExist.blah' % (dir_of_the_current_test,delimiter())) #caused unittest to fail as expected (tried separately)
os.chdir(r"%s%sInvestigation.blah" % (dir_of_the_current_test, delimiter()))
os.remove("m_1.xls")
# os.remove('does_not_exist.xls') #caused unittest to fail as expected (tried separately)
os.chdir(dir_of_the_current_test)
os.rmdir("Investigation.blah")
os.chdir(cwd)
def test_archive2folder(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
from zipper import zipUtils
zip_archive = r'%s%sInvestigation.blah.zip' % (dir_of_the_current_test,
delimiter())
instOfzipUtils = zipUtils(delimiter_value=delimiter())
sub_folder_count = instOfzipUtils.archive2folder(zip_archive)
print 'sub_folder_count=', sub_folder_count
assert 0 == sub_folder_count
cwd = os.getcwd()
#os.chdir(r'%s%sdoesNotExist.blah' % (dir_of_the_current_test,delimiter())) #caused unittest to fail as expected (tried separately)
os.chdir(r'%s%sInvestigation.blah' %
(dir_of_the_current_test, delimiter()))
os.remove('m_1.xls')
#os.remove('does_not_exist.xls') #caused unittest to fail as expected (tried separately)
os.chdir(dir_of_the_current_test)
os.rmdir('Investigation.blah')
os.chdir(cwd)
def clean_up_if_all_checks_passed(
self,
specific_files_or_dirs_not_to_delete,
current_test_dir=dir_of_the_current_test):
all_files_or_dirs_to_delete = [
r'%s%s%s' % (current_test_dir, delimiter(), file_or_dir_name)
for file_or_dir_name in os.listdir(current_test_dir)
if not re.search('(.\py$)', file_or_dir_name) and not r'%s%s%s' %
(current_test_dir, delimiter(),
file_or_dir_name) in specific_files_or_dirs_not_to_delete
]
for FILE_OR_DIR_TO_DELETE in all_files_or_dirs_to_delete:
if os.path.isfile(FILE_OR_DIR_TO_DELETE):
os.remove(FILE_OR_DIR_TO_DELETE)
assert not os.path.exists(
FILE_OR_DIR_TO_DELETE
), " This still exists: \n %s" % FILE_OR_DIR_TO_DELETE
print 'Removed this temporary file: ', FILE_OR_DIR_TO_DELETE
else:
assert os.path.isdir(
FILE_OR_DIR_TO_DELETE
), "FILE_OR_DIR_TO_DELETE=%s; not a directory or a file???" % FILE_OR_DIR_TO_DELETE
cwd = os.getcwd()
os.chdir(FILE_OR_DIR_TO_DELETE)
for file in glob.glob('*'):
os.remove(file)
del file
os.chdir(cwd)
del cwd
os.rmdir(FILE_OR_DIR_TO_DELETE
) #this will only work on an empty directory!
def test_AtLeastOneInvestigationStudyAssayMaterialRequired_defaultOptions(self): ############################## print 'Running unittests for this project: ', project_name print 'Running this unittest: ', self._testMethodName ############################## non_problem_inputs = ["TOY.test_11.zip"] non_problem_inputs = [r'%s%s%s' % (dir_of_the_current_test,delimiter(),file) for file in non_problem_inputs] del file problem_inputs = ["TOY.test_11-no.Material.zip","TOY.test_11-no.Investigation.zip","TOY.test_11-no.Study.zip","TOY.test_11-no.Assay.zip"] problem_inputs = [r'%s%s%s' % (dir_of_the_current_test,delimiter(),file) for file in problem_inputs] del file for input in non_problem_inputs+problem_inputs: cmd = r'python "%s%sxls2txtISA.NANO.archive.py" -i "%s"' % (project_modules_to_test_dir,delimiter(),input) if not input in problem_inputs: assert input in non_problem_inputs,"input=%s???" % input assert 0 == os.system(cmd) else: assert input in problem_inputs,"input=%s???" % input assert not 0 == os.system(cmd) del cmd del input self.clean_up_if_all_checks_passed(specific_files_or_dirs_not_to_delete=non_problem_inputs+problem_inputs,current_test_dir=dir_of_the_current_test)
def test_checkDuplicatedColumnTitlesAreNotSuspicious_defaultOptions(self): ############################## print 'Running unittests for this project: ', project_name print 'Running this unittest: ', self._testMethodName ############################## non_problem_inputs = ["TOY.test_11.zip","TOY.test_11-two.Sample.Name.Cols.zip"] non_problem_inputs = [r'%s%s%s' % (dir_of_the_current_test,delimiter(),file) for file in non_problem_inputs] del file problem_inputs = ["TOY.test_11-dup.Factors.zip"] problem_inputs = [r'%s%s%s' % (dir_of_the_current_test,delimiter(),file) for file in problem_inputs] del file for input in non_problem_inputs+problem_inputs: cmd = r'python "%s%sxls2txtISA.NANO.archive.py" -i "%s"' % (project_modules_to_test_dir,delimiter(),input) if not input in problem_inputs: assert input in non_problem_inputs,"input=%s???" % input assert not 'WARNING: suspicious duplicates' in self.runCmdToInspectPrintedMsgs(cmd) else: assert input in problem_inputs,"input=%s???" % input assert 'WARNING: suspicious duplicates' in self.runCmdToInspectPrintedMsgs(cmd) del cmd del input self.clean_up_if_all_checks_passed(specific_files_or_dirs_not_to_delete=non_problem_inputs+problem_inputs,current_test_dir=dir_of_the_current_test)
def test_changeXls2txt(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
import itertools
from xls2txt import changeXls2txt
input_file_extensions = ['xls']
all_input_files = []
for extension in input_file_extensions:
extension_regex = re.compile('(\.%s$)' % extension)
for input_file in glob.glob(
r'%s%s*.%s' %
(dir_of_the_current_test, delimiter(), extension)):
no_nonblank_sheets = changeXls2txt(input_file, extension_regex)
#assert 1 == no_nonblank_sheets, "%d non-blank sheets in %s!" % (no_nonblank_sheets,input_file)
all_input_files.append(input_file)
del input_file
del extension
assert 1 == len(all_input_files)
all_new_files = list(
itertools.chain(*[[
re.sub('(\.%s)' % extension, '.txt', input_file)
for input_file in glob.glob(r'%s%s*.%s' %
(dir_of_the_current_test,
delimiter(), extension))
] for extension in input_file_extensions]))
self.checkStillWorks(all_input_files, all_new_files)
def idInputFiles(xls_folder):
instOfzipUtils = zipUtils(delimiter())
input_files = instOfzipUtils.getRelativeFileNames(xls_folder)
input_files = [
r'%s%s%s' % (xls_folder, delimiter(), file) for file in input_files
if fileNameRegexesDict['input_extension'].search(file)
]
del file
del instOfzipUtils
#non_xls_files = [file_name for file_name in input_files if not fileNameRegexesDict['input_extension'].search(file_name)]
#del file_name
#assert 0 == len(non_xls_files),"There are %d non-xls files in the folder %s created from the input archive." % (len(non_xls_files),xls_folder)
#del non_xls_files
fileType2No = {}
for fileType in all_file_types:
fileType2No[fileType] = len([
file_name for file_name in input_files
if fileNameRegexesDict[fileType].match(
file_name.split(delimiter())[-1])
])
assert not 0 == fileType2No[
fileType], "Zero %s input files in the folder created from the input archive!" % fileType
print "%d %s input files in the folder created from the input archive!" % (
fileType2No[fileType], fileType)
del fileType2No
return input_files #,non_xls_files #non_xls_files should just be copied across to the final zip archive without modification -see "def createFlatTxtArchive(xls_folder):"
def test_convertTOYtest11_removeComments(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
##########################
#IMPORTANT: TOY.test_11.zip JUST COPIED FROM test_11 WITHOUT EDITING; EXPECTED OUTPUT [* - Copy.txt] ALSO COPIED, BUT MANUALLY EDITED [WITHOUT CHANGING FILE NAMES!] IN ACCORDANCE WITH EXPECTED CHANGES NOW THAT "-c" FLAG IS BEING USED!
#########################
cmd = r'python "%s%sxls2txtISA.NANO.archive.py" -i "%s" -c' % (project_modules_to_test_dir,delimiter(),example_input)
assert 0 == os.system(cmd)
instOfzipUtils = zipUtils(delimiter_value=delimiter())
sub_folder_count = instOfzipUtils.archive2folder(re.sub('(\.zip$)','-txt_opt-c.zip',example_input))
cwd = os.getcwd()
os.chdir(re.sub('(\.zip$)','-txt_opt-c',example_input))
comparisons_count = 0
for orig_file in example_output_to_compare_to:
new_file = r'%s%s%s' % (os.getcwd(),delimiter(),re.sub('( - Copy\.txt)','.txt',orig_file.split(delimiter())[-1]))
self.compareOriginalAndNewFiles(orig_file,new_file)
os.remove(new_file)
comparisons_count += 1
assert expected_no_output_files == comparisons_count, "comparisons_count=%d;expected_no_output_files=%d" % (comparisons_count,expected_no_output_files)
os.chdir(cwd)
os.remove(re.sub('(\.zip$)','-txt_opt-c.zip',example_input))
os.rmdir(re.sub('(\.zip$)','-txt_opt-c',example_input))
def main():
global debug
global default_sig_tresh
global conc_dep_modelling_input
global loel_based_output_file
print __doc__
################
opts,args = getopt.getopt(sys.argv[1:],'di:s:',['dir_with_nbi_records=','default_sig_tresh='])
for o,v in opts:
if '-d' == o:
debug = True
if '-i' == o:
dir_with_nbi_records = r'%s' % re.sub('"','',v)
if '-s' == o:
default_sig_tresh = float(v)
#################
####################
assert re.search('(\.csv$)',conc_dep_modelling_input),"conc_dep_modelling_input=%s?" % conc_dep_modelling_input
conc_dep_modelling_input = re.sub('(\.csv$)','_s%f.csv' % default_sig_tresh,conc_dep_modelling_input)
assert re.search('(\.csv$)',loel_based_output_file),"loel_based_output_file=%s?" % loel_based_output_file
loel_based_output_file = re.sub('(\.csv$)','_s%f.csv' % default_sig_tresh,loel_based_output_file)
####################
print '='*50
print 'Parsing NBI Knowledgebase records found in this directory:',dir_with_nbi_records
print 'in order to generate %s' % conc_dep_raw_output_file
print '(prior to generating %s and %s)' % (conc_dep_modelling_input,loel_based_output_file)
start = time.clock()
ok_list = []
rejects_list = []
conc_dep_titles = None
for input_file in glob.glob(r'%s%snbi_*.xls' % (dir_with_nbi_records,delimiter())):
print '#'*50
anNBIrecord = NBIrecord(input_file)
try:
anNBIrecord.extractData()
conc_dep_titles = processData(anNBIrecord.dataDict,conc_dep_titles,commonTitle2Location,concDepTitle2Location,effect_specific_regex,nmLocation2ID)
ok_list.append(input_file.split(delimiter())[-1])
except Exception,e:
print '!'*50
print 'Problem parsing this file: ',input_file
logging.exception(e)
del e
rejects_list.append(input_file.split(delimiter())[-1])
print '!'*50
anNBIrecord.cleanUp()
del anNBIrecord
print '#'*50
def createFlatTxtArchive(xls_folder, mustEditAccessionCodes,
mustRemoveComments,
mustMakeNanoPUZZLESspecificChanges):
flat_txt_archive = xls_folder + "-txt.zip"
###########
#Rename the output file if non-default options are used
if mustEditAccessionCodes:
flat_txt_archive = re.sub('(\.zip$)', '_opt-a.zip', flat_txt_archive)
if mustRemoveComments:
flat_txt_archive = re.sub('(\.zip$)', '_opt-c.zip', flat_txt_archive)
if mustMakeNanoPUZZLESspecificChanges:
flat_txt_archive = re.sub('(\.zip$)', '_opt-N.zip', flat_txt_archive)
###########
cwd = os.getcwd()
os.chdir(xls_folder)
for xls_file in glob.glob('*.xls'):
os.remove(xls_file)
os.chdir(cwd)
del cwd, xls_file
instOfzipUtils = zipUtils(delimiter_value=delimiter())
instOfzipUtils.filesIntoFlatArchive(folder_name=xls_folder,
zip_archive=flat_txt_archive)
del instOfzipUtils
def run_all_unit_tests():
import unittest
import glob
all_files_and_dirs_in_dir_of_this_script_prior_to_running_unit_tests = report_all_files_and_dirs_in_dir_of_this_script_prior_to_running_unit_tests()
CWD = os.getcwd()
os.chdir(dir_of_this_script)
test_dirs = [file_or_dir_name for file_or_dir_name in os.listdir(r'%s' % os.getcwd()) if re.match('(test_[0-9]+$)',file_or_dir_name)]# and 'test_6' == file_or_dir_name]
#print 'test_dirs = ', test_dirs
#sys.exit(1)
########################################
#The following code was written based on the answer provided by Stephen Cagle[http://stackoverflow.com/users/21317/stephen-cagle]: http://stackoverflow.com/questions/1732438/how-to-run-all-python-unit-tests-in-a-directory
test_file_names = []
for TEST_DIR in test_dirs:
sys.path.append(r'%s%s%s' % (dir_of_this_script,delimiter(),TEST_DIR))
os.chdir(TEST_DIR)
test_file_names += glob.glob('test_*.py')
os.chdir("..")
del test_dirs
del TEST_DIR
test_module_names = [name[0:len(name)-3] for name in test_file_names]
del name
loadedTests = [unittest.defaultTestLoader.loadTestsFromName(name) for name in test_module_names]
del name
testsReady2Run = unittest.TestSuite(loadedTests)
unittest.TextTestRunner().run(testsReady2Run)
########################################
os.chdir(CWD)
cleanUp(all_files_and_dirs_in_dir_of_this_script_prior_to_running_unit_tests)
def main():
################
opts,args = getopt.getopt(sys.argv[1:],'d:',['dir_with_nbi_records='])
for o,v in opts:
if '-d' == o:
dir_with_nbi_records = r'%s' % re.sub('"','',v)
#################
print '='*50
print 'Parsing NBI Knowledgebase records found in this directory:',dir_with_nbi_records
start = time.clock()
ok_parse_count = 0
bad_parse_count = 0
for input_file in glob.glob(r'%s%snbi_*.xls' % (dir_with_nbi_records,delimiter())):
print '#'*50
anNBIrecord = NBIrecord(input_file)
try:
anNBIrecord.extractData()
anNBIrecord.cleanUp()
ok_parse_count += 1
except Exception,err_msg:
print '!'*50
print 'Problem parsing this file: ',input_file
print err_msg
bad_parse_count += 1
print '!'*50
del anNBIrecord
print '#'*50
def createFlatTxtArchive(xls_folder,mustEditAccessionCodes,mustRemoveComments,mustMakeNanoPUZZLESspecificChanges):
flat_txt_archive = xls_folder+"-txt.zip"
###########
#Rename the output file if non-default options are used
if mustEditAccessionCodes:
flat_txt_archive = re.sub('(\.zip$)','_opt-a.zip',flat_txt_archive)
if mustRemoveComments:
flat_txt_archive = re.sub('(\.zip$)','_opt-c.zip',flat_txt_archive)
if mustMakeNanoPUZZLESspecificChanges:
flat_txt_archive = re.sub('(\.zip$)','_opt-N.zip',flat_txt_archive)
###########
cwd = os.getcwd()
os.chdir(xls_folder)
for xls_file in glob.glob('*.xls'):
os.remove(xls_file)
os.chdir(cwd)
del cwd,xls_file
instOfzipUtils = zipUtils(delimiter_value=delimiter())
instOfzipUtils.filesIntoFlatArchive(folder_name=xls_folder,zip_archive=flat_txt_archive)
del instOfzipUtils
def test_filesIntoFlatArchive(self): ############################## print 'Running unittests for this project: ', project_name print 'Running this unittest: ', self._testMethodName ############################## from zipper import zipUtils folder = r'%s%sInvestigation.blah-TXT' % (dir_of_the_current_test,delimiter()) instOfzipUtils = zipUtils(delimiter_value=delimiter()) instOfzipUtils.filesIntoFlatArchive(folder_name=folder,zip_archive=folder+".zip") del instOfzipUtils os.remove(r'%s%sInvestigation.blah-TXT.zip' % (dir_of_the_current_test,delimiter())) #when this was commented, archive looked as expected (flat archive containing a single text file)
def cleanUp(self): print 'Deleting text files used to read data into instance of NBIrecord() class' for file in self.txt_sheets: assert os.path.isfile(file), r"self.txt_sheets entry %s is not a file???" % file os.remove(file) del file print 'Deleting pyc files in the directory of this module file (os.path.abspath(__file__) will not work once .py compiled to .pyc!)' for file in glob.glob(r'%s%s*pyc' % (dir_of_this_file,delimiter())): os.remove(file)
def extractXlsFolder(xls_archive): instOfzipUtils = zipUtils(delimiter()) sub_folder_count = instOfzipUtils.archive2folder(xls_archive) assert 0 == sub_folder_count return instOfzipUtils.folder_name
def extractXlsFolder(xls_archive):
instOfzipUtils = zipUtils(delimiter())
sub_folder_count = instOfzipUtils.archive2folder(xls_archive)
assert 0 == sub_folder_count
return instOfzipUtils.folder_name
def test_NanoPUZZLES_inconsistency_fix_3(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
##########################
#This unit test is designed to check (an aspect of) the "-N" option for this program i.e. the conversion of potentially inconsistent fields in datasets arising from older versions of the NanoPUZZLES ISA-TAB-Nano templates
#N.B. The "....TOY.test_11... - Copy.txt" files (which were checked to make sure they were not inconsistent with the expected changes to be made via the "-N" option) were just renamed and the "TOY.test_11.zip" Excel files were updated to make sure they contained (one of) the inconsistencies that the "-N" option is designed to fix, then all such files were renamed to give "TOY.test_17.zip".
#[*] In addition, given the changes to the file names, the internal contents of the files (both Excel and expected text output) needed to be edited such that "TOY.test_11" was replaced with "TOY.test_17" for consistency.
#########################
##############################
#test_17: inconsistency(ies) fix which is (are) being tested: replace "Characteristics[shape]" fields with "Characteristics [shape {NPO:http://purl.bioontology.org/ontology/npo#NPO_274}]"
##############################
cmd = r'python "%s%sxls2txtISA.NANO.archive.py" -i "%s" -N' % (
project_modules_to_test_dir, delimiter(), example_input)
assert 0 == os.system(cmd)
instOfzipUtils = zipUtils(delimiter_value=delimiter())
sub_folder_count = instOfzipUtils.archive2folder(
re.sub('(\.zip$)', '-txt_opt-N.zip', example_input))
cwd = os.getcwd()
os.chdir(re.sub('(\.zip$)', '-txt_opt-N', example_input))
comparisons_count = 0 #This line would actually be useful in earlier unit tests!
for orig_file in example_output_to_compare_to:
new_file = r'%s%s%s' % (os.getcwd(), delimiter(),
re.sub('( - Copy\.txt)', '.txt',
orig_file.split(delimiter())[-1]))
self.compareOriginalAndNewFiles(orig_file, new_file)
os.remove(new_file)
comparisons_count += 1 #This line would actually be useful in earlier unit tests!
assert expected_no_output_files == comparisons_count, "comparisons_count=%d;expected_no_output_files=%d" % (
comparisons_count, expected_no_output_files
) #This line would actually be useful in earlier unit tests!
os.chdir(cwd)
os.remove(re.sub('(\.zip$)', '-txt_opt-N.zip', example_input))
os.rmdir(re.sub('(\.zip$)', '-txt_opt-N', example_input))
def test_convertTOYtest11_defaultOptions(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
##########################
#Observations regarding TOY.test_11.zip files which are relevant to testing capabilities of the code to fix xls errors:
#s_TOY.test_11_InVitro.CB.xls => "Factor Value[culture medium]" : should be converted to "Factor Value [culture medium]" in txt version
#a_TOY.test_11_PC_size_TEM.xls => "Parameter Value[Instrument Version]" : ditto "Parameter Value [Instrument Version]"
#ditto => "Measurement Value[maximum(diameter)]" ditto "Measurement Value [maximum(diameter)]"
#m_TiO2_TOY.test_11.xls -> Excel 2010 saved as tab delimited text => "Characteristics [Product impurities found {MEDDRA:\nhttp://purl.bioontology.org/ontology/MDR/10069178}]" i.e. this field contained a line ending inside a field - which should be removed in code created version!
#ditto => Characteristics[purity {NPO: http://purl.bioontology.org/ontology/npo#NPO_1345}] : should be converted to "Characteristics [purity {NPO:http://purl.bioontology.org/ontology/npo#NPO_1345}]"
#########################
cmd = r'python "%s%sxls2txtISA.NANO.archive.py" -i "%s"' % (
project_modules_to_test_dir, delimiter(), example_input)
assert 0 == os.system(cmd)
instOfzipUtils = zipUtils(delimiter_value=delimiter())
sub_folder_count = instOfzipUtils.archive2folder(
re.sub('(\.zip$)', '-txt.zip', example_input))
cwd = os.getcwd()
os.chdir(re.sub('(\.zip$)', '-txt', example_input))
comparisons_count = 0
for orig_file in example_output_to_compare_to:
new_file = r'%s%s%s' % (os.getcwd(), delimiter(),
re.sub('( - Copy\.txt)', '.txt',
orig_file.split(delimiter())[-1]))
self.compareOriginalAndNewFiles(orig_file, new_file)
os.remove(new_file)
comparisons_count += 1
assert expected_no_output_files == comparisons_count, "comparisons_count=%d;expected_no_output_files=%d" % (
comparisons_count, expected_no_output_files)
os.chdir(cwd)
os.remove(re.sub('(\.zip$)', '-txt.zip', example_input))
os.rmdir(re.sub('(\.zip$)', '-txt', example_input))
def test_xls2txtISANANOarchive_entire_workflow(self): ############################## print 'Running unittests for this project: ', project_name print 'Running this unittest: ', self._testMethodName ############################## cmd = r'python "%s%sxls2txtISA.NANO.archive.py" -i "%s%sInvestigation.ID.zip"' % (project_modules_to_test_dir,delimiter(),dir_of_the_current_test,delimiter()) assert 0 == os.system(cmd) os.remove(r'%s%sInvestigation.ID-txt.zip' % (dir_of_the_current_test,delimiter()))#when commented, output files were as expected (no consideration of internal contents of txt files!)
def test_checkDuplicatedColumnTitlesAreNotSuspicious_defaultOptions(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
non_problem_inputs = [
"TOY.test_11.zip", "TOY.test_11-two.Sample.Name.Cols.zip"
]
non_problem_inputs = [
r'%s%s%s' % (dir_of_the_current_test, delimiter(), file)
for file in non_problem_inputs
]
del file
problem_inputs = ["TOY.test_11-dup.Factors.zip"]
problem_inputs = [
r'%s%s%s' % (dir_of_the_current_test, delimiter(), file)
for file in problem_inputs
]
del file
for input in non_problem_inputs + problem_inputs:
cmd = r'python "%s%sxls2txtISA.NANO.archive.py" -i "%s"' % (
project_modules_to_test_dir, delimiter(), input)
if not input in problem_inputs:
assert input in non_problem_inputs, "input=%s???" % input
assert not 'WARNING: suspicious duplicates' in self.runCmdToInspectPrintedMsgs(
cmd)
else:
assert input in problem_inputs, "input=%s???" % input
assert 'WARNING: suspicious duplicates' in self.runCmdToInspectPrintedMsgs(
cmd)
del cmd
del input
self.clean_up_if_all_checks_passed(
specific_files_or_dirs_not_to_delete=non_problem_inputs +
problem_inputs,
current_test_dir=dir_of_the_current_test)
def test_filesIntoFlatArchive(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
from zipper import zipUtils
folder = r'%s%sInvestigation.blah-TXT' % (dir_of_the_current_test,
delimiter())
instOfzipUtils = zipUtils(delimiter_value=delimiter())
instOfzipUtils.filesIntoFlatArchive(folder_name=folder,
zip_archive=folder + ".zip")
del instOfzipUtils
os.remove(
r'%s%sInvestigation.blah-TXT.zip' %
(dir_of_the_current_test, delimiter())
) #when this was commented, archive looked as expected (flat archive containing a single text file)
def test_convertTOYtest11_defaultOptions(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
##########################
#Observations regarding TOY.test_11.zip files which are relevant to testing capabilities of the code to fix xls errors:
#s_TOY.test_11_InVitro.CB.xls => "Factor Value[culture medium]" : should be converted to "Factor Value [culture medium]" in txt version
#a_TOY.test_11_PC_size_TEM.xls => "Parameter Value[Instrument Version]" : ditto "Parameter Value [Instrument Version]"
#ditto => "Measurement Value[maximum(diameter)]" ditto "Measurement Value [maximum(diameter)]"
#m_TiO2_TOY.test_11.xls -> Excel 2010 saved as tab delimited text => "Characteristics [Product impurities found {MEDDRA:\nhttp://purl.bioontology.org/ontology/MDR/10069178}]" i.e. this field contained a line ending inside a field - which should be removed in code created version!
#ditto => Characteristics[purity {NPO: http://purl.bioontology.org/ontology/npo#NPO_1345}] : should be converted to "Characteristics [purity {NPO:http://purl.bioontology.org/ontology/npo#NPO_1345}]"
#########################
cmd = r'python "%s%sxls2txtISA.NANO.archive.py" -i "%s"' % (project_modules_to_test_dir,delimiter(),example_input)
assert 0 == os.system(cmd)
instOfzipUtils = zipUtils(delimiter_value=delimiter())
sub_folder_count = instOfzipUtils.archive2folder(re.sub('(\.zip$)','-txt.zip',example_input))
cwd = os.getcwd()
os.chdir(re.sub('(\.zip$)','-txt',example_input))
comparisons_count = 0
for orig_file in example_output_to_compare_to:
new_file = r'%s%s%s' % (os.getcwd(),delimiter(),re.sub('( - Copy\.txt)','.txt',orig_file.split(delimiter())[-1]))
self.compareOriginalAndNewFiles(orig_file,new_file)
os.remove(new_file)
comparisons_count += 1
assert expected_no_output_files == comparisons_count, "comparisons_count=%d;expected_no_output_files=%d" % (comparisons_count,expected_no_output_files)
os.chdir(cwd)
os.remove(re.sub('(\.zip$)','-txt.zip',example_input))
os.rmdir(re.sub('(\.zip$)','-txt',example_input))
def test_NanoPUZZLES_inconsistency_fix_1(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
##########################
#This unit test is designed to check (an aspect of) the "-N" option for this program i.e. the conversion of potentially inconsistent fields in datasets arising from older versions of the NanoPUZZLES ISA-TAB-Nano templates
#N.B. The "....TOY.test_11... - Copy.txt" files (which were checked to make sure they were not inconsistent with the expected changes to be made via the "-N" option) were just renamed and the "TOY.test_11.zip" Excel files were updated to make sure they contained (one of) the inconsistencies that the "-N" option is designed to fix, then all such files were renamed to give "TOY.test_15.zip".
#[*] In addition, given the changes to the file names, the internal contents of the files (both Excel and expected text output) needed to be edited such that "TOY.test_11" was replaced with "TOY.test_15" for consistency.
#########################
##############################
#test_15: inconsistency(ies) fix which is (are) being tested: removal of "Manufacturer supplied " prefixes for Material file "Characteristics [...]" and corresponding "Comment [...:from graph]" fields
##############################
#cmd = r'python "%s%sxls2txtISA.NANO.archive.py" -i "%s"' % (project_modules_to_test_dir,delimiter(),example_input) #[*] To check no problems with updating names from test_11 files, this test was initially run without making any changes except replacing "TOY.test_11" with "TOY.test_15" in file names and internal contents => OK [test output scrolled through to see that expected comparisons were being made]. Also, a minor error was introduced to check that self.compareOriginalAndNewFiles(orig_file,new_file) would fail as expected for one file => OK [this error was then fixed, this command was ran again with no errors and the files were further updated for the purpose of this test].
cmd = r'python "%s%sxls2txtISA.NANO.archive.py" -i "%s" -N' % (project_modules_to_test_dir,delimiter(),example_input)
assert 0 == os.system(cmd)
instOfzipUtils = zipUtils(delimiter_value=delimiter())
sub_folder_count = instOfzipUtils.archive2folder(re.sub('(\.zip$)','-txt_opt-N.zip',example_input))
cwd = os.getcwd()
os.chdir(re.sub('(\.zip$)','-txt_opt-N',example_input))
comparisons_count = 0 #This line would actually be useful in earlier unit tests!
for orig_file in example_output_to_compare_to:
new_file = r'%s%s%s' % (os.getcwd(),delimiter(),re.sub('( - Copy\.txt)','.txt',orig_file.split(delimiter())[-1]))
self.compareOriginalAndNewFiles(orig_file,new_file)
os.remove(new_file)
comparisons_count += 1 #This line would actually be useful in earlier unit tests!
assert expected_no_output_files == comparisons_count, "comparisons_count=%d;expected_no_output_files=%d" % (comparisons_count,expected_no_output_files) #This line would actually be useful in earlier unit tests!
os.chdir(cwd)
os.remove(re.sub('(\.zip$)','-txt_opt-N.zip',example_input))
os.rmdir(re.sub('(\.zip$)','-txt_opt-N',example_input))
def test_NanoPUZZLES_inconsistency_fix_5(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
##########################
#This unit test is designed to check (an aspect of) the "-N" option for this program i.e. the conversion of potentially inconsistent fields in datasets arising from older versions of the NanoPUZZLES ISA-TAB-Nano templates
#N.B. The "....TOY.test_11... - Copy.txt" files (which were checked to make sure they were not inconsistent with the expected changes to be made via the "-N" option) were just renamed and the "TOY.test_11.zip" Excel files were updated to make sure they contained (one of) the inconsistencies that the "-N" option is designed to fix, then all such files were renamed to give "TOY.test_19.zip".
#[*] In addition, given the changes to the file names, the internal contents of the files (both Excel and expected text output) needed to be edited such that "TOY.test_11" was replaced with "TOY.test_19" for consistency.
#########################
##############################
#test_19: inconsistency(ies) fix which is (are) being tested: replace "nanoparticle sample" with "nanomaterial" and (correspondingly) "http://purl.bioontology.org/ontology/npo#NPO_1404" with "http://purl.bioontology.org/ontology/npo#NPO_199". In practice, this should only affect old biological Study files (name replacements), Material files (name replacements and ontology code replacements) and Investigation files (name replacements and ontology code replacements).
##############################
cmd = r'python "%s%sxls2txtISA.NANO.archive.py" -i "%s" -N' % (project_modules_to_test_dir,delimiter(),example_input)
assert 0 == os.system(cmd)
instOfzipUtils = zipUtils(delimiter_value=delimiter())
sub_folder_count = instOfzipUtils.archive2folder(re.sub('(\.zip$)','-txt_opt-N.zip',example_input))
cwd = os.getcwd()
os.chdir(re.sub('(\.zip$)','-txt_opt-N',example_input))
comparisons_count = 0 #This line would actually be useful in earlier unit tests!
for orig_file in example_output_to_compare_to:
new_file = r'%s%s%s' % (os.getcwd(),delimiter(),re.sub('( - Copy\.txt)','.txt',orig_file.split(delimiter())[-1]))
self.compareOriginalAndNewFiles(orig_file,new_file)
os.remove(new_file)
comparisons_count += 1 #This line would actually be useful in earlier unit tests!
assert expected_no_output_files == comparisons_count, "comparisons_count=%d;expected_no_output_files=%d" % (comparisons_count,expected_no_output_files) #This line would actually be useful in earlier unit tests!
os.chdir(cwd)
os.remove(re.sub('(\.zip$)','-txt_opt-N.zip',example_input))
os.rmdir(re.sub('(\.zip$)','-txt_opt-N',example_input))
def test_convertTOYtest11_removeComments(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
##########################
#IMPORTANT: TOY.test_11.zip JUST COPIED FROM test_11 WITHOUT EDITING; EXPECTED OUTPUT [* - Copy.txt] ALSO COPIED, BUT MANUALLY EDITED [WITHOUT CHANGING FILE NAMES!] IN ACCORDANCE WITH EXPECTED CHANGES NOW THAT "-c" FLAG IS BEING USED!
#########################
cmd = r'python "%s%sxls2txtISA.NANO.archive.py" -i "%s" -c' % (
project_modules_to_test_dir, delimiter(), example_input)
assert 0 == os.system(cmd)
instOfzipUtils = zipUtils(delimiter_value=delimiter())
sub_folder_count = instOfzipUtils.archive2folder(
re.sub('(\.zip$)', '-txt_opt-c.zip', example_input))
cwd = os.getcwd()
os.chdir(re.sub('(\.zip$)', '-txt_opt-c', example_input))
comparisons_count = 0
for orig_file in example_output_to_compare_to:
new_file = r'%s%s%s' % (os.getcwd(), delimiter(),
re.sub('( - Copy\.txt)', '.txt',
orig_file.split(delimiter())[-1]))
self.compareOriginalAndNewFiles(orig_file, new_file)
os.remove(new_file)
comparisons_count += 1
assert expected_no_output_files == comparisons_count, "comparisons_count=%d;expected_no_output_files=%d" % (
comparisons_count, expected_no_output_files)
os.chdir(cwd)
os.remove(re.sub('(\.zip$)', '-txt_opt-c.zip', example_input))
os.rmdir(re.sub('(\.zip$)', '-txt_opt-c', example_input))
def idInputFiles(xls_folder):
instOfzipUtils = zipUtils(delimiter())
input_files = instOfzipUtils.getRelativeFileNames(xls_folder)
input_files = [r'%s%s%s' % (xls_folder,delimiter(),file) for file in input_files if fileNameRegexesDict['input_extension'].search(file)]
del file
del instOfzipUtils
#non_xls_files = [file_name for file_name in input_files if not fileNameRegexesDict['input_extension'].search(file_name)]
#del file_name
#assert 0 == len(non_xls_files),"There are %d non-xls files in the folder %s created from the input archive." % (len(non_xls_files),xls_folder)
#del non_xls_files
fileType2No = {}
for fileType in all_file_types:
fileType2No[fileType] = len([file_name for file_name in input_files if fileNameRegexesDict[fileType].match(file_name.split(delimiter())[-1])])
assert not 0 == fileType2No[fileType], "Zero %s input files in the folder created from the input archive!" % fileType
print "%d %s input files in the folder created from the input archive!" % (fileType2No[fileType],fileType)
del fileType2No
return input_files#,non_xls_files #non_xls_files should just be copied across to the final zip archive without modification -see "def createFlatTxtArchive(xls_folder):"
def test_getRows_example_1(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
example_file = '%s%sexample_no_line_endings_in_col_titles.txt' % (
dir_of_the_current_test, delimiter())
expected_col_titles = [
'A', 'B', 'C', 'Unit', 'D', 'Unit', 'C plus D', 'Unit', 'E'
]
expected_data_row = [
'M1_ID', 'M1', '10', 'nanometers', '20', 'nanometers', '30',
'nanometers', 'Hello'
]
assert [expected_col_titles, expected_data_row] == getRows(
example_file), "file=%s\nexpected rows=%s\nextracted rows=%s\n" % (
example_file, str([expected_col_titles, expected_data_row
]), str(getRows(example_file)))
def test_getRows_example_2(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
##############################
example_file = '%s%sexample_with_line_endings_in_quoted_col_titles.txt' % (
dir_of_the_current_test, delimiter())
expected_col_titles = [
'A', 'B', 'C', 'Unit', 'D', 'Unit', 'C \nplus D', 'Unit', 'E'
] #It seems that csv.reader(...) converts "\r\n" inside quoted column title to "\n"![using Python 2.7.3]
expected_data_row = [
'M1_ID', 'M1', '10', 'nanometers', '20', 'nanometers', '30',
'nanometers', 'Hello'
]
assert [expected_col_titles, expected_data_row] == getRows(
example_file), "file=%s\nexpected rows=%s\nextracted rows=%s\n" % (
example_file, str([expected_col_titles, expected_data_row
]), str(getRows(example_file)))
def extractData_from_EMZdata_sheet(self,txt_sheet_name): assert 'NBI-EMZ Data' == self.idTxtSheetType(txt_sheet_name), "%s is NOT a NBI-EMZ Data sheet!" % txt_sheet_name print '-'*50 print 'Extracting data from this NBI-EMZ Data sheet:',txt_sheet_name rows = self.extractRows(txt_sheet_name) assert not 0 == len(rows) main_titles_row_index = self.idEMZdataMainTitlesRow(rows) max_dc_row_index = self.idEMZdataMaxDosageConcRow(main_titles_row_index,rows) hpf_24_col_index,hpf_120_col_index = self.idEMZdataHpfCols(main_titles_row_index,rows) self.dataDict[self.idTxtSheetType(txt_sheet_name)] = self.matchEMZdataRowId2ExperiVarName2Value(max_dc_row_index,main_titles_row_index,hpf_24_col_index,hpf_120_col_index,rows) #<TO DO?>:USE DOSAGE CONCENTRATION VALUES AS KEYS RATHER THAN row IDs if 'nbi_1.xls' == self.nbi_xls_file.split(delimiter())[-1]:#<TO DO?>:ASSUME THE SAME NUMBER OF DOSAGE CONCENTRATIONS ARE ALWAYS TESTED AND ALWAYS APPLY THIS TEST print 'Checking self.dataDict[%s] entry against expected number of evaluated dosage concentrations for nbi_1.xls' % self.idTxtSheetType(txt_sheet_name) assert 8 == len(self.dataDict[self.idTxtSheetType(txt_sheet_name)].keys()), "len(self.dataDict[self.idTxtSheetType(txt_sheet_name)].keys())=%d???" % len(self.dataDict[self.idTxtSheetType(txt_sheet_name)].keys()) print '-'*50
def createAllTxt(xls_folder, mustEditAccessionCodes, mustRemoveComments,
mustMakeNanoPUZZLESspecificChanges):
abs_name_input_files = idInputFiles(xls_folder)
for xls_file in abs_name_input_files:
txt_file = changeXls2txt(xls_file,
fileNameRegexesDict['input_extension'])
applicable_standard_file_types = [
ft for ft in all_file_types
if fileNameRegexesDict[ft].match(txt_file.split(delimiter())[-1])
]
del ft
assert 1 >= len(applicable_standard_file_types
), "txt_file=%s,applicable_standard_file_types=%s" % (
txt_file, str(applicable_standard_file_types))
if 1 == len(applicable_standard_file_types):
current_file_type = applicable_standard_file_types[0]
else:
assert 0 == len(
applicable_standard_file_types
), "txt_file=%s,applicable_standard_file_types=%s" % (
txt_file, str(applicable_standard_file_types))
current_file_type = 'NonStandard'
del applicable_standard_file_types
fixContents(input_file=txt_file,
out_name=None,
del_intermediates=True,
file_type=current_file_type,
shouldEditAccessionCodes=mustEditAccessionCodes,
shouldRemoveComments=mustRemoveComments,
shouldMakeNanoPUZZLESspecificChanges=
mustMakeNanoPUZZLESspecificChanges)
run_tests_levels_below_top_dir = 1
this_test_levels_below_top_dir = 2
#########################
#************************
import sys,re,os,glob
cwd = os.getcwd()
for level in range(1,(run_tests_levels_below_top_dir+1)):
os.chdir('..')
#print os.getcwd()
del level
sys.path.append('utils')
from os_ind_delimiter import delimiter
from zipper import zipUtils
os.chdir(cwd)
del cwd
project_modules_to_test_dir = delimiter().join(os.path.abspath(__file__).split(delimiter())[:-(this_test_levels_below_top_dir+1)])
print 'project_modules_to_test_dir=',project_modules_to_test_dir
sys.path.append(project_modules_to_test_dir)
sys.path.append(r'%s%sutils' %(project_modules_to_test_dir,delimiter()))
dir_of_the_current_test = delimiter().join(os.path.abspath(__file__).split(delimiter())[:-1])
print 'dir_of_the_current_test=',dir_of_the_current_test
import unittest
#************************
sys.path.append(r'%s%stests%stest_1' % (project_modules_to_test_dir,delimiter(),delimiter()))
from test_1 import test_1
import subprocess
class test_8(test_1):
def runCmdToInspectPrintedMsgs(self,cmd):
#N.B. - see http://stackoverflow.com/questions/2502833/store-output-of-subprocess-popen-call-in-a-string
output,errors = subprocess.Popen(cmd,stdout=subprocess.PIPE).communicate()
def createAllTxt(xls_folder,mustEditAccessionCodes,mustRemoveComments,mustMakeNanoPUZZLESspecificChanges): abs_name_input_files = idInputFiles(xls_folder) for xls_file in abs_name_input_files: txt_file = changeXls2txt(xls_file,fileNameRegexesDict['input_extension']) applicable_standard_file_types = [ft for ft in all_file_types if fileNameRegexesDict[ft].match(txt_file.split(delimiter())[-1])] del ft assert 1 >= len(applicable_standard_file_types),"txt_file=%s,applicable_standard_file_types=%s" % (txt_file,str(applicable_standard_file_types)) if 1 == len(applicable_standard_file_types): current_file_type = applicable_standard_file_types[0] else: assert 0 == len(applicable_standard_file_types),"txt_file=%s,applicable_standard_file_types=%s" % (txt_file,str(applicable_standard_file_types)) current_file_type = 'NonStandard' del applicable_standard_file_types fixContents(input_file=txt_file,out_name=None,del_intermediates=True,file_type=current_file_type,shouldEditAccessionCodes=mustEditAccessionCodes,shouldRemoveComments=mustRemoveComments,shouldMakeNanoPUZZLESspecificChanges=mustMakeNanoPUZZLESspecificChanges)
def report_all_files_and_dirs_in_dir_of_this_script_prior_to_running_unit_tests(): return [r'%s%s%s' % (dir_of_this_script,delimiter(),file_or_dir_name) for file_or_dir_name in os.listdir(r'%s' % dir_of_this_script)]
run_tests_levels_below_top_dir = 1
this_test_levels_below_top_dir = 2
#########################
#************************
import sys,re,os,glob
cwd = os.getcwd()
for level in range(1,(run_tests_levels_below_top_dir+1)):
os.chdir('..')
#print os.getcwd()
del level
sys.path.append('utils')
from os_ind_delimiter import delimiter
from zipper import zipUtils
os.chdir(cwd)
del cwd
project_modules_to_test_dir = delimiter().join(os.path.abspath(__file__).split(delimiter())[:-(this_test_levels_below_top_dir+1)])
print 'project_modules_to_test_dir=',project_modules_to_test_dir
sys.path.append(project_modules_to_test_dir)
sys.path.append(r'%s%sutils' %(project_modules_to_test_dir,delimiter()))
dir_of_the_current_test = delimiter().join(os.path.abspath(__file__).split(delimiter())[:-1])
print 'dir_of_the_current_test=',dir_of_the_current_test
import unittest
#************************
sys.path.append(r'%s%stests%stest_1' % (project_modules_to_test_dir,delimiter(),delimiter()))
from test_1 import test_1
example_input = '%s%sTOY.test_19.zip' % (dir_of_the_current_test,delimiter())
example_output_to_compare_to = glob.glob(r'%s%s* - Copy.txt' % (dir_of_the_current_test,delimiter()))
expected_no_output_files = 8
assert expected_no_output_files == len(example_output_to_compare_to) #This line would actually be useful in earlier unit tests!
assert expected_no_output_files == len([file for file in example_output_to_compare_to if os.path.exists(file)]), "%s???" % str(example_output_to_compare_to) #This line would actually be useful in earlier unit tests!
del file #This line would actually be useful in earlier unit tests!
project_name = 'xls2txtISA.NANO.archive'
run_tests_levels_below_top_dir = 1
this_test_levels_below_top_dir = 2
#########################
#************************
import sys,re,os,glob
cwd = os.getcwd()
for level in range(1,(run_tests_levels_below_top_dir+1)):
os.chdir('..')
#print os.getcwd()
del level
sys.path.append('utils')
from os_ind_delimiter import delimiter
os.chdir(cwd)
del cwd
project_modules_to_test_dir = delimiter().join(os.path.abspath(__file__).split(delimiter())[:-(this_test_levels_below_top_dir+1)])
print 'project_modules_to_test_dir=',project_modules_to_test_dir
sys.path.append(project_modules_to_test_dir)
sys.path.append(r'%s%sutils' %(project_modules_to_test_dir,delimiter()))
dir_of_the_current_test = delimiter().join(os.path.abspath(__file__).split(delimiter())[:-1])
print 'dir_of_the_current_test=',dir_of_the_current_test
import unittest
#************************
class test_4(unittest.TestCase):
def test_xls2txtISANANOarchive_entire_workflow(self):
##############################
print 'Running unittests for this project: ', project_name
print 'Running this unittest: ', self._testMethodName
def test_getRows_example_1(self): ############################## print 'Running unittests for this project: ', project_name print 'Running this unittest: ', self._testMethodName ############################## example_file = '%s%sexample_no_line_endings_in_col_titles.txt' % (dir_of_the_current_test,delimiter()) expected_col_titles = ['A','B','C','Unit','D','Unit','C plus D','Unit','E'] expected_data_row = ['M1_ID','M1','10','nanometers','20','nanometers','30','nanometers','Hello'] assert [expected_col_titles,expected_data_row] == getRows(example_file), "file=%s\nexpected rows=%s\nextracted rows=%s\n" % (example_file,str([expected_col_titles,expected_data_row]),str(getRows(example_file)))
'''
#########################
run_tests_levels_below_top_dir = 1
#########################
#************************
import sys,re,os,glob,getopt
cwd = os.getcwd()
for level in range(1,(run_tests_levels_below_top_dir+1)):
os.chdir('..')
#print os.getcwd()
del level
sys.path.append('utils')
from os_ind_delimiter import delimiter
os.chdir(cwd)
del cwd
dir_of_this_script = delimiter().join(os.path.abspath(__file__).split(delimiter())[:-1])
print 'dir_of_this_script=',dir_of_this_script
import unittest
#************************
def report_all_files_and_dirs_in_dir_of_this_script_prior_to_running_unit_tests():
return [r'%s%s%s' % (dir_of_this_script,delimiter(),file_or_dir_name) for file_or_dir_name in os.listdir(r'%s' % dir_of_this_script)]
def cleanUp(all_files_and_dirs_in_dir_of_this_script_prior_to_running_unit_tests):
import glob
#some unit tests may actually write intermediate temporary files to dir_of_this_script - hence make sure that these have all been deleted after all unit tests have been carried out!
unit_test_temp_files_written_to_dir_of_this_script = [file_name for file_name in glob.glob(r'%s%s*' % (dir_of_this_script,delimiter())) if not file_name in all_files_and_dirs_in_dir_of_this_script_prior_to_running_unit_tests]
for UNIT_TEST_TEMP_FILE_WRITTEN_TO_DIR_OF_THIS_SCRIPT in unit_test_temp_files_written_to_dir_of_this_script:
print '='*50
run_tests_levels_below_top_dir = 1
this_test_levels_below_top_dir = 2
#########################
#************************
import sys,re,os,glob
cwd = os.getcwd()
for level in range(1,(run_tests_levels_below_top_dir+1)):
os.chdir('..')
#print os.getcwd()
del level
sys.path.append('utils')
from os_ind_delimiter import delimiter
from zipper import zipUtils
os.chdir(cwd)
del cwd
project_modules_to_test_dir = delimiter().join(os.path.abspath(__file__).split(delimiter())[:-(this_test_levels_below_top_dir+1)])
print 'project_modules_to_test_dir=',project_modules_to_test_dir
sys.path.append(project_modules_to_test_dir)
sys.path.append(r'%s%sutils' %(project_modules_to_test_dir,delimiter()))
dir_of_the_current_test = delimiter().join(os.path.abspath(__file__).split(delimiter())[:-1])
print 'dir_of_the_current_test=',dir_of_the_current_test
import unittest
#************************
sys.path.append(r'%s%stests%stest_1' % (project_modules_to_test_dir,delimiter(),delimiter()))
from test_1 import test_1
example_input = '%s%sTOY.test_15.zip' % (dir_of_the_current_test,delimiter())
example_output_to_compare_to = glob.glob(r'%s%s* - Copy.txt' % (dir_of_the_current_test,delimiter()))
expected_no_output_files = 8
assert expected_no_output_files == len(example_output_to_compare_to) #This line would actually be useful in earlier unit tests!
assert expected_no_output_files == len([file for file in example_output_to_compare_to if os.path.exists(file)]), "%s???" % str(example_output_to_compare_to) #This line would actually be useful in earlier unit tests!
del file #This line would actually be useful in earlier unit tests!
def test_getRows_example_2(self): ############################## print 'Running unittests for this project: ', project_name print 'Running this unittest: ', self._testMethodName ############################## example_file = '%s%sexample_with_line_endings_in_quoted_col_titles.txt' % (dir_of_the_current_test,delimiter()) expected_col_titles = ['A','B','C','Unit','D','Unit','C \nplus D','Unit','E'] #It seems that csv.reader(...) converts "\r\n" inside quoted column title to "\n"![using Python 2.7.3] expected_data_row = ['M1_ID','M1','10','nanometers','20','nanometers','30','nanometers','Hello'] assert [expected_col_titles,expected_data_row] == getRows(example_file), "file=%s\nexpected rows=%s\nextracted rows=%s\n" % (example_file,str([expected_col_titles,expected_data_row]),str(getRows(example_file)))
def cleanUp(all_files_and_dirs_in_dir_of_this_script_prior_to_running_unit_tests): import glob #some unit tests may actually write intermediate temporary files to dir_of_this_script - hence make sure that these have all been deleted after all unit tests have been carried out! unit_test_temp_files_written_to_dir_of_this_script = [file_name for file_name in glob.glob(r'%s%s*' % (dir_of_this_script,delimiter())) if not file_name in all_files_and_dirs_in_dir_of_this_script_prior_to_running_unit_tests] for UNIT_TEST_TEMP_FILE_WRITTEN_TO_DIR_OF_THIS_SCRIPT in unit_test_temp_files_written_to_dir_of_this_script: print '='*50 print 'Removing this temporary file written to the directory of run_tests.py: ', UNIT_TEST_TEMP_FILE_WRITTEN_TO_DIR_OF_THIS_SCRIPT os.remove(UNIT_TEST_TEMP_FILE_WRITTEN_TO_DIR_OF_THIS_SCRIPT) print '='*50
