def setUp(self):
# Make test directories
self.empty_dir1 = TestUtils.make_dir()
self.empty_dir2 = TestUtils.make_dir()
self.dir1 = ExampleDirScooby()
self.dir2 = ExampleDirScooby()
self.dir1.create_directory()
self.dir2.create_directory()
def test_cmp_filepair_different_files(self):
"""cmp_filepair flags mismatch between differing files
"""
# Make two different files and compare them
f1 = TestUtils.make_file('test_file1',"Lorum ipsum",basedir=self.wd)
f2 = TestUtils.make_file('test_file2',"lorum ipsum",basedir=self.wd)
result = cmp_filepair((f1,f2))
self.assertEqual(result.status,Md5Checker.MD5_FAILED)
def test_cmp_filepair_identical_links(self):
"""cmp_filepair matches identical links
"""
# Make two identical symlinks and compare them
f1 = TestUtils.make_sym_link('/dummy/file',link_name='test_link1',basedir=self.wd)
f2 = TestUtils.make_sym_link('/dummy/file',link_name='test_link2',basedir=self.wd)
result = cmp_filepair((f1,f2))
self.assertEqual(result.status,Md5Checker.LINKS_SAME)
def test_cmp_filepair_different_links(self):
"""cmp_filepair flags mismatch between differing links
"""
# Make two identical symlinks and compare them
f1 = TestUtils.make_sym_link('/dummy/file1',link_name='test_link1',basedir=self.wd)
f2 = TestUtils.make_sym_link('/dummy/file2',link_name='test_link2',basedir=self.wd)
result = cmp_filepair((f1,f2))
self.assertEqual(result.status,Md5Checker.LINKS_DIFFER)
def setUp(self):
# Make test directories
self.empty_dir1 = TestUtils.make_dir()
self.empty_dir2 = TestUtils.make_dir()
self.dir1 = ExampleDirScooby()
self.dir2 = ExampleDirScooby()
self.dir1.create_directory()
self.dir2.create_directory()
def test_cmp_filepair_file_to_link(self):
"""cmp_file flags mismatch between file and link
"""
# Make file and link
f1 = TestUtils.make_file('test_file1',"Lorum ipsum",basedir=self.wd)
f2 = TestUtils.make_sym_link('/dummy/file',link_name='test_link2',basedir=self.wd)
result = cmp_filepair((f1,f2))
self.assertEqual(result.status,Md5Checker.MD5_ERROR)
def test_cmp_filepair_identical_files(self):
"""cmp_filepair matches identical files
"""
# Make two identical files and compare them
f1 = TestUtils.make_file('test_file1',"Lorum ipsum",basedir=self.wd)
f2 = TestUtils.make_file('test_file2',"Lorum ipsum",basedir=self.wd)
result = cmp_filepair((f1,f2))
self.assertEqual(result.status,Md5Checker.MD5_OK)
def test_cmp_filepair_link_to_file(self):
"""cmp_file flags mismatch between link and file
"""
# Make file and link
f1 = TestUtils.make_sym_link('/dummy/file',link_name='test_link1',basedir=self.wd)
f2 = TestUtils.make_file('test_file2',"Lorum ipsum",basedir=self.wd)
result = cmp_filepair((f1,f2))
self.assertEqual(result.status,Md5Checker.TYPES_DIFFER)
def setUp(self):
# Make an example directory with sample files
# structured as for Illumina data
self.d = TestUtils.make_dir()
# Add fastq files
self.fastq_dir = TestUtils.make_sub_dir(self.d, 'fastqs')
for f in ILLUMINA_FILES.split():
TestUtils.make_file(f, "lorem ipsum", basedir=self.fastq_dir)
# Make an example QC dir
self.qc_dir = TestUtils.make_sub_dir(self.d, 'qc')
for f in ILLUMINA_QC_FILES.split():
TestUtils.make_file(f, "lorem ipsum", basedir=self.qc_dir)
for d in ILLUMINA_FASTQC_DIRS.split():
TestUtils.make_sub_dir(self.qc_dir, d)
def setUp(self):
# Make an example directory with sample files
# structured as for Illumina data
self.d = TestUtils.make_dir()
# Add fastq files
self.fastq_dir = TestUtils.make_sub_dir(self.d,'fastqs')
for f in ILLUMINA_FILES.split():
TestUtils.make_file(f,"lorem ipsum",basedir=self.fastq_dir)
# Make an example QC dir
self.qc_dir = TestUtils.make_sub_dir(self.d,'qc')
for f in ILLUMINA_QC_FILES.split():
TestUtils.make_file(f,"lorem ipsum",basedir=self.qc_dir)
for d in ILLUMINA_FASTQC_DIRS.split():
TestUtils.make_sub_dir(self.qc_dir,d)
def setUp(self):
# Make an example directory with sample files
# structured as for SOLiD data
self.d = TestUtils.make_dir()
# Add files
for f in SOLID_FILES.split():
TestUtils.make_file(f,"lorem ipsum",basedir=self.d)
# Make an example QC dir
self.qc_dir = TestUtils.make_sub_dir(self.d,'qc')
for f in SOLID_QC_FILES.split():
TestUtils.make_file(f,"lorem ipsum",basedir=self.qc_dir)
def setUp(self):
# Make an example directory with sample files
# structured as for SOLiD data
self.d = TestUtils.make_dir()
# Add files
for f in SOLID_FILES.split():
TestUtils.make_file(f, "lorem ipsum", basedir=self.d)
# Make an example QC dir
self.qc_dir = TestUtils.make_sub_dir(self.d, 'qc')
for f in SOLID_QC_FILES.split():
TestUtils.make_file(f, "lorem ipsum", basedir=self.qc_dir)
def tearDown(self):
# Remove the example dir
TestUtils.remove_dir(self.d)
def tearDown(self):
# Remove the example dir
TestUtils.remove_dir(self.d)
def setUp(self):
# Create a set of files to compare
self.file1 = TestUtils.make_file(None,"This is a test file")
self.file2 = TestUtils.make_file(None,"This is a test file")
self.file3 = TestUtils.make_file(None,"This is another test file")
def setUp(self):
# Create a set of files to compare
self.file1 = TestUtils.make_file(None, "This is a test file")
self.file2 = TestUtils.make_file(None, "This is a test file")
self.file3 = TestUtils.make_file(None, "This is another test file")
def setUp(self):
# Create working directory for test files etc
self.wd = TestUtils.make_dir()
def tearDown(self):
# Remove the container dir
TestUtils.remove_dir(self.wd)