def setUp(self):
super(CleanTest, self).setUp()
## Setup pre-casava results
for k in self.RESULT_FILES.keys():
for f in self.RESULT_FILES[k]:
outfile = os.path.join(intermediate, flowcell, f)
if not os.path.exists(os.path.dirname(outfile)):
safe_makedir(os.path.dirname(outfile))
exit_code = shell.exec_cmd2(['touch', outfile])
for k in self.INPUT_FILES.keys():
for f in self.INPUT_FILES[k]:
outfile = os.path.join(data, flowcell, '1_120829_AA001AAAXX_barcode', f)
if not os.path.exists(os.path.dirname(outfile)):
safe_makedir(os.path.dirname(outfile))
exit_code = shell.exec_cmd2(['touch', outfile])
## Setup casava results
for k in self.RESULT_FILES.keys():
for f in self.RESULT_FILES[k]:
outfile = os.path.join(data, k, flowcell, f)
if not os.path.exists(os.path.dirname(outfile)):
safe_makedir(os.path.dirname(outfile))
exit_code = shell.exec_cmd2(['touch', outfile])
for k in self.INPUT_FILES.keys():
for f in self.INPUT_FILES[k]:
outfile = os.path.join(data, k, flowcell, '1_120829_AA001AAAXX_barcode', f)
if not os.path.exists(os.path.dirname(outfile)):
safe_makedir(os.path.dirname(outfile))
exit_code = shell.exec_cmd2(['touch', outfile])
def setUp(self):
super(CleanTest, self).setUp()
## Setup pre-casava results
for k in self.RESULT_FILES.keys():
for f in self.RESULT_FILES[k]:
outfile = os.path.join(intermediate, flowcell, f)
if not os.path.exists(os.path.dirname(outfile)):
safe_makedir(os.path.dirname(outfile))
exit_code = shell.exec_cmd2(['touch', outfile])
for k in self.INPUT_FILES.keys():
for f in self.INPUT_FILES[k]:
outfile = os.path.join(data, flowcell,
'1_120829_AA001AAAXX_barcode', f)
if not os.path.exists(os.path.dirname(outfile)):
safe_makedir(os.path.dirname(outfile))
exit_code = shell.exec_cmd2(['touch', outfile])
## Setup casava results
for k in self.RESULT_FILES.keys():
for f in self.RESULT_FILES[k]:
outfile = os.path.join(data, k, flowcell, f)
if not os.path.exists(os.path.dirname(outfile)):
safe_makedir(os.path.dirname(outfile))
exit_code = shell.exec_cmd2(['touch', outfile])
for k in self.INPUT_FILES.keys():
for f in self.INPUT_FILES[k]:
outfile = os.path.join(data, k, flowcell,
'1_120829_AA001AAAXX_barcode', f)
if not os.path.exists(os.path.dirname(outfile)):
safe_makedir(os.path.dirname(outfile))
exit_code = shell.exec_cmd2(['touch', outfile])
def setUp(self):
super(ProjectTest, self).setUp()
## FIX ME: deliver data first - serves as test data
self.app = self.make_app(argv = [])
self.app.setup()
self.fastq_dir = os.path.join(self.app.config.get("project", "root"), "j_doe_00_01", "data", flowcell)
safe_makedir(self.fastq_dir)
for f in self.COMPRESS_FILES:
m = glob.glob("{}*".format(os.path.join(self.fastq_dir, f)))
if not m:
exit_code = shell.exec_cmd2(['touch', os.path.join(self.fastq_dir, f)])
flist = walk(j_doe_00_04['data'])
for f in flist:
os.unlink(f)
def setUp(self):
super(ProjectTest, self).setUp()
## FIX ME: deliver data first - serves as test data
self.app = self.make_app(argv=[])
self.app.setup()
self.fastq_dir = os.path.join(self.app.config.get("project", "root"),
"j_doe_00_01", "data", flowcell)
safe_makedir(self.fastq_dir)
for f in self.COMPRESS_FILES:
m = glob.glob("{}*".format(os.path.join(self.fastq_dir, f)))
if not m:
exit_code = shell.exec_cmd2(
['touch', os.path.join(self.fastq_dir, f)])
flist = walk(j_doe_00_04['data'])
for f in flist:
os.unlink(f)
