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 sync(self, source):
sources = self.app.db['sources']
src = self.app.db['sources'][source]
if not src['is_local']:
if not os.path.exists(os.path.join(src['cache'], '.git')):
shell.exec_cmd2([ 'git', 'clone',
src['path'], src['cache'] ])
else:
os.chdir(src['cache'])
shell.exec_cmd2(['git', 'pull'])
src['last_sync_time'] = datetime.now()
sources[source] = src
self.app.db['sources'] = sources
def unpack(self):
cmd = ['java', '-jar', 'lib/abe.jar', 'unpack', self.options.in_backup[0], self.options.out_archive[0]]
exitcode = shell.exec_cmd2(cmd)
self.log.debug('abe exit: %d.' % exitcode, __name__)
if exitcode == 0:
# self.log.info('Done.')
# self.log.info('tar archive is saved as: %s' % self.options.out_archive[0])
CoreUtil.hash(self.options.out_archive[0])
else:
self.log.warning('Backup Unpack module exit unexpectedly: %d.' % exitcode)
def sync(self, source):
sources = self.app.db['sources']
src = self.app.db['sources'][source]
if not src['is_local']:
if not os.path.exists(os.path.join(src['cache'], '.git')):
shell.exec_cmd2(['git', 'clone', src['path'], src['cache']])
else:
orig_dir = fs.abspath(os.curdir)
try:
os.chdir(src['cache'])
shell.exec_cmd2(['git', 'pull'])
os.chdir(orig_dir)
finally:
os.chdir(orig_dir)
src['last_sync_time'] = datetime.now()
sources[source] = src
self.app.db['sources'] = sources
def sync(self, source):
sources = self.app.db["sources"]
src = self.app.db["sources"][source]
if not src["is_local"]:
if not os.path.exists(os.path.join(src["cache"], ".git")):
shell.exec_cmd2(["git", "clone", src["path"], src["cache"]])
else:
orig_dir = fs.abspath(os.curdir)
try:
os.chdir(src["cache"])
shell.exec_cmd2(["git", "pull"])
os.chdir(orig_dir)
finally:
os.chdir(orig_dir)
src["last_sync_time"] = datetime.now()
sources[source] = src
self.app.db["sources"] = sources
def _do_tests(self):
print('Running Nose Tests')
out, err, res = shell.exec_cmd(['which', 'nosetests'])
nose = out.decode('utf-8').strip()
if self.app.pargs.loud:
cmd_args = ['coverage', 'run', nose, '--verbosity=3']
res = shell.exec_cmd2(cmd_args)
else:
cmd_args = ['coverage', 'run', nose, '--verbosity=0']
out, err, res = shell.exec_cmd(cmd_args)
if res > 0:
self._do_error("\n\nNose tests did not pass.\n\n" +
"$ %s\n%s" % (' '.join(cmd_args), err))
def _do_tests(self):
print('Running Nose Tests')
out, err, res = shell.exec_cmd(['which', 'nosetests'])
if self.app.pargs.loud:
cmd_args = ['coverage', 'run', out.strip(), '--verbosity=3']
res = shell.exec_cmd2(cmd_args)
else:
cmd_args = ['coverage', 'run', out.strip(), '--verbosity=0']
out, err, res = shell.exec_cmd(cmd_args)
if res > 0:
self._do_error("\n\nNose tests did not pass.\n\n" +
"$ %s\n%s" % (' '.join(cmd_args), err))
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)
def execute(self):
cmd = ['adb', 'backup']
if self.options.apk:
cmd.append('-apk')
if self.options.all:
cmd.append('-all')
if self.options.system:
cmd.append('-system')
if self.options.obb:
cmd.append('-obb')
if self.options.shared:
cmd.append('-shared')
if self.options.filename:
cmd.append('-f %s' % self.options.filename)
exitcode = shell.exec_cmd2(cmd)
self.log.debug('adb backup exit: %d.' % exitcode, __name__)
if exitcode == 0:
# self.log.info('Done.')
# self.log.info('Backup is saved as: %s' % self.options.filename)
CoreUtil.hash(self.options.filename)
else:
self.log.warning('Logical Acquisition module exit unexpectedly: %d.' % exitcode)
def list(self):
cmd = ['adb', 'shell', 'pm', 'list', 'packages', '-u', '-f']
shell.exec_cmd2(cmd)
def test_exec_cmd2_bad_command(self):
ret = shell.exec_cmd2(['false'])
self.eq(ret, 1)
def test_exec_cmd2_shell_true(self):
ret = shell.exec_cmd2(['echo johnny'], shell=True)
self.eq(ret, 0)
def test_exec_cmd2(self):
ret = shell.exec_cmd2(['echo'])
self.eq(ret, 0)
def test_exec_cmd2_bad_command():
ret = shell.exec_cmd2(['false'])
assert ret == 1
def test_exec_cmd2_shell_true():
ret = shell.exec_cmd2(['echo johnny'], shell=True)
assert ret == 0
def test_exec_cmd2():
ret = shell.exec_cmd2(['echo'])
assert ret == 0
def test_exec_cmd2():
ret = shell.exec_cmd2(['echo'])
assert ret == 0
def test_exec_cmd2_shell_true():
ret = shell.exec_cmd2(['echo johnny'], shell=True)
assert ret == 0
def test_exec_cmd2_bad_command():
ret = shell.exec_cmd2(['false'])
assert ret == 1
