def test_cli(self):
Path('/tmp/test_remote/').rmtree_p()
stdout = LoggedShellCommand([
'python3','-m','spiper run',
'spiper_mock_flow@https://github.com/shouldsee/spiper_mock_flow/tarball/8b01372',
'TOPLEVEL:run_and_backup',
'/tmp/test_remote/root','1','2','/tmp/test_remote/root.backup'
])
assert '[workflow]done' in stdout.splitlines()[-1]
def tarball_dangerous_cache(self,prefix,
input_prefix = File,
_output=[
File('tar_gz'),
File('cmd')]):
with input_prefix.dirname():
stdout = LoggedShellCommand([
'tar', '-cvzf', self.output.tar_gz, input_prefix.basename()+'*',
],
self.output.cmd)
return self
def workflow(self, prefix, seed =int , L=int,
_output = [
File('log'),
]):
print('\n[Flow running] mock=%s'%getattr(self.runner.func,'__name__','None'))
curr = self.runner(random_seq, prefix, seed, L)
curr1 = self.config_runner(tag='const')(random_seq, prefix, 0, 100)
curr = self.runner(transcribe, prefix, curr.output.seq,)
curr = self.runner(mutate, prefix, curr.output.fasta)
stdout = LoggedShellCommand(['ls -lhtr',prefix.dirname()], self.output.log).rstrip()
self.runner(copy_file, prefix+'.source.py', __file__)
return self
def get_genepred(self,prefix,
_resp = spiper.types.HttpResponseContentHeader('https://hgdownload.soe.ucsc.edu/goldenPath/currentGenomes/Wuhan_seafood_market_pneumonia_virus/database/ncbiGene.txt.gz'),
_IMAGE = Depend('docker://quay.io/biocontainers/ucsc-genepredtogtf:377--h35c10e6_2'),
_output = ['genepred','gtf','cmd'],
):
CMD = ['curl','-LC0',_resp.url,
'|','gzip -d | cut -f2- >',self.output.genepred,
]
LoggedShellCommand(CMD, self.output.cmd,mode='w')
CMD = ['genePredToGtf','file',self.output.genepred, self.output.gtf]
LoggedSingularityCommand(CMD, _IMAGE, self.output.cmd,mode='a')
def workflow(self, prefix, seed =int , L=int,
_output = [
File('log'),
]):
_ = '''
A workflow is not a Node()
'''
print('\n[Flow running] mock=%s'%getattr(self.runner.func,'__name__','None'))
### [ToDo] (func, prefix) must be unique within each workflow
# self.data = {}
curr = self.runner(random_seq, prefix, seed, L)
curr1 = self.config_runner(tag='temp')(random_seq, prefix, 0, 100)
curr = self.runner(transcribe, prefix, curr.output.seq,)
curr = self.runner(mutate, prefix, curr.output.fasta)
stdout = LoggedShellCommand(['ls -lhtr',prefix.dirname()],).rstrip()
return self
def main(force_run=force_run,prefix=None):
# spiper.rcParams['dir_layout'] = dir_layout
if prefix is None:
prefix = Path('/tmp/spiper.test_run/root')
prefix.dirname().rmtree_p()
print('\n---------------------Run1---\n## got') if __name__ == '__main__' else None
res1 = force_run(gen_files, prefix,verbose=0)
res2 = force_run(tarball_dangerous_cache, prefix, res1.prefix_named, verbose=1)
res1 = force_run(gen_files, prefix,verbose=0)
res2 = force_run(tarball_dangerous_cache, prefix, res1.prefix_named, verbose=1)
s = '''
## expect
[cache_run] {"job_name"="tarball_dangerous_cache"_"input_ident_changed"=1_"output_ident_chanegd"=0}
* This change to input is ignored because tarball_dangerous_cache(input_prefix=File) would not expand to match the files during input validation The type specified in def line will be used for detecting a timestamp/filesize change
'''.strip()
print(s) if __name__ == '__main__' else None
print('---------------------Run2---\n## got') if __name__ == '__main__' else None
res1 = force_run(gen_files, prefix)
res2 = force_run(tarball_prefix_cache, prefix, res1.prefix_named, verbose=1)
res1 = force_run(gen_files, prefix)
res2 = force_run(tarball_prefix_cache, prefix, res1.prefix_named, verbose=1)
s = '''
## expect
[cache_run] {"job_name"="tarball_prefix_cache"_"input_ident_changed"=1_"output_ident_chanegd"=0}
* Because tarball_prefix_cache(input_prefix=Prefix) is expanded into the appropriate files during input validation.
* Note that the Prefix only expands into a shallow match and does not recurse into sub-directory during input validation
'''.strip()
print(s) if __name__ == '__main__' else None
print('------Output Directory. (dir_layout={spiper.rcParams.dir_layout})--------\n'.format(spiper=spiper),
LoggedShellCommand(['echo [ls]',prefix,'&&','ls','-lhtr',prefix.dirname(),],'/dev/null'))
return res1,res2
def make_tar( self, prefix, input_file=File, _output=['tar_gz'] ):
with input_file.dirname() as d:
print('taring %r'%d)
stdout = LoggedShellCommand(['tar','-zvcf',self.output.tar_gz, '*'], '/dev/null')
return self