How to use sos - 10 common examples

## (at your option) any later version.

## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
## GNU General Public License for more details.

## You should have received a copy of the GNU General Public License
## along with this program; if not, write to the Free Software
## Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.

import sys
import sos.plugintools
from sos.helpers import *

class tarball(sos.plugintools.PluginBase):
    """This plugin tars up the information gathered by sosreport
    """
    def postproc(self, dstroot):
        print "Please enter your first initial and last name (jsmith): ",
        name = sys.stdin.readline()[:-1]

        print "Please enter the case number that you are generating this",
        print "report for: ",
        ticketNumber = sys.stdin.readline()[:-1]

        dirName = name + "." + ticketNumber
        self.callExtProg("/bin/mkdir /tmp/%s" % dirName)
        self.callExtProg("/bin/mv %s/* /tmp/%s"
                       % (dstroot, dirName))
        self.callExtProg("/bin/rm -rf %s" % dstroot)
        self.callExtProg("/bin/tar --directory /tmp -jcf "

'''Test workdir option for runtime environment'''
        import tempfile
        tdir = tempfile.mkdtemp()
        with open(os.path.join(tdir, 'aaa.pp'), 'w') as aaa:
            aaa.write('something')
        script = r"""
import os
[0]
task: workdir={0!r}

with open(os.path.join({1!r}, 'result.txt'), 'w') as res:
   for file in os.listdir({1!r}):
       res.write(file + '\n')
""".format(os.path.split(tdir)[0],
           os.path.split(tdir)[1])
        wf = SoS_Script(script).workflow()
        env.config['sig_mode'] = 'force'
        Base_Executor(wf, config={'default_queue': 'localhost'}).run()
        with open(os.path.join(tdir, 'result.txt')) as res:
            content = [x.strip() for x in res.readlines()]
            self.assertTrue('aaa.pp' in content)

def testBash(self):
        '''Test action bash'''
        script = SoS_Script(r'''
[0]
bash:
echo 'Echo'
''')
        wf = script.workflow()
        Base_Executor(wf).run()
        script = SoS_Script(r'''
[0]
bash:
echo 'Echo
''')
        wf = script.workflow()
        self.assertRaises(Exception, Base_Executor(wf).run)

def testProgressBar(self):
        '''Test progress bar'''
        env.verbosity = 1
        #
        script = SoS_Script('''

[1]
[2]
[3]
[4]
[5]
''')
        wf = script.workflow()
        Base_Executor(wf).run()

def testChainedDepends(self):
        '''Test chain dependent'''
        script = SoS_Script(r'''
# this step provides variable `var`
[index: provides='{filename}.bam.bai']
input: f"{filename}.bam"
run: expand=True
   echo "Generating {_output}"
   touch {_output}

[call: provides='{filename}.vcf']
input:   f"{filename}.bam"
depends: f"{_input}.bai"
run: expand=True
   echo "Calling variants from {_input} with {_depends} to {_output}"
   touch {_output}
''')
        if file_target('a.bam.bai').exists():
            file_target('a.bam.bai').unlink()

def testTrunkSizeWithStopIf(self):
        '''Test a case when some tasks are not submitted due to holes in slots #1159'''
        for i in range(5):
            f = f'{i+1}.txt'
            if os.path.isfile(f):
                os.remove(f)
        script = SoS_Script('''\
[1]
output: [f'{x+1}.txt' for x in range(5)]
for i in range(5):
  name = f'{i+1}.txt'
  if i not in [0,1,2]:
    path(name).touch()
  else:
    with open(name, 'w') as f:
      f.write('test it')

[2]
input: group_by = 1
output: f'{_input:n}.out'
stop_if(_input.stat().st_size==0, no_output=True)

task: trunk_size = 80

script.workflow()
        #
        # script with first-line indent
        #
        script = SoS_Script('''
[0]
sh:
  echo "a"

sh('echo "b"')
''')
        script.workflow()
        #
        # script with triple quote and format string
        # #1211
        script = SoS_Script('''
[1]
python3: expand = "${ }"

  ld = ${'100'}
  a =  """doc"""

''')
        wf = script.workflow()
        Base_Executor(wf).run()
        script = SoS_Script('''
[default]
report: expand = "${ }"
  ld_file = ${_input['']:r}
  """ \'\'\'
  {}, ${_output:r},

files = ['a.txt', 'b.txt']
vars = [1, 2]

input: files, paired_with='vars', group_by=1
output: f"{_input}{_vars[0]}"
run: expand=True
    touch {_output}
''')
        wf = script.workflow()
        Base_Executor(wf).run()
        for ofile in ['a.txt1', 'b.txt2']:
            self.assertTrue(file_target(ofile).target_exists('target'))
            file_target(ofile).unlink()
        #
        # list input
        script = SoS_Script(r'''
[0]
files = ['a.txt', 'b.txt']
vars = [1, 2]
vars2 = ['a', 'b']

input: files, paired_with=('vars', 'vars2'), group_by=1
output: f"{_input}{_vars[0]}"
run: expand=True
    touch {_output}
''')
        wf = script.workflow()
        Base_Executor(wf).run()
        for ofile in ['a.txt1', 'b.txt2']:
            self.assertTrue(file_target(ofile).target_exists('target'))
            file_target(ofile).unlink()
        #

def testTypeTraitParameter(self):
        # type trait
        script = SoS_Script('''
parameter: b
[0]
''')
        wf = script.workflow()
        Base_Executor(wf, args=['--b', '5']).run(mode='dryrun')
        self.assertEqual(env.sos_dict['b'], '5')
        #
        script = SoS_Script('''
parameter: b :str
[0]
''')
        wf = script.workflow()
        Base_Executor(wf, args=['--b', '5']).run(mode='dryrun')
        self.assertEqual(env.sos_dict['b'], '5')
        #
        script = SoS_Script('''
parameter: b : list
[0]
''')
        wf = script.workflow()
        Base_Executor(wf, args=['--b', '5']).run(mode='dryrun')
        self.assertEqual(env.sos_dict['b'], ['5'])

        #

executed = []
input: ['a{}.txt'.format(x) for x in range(1, 10)], group_by=3

executed.append(_input)

''')
        wf = script.workflow()
        Base_Executor(wf).run(mode='dryrun')
        self.assertEqual(env.sos_dict['executed'], [
            sos_targets('a1.txt', 'a2.txt', 'a3.txt'),
            sos_targets('a4.txt', 'a5.txt', 'a6.txt'),
            sos_targets('a7.txt', 'a8.txt', 'a9.txt')
        ])
        # group_by chunks specified as integer strings
        script = SoS_Script('''
[0: shared='executed']

executed = []
input: ['a{}.txt'.format(x) for x in range(1, 10)], group_by='3'

executed.append(_input)

''')
        wf = script.workflow()
        Base_Executor(wf).run(mode='dryrun')
        self.assertEqual(env.sos_dict['executed'], [
            sos_targets('a1.txt', 'a2.txt', 'a3.txt'),
            sos_targets('a4.txt', 'a5.txt', 'a6.txt'),
            sos_targets('a7.txt', 'a8.txt', 'a9.txt')
        ])
        # number of files should be divisible by group_by