How to use the ipykernel.tests.utils.assemble_output function in ipykernel

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github vatlab / sos / test / jupyter / test_sos_kernel.py View on Github external
'''Test magic use to create new kernels'''
        with sos_kernel() as kc:
            iopub = kc.iopub_channel
            # create a data frame
            execute(kc=kc, code='%use R2 -l R')
            wait_for_idle(kc)
            execute(kc=kc, code='%use R3 -l R -c black')
            wait_for_idle(kc)
            execute(kc=kc, code='%use R4 -k ir -l R -c green')
            wait_for_idle(kc)
            execute(kc=kc, code='%use R4 -c cyan')
            wait_for_idle(kc)
            execute(kc=kc, code='%with R5 -l sos.R:sos_R -c default')
            wait_for_idle(kc)
            execute(kc=kc, code='%with R6 -l unknown -c default')
            _, stderr = assemble_output(iopub)
            self.assertTrue('Failed to switch' in stderr, 'expect error {}'.format(stderr))
            execute(kc=kc, code="%use sos")
            wait_for_idle(kc)
github vatlab / sos / test / jupyter / test_sos_kernel.py View on Github external
def testCD(self):
        with sos_kernel() as kc:
            iopub = kc.iopub_channel
            execute(kc=kc, code="%cd ..")
            wait_for_idle(kc)
            execute(kc=kc, code="print(os.getcwd())")
            stdout, stderr = assemble_output(iopub)
            self.assertFalse(stdout.strip().endswith('jupyter'))
            self.assertEqual(stderr, '')
            execute(kc=kc, code="%cd jupyter")
github vatlab / sos / test / jupyter / test_sos_magics.py View on Github external
hello
world
""")
''')
            stdout, stderr = assemble_output(iopub)
            self.assertEqual(stderr, '')
            self.assertTrue('world' in stdout, 'Expect preview {}'.format(stdout))
            # preview zip
            execute(kc=kc, code='''
%preview -n a.zip
import zipfile

with zipfile.ZipFile('a.zip', 'w') as zfile:
    zfile.write('a.csv')
''')
            stdout, stderr = assemble_output(iopub)
            self.assertEqual(stderr, '')
            self.assertTrue('a.csv' in stdout, 'Expect preview {}'.format(stdout))
            # preview tar
            execute(kc=kc, code='''
%preview -n a.tar
import tarfile

with tarfile.open('a.tar', 'w') as tar:
    tar.add('a.csv')

''')
            stdout, stderr = assemble_output(iopub)
            self.assertEqual(stderr, '')
            self.assertTrue('a.csv' in stdout, 'Expect preview {}'.format(stdout))
            # preview tar.gz
            execute(kc=kc, code='''
github vatlab / jupyterlab-sos / test / test_utils.py View on Github external
def get_std_output(iopub):
    '''Obtain stderr and remove some unnecessary warning from
    https://github.com/jupyter/jupyter_client/pull/201#issuecomment-314269710'''
    stdout, stderr = test_utils.assemble_output(iopub)
    return stdout, '\n'.join([
        x for x in stderr.splitlines() if 'sticky' not in x and
        'RuntimeWarning' not in x and 'communicator' not in x
    ])
github vatlab / sos / test / jupyter / test_sos_magics.py View on Github external
def testMagicSet(self):
        # test preview of remote file
        with sos_kernel() as kc:
            iopub = kc.iopub_channel
            # preview variable
            execute(kc=kc, code='''
%set
%set -v2
%set
%set -v1
''')
        stdout, stderr = assemble_output(iopub)
        self.assertEqual(stderr, '', 'Got {}'.format(stderr))
        self.assertTrue('set' in stdout, 'Got {}'.format(stdout))
github vatlab / sos / test / jupyter / test_jupyter_sos.py View on Github external
def testReadonlyALLCAPVars(self):
        subprocess.call('sos config --global --set sos.change_all_cap_vars warning', shell=True)
        with sos_kernel() as kc:
            iopub = kc.iopub_channel
            execute(kc=kc, code='''
%run
A=10

[default]
A=20
''')
            _, stderr = assemble_output(iopub)
            self.assertTrue('A' in stderr, 'Expect an error {}'.format(stderr))
        subprocess.call('sos config --global --unset sos.change_all_cap_vars', shell=True)
github vatlab / sos-notebook / src / sos_notebook / test_utils.py View on Github external
def get_std_output(iopub):
    '''Obtain stderr and remove some unnecessary warning from
    https://github.com/jupyter/jupyter_client/pull/201#issuecomment-314269710'''
    stdout, stderr = test_utils.assemble_output(iopub)
    return stdout, '\n'.join([
        x for x in stderr.splitlines() if 'sticky' not in x and
        'RuntimeWarning' not in x and 'communicator' not in x
    ])
github vatlab / sos / test / jupyter / test_sos_kernel.py View on Github external
def testShell(self):
        with sos_kernel() as kc:
            iopub = kc.iopub_channel
            execute(kc=kc, code="!echo ha ha")
            stdout, stderr = assemble_output(iopub)
            self.assertTrue('ha ha' in stdout, "GOT ERROR {}".format(stderr))
            self.assertEqual(stderr, '')
github vatlab / sos / test / bioinfo / test_preview.py View on Github external
def testMagicPreview(self):
        with sos_kernel() as kc:
            # preview bam file
            iopub = kc.iopub_channel
            execute(kc=kc, code='''
%preview -n {}/sim_reads_aligned.bam
'''.format(self.resource_dir))
            stdout, stderr = assemble_output(iopub)
            self.assertEqual(stderr, '')
            self.assertTrue('PG' in stdout)

            # preview sam file
            execute(kc=kc, code='''
%preview -n {}/sim_reads_aligned.sam
'''.format(self.resource_dir))
            stdout, stderr = assemble_output(iopub)
            self.assertEqual(stderr, '')
            self.assertTrue('PG' in stdout)
github vatlab / sos / test / jupyter / test_sos_kernel.py View on Github external
def testMagicUse(self):
        with sos_kernel() as kc:
            iopub = kc.iopub_channel
            execute(kc=kc, code="%use R0 -l sos.R.kernel:sos_R -c #CCCCCC")
            _, stderr = assemble_output(iopub)
            self.assertEqual(stderr, '')
            execute(kc=kc, code="%use R1 -l sos.R.kernel:sos_R -k ir -c #CCCCCC")
            _, stderr = assemble_output(iopub)
            self.assertEqual(stderr, '')
            execute(kc=kc, code="%use R2 -k ir")
            _, stderr = assemble_output(iopub)
            self.assertEqual(stderr, '')
            execute(kc=kc, code="a <- 1024")
            wait_for_idle(kc)
            execute(kc=kc, code="a")
            res = get_display_data(iopub)
            self.assertEqual(res, '[1] 1024')
            execute(kc=kc, code="%use R3 -k ir -l R")
            _, stderr = assemble_output(iopub)
            self.assertEqual(stderr, '')
            execute(kc=kc, code="a <- 233")