projects
/
htsworkflow.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
af16081
)
convert several not covered by unit-test modules to use print function
author
Diane Trout
<diane@ghic.org>
Mon, 6 Apr 2015 21:50:03 +0000
(14:50 -0700)
committer
Diane Trout
<diane@ghic.org>
Mon, 6 Apr 2015 21:50:03 +0000
(14:50 -0700)
htsworkflow/automation/runner.py
patch
|
blob
|
history
htsworkflow/pipelines/configure_run.py
patch
|
blob
|
history
htsworkflow/pipelines/fastq.py
patch
|
blob
|
history
htsworkflow/pipelines/run_status.py
patch
|
blob
|
history
htsworkflow/submission/geo.py
patch
|
blob
|
history
htsworkflow/submission/trackhub_submission.py
patch
|
blob
|
history
test/tree.py
patch
|
blob
|
history
version.py
patch
|
blob
|
history
diff --git
a/htsworkflow/automation/runner.py
b/htsworkflow/automation/runner.py
index 7b0c4c9d7ca6b47e59254b27e2171876525e6715..073a6e7a6861ec8f4b544a64978eca129628bd40 100644
(file)
--- a/
htsworkflow/automation/runner.py
+++ b/
htsworkflow/automation/runner.py
@@
-1,4
+1,5
@@
#!/usr/bin/env python
#!/usr/bin/env python
+from __future__ import print_function
from glob import glob
import logging
import os
from glob import glob
import logging
import os
@@
-196,7
+197,7
@@
class Runner(rpc.XmlRpcBot):
#startCmdLineStatusMonitor(ci)
# running step
#startCmdLineStatusMonitor(ci)
# running step
- print
'Running pipeline now!'
+ print
('Running pipeline now!')
run_status = run_pipeline(conf_info)
if run_status is True:
LOGGER.info('Runner: Pipeline: success')
run_status = run_pipeline(conf_info)
if run_status is True:
LOGGER.info('Runner: Pipeline: success')
@@
-223,4
+224,3
@@
def main(args=None):
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))
-
diff --git
a/htsworkflow/pipelines/configure_run.py
b/htsworkflow/pipelines/configure_run.py
index d0d43d25e579e62e7a7ddceb6774d187457a118b..324f53b4cdffa25906275e3865d4b1137f5a7e6f 100644
(file)
--- a/
htsworkflow/pipelines/configure_run.py
+++ b/
htsworkflow/pipelines/configure_run.py
@@
-1,4
+1,6
@@
#!/usr/bin/python
#!/usr/bin/python
+from __future__ import print_function
+
__docformat__ = "restructuredtext en"
import subprocess
__docformat__ = "restructuredtext en"
import subprocess
@@
-243,7
+245,7
@@
def config_stdout_handler(line, conf_info):
#Standard output handling
else:
#Standard output handling
else:
- print
'Sequence line:', line
+ print
('Sequence line:', line)
mo = s_seq_folder.search(line)
conf_info.bustard_path = line[mo.end():]
conf_info.run_path, temp = os.path.split(conf_info.bustard_path)
mo = s_seq_folder.search(line)
conf_info.bustard_path = line[mo.end():]
conf_info.run_path, temp = os.path.split(conf_info.bustard_path)
@@
-458,7
+460,7
@@
def configure(conf_info):
stdout=fout,
stderr=ferr)
stdout=fout,
stderr=ferr)
- print
"Configuring pipeline: %s" % (time.ctime(
))
+ print
("Configuring pipeline: %s" % (time.ctime()
))
error_code = pipe.wait()
# Clean up
error_code = pipe.wait()
# Clean up
@@
-509,8
+511,8
@@
def configure(conf_info):
# 1) The stdout completed without error
# 2) The program exited with status 0
# 3) No errors found in stdout
# 1) The stdout completed without error
# 2) The program exited with status 0
# 3) No errors found in stdout
- print
'#Expect: True, False, True, True'
- print
complete, bool(error_code), abort != RUN_ABORT, stderr_success is True
+ print
('#Expect: True, False, True, True')
+ print
(complete, bool(error_code), abort != RUN_ABORT, stderr_success is True)
status = complete is True and \
bool(error_code) is False and \
abort != RUN_ABORT and \
status = complete is True and \
bool(error_code) is False and \
abort != RUN_ABORT and \
@@
-592,9
+594,9
@@
def run_pipeline(conf_info):
ferr.close()
# Finished file check!
ferr.close()
# Finished file check!
- print
'RUN SUCCESS CHECK:'
+ print
('RUN SUCCESS CHECK:')
for key, value in event.run_status_dict.items():
for key, value in event.run_status_dict.items():
- print
' %s: %s' % (key, value
)
+ print
(' %s: %s' % (key, value)
)
dstatus = event.run_status_dict
dstatus = event.run_status_dict
diff --git
a/htsworkflow/pipelines/fastq.py
b/htsworkflow/pipelines/fastq.py
index 47b2f8300d553d6ba944c1309ec5c233ad1f4951..fce8993e10a0946115382c702da22edf98c40bfc 100644
(file)
--- a/
htsworkflow/pipelines/fastq.py
+++ b/
htsworkflow/pipelines/fastq.py
@@
-1,5
+1,7
@@
'''summarize fastq file
'''
'''summarize fastq file
'''
+from __future__ import print_function
+
import os
import numpy
import os
import numpy
@@
-42,4
+44,4
@@
if __name__ == '__main__':
import sys
from autoopen import autoopen
with autoopen(sys.argv[1], 'r') as instream:
import sys
from autoopen import autoopen
with autoopen(sys.argv[1], 'r') as instream:
- print
summarize_hiseq_fastq(instream
)
+ print
(summarize_hiseq_fastq(instream)
)
diff --git
a/htsworkflow/pipelines/run_status.py
b/htsworkflow/pipelines/run_status.py
index e6a3ed8e6b2f41793f1109dac1334900860e8eaf..46e400726fd3342578c839c8772e65e509cdbc01 100644
(file)
--- a/
htsworkflow/pipelines/run_status.py
+++ b/
htsworkflow/pipelines/run_status.py
@@
-1,3
+1,5
@@
+from __future__ import print_function
+
__docformat__ = "restructuredtext en"
import glob
__docformat__ = "restructuredtext en"
import glob
@@
-104,7
+106,7
@@
class GARunStatus(object):
during a run and provides methods for retrieving
(completed, total) for each step or entire run.
"""
during a run and provides methods for retrieving
(completed, total) for each step or entire run.
"""
- #print
'self._conf_filepath = %s' % (conf_filepath
)
+ #print
('self._conf_filepath = %s' % (conf_filepath)
)
self._conf_filepath = conf_filepath
self._base_dir, junk = os.path.split(conf_filepath)
self._image_dir = os.path.join(self._base_dir, 'Images')
self._conf_filepath = conf_filepath
self._base_dir, junk = os.path.split(conf_filepath)
self._image_dir = os.path.join(self._base_dir, 'Images')
@@
-178,9
+180,9
@@
class GARunStatus(object):
"""
Figures out the number of cycles that are available
"""
"""
Figures out the number of cycles that are available
"""
- #print
'self._image_dir = %s' % (self._image_dir
)
+ #print
('self._image_dir = %s' % (self._image_dir)
)
cycle_dirs = glob.glob(os.path.join(self._image_dir, 'L001', 'C*.1'))
cycle_dirs = glob.glob(os.path.join(self._image_dir, 'L001', 'C*.1'))
- #print
'cycle_dirs = %s' % (cycle_dirs
)
+ #print
('cycle_dirs = %s' % (cycle_dirs)
)
cycle_list = []
for cycle_dir in cycle_dirs:
junk, c = os.path.split(cycle_dir)
cycle_list = []
for cycle_dir in cycle_dirs:
junk, c = os.path.split(cycle_dir)
@@
-410,13
+412,13
@@
def _cmdLineStatusMonitorFunc(conf_info):
while 1:
if conf_info.status is None:
while 1:
if conf_info.status is None:
- print
"No status object yet."
+ print
("No status object yet.")
time.sleep(SLEEP_AMOUNT)
continue
report = conf_info.status.statusReport()
time.sleep(SLEEP_AMOUNT)
continue
report = conf_info.status.statusReport()
- print
os.linesep.join(report
)
- print
+ print
( os.linesep.join(report)
)
+ print
()
time.sleep(SLEEP_AMOUNT)
time.sleep(SLEEP_AMOUNT)
@@
-446,9
+448,8
@@
def main(cmdline=None):
parser.error("need name of configuration file")
status = GARunStatus(args[0])
parser.error("need name of configuration file")
status = GARunStatus(args[0])
- print
os.linesep.join(status.statusReport(
))
+ print
(os.linesep.join(status.statusReport()
))
return 0
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))
return 0
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))
-
diff --git
a/htsworkflow/submission/geo.py
b/htsworkflow/submission/geo.py
index 1d98bd5c9550e36408b3ba4faed02ee8d28cedee..15d5b747bab1d1520757f1277ae3cb4f97ffbe26 100644
(file)
--- a/
htsworkflow/submission/geo.py
+++ b/
htsworkflow/submission/geo.py
@@
-1,3
+1,5
@@
+from __future__ import print_function
+
import logging
import os
import logging
import os
@@
-52,7
+54,7
@@
class GEOSubmission(Submission):
'platform_id': platform_id,
'series_id': series_id,
})
'platform_id': platform_id,
'series_id': series_id,
})
- print
str(soft_template.render(context
))
+ print
(str(soft_template.render(context)
))
def check_for_name(self, analysis_node):
name = fromTypedNode(
def check_for_name(self, analysis_node):
name = fromTypedNode(
diff --git
a/htsworkflow/submission/trackhub_submission.py
b/htsworkflow/submission/trackhub_submission.py
index 3aa4a96ae26fa96c44e0c0f58c67503890fe38dc..c771b165a52e7b1e57072baa332f2f63ee3dff1a 100644
(file)
--- a/
htsworkflow/submission/trackhub_submission.py
+++ b/
htsworkflow/submission/trackhub_submission.py
@@
-1,3
+1,4
@@
+from __future__ import print_function
import logging
import os
from pprint import pformat
import logging
import os
from pprint import pformat
@@
-41,7
+42,7
@@
class TrackHubSubmission(Submission):
self.baseurl = os.path.join(baseurl, self.name)
if baseupload:
sshurl = parse_ssh_url(baseupload)
self.baseurl = os.path.join(baseurl, self.name)
if baseupload:
sshurl = parse_ssh_url(baseupload)
- print
sshurl
+ print
(sshurl)
self.user = sshurl.user
self.host = sshurl.host
self.uploadpath = sshurl.path
self.user = sshurl.user
self.host = sshurl.host
self.uploadpath = sshurl.path
diff --git
a/test/tree.py
b/test/tree.py
index 4f666cc14a3b4f3326a66ecec138572a5a8bd05a..37d3fd44c0f7673eeb8c975c514dcbd647521fa2 100644
(file)
--- a/
test/tree.py
+++ b/
test/tree.py
@@
-1,8
+1,8
@@
#!/usr/bin/env python
#!/usr/bin/env python
-
"""
Build a fake directory tree for testing rsync management code.
"""
"""
Build a fake directory tree for testing rsync management code.
"""
+from __future__ import print_function
import os
import random
import os
import random
@@
-77,5
+77,5
@@
def compare_tree(root, paths, verbose=False):
difference = experimental_set - theoretical_set
issame = (len(difference) == 0)
if verbose and not issame:
difference = experimental_set - theoretical_set
issame = (len(difference) == 0)
if verbose and not issame:
- print
difference
+ print
(difference)
return issame
return issame
diff --git
a/version.py
b/version.py
index b850b4a713a17a4b289a82d9aae97f6ef79cd883..4856928c7e74680578672a60916a1f11131d65fb 100644
(file)
--- a/
version.py
+++ b/
version.py
@@
-30,6
+30,7
@@
# contains the following line:
#
# include RELEASE-VERSION
# contains the following line:
#
# include RELEASE-VERSION
+from __future__ import print_function
__all__ = ("get_git_version")
__all__ = ("get_git_version")
@@
-101,4
+102,4
@@
def get_git_version(abbrev=4):
if __name__ == "__main__":
if __name__ == "__main__":
- print
get_git_version(
)
+ print
(get_git_version()
)