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Initial port to python3
[htsworkflow.git]
/
htsworkflow
/
pipelines
/
configure_run.py
diff --git
a/htsworkflow/pipelines/configure_run.py
b/htsworkflow/pipelines/configure_run.py
index 83c7569d2816b03e3a67a3fb4f376589ae472a5f..02d0adfc1619035a007849b0e7e4e24b81254e67 100644
(file)
--- a/
htsworkflow/pipelines/configure_run.py
+++ b/
htsworkflow/pipelines/configure_run.py
@@
-243,7
+243,7
@@
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)
@@
-377,16
+377,16
@@
def retrieve_config(conf_info, flowcell, cfg_filepath, genome_dir):
try:
saveConfigFile(flowcell, options.url, cfg_filepath)
conf_info.config_filepath = cfg_filepath
try:
saveConfigFile(flowcell, options.url, cfg_filepath)
conf_info.config_filepath = cfg_filepath
- except FlowCellNotFound
,
e:
+ except FlowCellNotFound
as
e:
LOGGER.error(e)
return False
LOGGER.error(e)
return False
- except WebError404
,
e:
+ except WebError404
as
e:
LOGGER.error(e)
return False
LOGGER.error(e)
return False
- except IOError
,
e:
+ except IOError
as
e:
LOGGER.error(e)
return False
LOGGER.error(e)
return False
- except Exception
,
e:
+ except Exception
as
e:
LOGGER.error(e)
return False
LOGGER.error(e)
return False
@@
-458,7
+458,7
@@
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
+509,8
@@
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
+592,9
@@
def run_pipeline(conf_info):
ferr.close()
# Finished file check!
ferr.close()
# Finished file check!
- print
'RUN SUCCESS CHECK:'
- for key, value in
event.run_status_dict.items(
):
- print
' %s: %s' % (key, value
)
+ print
('RUN SUCCESS CHECK:')
+ for key, value in
list(event.run_status_dict.items()
):
+ print
(' %s: %s' % (key, value)
)
dstatus = event.run_status_dict
dstatus = event.run_status_dict