def _write_bash_header(self, script):
# bash_line = '#PBS -S /bin/bash'
bash_line = '#!/bin/bash'
file_utils.wl(script, bash_line)
file_utils.wl(script, '')
def _write_bash_header(self, script):
# bash_line = '#PBS -S /bin/bash'
bash_line = '#!/bin/bash'
file_utils.wl(script, bash_line)
file_utils.wl(script, '')
def _write_die_function(self, script):
file_utils.wl(script, 'die()')
file_utils.wl(script, '{')
# file_utils.wl(script, ' xnat_workflow_fail ' + str_utils.get_server_name(self.server)
# + ' ' + self.username + ' ' + self.password + ' ' + self._workflow_id)
file_utils.wl(script, ' exit 1')
file_utils.wl(script, '}')
file_utils.wl(script, '')
def _write_die_function(self, script):
file_utils.wl(script, 'die()')
file_utils.wl(script, '{')
# file_utils.wl(script, ' xnat_workflow_fail ' + str_utils.get_server_name(self.server)
# + ' ' + self.username + ' ' + self.password + ' ' + self._workflow_id)
file_utils.wl(script, ' exit 1')
file_utils.wl(script, '}')
file_utils.wl(script, '')
def _write_env_setup(self, script):
setup_file = open(self.setup_script, 'r')
for line in setup_file:
script.write(line)
file_utils.wl(script, '')
setup_file.close()
def _write_env_setup(self, script):
setup_file = open(self.setup_script, 'r')
for line in setup_file:
script.write(line)
file_utils.wl(script, '')
setup_file.close()
def _write_bedpostx_call(self, script):
bedpostx_call_line = '${FSLDIR}/bin/bedpostx_gpu.tbb' + ' '
bedpostx_call_line += self._working_directory_name + os.sep
bedpostx_call_line += self.subject + os.sep
bedpostx_call_line += 'T1w' + os.sep + 'Diffusion' + ' '
bedpostx_call_line += '-n 3 -b 3000 -model 3 -g --rician'
file_utils.wl(script, 'echo "Calling bedpostx_gpu"')
file_utils.wl(script, bedpostx_call_line)
file_utils.wl(script, '')
def _write_bedpostx_call(self, script):
bedpostx_call_line = '${FSLDIR}/bin/bedpostx_gpu.tbb' + ' '
bedpostx_call_line += self._working_directory_name + os.sep
bedpostx_call_line += self.subject + os.sep
bedpostx_call_line += 'T1w' + os.sep + 'Diffusion' + ' '
bedpostx_call_line += '-n 3 -b 3000 -model 3 -g --rician'
file_utils.wl(script, 'echo "Calling bedpostx_gpu"')
file_utils.wl(script, bedpostx_call_line)
file_utils.wl(script, '')
def _write_rm_old_starttime_file_section(self, script):
file_utils.wl(script, 'echo "Create a start time file"')
file_utils.wl(script, 'start_time_file=' + self._starttime_file_name())
file_utils.wl(script, 'if [ -e "${start_time_file}" ]; then')
file_utils.wl(script, ' echo "Removing old ${start_time_file}"')
file_utils.wl(script, ' rm -f ${start_time_file}')
file_utils.wl(script, 'fi')
file_utils.wl(script, '')
def _write_platform_info_section(self, script):
file_utils.wl(script, 'echo "----- Platform Information: Begin -----"')
file_utils.wl(script, 'uname -a')
file_utils.wl(script, 'echo "----- Platform Information: End -----"')
file_utils.wl(script, '')
def _write_host_id_section(self, script):
file_utils.wl(script, 'echo "Job started on `hostname` at `date`"')
file_utils.wl(script, '')
def _write_platform_info_section(self, script):
file_utils.wl(script, 'echo "----- Platform Information: Begin -----"')
file_utils.wl(script, 'uname -a')
file_utils.wl(script, 'echo "----- Platform Information: End -----"')
file_utils.wl(script, '')
def _write_doc_header(self, script):
file_utils.wl(script, '')
file_utils.wl(
script, "# Copyright (C) " + str(datetime.datetime.now().year) +
" The Human Connectome Project")
file_utils.wl(script, "#")
file_utils.wl(
script, "# This file was autogenerated to run the " +
self.PIPELINE_NAME + " pipeline")
file_utils.wl(script, "# for subject: " + self.subject)
file_utils.wl(script, '')
def _write_starttime_creation_section(self, script):
file_utils.wl(script, 'echo "Creating start time file: ${start_time_file}"')
file_utils.wl(script, 'touch ${start_time_file} || die')
file_utils.wl(script, 'ls -l ${start_time_file}')
file_utils.wl(script, '')
def _write_starttime_creation_section(self, script):
file_utils.wl(script,
'echo "Creating start time file: ${start_time_file}"')
file_utils.wl(script, 'touch ${start_time_file} || die')
file_utils.wl(script, 'ls -l ${start_time_file}')
file_utils.wl(script, '')
def _write_bash_header(self, script):
bash_line = "#PBS -S /bin/bash"
file_utils.wl(script, bash_line)
def _write_doc_header(self, script):
file_utils.wl(script, '')
file_utils.wl(script, "# Copyright (C) " + str(datetime.datetime.now().year) + " The Human Connectome Project")
file_utils.wl(script, "#")
file_utils.wl(script, "# This file was autogenerated to run the " + self.PIPELINE_NAME + " pipeline")
file_utils.wl(script, "# for subject: " + self.subject)
file_utils.wl(script, '')
def _create_work_script(self):
logger.debug(debug_utils.get_name())
script_name = self._work_script_name()
with contextlib.suppress(FileNotFoundError):
os.remove(script_name)
walltime_limit = str(self.walltime_limit_hours) + ':00:00'
vmem_limit = str(self.vmem_limit_gbs) + 'gb'
resources_line = '#PBS -l nodes=1:ppn=1,walltime=' + walltime_limit + ',vmem=' + vmem_limit
stdout_line = '#PBS -o ' + self._working_directory_name
stderr_line = '#PBS -e ' + self._working_directory_name
script_line = self.xnat_pbs_jobs_home + os.sep + self.PIPELINE_NAME + os.sep + self.PIPELINE_NAME + '.XNAT.sh'
user_line = ' --user='******' --password='******' --server=' + str_utils.get_server_name(self.server)
project_line = ' --project=' + self.project
subject_line = ' --subject=' + self.subject
session_line = ' --session=' + self.session
scan_line = ' --scan=' + self.scan
wdir_line = ' --working-dir=' + self._working_directory_name
setup_line = ' --setup-script=' + self.xnat_pbs_jobs_home + os.sep + self.PIPELINE_NAME + os.sep + self.setup_script
reg_name_line = ' --reg-name=' + self.reg_name
work_script = open(self._work_script_name(), 'w')
futils.wl(work_script, resources_line)
futils.wl(work_script, stdout_line)
futils.wl(work_script, stderr_line)
futils.wl(work_script, '')
futils.wl(work_script, script_line + self._continue)
futils.wl(work_script, user_line + self._continue)
futils.wl(work_script, password_line + self._continue)
futils.wl(work_script, server_line + self._continue)
futils.wl(work_script, project_line + self._continue)
futils.wl(work_script, subject_line + self._continue)
futils.wl(work_script, session_line + self._continue)
futils.wl(work_script, scan_line + self._continue)
futils.wl(work_script, wdir_line + self._continue)
if self.reg_name != 'MSMSulc':
futils.wl(work_script, reg_name_line + self._continue)
futils.wl(work_script, setup_line)
work_script.close()
os.chmod(self._work_script_name(), stat.S_IRWXU | stat.S_IRWXG)
def _create_work_script(self, scan):
logger.debug("_create_work_script - scan: " + scan)
with contextlib.suppress(FileNotFoundError):
os.remove(self._work_script_name(scan))
walltime_limit = str(self.walltime_limit_hours) + ':00:00'
vmem_limit = str(self.vmem_limit_gbs) + 'gb'
resources_line = '#PBS -l nodes=1:ppn=1,walltime=' + walltime_limit
resources_line += ',vmem=' + vmem_limit
stdout_line = '#PBS -o ' + self._working_directory_name
stderr_line = '#PBS -e ' + self._working_directory_name
script_line = self.xnat_pbs_jobs_home + os.sep + '7T' + os.sep
script_line += self.PIPELINE_NAME + os.sep + self.PIPELINE_NAME + '.XNAT.sh'
user_line = ' --user='******' --password='******' --server=' + str_utils.get_server_name(self.server)
project_line = ' --project=' + self.project
subject_line = ' --subject=' + self.subject
session_line = ' --session=' + self.session
ref_proj_line = ' --structural-reference-project=' + self.structural_reference_project
ref_sess_line = ' --structural-reference-session=' + self.structural_reference_session
scan_line = ' --scan=' + scan
wdir_line = ' --working-dir=' + self._working_directory_name
workflow_line = ' --workflow-id=' + self._workflow_id
setup_line = ' --setup-script=' + self.setup_script
work_script = open(self._work_script_name(scan), 'w')
futils.wl(work_script, resources_line)
futils.wl(work_script, stdout_line)
futils.wl(work_script, stderr_line)
futils.wl(work_script, '')
futils.wl(work_script, script_line + self._continue)
futils.wl(work_script, user_line + self._continue)
futils.wl(work_script, password_line + self._continue)
futils.wl(work_script, server_line + self._continue)
futils.wl(work_script, project_line + self._continue)
futils.wl(work_script, subject_line + self._continue)
futils.wl(work_script, session_line + self._continue)
futils.wl(work_script, ref_proj_line + self._continue)
futils.wl(work_script, ref_sess_line + self._continue)
futils.wl(work_script, scan_line + self._continue)
futils.wl(work_script, wdir_line + self._continue)
futils.wl(work_script, workflow_line + self._continue)
futils.wl(work_script, setup_line)
work_script.close()
os.chmod(self._work_script_name(scan), stat.S_IRWXU | stat.S_IRWXG)
def _create_post_eddy_script(self):
_debug("_create_post_eddy_script")
with contextlib.suppress(FileNotFoundError):
os.remove(self._post_eddy_script_name)
walltime_limit = str(self.post_eddy_walltime_limit_hours) + ':00:00'
vmem_limit = str(self.post_eddy_vmem_limit_gbs) + 'gb'
resources_line = '#PBS -l nodes=1:ppn=1,walltime=' + walltime_limit
resources_line += ',vmem=' + vmem_limit
stdout_line = '#PBS -o ' + self._working_directory_name
stderr_line = '#PBS -e ' + self._working_directory_name
script_line = self.xnat_pbs_jobs_home + os.sep + '7T' + os.sep
script_line += 'DiffusionPreprocessingHCP7T' + os.sep
script_line += 'DiffusionPreprocessingHCP7T_PostEddy.XNAT.sh'
user_line = ' --user="******"'
password_line = ' --password="******"'
server_line = ' --server="' + str_utils.get_server_name(
self.server) + '"'
subject_line = ' --subject="' + self.subject + '"'
wdir_line = ' --working-dir="' + self._working_directory_name + '"'
workflow_line = ' --workflow-id="' + self._workflow_id + '"'
setup_line = ' --setup-script=' + self.setup_script
post_eddy_script = open(self._post_eddy_script_name, 'w')
futils.wl(post_eddy_script, resources_line)
futils.wl(post_eddy_script, stdout_line)
futils.wl(post_eddy_script, stderr_line)
futils.wl(post_eddy_script, '')
futils.wl(post_eddy_script, script_line + self._continue)
futils.wl(post_eddy_script, user_line + self._continue)
futils.wl(post_eddy_script, password_line + self._continue)
futils.wl(post_eddy_script, server_line + self._continue)
futils.wl(post_eddy_script, subject_line + self._continue)
futils.wl(post_eddy_script, wdir_line + self._continue)
futils.wl(post_eddy_script, workflow_line + self._continue)
futils.wl(post_eddy_script, setup_line)
post_eddy_script.close()
os.chmod(self._post_eddy_script_name, stat.S_IRWXU | stat.S_IRWXG)
def _write_sleep_section(self, script):
file_utils.wl(script, 'echo "Sleep for 1 minute"')
file_utils.wl(script, 'sleep 1m || die')
file_utils.wl(script, '')
def _write_doc_header(self, script):
file_utils.wl(
script, "# Copyright (C) " + str(datetime.datetime.now().year) +
" The Human Connectome Project")
file_utils.wl(script, "#")
file_utils.wl(
script, "# This file was autogenerated to run the " +
self.WORK_DESC + " for")
file_utils.wl(script, "# subject: " + self.subject)
file_utils.wl(script, "# project: " + self.project)
file_utils.wl(script, "# session: " + self.session)
file_utils.wl(script, "")
def _write_host_id_section(self, script):
file_utils.wl(script, 'echo "Job started on `hostname` at `date`"')
file_utils.wl(script, '')
def _write_rm_old_starttime_file_section(self, script):
file_utils.wl(script, 'echo "Create a start time file"')
file_utils.wl(script, 'start_time_file=' + self._starttime_file_name())
file_utils.wl(script, 'if [ -e "${start_time_file}" ]; then')
file_utils.wl(script, ' echo "Removing old ${start_time_file}"')
file_utils.wl(script, ' rm -f ${start_time_file}')
file_utils.wl(script, 'fi')
file_utils.wl(script, '')
def _create_post_eddy_script(self):
_debug("_create_post_eddy_script")
with contextlib.suppress(FileNotFoundError):
os.remove(self._post_eddy_script_name)
walltime_limit = str(self.post_eddy_walltime_limit_hours) + ':00:00'
vmem_limit = str(self.post_eddy_vmem_limit_gbs) + 'gb'
resources_line = '#PBS -l nodes=1:ppn=1,walltime=' + walltime_limit
resources_line += ',vmem=' + vmem_limit
stdout_line = '#PBS -o ' + self._working_directory_name
stderr_line = '#PBS -e ' + self._working_directory_name
script_line = self.xnat_pbs_jobs_home + os.sep + '7T' + os.sep
script_line += 'DiffusionPreprocessingHCP7T' + os.sep
script_line += 'DiffusionPreprocessingHCP7T_PostEddy.XNAT.sh'
user_line = ' --user="******"'
password_line = ' --password="******"'
server_line = ' --server="' + str_utils.get_server_name(self.server) + '"'
subject_line = ' --subject="' + self.subject + '"'
wdir_line = ' --working-dir="' + self._working_directory_name + '"'
workflow_line = ' --workflow-id="' + self._workflow_id + '"'
setup_line = ' --setup-script=' + self.setup_script
post_eddy_script = open(self._post_eddy_script_name, 'w')
futils.wl(post_eddy_script, resources_line)
futils.wl(post_eddy_script, stdout_line)
futils.wl(post_eddy_script, stderr_line)
futils.wl(post_eddy_script, '')
futils.wl(post_eddy_script, script_line + self._continue)
futils.wl(post_eddy_script, user_line + self._continue)
futils.wl(post_eddy_script, password_line + self._continue)
futils.wl(post_eddy_script, server_line + self._continue)
futils.wl(post_eddy_script, subject_line + self._continue)
futils.wl(post_eddy_script, wdir_line + self._continue)
futils.wl(post_eddy_script, workflow_line + self._continue)
futils.wl(post_eddy_script, setup_line)
post_eddy_script.close()
os.chmod(self._post_eddy_script_name, stat.S_IRWXU | stat.S_IRWXG)
def _write_sleep_section(self, script):
file_utils.wl(script, 'echo "Sleep for 1 minute"')
file_utils.wl(script, 'sleep 1m || die')
file_utils.wl(script, '')