def main(args):
if workflow.parse_workflow_commands():
return
options = parse_dimple_commands(args)
check_ccp4_envvars()
wf = workflow.Workflow(options.output_dir, from_job=options.from_step)
utils.start_log(os.path.join(options.output_dir, "dimple.log"),
output_dir=options.output_dir)
utils.log_value("version", __version__)
utils.start_log_screen(os.path.join(options.output_dir, "screen.log"))
try:
dimple(wf=wf, opt=options)
check_contaminants_if_bad(wf, mtz=options.mtz)
exit_status = 0
except workflow.JobError as e:
put_error(e.msg, comment=e.note)
try:
utils.report_disk_space([wf.output_dir, os.getenv("CCP4_SCR")])
except KeyboardInterrupt:
comment("\nok, exiting...")
exit_status = 1
except RuntimeError as e:
put_error(e)
exit_status = 1
finally:
comment("\n")
if options.cleanup:
wf.delete_files(wf.temporary_files)
wf.options = options
wf.dump_pickle()
return exit_status
def main(args):
if workflow.parse_workflow_commands():
return
options = parse_dimple_commands(args)
for necessary_var in ("CCP4", "CCP4_SCR"):
if necessary_var not in os.environ:
put_error('$%s not found, giving up' % necessary_var)
sys.exit(1)
if not os.path.isdir(os.environ["CCP4_SCR"]):
put_error('No such directory: $CCP4_SCR, refmac shall not work!')
wf = workflow.Workflow(options.output_dir, from_job=options.from_step)
utils.start_log(os.path.join(options.output_dir, "dimple.log"),
output_dir=options.output_dir)
utils.log_value("version", __version__)
utils.start_log_screen(os.path.join(options.output_dir, "screen.log"))
try:
dimple(wf=wf, opt=options)
exit_status = 0
except workflow.JobError as e:
put_error(e.msg, comment=e.note)
try:
utils.report_disk_space([wf.output_dir, os.getenv("CCP4_SCR")])
except KeyboardInterrupt:
comment("\nok, exiting...")
exit_status = 1
except RuntimeError as e:
put_error(e)
exit_status = 1
finally:
comment("\n")
if options.cleanup:
wf.delete_files(wf.temporary_files)
wf.options = options
wf.dump_pickle()
return exit_status
def main(args):
if workflow.parse_workflow_commands():
return
options = parse_dimple_commands(args)
check_ccp4_envvars()
try:
wf = workflow.Workflow(options.output_dir, from_job=options.from_step)
utils.start_log(os.path.join(options.output_dir, 'dimple.log'),
output_dir=options.output_dir)
utils.log_value('version', __version__)
utils.start_log_screen(os.path.join(options.output_dir, 'screen.log'))
dimple(wf=wf, opt=options)
check_contaminants_if_bad(wf, mtz=options.mtz)
exit_status = 0
except workflow.JobError as e:
put_error(e.msg, comment=e.note)
try:
utils.report_disk_space([wf.output_dir, os.getenv('CCP4_SCR')])
except KeyboardInterrupt:
comment('\nok, exiting...')
exit_status = 1
except (RuntimeError, IOError, OSError) as e:
put_error(e)
exit_status = 1
finally:
comment('\n')
if options.cleanup:
wf.delete_files(wf.temporary_files)
wf.options = options
try:
wf.dump_pickle()
except IOError as e:
put_error(e)
exit_status = 1
return exit_status