def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_params, script_name="tool_script.sh"):
local_container_script = join( job_wrapper.working_directory, script_name )
tool_commands = commands_builder.build()
config = job_wrapper.app.config
integrity_injection = ""
# Setting shell to none in job_conf.xml disables creating a tool command script,
# set -e doesn't work for composite commands but this is necessary for Windows jobs
# for instance.
if shell and shell.lower() == 'none':
return tool_commands
if check_script_integrity(config):
integrity_injection = INTEGRITY_INJECTION
set_e = ""
if job_wrapper.strict_shell:
set_e = "set -e\n"
script_contents = u"#!%s\n%s%s%s" % (
shell,
integrity_injection,
set_e,
tool_commands
)
write_script(local_container_script, script_contents, config)
commands = local_container_script
if 'working_directory' in remote_command_params:
commands = "%s %s" % (shell, join(remote_command_params['working_directory'], script_name))
log.info("Built script [%s] for tool command[%s]" % (local_container_script, tool_commands))
return commands
def __externalize_commands(job_wrapper,
shell,
commands_builder,
remote_command_params,
script_name="tool_script.sh"):
local_container_script = join(job_wrapper.working_directory, script_name)
tool_commands = commands_builder.build()
config = job_wrapper.app.config
integrity_injection = ""
# Setting shell to none in job_conf.xml disables creating a tool command script,
# set -e doesn't work for composite commands but this is necessary for Windows jobs
# for instance.
if shell and shell.lower() == 'none':
return tool_commands
if check_script_integrity(config):
integrity_injection = INTEGRITY_INJECTION
set_e = ""
if job_wrapper.strict_shell:
set_e = "set -e\n"
script_contents = u"#!%s\n%s%s%s" % (shell, integrity_injection, set_e,
tool_commands)
write_script(local_container_script, script_contents, config)
commands = local_container_script
if 'working_directory' in remote_command_params:
commands = "%s %s" % (shell,
join(remote_command_params['working_directory'],
script_name))
log.info("Built script [%s] for tool command [%s]" %
(local_container_script, tool_commands))
return commands
def __externalize_commands(job_wrapper,
shell,
commands_builder,
remote_command_params,
script_name="tool_script.sh"):
local_container_script = join(job_wrapper.working_directory, script_name)
tool_commands = commands_builder.build()
config = job_wrapper.app.config
integrity_injection = ""
if check_script_integrity(config):
integrity_injection = INTEGRITY_INJECTION
set_e = ""
if job_wrapper.strict_shell:
set_e = "set -e\n"
script_contents = u"#!%s\n%s%s%s" % (shell, integrity_injection, set_e,
tool_commands)
write_script(local_container_script, script_contents, config)
commands = local_container_script
if 'working_directory' in remote_command_params:
commands = "%s %s" % (shell,
join(remote_command_params['working_directory'],
script_name))
log.info("Built script [%s] for tool command[%s]" %
(local_container_script, tool_commands))
return commands
def __externalize_commands(job_wrapper,
shell,
commands_builder,
remote_command_params,
script_name="tool_script.sh",
container=None):
local_container_script = join(job_wrapper.working_directory, script_name)
tool_commands = commands_builder.build()
config = job_wrapper.app.config
integrity_injection = ""
# Setting shell to none in job_conf.xml disables creating a tool command script,
# set -e doesn't work for composite commands but this is necessary for Windows jobs
# for instance.
if shell and shell.lower() == 'none':
return tool_commands
if check_script_integrity(config):
integrity_injection = INTEGRITY_INJECTION
set_e = ""
if job_wrapper.strict_shell:
set_e = "set -e\n"
source_command = ""
if container:
source_command = container.source_environment
script_contents = "#!{}\n{}{}{}{}".format(
shell,
integrity_injection,
set_e,
source_command,
tool_commands,
)
write_script(local_container_script, script_contents, config)
commands = "{} {}".format(shell, local_container_script)
# TODO: Cleanup for_pulsar hack.
# - Integrate Pulsar sending tool_stdout/tool_stderr back
# https://github.com/galaxyproject/pulsar/pull/202
# *and*
# - Get Galaxy to write these files to an output directory so the container itself
# doesn't need to mount the job directory (rw) and then eliminate this hack
# (or restrict to older Pulsar versions).
# https://github.com/galaxyproject/galaxy/pull/8449
for_pulsar = False
if 'script_directory' in remote_command_params:
commands = "{} {}".format(
shell, join(remote_command_params['script_directory'],
script_name))
for_pulsar = True
if not for_pulsar:
commands += " > ../outputs/tool_stdout 2> ../outputs/tool_stderr"
log.info("Built script [{}] for tool command [{}]".format(
local_container_script, tool_commands))
return commands
def __externalize_commands(job_wrapper, passwordIS, shell, commands_builder, remote_command_params, script_name="tool_script.sh"):
local_container_script = join( job_wrapper.working_directory, script_name )
tool_commands = commands_builder.build()
config = job_wrapper.app.config
integrity_injection = ""
# Setting shell to none in job_conf.xml disables creating a tool command script,
# set -e doesn't work for composite commands but this is necessary for Windows jobs
# for instance.
if shell and shell.lower() == 'none':
return tool_commands
if check_script_integrity(config):
integrity_injection = INTEGRITY_INJECTION
set_e = ""
if job_wrapper.strict_shell:
set_e = "set -e\n"
####
# tool_commands = str(tool_commands)
envVar = ''
envVar = "PASS="******"PASS="******"'+passVar + '"'
# indexSoFar = end +1
# tool_commands = tool_commands.replace(passVar, '$PASS')
# tool_commands = tool_commands.replace('JPCNn681vcGV4KuvuT16 ', '')
####
script_contents = u"#!%s\n%s%s%s\n%s" % (
shell,
integrity_injection,
set_e,
envVar,
tool_commands
)
write_script(local_container_script, script_contents, config)
#print local_container_script
commands = local_container_script
#print "From command factory, commands: " + commands
if 'working_directory' in remote_command_params:
commands = "%s %s" % (shell, join(remote_command_params['working_directory'], script_name))
log.info("Built script [%s] for tool command[%s]" % (local_container_script, tool_commands))
return commands
def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_params, script_name="tool_script.sh"):
local_container_script = join( job_wrapper.working_directory, script_name )
tool_commands = commands_builder.build()
config = job_wrapper.app.config
integrity_injection = ""
if check_script_integrity(config):
integrity_injection = INTEGRITY_INJECTION
script_contents = u"#!%s\n%s%s" % (shell, integrity_injection, tool_commands)
write_script(local_container_script, script_contents, config)
commands = local_container_script
if 'working_directory' in remote_command_params:
commands = "%s %s" % (shell, join(remote_command_params['working_directory'], script_name))
log.info("Built script [%s] for tool command[%s]" % (local_container_script, tool_commands))
return commands
