def test_commandtool(self):
c = cwlgen.CommandLineTool("reqs")
docker = cwlgen.DockerRequirement(docker_pull="ubuntu:latest")
c.requirements.append(docker)
d = c.get_dict()
self.assertIn("requirements", d)
self.assertIn(docker.get_class(), d["requirements"])
def setUp(self):
self.dock_req = cwlgen.DockerRequirement(
docker_pull='pull',
docker_load='load',
docker_file='file',
docker_import='import',
docker_image_id='id',
docker_output_dir='dir'
)
def createGenericStep(id, docker_image, base_command, type, doc, input_doc,
extension, output_doc):
cwl_tool = cwlgen.CommandLineTool(tool_id=id, base_command=base_command)
cwl_tool_docker = cwlgen.DockerRequirement(docker_pull=docker_image)
implementation_file_binding = cwlgen.CommandLineBinding(position=1)
cases_file_binding = cwlgen.CommandLineBinding(position=2)
return createStep(cwl_tool, cwl_tool_docker, implementation_file_binding,
cases_file_binding, type, doc, input_doc, extension,
output_doc, base_command)
def createKNIMEStep(id, type, doc, input_doc, extension, output_doc):
cwl_tool = cwlgen.CommandLineTool(
tool_id=id, base_command='/home/kclhi/knime_4.1.1/knime')
cwl_tool_docker = cwlgen.DockerRequirement(
docker_pull="kclhi/knime:amia",
docker_output_dir="/home/kclhi/.eclipse")
cwl_tool.arguments = [
'-data', '/home/kclhi/.eclipse', '-reset', '-nosplash', '-nosave',
'-application', 'org.knime.product.KNIME_BATCH_APPLICATION'
]
implementation_file_binding = cwlgen.CommandLineBinding(
prefix="-workflowFile=", separate=False)
cases_file_binding = cwlgen.CommandLineBinding(
prefix="-workflow.variable=dm_potential_cases,file://",
separate=False,
value_from=" $(inputs.potentialCases.path),String")
return createStep(cwl_tool, cwl_tool_docker, implementation_file_binding,
cases_file_binding, type, doc, input_doc, extension,
output_doc, "knime")
def test_missing_export(self):
dr = cwlgen.DockerRequirement()
self.assertDictEqual(dr.get_dict(), {})
def translate_tool_internal(cls,
tool,
with_docker=True,
with_resource_overrides=False):
metadata = tool.metadata if tool.metadata else ToolMetadata()
stdouts = [
o.output_type for o in tool.outputs()
if isinstance(o.output_type, Stdout) and o.output_type.stdoutname
]
stdout = stdouts[0].stdoutname if len(stdouts) > 0 else None
if isinstance(stdout, InputSelector):
stdout = translate_input_selector(stdout, code_environment=False)
tool_cwl = cwlgen.CommandLineTool(
tool_id=tool.id(),
base_command=tool.base_command(),
label=tool.id(),
doc=metadata.documentation,
cwl_version=CWL_VERSION,
stdin=None,
stderr=None,
stdout=stdout,
)
# if any(not i.shell_quote for i in tool.inputs()):
tool_cwl.requirements.append(cwlgen.ShellCommandRequirement())
tool_cwl.requirements.extend([cwlgen.InlineJavascriptReq()])
inputs_that_require_localisation = [
ti for ti in tool.inputs()
if ti.localise_file and (issubclass(type(ti.input_type), File) or (
issubclass(type(ti.input_type), Array)
) and issubclass(type(ti.input_type.subtype()), File))
]
if inputs_that_require_localisation:
tool_cwl.requirements.append(
cwlgen.InitialWorkDirRequirement([
"$(inputs.%s)" % ti.id()
for ti in inputs_that_require_localisation
]))
if with_docker:
tool_cwl.requirements.append(
cwlgen.DockerRequirement(
docker_pull=tool.container(),
# docker_load=None,
# docker_file=None,
# docker_import=None,
# docker_image_id=None,
# docker_output_dir=None
))
tool_cwl.inputs.extend(translate_tool_input(i) for i in tool.inputs())
tool_cwl.outputs.extend(
translate_tool_output(o, tool=tool.id()) for o in tool.outputs())
args = tool.arguments()
if args:
tool_cwl.arguments.extend(
translate_tool_argument(a) for a in tool.arguments())
if with_resource_overrides:
# work out whether (the tool of) s is a workflow or tool
tool_cwl.inputs.extend([
cwlgen.CommandInputParameter("runtime_memory",
param_type="float?"),
cwlgen.CommandInputParameter("runtime_cpu", param_type="int?"),
# cwlgen.CommandInputParameter("runtime_disks", param_type="string?"),
])
tool_cwl.requirements.append(
cwlgen.ResourceRequirement(
cores_min="$(inputs.runtime_cpu ? inputs.runtime_cpu : 1)",
ram_min=
"$(inputs.runtime_memory ? Math.floor(1024 * inputs.runtime_memory) : 4096)",
))
return tool_cwl