def to_script(ctx, path, job_path, **kwds):
if schema_salad is None:
raise Exception(
"This functionality requires schema_salad and Python 2.7.")
if cwltool is None:
raise Exception("This functionality requires cwltool and Python 2.7.")
uri = "file://" + os.path.abspath(job_path)
loader = schema_salad.ref_resolver.Loader({
"@base": uri,
"path": {
"@type": "@id"
}
})
job, _ = loader.resolve_ref(uri)
t = load_tool(path, False, False, cwltool.workflow.defaultMakeTool, True)
if type(t) == int:
return t
process.checkRequirements(t.tool, cwl2script.supportedProcessRequirements)
for inp in t.tool["inputs"]:
if process.shortname(inp["id"]) in job:
pass
elif process.shortname(inp["id"]) not in job and "default" in inp:
job[process.shortname(inp["id"])] = copy.copy(inp["default"])
elif process.shortname(
inp["id"]) not in job and inp["type"][0] == "null":
pass
else:
raise Exception("Missing inputs `%s`" %
process.shortname(inp["id"]))
if not kwds.get("basedir", None):
kwds["basedir"] = os.path.dirname(os.path.abspath(job_path))
outdir = kwds.get("outdir")
if t.tool["class"] == "Workflow":
print(cwl2script.generateScriptForWorkflow(t, job, outdir))
elif t.tool["class"] == "CommandLineTool":
print(cwl2script.generateScriptForTool(t, job, outdir))
return 0
def to_script(ctx, path, job_path, **kwds):
if schema_salad is None:
raise Exception("This functionality requires schema_salad and Python 2.7.")
if cwltool is None:
raise Exception("This functionality requires cwltool and Python 2.7.")
uri = "file://" + os.path.abspath(job_path)
loader = schema_salad.ref_resolver.Loader({
"@base": uri,
"path": {
"@type": "@id"
}
})
job, _ = loader.resolve_ref(uri)
t = load_tool(path, False, False, cwltool.workflow.defaultMakeTool, True)
if type(t) == int:
return t
process.checkRequirements(t.tool, cwl2script.supportedProcessRequirements)
for inp in t.tool["inputs"]:
if process.shortname(inp["id"]) in job:
pass
elif process.shortname(inp["id"]) not in job and "default" in inp:
job[process.shortname(inp["id"])] = copy.copy(inp["default"])
elif process.shortname(inp["id"]) not in job and inp["type"][0] == "null":
pass
else:
raise Exception("Missing inputs `%s`" % process.shortname(inp["id"]))
if not kwds.get("basedir", None):
kwds["basedir"] = os.path.dirname(os.path.abspath(job_path))
outdir = kwds.get("outdir")
if t.tool["class"] == "Workflow":
print(cwl2script.generateScriptForWorkflow(t, job, outdir))
elif t.tool["class"] == "CommandLineTool":
print(cwl2script.generateScriptForTool(t, job, outdir))
return 0
def main(args=None):
parser = argparse.ArgumentParser()
parser.add_argument("cwltool", type=str)
parser.add_argument("cwljob", type=str)
parser.add_argument("--conformance-test", action="store_true")
parser.add_argument("--no-container", action="store_true")
parser.add_argument("--basedir", type=str)
parser.add_argument("--outdir", type=str, default=os.getcwd())
options = parser.parse_args(args)
uri = "file://" + os.path.abspath(options.cwljob)
if options.conformance_test:
loader = schema_salad.ref_resolver.Loader({})
else:
loader = schema_salad.ref_resolver.Loader({
"@base": uri,
"path": {
"@type": "@id"
}
})
job, _ = loader.resolve_ref(uri)
t = cwltool.main.load_tool(options.cwltool, False, False, cwltool.workflow.defaultMakeTool, True)
if type(t) == int:
return t
try:
checkRequirements(t.tool, supportedProcessRequirements)
except Exception as e:
logging.error(e)
return 33
for inp in t.tool["inputs"]:
if shortname(inp["id"]) in job:
pass
elif shortname(inp["id"]) not in job and "default" in inp:
job[shortname(inp["id"])] = copy.copy(inp["default"])
elif shortname(inp["id"]) not in job and inp["type"][0] == "null":
pass
else:
raise Exception("Missing inputs `%s`" % shortname(inp["id"]))
if options.conformance_test:
sys.stdout.write(json.dumps(cwltool.main.single_job_executor(t, job, options.basedir, options, conformance_test=True), indent=4))
return 0
if not options.basedir:
options.basedir = os.path.dirname(os.path.abspath(options.cwljob))
outdir = options.outdir
if t.tool["class"] == "Workflow":
print generateScriptForWorkflow(t, job, outdir)
elif t.tool["class"] == "CommandLineTool":
print generateScriptForTool(t, job, outdir)
return 0
