def add_arv_hints():
cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE
- res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
- use_custom_schema("v1.0", "http://arvados.org/cwl", res.read())
+ res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.0.yml')
+ res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.1.yml')
+ customschema = res.read()
+ use_custom_schema("v1.0", "http://arvados.org/cwl", customschema)
+ use_custom_schema("v1.1.0-dev1", "http://arvados.org/cwl", customschema)
res.close()
cwltool.process.supportedProcessRequirements.extend([
"http://arvados.org/cwl#RunInSingleContainer",
logger.exception("Error creating the Arvados CWL Executor")
return 1
- # Note that unless in debug mode, some stack traces related to user
+ # Note that unless in debug mode, some stack traces related to user
# workflow errors may be suppressed. See ArvadosJob.done().
if arvargs.debug:
logger.setLevel(logging.DEBUG)
else:
arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
+ if stdout is sys.stdout:
+ # cwltool.main has code to work around encoding issues with
+ # sys.stdout and unix pipes (they default to ASCII encoding,
+ # we want utf-8), so when stdout is sys.stdout set it to None
+ # to take advantage of that. Don't override it for all cases
+ # since we still want to be able to capture stdout for the
+ # unit tests.
+ stdout = None
+
return cwltool.main.main(args=arvargs,
stdout=stdout,
stderr=stderr,