from schema_salad.sourceline import SourceLine, cmap
from cwltool.command_line_tool import CommandLineTool
import cwltool.workflow
from schema_salad.sourceline import SourceLine, cmap
from cwltool.command_line_tool import CommandLineTool
import cwltool.workflow
-from cwltool.process import scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname
+from cwltool.process import scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname, Process
from cwltool.load_tool import fetch_document
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
from cwltool.utils import aslist
from cwltool.load_tool import fetch_document
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
from cwltool.utils import aslist
visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
# Only interested in discovered secondaryFiles which are local
# files that need to be uploaded.
if d.startswith("file:"):
# Only interested in discovered secondaryFiles which are local
# files that need to be uploaded.
if d.startswith("file:"):
packed = pack(tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]),
tool.tool["id"], tool.metadata, rewrite_out=rewrites)
packed = pack(tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]),
tool.tool["id"], tool.metadata, rewrite_out=rewrites)
"""Base class for runner processes, which submit an instance of
arvados-cwl-runner and wait for the final result."""
"""Base class for runner processes, which submit an instance of
arvados-cwl-runner and wait for the final result."""
- def __init__(self, runner, tool, job_order, enable_reuse,
+ def __init__(self, runner, tool, loadingContext, enable_reuse,
output_name, output_tags, submit_runner_ram=0,
name=None, on_error=None, submit_runner_image=None,
intermediate_output_ttl=0, merged_map=None,
priority=None, secret_store=None,
collection_cache_size=256,
collection_cache_is_default=True):
output_name, output_tags, submit_runner_ram=0,
name=None, on_error=None, submit_runner_image=None,
intermediate_output_ttl=0, merged_map=None,
priority=None, secret_store=None,
collection_cache_size=256,
collection_cache_is_default=True):
self.running = False
if enable_reuse:
# If reuse is permitted by command line arguments but
# disabled by the workflow itself, disable it.
self.running = False
if enable_reuse:
# If reuse is permitted by command line arguments but
# disabled by the workflow itself, disable it.
+ def job(self,
+ job_order, # type: Mapping[Text, Text]
+ output_callbacks, # type: Callable[[Any, Any], Any]
+ runtimeContext # type: RuntimeContext
+ ): # type: (...) -> Generator[Any, None, None]
+ self.job_order = job_order
+ self._init_job(job_order, runtimeContext)
+ yield self
+
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
if "cwl.output.json" in outc:
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
if "cwl.output.json" in outc: