diff env/lib/python3.7/site-packages/cwltool/procgenerator.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"

--- a/env/lib/python3.7/site-packages/cwltool/procgenerator.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,123 +0,0 @@
-import copy
-from .process import Process, shortname
-from .load_tool import load_tool
-from schema_salad import validate
-from schema_salad.sourceline import indent
-from .errors import WorkflowException
-from .context import RuntimeContext, LoadingContext
-from typing import (Any, Callable, Dict, Generator, Iterable, List,
-                    Mapping, MutableMapping, MutableSequence,
-                    Optional, Tuple, Union, cast)
-from .loghandler import _logger
-from typing_extensions import Text  # pylint: disable=unused-import
-
-class ProcessGeneratorJob(object):
-    def __init__(self, procgenerator):
-        # type: (ProcessGenerator) -> None
-        self.procgenerator = procgenerator
-        self.jobout = None         # type: Optional[Dict[Text, Any]]
-        self.processStatus = None  # type: Optional[Text]
-
-    def receive_output(self, jobout, processStatus):
-        # type: (Dict[Text, Any], Text) -> None
-        self.jobout = jobout
-        self.processStatus = processStatus
-
-    def job(self,
-            job_order,         # type: Mapping[Text, Any]
-            output_callbacks,  # type: Callable[[Any, Any], Any]
-            runtimeContext     # type: RuntimeContext
-           ):  # type: (...) -> Generator[Any, None, None]
-        # FIXME: Declare base type for what Generator yields
-
-        try:
-            for tool in self.procgenerator.embedded_tool.job(
-                    job_order,
-                    self.receive_output,
-                    runtimeContext):
-                yield tool
-
-            while self.processStatus is None:
-                yield None
-
-            if self.processStatus != "success":
-                output_callbacks(self.jobout, self.processStatus)
-                return
-
-            if self.jobout is None:
-                raise WorkflowException("jobout should not be None")
-
-            created_tool, runinputs = self.procgenerator.result(job_order, self.jobout, runtimeContext)
-
-            for tool in created_tool.job(
-                    runinputs,
-                    output_callbacks,
-                    runtimeContext):
-                yield tool
-
-        except WorkflowException:
-            raise
-        except Exception as exc:
-            _logger.exception("Unexpected exception")
-            raise WorkflowException(Text(exc))
-
-
-class ProcessGenerator(Process):
-    def __init__(self,
-                 toolpath_object,      # type: MutableMapping[Text, Any]
-                 loadingContext        # type: LoadingContext
-    ):  # type: (...) -> None
-        super(ProcessGenerator, self).__init__(
-            toolpath_object, loadingContext)
-        self.loadingContext = loadingContext  # type: LoadingContext
-        try:
-            if isinstance(toolpath_object["run"], MutableMapping):
-                self.embedded_tool = loadingContext.construct_tool_object(
-                    toolpath_object["run"], loadingContext)  # type: Process
-            else:
-                loadingContext.metadata = {}
-                self.embedded_tool = load_tool(
-                    toolpath_object["run"], loadingContext)
-        except validate.ValidationException as vexc:
-            if loadingContext.debug:
-                _logger.exception("Validation exception")
-            raise WorkflowException(
-                u"Tool definition %s failed validation:\n%s" %
-                (toolpath_object["run"], indent(str(vexc))))
-
-    def job(self,
-            job_order,         # type: Mapping[Text, Text]
-            output_callbacks,  # type: Callable[[Any, Any], Any]
-            runtimeContext     # type: RuntimeContext
-           ):  # type: (...) -> Generator[Any, None, None]
-        # FIXME: Declare base type for what Generator yields
-        return ProcessGeneratorJob(self).job(job_order, output_callbacks, runtimeContext)
-
-    def result(self,
-            job_order,      # type: Mapping[Text, Any]
-            jobout,         # type: Mapping[Text, Any]
-            runtimeContext  # type: RuntimeContext
-    ):  # type: (...) -> Tuple[Process, MutableMapping[Text, Any]]
-        try:
-            loadingContext = self.loadingContext.copy()
-            loadingContext.metadata = {}
-            embedded_tool = load_tool(
-                jobout["runProcess"]["location"], loadingContext)
-        except validate.ValidationException as vexc:
-            if runtimeContext.debug:
-                _logger.exception("Validation exception")
-            raise WorkflowException(
-                u"Tool definition %s failed validation:\n%s" %
-                (jobout["runProcess"], indent(str(vexc))))
-
-        if "runInputs" in jobout:
-            runinputs = cast(MutableMapping[Text, Any], jobout["runInputs"])
-        else:
-            runinputs = cast(MutableMapping[Text, Any], copy.deepcopy(job_order))
-            for i in self.embedded_tool.tool["inputs"]:
-                if shortname(i["id"]) in runinputs:
-                    del runinputs[shortname(i["id"])]
-            if "id" in runinputs:
-                del runinputs["id"]
-
-        return embedded_tool, runinputs