--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/cwltool/workflow.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,446 @@
+import copy
+import datetime
+import functools
+import logging
+import random
+from typing import (
+    Callable,
+    Dict,
+    List,
+    Mapping,
+    MutableMapping,
+    MutableSequence,
+    Optional,
+    cast,
+)
+from uuid import UUID
+
+from ruamel.yaml.comments import CommentedMap
+from schema_salad.exceptions import ValidationException
+from schema_salad.sourceline import SourceLine, indent
+
+from . import command_line_tool, context, procgenerator
+from .checker import static_checker
+from .context import LoadingContext, RuntimeContext, getdefault
+from .errors import WorkflowException
+from .load_tool import load_tool
+from .loghandler import _logger
+from .process import Process, get_overrides, shortname
+from .provenance_profile import ProvenanceProfile
+from .utils import (
+    CWLObjectType,
+    JobsGeneratorType,
+    OutputCallbackType,
+    StepType,
+    aslist,
+)
+from .workflow_job import WorkflowJob
+
+
+def default_make_tool(
+    toolpath_object: CommentedMap, loadingContext: LoadingContext
+) -> Process:
+    if not isinstance(toolpath_object, MutableMapping):
+        raise WorkflowException("Not a dict: '%s'" % toolpath_object)
+    if "class" in toolpath_object:
+        if toolpath_object["class"] == "CommandLineTool":
+            return command_line_tool.CommandLineTool(toolpath_object, loadingContext)
+        if toolpath_object["class"] == "ExpressionTool":
+            return command_line_tool.ExpressionTool(toolpath_object, loadingContext)
+        if toolpath_object["class"] == "Workflow":
+            return Workflow(toolpath_object, loadingContext)
+        if toolpath_object["class"] == "ProcessGenerator":
+            return procgenerator.ProcessGenerator(toolpath_object, loadingContext)
+        if toolpath_object["class"] == "Operation":
+            return command_line_tool.AbstractOperation(toolpath_object, loadingContext)
+
+    raise WorkflowException(
+        "Missing or invalid 'class' field in "
+        "%s, expecting one of: CommandLineTool, ExpressionTool, Workflow"
+        % toolpath_object["id"]
+    )
+
+
+context.default_make_tool = default_make_tool
+
+
+class Workflow(Process):
+    def __init__(
+        self,
+        toolpath_object: CommentedMap,
+        loadingContext: LoadingContext,
+    ) -> None:
+        """Initialize this Workflow."""
+        super().__init__(toolpath_object, loadingContext)
+        self.provenance_object = None  # type: Optional[ProvenanceProfile]
+        if loadingContext.research_obj is not None:
+            run_uuid = None  # type: Optional[UUID]
+            is_main = not loadingContext.prov_obj  # Not yet set
+            if is_main:
+                run_uuid = loadingContext.research_obj.ro_uuid
+
+            self.provenance_object = ProvenanceProfile(
+                loadingContext.research_obj,
+                full_name=loadingContext.cwl_full_name,
+                host_provenance=loadingContext.host_provenance,
+                user_provenance=loadingContext.user_provenance,
+                orcid=loadingContext.orcid,
+                run_uuid=run_uuid,
+                fsaccess=loadingContext.research_obj.fsaccess,
+            )  # inherit RO UUID for main wf run
+            # TODO: Is Workflow(..) only called when we are the main workflow?
+            self.parent_wf = self.provenance_object
+
+        # FIXME: Won't this overwrite prov_obj for nested workflows?
+        loadingContext.prov_obj = self.provenance_object
+        loadingContext = loadingContext.copy()
+        loadingContext.requirements = self.requirements
+        loadingContext.hints = self.hints
+
+        self.steps = []  # type: List[WorkflowStep]
+        validation_errors = []
+        for index, step in enumerate(self.tool.get("steps", [])):
+            try:
+                self.steps.append(
+                    self.make_workflow_step(
+                        step, index, loadingContext, loadingContext.prov_obj
+                    )
+                )
+            except ValidationException as vexc:
+                if _logger.isEnabledFor(logging.DEBUG):
+                    _logger.exception("Validation failed at")
+                validation_errors.append(vexc)
+
+        if validation_errors:
+            raise ValidationException("\n".join(str(v) for v in validation_errors))
+
+        random.shuffle(self.steps)
+
+        # statically validate data links instead of doing it at runtime.
+        workflow_inputs = self.tool["inputs"]
+        workflow_outputs = self.tool["outputs"]
+
+        step_inputs = []  # type: List[CWLObjectType]
+        step_outputs = []  # type: List[CWLObjectType]
+        param_to_step = {}  # type: Dict[str, CWLObjectType]
+        for step in self.steps:
+            step_inputs.extend(step.tool["inputs"])
+            step_outputs.extend(step.tool["outputs"])
+            for s in step.tool["inputs"]:
+                param_to_step[s["id"]] = step.tool
+            for s in step.tool["outputs"]:
+                param_to_step[s["id"]] = step.tool
+
+        if getdefault(loadingContext.do_validate, True):
+            static_checker(
+                workflow_inputs,
+                workflow_outputs,
+                step_inputs,
+                step_outputs,
+                param_to_step,
+            )
+
+    def make_workflow_step(
+        self,
+        toolpath_object: CommentedMap,
+        pos: int,
+        loadingContext: LoadingContext,
+        parentworkflowProv: Optional[ProvenanceProfile] = None,
+    ) -> "WorkflowStep":
+        return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv)
+
+    def job(
+        self,
+        job_order: CWLObjectType,
+        output_callbacks: Optional[OutputCallbackType],
+        runtimeContext: RuntimeContext,
+    ) -> JobsGeneratorType:
+        builder = self._init_job(job_order, runtimeContext)
+
+        if runtimeContext.research_obj is not None:
+            if runtimeContext.toplevel:
+                # Record primary-job.json
+                runtimeContext.research_obj.fsaccess = runtimeContext.make_fs_access("")
+                runtimeContext.research_obj.create_job(builder.job)
+
+        job = WorkflowJob(self, runtimeContext)
+        yield job
+
+        runtimeContext = runtimeContext.copy()
+        runtimeContext.part_of = "workflow %s" % job.name
+        runtimeContext.toplevel = False
+
+        yield from job.job(builder.job, output_callbacks, runtimeContext)
+
+    def visit(self, op: Callable[[CommentedMap], None]) -> None:
+        op(self.tool)
+        for step in self.steps:
+            step.visit(op)
+
+
+def used_by_step(step: StepType, shortinputid: str) -> bool:
+    for st in cast(MutableSequence[CWLObjectType], step["in"]):
+        if st.get("valueFrom"):
+            if ("inputs.%s" % shortinputid) in cast(str, st.get("valueFrom")):
+                return True
+    if step.get("when"):
+        if ("inputs.%s" % shortinputid) in cast(str, step.get("when")):
+            return True
+    return False
+
+
+class WorkflowStep(Process):
+    def __init__(
+        self,
+        toolpath_object: CommentedMap,
+        pos: int,
+        loadingContext: LoadingContext,
+        parentworkflowProv: Optional[ProvenanceProfile] = None,
+    ) -> None:
+        """Initialize this WorkflowStep."""
+        if "id" in toolpath_object:
+            self.id = toolpath_object["id"]
+        else:
+            self.id = "#step" + str(pos)
+
+        loadingContext = loadingContext.copy()
+
+        loadingContext.requirements = copy.deepcopy(
+            getdefault(loadingContext.requirements, [])
+        )
+        assert loadingContext.requirements is not None  # nosec
+        loadingContext.requirements.extend(toolpath_object.get("requirements", []))
+        loadingContext.requirements.extend(
+            cast(
+                List[CWLObjectType],
+                get_overrides(
+                    getdefault(loadingContext.overrides_list, []), self.id
+                ).get("requirements", []),
+            )
+        )
+
+        hints = copy.deepcopy(getdefault(loadingContext.hints, []))
+        hints.extend(toolpath_object.get("hints", []))
+        loadingContext.hints = hints
+
+        try:
+            if isinstance(toolpath_object["run"], CommentedMap):
+                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 ValidationException as vexc:
+            if loadingContext.debug:
+                _logger.exception("Validation exception")
+            raise WorkflowException(
+                "Tool definition %s failed validation:\n%s"
+                % (toolpath_object["run"], indent(str(vexc)))
+            ) from vexc
+
+        validation_errors = []
+        self.tool = toolpath_object = copy.deepcopy(toolpath_object)
+        bound = set()
+        for stepfield, toolfield in (("in", "inputs"), ("out", "outputs")):
+            toolpath_object[toolfield] = []
+            for index, step_entry in enumerate(toolpath_object[stepfield]):
+                if isinstance(step_entry, str):
+                    param = CommentedMap()  # type: CommentedMap
+                    inputid = step_entry
+                else:
+                    param = CommentedMap(step_entry.items())
+                    inputid = step_entry["id"]
+
+                shortinputid = shortname(inputid)
+                found = False
+                for tool_entry in self.embedded_tool.tool[toolfield]:
+                    frag = shortname(tool_entry["id"])
+                    if frag == shortinputid:
+                        # if the case that the step has a default for a parameter,
+                        # we do not want the default of the tool to override it
+                        step_default = None
+                        if "default" in param and "default" in tool_entry:
+                            step_default = param["default"]
+                        param.update(tool_entry)
+                        param["_tool_entry"] = tool_entry
+                        if step_default is not None:
+                            param["default"] = step_default
+                        found = True
+                        bound.add(frag)
+                        break
+                if not found:
+                    if stepfield == "in":
+                        param["type"] = "Any"
+                        param["used_by_step"] = used_by_step(self.tool, shortinputid)
+                        param["not_connected"] = True
+                    else:
+                        if isinstance(step_entry, Mapping):
+                            step_entry_name = step_entry["id"]
+                        else:
+                            step_entry_name = step_entry
+                        validation_errors.append(
+                            SourceLine(self.tool["out"], index).makeError(
+                                "Workflow step output '%s' does not correspond to"
+                                % shortname(step_entry_name)
+                            )
+                            + "\n"
+                            + SourceLine(self.embedded_tool.tool, "outputs").makeError(
+                                "  tool output (expected '%s')"
+                                % (
+                                    "', '".join(
+                                        [
+                                            shortname(tool_entry["id"])
+                                            for tool_entry in self.embedded_tool.tool[
+                                                "outputs"
+                                            ]
+                                        ]
+                                    )
+                                )
+                            )
+                        )
+                param["id"] = inputid
+                param.lc.line = toolpath_object[stepfield].lc.data[index][0]
+                param.lc.col = toolpath_object[stepfield].lc.data[index][1]
+                param.lc.filename = toolpath_object[stepfield].lc.filename
+                toolpath_object[toolfield].append(param)
+
+        missing_values = []
+        for _, tool_entry in enumerate(self.embedded_tool.tool["inputs"]):
+            if shortname(tool_entry["id"]) not in bound:
+                if "null" not in tool_entry["type"] and "default" not in tool_entry:
+                    missing_values.append(shortname(tool_entry["id"]))
+
+        if missing_values:
+            validation_errors.append(
+                SourceLine(self.tool, "in").makeError(
+                    "Step is missing required parameter%s '%s'"
+                    % (
+                        "s" if len(missing_values) > 1 else "",
+                        "', '".join(missing_values),
+                    )
+                )
+            )
+
+        if validation_errors:
+            raise ValidationException("\n".join(validation_errors))
+
+        super().__init__(toolpath_object, loadingContext)
+
+        if self.embedded_tool.tool["class"] == "Workflow":
+            (feature, _) = self.get_requirement("SubworkflowFeatureRequirement")
+            if not feature:
+                raise WorkflowException(
+                    "Workflow contains embedded workflow but "
+                    "SubworkflowFeatureRequirement not in requirements"
+                )
+
+        if "scatter" in self.tool:
+            (feature, _) = self.get_requirement("ScatterFeatureRequirement")
+            if not feature:
+                raise WorkflowException(
+                    "Workflow contains scatter but ScatterFeatureRequirement "
+                    "not in requirements"
+                )
+
+            inputparms = copy.deepcopy(self.tool["inputs"])
+            outputparms = copy.deepcopy(self.tool["outputs"])
+            scatter = aslist(self.tool["scatter"])
+
+            method = self.tool.get("scatterMethod")
+            if method is None and len(scatter) != 1:
+                raise ValidationException(
+                    "Must specify scatterMethod when scattering over multiple inputs"
+                )
+
+            inp_map = {i["id"]: i for i in inputparms}
+            for inp in scatter:
+                if inp not in inp_map:
+                    raise ValidationException(
+                        SourceLine(self.tool, "scatter").makeError(
+                            "Scatter parameter '%s' does not correspond to "
+                            "an input parameter of this step, expecting '%s'"
+                            % (
+                                shortname(inp),
+                                "', '".join(shortname(k) for k in inp_map.keys()),
+                            )
+                        )
+                    )
+
+                inp_map[inp]["type"] = {"type": "array", "items": inp_map[inp]["type"]}
+
+            if self.tool.get("scatterMethod") == "nested_crossproduct":
+                nesting = len(scatter)
+            else:
+                nesting = 1
+
+            for _ in range(0, nesting):
+                for oparam in outputparms:
+                    oparam["type"] = {"type": "array", "items": oparam["type"]}
+            self.tool["inputs"] = inputparms
+            self.tool["outputs"] = outputparms
+        self.prov_obj = None  # type: Optional[ProvenanceProfile]
+        if loadingContext.research_obj is not None:
+            self.prov_obj = parentworkflowProv
+            if self.embedded_tool.tool["class"] == "Workflow":
+                self.parent_wf = self.embedded_tool.parent_wf
+            else:
+                self.parent_wf = self.prov_obj
+
+    def receive_output(
+        self,
+        output_callback: OutputCallbackType,
+        jobout: CWLObjectType,
+        processStatus: str,
+    ) -> None:
+        output = {}
+        for i in self.tool["outputs"]:
+            field = shortname(i["id"])
+            if field in jobout:
+                output[i["id"]] = jobout[field]
+            else:
+                processStatus = "permanentFail"
+        output_callback(output, processStatus)
+
+    def job(
+        self,
+        job_order: CWLObjectType,
+        output_callbacks: Optional[OutputCallbackType],
+        runtimeContext: RuntimeContext,
+    ) -> JobsGeneratorType:
+        """Initialize sub-workflow as a step in the parent profile."""
+        if (
+            self.embedded_tool.tool["class"] == "Workflow"
+            and runtimeContext.research_obj
+            and self.prov_obj
+            and self.embedded_tool.provenance_object
+        ):
+            self.embedded_tool.parent_wf = self.prov_obj
+            process_name = self.tool["id"].split("#")[1]
+            self.prov_obj.start_process(
+                process_name,
+                datetime.datetime.now(),
+                self.embedded_tool.provenance_object.workflow_run_uri,
+            )
+
+        step_input = {}
+        for inp in self.tool["inputs"]:
+            field = shortname(inp["id"])
+            if not inp.get("not_connected"):
+                step_input[field] = job_order[inp["id"]]
+
+        try:
+            yield from self.embedded_tool.job(
+                step_input,
+                functools.partial(self.receive_output, output_callbacks),
+                runtimeContext,
+            )
+        except WorkflowException:
+            _logger.error("Exception on step '%s'", runtimeContext.name)
+            raise
+        except Exception as exc:
+            _logger.exception("Unexpected exception")
+            raise WorkflowException(str(exc)) from exc
+
+    def visit(self, op: Callable[[CommentedMap], None]) -> None:
+        self.embedded_tool.visit(op)