arctrl 3.0.0__py3-none-any.whl

arctrl/py/WorkflowGraph/workflow_graph.py

@@ -0,0 +1,119 @@
+from __future__ import annotations
+from collections.abc import Callable
+from ..fable_modules.fable_library.list import FSharpList
+from ..fable_modules.fable_library.result import FSharpResult_2
+from ..fable_modules.siren.siren_types import SirenElement
+from ..Core.arc_types import (ArcWorkflow, ArcRun, ArcInvestigation)
+from ..CWL.cwlprocessing_unit import CWLProcessingUnit
+from .adapters import (of_workflow as of_workflow_1, of_run as of_run_1, of_investigation as of_investigation_1)
+from .builder import (build as build_1, build_with as build_with_1)
+from .build_options import WorkflowGraphBuildOptions
+from .graph_types import (WorkflowGraph, GraphBuildIssue, WorkflowGraphIndex, WorkflowGraphNode, NodeKind, WorkflowGraphEdge, EdgeKind)
+from .query_helpers import (try_find_node as try_find_node_1, get_nodes as get_nodes_1, get_edges_from as get_edges_from_1, get_edges_to as get_edges_to_1, get_edges_by_kind as get_edges_by_kind_1, get_input_ports as get_input_ports_1, get_output_ports as get_output_ports_1)
+from .visualization_siren import (WorkflowGraphSiren_fromGraph, WorkflowGraphSiren_toMermaid, WorkflowGraphSiren_toMarkdown, WorkflowGraphSiren_fromProcessingUnit, WorkflowGraphSiren_fromProcessingUnitResolved)
+
+build: Callable[[CWLProcessingUnit], WorkflowGraph] = build_1
+
+def _arrow1390(options: WorkflowGraphBuildOptions) -> Callable[[CWLProcessingUnit], WorkflowGraph]:
+    def _arrow1389(processing_unit: CWLProcessingUnit) -> WorkflowGraph:
+        return build_with_1(options, processing_unit)
+
+    return _arrow1389
+
+
+build_with: Callable[[WorkflowGraphBuildOptions, CWLProcessingUnit], WorkflowGraph] = _arrow1390
+
+of_workflow: Callable[[ArcWorkflow], FSharpResult_2[WorkflowGraph, GraphBuildIssue]] = of_workflow_1
+
+of_run: Callable[[ArcRun], FSharpResult_2[WorkflowGraph, GraphBuildIssue]] = of_run_1
+
+of_investigation: Callable[[ArcInvestigation], WorkflowGraphIndex] = of_investigation_1
+
+def _arrow1392(node_id: str) -> Callable[[WorkflowGraph], WorkflowGraphNode | None]:
+    def _arrow1391(graph: WorkflowGraph) -> WorkflowGraphNode | None:
+        return try_find_node_1(node_id, graph)
+
+    return _arrow1391
+
+
+try_find_node: Callable[[str, WorkflowGraph], WorkflowGraphNode | None] = _arrow1392
+
+def _arrow1394(kind: NodeKind) -> Callable[[WorkflowGraph], FSharpList[WorkflowGraphNode]]:
+    def _arrow1393(graph: WorkflowGraph) -> FSharpList[WorkflowGraphNode]:
+        return get_nodes_1(kind, graph)
+
+    return _arrow1393
+
+
+get_nodes: Callable[[NodeKind, WorkflowGraph], FSharpList[WorkflowGraphNode]] = _arrow1394
+
+def _arrow1396(node_id: str) -> Callable[[WorkflowGraph], FSharpList[WorkflowGraphEdge]]:
+    def _arrow1395(graph: WorkflowGraph) -> FSharpList[WorkflowGraphEdge]:
+        return get_edges_from_1(node_id, graph)
+
+    return _arrow1395
+
+
+get_edges_from: Callable[[str, WorkflowGraph], FSharpList[WorkflowGraphEdge]] = _arrow1396
+
+def _arrow1398(node_id: str) -> Callable[[WorkflowGraph], FSharpList[WorkflowGraphEdge]]:
+    def _arrow1397(graph: WorkflowGraph) -> FSharpList[WorkflowGraphEdge]:
+        return get_edges_to_1(node_id, graph)
+
+    return _arrow1397
+
+
+get_edges_to: Callable[[str, WorkflowGraph], FSharpList[WorkflowGraphEdge]] = _arrow1398
+
+def _arrow1400(kind: EdgeKind) -> Callable[[WorkflowGraph], FSharpList[WorkflowGraphEdge]]:
+    def _arrow1399(graph: WorkflowGraph) -> FSharpList[WorkflowGraphEdge]:
+        return get_edges_by_kind_1(kind, graph)
+
+    return _arrow1399
+
+
+get_edges_by_kind: Callable[[EdgeKind, WorkflowGraph], FSharpList[WorkflowGraphEdge]] = _arrow1400
+
+def _arrow1402(owner_node_id: str) -> Callable[[WorkflowGraph], FSharpList[WorkflowGraphNode]]:
+    def _arrow1401(graph: WorkflowGraph) -> FSharpList[WorkflowGraphNode]:
+        return get_input_ports_1(owner_node_id, graph)
+
+    return _arrow1401
+
+
+get_input_ports: Callable[[str, WorkflowGraph], FSharpList[WorkflowGraphNode]] = _arrow1402
+
+def _arrow1404(owner_node_id: str) -> Callable[[WorkflowGraph], FSharpList[WorkflowGraphNode]]:
+    def _arrow1403(graph: WorkflowGraph) -> FSharpList[WorkflowGraphNode]:
+        return get_output_ports_1(owner_node_id, graph)
+
+    return _arrow1403
+
+
+get_output_ports: Callable[[str, WorkflowGraph], FSharpList[WorkflowGraphNode]] = _arrow1404
+
+from_graph_to_siren: Callable[[WorkflowGraph], SirenElement] = WorkflowGraphSiren_fromGraph
+
+to_mermaid: Callable[[WorkflowGraph], str] = WorkflowGraphSiren_toMermaid
+
+to_markdown: Callable[[WorkflowGraph], str] = WorkflowGraphSiren_toMarkdown
+
+from_processing_unit_to_siren: Callable[[CWLProcessingUnit], SirenElement] = WorkflowGraphSiren_fromProcessingUnit
+
+def _arrow1408(build_options: WorkflowGraphBuildOptions) -> Callable[[CWLProcessingUnit], SirenElement]:
+    def _arrow1407(processing_unit: CWLProcessingUnit) -> SirenElement:
+        return WorkflowGraphSiren_fromProcessingUnitResolved(build_options, processing_unit)
+
+    return _arrow1407
+
+
+from_processing_unit_to_siren_resolved: Callable[[WorkflowGraphBuildOptions, CWLProcessingUnit], SirenElement] = _arrow1408
+
+from_arc_workflow: Callable[[ArcWorkflow], FSharpResult_2[WorkflowGraph, GraphBuildIssue]] = of_workflow
+
+from_arc_run: Callable[[ArcRun], FSharpResult_2[WorkflowGraph, GraphBuildIssue]] = of_run
+
+from_arc_investigation: Callable[[ArcInvestigation], WorkflowGraphIndex] = of_investigation
+
+__all__ = ["build", "build_with", "of_workflow", "of_run", "of_investigation", "try_find_node", "get_nodes", "get_edges_from", "get_edges_to", "get_edges_by_kind", "get_input_ports", "get_output_ports", "from_graph_to_siren", "to_mermaid", "to_markdown", "from_processing_unit_to_siren", "from_processing_unit_to_siren_resolved", "from_arc_workflow", "from_arc_run", "from_arc_investigation"]
+

arctrl/py/Yaml/decode.py

@@ -0,0 +1 @@
+

arctrl/py/Yaml/encode.py

@@ -0,0 +1,10 @@
+from ..fable_modules.fable_library.option import default_arg
+
+DefaultWhitespace: int = 2
+
+def default_whitespace(spaces: int | None=None) -> int:
+    return default_arg(spaces, DefaultWhitespace)
+
+
+__all__ = ["DefaultWhitespace", "default_whitespace"]
+

arctrl/py/Yaml/validation_package.py

@@ -0,0 +1,77 @@
+from __future__ import annotations
+from collections.abc import Callable
+from typing import Any
+from ..fable_modules.fable_library.list import (choose, of_array, FSharpList)
+from ..fable_modules.fable_library.seq import (to_list, delay, collect, singleton)
+from ..fable_modules.fable_library.util import (equals, IEnumerable_1)
+from ..fable_modules.yamlicious.yamlicious_types import YAMLContent_create_27AED5E3
+from ..fable_modules.yamlicious.decode import (object, IRequiredGetter, string as string_1, IOptionalGetter, IGetters)
+from ..fable_modules.yamlicious.encode import (string, try_include)
+from ..fable_modules.yamlicious.reader import read
+from ..fable_modules.yamlicious.writer import write
+from ..fable_modules.yamlicious.yamlicious_types import (YAMLElement, Config)
+from ..ValidationPackages.validation_package import ValidationPackage
+from .encode import default_whitespace
+
+def ValidationPackage_encoder(validationpackage: ValidationPackage) -> YAMLElement:
+    def chooser(tupled_arg: tuple[str, YAMLElement], validationpackage: Any=validationpackage) -> tuple[str, YAMLElement] | None:
+        v: YAMLElement = tupled_arg[1]
+        if equals(v, YAMLElement(5)):
+            return None
+
+        else: 
+            return (tupled_arg[0], v)
+
+
+    def _arrow3952(value: str, validationpackage: Any=validationpackage) -> YAMLElement:
+        return string(value)
+
+    obj_seq: FSharpList[tuple[str, YAMLElement]] = choose(chooser, of_array([("name", string(validationpackage.Name)), try_include("version", _arrow3952, validationpackage.Version)]))
+    def _arrow3954(__unit: None=None, validationpackage: Any=validationpackage) -> IEnumerable_1[YAMLElement]:
+        def _arrow3953(match_value: tuple[str, YAMLElement]) -> IEnumerable_1[YAMLElement]:
+            return singleton(YAMLElement(0, YAMLContent_create_27AED5E3(match_value[0]), match_value[1]))
+
+        return collect(_arrow3953, obj_seq)
+
+    return YAMLElement(3, to_list(delay(_arrow3954)))
+
+
+def _arrow3957(value_2: YAMLElement) -> ValidationPackage:
+    def getter(get: IGetters) -> ValidationPackage:
+        def _arrow3955(__unit: None=None, get: Any=get) -> str:
+            object_arg: IRequiredGetter = get.Required
+            return object_arg.Field("name", string_1)
+
+        def _arrow3956(__unit: None=None, get: Any=get) -> str | None:
+            object_arg_1: IOptionalGetter = get.Optional
+            return object_arg_1.Field("version", string_1)
+
+        return ValidationPackage(_arrow3955(), _arrow3956())
+
+    return object(getter, value_2)
+
+
+ValidationPackage_decoder: Callable[[YAMLElement], ValidationPackage] = _arrow3957
+
+def ARCtrl_ValidationPackages_ValidationPackage__ValidationPackage_fromYamlString_Static_Z721C83C5(s: str) -> ValidationPackage:
+    return ValidationPackage_decoder(read(s))
+
+
+def ARCtrl_ValidationPackages_ValidationPackage__ValidationPackage_toYamlString_Static_71136F3F(whitespace: int | None=None) -> Callable[[ValidationPackage], str]:
+    def _arrow3959(vp: ValidationPackage, whitespace: Any=whitespace) -> str:
+        element: YAMLElement = ValidationPackage_encoder(vp)
+        whitespace_1: int = default_whitespace(whitespace) or 0
+        def _arrow3958(c: Config) -> Config:
+            return Config(whitespace_1, c.Level)
+
+        return write(element, _arrow3958)
+
+    return _arrow3959
+
+
+def ARCtrl_ValidationPackages_ValidationPackage__ValidationPackage_toYamlString_71136F3F(this: ValidationPackage, whitespace: int | None=None) -> str:
+    return ARCtrl_ValidationPackages_ValidationPackage__ValidationPackage_toYamlString_Static_71136F3F(whitespace)(this)
+
+
+__all__ = ["ValidationPackage_encoder", "ValidationPackage_decoder", "ARCtrl_ValidationPackages_ValidationPackage__ValidationPackage_fromYamlString_Static_Z721C83C5", "ARCtrl_ValidationPackages_ValidationPackage__ValidationPackage_toYamlString_Static_71136F3F", "ARCtrl_ValidationPackages_ValidationPackage__ValidationPackage_toYamlString_71136F3F"]
+

arctrl/py/Yaml/validation_packages_config.py

@@ -0,0 +1,86 @@
+from __future__ import annotations
+from collections.abc import Callable
+from typing import Any
+from ..fable_modules.fable_library.list import (choose, of_array, FSharpList)
+from ..fable_modules.fable_library.seq import (to_list, delay, collect, singleton)
+from ..fable_modules.fable_library.types import Array
+from ..fable_modules.fable_library.util import (equals, IEnumerable_1)
+from ..fable_modules.yamlicious.yamlicious_types import YAMLContent_create_27AED5E3
+from ..fable_modules.yamlicious.decode import (object, IRequiredGetter, resizearray as resizearray_1, IOptionalGetter, string as string_1, IGetters)
+from ..fable_modules.yamlicious.encode import (try_include, string, resizearray)
+from ..fable_modules.yamlicious.reader import read
+from ..fable_modules.yamlicious.writer import write
+from ..fable_modules.yamlicious.yamlicious_types import (YAMLElement, Config)
+from ..ValidationPackages.validation_package import ValidationPackage
+from ..ValidationPackages.validation_packages_config import ValidationPackagesConfig
+from .encode import default_whitespace
+from .validation_package import (ValidationPackage_encoder, ValidationPackage_decoder)
+
+def ValidationPackagesConfig_encoder(validationpackage: ValidationPackagesConfig) -> YAMLElement:
+    def chooser(tupled_arg: tuple[str, YAMLElement], validationpackage: Any=validationpackage) -> tuple[str, YAMLElement] | None:
+        v: YAMLElement = tupled_arg[1]
+        if equals(v, YAMLElement(5)):
+            return None
+
+        else: 
+            return (tupled_arg[0], v)
+
+
+    def _arrow3961(value: str, validationpackage: Any=validationpackage) -> YAMLElement:
+        return string(value)
+
+    def _arrow3962(validationpackage_1: ValidationPackage, validationpackage: Any=validationpackage) -> YAMLElement:
+        return ValidationPackage_encoder(validationpackage_1)
+
+    obj_seq: FSharpList[tuple[str, YAMLElement]] = choose(chooser, of_array([try_include("arc_specification", _arrow3961, validationpackage.ARCSpecification), ("validation_packages", resizearray(_arrow3962, validationpackage.ValidationPackages))]))
+    def _arrow3964(__unit: None=None, validationpackage: Any=validationpackage) -> IEnumerable_1[YAMLElement]:
+        def _arrow3963(match_value: tuple[str, YAMLElement]) -> IEnumerable_1[YAMLElement]:
+            return singleton(YAMLElement(0, YAMLContent_create_27AED5E3(match_value[0]), match_value[1]))
+
+        return collect(_arrow3963, obj_seq)
+
+    return YAMLElement(3, to_list(delay(_arrow3964)))
+
+
+def _arrow3967(value_2: YAMLElement) -> ValidationPackagesConfig:
+    def getter(get: IGetters) -> ValidationPackagesConfig:
+        def _arrow3965(__unit: None=None, get: Any=get) -> Array[ValidationPackage]:
+            object_arg: IRequiredGetter = get.Required
+            def arg_1(value: YAMLElement) -> Array[ValidationPackage]:
+                return resizearray_1(ValidationPackage_decoder, value)
+
+            return object_arg.Field("validation_packages", arg_1)
+
+        def _arrow3966(__unit: None=None, get: Any=get) -> str | None:
+            object_arg_1: IOptionalGetter = get.Optional
+            return object_arg_1.Field("arc_specification", string_1)
+
+        return ValidationPackagesConfig(_arrow3965(), _arrow3966())
+
+    return object(getter, value_2)
+
+
+ValidationPackagesConfig_decoder: Callable[[YAMLElement], ValidationPackagesConfig] = _arrow3967
+
+def ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_fromYamlString_Static_Z721C83C5(s: str) -> ValidationPackagesConfig:
+    return ValidationPackagesConfig_decoder(read(s))
+
+
+def ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toYamlString_Static_71136F3F(whitespace: int | None=None) -> Callable[[ValidationPackagesConfig], str]:
+    def _arrow3969(vp: ValidationPackagesConfig, whitespace: Any=whitespace) -> str:
+        element: YAMLElement = ValidationPackagesConfig_encoder(vp)
+        whitespace_1: int = default_whitespace(whitespace) or 0
+        def _arrow3968(c: Config) -> Config:
+            return Config(whitespace_1, c.Level)
+
+        return write(element, _arrow3968)
+
+    return _arrow3969
+
+
+def ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toYamlString_71136F3F(this: ValidationPackagesConfig, whitespace: int | None=None) -> str:
+    return ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toYamlString_Static_71136F3F(whitespace)(this)
+
+
+__all__ = ["ValidationPackagesConfig_encoder", "ValidationPackagesConfig_decoder", "ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_fromYamlString_Static_Z721C83C5", "ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toYamlString_Static_71136F3F", "ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toYamlString_71136F3F"]
+