ARCtrl 2.2.2__tar.gz → 2.2.4__tar.gz

{arctrl-2.2.2 → arctrl-2.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ARCtrl
-Version: 2.2.2
+Version: 2.2.4
 Summary: Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtimer agnostic contract systems.
 Home-page: https://github.com/nfdi4plants/ARCtrl
 Keywords: arc,annotated research context,isa,research data,multi platform
@@ -12,7 +12,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: requests (==2.28.1)
+Requires-Dist: requests (>=2.28.1,<3.0.0)
 Project-URL: Repository, https://github.com/nfdi4plants/ARCtrl
 Description-Content-Type: text/markdown
 

{arctrl-2.2.2 → arctrl-2.2.4}/arctrl/CWL/cwltypes.py

@@ -6,7 +6,7 @@ from ..fable_modules.dynamic_obj.dyn_obj import set_property
 from ..fable_modules.fable_library.reflection import (TypeInfo, class_type, string_type, option_type, bool_type, record_type, union_type, array_type)
 from ..fable_modules.fable_library.types import (Record, Array, Union, FSharpRef)
 
-def _expr431() -> TypeInfo:
+def _expr427() -> TypeInfo:
     return class_type("ARCtrl.CWL.FileInstance", None, FileInstance, DynamicObj_reflection())
 
 
@@ -16,13 +16,13 @@ class FileInstance(DynamicObj):
         pass
 
 
-FileInstance_reflection = _expr431
+FileInstance_reflection = _expr427
 
 def FileInstance__ctor(__unit: None=None) -> FileInstance:
     return FileInstance(__unit)
 
 
-def _expr433() -> TypeInfo:
+def _expr428() -> TypeInfo:
     return class_type("ARCtrl.CWL.DirectoryInstance", None, DirectoryInstance, DynamicObj_reflection())
 
 
@@ -32,13 +32,13 @@ class DirectoryInstance(DynamicObj):
         pass
 
 
-DirectoryInstance_reflection = _expr433
+DirectoryInstance_reflection = _expr428
 
 def DirectoryInstance__ctor(__unit: None=None) -> DirectoryInstance:
     return DirectoryInstance(__unit)
 
 
-def _expr434() -> TypeInfo:
+def _expr429() -> TypeInfo:
     return record_type("ARCtrl.CWL.DirentInstance", [], DirentInstance, lambda: [("Entry", string_type), ("Entryname", option_type(string_type)), ("Writable", option_type(bool_type))])
 
 
@@ -48,9 +48,9 @@ class DirentInstance(Record):
     Entryname: str | None
     Writable: bool | None
 
-DirentInstance_reflection = _expr434
+DirentInstance_reflection = _expr429
 
-def _expr435() -> TypeInfo:
+def _expr430() -> TypeInfo:
     return union_type("ARCtrl.CWL.CWLType", [], CWLType, lambda: [[("Item", FileInstance_reflection())], [("Item", DirectoryInstance_reflection())], [("Item", DirentInstance_reflection())], [], [], [], [], [], [], [], [], [("Item", CWLType_reflection())]])
 
 
@@ -65,9 +65,9 @@ class CWLType(Union):
         return ["File", "Directory", "Dirent", "String", "Int", "Long", "Float", "Double", "Boolean", "Stdout", "Null", "Array"]
 
 
-CWLType_reflection = _expr435
+CWLType_reflection = _expr430
 
-def _expr438() -> TypeInfo:
+def _expr431() -> TypeInfo:
     return class_type("ARCtrl.CWL.InputRecordSchema", None, InputRecordSchema, DynamicObj_reflection())
 
 
@@ -77,13 +77,13 @@ class InputRecordSchema(DynamicObj):
         pass
 
 
-InputRecordSchema_reflection = _expr438
+InputRecordSchema_reflection = _expr431
 
 def InputRecordSchema__ctor(__unit: None=None) -> InputRecordSchema:
     return InputRecordSchema(__unit)
 
 
-def _expr441() -> TypeInfo:
+def _expr432() -> TypeInfo:
     return class_type("ARCtrl.CWL.InputEnumSchema", None, InputEnumSchema, DynamicObj_reflection())
 
 
@@ -93,13 +93,13 @@ class InputEnumSchema(DynamicObj):
         pass
 
 
-InputEnumSchema_reflection = _expr441
+InputEnumSchema_reflection = _expr432
 
 def InputEnumSchema__ctor(__unit: None=None) -> InputEnumSchema:
     return InputEnumSchema(__unit)
 
 
-def _expr445() -> TypeInfo:
+def _expr433() -> TypeInfo:
     return class_type("ARCtrl.CWL.InputArraySchema", None, InputArraySchema, DynamicObj_reflection())
 
 
@@ -109,13 +109,13 @@ class InputArraySchema(DynamicObj):
         pass
 
 
-InputArraySchema_reflection = _expr445
+InputArraySchema_reflection = _expr433
 
 def InputArraySchema__ctor(__unit: None=None) -> InputArraySchema:
     return InputArraySchema(__unit)
 
 
-def _expr446() -> TypeInfo:
+def _expr435() -> TypeInfo:
     return class_type("ARCtrl.CWL.SchemaDefRequirementType", None, SchemaDefRequirementType, DynamicObj_reflection())
 
 
@@ -128,13 +128,13 @@ class SchemaDefRequirementType(DynamicObj):
         set_property("types", definitions, this.contents)
 
 
-SchemaDefRequirementType_reflection = _expr446
+SchemaDefRequirementType_reflection = _expr435
 
 def SchemaDefRequirementType__ctor_541DA560(types: Any=None, definitions: Any=None) -> SchemaDefRequirementType:
     return SchemaDefRequirementType(types, definitions)
 
 
-def _expr448() -> TypeInfo:
+def _expr436() -> TypeInfo:
     return record_type("ARCtrl.CWL.SoftwarePackage", [], SoftwarePackage, lambda: [("Package", string_type), ("Version", option_type(array_type(string_type))), ("Specs", option_type(array_type(string_type)))])
 
 
@@ -144,7 +144,7 @@ class SoftwarePackage(Record):
     Version: Array[str] | None
     Specs: Array[str] | None
 
-SoftwarePackage_reflection = _expr448
+SoftwarePackage_reflection = _expr436
 
 __all__ = ["FileInstance_reflection", "DirectoryInstance_reflection", "DirentInstance_reflection", "CWLType_reflection", "InputRecordSchema_reflection", "InputEnumSchema_reflection", "InputArraySchema_reflection", "SchemaDefRequirementType_reflection", "SoftwarePackage_reflection"]
 

{arctrl-2.2.2 → arctrl-2.2.4}/arctrl/CWL/decode.py

@@ -172,20 +172,20 @@ def Decode_decodeStringOrExpression(y_ele: YAMLElement) -> str:
 
 
 
-def _arrow515(value_1: YAMLElement) -> OutputBinding:
+def _arrow518(value_1: YAMLElement) -> OutputBinding:
     def getter(get: IGetters) -> OutputBinding:
-        def _arrow514(__unit: None=None, get: Any=get) -> str | None:
+        def _arrow517(__unit: None=None, get: Any=get) -> str | None:
             object_arg: IOptionalGetter = get.Optional
             return object_arg.Field("glob", string)
 
-        return OutputBinding(_arrow514())
+        return OutputBinding(_arrow517())
 
     return object(getter, value_1)
 
 
-Decode_outputBindingGlobDecoder: Callable[[YAMLElement], OutputBinding] = _arrow515
+Decode_outputBindingGlobDecoder: Callable[[YAMLElement], OutputBinding] = _arrow518
 
-def _arrow516(value: YAMLElement) -> OutputBinding | None:
+def _arrow519(value: YAMLElement) -> OutputBinding | None:
     def getter(get: IGetters) -> OutputBinding | None:
         object_arg: IOptionalGetter = get.Optional
         return object_arg.Field("outputBinding", Decode_outputBindingGlobDecoder)
@@ -193,30 +193,30 @@ def _arrow516(value: YAMLElement) -> OutputBinding | None:
     return object(getter, value)
 
 
-Decode_outputBindingDecoder: Callable[[YAMLElement], OutputBinding | None] = _arrow516
+Decode_outputBindingDecoder: Callable[[YAMLElement], OutputBinding | None] = _arrow519
 
-def _arrow520(value_1: YAMLElement) -> CWLType:
+def _arrow523(value_1: YAMLElement) -> CWLType:
     def getter(get: IGetters) -> CWLType:
-        def _arrow517(__unit: None=None, get: Any=get) -> str:
+        def _arrow520(__unit: None=None, get: Any=get) -> str:
             object_arg: IRequiredGetter = get.Required
             return object_arg.Field("entry", Decode_decodeStringOrExpression)
 
-        def _arrow518(__unit: None=None, get: Any=get) -> str | None:
+        def _arrow521(__unit: None=None, get: Any=get) -> str | None:
             object_arg_1: IOptionalGetter = get.Optional
             return object_arg_1.Field("entryname", Decode_decodeStringOrExpression)
 
-        def _arrow519(__unit: None=None, get: Any=get) -> bool | None:
+        def _arrow522(__unit: None=None, get: Any=get) -> bool | None:
             object_arg_2: IOptionalGetter = get.Optional
             return object_arg_2.Field("writable", bool_1)
 
-        return CWLType(2, DirentInstance(_arrow517(), _arrow518(), _arrow519()))
+        return CWLType(2, DirentInstance(_arrow520(), _arrow521(), _arrow522()))
 
     return object(getter, value_1)
 
 
-Decode_direntDecoder: Callable[[YAMLElement], CWLType] = _arrow520
+Decode_direntDecoder: Callable[[YAMLElement], CWLType] = _arrow523
 
-def _arrow522(value_1: YAMLElement) -> CWLType:
+def _arrow525(value_1: YAMLElement) -> CWLType:
     def getter(get: IGetters) -> CWLType:
         items: str
         object_arg: IRequiredGetter = get.Required
@@ -231,11 +231,11 @@ def _arrow522(value_1: YAMLElement) -> CWLType:
             return CWLType(11, CWLType(1, DirectoryInstance__ctor()))
 
         elif items == "Dirent":
-            def _arrow521(__unit: None=None, get: Any=get) -> CWLType:
+            def _arrow524(__unit: None=None, get: Any=get) -> CWLType:
                 object_arg_1: IRequiredGetter = get.Required
                 return object_arg_1.Field("listing", Decode_direntDecoder)
 
-            return CWLType(11, _arrow521())
+            return CWLType(11, _arrow524())
 
         elif items == "string":
             return CWLType(11, CWLType(3))
@@ -262,26 +262,26 @@ def _arrow522(value_1: YAMLElement) -> CWLType:
     return object(getter, value_1)
 
 
-Decode_cwlArrayTypeDecoder: Callable[[YAMLElement], CWLType] = _arrow522
+Decode_cwlArrayTypeDecoder: Callable[[YAMLElement], CWLType] = _arrow525
 
 def Decode_cwlTypeStringMatcher(t: str, get: IGetters) -> tuple[CWLType, bool]:
     pattern_input: tuple[bool, str] = ((True, replace(t, "?", ""))) if ends_with(t, "?") else ((False, t))
     new_t: str = pattern_input[1]
-    def _arrow523(__unit: None=None, t: Any=t, get: Any=get) -> CWLType:
+    def _arrow526(__unit: None=None, t: Any=t, get: Any=get) -> CWLType:
         object_arg: IRequiredGetter = get.Required
         return object_arg.Field("listing", Decode_direntDecoder)
 
-    def _arrow524(__unit: None=None, t: Any=t, get: Any=get) -> CWLType:
+    def _arrow527(__unit: None=None, t: Any=t, get: Any=get) -> CWLType:
         object_arg_1: IRequiredGetter = get.Required
         return object_arg_1.Field("listing", Decode_direntDecoder)
 
-    def _arrow525(__unit: None=None, t: Any=t, get: Any=get) -> CWLType:
+    def _arrow528(__unit: None=None, t: Any=t, get: Any=get) -> CWLType:
         raise Exception("Invalid CWL type")
 
-    return (CWLType(0, FileInstance__ctor()) if (new_t == "File") else (CWLType(1, DirectoryInstance__ctor()) if (new_t == "Directory") else (_arrow523() if (new_t == "Dirent") else (CWLType(3) if (new_t == "string") else (CWLType(4) if (new_t == "int") else (CWLType(5) if (new_t == "long") else (CWLType(6) if (new_t == "float") else (CWLType(7) if (new_t == "double") else (CWLType(8) if (new_t == "boolean") else (CWLType(11, CWLType(0, FileInstance__ctor())) if (new_t == "File[]") else (CWLType(11, CWLType(1, DirectoryInstance__ctor())) if (new_t == "Directory[]") else (CWLType(11, _arrow524()) if (new_t == "Dirent[]") else (CWLType(11, CWLType(3)) if (new_t == "string[]") else (CWLType(11, CWLType(4)) if (new_t == "int[]") else (CWLType(11, CWLType(5)) if (new_t == "long[]") else (CWLType(11, CWLType(6)) if (new_t == "float[]") else (CWLType(11, CWLType(7)) if (new_t == "double[]") else (CWLType(11, CWLType(8)) if (new_t == "boolean[]") else (CWLType(9) if (new_t == "stdout") else (CWLType(10) if (new_t == "null") else _arrow525()))))))))))))))))))), pattern_input[0])
+    return (CWLType(0, FileInstance__ctor()) if (new_t == "File") else (CWLType(1, DirectoryInstance__ctor()) if (new_t == "Directory") else (_arrow526() if (new_t == "Dirent") else (CWLType(3) if (new_t == "string") else (CWLType(4) if (new_t == "int") else (CWLType(5) if (new_t == "long") else (CWLType(6) if (new_t == "float") else (CWLType(7) if (new_t == "double") else (CWLType(8) if (new_t == "boolean") else (CWLType(11, CWLType(0, FileInstance__ctor())) if (new_t == "File[]") else (CWLType(11, CWLType(1, DirectoryInstance__ctor())) if (new_t == "Directory[]") else (CWLType(11, _arrow527()) if (new_t == "Dirent[]") else (CWLType(11, CWLType(3)) if (new_t == "string[]") else (CWLType(11, CWLType(4)) if (new_t == "int[]") else (CWLType(11, CWLType(5)) if (new_t == "long[]") else (CWLType(11, CWLType(6)) if (new_t == "float[]") else (CWLType(11, CWLType(7)) if (new_t == "double[]") else (CWLType(11, CWLType(8)) if (new_t == "boolean[]") else (CWLType(9) if (new_t == "stdout") else (CWLType(10) if (new_t == "null") else _arrow528()))))))))))))))))))), pattern_input[0])
 
 
-def _arrow527(value_1: YAMLElement) -> tuple[CWLType, bool]:
+def _arrow530(value_1: YAMLElement) -> tuple[CWLType, bool]:
     def getter(get: IGetters) -> tuple[CWLType, bool]:
         cwl_type: str | None
         object_arg: IRequiredGetter = get.Required
@@ -325,11 +325,11 @@ def _arrow527(value_1: YAMLElement) -> tuple[CWLType, bool]:
 
         cwl_type = object_arg.Field("type", arg_1)
         if cwl_type is None:
-            def _arrow526(__unit: None=None, get: Any=get) -> CWLType:
+            def _arrow529(__unit: None=None, get: Any=get) -> CWLType:
                 object_arg_1: IRequiredGetter = get.Required
                 return object_arg_1.Field("type", Decode_cwlArrayTypeDecoder)
 
-            return (_arrow526(), False)
+            return (_arrow529(), False)
 
         else: 
             return Decode_cwlTypeStringMatcher(cwl_type, get)
@@ -338,7 +338,7 @@ def _arrow527(value_1: YAMLElement) -> tuple[CWLType, bool]:
     return object(getter, value_1)
 
 
-Decode_cwlTypeDecoder: Callable[[YAMLElement], tuple[CWLType, bool]] = _arrow527
+Decode_cwlTypeDecoder: Callable[[YAMLElement], tuple[CWLType, bool]] = _arrow530
 
 def _arrow537(value_2: YAMLElement) -> Array[CWLOutput]:
     def getter(get: IGetters) -> Array[CWLOutput]:

{arctrl-2.2.2 → arctrl-2.2.4}/arctrl/Contract/datamap.py

@@ -168,11 +168,11 @@ def ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static(study_identifier:
             if c.DTOType.tag == 3:
                 if c.DTO is not None:
                     if c.DTO.tag == 0:
-                        def _arrow3082(__unit: None=None, study_identifier: Any=study_identifier, c: Any=c) -> bool:
+                        def _arrow3083(__unit: None=None, study_identifier: Any=study_identifier, c: Any=c) -> bool:
                             fsworkbook: Any = c.DTO.fields[0]
                             return c.Path == path
 
-                        if _arrow3082():
+                        if _arrow3083():
                             pattern_matching_result = 0
                             fsworkbook_1 = c.DTO.fields[0]
                             p_1 = c.Path

{arctrl-2.2.2 → arctrl-2.2.4}/arctrl/Contract/validation_packages_config.py

@@ -13,10 +13,10 @@ ValidationPackagesConfigHelper_ReadContract: Contract = Contract("READ", Validat
 
 def ValidationPackagesConfigExtensions__007CValidationPackagesYamlPath_007C__007C(input: Array[str]) -> str | None:
     (pattern_matching_result,) = (None,)
-    def _arrow3083(x: str, y: str, input: Any=input) -> bool:
+    def _arrow3082(x: str, y: str, input: Any=input) -> bool:
         return x == y
 
-    if (len(input) == 2) if (not equals_with(_arrow3083, input, None)) else False:
+    if (len(input) == 2) if (not equals_with(_arrow3082, input, None)) else False:
         if input[0] == ".arc":
             if input[1] == "validation_packages.yml":
                 pattern_matching_result = 0

{arctrl-2.2.2 → arctrl-2.2.4}/arctrl/Core/Helper/hash_codes.py

@@ -31,15 +31,15 @@ def hash_1(obj: Any | None=None) -> int:
 
 
 def box_hash_option(a: Any | None=None) -> Any:
-    def _arrow528(__unit: None=None, a: Any=a) -> int:
+    def _arrow514(__unit: None=None, a: Any=a) -> int:
         copy_of_struct: _A = value_1(a)
         return identity_hash(copy_of_struct)
 
-    def _arrow529(__unit: None=None, a: Any=a) -> int:
+    def _arrow515(__unit: None=None, a: Any=a) -> int:
         copy_of_struct_1: int = 0
         return number_hash(copy_of_struct_1)
 
-    return _arrow528() if (a is not None) else _arrow529()
+    return _arrow514() if (a is not None) else _arrow515()
 
 
 def box_hash_array(a: Array[Any]) -> Any:

{arctrl-2.2.2 → arctrl-2.2.4}/arctrl/Core/Helper/identifier.py

@@ -23,11 +23,11 @@ def check_valid_characters(identifier: str) -> None:
 
 
 def create_missing_identifier(__unit: None=None) -> str:
-    def _arrow530(__unit: None=None) -> str:
+    def _arrow516(__unit: None=None) -> str:
         copy_of_struct: str = new_guid()
         return str(copy_of_struct)
 
-    return "MISSING_IDENTIFIER_" + _arrow530()
+    return "MISSING_IDENTIFIER_" + _arrow516()
 
 
 def is_missing_identifier(str_1: str) -> bool:

{arctrl-2.2.2 → arctrl-2.2.4}/arctrl/Core/Process/component.py

@@ -13,7 +13,7 @@ from ..Helper.regex import ActivePatterns__007CRegex_007C__007C
 from ..ontology_annotation import (OntologyAnnotation, OntologyAnnotation_reflection)
 from ..value import (Value, Value_reflection)
 
-def _expr659() -> TypeInfo:
+def _expr660() -> TypeInfo:
     return record_type("ARCtrl.Process.Component", [], Component, lambda: [("ComponentValue", option_type(Value_reflection())), ("ComponentUnit", option_type(OntologyAnnotation_reflection())), ("ComponentType", option_type(OntologyAnnotation_reflection()))])
 
 
@@ -48,7 +48,7 @@ class Component(Record):
         return this.ComponentUnit
 
 
-Component_reflection = _expr659
+Component_reflection = _expr660
 
 def Component__get_ComponentName(this: Component) -> str | None:
     def mapping(v: Value, this: Any=this) -> str:

{arctrl-2.2.2 → arctrl-2.2.4}/arctrl/Core/Process/protocol_parameter.py

@@ -9,7 +9,7 @@ from ..comment import Comment
 from ..Helper.collections_ import Option_fromValueWithDefault
 from ..ontology_annotation import (OntologyAnnotation, OntologyAnnotation_reflection)
 
-def _expr660() -> TypeInfo:
+def _expr659() -> TypeInfo:
     return record_type("ARCtrl.Process.ProtocolParameter", [], ProtocolParameter, lambda: [("ID", option_type(string_type)), ("ParameterName", option_type(OntologyAnnotation_reflection()))])
 
 
@@ -92,7 +92,7 @@ class ProtocolParameter(Record):
         return "OA " + this.NameText
 
 
-ProtocolParameter_reflection = _expr660
+ProtocolParameter_reflection = _expr659
 
 __all__ = ["ProtocolParameter_reflection"]
 

{arctrl-2.2.2 → arctrl-2.2.4}/arctrl/Core/Table/composite_column.py

@@ -9,7 +9,7 @@ from ..ontology_annotation import OntologyAnnotation
 from .composite_cell import (CompositeCell, CompositeCell_reflection)
 from .composite_header import (CompositeHeader, CompositeHeader_reflection)
 
-def _expr714() -> TypeInfo:
+def _expr713() -> TypeInfo:
     return record_type("ARCtrl.CompositeColumn", [], CompositeColumn, lambda: [("Header", CompositeHeader_reflection()), ("Cells", array_type(CompositeCell_reflection()))])
 
 
@@ -67,7 +67,7 @@ class CompositeColumn(Record):
         return this.Header.IsUnique
 
 
-CompositeColumn_reflection = _expr714
+CompositeColumn_reflection = _expr713
 
 __all__ = ["CompositeColumn_reflection"]
 

{arctrl-2.2.2 → arctrl-2.2.4}/arctrl/Core/Table/composite_header.py

@@ -40,11 +40,11 @@ class IOType(Union):
     def as_input(self, __unit: None=None) -> str:
         this: IOType = self
         def string_create(x: Any | None=None) -> str:
-            def _arrow713(__unit: None=None, x: Any=x) -> str:
+            def _arrow714(__unit: None=None, x: Any=x) -> str:
                 copy_of_struct: __A = x
                 return to_string(copy_of_struct)
 
-            return ("Input [" + _arrow713()) + "]"
+            return ("Input [" + _arrow714()) + "]"
 
         return string_create(this.fields[0]) if (this.tag == 4) else string_create(this)