arctrl 3.0.0a3__py3-none-any.whl

arctrl/py/Json/ontology_annotation.py

@@ -0,0 +1,404 @@
+from __future__ import annotations
+from collections.abc import Callable
+from typing import (Any, TypeVar)
+from ..fable_modules.fable_library.list import (of_array, choose, FSharpList)
+from ..fable_modules.fable_library.option import map as map_1
+from ..fable_modules.fable_library.seq import (map as map_2, filter)
+from ..fable_modules.fable_library.string_ import replace
+from ..fable_modules.fable_library.types import (to_string, Array)
+from ..fable_modules.fable_library.util import (int32_to_string, IEnumerable_1)
+from ..fable_modules.thoth_json_core.decode import (one_of, map, int_1, float_1, string, object, IOptionalGetter, resize_array, IGetters)
+from ..fable_modules.thoth_json_core.types import (Decoder_1, IEncodable, IEncoderHelpers_1)
+from ..Core.comment import Comment
+from ..Core.ontology_annotation import OntologyAnnotation
+from ..Core.Process.column_index import order_name
+from ..Core.uri import URIModule_toString
+from .comment import (encoder, decoder, ROCrate_encoderDisambiguatingDescription, ROCrate_decoderDisambiguatingDescription)
+from .context.rocrate.isa_ontology_annotation_context import context_jsonvalue
+from .context.rocrate.property_value_context import context_jsonvalue as context_jsonvalue_1
+from .encode import (try_include, try_include_seq)
+from .idtable import encode
+from .string_table import (encode_string, decode_string)
+
+__A_ = TypeVar("__A_")
+
+AnnotationValue_decoder: Decoder_1[str] = one_of(of_array([map(int32_to_string, int_1), map(to_string, float_1), string]))
+
+def OntologyAnnotation_encoder(oa: OntologyAnnotation) -> IEncodable:
+    def chooser(tupled_arg: tuple[str, IEncodable | None], oa: Any=oa) -> tuple[str, IEncodable] | None:
+        def mapping(v_1: IEncodable, tupled_arg: Any=tupled_arg) -> tuple[str, IEncodable]:
+            return (tupled_arg[0], v_1)
+
+        return map_1(mapping, tupled_arg[1])
+
+    def _arrow2007(value: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2006(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr2006()
+
+    def _arrow2009(value_2: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2008(IEncodable):
+            def Encode(self, helpers_1: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_1.encode_string(value_2)
+
+        return ObjectExpr2008()
+
+    def _arrow2011(value_4: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2010(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_4)
+
+        return ObjectExpr2010()
+
+    def _arrow2012(comment: Comment, oa: Any=oa) -> IEncodable:
+        return encoder(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([try_include("annotationValue", _arrow2007, oa.Name), try_include("termSource", _arrow2009, oa.TermSourceREF), try_include("termAccession", _arrow2011, oa.TermAccessionNumber), try_include_seq("comments", _arrow2012, oa.Comments)]))
+    class ObjectExpr2013(IEncodable):
+        def Encode(self, helpers_3: IEncoderHelpers_1[Any], oa: Any=oa) -> Any:
+            def mapping_1(tupled_arg_1: tuple[str, IEncodable]) -> tuple[str, __A_]:
+                return (tupled_arg_1[0], tupled_arg_1[1].Encode(helpers_3))
+
+            arg: IEnumerable_1[tuple[str, __A_]] = map_2(mapping_1, values)
+            return helpers_3.encode_object(arg)
+
+    return ObjectExpr2013()
+
+
+def _arrow2018(get: IGetters) -> OntologyAnnotation:
+    def _arrow2014(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("annotationValue", AnnotationValue_decoder)
+
+    def _arrow2015(__unit: None=None) -> str | None:
+        object_arg_1: IOptionalGetter = get.Optional
+        return object_arg_1.Field("termSource", string)
+
+    def _arrow2016(__unit: None=None) -> str | None:
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("termAccession", string)
+
+    def _arrow2017(__unit: None=None) -> Array[Comment] | None:
+        arg_7: Decoder_1[Array[Comment]] = resize_array(decoder)
+        object_arg_3: IOptionalGetter = get.Optional
+        return object_arg_3.Field("comments", arg_7)
+
+    return OntologyAnnotation.create(_arrow2014(), _arrow2015(), _arrow2016(), _arrow2017())
+
+
+OntologyAnnotation_decoder: Decoder_1[OntologyAnnotation] = object(_arrow2018)
+
+def OntologyAnnotation_compressedEncoder(string_table: Any, oa: OntologyAnnotation) -> IEncodable:
+    def chooser(tupled_arg: tuple[str, IEncodable | None], string_table: Any=string_table, oa: Any=oa) -> tuple[str, IEncodable] | None:
+        def mapping(v_1: IEncodable, tupled_arg: Any=tupled_arg) -> tuple[str, IEncodable]:
+            return (tupled_arg[0], v_1)
+
+        return map_1(mapping, tupled_arg[1])
+
+    def _arrow2020(s: str, string_table: Any=string_table, oa: Any=oa) -> IEncodable:
+        return encode_string(string_table, s)
+
+    def _arrow2021(s_1: str, string_table: Any=string_table, oa: Any=oa) -> IEncodable:
+        return encode_string(string_table, s_1)
+
+    def _arrow2022(s_2: str, string_table: Any=string_table, oa: Any=oa) -> IEncodable:
+        return encode_string(string_table, s_2)
+
+    def _arrow2023(comment: Comment, string_table: Any=string_table, oa: Any=oa) -> IEncodable:
+        return encoder(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([try_include("a", _arrow2020, oa.Name), try_include("ts", _arrow2021, oa.TermSourceREF), try_include("ta", _arrow2022, oa.TermAccessionNumber), try_include_seq("comments", _arrow2023, oa.Comments)]))
+    class ObjectExpr2024(IEncodable):
+        def Encode(self, helpers: IEncoderHelpers_1[Any], string_table: Any=string_table, oa: Any=oa) -> Any:
+            def mapping_1(tupled_arg_1: tuple[str, IEncodable]) -> tuple[str, __A_]:
+                return (tupled_arg_1[0], tupled_arg_1[1].Encode(helpers))
+
+            arg: IEnumerable_1[tuple[str, __A_]] = map_2(mapping_1, values)
+            return helpers.encode_object(arg)
+
+    return ObjectExpr2024()
+
+
+def OntologyAnnotation_compressedDecoder(string_table: Array[str]) -> Decoder_1[OntologyAnnotation]:
+    def _arrow2029(get: IGetters, string_table: Any=string_table) -> OntologyAnnotation:
+        def _arrow2025(__unit: None=None) -> str | None:
+            arg_1: Decoder_1[str] = decode_string(string_table)
+            object_arg: IOptionalGetter = get.Optional
+            return object_arg.Field("a", arg_1)
+
+        def _arrow2026(__unit: None=None) -> str | None:
+            arg_3: Decoder_1[str] = decode_string(string_table)
+            object_arg_1: IOptionalGetter = get.Optional
+            return object_arg_1.Field("ts", arg_3)
+
+        def _arrow2027(__unit: None=None) -> str | None:
+            arg_5: Decoder_1[str] = decode_string(string_table)
+            object_arg_2: IOptionalGetter = get.Optional
+            return object_arg_2.Field("ta", arg_5)
+
+        def _arrow2028(__unit: None=None) -> Array[Comment] | None:
+            arg_7: Decoder_1[Array[Comment]] = resize_array(decoder)
+            object_arg_3: IOptionalGetter = get.Optional
+            return object_arg_3.Field("comments", arg_7)
+
+        return OntologyAnnotation(_arrow2025(), _arrow2026(), _arrow2027(), _arrow2028())
+
+    return object(_arrow2029)
+
+
+def OntologyAnnotation_ROCrate_genID(o: OntologyAnnotation) -> str:
+    match_value: str | None = o.TermAccessionNumber
+    if match_value is None:
+        match_value_1: str | None = o.TermSourceREF
+        if match_value_1 is None:
+            match_value_2: str | None = o.Name
+            if match_value_2 is None:
+                return "#DummyOntologyAnnotation"
+
+            else: 
+                return "#UserTerm_" + replace(match_value_2, " ", "_")
+
+
+        else: 
+            return "#" + replace(match_value_1, " ", "_")
+
+
+    else: 
+        return URIModule_toString(match_value)
+
+
+
+def OntologyAnnotation_ROCrate_encoderDefinedTerm(oa: OntologyAnnotation) -> IEncodable:
+    def chooser(tupled_arg: tuple[str, IEncodable | None], oa: Any=oa) -> tuple[str, IEncodable] | None:
+        def mapping(v_1: IEncodable, tupled_arg: Any=tupled_arg) -> tuple[str, IEncodable]:
+            return (tupled_arg[0], v_1)
+
+        return map_1(mapping, tupled_arg[1])
+
+    def _arrow2033(__unit: None=None, oa: Any=oa) -> IEncodable:
+        value: str = OntologyAnnotation_ROCrate_genID(oa)
+        class ObjectExpr2032(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr2032()
+
+    class ObjectExpr2034(IEncodable):
+        def Encode(self, helpers_1: IEncoderHelpers_1[Any], oa: Any=oa) -> Any:
+            return helpers_1.encode_string("OntologyAnnotation")
+
+    def _arrow2036(value_2: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2035(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_2)
+
+        return ObjectExpr2035()
+
+    def _arrow2038(value_4: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2037(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_4)
+
+        return ObjectExpr2037()
+
+    def _arrow2040(value_6: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2039(IEncodable):
+            def Encode(self, helpers_4: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_4.encode_string(value_6)
+
+        return ObjectExpr2039()
+
+    def _arrow2041(comment: Comment, oa: Any=oa) -> IEncodable:
+        return ROCrate_encoderDisambiguatingDescription(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([("@id", _arrow2033()), ("@type", ObjectExpr2034()), try_include("annotationValue", _arrow2036, oa.Name), try_include("termSource", _arrow2038, oa.TermSourceREF), try_include("termAccession", _arrow2040, oa.TermAccessionNumber), try_include_seq("comments", _arrow2041, oa.Comments), ("@context", context_jsonvalue)]))
+    class ObjectExpr2042(IEncodable):
+        def Encode(self, helpers_5: IEncoderHelpers_1[Any], oa: Any=oa) -> Any:
+            def mapping_1(tupled_arg_1: tuple[str, IEncodable]) -> tuple[str, __A_]:
+                return (tupled_arg_1[0], tupled_arg_1[1].Encode(helpers_5))
+
+            arg: IEnumerable_1[tuple[str, __A_]] = map_2(mapping_1, values)
+            return helpers_5.encode_object(arg)
+
+    return ObjectExpr2042()
+
+
+def _arrow2047(get: IGetters) -> OntologyAnnotation:
+    def _arrow2043(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("annotationValue", AnnotationValue_decoder)
+
+    def _arrow2044(__unit: None=None) -> str | None:
+        object_arg_1: IOptionalGetter = get.Optional
+        return object_arg_1.Field("termSource", string)
+
+    def _arrow2045(__unit: None=None) -> str | None:
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("termAccession", string)
+
+    def _arrow2046(__unit: None=None) -> Array[Comment] | None:
+        arg_7: Decoder_1[Array[Comment]] = resize_array(ROCrate_decoderDisambiguatingDescription)
+        object_arg_3: IOptionalGetter = get.Optional
+        return object_arg_3.Field("comments", arg_7)
+
+    return OntologyAnnotation.create(_arrow2043(), _arrow2044(), _arrow2045(), _arrow2046())
+
+
+OntologyAnnotation_ROCrate_decoderDefinedTerm: Decoder_1[OntologyAnnotation] = object(_arrow2047)
+
+def OntologyAnnotation_ROCrate_encoderPropertyValue(oa: OntologyAnnotation) -> IEncodable:
+    def chooser(tupled_arg: tuple[str, IEncodable | None], oa: Any=oa) -> tuple[str, IEncodable] | None:
+        def mapping(v_1: IEncodable, tupled_arg: Any=tupled_arg) -> tuple[str, IEncodable]:
+            return (tupled_arg[0], v_1)
+
+        return map_1(mapping, tupled_arg[1])
+
+    def _arrow2051(__unit: None=None, oa: Any=oa) -> IEncodable:
+        value: str = OntologyAnnotation_ROCrate_genID(oa)
+        class ObjectExpr2050(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr2050()
+
+    class ObjectExpr2052(IEncodable):
+        def Encode(self, helpers_1: IEncoderHelpers_1[Any], oa: Any=oa) -> Any:
+            return helpers_1.encode_string("PropertyValue")
+
+    def _arrow2054(value_2: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2053(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_2)
+
+        return ObjectExpr2053()
+
+    def _arrow2056(value_4: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2055(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_4)
+
+        return ObjectExpr2055()
+
+    def _arrow2057(comment: Comment, oa: Any=oa) -> IEncodable:
+        return ROCrate_encoderDisambiguatingDescription(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([("@id", _arrow2051()), ("@type", ObjectExpr2052()), try_include("category", _arrow2054, oa.Name), try_include("categoryCode", _arrow2056, oa.TermAccessionNumber), try_include_seq("comments", _arrow2057, oa.Comments), ("@context", context_jsonvalue_1)]))
+    class ObjectExpr2058(IEncodable):
+        def Encode(self, helpers_4: IEncoderHelpers_1[Any], oa: Any=oa) -> Any:
+            def mapping_1(tupled_arg_1: tuple[str, IEncodable]) -> tuple[str, __A_]:
+                return (tupled_arg_1[0], tupled_arg_1[1].Encode(helpers_4))
+
+            arg: IEnumerable_1[tuple[str, __A_]] = map_2(mapping_1, values)
+            return helpers_4.encode_object(arg)
+
+    return ObjectExpr2058()
+
+
+def _arrow2062(get: IGetters) -> OntologyAnnotation:
+    def _arrow2059(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("category", string)
+
+    def _arrow2060(__unit: None=None) -> str | None:
+        object_arg_1: IOptionalGetter = get.Optional
+        return object_arg_1.Field("categoryCode", string)
+
+    def _arrow2061(__unit: None=None) -> Array[Comment] | None:
+        arg_5: Decoder_1[Array[Comment]] = resize_array(ROCrate_decoderDisambiguatingDescription)
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("comments", arg_5)
+
+    return OntologyAnnotation.create(_arrow2059(), None, _arrow2060(), _arrow2061())
+
+
+OntologyAnnotation_ROCrate_decoderPropertyValue: Decoder_1[OntologyAnnotation] = object(_arrow2062)
+
+def OntologyAnnotation_ISAJson_encoder(id_map: Any | None, oa: OntologyAnnotation) -> IEncodable:
+    def f(oa_1: OntologyAnnotation, id_map: Any=id_map, oa: Any=oa) -> IEncodable:
+        def predicate(c: Comment, oa_1: Any=oa_1) -> bool:
+            match_value: str | None = c.Name
+            (pattern_matching_result,) = (None,)
+            if match_value is not None:
+                if match_value == order_name:
+                    pattern_matching_result = 0
+
+                else: 
+                    pattern_matching_result = 1
+
+
+            else: 
+                pattern_matching_result = 1
+
+            if pattern_matching_result == 0:
+                return False
+
+            elif pattern_matching_result == 1:
+                return True
+
+
+        comments: IEnumerable_1[Comment] = filter(predicate, oa_1.Comments)
+        def chooser(tupled_arg: tuple[str, IEncodable | None], oa_1: Any=oa_1) -> tuple[str, IEncodable] | None:
+            def mapping(v_1: IEncodable, tupled_arg: Any=tupled_arg) -> tuple[str, IEncodable]:
+                return (tupled_arg[0], v_1)
+
+            return map_1(mapping, tupled_arg[1])
+
+        def _arrow2066(value: str, oa_1: Any=oa_1) -> IEncodable:
+            class ObjectExpr2065(IEncodable):
+                def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers.encode_string(value)
+
+            return ObjectExpr2065()
+
+        def _arrow2068(value_2: str, oa_1: Any=oa_1) -> IEncodable:
+            class ObjectExpr2067(IEncodable):
+                def Encode(self, helpers_1: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_1.encode_string(value_2)
+
+            return ObjectExpr2067()
+
+        def _arrow2070(value_4: str, oa_1: Any=oa_1) -> IEncodable:
+            class ObjectExpr2069(IEncodable):
+                def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_2.encode_string(value_4)
+
+            return ObjectExpr2069()
+
+        def _arrow2072(value_6: str, oa_1: Any=oa_1) -> IEncodable:
+            class ObjectExpr2071(IEncodable):
+                def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_3.encode_string(value_6)
+
+            return ObjectExpr2071()
+
+        def _arrow2073(comment: Comment, oa_1: Any=oa_1) -> IEncodable:
+            return encoder(comment)
+
+        values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([try_include("@id", _arrow2066, OntologyAnnotation_ROCrate_genID(oa_1)), try_include("annotationValue", _arrow2068, oa_1.Name), try_include("termSource", _arrow2070, oa_1.TermSourceREF), try_include("termAccession", _arrow2072, oa_1.TermAccessionNumber), try_include_seq("comments", _arrow2073, comments)]))
+        class ObjectExpr2074(IEncodable):
+            def Encode(self, helpers_4: IEncoderHelpers_1[Any], oa_1: Any=oa_1) -> Any:
+                def mapping_1(tupled_arg_1: tuple[str, IEncodable]) -> tuple[str, __A_]:
+                    return (tupled_arg_1[0], tupled_arg_1[1].Encode(helpers_4))
+
+                arg: IEnumerable_1[tuple[str, __A_]] = map_2(mapping_1, values)
+                return helpers_4.encode_object(arg)
+
+        return ObjectExpr2074()
+
+    if id_map is not None:
+        def _arrow2075(o: OntologyAnnotation, id_map: Any=id_map, oa: Any=oa) -> str:
+            return OntologyAnnotation_ROCrate_genID(o)
+
+        return encode(_arrow2075, f, oa, id_map)
+
+    else: 
+        return f(oa)
+
+
+
+OntologyAnnotation_ISAJson_decoder: Decoder_1[OntologyAnnotation] = OntologyAnnotation_decoder
+
+__all__ = ["AnnotationValue_decoder", "OntologyAnnotation_encoder", "OntologyAnnotation_decoder", "OntologyAnnotation_compressedEncoder", "OntologyAnnotation_compressedDecoder", "OntologyAnnotation_ROCrate_genID", "OntologyAnnotation_ROCrate_encoderDefinedTerm", "OntologyAnnotation_ROCrate_decoderDefinedTerm", "OntologyAnnotation_ROCrate_encoderPropertyValue", "OntologyAnnotation_ROCrate_decoderPropertyValue", "OntologyAnnotation_ISAJson_encoder", "OntologyAnnotation_ISAJson_decoder"]
+

arctrl/py/Json/ontology_source_reference.py

@@ -0,0 +1,255 @@
+from __future__ import annotations
+from typing import (Any, TypeVar)
+from ..fable_modules.fable_library.list import (choose, of_array, FSharpList)
+from ..fable_modules.fable_library.option import map
+from ..fable_modules.fable_library.seq import map as map_1
+from ..fable_modules.fable_library.string_ import replace
+from ..fable_modules.fable_library.types import Array
+from ..fable_modules.fable_library.util import IEnumerable_1
+from ..fable_modules.thoth_json_core.decode import (object, IOptionalGetter, string, resize_array, IGetters)
+from ..fable_modules.thoth_json_core.types import (IEncodable, IEncoderHelpers_1, Decoder_1)
+from ..Core.comment import Comment
+from ..Core.ontology_source_reference import OntologySourceReference
+from .comment import (encoder as encoder_1, decoder as decoder_1, ISAJson_encoder as ISAJson_encoder_1)
+from .context.rocrate.isa_ontology_source_reference_context import context_jsonvalue
+from .decode import Decode_uri
+from .encode import (try_include, try_include_seq)
+
+__A_ = TypeVar("__A_")
+
+def encoder(osr: OntologySourceReference) -> IEncodable:
+    def chooser(tupled_arg: tuple[str, IEncodable | None], osr: Any=osr) -> tuple[str, IEncodable] | None:
+        def mapping(v_1: IEncodable, tupled_arg: Any=tupled_arg) -> tuple[str, IEncodable]:
+            return (tupled_arg[0], v_1)
+
+        return map(mapping, tupled_arg[1])
+
+    def _arrow2116(value: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2115(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr2115()
+
+    def _arrow2118(value_2: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2117(IEncodable):
+            def Encode(self, helpers_1: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_1.encode_string(value_2)
+
+        return ObjectExpr2117()
+
+    def _arrow2120(value_4: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2119(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_4)
+
+        return ObjectExpr2119()
+
+    def _arrow2122(value_6: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2121(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_6)
+
+        return ObjectExpr2121()
+
+    def _arrow2123(comment: Comment, osr: Any=osr) -> IEncodable:
+        return encoder_1(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([try_include("description", _arrow2116, osr.Description), try_include("file", _arrow2118, osr.File), try_include("name", _arrow2120, osr.Name), try_include("version", _arrow2122, osr.Version), try_include_seq("comments", _arrow2123, osr.Comments)]))
+    class ObjectExpr2124(IEncodable):
+        def Encode(self, helpers_4: IEncoderHelpers_1[Any], osr: Any=osr) -> Any:
+            def mapping_1(tupled_arg_1: tuple[str, IEncodable]) -> tuple[str, __A_]:
+                return (tupled_arg_1[0], tupled_arg_1[1].Encode(helpers_4))
+
+            arg: IEnumerable_1[tuple[str, __A_]] = map_1(mapping_1, values)
+            return helpers_4.encode_object(arg)
+
+    return ObjectExpr2124()
+
+
+def _arrow2130(get: IGetters) -> OntologySourceReference:
+    def _arrow2125(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("description", Decode_uri)
+
+    def _arrow2126(__unit: None=None) -> str | None:
+        object_arg_1: IOptionalGetter = get.Optional
+        return object_arg_1.Field("file", string)
+
+    def _arrow2127(__unit: None=None) -> str | None:
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("name", string)
+
+    def _arrow2128(__unit: None=None) -> str | None:
+        object_arg_3: IOptionalGetter = get.Optional
+        return object_arg_3.Field("version", string)
+
+    def _arrow2129(__unit: None=None) -> Array[Comment] | None:
+        arg_9: Decoder_1[Array[Comment]] = resize_array(decoder_1)
+        object_arg_4: IOptionalGetter = get.Optional
+        return object_arg_4.Field("comments", arg_9)
+
+    return OntologySourceReference(_arrow2125(), _arrow2126(), _arrow2127(), _arrow2128(), _arrow2129())
+
+
+decoder: Decoder_1[OntologySourceReference] = object(_arrow2130)
+
+def ROCrate_genID(o: OntologySourceReference) -> str:
+    match_value: str | None = o.File
+    if match_value is None:
+        match_value_1: str | None = o.Name
+        if match_value_1 is None:
+            return "#DummyOntologySourceRef"
+
+        else: 
+            return "#OntologySourceRef_" + replace(match_value_1, " ", "_")
+
+
+    else: 
+        return match_value
+
+
+
+def ROCrate_encoder(osr: OntologySourceReference) -> IEncodable:
+    def chooser(tupled_arg: tuple[str, IEncodable | None], osr: Any=osr) -> tuple[str, IEncodable] | None:
+        def mapping(v_1: IEncodable, tupled_arg: Any=tupled_arg) -> tuple[str, IEncodable]:
+            return (tupled_arg[0], v_1)
+
+        return map(mapping, tupled_arg[1])
+
+    def _arrow2134(__unit: None=None, osr: Any=osr) -> IEncodable:
+        value: str = ROCrate_genID(osr)
+        class ObjectExpr2133(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr2133()
+
+    class ObjectExpr2135(IEncodable):
+        def Encode(self, helpers_1: IEncoderHelpers_1[Any], osr: Any=osr) -> Any:
+            return helpers_1.encode_string("OntologySourceReference")
+
+    def _arrow2137(value_2: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2136(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_2)
+
+        return ObjectExpr2136()
+
+    def _arrow2139(value_4: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2138(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_4)
+
+        return ObjectExpr2138()
+
+    def _arrow2141(value_6: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2140(IEncodable):
+            def Encode(self, helpers_4: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_4.encode_string(value_6)
+
+        return ObjectExpr2140()
+
+    def _arrow2143(value_8: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2142(IEncodable):
+            def Encode(self, helpers_5: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_5.encode_string(value_8)
+
+        return ObjectExpr2142()
+
+    def _arrow2144(comment: Comment, osr: Any=osr) -> IEncodable:
+        return encoder_1(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([("@id", _arrow2134()), ("@type", ObjectExpr2135()), try_include("description", _arrow2137, osr.Description), try_include("file", _arrow2139, osr.File), try_include("name", _arrow2141, osr.Name), try_include("version", _arrow2143, osr.Version), try_include_seq("comments", _arrow2144, osr.Comments), ("@context", context_jsonvalue)]))
+    class ObjectExpr2145(IEncodable):
+        def Encode(self, helpers_6: IEncoderHelpers_1[Any], osr: Any=osr) -> Any:
+            def mapping_1(tupled_arg_1: tuple[str, IEncodable]) -> tuple[str, __A_]:
+                return (tupled_arg_1[0], tupled_arg_1[1].Encode(helpers_6))
+
+            arg: IEnumerable_1[tuple[str, __A_]] = map_1(mapping_1, values)
+            return helpers_6.encode_object(arg)
+
+    return ObjectExpr2145()
+
+
+def _arrow2151(get: IGetters) -> OntologySourceReference:
+    def _arrow2146(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("description", Decode_uri)
+
+    def _arrow2147(__unit: None=None) -> str | None:
+        object_arg_1: IOptionalGetter = get.Optional
+        return object_arg_1.Field("file", string)
+
+    def _arrow2148(__unit: None=None) -> str | None:
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("name", string)
+
+    def _arrow2149(__unit: None=None) -> str | None:
+        object_arg_3: IOptionalGetter = get.Optional
+        return object_arg_3.Field("version", string)
+
+    def _arrow2150(__unit: None=None) -> Array[Comment] | None:
+        arg_9: Decoder_1[Array[Comment]] = resize_array(decoder_1)
+        object_arg_4: IOptionalGetter = get.Optional
+        return object_arg_4.Field("comments", arg_9)
+
+    return OntologySourceReference(_arrow2146(), _arrow2147(), _arrow2148(), _arrow2149(), _arrow2150())
+
+
+ROCrate_decoder: Decoder_1[OntologySourceReference] = object(_arrow2151)
+
+def ISAJson_encoder(id_map: Any | None, osr: OntologySourceReference) -> IEncodable:
+    def chooser(tupled_arg: tuple[str, IEncodable | None], id_map: Any=id_map, osr: Any=osr) -> tuple[str, IEncodable] | None:
+        def mapping(v_1: IEncodable, tupled_arg: Any=tupled_arg) -> tuple[str, IEncodable]:
+            return (tupled_arg[0], v_1)
+
+        return map(mapping, tupled_arg[1])
+
+    def _arrow2155(value: str, id_map: Any=id_map, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2154(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr2154()
+
+    def _arrow2157(value_2: str, id_map: Any=id_map, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2156(IEncodable):
+            def Encode(self, helpers_1: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_1.encode_string(value_2)
+
+        return ObjectExpr2156()
+
+    def _arrow2159(value_4: str, id_map: Any=id_map, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2158(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_4)
+
+        return ObjectExpr2158()
+
+    def _arrow2161(value_6: str, id_map: Any=id_map, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2160(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_6)
+
+        return ObjectExpr2160()
+
+    def _arrow2162(comment: Comment, id_map: Any=id_map, osr: Any=osr) -> IEncodable:
+        return ISAJson_encoder_1(id_map, comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([try_include("description", _arrow2155, osr.Description), try_include("file", _arrow2157, osr.File), try_include("name", _arrow2159, osr.Name), try_include("version", _arrow2161, osr.Version), try_include_seq("comments", _arrow2162, osr.Comments)]))
+    class ObjectExpr2163(IEncodable):
+        def Encode(self, helpers_4: IEncoderHelpers_1[Any], id_map: Any=id_map, osr: Any=osr) -> Any:
+            def mapping_1(tupled_arg_1: tuple[str, IEncodable]) -> tuple[str, __A_]:
+                return (tupled_arg_1[0], tupled_arg_1[1].Encode(helpers_4))
+
+            arg: IEnumerable_1[tuple[str, __A_]] = map_1(mapping_1, values)
+            return helpers_4.encode_object(arg)
+
+    return ObjectExpr2163()
+
+
+ISAJson_decoder: Decoder_1[OntologySourceReference] = decoder
+
+__all__ = ["encoder", "decoder", "ROCrate_genID", "ROCrate_encoder", "ROCrate_decoder", "ISAJson_encoder", "ISAJson_decoder"]
+