arctrl 3.0.0__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 _arrow2676(value: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2675(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr2675()
+
+    def _arrow2678(value_2: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2677(IEncodable):
+            def Encode(self, helpers_1: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_1.encode_string(value_2)
+
+        return ObjectExpr2677()
+
+    def _arrow2680(value_4: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2679(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_4)
+
+        return ObjectExpr2679()
+
+    def _arrow2681(comment: Comment, oa: Any=oa) -> IEncodable:
+        return encoder(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([try_include("annotationValue", _arrow2676, oa.Name), try_include("termSource", _arrow2678, oa.TermSourceREF), try_include("termAccession", _arrow2680, oa.TermAccessionNumber), try_include_seq("comments", _arrow2681, oa.Comments)]))
+    class ObjectExpr2682(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 ObjectExpr2682()
+
+
+def _arrow2687(get: IGetters) -> OntologyAnnotation:
+    def _arrow2683(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("annotationValue", AnnotationValue_decoder)
+
+    def _arrow2684(__unit: None=None) -> str | None:
+        object_arg_1: IOptionalGetter = get.Optional
+        return object_arg_1.Field("termSource", string)
+
+    def _arrow2685(__unit: None=None) -> str | None:
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("termAccession", string)
+
+    def _arrow2686(__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(_arrow2683(), _arrow2684(), _arrow2685(), _arrow2686())
+
+
+OntologyAnnotation_decoder: Decoder_1[OntologyAnnotation] = object(_arrow2687)
+
+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 _arrow2689(s: str, string_table: Any=string_table, oa: Any=oa) -> IEncodable:
+        return encode_string(string_table, s)
+
+    def _arrow2690(s_1: str, string_table: Any=string_table, oa: Any=oa) -> IEncodable:
+        return encode_string(string_table, s_1)
+
+    def _arrow2691(s_2: str, string_table: Any=string_table, oa: Any=oa) -> IEncodable:
+        return encode_string(string_table, s_2)
+
+    def _arrow2692(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", _arrow2689, oa.Name), try_include("ts", _arrow2690, oa.TermSourceREF), try_include("ta", _arrow2691, oa.TermAccessionNumber), try_include_seq("comments", _arrow2692, oa.Comments)]))
+    class ObjectExpr2693(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 ObjectExpr2693()
+
+
+def OntologyAnnotation_compressedDecoder(string_table: Array[str]) -> Decoder_1[OntologyAnnotation]:
+    def _arrow2698(get: IGetters, string_table: Any=string_table) -> OntologyAnnotation:
+        def _arrow2694(__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 _arrow2695(__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 _arrow2696(__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 _arrow2697(__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(_arrow2694(), _arrow2695(), _arrow2696(), _arrow2697())
+
+    return object(_arrow2698)
+
+
+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 _arrow2702(__unit: None=None, oa: Any=oa) -> IEncodable:
+        value: str = OntologyAnnotation_ROCrate_genID(oa)
+        class ObjectExpr2701(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr2701()
+
+    class ObjectExpr2703(IEncodable):
+        def Encode(self, helpers_1: IEncoderHelpers_1[Any], oa: Any=oa) -> Any:
+            return helpers_1.encode_string("OntologyAnnotation")
+
+    def _arrow2705(value_2: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2704(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_2)
+
+        return ObjectExpr2704()
+
+    def _arrow2707(value_4: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2706(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_4)
+
+        return ObjectExpr2706()
+
+    def _arrow2709(value_6: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2708(IEncodable):
+            def Encode(self, helpers_4: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_4.encode_string(value_6)
+
+        return ObjectExpr2708()
+
+    def _arrow2710(comment: Comment, oa: Any=oa) -> IEncodable:
+        return ROCrate_encoderDisambiguatingDescription(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([("@id", _arrow2702()), ("@type", ObjectExpr2703()), try_include("annotationValue", _arrow2705, oa.Name), try_include("termSource", _arrow2707, oa.TermSourceREF), try_include("termAccession", _arrow2709, oa.TermAccessionNumber), try_include_seq("comments", _arrow2710, oa.Comments), ("@context", context_jsonvalue)]))
+    class ObjectExpr2711(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 ObjectExpr2711()
+
+
+def _arrow2716(get: IGetters) -> OntologyAnnotation:
+    def _arrow2712(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("annotationValue", AnnotationValue_decoder)
+
+    def _arrow2713(__unit: None=None) -> str | None:
+        object_arg_1: IOptionalGetter = get.Optional
+        return object_arg_1.Field("termSource", string)
+
+    def _arrow2714(__unit: None=None) -> str | None:
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("termAccession", string)
+
+    def _arrow2715(__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(_arrow2712(), _arrow2713(), _arrow2714(), _arrow2715())
+
+
+OntologyAnnotation_ROCrate_decoderDefinedTerm: Decoder_1[OntologyAnnotation] = object(_arrow2716)
+
+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 _arrow2720(__unit: None=None, oa: Any=oa) -> IEncodable:
+        value: str = OntologyAnnotation_ROCrate_genID(oa)
+        class ObjectExpr2719(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr2719()
+
+    class ObjectExpr2721(IEncodable):
+        def Encode(self, helpers_1: IEncoderHelpers_1[Any], oa: Any=oa) -> Any:
+            return helpers_1.encode_string("PropertyValue")
+
+    def _arrow2723(value_2: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2722(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_2)
+
+        return ObjectExpr2722()
+
+    def _arrow2725(value_4: str, oa: Any=oa) -> IEncodable:
+        class ObjectExpr2724(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_4)
+
+        return ObjectExpr2724()
+
+    def _arrow2726(comment: Comment, oa: Any=oa) -> IEncodable:
+        return ROCrate_encoderDisambiguatingDescription(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([("@id", _arrow2720()), ("@type", ObjectExpr2721()), try_include("category", _arrow2723, oa.Name), try_include("categoryCode", _arrow2725, oa.TermAccessionNumber), try_include_seq("comments", _arrow2726, oa.Comments), ("@context", context_jsonvalue_1)]))
+    class ObjectExpr2727(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 ObjectExpr2727()
+
+
+def _arrow2731(get: IGetters) -> OntologyAnnotation:
+    def _arrow2728(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("category", string)
+
+    def _arrow2729(__unit: None=None) -> str | None:
+        object_arg_1: IOptionalGetter = get.Optional
+        return object_arg_1.Field("categoryCode", string)
+
+    def _arrow2730(__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(_arrow2728(), None, _arrow2729(), _arrow2730())
+
+
+OntologyAnnotation_ROCrate_decoderPropertyValue: Decoder_1[OntologyAnnotation] = object(_arrow2731)
+
+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 _arrow2735(value: str, oa_1: Any=oa_1) -> IEncodable:
+            class ObjectExpr2734(IEncodable):
+                def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers.encode_string(value)
+
+            return ObjectExpr2734()
+
+        def _arrow2737(value_2: str, oa_1: Any=oa_1) -> IEncodable:
+            class ObjectExpr2736(IEncodable):
+                def Encode(self, helpers_1: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_1.encode_string(value_2)
+
+            return ObjectExpr2736()
+
+        def _arrow2739(value_4: str, oa_1: Any=oa_1) -> IEncodable:
+            class ObjectExpr2738(IEncodable):
+                def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_2.encode_string(value_4)
+
+            return ObjectExpr2738()
+
+        def _arrow2741(value_6: str, oa_1: Any=oa_1) -> IEncodable:
+            class ObjectExpr2740(IEncodable):
+                def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_3.encode_string(value_6)
+
+            return ObjectExpr2740()
+
+        def _arrow2742(comment: Comment, oa_1: Any=oa_1) -> IEncodable:
+            return encoder(comment)
+
+        values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([try_include("@id", _arrow2735, OntologyAnnotation_ROCrate_genID(oa_1)), try_include("annotationValue", _arrow2737, oa_1.Name), try_include("termSource", _arrow2739, oa_1.TermSourceREF), try_include("termAccession", _arrow2741, oa_1.TermAccessionNumber), try_include_seq("comments", _arrow2742, comments)]))
+        class ObjectExpr2743(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 ObjectExpr2743()
+
+    if id_map is not None:
+        def _arrow2744(o: OntologyAnnotation, id_map: Any=id_map, oa: Any=oa) -> str:
+            return OntologyAnnotation_ROCrate_genID(o)
+
+        return encode(_arrow2744, 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 _arrow2785(value: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2784(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr2784()
+
+    def _arrow2787(value_2: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2786(IEncodable):
+            def Encode(self, helpers_1: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_1.encode_string(value_2)
+
+        return ObjectExpr2786()
+
+    def _arrow2789(value_4: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2788(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_4)
+
+        return ObjectExpr2788()
+
+    def _arrow2791(value_6: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2790(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_6)
+
+        return ObjectExpr2790()
+
+    def _arrow2792(comment: Comment, osr: Any=osr) -> IEncodable:
+        return encoder_1(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([try_include("description", _arrow2785, osr.Description), try_include("file", _arrow2787, osr.File), try_include("name", _arrow2789, osr.Name), try_include("version", _arrow2791, osr.Version), try_include_seq("comments", _arrow2792, osr.Comments)]))
+    class ObjectExpr2793(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 ObjectExpr2793()
+
+
+def _arrow2799(get: IGetters) -> OntologySourceReference:
+    def _arrow2794(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("description", Decode_uri)
+
+    def _arrow2795(__unit: None=None) -> str | None:
+        object_arg_1: IOptionalGetter = get.Optional
+        return object_arg_1.Field("file", string)
+
+    def _arrow2796(__unit: None=None) -> str | None:
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("name", string)
+
+    def _arrow2797(__unit: None=None) -> str | None:
+        object_arg_3: IOptionalGetter = get.Optional
+        return object_arg_3.Field("version", string)
+
+    def _arrow2798(__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(_arrow2794(), _arrow2795(), _arrow2796(), _arrow2797(), _arrow2798())
+
+
+decoder: Decoder_1[OntologySourceReference] = object(_arrow2799)
+
+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 _arrow2803(__unit: None=None, osr: Any=osr) -> IEncodable:
+        value: str = ROCrate_genID(osr)
+        class ObjectExpr2802(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr2802()
+
+    class ObjectExpr2804(IEncodable):
+        def Encode(self, helpers_1: IEncoderHelpers_1[Any], osr: Any=osr) -> Any:
+            return helpers_1.encode_string("OntologySourceReference")
+
+    def _arrow2806(value_2: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2805(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_2)
+
+        return ObjectExpr2805()
+
+    def _arrow2808(value_4: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2807(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_4)
+
+        return ObjectExpr2807()
+
+    def _arrow2810(value_6: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2809(IEncodable):
+            def Encode(self, helpers_4: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_4.encode_string(value_6)
+
+        return ObjectExpr2809()
+
+    def _arrow2812(value_8: str, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2811(IEncodable):
+            def Encode(self, helpers_5: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_5.encode_string(value_8)
+
+        return ObjectExpr2811()
+
+    def _arrow2813(comment: Comment, osr: Any=osr) -> IEncodable:
+        return encoder_1(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([("@id", _arrow2803()), ("@type", ObjectExpr2804()), try_include("description", _arrow2806, osr.Description), try_include("file", _arrow2808, osr.File), try_include("name", _arrow2810, osr.Name), try_include("version", _arrow2812, osr.Version), try_include_seq("comments", _arrow2813, osr.Comments), ("@context", context_jsonvalue)]))
+    class ObjectExpr2814(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 ObjectExpr2814()
+
+
+def _arrow2820(get: IGetters) -> OntologySourceReference:
+    def _arrow2815(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("description", Decode_uri)
+
+    def _arrow2816(__unit: None=None) -> str | None:
+        object_arg_1: IOptionalGetter = get.Optional
+        return object_arg_1.Field("file", string)
+
+    def _arrow2817(__unit: None=None) -> str | None:
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("name", string)
+
+    def _arrow2818(__unit: None=None) -> str | None:
+        object_arg_3: IOptionalGetter = get.Optional
+        return object_arg_3.Field("version", string)
+
+    def _arrow2819(__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(_arrow2815(), _arrow2816(), _arrow2817(), _arrow2818(), _arrow2819())
+
+
+ROCrate_decoder: Decoder_1[OntologySourceReference] = object(_arrow2820)
+
+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 _arrow2824(value: str, id_map: Any=id_map, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2823(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr2823()
+
+    def _arrow2826(value_2: str, id_map: Any=id_map, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2825(IEncodable):
+            def Encode(self, helpers_1: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_1.encode_string(value_2)
+
+        return ObjectExpr2825()
+
+    def _arrow2828(value_4: str, id_map: Any=id_map, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2827(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_4)
+
+        return ObjectExpr2827()
+
+    def _arrow2830(value_6: str, id_map: Any=id_map, osr: Any=osr) -> IEncodable:
+        class ObjectExpr2829(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_6)
+
+        return ObjectExpr2829()
+
+    def _arrow2831(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", _arrow2824, osr.Description), try_include("file", _arrow2826, osr.File), try_include("name", _arrow2828, osr.Name), try_include("version", _arrow2830, osr.Version), try_include_seq("comments", _arrow2831, osr.Comments)]))
+    class ObjectExpr2832(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 ObjectExpr2832()
+
+
+ISAJson_decoder: Decoder_1[OntologySourceReference] = decoder
+
+__all__ = ["encoder", "decoder", "ROCrate_genID", "ROCrate_encoder", "ROCrate_decoder", "ISAJson_encoder", "ISAJson_decoder"]
+