arctrl 3.0.0a3__py3-none-any.whl

arctrl/py/Json/study.py

@@ -0,0 +1,793 @@
+from __future__ import annotations
+from collections.abc import Callable
+from typing import (Any, TypeVar)
+from ..fable_modules.fable_library.list import (try_find, FSharpList, choose, of_array, singleton, map as map_2, empty)
+from ..fable_modules.fable_library.option import (default_arg, value as value_17, map, bind, default_arg_with)
+from ..fable_modules.fable_library.seq import (map as map_1, is_empty)
+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, get_enumerator, dispose)
+from ..fable_modules.thoth_json_core.decode import (object, IRequiredGetter, string, IOptionalGetter, resize_array, IGetters, list_1 as list_1_2)
+from ..fable_modules.thoth_json_core.encode import list_1 as list_1_1
+from ..fable_modules.thoth_json_core.types import (IEncodable, IEncoderHelpers_1, Decoder_1)
+from ..Core.arc_types import (ArcAssay, ArcStudy)
+from ..Core.comment import Comment
+from ..Core.conversion import (ARCtrl_ArcTables__ArcTables_GetProcesses, ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D, Person_setSourceAssayComment, Person_getSourceAssayIdentifiersFromComments, Person_removeSourceAssayComments)
+from ..Core.data import Data
+from ..Core.data_map import DataMap
+from ..Core.Helper.collections_ import (ResizeArray_map, Option_fromValueWithDefault)
+from ..Core.Helper.identifier import (Study_tryFileNameFromIdentifier, Study_tryIdentifierFromFileName, create_missing_identifier, Study_fileNameFromIdentifier)
+from ..Core.ontology_annotation import OntologyAnnotation
+from ..Core.person import Person
+from ..Core.Process.factor import Factor
+from ..Core.Process.material_attribute import MaterialAttribute
+from ..Core.Process.process import Process
+from ..Core.Process.process_sequence import (get_data, get_units, get_factors, get_characteristics, get_protocols)
+from ..Core.Process.protocol import Protocol
+from ..Core.publication import Publication
+from ..Core.Table.arc_table import ArcTable
+from ..Core.Table.arc_tables import ArcTables
+from ..Core.Table.composite_cell import CompositeCell
+from .assay import (ROCrate_encoder as ROCrate_encoder_4, ROCrate_decoder as ROCrate_decoder_1, ISAJson_encoder as ISAJson_encoder_5, ISAJson_decoder as ISAJson_decoder_2)
+from .comment import (encoder as encoder_9, decoder as decoder_6, ROCrate_encoder as ROCrate_encoder_6, ROCrate_decoder as ROCrate_decoder_5, ISAJson_encoder as ISAJson_encoder_6, ISAJson_decoder as ISAJson_decoder_5)
+from .context.rocrate.isa_study_context import context_jsonvalue
+from .data import ROCrate_encoder as ROCrate_encoder_5
+from .DataMap.data_map import (encoder as encoder_8, decoder as decoder_5, encoder_compressed as encoder_compressed_2, decoder_compressed as decoder_compressed_2)
+from .decode import Decode_objectNoAdditionalProperties
+from .encode import (try_include, try_include_seq, try_include_list)
+from .idtable import encode
+from .ontology_annotation import (OntologyAnnotation_encoder, OntologyAnnotation_decoder, OntologyAnnotation_ROCrate_encoderDefinedTerm, OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_ISAJson_encoder, OntologyAnnotation_ISAJson_decoder)
+from .person import (encoder as encoder_6, decoder as decoder_3, ROCrate_encoder as ROCrate_encoder_2, ROCrate_decoder as ROCrate_decoder_4, ISAJson_encoder as ISAJson_encoder_3, ISAJson_decoder as ISAJson_decoder_3)
+from .Process.factor import encoder as encoder_10
+from .Process.material_attribute import encoder as encoder_11
+from .Process.process import (ROCrate_encoder as ROCrate_encoder_3, ROCrate_decoder as ROCrate_decoder_2, ISAJson_encoder as ISAJson_encoder_4, ISAJson_decoder as ISAJson_decoder_1)
+from .Process.protocol import ISAJson_encoder as ISAJson_encoder_1
+from .Process.study_materials import encoder as encoder_12
+from .publication import (encoder as encoder_5, decoder as decoder_2, ROCrate_encoder as ROCrate_encoder_1, ROCrate_decoder as ROCrate_decoder_3, ISAJson_encoder as ISAJson_encoder_2, ISAJson_decoder as ISAJson_decoder_4)
+from .Table.arc_table import (encoder as encoder_7, decoder as decoder_4, encoder_compressed as encoder_compressed_1, decoder_compressed as decoder_compressed_1)
+
+__A_ = TypeVar("__A_")
+
+def Helper_getAssayInformation(assays: FSharpList[ArcAssay] | None, study: ArcStudy) -> Array[ArcAssay]:
+    if assays is not None:
+        def f(assay_id: str, assays: Any=assays, study: Any=study) -> ArcAssay:
+            def predicate(a: ArcAssay, assay_id: Any=assay_id) -> bool:
+                return a.Identifier == assay_id
+
+            return default_arg(try_find(predicate, value_17(assays)), ArcAssay.init(assay_id))
+
+        return ResizeArray_map(f, study.RegisteredAssayIdentifiers)
+
+    else: 
+        return study.GetRegisteredAssaysOrIdentifier()
+
+
+
+def encoder(study: ArcStudy) -> IEncodable:
+    def chooser(tupled_arg: tuple[str, IEncodable | None], study: Any=study) -> 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 _arrow3010(__unit: None=None, study: Any=study) -> IEncodable:
+        value: str = study.Identifier
+        class ObjectExpr3009(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr3009()
+
+    def _arrow3012(value_1: str, study: Any=study) -> IEncodable:
+        class ObjectExpr3011(IEncodable):
+            def Encode(self, helpers_1: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_1.encode_string(value_1)
+
+        return ObjectExpr3011()
+
+    def _arrow3014(value_3: str, study: Any=study) -> IEncodable:
+        class ObjectExpr3013(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_3)
+
+        return ObjectExpr3013()
+
+    def _arrow3016(value_5: str, study: Any=study) -> IEncodable:
+        class ObjectExpr3015(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_5)
+
+        return ObjectExpr3015()
+
+    def _arrow3018(value_7: str, study: Any=study) -> IEncodable:
+        class ObjectExpr3017(IEncodable):
+            def Encode(self, helpers_4: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_4.encode_string(value_7)
+
+        return ObjectExpr3017()
+
+    def _arrow3019(oa: Publication, study: Any=study) -> IEncodable:
+        return encoder_5(oa)
+
+    def _arrow3020(person: Person, study: Any=study) -> IEncodable:
+        return encoder_6(person)
+
+    def _arrow3021(oa_1: OntologyAnnotation, study: Any=study) -> IEncodable:
+        return OntologyAnnotation_encoder(oa_1)
+
+    def _arrow3022(table: ArcTable, study: Any=study) -> IEncodable:
+        return encoder_7(table)
+
+    def _arrow3023(dm: DataMap, study: Any=study) -> IEncodable:
+        return encoder_8(dm)
+
+    def _arrow3025(value_9: str, study: Any=study) -> IEncodable:
+        class ObjectExpr3024(IEncodable):
+            def Encode(self, helpers_5: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_5.encode_string(value_9)
+
+        return ObjectExpr3024()
+
+    def _arrow3026(comment: Comment, study: Any=study) -> IEncodable:
+        return encoder_9(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([("Identifier", _arrow3010()), try_include("Title", _arrow3012, study.Title), try_include("Description", _arrow3014, study.Description), try_include("SubmissionDate", _arrow3016, study.SubmissionDate), try_include("PublicReleaseDate", _arrow3018, study.PublicReleaseDate), try_include_seq("Publications", _arrow3019, study.Publications), try_include_seq("Contacts", _arrow3020, study.Contacts), try_include_seq("StudyDesignDescriptors", _arrow3021, study.StudyDesignDescriptors), try_include_seq("Tables", _arrow3022, study.Tables), try_include("DataMap", _arrow3023, study.DataMap), try_include_seq("RegisteredAssayIdentifiers", _arrow3025, study.RegisteredAssayIdentifiers), try_include_seq("Comments", _arrow3026, study.Comments)]))
+    class ObjectExpr3027(IEncodable):
+        def Encode(self, helpers_6: IEncoderHelpers_1[Any], study: Any=study) -> 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 ObjectExpr3027()
+
+
+def _arrow3040(get: IGetters) -> ArcStudy:
+    def _arrow3028(__unit: None=None) -> str:
+        object_arg: IRequiredGetter = get.Required
+        return object_arg.Field("Identifier", string)
+
+    def _arrow3029(__unit: None=None) -> str | None:
+        object_arg_1: IOptionalGetter = get.Optional
+        return object_arg_1.Field("Title", string)
+
+    def _arrow3030(__unit: None=None) -> str | None:
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("Description", string)
+
+    def _arrow3031(__unit: None=None) -> str | None:
+        object_arg_3: IOptionalGetter = get.Optional
+        return object_arg_3.Field("SubmissionDate", string)
+
+    def _arrow3032(__unit: None=None) -> str | None:
+        object_arg_4: IOptionalGetter = get.Optional
+        return object_arg_4.Field("PublicReleaseDate", string)
+
+    def _arrow3033(__unit: None=None) -> Array[Publication] | None:
+        arg_11: Decoder_1[Array[Publication]] = resize_array(decoder_2)
+        object_arg_5: IOptionalGetter = get.Optional
+        return object_arg_5.Field("Publications", arg_11)
+
+    def _arrow3034(__unit: None=None) -> Array[Person] | None:
+        arg_13: Decoder_1[Array[Person]] = resize_array(decoder_3)
+        object_arg_6: IOptionalGetter = get.Optional
+        return object_arg_6.Field("Contacts", arg_13)
+
+    def _arrow3035(__unit: None=None) -> Array[OntologyAnnotation] | None:
+        arg_15: Decoder_1[Array[OntologyAnnotation]] = resize_array(OntologyAnnotation_decoder)
+        object_arg_7: IOptionalGetter = get.Optional
+        return object_arg_7.Field("StudyDesignDescriptors", arg_15)
+
+    def _arrow3036(__unit: None=None) -> Array[ArcTable] | None:
+        arg_17: Decoder_1[Array[ArcTable]] = resize_array(decoder_4)
+        object_arg_8: IOptionalGetter = get.Optional
+        return object_arg_8.Field("Tables", arg_17)
+
+    def _arrow3037(__unit: None=None) -> DataMap | None:
+        object_arg_9: IOptionalGetter = get.Optional
+        return object_arg_9.Field("DataMap", decoder_5)
+
+    def _arrow3038(__unit: None=None) -> Array[str] | None:
+        arg_21: Decoder_1[Array[str]] = resize_array(string)
+        object_arg_10: IOptionalGetter = get.Optional
+        return object_arg_10.Field("RegisteredAssayIdentifiers", arg_21)
+
+    def _arrow3039(__unit: None=None) -> Array[Comment] | None:
+        arg_23: Decoder_1[Array[Comment]] = resize_array(decoder_6)
+        object_arg_11: IOptionalGetter = get.Optional
+        return object_arg_11.Field("Comments", arg_23)
+
+    return ArcStudy(_arrow3028(), _arrow3029(), _arrow3030(), _arrow3031(), _arrow3032(), _arrow3033(), _arrow3034(), _arrow3035(), _arrow3036(), _arrow3037(), _arrow3038(), _arrow3039())
+
+
+decoder: Decoder_1[ArcStudy] = object(_arrow3040)
+
+def encoder_compressed(string_table: Any, oa_table: Any, cell_table: Any, study: ArcStudy) -> IEncodable:
+    def chooser(tupled_arg: tuple[str, IEncodable | None], string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> 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 _arrow3044(__unit: None=None, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        value: str = study.Identifier
+        class ObjectExpr3043(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr3043()
+
+    def _arrow3046(value_1: str, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        class ObjectExpr3045(IEncodable):
+            def Encode(self, helpers_1: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_1.encode_string(value_1)
+
+        return ObjectExpr3045()
+
+    def _arrow3048(value_3: str, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        class ObjectExpr3047(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_3)
+
+        return ObjectExpr3047()
+
+    def _arrow3050(value_5: str, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        class ObjectExpr3049(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_5)
+
+        return ObjectExpr3049()
+
+    def _arrow3052(value_7: str, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        class ObjectExpr3051(IEncodable):
+            def Encode(self, helpers_4: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_4.encode_string(value_7)
+
+        return ObjectExpr3051()
+
+    def _arrow3053(oa: Publication, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        return encoder_5(oa)
+
+    def _arrow3054(person: Person, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        return encoder_6(person)
+
+    def _arrow3055(oa_1: OntologyAnnotation, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        return OntologyAnnotation_encoder(oa_1)
+
+    def _arrow3056(table: ArcTable, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        return encoder_compressed_1(string_table, oa_table, cell_table, table)
+
+    def _arrow3057(dm: DataMap, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        return encoder_compressed_2(string_table, oa_table, cell_table, dm)
+
+    def _arrow3059(value_9: str, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        class ObjectExpr3058(IEncodable):
+            def Encode(self, helpers_5: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_5.encode_string(value_9)
+
+        return ObjectExpr3058()
+
+    def _arrow3060(comment: Comment, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        return encoder_9(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([("Identifier", _arrow3044()), try_include("Title", _arrow3046, study.Title), try_include("Description", _arrow3048, study.Description), try_include("SubmissionDate", _arrow3050, study.SubmissionDate), try_include("PublicReleaseDate", _arrow3052, study.PublicReleaseDate), try_include_seq("Publications", _arrow3053, study.Publications), try_include_seq("Contacts", _arrow3054, study.Contacts), try_include_seq("StudyDesignDescriptors", _arrow3055, study.StudyDesignDescriptors), try_include_seq("Tables", _arrow3056, study.Tables), try_include("DataMap", _arrow3057, study.DataMap), try_include_seq("RegisteredAssayIdentifiers", _arrow3059, study.RegisteredAssayIdentifiers), try_include_seq("Comments", _arrow3060, study.Comments)]))
+    class ObjectExpr3061(IEncodable):
+        def Encode(self, helpers_6: IEncoderHelpers_1[Any], string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> 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 ObjectExpr3061()
+
+
+def decoder_compressed(string_table: Array[str], oa_table: Array[OntologyAnnotation], cell_table: Array[CompositeCell]) -> Decoder_1[ArcStudy]:
+    def _arrow3074(get: IGetters, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table) -> ArcStudy:
+        def _arrow3062(__unit: None=None) -> str:
+            object_arg: IRequiredGetter = get.Required
+            return object_arg.Field("Identifier", string)
+
+        def _arrow3063(__unit: None=None) -> str | None:
+            object_arg_1: IOptionalGetter = get.Optional
+            return object_arg_1.Field("Title", string)
+
+        def _arrow3064(__unit: None=None) -> str | None:
+            object_arg_2: IOptionalGetter = get.Optional
+            return object_arg_2.Field("Description", string)
+
+        def _arrow3065(__unit: None=None) -> str | None:
+            object_arg_3: IOptionalGetter = get.Optional
+            return object_arg_3.Field("SubmissionDate", string)
+
+        def _arrow3066(__unit: None=None) -> str | None:
+            object_arg_4: IOptionalGetter = get.Optional
+            return object_arg_4.Field("PublicReleaseDate", string)
+
+        def _arrow3067(__unit: None=None) -> Array[Publication] | None:
+            arg_11: Decoder_1[Array[Publication]] = resize_array(decoder_2)
+            object_arg_5: IOptionalGetter = get.Optional
+            return object_arg_5.Field("Publications", arg_11)
+
+        def _arrow3068(__unit: None=None) -> Array[Person] | None:
+            arg_13: Decoder_1[Array[Person]] = resize_array(decoder_3)
+            object_arg_6: IOptionalGetter = get.Optional
+            return object_arg_6.Field("Contacts", arg_13)
+
+        def _arrow3069(__unit: None=None) -> Array[OntologyAnnotation] | None:
+            arg_15: Decoder_1[Array[OntologyAnnotation]] = resize_array(OntologyAnnotation_decoder)
+            object_arg_7: IOptionalGetter = get.Optional
+            return object_arg_7.Field("StudyDesignDescriptors", arg_15)
+
+        def _arrow3070(__unit: None=None) -> Array[ArcTable] | None:
+            arg_17: Decoder_1[Array[ArcTable]] = resize_array(decoder_compressed_1(string_table, oa_table, cell_table))
+            object_arg_8: IOptionalGetter = get.Optional
+            return object_arg_8.Field("Tables", arg_17)
+
+        def _arrow3071(__unit: None=None) -> DataMap | None:
+            arg_19: Decoder_1[DataMap] = decoder_compressed_2(string_table, oa_table, cell_table)
+            object_arg_9: IOptionalGetter = get.Optional
+            return object_arg_9.Field("DataMap", arg_19)
+
+        def _arrow3072(__unit: None=None) -> Array[str] | None:
+            arg_21: Decoder_1[Array[str]] = resize_array(string)
+            object_arg_10: IOptionalGetter = get.Optional
+            return object_arg_10.Field("RegisteredAssayIdentifiers", arg_21)
+
+        def _arrow3073(__unit: None=None) -> Array[Comment] | None:
+            arg_23: Decoder_1[Array[Comment]] = resize_array(decoder_6)
+            object_arg_11: IOptionalGetter = get.Optional
+            return object_arg_11.Field("Comments", arg_23)
+
+        return ArcStudy(_arrow3062(), _arrow3063(), _arrow3064(), _arrow3065(), _arrow3066(), _arrow3067(), _arrow3068(), _arrow3069(), _arrow3070(), _arrow3071(), _arrow3072(), _arrow3073())
+
+    return object(_arrow3074)
+
+
+def ROCrate_genID(a: ArcStudy) -> str:
+    match_value: str = a.Identifier
+    if match_value == "":
+        return "#EmptyStudy"
+
+    else: 
+        return ("studies/" + replace(match_value, " ", "_")) + "/"
+
+
+
+def ROCrate_encoder(assays: FSharpList[ArcAssay] | None, s: ArcStudy) -> IEncodable:
+    file_name: str | None = Study_tryFileNameFromIdentifier(s.Identifier)
+    processes: FSharpList[Process] = ARCtrl_ArcTables__ArcTables_GetProcesses(s)
+    assays_1: Array[ArcAssay] = Helper_getAssayInformation(assays, s)
+    def chooser(tupled_arg: tuple[str, IEncodable | None], assays: Any=assays, s: Any=s) -> 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 _arrow3078(__unit: None=None, assays: Any=assays, s: Any=s) -> IEncodable:
+        value: str = ROCrate_genID(s)
+        class ObjectExpr3077(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr3077()
+
+    class ObjectExpr3079(IEncodable):
+        def Encode(self, helpers_1: IEncoderHelpers_1[Any], assays: Any=assays, s: Any=s) -> Any:
+            return helpers_1.encode_string("Study")
+
+    class ObjectExpr3080(IEncodable):
+        def Encode(self, helpers_2: IEncoderHelpers_1[Any], assays: Any=assays, s: Any=s) -> Any:
+            return helpers_2.encode_string("Study")
+
+    def _arrow3082(__unit: None=None, assays: Any=assays, s: Any=s) -> IEncodable:
+        value_3: str = s.Identifier
+        class ObjectExpr3081(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_3)
+
+        return ObjectExpr3081()
+
+    def _arrow3084(value_4: str, assays: Any=assays, s: Any=s) -> IEncodable:
+        class ObjectExpr3083(IEncodable):
+            def Encode(self, helpers_4: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_4.encode_string(value_4)
+
+        return ObjectExpr3083()
+
+    def _arrow3086(value_6: str, assays: Any=assays, s: Any=s) -> IEncodable:
+        class ObjectExpr3085(IEncodable):
+            def Encode(self, helpers_5: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_5.encode_string(value_6)
+
+        return ObjectExpr3085()
+
+    def _arrow3088(value_8: str, assays: Any=assays, s: Any=s) -> IEncodable:
+        class ObjectExpr3087(IEncodable):
+            def Encode(self, helpers_6: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_6.encode_string(value_8)
+
+        return ObjectExpr3087()
+
+    def _arrow3089(oa: OntologyAnnotation, assays: Any=assays, s: Any=s) -> IEncodable:
+        return OntologyAnnotation_ROCrate_encoderDefinedTerm(oa)
+
+    def _arrow3091(value_10: str, assays: Any=assays, s: Any=s) -> IEncodable:
+        class ObjectExpr3090(IEncodable):
+            def Encode(self, helpers_7: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_7.encode_string(value_10)
+
+        return ObjectExpr3090()
+
+    def _arrow3093(value_12: str, assays: Any=assays, s: Any=s) -> IEncodable:
+        class ObjectExpr3092(IEncodable):
+            def Encode(self, helpers_8: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_8.encode_string(value_12)
+
+        return ObjectExpr3092()
+
+    def _arrow3094(oa_1: Publication, assays: Any=assays, s: Any=s) -> IEncodable:
+        return ROCrate_encoder_1(oa_1)
+
+    def _arrow3095(oa_2: Person, assays: Any=assays, s: Any=s) -> IEncodable:
+        return ROCrate_encoder_2(oa_2)
+
+    def _arrow3097(__unit: None=None, assays: Any=assays, s: Any=s) -> Callable[[Process], IEncodable]:
+        study_name: str | None = s.Identifier
+        def _arrow3096(oa_3: Process) -> IEncodable:
+            return ROCrate_encoder_3(study_name, None, oa_3)
+
+        return _arrow3096
+
+    def _arrow3099(__unit: None=None, assays: Any=assays, s: Any=s) -> Callable[[ArcAssay], IEncodable]:
+        study_name_1: str | None = s.Identifier
+        def _arrow3098(a_1: ArcAssay) -> IEncodable:
+            return ROCrate_encoder_4(study_name_1, a_1)
+
+        return _arrow3098
+
+    def _arrow3100(oa_4: Data, assays: Any=assays, s: Any=s) -> IEncodable:
+        return ROCrate_encoder_5(oa_4)
+
+    def _arrow3101(comment: Comment, assays: Any=assays, s: Any=s) -> IEncodable:
+        return ROCrate_encoder_6(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([("@id", _arrow3078()), ("@type", list_1_1(singleton(ObjectExpr3079()))), ("additionalType", ObjectExpr3080()), ("identifier", _arrow3082()), try_include("filename", _arrow3084, file_name), try_include("title", _arrow3086, s.Title), try_include("description", _arrow3088, s.Description), try_include_seq("studyDesignDescriptors", _arrow3089, s.StudyDesignDescriptors), try_include("submissionDate", _arrow3091, s.SubmissionDate), try_include("publicReleaseDate", _arrow3093, s.PublicReleaseDate), try_include_seq("publications", _arrow3094, s.Publications), try_include_seq("people", _arrow3095, s.Contacts), try_include_list("processSequence", _arrow3097(), processes), try_include_seq("assays", _arrow3099(), assays_1), try_include_list("dataFiles", _arrow3100, get_data(processes)), try_include_seq("comments", _arrow3101, s.Comments), ("@context", context_jsonvalue)]))
+    class ObjectExpr3102(IEncodable):
+        def Encode(self, helpers_9: IEncoderHelpers_1[Any], assays: Any=assays, s: Any=s) -> Any:
+            def mapping_1(tupled_arg_1: tuple[str, IEncodable]) -> tuple[str, __A_]:
+                return (tupled_arg_1[0], tupled_arg_1[1].Encode(helpers_9))
+
+            arg: IEnumerable_1[tuple[str, __A_]] = map_1(mapping_1, values)
+            return helpers_9.encode_object(arg)
+
+    return ObjectExpr3102()
+
+
+def _arrow3113(get: IGetters) -> tuple[ArcStudy, FSharpList[ArcAssay]]:
+    def _arrow3103(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("filename", string)
+
+    identifier: str = default_arg(bind(Study_tryIdentifierFromFileName, _arrow3103()), create_missing_identifier())
+    assays: FSharpList[ArcAssay] | None
+    arg_3: Decoder_1[FSharpList[ArcAssay]] = list_1_2(ROCrate_decoder_1)
+    object_arg_1: IOptionalGetter = get.Optional
+    assays = object_arg_1.Field("assays", arg_3)
+    def mapping_1(arg_4: FSharpList[ArcAssay]) -> Array[str]:
+        def mapping(a: ArcAssay, arg_4: Any=arg_4) -> str:
+            return a.Identifier
+
+        return list(map_2(mapping, arg_4))
+
+    assay_identifiers: Array[str] | None = map(mapping_1, assays)
+    def mapping_2(ps: FSharpList[Process]) -> Array[ArcTable]:
+        return ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(ps).Tables
+
+    def _arrow3104(__unit: None=None) -> FSharpList[Process] | None:
+        arg_6: Decoder_1[FSharpList[Process]] = list_1_2(ROCrate_decoder_2)
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("processSequence", arg_6)
+
+    tables: Array[ArcTable] | None = map(mapping_2, _arrow3104())
+    def _arrow3105(__unit: None=None) -> str | None:
+        object_arg_3: IOptionalGetter = get.Optional
+        return object_arg_3.Field("title", string)
+
+    def _arrow3106(__unit: None=None) -> str | None:
+        object_arg_4: IOptionalGetter = get.Optional
+        return object_arg_4.Field("description", string)
+
+    def _arrow3107(__unit: None=None) -> str | None:
+        object_arg_5: IOptionalGetter = get.Optional
+        return object_arg_5.Field("submissionDate", string)
+
+    def _arrow3108(__unit: None=None) -> str | None:
+        object_arg_6: IOptionalGetter = get.Optional
+        return object_arg_6.Field("publicReleaseDate", string)
+
+    def _arrow3109(__unit: None=None) -> Array[Publication] | None:
+        arg_16: Decoder_1[Array[Publication]] = resize_array(ROCrate_decoder_3)
+        object_arg_7: IOptionalGetter = get.Optional
+        return object_arg_7.Field("publications", arg_16)
+
+    def _arrow3110(__unit: None=None) -> Array[Person] | None:
+        arg_18: Decoder_1[Array[Person]] = resize_array(ROCrate_decoder_4)
+        object_arg_8: IOptionalGetter = get.Optional
+        return object_arg_8.Field("people", arg_18)
+
+    def _arrow3111(__unit: None=None) -> Array[OntologyAnnotation] | None:
+        arg_20: Decoder_1[Array[OntologyAnnotation]] = resize_array(OntologyAnnotation_ROCrate_decoderDefinedTerm)
+        object_arg_9: IOptionalGetter = get.Optional
+        return object_arg_9.Field("studyDesignDescriptors", arg_20)
+
+    def _arrow3112(__unit: None=None) -> Array[Comment] | None:
+        arg_22: Decoder_1[Array[Comment]] = resize_array(ROCrate_decoder_5)
+        object_arg_10: IOptionalGetter = get.Optional
+        return object_arg_10.Field("comments", arg_22)
+
+    return (ArcStudy(identifier, _arrow3105(), _arrow3106(), _arrow3107(), _arrow3108(), _arrow3109(), _arrow3110(), _arrow3111(), tables, None, assay_identifiers, _arrow3112()), default_arg(assays, empty()))
+
+
+ROCrate_decoder: Decoder_1[tuple[ArcStudy, FSharpList[ArcAssay]]] = object(_arrow3113)
+
+def ISAJson_encoder(id_map: Any | None, assays: FSharpList[ArcAssay] | None, s: ArcStudy) -> IEncodable:
+    def f(s_1: ArcStudy, id_map: Any=id_map, assays: Any=assays, s: Any=s) -> IEncodable:
+        study: ArcStudy = s_1.Copy(True)
+        file_name: str = Study_fileNameFromIdentifier(study.Identifier)
+        assays_1: Array[ArcAssay]
+        n: Array[ArcAssay] = []
+        enumerator: Any = get_enumerator(Helper_getAssayInformation(assays, study))
+        try: 
+            while enumerator.System_Collections_IEnumerator_MoveNext():
+                a: ArcAssay = enumerator.System_Collections_Generic_IEnumerator_1_get_Current()
+                assay: ArcAssay = a.Copy()
+                enumerator_1: Any = get_enumerator(assay.Performers)
+                try: 
+                    while enumerator_1.System_Collections_IEnumerator_MoveNext():
+                        person_1: Person = Person_setSourceAssayComment(enumerator_1.System_Collections_Generic_IEnumerator_1_get_Current(), assay.Identifier)
+                        (study.Contacts.append(person_1))
+
+                finally: 
+                    dispose(enumerator_1)
+
+                assay.Performers = []
+                (n.append(assay))
+
+        finally: 
+            dispose(enumerator)
+
+        assays_1 = n
+        processes: FSharpList[Process] = ARCtrl_ArcTables__ArcTables_GetProcesses(study)
+        def encoder_1(oa: OntologyAnnotation, s_1: Any=s_1) -> IEncodable:
+            return OntologyAnnotation_ISAJson_encoder(id_map, oa)
+
+        encoded_units: tuple[str, IEncodable | None] = try_include_list("unitCategories", encoder_1, get_units(processes))
+        def encoder_2(value_1: Factor, s_1: Any=s_1) -> IEncodable:
+            return encoder_10(id_map, value_1)
+
+        encoded_factors: tuple[str, IEncodable | None] = try_include_list("factors", encoder_2, get_factors(processes))
+        def encoder_3(value_3: MaterialAttribute, s_1: Any=s_1) -> IEncodable:
+            return encoder_11(id_map, value_3)
+
+        encoded_characteristics: tuple[str, IEncodable | None] = try_include_list("characteristicCategories", encoder_3, get_characteristics(processes))
+        def _arrow3114(ps: FSharpList[Process], s_1: Any=s_1) -> IEncodable:
+            return encoder_12(id_map, ps)
+
+        encoded_materials: tuple[str, IEncodable | None] = try_include("materials", _arrow3114, Option_fromValueWithDefault(empty(), processes))
+        encoded_protocols: tuple[str, IEncodable | None]
+        value_5: FSharpList[Protocol] = get_protocols(processes)
+        def _arrow3116(__unit: None=None, s_1: Any=s_1) -> Callable[[Protocol], IEncodable]:
+            study_name: str | None = s_1.Identifier
+            def _arrow3115(oa_1: Protocol) -> IEncodable:
+                return ISAJson_encoder_1(study_name, None, None, id_map, oa_1)
+
+            return _arrow3115
+
+        encoded_protocols = try_include_list("protocols", _arrow3116(), value_5)
+        def chooser(tupled_arg: tuple[str, IEncodable | None], s_1: Any=s_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(mapping, tupled_arg[1])
+
+        def _arrow3120(__unit: None=None, s_1: Any=s_1) -> IEncodable:
+            value_6: str = ROCrate_genID(study)
+            class ObjectExpr3119(IEncodable):
+                def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers.encode_string(value_6)
+
+            return ObjectExpr3119()
+
+        class ObjectExpr3121(IEncodable):
+            def Encode(self, helpers_1: IEncoderHelpers_1[Any], s_1: Any=s_1) -> Any:
+                return helpers_1.encode_string(file_name)
+
+        def _arrow3123(__unit: None=None, s_1: Any=s_1) -> IEncodable:
+            value_8: str = study.Identifier
+            class ObjectExpr3122(IEncodable):
+                def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_2.encode_string(value_8)
+
+            return ObjectExpr3122()
+
+        def _arrow3125(value_9: str, s_1: Any=s_1) -> IEncodable:
+            class ObjectExpr3124(IEncodable):
+                def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_3.encode_string(value_9)
+
+            return ObjectExpr3124()
+
+        def _arrow3127(value_11: str, s_1: Any=s_1) -> IEncodable:
+            class ObjectExpr3126(IEncodable):
+                def Encode(self, helpers_4: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_4.encode_string(value_11)
+
+            return ObjectExpr3126()
+
+        def _arrow3129(value_13: str, s_1: Any=s_1) -> IEncodable:
+            class ObjectExpr3128(IEncodable):
+                def Encode(self, helpers_5: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_5.encode_string(value_13)
+
+            return ObjectExpr3128()
+
+        def _arrow3131(value_15: str, s_1: Any=s_1) -> IEncodable:
+            class ObjectExpr3130(IEncodable):
+                def Encode(self, helpers_6: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_6.encode_string(value_15)
+
+            return ObjectExpr3130()
+
+        def _arrow3132(oa_2: Publication, s_1: Any=s_1) -> IEncodable:
+            return ISAJson_encoder_2(id_map, oa_2)
+
+        def _arrow3133(person_2: Person, s_1: Any=s_1) -> IEncodable:
+            return ISAJson_encoder_3(id_map, person_2)
+
+        def _arrow3134(oa_3: OntologyAnnotation, s_1: Any=s_1) -> IEncodable:
+            return OntologyAnnotation_ISAJson_encoder(id_map, oa_3)
+
+        def _arrow3136(__unit: None=None, s_1: Any=s_1) -> Callable[[Process], IEncodable]:
+            study_name_1: str | None = s_1.Identifier
+            def _arrow3135(oa_4: Process) -> IEncodable:
+                return ISAJson_encoder_4(study_name_1, None, id_map, oa_4)
+
+            return _arrow3135
+
+        def _arrow3138(__unit: None=None, s_1: Any=s_1) -> Callable[[ArcAssay], IEncodable]:
+            study_name_2: str | None = s_1.Identifier
+            def _arrow3137(a_2: ArcAssay) -> IEncodable:
+                return ISAJson_encoder_5(study_name_2, id_map, a_2)
+
+            return _arrow3137
+
+        def _arrow3139(comment: Comment, s_1: Any=s_1) -> IEncodable:
+            return ISAJson_encoder_6(id_map, comment)
+
+        values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([("@id", _arrow3120()), ("filename", ObjectExpr3121()), ("identifier", _arrow3123()), try_include("title", _arrow3125, study.Title), try_include("description", _arrow3127, study.Description), try_include("submissionDate", _arrow3129, study.SubmissionDate), try_include("publicReleaseDate", _arrow3131, study.PublicReleaseDate), try_include_seq("publications", _arrow3132, study.Publications), try_include_seq("people", _arrow3133, study.Contacts), try_include_seq("studyDesignDescriptors", _arrow3134, study.StudyDesignDescriptors), encoded_protocols, encoded_materials, try_include_list("processSequence", _arrow3136(), processes), try_include_seq("assays", _arrow3138(), assays_1), encoded_factors, encoded_characteristics, encoded_units, try_include_seq("comments", _arrow3139, study.Comments)]))
+        class ObjectExpr3140(IEncodable):
+            def Encode(self, helpers_7: IEncoderHelpers_1[Any], s_1: Any=s_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_7))
+
+                arg: IEnumerable_1[tuple[str, __A_]] = map_1(mapping_1, values)
+                return helpers_7.encode_object(arg)
+
+        return ObjectExpr3140()
+
+    if id_map is not None:
+        def _arrow3141(s_2: ArcStudy, id_map: Any=id_map, assays: Any=assays, s: Any=s) -> str:
+            return ROCrate_genID(s_2)
+
+        return encode(_arrow3141, f, s, id_map)
+
+    else: 
+        return f(s)
+
+
+
+ISAJson_allowedFields: FSharpList[str] = of_array(["@id", "filename", "identifier", "title", "description", "submissionDate", "publicReleaseDate", "publications", "people", "studyDesignDescriptors", "protocols", "materials", "assays", "factors", "characteristicCategories", "unitCategories", "processSequence", "comments", "@type", "@context"])
+
+def _arrow3156(get: IGetters) -> tuple[ArcStudy, FSharpList[ArcAssay]]:
+    def _arrow3144(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("identifier", string)
+
+    def def_thunk(__unit: None=None) -> str:
+        def _arrow3145(__unit: None=None) -> str | None:
+            object_arg_1: IOptionalGetter = get.Optional
+            return object_arg_1.Field("filename", string)
+
+        return default_arg(bind(Study_tryIdentifierFromFileName, _arrow3145()), create_missing_identifier())
+
+    identifier: str = default_arg_with(_arrow3144(), def_thunk)
+    def mapping(arg_6: FSharpList[Process]) -> Array[ArcTable]:
+        a: ArcTables = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(arg_6)
+        return a.Tables
+
+    def _arrow3146(__unit: None=None) -> FSharpList[Process] | None:
+        arg_5: Decoder_1[FSharpList[Process]] = list_1_2(ISAJson_decoder_1)
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("processSequence", arg_5)
+
+    tables: Array[ArcTable] | None = map(mapping, _arrow3146())
+    assays: FSharpList[ArcAssay] | None
+    arg_8: Decoder_1[FSharpList[ArcAssay]] = list_1_2(ISAJson_decoder_2)
+    object_arg_3: IOptionalGetter = get.Optional
+    assays = object_arg_3.Field("assays", arg_8)
+    persons_raw: Array[Person] | None
+    arg_10: Decoder_1[Array[Person]] = resize_array(ISAJson_decoder_3)
+    object_arg_4: IOptionalGetter = get.Optional
+    persons_raw = object_arg_4.Field("people", arg_10)
+    persons: Array[Person] = []
+    if persons_raw is not None:
+        enumerator: Any = get_enumerator(value_17(persons_raw))
+        try: 
+            while enumerator.System_Collections_IEnumerator_MoveNext():
+                person: Person = enumerator.System_Collections_Generic_IEnumerator_1_get_Current()
+                source_assays: IEnumerable_1[str] = Person_getSourceAssayIdentifiersFromComments(person)
+                with get_enumerator(source_assays) as enumerator_1:
+                    while enumerator_1.System_Collections_IEnumerator_MoveNext():
+                        assay_identifier: str = enumerator_1.System_Collections_Generic_IEnumerator_1_get_Current()
+                        with get_enumerator(value_17(assays)) as enumerator_2:
+                            while enumerator_2.System_Collections_IEnumerator_MoveNext():
+                                assay: ArcAssay = enumerator_2.System_Collections_Generic_IEnumerator_1_get_Current()
+                                if assay.Identifier == assay_identifier:
+                                    (assay.Performers.append(person))
+
+                person.Comments = Person_removeSourceAssayComments(person)
+                if is_empty(source_assays):
+                    (persons.append(person))
+
+
+        finally: 
+            dispose(enumerator)
+
+
+    def mapping_2(arg_11: FSharpList[ArcAssay]) -> Array[str]:
+        def mapping_1(a_1: ArcAssay, arg_11: Any=arg_11) -> str:
+            return a_1.Identifier
+
+        return list(map_2(mapping_1, arg_11))
+
+    assay_identifiers: Array[str] | None = map(mapping_2, assays)
+    def _arrow3149(__unit: None=None) -> str | None:
+        object_arg_5: IOptionalGetter = get.Optional
+        return object_arg_5.Field("title", string)
+
+    def _arrow3150(__unit: None=None) -> str | None:
+        object_arg_6: IOptionalGetter = get.Optional
+        return object_arg_6.Field("description", string)
+
+    def _arrow3151(__unit: None=None) -> str | None:
+        object_arg_7: IOptionalGetter = get.Optional
+        return object_arg_7.Field("submissionDate", string)
+
+    def _arrow3152(__unit: None=None) -> str | None:
+        object_arg_8: IOptionalGetter = get.Optional
+        return object_arg_8.Field("publicReleaseDate", string)
+
+    def _arrow3153(__unit: None=None) -> Array[Publication] | None:
+        arg_21: Decoder_1[Array[Publication]] = resize_array(ISAJson_decoder_4)
+        object_arg_9: IOptionalGetter = get.Optional
+        return object_arg_9.Field("publications", arg_21)
+
+    def _arrow3154(__unit: None=None) -> Array[OntologyAnnotation] | None:
+        arg_23: Decoder_1[Array[OntologyAnnotation]] = resize_array(OntologyAnnotation_ISAJson_decoder)
+        object_arg_10: IOptionalGetter = get.Optional
+        return object_arg_10.Field("studyDesignDescriptors", arg_23)
+
+    def _arrow3155(__unit: None=None) -> Array[Comment] | None:
+        arg_25: Decoder_1[Array[Comment]] = resize_array(ISAJson_decoder_5)
+        object_arg_11: IOptionalGetter = get.Optional
+        return object_arg_11.Field("comments", arg_25)
+
+    return (ArcStudy(identifier, _arrow3149(), _arrow3150(), _arrow3151(), _arrow3152(), _arrow3153(), None if (len(persons) == 0) else persons, _arrow3154(), tables, None, assay_identifiers, _arrow3155()), default_arg(assays, empty()))
+
+
+ISAJson_decoder: Decoder_1[tuple[ArcStudy, FSharpList[ArcAssay]]] = Decode_objectNoAdditionalProperties(ISAJson_allowedFields, _arrow3156)
+
+__all__ = ["Helper_getAssayInformation", "encoder", "decoder", "encoder_compressed", "decoder_compressed", "ROCrate_genID", "ROCrate_encoder", "ROCrate_decoder", "ISAJson_encoder", "ISAJson_allowedFields", "ISAJson_decoder"]
+