arctrl 3.0.0__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.datamap 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.datamap 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 _arrow3743(__unit: None=None, study: Any=study) -> IEncodable:
+        value: str = study.Identifier
+        class ObjectExpr3742(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr3742()
+
+    def _arrow3748(value_1: str, study: Any=study) -> IEncodable:
+        class ObjectExpr3746(IEncodable):
+            def Encode(self, helpers_1: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_1.encode_string(value_1)
+
+        return ObjectExpr3746()
+
+    def _arrow3752(value_3: str, study: Any=study) -> IEncodable:
+        class ObjectExpr3749(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_3)
+
+        return ObjectExpr3749()
+
+    def _arrow3756(value_5: str, study: Any=study) -> IEncodable:
+        class ObjectExpr3755(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_5)
+
+        return ObjectExpr3755()
+
+    def _arrow3759(value_7: str, study: Any=study) -> IEncodable:
+        class ObjectExpr3758(IEncodable):
+            def Encode(self, helpers_4: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_4.encode_string(value_7)
+
+        return ObjectExpr3758()
+
+    def _arrow3760(oa: Publication, study: Any=study) -> IEncodable:
+        return encoder_5(oa)
+
+    def _arrow3761(person: Person, study: Any=study) -> IEncodable:
+        return encoder_6(person)
+
+    def _arrow3763(oa_1: OntologyAnnotation, study: Any=study) -> IEncodable:
+        return OntologyAnnotation_encoder(oa_1)
+
+    def _arrow3764(table: ArcTable, study: Any=study) -> IEncodable:
+        return encoder_7(table)
+
+    def _arrow3765(dm: Datamap, study: Any=study) -> IEncodable:
+        return encoder_8(dm)
+
+    def _arrow3767(value_9: str, study: Any=study) -> IEncodable:
+        class ObjectExpr3766(IEncodable):
+            def Encode(self, helpers_5: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_5.encode_string(value_9)
+
+        return ObjectExpr3766()
+
+    def _arrow3768(comment: Comment, study: Any=study) -> IEncodable:
+        return encoder_9(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([("Identifier", _arrow3743()), try_include("Title", _arrow3748, study.Title), try_include("Description", _arrow3752, study.Description), try_include("SubmissionDate", _arrow3756, study.SubmissionDate), try_include("PublicReleaseDate", _arrow3759, study.PublicReleaseDate), try_include_seq("Publications", _arrow3760, study.Publications), try_include_seq("Contacts", _arrow3761, study.Contacts), try_include_seq("StudyDesignDescriptors", _arrow3763, study.StudyDesignDescriptors), try_include_seq("Tables", _arrow3764, study.Tables), try_include("Datamap", _arrow3765, study.Datamap), try_include_seq("RegisteredAssayIdentifiers", _arrow3767, study.RegisteredAssayIdentifiers), try_include_seq("Comments", _arrow3768, study.Comments)]))
+    class ObjectExpr3774(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 ObjectExpr3774()
+
+
+def _arrow3802(get: IGetters) -> ArcStudy:
+    def _arrow3779(__unit: None=None) -> str:
+        object_arg: IRequiredGetter = get.Required
+        return object_arg.Field("Identifier", string)
+
+    def _arrow3781(__unit: None=None) -> str | None:
+        object_arg_1: IOptionalGetter = get.Optional
+        return object_arg_1.Field("Title", string)
+
+    def _arrow3782(__unit: None=None) -> str | None:
+        object_arg_2: IOptionalGetter = get.Optional
+        return object_arg_2.Field("Description", string)
+
+    def _arrow3785(__unit: None=None) -> str | None:
+        object_arg_3: IOptionalGetter = get.Optional
+        return object_arg_3.Field("SubmissionDate", string)
+
+    def _arrow3786(__unit: None=None) -> str | None:
+        object_arg_4: IOptionalGetter = get.Optional
+        return object_arg_4.Field("PublicReleaseDate", string)
+
+    def _arrow3787(__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 _arrow3789(__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 _arrow3791(__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 _arrow3794(__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 _arrow3795(__unit: None=None) -> Datamap | None:
+        object_arg_9: IOptionalGetter = get.Optional
+        return object_arg_9.Field("Datamap", decoder_5)
+
+    def _arrow3798(__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 _arrow3799(__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(_arrow3779(), _arrow3781(), _arrow3782(), _arrow3785(), _arrow3786(), _arrow3787(), _arrow3789(), _arrow3791(), _arrow3794(), _arrow3795(), _arrow3798(), _arrow3799())
+
+
+decoder: Decoder_1[ArcStudy] = object(_arrow3802)
+
+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 _arrow3812(__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 ObjectExpr3811(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr3811()
+
+    def _arrow3817(value_1: str, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        class ObjectExpr3816(IEncodable):
+            def Encode(self, helpers_1: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_1.encode_string(value_1)
+
+        return ObjectExpr3816()
+
+    def _arrow3819(value_3: str, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        class ObjectExpr3818(IEncodable):
+            def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_2.encode_string(value_3)
+
+        return ObjectExpr3818()
+
+    def _arrow3822(value_5: str, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        class ObjectExpr3821(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_5)
+
+        return ObjectExpr3821()
+
+    def _arrow3824(value_7: str, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        class ObjectExpr3823(IEncodable):
+            def Encode(self, helpers_4: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_4.encode_string(value_7)
+
+        return ObjectExpr3823()
+
+    def _arrow3825(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 _arrow3826(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 _arrow3827(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 _arrow3828(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 _arrow3830(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 _arrow3835(value_9: str, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table, study: Any=study) -> IEncodable:
+        class ObjectExpr3834(IEncodable):
+            def Encode(self, helpers_5: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_5.encode_string(value_9)
+
+        return ObjectExpr3834()
+
+    def _arrow3836(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", _arrow3812()), try_include("Title", _arrow3817, study.Title), try_include("Description", _arrow3819, study.Description), try_include("SubmissionDate", _arrow3822, study.SubmissionDate), try_include("PublicReleaseDate", _arrow3824, study.PublicReleaseDate), try_include_seq("Publications", _arrow3825, study.Publications), try_include_seq("Contacts", _arrow3826, study.Contacts), try_include_seq("StudyDesignDescriptors", _arrow3827, study.StudyDesignDescriptors), try_include_seq("Tables", _arrow3828, study.Tables), try_include("Datamap", _arrow3830, study.Datamap), try_include_seq("RegisteredAssayIdentifiers", _arrow3835, study.RegisteredAssayIdentifiers), try_include_seq("Comments", _arrow3836, study.Comments)]))
+    class ObjectExpr3839(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 ObjectExpr3839()
+
+
+def decoder_compressed(string_table: Array[str], oa_table: Array[OntologyAnnotation], cell_table: Array[CompositeCell]) -> Decoder_1[ArcStudy]:
+    def _arrow3858(get: IGetters, string_table: Any=string_table, oa_table: Any=oa_table, cell_table: Any=cell_table) -> ArcStudy:
+        def _arrow3845(__unit: None=None) -> str:
+            object_arg: IRequiredGetter = get.Required
+            return object_arg.Field("Identifier", string)
+
+        def _arrow3847(__unit: None=None) -> str | None:
+            object_arg_1: IOptionalGetter = get.Optional
+            return object_arg_1.Field("Title", string)
+
+        def _arrow3848(__unit: None=None) -> str | None:
+            object_arg_2: IOptionalGetter = get.Optional
+            return object_arg_2.Field("Description", string)
+
+        def _arrow3849(__unit: None=None) -> str | None:
+            object_arg_3: IOptionalGetter = get.Optional
+            return object_arg_3.Field("SubmissionDate", string)
+
+        def _arrow3850(__unit: None=None) -> str | None:
+            object_arg_4: IOptionalGetter = get.Optional
+            return object_arg_4.Field("PublicReleaseDate", string)
+
+        def _arrow3851(__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 _arrow3852(__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 _arrow3853(__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 _arrow3854(__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 _arrow3855(__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 _arrow3856(__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 _arrow3857(__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(_arrow3845(), _arrow3847(), _arrow3848(), _arrow3849(), _arrow3850(), _arrow3851(), _arrow3852(), _arrow3853(), _arrow3854(), _arrow3855(), _arrow3856(), _arrow3857())
+
+    return object(_arrow3858)
+
+
+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 _arrow3862(__unit: None=None, assays: Any=assays, s: Any=s) -> IEncodable:
+        value: str = ROCrate_genID(s)
+        class ObjectExpr3861(IEncodable):
+            def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                return helpers.encode_string(value)
+
+        return ObjectExpr3861()
+
+    class ObjectExpr3863(IEncodable):
+        def Encode(self, helpers_1: IEncoderHelpers_1[Any], assays: Any=assays, s: Any=s) -> Any:
+            return helpers_1.encode_string("Study")
+
+    class ObjectExpr3864(IEncodable):
+        def Encode(self, helpers_2: IEncoderHelpers_1[Any], assays: Any=assays, s: Any=s) -> Any:
+            return helpers_2.encode_string("Study")
+
+    def _arrow3866(__unit: None=None, assays: Any=assays, s: Any=s) -> IEncodable:
+        value_3: str = s.Identifier
+        class ObjectExpr3865(IEncodable):
+            def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_3.encode_string(value_3)
+
+        return ObjectExpr3865()
+
+    def _arrow3868(value_4: str, assays: Any=assays, s: Any=s) -> IEncodable:
+        class ObjectExpr3867(IEncodable):
+            def Encode(self, helpers_4: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_4.encode_string(value_4)
+
+        return ObjectExpr3867()
+
+    def _arrow3870(value_6: str, assays: Any=assays, s: Any=s) -> IEncodable:
+        class ObjectExpr3869(IEncodable):
+            def Encode(self, helpers_5: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_5.encode_string(value_6)
+
+        return ObjectExpr3869()
+
+    def _arrow3872(value_8: str, assays: Any=assays, s: Any=s) -> IEncodable:
+        class ObjectExpr3871(IEncodable):
+            def Encode(self, helpers_6: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_6.encode_string(value_8)
+
+        return ObjectExpr3871()
+
+    def _arrow3873(oa: OntologyAnnotation, assays: Any=assays, s: Any=s) -> IEncodable:
+        return OntologyAnnotation_ROCrate_encoderDefinedTerm(oa)
+
+    def _arrow3875(value_10: str, assays: Any=assays, s: Any=s) -> IEncodable:
+        class ObjectExpr3874(IEncodable):
+            def Encode(self, helpers_7: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_7.encode_string(value_10)
+
+        return ObjectExpr3874()
+
+    def _arrow3877(value_12: str, assays: Any=assays, s: Any=s) -> IEncodable:
+        class ObjectExpr3876(IEncodable):
+            def Encode(self, helpers_8: IEncoderHelpers_1[Any]) -> Any:
+                return helpers_8.encode_string(value_12)
+
+        return ObjectExpr3876()
+
+    def _arrow3878(oa_1: Publication, assays: Any=assays, s: Any=s) -> IEncodable:
+        return ROCrate_encoder_1(oa_1)
+
+    def _arrow3879(oa_2: Person, assays: Any=assays, s: Any=s) -> IEncodable:
+        return ROCrate_encoder_2(oa_2)
+
+    def _arrow3881(__unit: None=None, assays: Any=assays, s: Any=s) -> Callable[[Process], IEncodable]:
+        study_name: str | None = s.Identifier
+        def _arrow3880(oa_3: Process) -> IEncodable:
+            return ROCrate_encoder_3(study_name, None, oa_3)
+
+        return _arrow3880
+
+    def _arrow3883(__unit: None=None, assays: Any=assays, s: Any=s) -> Callable[[ArcAssay], IEncodable]:
+        assay_name_1: str | None = s.Identifier
+        def _arrow3882(a_1: ArcAssay) -> IEncodable:
+            return ROCrate_encoder_4(assay_name_1, a_1)
+
+        return _arrow3882
+
+    def _arrow3884(oa_4: Data, assays: Any=assays, s: Any=s) -> IEncodable:
+        return ROCrate_encoder_5(oa_4)
+
+    def _arrow3885(comment: Comment, assays: Any=assays, s: Any=s) -> IEncodable:
+        return ROCrate_encoder_6(comment)
+
+    values: FSharpList[tuple[str, IEncodable]] = choose(chooser, of_array([("@id", _arrow3862()), ("@type", list_1_1(singleton(ObjectExpr3863()))), ("additionalType", ObjectExpr3864()), ("identifier", _arrow3866()), try_include("filename", _arrow3868, file_name), try_include("title", _arrow3870, s.Title), try_include("description", _arrow3872, s.Description), try_include_seq("studyDesignDescriptors", _arrow3873, s.StudyDesignDescriptors), try_include("submissionDate", _arrow3875, s.SubmissionDate), try_include("publicReleaseDate", _arrow3877, s.PublicReleaseDate), try_include_seq("publications", _arrow3878, s.Publications), try_include_seq("people", _arrow3879, s.Contacts), try_include_list("processSequence", _arrow3881(), processes), try_include_seq("assays", _arrow3883(), assays_1), try_include_list("dataFiles", _arrow3884, get_data(processes)), try_include_seq("comments", _arrow3885, s.Comments), ("@context", context_jsonvalue)]))
+    class ObjectExpr3886(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 ObjectExpr3886()
+
+
+def _arrow3897(get: IGetters) -> tuple[ArcStudy, FSharpList[ArcAssay]]:
+    def _arrow3887(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("filename", string)
+
+    identifier: str = default_arg(bind(Study_tryIdentifierFromFileName, _arrow3887()), 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 _arrow3888(__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, _arrow3888())
+    def _arrow3889(__unit: None=None) -> str | None:
+        object_arg_3: IOptionalGetter = get.Optional
+        return object_arg_3.Field("title", string)
+
+    def _arrow3890(__unit: None=None) -> str | None:
+        object_arg_4: IOptionalGetter = get.Optional
+        return object_arg_4.Field("description", string)
+
+    def _arrow3891(__unit: None=None) -> str | None:
+        object_arg_5: IOptionalGetter = get.Optional
+        return object_arg_5.Field("submissionDate", string)
+
+    def _arrow3892(__unit: None=None) -> str | None:
+        object_arg_6: IOptionalGetter = get.Optional
+        return object_arg_6.Field("publicReleaseDate", string)
+
+    def _arrow3893(__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 _arrow3894(__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 _arrow3895(__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 _arrow3896(__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, _arrow3889(), _arrow3890(), _arrow3891(), _arrow3892(), _arrow3893(), _arrow3894(), _arrow3895(), tables, None, assay_identifiers, _arrow3896()), default_arg(assays, empty()))
+
+
+ROCrate_decoder: Decoder_1[tuple[ArcStudy, FSharpList[ArcAssay]]] = object(_arrow3897)
+
+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 _arrow3898(ps: FSharpList[Process], s_1: Any=s_1) -> IEncodable:
+            return encoder_12(id_map, ps)
+
+        encoded_materials: tuple[str, IEncodable | None] = try_include("materials", _arrow3898, Option_fromValueWithDefault(empty(), processes))
+        encoded_protocols: tuple[str, IEncodable | None]
+        value_5: FSharpList[Protocol] = get_protocols(processes)
+        def _arrow3900(__unit: None=None, s_1: Any=s_1) -> Callable[[Protocol], IEncodable]:
+            study_name: str | None = s_1.Identifier
+            def _arrow3899(oa_1: Protocol) -> IEncodable:
+                return ISAJson_encoder_1(study_name, None, None, id_map, oa_1)
+
+            return _arrow3899
+
+        encoded_protocols = try_include_list("protocols", _arrow3900(), 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 _arrow3904(__unit: None=None, s_1: Any=s_1) -> IEncodable:
+            value_6: str = ROCrate_genID(study)
+            class ObjectExpr3903(IEncodable):
+                def Encode(self, helpers: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers.encode_string(value_6)
+
+            return ObjectExpr3903()
+
+        class ObjectExpr3905(IEncodable):
+            def Encode(self, helpers_1: IEncoderHelpers_1[Any], s_1: Any=s_1) -> Any:
+                return helpers_1.encode_string(file_name)
+
+        def _arrow3907(__unit: None=None, s_1: Any=s_1) -> IEncodable:
+            value_8: str = study.Identifier
+            class ObjectExpr3906(IEncodable):
+                def Encode(self, helpers_2: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_2.encode_string(value_8)
+
+            return ObjectExpr3906()
+
+        def _arrow3909(value_9: str, s_1: Any=s_1) -> IEncodable:
+            class ObjectExpr3908(IEncodable):
+                def Encode(self, helpers_3: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_3.encode_string(value_9)
+
+            return ObjectExpr3908()
+
+        def _arrow3911(value_11: str, s_1: Any=s_1) -> IEncodable:
+            class ObjectExpr3910(IEncodable):
+                def Encode(self, helpers_4: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_4.encode_string(value_11)
+
+            return ObjectExpr3910()
+
+        def _arrow3913(value_13: str, s_1: Any=s_1) -> IEncodable:
+            class ObjectExpr3912(IEncodable):
+                def Encode(self, helpers_5: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_5.encode_string(value_13)
+
+            return ObjectExpr3912()
+
+        def _arrow3915(value_15: str, s_1: Any=s_1) -> IEncodable:
+            class ObjectExpr3914(IEncodable):
+                def Encode(self, helpers_6: IEncoderHelpers_1[Any]) -> Any:
+                    return helpers_6.encode_string(value_15)
+
+            return ObjectExpr3914()
+
+        def _arrow3916(oa_2: Publication, s_1: Any=s_1) -> IEncodable:
+            return ISAJson_encoder_2(id_map, oa_2)
+
+        def _arrow3917(person_2: Person, s_1: Any=s_1) -> IEncodable:
+            return ISAJson_encoder_3(id_map, person_2)
+
+        def _arrow3918(oa_3: OntologyAnnotation, s_1: Any=s_1) -> IEncodable:
+            return OntologyAnnotation_ISAJson_encoder(id_map, oa_3)
+
+        def _arrow3920(__unit: None=None, s_1: Any=s_1) -> Callable[[Process], IEncodable]:
+            study_name_1: str | None = s_1.Identifier
+            def _arrow3919(oa_4: Process) -> IEncodable:
+                return ISAJson_encoder_4(study_name_1, None, id_map, oa_4)
+
+            return _arrow3919
+
+        def _arrow3922(__unit: None=None, s_1: Any=s_1) -> Callable[[ArcAssay], IEncodable]:
+            study_name_2: str | None = s_1.Identifier
+            def _arrow3921(a_2: ArcAssay) -> IEncodable:
+                return ISAJson_encoder_5(study_name_2, id_map, a_2)
+
+            return _arrow3921
+
+        def _arrow3923(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", _arrow3904()), ("filename", ObjectExpr3905()), ("identifier", _arrow3907()), try_include("title", _arrow3909, study.Title), try_include("description", _arrow3911, study.Description), try_include("submissionDate", _arrow3913, study.SubmissionDate), try_include("publicReleaseDate", _arrow3915, study.PublicReleaseDate), try_include_seq("publications", _arrow3916, study.Publications), try_include_seq("people", _arrow3917, study.Contacts), try_include_seq("studyDesignDescriptors", _arrow3918, study.StudyDesignDescriptors), encoded_protocols, encoded_materials, try_include_list("processSequence", _arrow3920(), processes), try_include_seq("assays", _arrow3922(), assays_1), encoded_factors, encoded_characteristics, encoded_units, try_include_seq("comments", _arrow3923, study.Comments)]))
+        class ObjectExpr3924(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 ObjectExpr3924()
+
+    if id_map is not None:
+        def _arrow3925(s_2: ArcStudy, id_map: Any=id_map, assays: Any=assays, s: Any=s) -> str:
+            return ROCrate_genID(s_2)
+
+        return encode(_arrow3925, 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 _arrow3936(get: IGetters) -> tuple[ArcStudy, FSharpList[ArcAssay]]:
+    def _arrow3926(__unit: None=None) -> str | None:
+        object_arg: IOptionalGetter = get.Optional
+        return object_arg.Field("identifier", string)
+
+    def def_thunk(__unit: None=None) -> str:
+        def _arrow3927(__unit: None=None) -> str | None:
+            object_arg_1: IOptionalGetter = get.Optional
+            return object_arg_1.Field("filename", string)
+
+        return default_arg(bind(Study_tryIdentifierFromFileName, _arrow3927()), create_missing_identifier())
+
+    identifier: str = default_arg_with(_arrow3926(), def_thunk)
+    def mapping(arg_6: FSharpList[Process]) -> Array[ArcTable]:
+        a: ArcTables = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(arg_6)
+        return a.Tables
+
+    def _arrow3928(__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, _arrow3928())
+    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 _arrow3929(__unit: None=None) -> str | None:
+        object_arg_5: IOptionalGetter = get.Optional
+        return object_arg_5.Field("title", string)
+
+    def _arrow3930(__unit: None=None) -> str | None:
+        object_arg_6: IOptionalGetter = get.Optional
+        return object_arg_6.Field("description", string)
+
+    def _arrow3931(__unit: None=None) -> str | None:
+        object_arg_7: IOptionalGetter = get.Optional
+        return object_arg_7.Field("submissionDate", string)
+
+    def _arrow3932(__unit: None=None) -> str | None:
+        object_arg_8: IOptionalGetter = get.Optional
+        return object_arg_8.Field("publicReleaseDate", string)
+
+    def _arrow3933(__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 _arrow3934(__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 _arrow3935(__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, _arrow3929(), _arrow3930(), _arrow3931(), _arrow3932(), _arrow3933(), None if (len(persons) == 0) else persons, _arrow3934(), tables, None, assay_identifiers, _arrow3935()), default_arg(assays, empty()))
+
+
+ISAJson_decoder: Decoder_1[tuple[ArcStudy, FSharpList[ArcAssay]]] = Decode_objectNoAdditionalProperties(ISAJson_allowedFields, _arrow3936)
+
+__all__ = ["Helper_getAssayInformation", "encoder", "decoder", "encoder_compressed", "decoder_compressed", "ROCrate_genID", "ROCrate_encoder", "ROCrate_decoder", "ISAJson_encoder", "ISAJson_allowedFields", "ISAJson_decoder"]
+