arctrl 3.0.0a3__py3-none-any.whl

arctrl/py/json.py

@@ -0,0 +1,213 @@
+from __future__ import annotations
+from collections.abc import Callable
+from .Core.arc_types import (ArcAssay, ArcStudy, ArcInvestigation)
+from .Core.ontology_annotation import OntologyAnnotation
+from .arc import ARC
+from .JsonIO.assay import (ARCtrl_ArcAssay__ArcAssay_fromJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_toJsonString_Static_71136F3F, ARCtrl_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_Z3B036AA, ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47)
+from .JsonIO.investigation import (ARCtrl_ArcInvestigation__ArcInvestigation_fromJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_toJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_Z3B036AA, ARCtrl_ArcInvestigation__ArcInvestigation_toROCrateJsonString_Static_71136F3F)
+from .JsonIO.ontology_annotation import (ARCtrl_OntologyAnnotation__OntologyAnnotation_fromJsonString_Static_Z721C83C5, ARCtrl_OntologyAnnotation__OntologyAnnotation_fromISAJsonString_Static_Z721C83C5, ARCtrl_OntologyAnnotation__OntologyAnnotation_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_OntologyAnnotation__OntologyAnnotation_toJsonString_Static_71136F3F, ARCtrl_OntologyAnnotation__OntologyAnnotation_toISAJsonString_Static_71136F3F, ARCtrl_OntologyAnnotation__OntologyAnnotation_toROCrateJsonString_Static_71136F3F)
+from .JsonIO.study import (ARCtrl_ArcStudy__ArcStudy_fromJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_toJsonString_Static_71136F3F, ARCtrl_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_Z3FD920F1, ARCtrl_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086)
+from .fable_modules.fable_library.list import FSharpList
+from .fable_modules.fable_library.reflection import (TypeInfo, class_type)
+
+def _expr3761() -> TypeInfo:
+    return class_type("ARCtrl.JsonHelper.OntologyAnnotationJson", None, JsonHelper_OntologyAnnotationJson)
+
+
+class JsonHelper_OntologyAnnotationJson:
+    def __init__(self, __unit: None=None) -> None:
+        pass
+
+    def from_json_string(self, s: str) -> OntologyAnnotation:
+        return ARCtrl_OntologyAnnotation__OntologyAnnotation_fromJsonString_Static_Z721C83C5(s)
+
+    def from_isajson_string(self, s: str) -> OntologyAnnotation:
+        return ARCtrl_OntologyAnnotation__OntologyAnnotation_fromISAJsonString_Static_Z721C83C5(s)
+
+    def from_rocrate_json_string(self, s: str) -> OntologyAnnotation:
+        return ARCtrl_OntologyAnnotation__OntologyAnnotation_fromROCrateJsonString_Static_Z721C83C5(s)
+
+    def to_json_string(self, oa: OntologyAnnotation, spaces: int | None=None) -> str:
+        return ARCtrl_OntologyAnnotation__OntologyAnnotation_toJsonString_Static_71136F3F(spaces)(oa)
+
+    def to_isajson_string(self, oa: OntologyAnnotation, spaces: int | None=None) -> str:
+        return ARCtrl_OntologyAnnotation__OntologyAnnotation_toISAJsonString_Static_71136F3F(spaces)(oa)
+
+    def to_rocrate_json_string(self, oa: OntologyAnnotation, spaces: int | None=None) -> str:
+        return ARCtrl_OntologyAnnotation__OntologyAnnotation_toROCrateJsonString_Static_71136F3F(spaces)(oa)
+
+
+JsonHelper_OntologyAnnotationJson_reflection = _expr3761
+
+def JsonHelper_OntologyAnnotationJson__ctor(__unit: None=None) -> JsonHelper_OntologyAnnotationJson:
+    return JsonHelper_OntologyAnnotationJson(__unit)
+
+
+def _expr3762() -> TypeInfo:
+    return class_type("ARCtrl.JsonHelper.AssayJson", None, JsonHelper_AssayJson)
+
+
+class JsonHelper_AssayJson:
+    def __init__(self, __unit: None=None) -> None:
+        pass
+
+    def from_json_string(self, s: str) -> ArcAssay:
+        return ARCtrl_ArcAssay__ArcAssay_fromJsonString_Static_Z721C83C5(s)
+
+    def from_compressed_json_string(self, s: str) -> ArcAssay:
+        return ARCtrl_ArcAssay__ArcAssay_fromCompressedJsonString_Static_Z721C83C5(s)
+
+    def from_isajson_string(self, s: str) -> ArcAssay:
+        return ARCtrl_ArcAssay__ArcAssay_fromISAJsonString_Static_Z721C83C5(s)
+
+    def from_rocrate_json_string(self, s: str) -> ArcAssay:
+        return ARCtrl_ArcAssay__ArcAssay_fromROCrateJsonString_Static_Z721C83C5(s)
+
+    def to_json_string(self, assay: ArcAssay, spaces: int | None=None) -> str:
+        return ARCtrl_ArcAssay__ArcAssay_toJsonString_Static_71136F3F(spaces)(assay)
+
+    def to_compressed_json_string(self, assay: ArcAssay, spaces: int | None=None) -> str:
+        return ARCtrl_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F(spaces)(assay)
+
+    def to_isajson_string(self, assay: ArcAssay, spaces: int | None=None, use_idreferencing: bool | None=None) -> str:
+        return ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_Z3B036AA(spaces, use_idreferencing)(assay)
+
+    def to_rocrate_json_string(self, assay: ArcAssay, study_name: str, spaces: int | None=None) -> str:
+        return ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47(study_name, spaces)(assay)
+
+
+JsonHelper_AssayJson_reflection = _expr3762
+
+def JsonHelper_AssayJson__ctor(__unit: None=None) -> JsonHelper_AssayJson:
+    return JsonHelper_AssayJson(__unit)
+
+
+def _expr3763() -> TypeInfo:
+    return class_type("ARCtrl.JsonHelper.StudyJson", None, JsonHelper_StudyJson)
+
+
+class JsonHelper_StudyJson:
+    def __init__(self, __unit: None=None) -> None:
+        pass
+
+    def from_json_string(self, s: str) -> ArcStudy:
+        return ARCtrl_ArcStudy__ArcStudy_fromJsonString_Static_Z721C83C5(s)
+
+    def from_compressed_json_string(self, s: str) -> ArcStudy:
+        return ARCtrl_ArcStudy__ArcStudy_fromCompressedJsonString_Static_Z721C83C5(s)
+
+    def from_isajson_string(self, s: str) -> tuple[ArcStudy, FSharpList[ArcAssay]]:
+        return ARCtrl_ArcStudy__ArcStudy_fromISAJsonString_Static_Z721C83C5(s)
+
+    def from_rocrate_json_string(self, s: str) -> tuple[ArcStudy, FSharpList[ArcAssay]]:
+        return ARCtrl_ArcStudy__ArcStudy_fromROCrateJsonString_Static_Z721C83C5(s)
+
+    def to_json_string(self, study: ArcStudy, spaces: int | None=None) -> str:
+        return ARCtrl_ArcStudy__ArcStudy_toJsonString_Static_71136F3F(spaces)(study)
+
+    def to_compressed_json_string(self, study: ArcStudy, spaces: int | None=None) -> str:
+        return ARCtrl_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F(spaces)(study)
+
+    def to_isajson_string(self, study: ArcStudy, assays: FSharpList[ArcAssay] | None=None, spaces: int | None=None, use_idreferencing: bool | None=None) -> str:
+        return ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_Z3FD920F1(assays, spaces, use_idreferencing)(study)
+
+    def to_rocrate_json_string(self, study: ArcStudy, assays: FSharpList[ArcAssay] | None=None, spaces: int | None=None) -> str:
+        return ARCtrl_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086(assays, spaces)(study)
+
+
+JsonHelper_StudyJson_reflection = _expr3763
+
+def JsonHelper_StudyJson__ctor(__unit: None=None) -> JsonHelper_StudyJson:
+    return JsonHelper_StudyJson(__unit)
+
+
+def _expr3764() -> TypeInfo:
+    return class_type("ARCtrl.JsonHelper.InvestigationJson", None, JsonHelper_InvestigationJson)
+
+
+class JsonHelper_InvestigationJson:
+    def __init__(self, __unit: None=None) -> None:
+        pass
+
+    def from_json_string(self, s: str) -> ArcInvestigation:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromJsonString_Static_Z721C83C5(s)
+
+    def from_compressed_json_string(self, s: str) -> ArcInvestigation:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromCompressedJsonString_Static_Z721C83C5(s)
+
+    def from_isajson_string(self, s: str) -> ArcInvestigation:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromISAJsonString_Static_Z721C83C5(s)
+
+    def from_rocrate_json_string(self, s: str) -> ArcInvestigation:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateJsonString_Static_Z721C83C5(s)
+
+    def to_json_string(self, investigation: ArcInvestigation, spaces: int | None=None) -> str:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_toJsonString_Static_71136F3F(spaces)(investigation)
+
+    def to_compressed_json_string(self, investigation: ArcInvestigation, spaces: int | None=None) -> str:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_toCompressedJsonString_Static_71136F3F(spaces)(investigation)
+
+    def to_isajson_string(self, investigation: ArcInvestigation, spaces: int | None=None, use_idreferencing: bool | None=None) -> str:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_Z3B036AA(spaces, use_idreferencing)(investigation)
+
+    def to_rocrate_json_string(self, investigation: ArcInvestigation, spaces: int | None=None) -> str:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_toROCrateJsonString_Static_71136F3F(spaces)(investigation)
+
+
+JsonHelper_InvestigationJson_reflection = _expr3764
+
+def JsonHelper_InvestigationJson__ctor(__unit: None=None) -> JsonHelper_InvestigationJson:
+    return JsonHelper_InvestigationJson(__unit)
+
+
+def _expr3765() -> TypeInfo:
+    return class_type("ARCtrl.JsonHelper.ARCJson", None, JsonHelper_ARCJson)
+
+
+class JsonHelper_ARCJson:
+    def __init__(self, __unit: None=None) -> None:
+        pass
+
+    def from_rocrate_json_string(self, s: str) -> ARC:
+        return ARC.from_rocrate_json_string(s)
+
+    def to_rocrate_json_string(self, spaces: int | None=None) -> Callable[[ARC], str]:
+        return ARC.to_rocrate_json_string(spaces)
+
+
+JsonHelper_ARCJson_reflection = _expr3765
+
+def JsonHelper_ARCJson__ctor(__unit: None=None) -> JsonHelper_ARCJson:
+    return JsonHelper_ARCJson(__unit)
+
+
+def _expr3766() -> TypeInfo:
+    return class_type("ARCtrl.JsonController", None, JsonController)
+
+
+class JsonController:
+    @staticmethod
+    def OntologyAnnotation() -> JsonHelper_OntologyAnnotationJson:
+        return JsonHelper_OntologyAnnotationJson()
+
+    @staticmethod
+    def Assay() -> JsonHelper_AssayJson:
+        return JsonHelper_AssayJson()
+
+    @staticmethod
+    def Study() -> JsonHelper_StudyJson:
+        return JsonHelper_StudyJson()
+
+    @staticmethod
+    def Investigation() -> JsonHelper_InvestigationJson:
+        return JsonHelper_InvestigationJson()
+
+    @staticmethod
+    def ARC() -> JsonHelper_ARCJson:
+        return JsonHelper_ARCJson()
+
+
+JsonController_reflection = _expr3766
+
+__all__ = ["JsonHelper_OntologyAnnotationJson_reflection", "JsonHelper_AssayJson_reflection", "JsonHelper_StudyJson_reflection", "JsonHelper_InvestigationJson_reflection", "JsonHelper_ARCJson_reflection", "JsonController_reflection"]
+

arctrl/py/rocrate_io.py

@@ -0,0 +1,72 @@
+from __future__ import annotations
+from typing import Any
+from .Core.arc_types import ArcInvestigation
+from .Json.ROCrate.ldgraph import (encoder, decoder)
+from .Json.ROCrate.ldnode import decoder as decoder_1
+from .ROCrate.Generic.dataset import LDDataset
+from .ROCrate.ldcontext import LDContext
+from .ROCrate.ldobject import (LDNode, LDRef, LDGraph)
+from .ROCrate.rocrate_context import (init_v1_1, init_bioschemas_context)
+from .conversion import (ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation, ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8)
+from .fable_modules.fable_library.date import now
+from .fable_modules.fable_library.option import value
+from .fable_modules.fable_library.reflection import (TypeInfo, class_type)
+from .fable_modules.fable_library.seq import exactly_one
+from .fable_modules.thoth_json_core.decode import map
+from .fable_modules.thoth_json_core.types import (IEncodable, Decoder_1)
+
+def _expr3578() -> TypeInfo:
+    return class_type("ARCtrl.Json.ARC.ROCrate", None, ROCrate)
+
+
+class ROCrate:
+    ...
+
+ROCrate_reflection = _expr3578
+
+def ROCrate_getDefaultLicense(__unit: None=None) -> str:
+    return "ALL RIGHTS RESERVED BY THE AUTHORS"
+
+
+def ROCrate_get_metadataFileDescriptor(__unit: None=None) -> LDNode:
+    node: LDNode = LDNode("ro-crate-metadata.json", ["http://schema.org/CreativeWork"])
+    node.SetProperty("http://purl.org/dc/terms/conformsTo", LDRef("https://w3id.org/ro/crate/1.1"))
+    node.SetProperty("http://schema.org/about", LDRef("./"))
+    return node
+
+
+def ROCrate_encoder_8A8D439(isa: ArcInvestigation, license: Any | None=None) -> IEncodable:
+    license_2: Any = ROCrate_getDefaultLicense() if (license is None) else value(license)
+    isa_1: LDNode = ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation(isa)
+    LDDataset.set_sddate_published_as_date_time(isa_1, now())
+    LDDataset.set_license_as_creative_work(isa_1, license_2)
+    graph: LDGraph = isa_1.Flatten()
+    context: LDContext = LDContext(None, [init_v1_1(), init_bioschemas_context()])
+    graph.SetContext(context)
+    graph.AddNode(ROCrate_get_metadataFileDescriptor())
+    graph.Compact_InPlace()
+    return encoder(graph)
+
+
+def ROCrate_get_decoder(__unit: None=None) -> Decoder_1[ArcInvestigation]:
+    def ctor(graph: LDGraph) -> ArcInvestigation:
+        match_value: LDNode | None = graph.TryGetNode("./")
+        if match_value is None:
+            raise Exception("RO-Crate graph did not contain root data Entity")
+
+        else: 
+            return ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(match_value, graph, graph.TryGetContext())
+
+
+    return map(ctor, decoder)
+
+
+def ROCrate_get_decoderDeprecated(__unit: None=None) -> Decoder_1[ArcInvestigation]:
+    def ctor(ldnode: LDNode) -> ArcInvestigation:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(exactly_one(LDDataset.get_abouts(ldnode)), None, init_v1_1())
+
+    return map(ctor, decoder_1)
+
+
+__all__ = ["ROCrate_reflection", "ROCrate_getDefaultLicense", "ROCrate_get_metadataFileDescriptor", "ROCrate_encoder_8A8D439", "ROCrate_get_decoder", "ROCrate_get_decoderDeprecated"]
+

arctrl/py/template_web.py

@@ -0,0 +1,23 @@
+from __future__ import annotations
+from typing import Any
+from .Core.template import Template
+from .JsonIO.Table.templates import Templates_fromJsonString
+from .fable_modules.fable_library.async_builder import (singleton, Async)
+from .fable_modules.fable_library.option import default_arg
+from .fable_modules.fable_library.types import Array
+from .WebRequest.web_request import download_file
+
+def get_templates(url: str | None=None) -> Async[Array[Template]]:
+    url_1: str = default_arg(url, "https://github.com/nfdi4plants/Swate-templates/releases/download/latest/templates_v2.0.0.json")
+    def _arrow3626(__unit: None=None, url: Any=url) -> Async[Array[Template]]:
+        def _arrow3625(_arg: str) -> Async[Array[Template]]:
+            map_result: Array[Template] = Templates_fromJsonString(_arg)
+            return singleton.Return(map_result)
+
+        return singleton.Bind(download_file(url_1), _arrow3625)
+
+    return singleton.Delay(_arrow3626)
+
+
+__all__ = ["get_templates"]
+

arctrl/py/xlsx.py

@@ -0,0 +1,148 @@
+from __future__ import annotations
+from .Core.arc_types import (ArcAssay, ArcStudy, ArcInvestigation)
+from .Core.data_map import DataMap
+from .Spreadsheet.arc_assay import (ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D, ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F)
+from .Spreadsheet.arc_investigation import (ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D, ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF)
+from .Spreadsheet.arc_study import (ARCtrl_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D, ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522)
+from .Spreadsheet.data_map import (from_fs_workbook, to_fs_workbook)
+from .fable_modules.fable_library.list import (FSharpList, of_seq)
+from .fable_modules.fable_library.option import map
+from .fable_modules.fable_library.reflection import (TypeInfo, class_type)
+from .fable_modules.fable_library.types import Array
+from .fable_modules.fs_spreadsheet.fs_workbook import FsWorkbook
+from .fable_modules.fs_spreadsheet_py.fs_extension import (FsSpreadsheet_FsWorkbook__FsWorkbook_fromXlsxFile_Static_Z721C83C5, FsSpreadsheet_FsWorkbook__FsWorkbook_toXlsxFile_Static)
+
+def _expr3767() -> TypeInfo:
+    return class_type("ARCtrl.XlsxHelper.DatamapXlsx", None, XlsxHelper_DatamapXlsx)
+
+
+class XlsxHelper_DatamapXlsx:
+    def __init__(self, __unit: None=None) -> None:
+        pass
+
+    def from_fs_workbook(self, fswb: FsWorkbook) -> DataMap:
+        return from_fs_workbook(fswb)
+
+    def to_fs_workbook(self, datamap: DataMap) -> FsWorkbook:
+        return to_fs_workbook(datamap)
+
+    def from_xlsx_file(self, path: str) -> DataMap:
+        return from_fs_workbook(FsSpreadsheet_FsWorkbook__FsWorkbook_fromXlsxFile_Static_Z721C83C5(path))
+
+    def to_xlsx_file(self, path: str, datamap: DataMap) -> None:
+        FsSpreadsheet_FsWorkbook__FsWorkbook_toXlsxFile_Static(path, to_fs_workbook(datamap))
+
+
+XlsxHelper_DatamapXlsx_reflection = _expr3767
+
+def XlsxHelper_DatamapXlsx__ctor(__unit: None=None) -> XlsxHelper_DatamapXlsx:
+    return XlsxHelper_DatamapXlsx(__unit)
+
+
+def _expr3768() -> TypeInfo:
+    return class_type("ARCtrl.XlsxHelper.AssayXlsx", None, XlsxHelper_AssayXlsx)
+
+
+class XlsxHelper_AssayXlsx:
+    def __init__(self, __unit: None=None) -> None:
+        pass
+
+    def from_fs_workbook(self, fswb: FsWorkbook) -> ArcAssay:
+        return ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D(fswb)
+
+    def to_fs_workbook(self, assay: ArcAssay) -> FsWorkbook:
+        return ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(assay)
+
+    def from_xlsx_file(self, path: str) -> ArcAssay:
+        return ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D(FsSpreadsheet_FsWorkbook__FsWorkbook_fromXlsxFile_Static_Z721C83C5(path))
+
+    def to_xlsx_file(self, path: str, assay: ArcAssay) -> None:
+        FsSpreadsheet_FsWorkbook__FsWorkbook_toXlsxFile_Static(path, ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(assay))
+
+
+XlsxHelper_AssayXlsx_reflection = _expr3768
+
+def XlsxHelper_AssayXlsx__ctor(__unit: None=None) -> XlsxHelper_AssayXlsx:
+    return XlsxHelper_AssayXlsx(__unit)
+
+
+def _expr3769() -> TypeInfo:
+    return class_type("ARCtrl.XlsxHelper.StudyXlsx", None, XlsxHelper_StudyXlsx)
+
+
+class XlsxHelper_StudyXlsx:
+    def __init__(self, __unit: None=None) -> None:
+        pass
+
+    def from_fs_workbook(self, fswb: FsWorkbook) -> tuple[ArcStudy, FSharpList[ArcAssay]]:
+        return ARCtrl_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(fswb)
+
+    def to_fs_workbook(self, study: ArcStudy, assays: Array[ArcAssay] | None=None) -> FsWorkbook:
+        return ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(study, map(of_seq, assays))
+
+    def from_xlsx_file(self, path: str) -> tuple[ArcStudy, FSharpList[ArcAssay]]:
+        return ARCtrl_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(FsSpreadsheet_FsWorkbook__FsWorkbook_fromXlsxFile_Static_Z721C83C5(path))
+
+    def to_xlsx_file(self, path: str, study: ArcStudy, assays: Array[ArcAssay] | None=None) -> None:
+        FsSpreadsheet_FsWorkbook__FsWorkbook_toXlsxFile_Static(path, ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(study, map(of_seq, assays)))
+
+
+XlsxHelper_StudyXlsx_reflection = _expr3769
+
+def XlsxHelper_StudyXlsx__ctor(__unit: None=None) -> XlsxHelper_StudyXlsx:
+    return XlsxHelper_StudyXlsx(__unit)
+
+
+def _expr3770() -> TypeInfo:
+    return class_type("ARCtrl.XlsxHelper.InvestigationXlsx", None, XlsxHelper_InvestigationXlsx)
+
+
+class XlsxHelper_InvestigationXlsx:
+    def __init__(self, __unit: None=None) -> None:
+        pass
+
+    def from_fs_workbook(self, fswb: FsWorkbook) -> ArcInvestigation:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D(fswb)
+
+    def to_fs_workbook(self, investigation: ArcInvestigation) -> FsWorkbook:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(investigation)
+
+    def from_xlsx_file(self, path: str) -> ArcInvestigation:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D(FsSpreadsheet_FsWorkbook__FsWorkbook_fromXlsxFile_Static_Z721C83C5(path))
+
+    def to_xlsx_file(self, path: str, investigation: ArcInvestigation) -> None:
+        FsSpreadsheet_FsWorkbook__FsWorkbook_toXlsxFile_Static(path, ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(investigation))
+
+
+XlsxHelper_InvestigationXlsx_reflection = _expr3770
+
+def XlsxHelper_InvestigationXlsx__ctor(__unit: None=None) -> XlsxHelper_InvestigationXlsx:
+    return XlsxHelper_InvestigationXlsx(__unit)
+
+
+def _expr3771() -> TypeInfo:
+    return class_type("ARCtrl.XlsxController", None, XlsxController)
+
+
+class XlsxController:
+    @staticmethod
+    def Datamap() -> XlsxHelper_DatamapXlsx:
+        return XlsxHelper_DatamapXlsx()
+
+    @staticmethod
+    def Assay() -> XlsxHelper_AssayXlsx:
+        return XlsxHelper_AssayXlsx()
+
+    @staticmethod
+    def Study() -> XlsxHelper_StudyXlsx:
+        return XlsxHelper_StudyXlsx()
+
+    @staticmethod
+    def Investigation() -> XlsxHelper_InvestigationXlsx:
+        return XlsxHelper_InvestigationXlsx()
+
+
+XlsxController_reflection = _expr3771
+
+__all__ = ["XlsxHelper_DatamapXlsx_reflection", "XlsxHelper_AssayXlsx_reflection", "XlsxHelper_StudyXlsx_reflection", "XlsxHelper_InvestigationXlsx_reflection", "XlsxController_reflection"]
+

arctrl/rocrate.py

@@ -0,0 +1,21 @@
+from __future__ import annotations
+from collections.abc import Callable
+from typing import Any
+from .py.ROCrate.ldobject import LDGraph, LDNode, LDValue, LDRef
+from .py.ROCrate.ldcontext import LDContext
+from .py.ROCrate.rocrate_context import init_v1_1, init_v1_2draft, init_bioschemas_context
+from .py.ROCrate.Generic.comment import LDComment
+from .py.ROCrate.Generic.defined_term import LDDefinedTerm
+from .py.ROCrate.Generic.file import LDFile
+from .py.ROCrate.Generic.lab_process import LDLabProcess
+from .py.ROCrate.Generic.lab_protocol import LDLabProtocol
+from .py.ROCrate.Generic.organization import LDOrganization
+from .py.ROCrate.Generic.person import LDPerson
+from .py.ROCrate.Generic.postal_address import LDPostalAddress
+from .py.ROCrate.Generic.property_value import LDPropertyValue
+from .py.ROCrate.Generic.sample import LDSample
+from .py.ROCrate.Generic.scholarly_article import LDScholarlyArticle
+from .py.ROCrate.Generic.dataset import LDDataset
+from .py.JsonIO.ldobject import LDGraphExtensions_PyJsInterop as LDGraphIO
+from .py.JsonIO.ldobject import LDNodeExtensions_PyJsInterop as LDNodeIO
+from .py.conversion import TypeExtensions_Conversion as Conversion

arctrl-3.0.0a3.dist-info/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 DataPLANT
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

arctrl-3.0.0a3.dist-info/METADATA

@@ -0,0 +1,119 @@
+Metadata-Version: 2.3
+Name: arctrl
+Version: 3.0.0a3
+Summary: Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtimer agnostic contract systems.
+Keywords: arc,annotated research context,isa,research data,multi platform
+Author: Heinrich Lukas Weil
+Author-email: weil@rptu.de
+Maintainer: Florian Wetzels
+Requires-Python: >=3.11
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: openpyxl (>=3.1.5,<4)
+Requires-Dist: requests (>=2.28.1,<3.0.0)
+Project-URL: Repository, https://github.com/nfdi4plants/ARCtrl
+Description-Content-Type: text/markdown
+
+
+![logo](logos/ARCtrl_horizontal.png)
+
+# ARCtrl
+
+> **ARCtrl** the easy way to read, manipulate and write ARCs in __.NET__, __JavaScript__ and __Python__! ❤️
+
+| Version | Downloads |
+| :--------|-----------:|
+|<a href="https://www.nuget.org/packages/ARCtrl/"><img alt="Nuget" src="https://img.shields.io/nuget/v/ARCtrl?logo=nuget&color=%234fb3d9"></a>|<a href="https://www.nuget.org/packages/ARCtrl/"><img alt="Nuget" src="https://img.shields.io/nuget/dt/ARCtrl?color=%234FB3D9"></a>|
+|<a href="https://www.npmjs.com/package/@nfdi4plants/arctrl"><img alt="NPM" src="https://img.shields.io/npm/v/%40nfdi4plants/arctrl?logo=npm&color=%234fb3d9"></a>|<a href="https://www.npmjs.com/package/@nfdi4plants/arctrl"><img alt="NPM" src="https://img.shields.io/npm/dt/%40nfdi4plants%2Farctrl?color=%234fb3d9"></a>|
+|<a href="https://pypi.org/project/ARCtrl/"><img alt="PyPI" src="https://img.shields.io/pypi/v/arctrl?logo=pypi&color=%234fb3d9"></a>|<a href="https://pypi.org/project/ARCtrl/"><img alt="PyPI" src="https://img.shields.io/pepy/dt/arctrl?color=%234fb3d9"></a>|
+
+## Install
+
+#### .NET
+
+```fsharp
+#r "nuget: ARCtrl"
+``` 
+
+```bash
+<PackageReference Include="ARCtrl" Version="1.1.0" />
+```
+
+#### JavaScript
+
+```bash
+npm i @nfdi4plants/arctrl
+```
+
+#### Python
+
+```bash
+pip install arctrl
+```
+
+## Docs
+
+Documentation can be found [here](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/arctrl/)
+
+## Development
+
+#### Requirements
+
+- [nodejs and npm](https://nodejs.org/en/download)
+    - verify with `node --version` (Tested with v18.16.1)
+    - verify with `npm --version` (Tested with v9.2.0)
+- [.NET SDK](https://dotnet.microsoft.com/en-us/download)
+    - verify with `dotnet --version` (Tested with 7.0.306)
+- [Python](https://www.python.org/downloads/)
+    - verify with `py --version` (Tested with 3.12.2, known to work only for >=3.11)
+
+#### Local Setup
+
+On windows you can use the `setup.cmd` to run the following steps automatically!
+
+1. Setup dotnet tools
+
+   `dotnet tool restore`
+
+
+2. Install NPM dependencies
+   
+    `npm install`
+
+3. Setup python environment
+    
+    `py -m venv .venv`
+
+4. Install [uv](https://docs.astral.sh/uv/) and dependencies
+
+   1. `.\.venv\Scripts\python.exe -m pip install -U pip setuptools`
+   2. `.\.venv\Scripts\python.exe -m pip install uv`
+   3. `.\.venv\Scripts\python.exe -m uv pip install -r pyproject.toml --group dev`
+
+Verify correct setup with `./build.cmd runtests` ✨
+
+## Branding
+
+Feel free to reference `ARCtrl` on slides or elsewhere using our logos:
+
+|Square | Horizontal | Vertical |
+| - | - | - |
+| ![square](logos/ARCtrl_square.png) | ![horizontal](logos/ARCtrl_horizontal.png) |  ![vertical](logos/ARCtrl_vertical.png) |
+
+## Performance
+
+Measured on 13th Gen Intel(R) Core(TM) i7-13800H
+
+| Name | Description | FSharp Time (ms) | JavaScript Time (ms) | Python Time (ms) |
+| --- | --- | --- | --- | --- |
+| Table_GetHashCode | From a table with 1 column and 10000 rows, retrieve the Hash Code |  5 | 21 | 226 |
+| Table_AddRows | Add 10000 rows to a table with 4 columns. |  15 | 22 | 289 |
+| Table_fillMissingCells | For a table 6 columns and 20000 rows, where each row has one missing value, fill those values with default values. | 49 | 108 | 4813 |
+| Table_ToJson | Serialize a table with 5 columns and 10000 rows to json. |  1099 | 481 | 6833 |
+| Table_ToCompressedJson | Serialize a table with 5 columns and 10000 rows to compressed json. |  261 |  2266 | 717334 |
+| Assay_toJson | Parse an assay with one table with 10000 rows and 6 columns to json |  915 | 2459 | 28799 |
+| Study_FromWorkbook | Parse a workbook with one study with 10000 rows and 6 columns to an ArcStudy |  97 | 87 | 1249 |
+| Investigation_ToWorkbook_ManyStudies | Parse an investigation with 1500 studies to a workbook |  621 | 379 | 9974 |
+