arctrl 3.0.0__py3-none-any.whl

arctrl/py/Core/data.py

@@ -0,0 +1,247 @@
+from __future__ import annotations
+from collections.abc import Callable
+from typing import Any
+from ..fable_modules.fable_library.option import default_arg
+from ..fable_modules.fable_library.reflection import (TypeInfo, class_type)
+from ..fable_modules.fable_library.string_ import (to_text, printf, trim, trim_start as trim_start_1, starts_with_exact, substring)
+from ..fable_modules.fable_library.types import (Array, to_string)
+from .comment import Comment
+from .data_file import (DataFile, DataFile__get_AsString)
+from .Helper.collections_ import ResizeArray_map
+from .Helper.hash_codes import (box_hash_array, box_hash_option, box_hash_seq, hash_1)
+
+def DataAux_nameFromPathAndSelector(path: str, selector: str) -> str:
+    return to_text(printf("%s#%s"))(path)(selector)
+
+
+def DataAux_pathAndSelectorFromName(name: str) -> tuple[str, str | None]:
+    name_1: str = trim(name, "#")
+    parts: Array[str] = name_1.split("#")
+    if len(parts) == 2:
+        return (parts[0], parts[1])
+
+    else: 
+        return (name_1, None)
+
+
+
+def _expr1055() -> TypeInfo:
+    return class_type("ARCtrl.Data", None, Data)
+
+
+class Data:
+    def __init__(self, id: str | None=None, name: str | None=None, data_type: DataFile | None=None, format: str | None=None, selector_format: str | None=None, comments: Array[Comment] | None=None) -> None:
+        self._id: str | None = id
+        pattern_input_1: tuple[str | None, str | None]
+        if name is None:
+            pattern_input_1 = (None, None)
+
+        else: 
+            pattern_input: tuple[str, str | None] = DataAux_pathAndSelectorFromName(name)
+            pattern_input_1 = (pattern_input[0], pattern_input[1])
+
+        self._selector: str | None = pattern_input_1[1]
+        self._filePath: str | None = pattern_input_1[0]
+        self._dataType: DataFile | None = data_type
+        self._format: str | None = format
+        self._selectorFormat: str | None = selector_format
+        self._comments: Array[Comment] = default_arg(comments, [])
+
+    @property
+    def ID(self, __unit: None=None) -> str | None:
+        this: Data = self
+        return this._id
+
+    @ID.setter
+    def ID(self, id: str | None=None) -> None:
+        this: Data = self
+        this._id = id
+
+    @property
+    def Name(self, __unit: None=None) -> str | None:
+        this: Data = self
+        match_value: str | None = this._filePath
+        match_value_1: str | None = this._selector
+        def _arrow1050(__unit: None=None) -> str | None:
+            p_1: str = match_value
+            return p_1
+
+        def _arrow1051(__unit: None=None) -> str | None:
+            p: str = match_value
+            s: str = match_value_1
+            return DataAux_nameFromPathAndSelector(p, s)
+
+        return None if (match_value is None) else (_arrow1050() if (match_value_1 is None) else _arrow1051())
+
+    @Name.setter
+    def Name(self, name: str | None=None) -> None:
+        this: Data = self
+        if name is None:
+            this._filePath = None
+            this._selector = None
+
+        else: 
+            pattern_input: tuple[str, str | None] = DataAux_pathAndSelectorFromName(name)
+            this._filePath = pattern_input[0]
+            this._selector = pattern_input[1]
+
+
+    @property
+    def FilePath(self, __unit: None=None) -> str | None:
+        this: Data = self
+        return this._filePath
+
+    @FilePath.setter
+    def FilePath(self, file_path: str | None=None) -> None:
+        this: Data = self
+        this._filePath = file_path
+
+    @property
+    def Selector(self, __unit: None=None) -> str | None:
+        this: Data = self
+        return this._selector
+
+    @Selector.setter
+    def Selector(self, selector: str | None=None) -> None:
+        this: Data = self
+        this._selector = selector
+
+    @property
+    def DataType(self, __unit: None=None) -> DataFile | None:
+        this: Data = self
+        return this._dataType
+
+    @DataType.setter
+    def DataType(self, data_type: DataFile | None=None) -> None:
+        this: Data = self
+        this._dataType = data_type
+
+    @property
+    def Format(self, __unit: None=None) -> str | None:
+        this: Data = self
+        return this._format
+
+    @Format.setter
+    def Format(self, format: str | None=None) -> None:
+        this: Data = self
+        this._format = format
+
+    @property
+    def SelectorFormat(self, __unit: None=None) -> str | None:
+        this: Data = self
+        return this._selectorFormat
+
+    @SelectorFormat.setter
+    def SelectorFormat(self, selector_format: str | None=None) -> None:
+        this: Data = self
+        this._selectorFormat = selector_format
+
+    @property
+    def Comments(self, __unit: None=None) -> Array[Comment]:
+        this: Data = self
+        return this._comments
+
+    @Comments.setter
+    def Comments(self, comments: Array[Comment]) -> None:
+        this: Data = self
+        this._comments = comments
+
+    @staticmethod
+    def make(id: str | None=None, name: str | None=None, data_type: DataFile | None=None, format: str | None=None, selector_format: str | None=None, comments: Array[Comment] | None=None) -> Data:
+        return Data(id, name, data_type, format, selector_format, comments)
+
+    @staticmethod
+    def create(Id: str | None=None, Name: str | None=None, DataType: DataFile | None=None, Format: str | None=None, SelectorFormat: str | None=None, Comments: Array[Comment] | None=None) -> Data:
+        return Data.make(Id, Name, DataType, Format, SelectorFormat, Comments)
+
+    @staticmethod
+    def empty() -> Data:
+        return Data.create()
+
+    @property
+    def NameText(self, __unit: None=None) -> str:
+        this: Data = self
+        return default_arg(this.Name, "")
+
+    def GetAbsolutePathBy(self, f: Callable[[str], str], check_existence_from_root: Callable[[str], bool] | None=None) -> str:
+        this: Data = self
+        def _arrow1052(_arg: str) -> bool:
+            return False
+
+        check_existence_from_root_1: Callable[[str], bool] = default_arg(check_existence_from_root, _arrow1052)
+        match_value: str | None = this.FilePath
+        if match_value is None:
+            raise Exception("Data does not have a file path")
+
+        else: 
+            p_3: str
+            s: str = trim_start_1(match_value, "/")
+            p_3 = substring(s, len("./")) if starts_with_exact(s, "./") else s
+            def _arrow1053(__unit: None=None) -> bool:
+                p: str = p_3
+                return True if (True if (True if starts_with_exact(p, "assays/") else starts_with_exact(p, "studies/")) else starts_with_exact(p, "workflows/")) else starts_with_exact(p, "runs/")
+
+            def _arrow1054(__unit: None=None) -> bool:
+                p_1: str = p_3
+                return True if starts_with_exact(p_1, "http:") else starts_with_exact(p_1, "https:")
+
+            return p_3 if (True if (True if check_existence_from_root_1(p_3) else _arrow1053()) else _arrow1054()) else f(p_3)
+
+
+    def GetAbsolutePathForAssay(self, assay_identifier: str, check_existence_from_root: Callable[[str], bool] | None=None) -> str:
+        this: Data = self
+        def f(p: str) -> str:
+            return (("assays/" + assay_identifier) + "/dataset/") + trim_start_1(p, "/")
+
+        return this.GetAbsolutePathBy(f, check_existence_from_root)
+
+    def GetAbsolutePathForStudy(self, study_identifier: str, check_existence_from_root: Callable[[str], bool] | None=None) -> str:
+        this: Data = self
+        def f(p: str) -> str:
+            return (("studies/" + study_identifier) + "/resources/") + trim_start_1(p, "/")
+
+        return this.GetAbsolutePathBy(f, check_existence_from_root)
+
+    def Copy(self, __unit: None=None) -> Data:
+        this: Data = self
+        def f(c: Comment) -> Comment:
+            return c.Copy()
+
+        next_comments: Array[Comment] = ResizeArray_map(f, this.Comments)
+        return Data(this.ID, this.Name, this.DataType, this.Format, this.SelectorFormat, next_comments)
+
+    def __hash__(self, __unit: None=None) -> Any:
+        this: Data = self
+        return box_hash_array([box_hash_option(this.ID), box_hash_option(this.Name), box_hash_option(this.DataType), box_hash_option(this.Format), box_hash_option(this.SelectorFormat), box_hash_seq(this.Comments)])
+
+    def __eq__(self, obj: Any=None) -> bool:
+        this: Data = self
+        return hash_1(this) == hash_1(obj)
+
+    def Print(self, __unit: None=None) -> str:
+        this: Data = self
+        return to_string(this)
+
+    def PrintCompact(self, __unit: None=None) -> str:
+        this: Data = self
+        match_value: DataFile | None = this.DataType
+        if match_value is None:
+            arg_2: str = this.NameText
+            return to_text(printf("%s"))(arg_2)
+
+        else: 
+            t: DataFile = match_value
+            arg: str = this.NameText
+            arg_1: str = DataFile__get_AsString(t)
+            return to_text(printf("%s [%s]"))(arg)(arg_1)
+
+
+
+Data_reflection = _expr1055
+
+def Data__ctor_5909441C(id: str | None=None, name: str | None=None, data_type: DataFile | None=None, format: str | None=None, selector_format: str | None=None, comments: Array[Comment] | None=None) -> Data:
+    return Data(id, name, data_type, format, selector_format, comments)
+
+
+__all__ = ["DataAux_nameFromPathAndSelector", "DataAux_pathAndSelectorFromName", "Data_reflection"]
+

arctrl/py/Core/data_context.py

@@ -0,0 +1,157 @@
+from __future__ import annotations
+from typing import Any
+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 .comment import Comment
+from .data import (Data, Data_reflection)
+from .data_file import DataFile
+from .Helper.hash_codes import (box_hash_array, box_hash_option, box_hash_seq, hash_1)
+from .ontology_annotation import OntologyAnnotation
+from .value import Value as Value_1
+
+def _expr1056() -> TypeInfo:
+    return class_type("ARCtrl.DataContext", None, DataContext, Data_reflection())
+
+
+class DataContext(Data):
+    def __init__(self, id: str | None=None, name: str | None=None, data_type: DataFile | None=None, format: str | None=None, selector_format: str | None=None, explication: OntologyAnnotation | None=None, unit: OntologyAnnotation | None=None, object_type: OntologyAnnotation | None=None, label: str | None=None, description: str | None=None, generated_by: str | None=None, comments: Array[Comment] | None=None) -> None:
+        super().__init__(id, name, data_type, format, selector_format, comments)
+        self._explication: OntologyAnnotation | None = explication
+        self._unit: OntologyAnnotation | None = unit
+        self._objectType: OntologyAnnotation | None = object_type
+        self._label: str | None = label
+        self._description: str | None = description
+        self._generatedBy: str | None = generated_by
+
+    def __hash__(self, __unit: None=None) -> Any:
+        this: DataContext = self
+        return box_hash_array([box_hash_option(this.ID), box_hash_option(this.Name), box_hash_option(this.DataType), box_hash_option(this.Format), box_hash_option(this.SelectorFormat), box_hash_seq(this.Comments), box_hash_option(DataContext__get_Explication(this)), box_hash_option(DataContext__get_Unit(this)), box_hash_option(DataContext__get_ObjectType(this)), box_hash_option(DataContext__get_Label(this)), box_hash_option(DataContext__get_Description(this)), box_hash_option(DataContext__get_GeneratedBy(this))])
+
+    def __eq__(self, obj: Any=None) -> bool:
+        this: DataContext = self
+        return hash_1(this) == hash_1(obj)
+
+    def AlternateName(self, __unit: None=None) -> str | None:
+        this: DataContext = self
+        return DataContext__get_Label(this)
+
+    def MeasurementMethod(self, __unit: None=None) -> str | None:
+        this: DataContext = self
+        return DataContext__get_GeneratedBy(this)
+
+    def GetCategory(self, __unit: None=None) -> OntologyAnnotation | None:
+        this: DataContext = self
+        return DataContext__get_Explication(this)
+
+    def GetValue(self, __unit: None=None) -> Value_1 | None:
+        this: DataContext = self
+        def mapping(Item: OntologyAnnotation) -> Value_1:
+            return Value_1(0, Item)
+
+        return map(mapping, DataContext__get_ObjectType(this))
+
+    def GetUnit(self, __unit: None=None) -> OntologyAnnotation | None:
+        this: DataContext = self
+        return DataContext__get_Unit(this)
+
+    def GetAdditionalType(self, __unit: None=None) -> str:
+        return "DataContext"
+
+    def Description(self, __unit: None=None) -> str | None:
+        this: DataContext = self
+        return DataContext__get_Description(this)
+
+
+DataContext_reflection = _expr1056
+
+def DataContext__ctor_Z780A8A2A(id: str | None=None, name: str | None=None, data_type: DataFile | None=None, format: str | None=None, selector_format: str | None=None, explication: OntologyAnnotation | None=None, unit: OntologyAnnotation | None=None, object_type: OntologyAnnotation | None=None, label: str | None=None, description: str | None=None, generated_by: str | None=None, comments: Array[Comment] | None=None) -> DataContext:
+    return DataContext(id, name, data_type, format, selector_format, explication, unit, object_type, label, description, generated_by, comments)
+
+
+def DataContext__get_Explication(this: DataContext) -> OntologyAnnotation | None:
+    return this._explication
+
+
+def DataContext__set_Explication_279AAFF2(this: DataContext, explication: OntologyAnnotation | None=None) -> None:
+    this._explication = explication
+
+
+def DataContext__get_Unit(this: DataContext) -> OntologyAnnotation | None:
+    return this._unit
+
+
+def DataContext__set_Unit_279AAFF2(this: DataContext, unit: OntologyAnnotation | None=None) -> None:
+    this._unit = unit
+
+
+def DataContext__get_ObjectType(this: DataContext) -> OntologyAnnotation | None:
+    return this._objectType
+
+
+def DataContext__set_ObjectType_279AAFF2(this: DataContext, object_type: OntologyAnnotation | None=None) -> None:
+    this._objectType = object_type
+
+
+def DataContext__get_Label(this: DataContext) -> str | None:
+    return this._label
+
+
+def DataContext__set_Label_6DFDD678(this: DataContext, label: str | None=None) -> None:
+    this._label = label
+
+
+def DataContext__get_Description(this: DataContext) -> str | None:
+    return this._description
+
+
+def DataContext__set_Description_6DFDD678(this: DataContext, description: str | None=None) -> None:
+    this._description = description
+
+
+def DataContext__get_GeneratedBy(this: DataContext) -> str | None:
+    return this._generatedBy
+
+
+def DataContext__set_GeneratedBy_6DFDD678(this: DataContext, generated_by: str | None=None) -> None:
+    this._generatedBy = generated_by
+
+
+def DataContext__AsData(this: DataContext) -> Data:
+    return Data(this.ID, this.Name, this.DataType, this.Format, this.SelectorFormat, this.Comments)
+
+
+def DataContext_fromData_Z7B4D7BF5(data: Data, explication: OntologyAnnotation | None=None, unit: OntologyAnnotation | None=None, object_type: OntologyAnnotation | None=None, label: str | None=None, description: str | None=None, generated_by: str | None=None) -> DataContext:
+    return DataContext__ctor_Z780A8A2A(data.ID, data.Name, data.DataType, data.Format, data.SelectorFormat, explication, unit, object_type, label, description, generated_by, data.Comments)
+
+
+def DataContext_createAsPV(alternate_name: str | None=None, measurement_method: str | None=None, description: str | None=None, category: OntologyAnnotation | None=None, value: Value_1 | None=None, unit: OntologyAnnotation | None=None) -> DataContext:
+    def _arrow1057(__unit: None=None, alternate_name: Any=alternate_name, measurement_method: Any=measurement_method, description: Any=description, category: Any=category, value: Any=value, unit: Any=unit) -> OntologyAnnotation | None:
+        oa: OntologyAnnotation = value.fields[0]
+        return oa
+
+    def _arrow1058(__unit: None=None, alternate_name: Any=alternate_name, measurement_method: Any=measurement_method, description: Any=description, category: Any=category, value: Any=value, unit: Any=unit) -> OntologyAnnotation | None:
+        v: Value_1 = value
+        return OntologyAnnotation(v.Text)
+
+    return DataContext__ctor_Z780A8A2A(None, None, None, None, None, category, unit, None if (value is None) else (_arrow1057() if (value.tag == 0) else _arrow1058()), alternate_name, description, measurement_method)
+
+
+def DataContext__Copy(this: DataContext) -> DataContext:
+    copy: DataContext = DataContext__ctor_Z780A8A2A()
+    copy.ID = this.ID
+    copy.Name = this.Name
+    copy.DataType = this.DataType
+    copy.Format = this.Format
+    copy.SelectorFormat = this.SelectorFormat
+    DataContext__set_Explication_279AAFF2(copy, DataContext__get_Explication(this))
+    DataContext__set_Unit_279AAFF2(copy, DataContext__get_Unit(this))
+    DataContext__set_ObjectType_279AAFF2(copy, DataContext__get_ObjectType(this))
+    DataContext__set_Description_6DFDD678(copy, DataContext__get_Description(this))
+    DataContext__set_GeneratedBy_6DFDD678(copy, DataContext__get_GeneratedBy(this))
+    copy.Comments = this.Comments
+    return copy
+
+
+__all__ = ["DataContext_reflection", "DataContext__get_Explication", "DataContext__set_Explication_279AAFF2", "DataContext__get_Unit", "DataContext__set_Unit_279AAFF2", "DataContext__get_ObjectType", "DataContext__set_ObjectType_279AAFF2", "DataContext__get_Label", "DataContext__set_Label_6DFDD678", "DataContext__get_Description", "DataContext__set_Description_6DFDD678", "DataContext__get_GeneratedBy", "DataContext__set_GeneratedBy_6DFDD678", "DataContext__AsData", "DataContext_fromData_Z7B4D7BF5", "DataContext_createAsPV", "DataContext__Copy"]
+

arctrl/py/Core/data_file.py

@@ -0,0 +1,112 @@
+from __future__ import annotations
+from typing import Any
+from ..fable_modules.fable_library.reflection import (TypeInfo, union_type)
+from ..fable_modules.fable_library.types import (Array, Union)
+
+def _expr977() -> TypeInfo:
+    return union_type("ARCtrl.DataFile", [], DataFile, lambda: [[], [], []])
+
+
+class DataFile(Union):
+    def __init__(self, tag: int, *fields: Any) -> None:
+        super().__init__()
+        self.tag: int = tag or 0
+        self.fields: Array[Any] = list(fields)
+
+    @staticmethod
+    def cases() -> list[str]:
+        return ["RawDataFile", "DerivedDataFile", "ImageFile"]
+
+
+DataFile_reflection = _expr977
+
+def DataFile_get_RawDataFileJson(__unit: None=None) -> str:
+    return "Raw Data File"
+
+
+def DataFile_get_DerivedDataFileJson(__unit: None=None) -> str:
+    return "Derived Data File"
+
+
+def DataFile_get_ImageFileJson(__unit: None=None) -> str:
+    return "Image File"
+
+
+def DataFile__get_AsString(this: DataFile) -> str:
+    if this.tag == 1:
+        return "Derived Data File"
+
+    elif this.tag == 2:
+        return "Image File"
+
+    else: 
+        return "Raw Data File"
+
+
+
+def DataFile_fromString_Z721C83C5(dt: str) -> DataFile:
+    (pattern_matching_result,) = (None,)
+    if dt == "RawDataFileJson":
+        pattern_matching_result = 0
+
+    elif dt == "Raw Data File":
+        pattern_matching_result = 0
+
+    elif dt == "DerivedDataFileJson":
+        pattern_matching_result = 1
+
+    elif dt == "Derived Data File":
+        pattern_matching_result = 1
+
+    elif dt == "ImageFileJson":
+        pattern_matching_result = 2
+
+    elif dt == "Image File":
+        pattern_matching_result = 2
+
+    else: 
+        pattern_matching_result = 3
+
+    if pattern_matching_result == 0:
+        return DataFile(0)
+
+    elif pattern_matching_result == 1:
+        return DataFile(1)
+
+    elif pattern_matching_result == 2:
+        return DataFile(2)
+
+    elif pattern_matching_result == 3:
+        raise Exception(("Invalid DataFile type: " + dt) + "")
+
+
+
+def DataFile__get_IsDerivedData(this: DataFile) -> bool:
+    if this.tag == 1:
+        return True
+
+    else: 
+        return False
+
+
+
+def DataFile__get_IsRawData(this: DataFile) -> bool:
+    if this.tag == 0:
+        return True
+
+    else: 
+        return False
+
+
+
+def DataFile__get_IsImage(this: DataFile) -> bool:
+    if this.tag == 2:
+        return True
+
+    else: 
+        return False
+
+
+
+__all__ = ["DataFile_reflection", "DataFile_get_RawDataFileJson", "DataFile_get_DerivedDataFileJson", "DataFile_get_ImageFileJson", "DataFile__get_AsString", "DataFile_fromString_Z721C83C5", "DataFile__get_IsDerivedData", "DataFile__get_IsRawData", "DataFile__get_IsImage"]
+