arctrl 3.0.0a3__py3-none-any.whl

arctrl/py/Core/Table/composite_header.py

@@ -0,0 +1,739 @@
+from __future__ import annotations
+from collections.abc import Callable
+from typing import (Any, TypeVar)
+from ...fable_modules.fable_library.array_ import map
+from ...fable_modules.fable_library.reflection import (name, get_union_cases, TypeInfo, string_type, union_type)
+from ...fable_modules.fable_library.reg_exp import (get_item, groups)
+from ...fable_modules.fable_library.string_ import (to_fail, printf)
+from ...fable_modules.fable_library.types import (Array, to_string, Union)
+from ..Helper.regex import (try_parse_iotype_header, ActivePatterns__007CRegex_007C__007C, Pattern_InputPattern, Pattern_OutputPattern, Pattern_CommentPattern, ActivePatterns__007CTermColumn_007C__007C)
+from ..ontology_annotation import (OntologyAnnotation, OntologyAnnotation_reflection)
+
+__A = TypeVar("__A")
+
+def _expr632() -> TypeInfo:
+    return union_type("ARCtrl.IOType", [], IOType, lambda: [[], [], [], [], [("Item", string_type)]])
+
+
+class IOType(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 ["Source", "Sample", "Data", "Material", "FreeText"]
+
+    @staticmethod
+    def All() -> Array[IOType]:
+        return [IOType(0), IOType(1), IOType(2), IOType(3)]
+
+    @staticmethod
+    def Cases() -> Array[tuple[int, str]]:
+        def mapping(x: Any) -> tuple[int, str]:
+            return (x.tag, name(x))
+
+        return map(mapping, get_union_cases(IOType_reflection()), None)
+
+    @property
+    def as_input(self, __unit: None=None) -> str:
+        this: IOType = self
+        def string_create(x: Any | None=None) -> str:
+            def _arrow630(__unit: None=None, x: Any=x) -> str:
+                copy_of_struct: __A = x
+                return to_string(copy_of_struct)
+
+            return ("Input [" + _arrow630()) + "]"
+
+        return string_create(this.fields[0]) if (this.tag == 4) else string_create(this)
+
+    @property
+    def as_output(self, __unit: None=None) -> str:
+        this: IOType = self
+        def string_create(x: Any | None=None) -> str:
+            def _arrow631(__unit: None=None, x: Any=x) -> str:
+                copy_of_struct: __A = x
+                return to_string(copy_of_struct)
+
+            return ("Output [" + _arrow631()) + "]"
+
+        return string_create(this.fields[0]) if (this.tag == 4) else string_create(this)
+
+    def Merge(self, other: IOType) -> IOType:
+        this: IOType = self
+        if this.tag == 2:
+            if other.tag == 0:
+                return IOType(2)
+
+            else: 
+                raise Exception(("Data IO column and " + str(other)) + " can not be merged")
+
+
+        elif this.tag == 1:
+            if other.tag == 0:
+                return IOType(1)
+
+            elif other.tag == 1:
+                return IOType(1)
+
+            else: 
+                raise Exception(("Sample IO column and " + str(other)) + " can not be merged")
+
+
+        elif this.tag == 0:
+            return IOType(0) if (other.tag == 0) else other
+
+        elif this.tag == 3:
+            if other.tag == 0:
+                return IOType(3)
+
+            elif other.tag == 3:
+                return IOType(3)
+
+            else: 
+                raise Exception(("Material IO column and " + str(other)) + " can not be merged")
+
+
+        elif other.tag == 4:
+            if this.fields[0] == other.fields[0]:
+                return IOType(4, this.fields[0])
+
+            else: 
+                raise Exception(((("FreeText IO column names " + this.fields[0]) + " and ") + other.fields[0]) + " do differ")
+
+
+        else: 
+            raise Exception(("FreeText IO column and " + str(other)) + " can not be merged")
+
+
+    def __str__(self, __unit: None=None) -> str:
+        this: IOType = self
+        if this.tag == 1:
+            return "Sample Name"
+
+        elif this.tag == 2:
+            return "Data"
+
+        elif this.tag == 3:
+            return "Material"
+
+        elif this.tag == 4:
+            return this.fields[0]
+
+        else: 
+            return "Source Name"
+
+
+    @staticmethod
+    def of_string(str_1: str) -> IOType:
+        return IOType(0) if (str_1 == "Source") else (IOType(0) if (str_1 == "Source Name") else (IOType(1) if (str_1 == "Sample") else (IOType(1) if (str_1 == "Sample Name") else (IOType(2) if (str_1 == "RawDataFile") else (IOType(2) if (str_1 == "Raw Data File") else (IOType(2) if (str_1 == "DerivedDataFile") else (IOType(2) if (str_1 == "Derived Data File") else (IOType(2) if (str_1 == "ImageFile") else (IOType(2) if (str_1 == "Image File") else (IOType(2) if (str_1 == "Data") else (IOType(3) if (str_1 == "Material") else IOType(4, str_1))))))))))))
+
+    @staticmethod
+    def try_of_header_string(str_1: str) -> IOType | None:
+        match_value: str | None = try_parse_iotype_header(str_1)
+        if match_value is None:
+            return None
+
+        else: 
+            s: str = match_value
+            return IOType.of_string(s)
+
+
+    @staticmethod
+    def source(__unit: None=None) -> IOType:
+        return IOType(0)
+
+    @staticmethod
+    def sample(__unit: None=None) -> IOType:
+        return IOType(1)
+
+    @staticmethod
+    def data(__unit: None=None) -> IOType:
+        return IOType(2)
+
+    @staticmethod
+    def material(__unit: None=None) -> IOType:
+        return IOType(3)
+
+    @staticmethod
+    def free_text(s: str) -> IOType:
+        return IOType(4, s)
+
+
+IOType_reflection = _expr632
+
+def _expr636() -> TypeInfo:
+    return union_type("ARCtrl.CompositeHeader", [], CompositeHeader, lambda: [[("Item", OntologyAnnotation_reflection())], [("Item", OntologyAnnotation_reflection())], [("Item", OntologyAnnotation_reflection())], [("Item", OntologyAnnotation_reflection())], [], [], [], [], [], [], [], [("Item", IOType_reflection())], [("Item", IOType_reflection())], [("Item", string_type)], [("Item", string_type)]])
+
+
+class CompositeHeader(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 ["Component", "Characteristic", "Factor", "Parameter", "ProtocolType", "ProtocolDescription", "ProtocolUri", "ProtocolVersion", "ProtocolREF", "Performer", "Date", "Input", "Output", "FreeText", "Comment"]
+
+    @staticmethod
+    def Cases() -> Array[tuple[int, str]]:
+        def mapping(x: Any) -> tuple[int, str]:
+            return (x.tag, name(x))
+
+        return map(mapping, get_union_cases(CompositeHeader_reflection()), None)
+
+    @staticmethod
+    def js_get_column_meta_type(inp: int) -> int:
+        return 1 if (inp == 0) else (1 if (inp == 1) else (1 if (inp == 2) else (1 if (inp == 3) else (0 if (inp == 4) else (0 if (inp == 5) else (0 if (inp == 6) else (0 if (inp == 7) else (0 if (inp == 8) else (0 if (inp == 9) else (0 if (inp == 10) else (2 if (inp == 11) else (2 if (inp == 12) else (3 if (inp == 13) else (3 if (inp == 14) else to_fail(printf("Cannot assign input `Tag` (%i) to `CompositeHeader`"))(inp)))))))))))))))
+
+    def __str__(self, __unit: None=None) -> str:
+        this: CompositeHeader = self
+        if this.tag == 2:
+            return ("Factor [" + this.fields[0].NameText) + "]"
+
+        elif this.tag == 1:
+            return ("Characteristic [" + this.fields[0].NameText) + "]"
+
+        elif this.tag == 0:
+            return ("Component [" + this.fields[0].NameText) + "]"
+
+        elif this.tag == 4:
+            return "Protocol Type"
+
+        elif this.tag == 8:
+            return "Protocol REF"
+
+        elif this.tag == 5:
+            return "Protocol Description"
+
+        elif this.tag == 6:
+            return "Protocol Uri"
+
+        elif this.tag == 7:
+            return "Protocol Version"
+
+        elif this.tag == 9:
+            return "Performer"
+
+        elif this.tag == 10:
+            return "Date"
+
+        elif this.tag == 11:
+            return this.fields[0].as_input
+
+        elif this.tag == 12:
+            return this.fields[0].as_output
+
+        elif this.tag == 14:
+            return ("Comment [" + this.fields[0]) + "]"
+
+        elif this.tag == 13:
+            return this.fields[0]
+
+        else: 
+            return ("Parameter [" + this.fields[0].NameText) + "]"
+
+
+    def ToTerm(self, __unit: None=None) -> OntologyAnnotation:
+        this: CompositeHeader = self
+        if this.tag == 2:
+            return this.fields[0]
+
+        elif this.tag == 1:
+            return this.fields[0]
+
+        elif this.tag == 0:
+            return this.fields[0]
+
+        elif this.tag == 4:
+            return OntologyAnnotation.create(to_string(this), None, this.GetFeaturedColumnAccession)
+
+        elif this.tag == 8:
+            return OntologyAnnotation.create(to_string(this))
+
+        elif this.tag == 5:
+            return OntologyAnnotation.create(to_string(this))
+
+        elif this.tag == 6:
+            return OntologyAnnotation.create(to_string(this))
+
+        elif this.tag == 7:
+            return OntologyAnnotation.create(to_string(this))
+
+        elif this.tag == 9:
+            return OntologyAnnotation.create(to_string(this))
+
+        elif this.tag == 10:
+            return OntologyAnnotation.create(to_string(this))
+
+        elif this.tag == 11:
+            return OntologyAnnotation.create(to_string(this))
+
+        elif this.tag == 12:
+            return OntologyAnnotation.create(to_string(this))
+
+        elif this.tag == 14:
+            return OntologyAnnotation.create(to_string(this))
+
+        elif this.tag == 13:
+            return OntologyAnnotation.create(to_string(this))
+
+        else: 
+            return this.fields[0]
+
+
+    @staticmethod
+    def OfHeaderString(str_1: str) -> CompositeHeader:
+        match_value: str = str_1.strip()
+        active_pattern_result: Any | None = ActivePatterns__007CRegex_007C__007C(Pattern_InputPattern, match_value)
+        if active_pattern_result is not None:
+            r: Any = active_pattern_result
+            iotype: str = get_item(groups(r), "iotype") or ""
+            return CompositeHeader(11, IOType.of_string(iotype))
+
+        else: 
+            active_pattern_result_1: Any | None = ActivePatterns__007CRegex_007C__007C(Pattern_OutputPattern, match_value)
+            if active_pattern_result_1 is not None:
+                r_1: Any = active_pattern_result_1
+                iotype_1: str = get_item(groups(r_1), "iotype") or ""
+                return CompositeHeader(12, IOType.of_string(iotype_1))
+
+            else: 
+                active_pattern_result_2: Any | None = ActivePatterns__007CRegex_007C__007C(Pattern_CommentPattern, match_value)
+                if active_pattern_result_2 is not None:
+                    r_2: Any = active_pattern_result_2
+                    return CompositeHeader(14, get_item(groups(r_2), "commentKey") or "")
+
+                else: 
+                    active_pattern_result_3: dict[str, Any] | None = ActivePatterns__007CTermColumn_007C__007C(match_value)
+                    if active_pattern_result_3 is not None:
+                        r_3: dict[str, Any] = active_pattern_result_3
+                        match_value_1: str = r_3["TermColumnType"]
+                        (pattern_matching_result,) = (None,)
+                        if match_value_1 == "Parameter":
+                            pattern_matching_result = 0
+
+                        elif match_value_1 == "Parameter Value":
+                            pattern_matching_result = 0
+
+                        elif match_value_1 == "Factor":
+                            pattern_matching_result = 1
+
+                        elif match_value_1 == "Factor Value":
+                            pattern_matching_result = 1
+
+                        elif match_value_1 == "Characteristic":
+                            pattern_matching_result = 2
+
+                        elif match_value_1 == "Characteristics":
+                            pattern_matching_result = 2
+
+                        elif match_value_1 == "Characteristics Value":
+                            pattern_matching_result = 2
+
+                        elif match_value_1 == "Component":
+                            pattern_matching_result = 3
+
+                        else: 
+                            pattern_matching_result = 4
+
+                        if pattern_matching_result == 0:
+                            return CompositeHeader(3, OntologyAnnotation.create(r_3["TermName"]))
+
+                        elif pattern_matching_result == 1:
+                            return CompositeHeader(2, OntologyAnnotation.create(r_3["TermName"]))
+
+                        elif pattern_matching_result == 2:
+                            return CompositeHeader(1, OntologyAnnotation.create(r_3["TermName"]))
+
+                        elif pattern_matching_result == 3:
+                            return CompositeHeader(0, OntologyAnnotation.create(r_3["TermName"]))
+
+                        elif pattern_matching_result == 4:
+                            return CompositeHeader(13, str_1)
+
+
+                    else: 
+                        return CompositeHeader(10) if (match_value == "Date") else (CompositeHeader(9) if (match_value == "Performer") else (CompositeHeader(5) if (match_value == "Protocol Description") else (CompositeHeader(6) if (match_value == "Protocol Uri") else (CompositeHeader(7) if (match_value == "Protocol Version") else (CompositeHeader(4) if (match_value == "Protocol Type") else (CompositeHeader(8) if (match_value == "Protocol REF") else CompositeHeader(13, match_value)))))))
+
+
+
+
+
+    @property
+    def IsDeprecated(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        (pattern_matching_result,) = (None,)
+        if this.tag == 13:
+            if this.fields[0].lower() == "sample name":
+                pattern_matching_result = 0
+
+            elif this.fields[0].lower() == "source name":
+                pattern_matching_result = 1
+
+            elif this.fields[0].lower() == "data file name":
+                pattern_matching_result = 2
+
+            elif this.fields[0].lower() == "derived data file":
+                pattern_matching_result = 3
+
+            else: 
+                pattern_matching_result = 4
+
+
+        else: 
+            pattern_matching_result = 4
+
+        if pattern_matching_result == 0:
+            return True
+
+        elif pattern_matching_result == 1:
+            return True
+
+        elif pattern_matching_result == 2:
+            return True
+
+        elif pattern_matching_result == 3:
+            return True
+
+        elif pattern_matching_result == 4:
+            return False
+
+
+    @property
+    def IsCvParamColumn(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        if (((this.tag == 3) or (this.tag == 2)) or (this.tag == 1)) or (this.tag == 0):
+            return True
+
+        else: 
+            return False
+
+
+    @property
+    def IsTermColumn(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        if ((((this.tag == 3) or (this.tag == 2)) or (this.tag == 1)) or (this.tag == 0)) or (this.tag == 4):
+            return True
+
+        else: 
+            return False
+
+
+    @property
+    def IsDataColumn(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        (pattern_matching_result,) = (None,)
+        if this.tag == 11:
+            if this.fields[0].tag == 2:
+                pattern_matching_result = 0
+
+            else: 
+                pattern_matching_result = 1
+
+
+        elif this.tag == 12:
+            if this.fields[0].tag == 2:
+                pattern_matching_result = 0
+
+            else: 
+                pattern_matching_result = 1
+
+
+        else: 
+            pattern_matching_result = 1
+
+        if pattern_matching_result == 0:
+            return True
+
+        elif pattern_matching_result == 1:
+            return False
+
+
+    @property
+    def IsFeaturedColumn(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 4) else False
+
+    @property
+    def GetFeaturedColumnAccession(self, __unit: None=None) -> str:
+        this: CompositeHeader = self
+        if this.tag == 4:
+            return "DPBO:1000161"
+
+        else: 
+            raise Exception(("Tried matching " + str(this)) + " in getFeaturedColumnAccession, but is not a featured column.")
+
+
+    @property
+    def GetColumnAccessionShort(self, __unit: None=None) -> str:
+        this: CompositeHeader = self
+        if this.tag == 4:
+            return this.GetFeaturedColumnAccession
+
+        elif this.tag == 3:
+            return this.fields[0].TermAccessionShort
+
+        elif this.tag == 2:
+            return this.fields[0].TermAccessionShort
+
+        elif this.tag == 1:
+            return this.fields[0].TermAccessionShort
+
+        elif this.tag == 0:
+            return this.fields[0].TermAccessionShort
+
+        else: 
+            raise Exception(("Tried matching " + str(this)) + ", but is not a column with an accession.")
+
+
+    @property
+    def IsSingleColumn(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        if (((((((((this.tag == 13) or (this.tag == 11)) or (this.tag == 12)) or (this.tag == 14)) or (this.tag == 8)) or (this.tag == 5)) or (this.tag == 6)) or (this.tag == 7)) or (this.tag == 9)) or (this.tag == 10):
+            return True
+
+        else: 
+            return False
+
+
+    @property
+    def IsIOType(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        if this.tag == 11:
+            return True
+
+        elif this.tag == 12:
+            return True
+
+        else: 
+            return False
+
+
+    @property
+    def is_input(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 11) else False
+
+    @property
+    def is_output(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 12) else False
+
+    @property
+    def is_parameter(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 3) else False
+
+    @property
+    def is_factor(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 2) else False
+
+    @property
+    def is_characteristic(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 1) else False
+
+    @property
+    def is_component(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 0) else False
+
+    @property
+    def is_protocol_type(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 4) else False
+
+    @property
+    def is_protocol_ref(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 8) else False
+
+    @property
+    def is_protocol_description(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 5) else False
+
+    @property
+    def is_protocol_uri(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 6) else False
+
+    @property
+    def is_protocol_version(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 7) else False
+
+    @property
+    def is_protocol_column(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        if ((((this.tag == 8) or (this.tag == 5)) or (this.tag == 6)) or (this.tag == 7)) or (this.tag == 4):
+            return True
+
+        else: 
+            return False
+
+
+    @property
+    def is_performer(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 9) else False
+
+    @property
+    def is_date(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 10) else False
+
+    @property
+    def is_comment(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 14) else False
+
+    @property
+    def is_free_text(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        return True if (this.tag == 13) else False
+
+    def TryInput(self, __unit: None=None) -> IOType | None:
+        this: CompositeHeader = self
+        return this.fields[0] if (this.tag == 11) else None
+
+    def TryOutput(self, __unit: None=None) -> IOType | None:
+        this: CompositeHeader = self
+        return this.fields[0] if (this.tag == 12) else None
+
+    def TryIOType(self, __unit: None=None) -> IOType | None:
+        this: CompositeHeader = self
+        (pattern_matching_result, io) = (None, None)
+        if this.tag == 12:
+            pattern_matching_result = 0
+            io = this.fields[0]
+
+        elif this.tag == 11:
+            pattern_matching_result = 0
+            io = this.fields[0]
+
+        else: 
+            pattern_matching_result = 1
+
+        if pattern_matching_result == 0:
+            return io
+
+        elif pattern_matching_result == 1:
+            return None
+
+
+    @property
+    def IsUnique(self, __unit: None=None) -> bool:
+        this: CompositeHeader = self
+        if ((((((((this.tag == 4) or (this.tag == 8)) or (this.tag == 5)) or (this.tag == 6)) or (this.tag == 7)) or (this.tag == 9)) or (this.tag == 10)) or (this.tag == 11)) or (this.tag == 12):
+            return True
+
+        else: 
+            return False
+
+
+    def Copy(self, __unit: None=None) -> CompositeHeader:
+        this: CompositeHeader = self
+        if this.tag == 3:
+            return CompositeHeader(3, this.fields[0].Copy())
+
+        elif this.tag == 2:
+            return CompositeHeader(2, this.fields[0].Copy())
+
+        elif this.tag == 1:
+            return CompositeHeader(1, this.fields[0].Copy())
+
+        elif this.tag == 0:
+            return CompositeHeader(0, this.fields[0].Copy())
+
+        else: 
+            return this
+
+
+    def TryGetTerm(self, __unit: None=None) -> OntologyAnnotation | None:
+        this: CompositeHeader = self
+        if this.tag == 3:
+            return this.fields[0]
+
+        elif this.tag == 2:
+            return this.fields[0]
+
+        elif this.tag == 1:
+            return this.fields[0]
+
+        elif this.tag == 0:
+            return this.fields[0]
+
+        else: 
+            return None
+
+
+    @staticmethod
+    def component(oa: OntologyAnnotation) -> CompositeHeader:
+        return CompositeHeader(0, oa)
+
+    @staticmethod
+    def characteristic(oa: OntologyAnnotation) -> CompositeHeader:
+        return CompositeHeader(1, oa)
+
+    @staticmethod
+    def factor(oa: OntologyAnnotation) -> CompositeHeader:
+        return CompositeHeader(2, oa)
+
+    @staticmethod
+    def parameter(oa: OntologyAnnotation) -> CompositeHeader:
+        return CompositeHeader(3, oa)
+
+    @staticmethod
+    def protocol_type(__unit: None=None) -> CompositeHeader:
+        return CompositeHeader(4)
+
+    @staticmethod
+    def protocol_description(__unit: None=None) -> CompositeHeader:
+        return CompositeHeader(5)
+
+    @staticmethod
+    def protocol_uri(__unit: None=None) -> CompositeHeader:
+        return CompositeHeader(6)
+
+    @staticmethod
+    def protocol_version(__unit: None=None) -> CompositeHeader:
+        return CompositeHeader(7)
+
+    @staticmethod
+    def protocol_ref(__unit: None=None) -> CompositeHeader:
+        return CompositeHeader(8)
+
+    @staticmethod
+    def performer(__unit: None=None) -> CompositeHeader:
+        return CompositeHeader(9)
+
+    @staticmethod
+    def date(__unit: None=None) -> CompositeHeader:
+        return CompositeHeader(10)
+
+    @staticmethod
+    def input(io: IOType) -> CompositeHeader:
+        return CompositeHeader(11, io)
+
+    @staticmethod
+    def output(io: IOType) -> CompositeHeader:
+        return CompositeHeader(12, io)
+
+    @staticmethod
+    def free_text(s: str) -> CompositeHeader:
+        return CompositeHeader(13, s)
+
+    @staticmethod
+    def comment(s: str) -> CompositeHeader:
+        return CompositeHeader(14, s)
+
+
+CompositeHeader_reflection = _expr636
+
+__all__ = ["IOType_reflection", "CompositeHeader_reflection"]
+