arctrl 3.0.0a3__py3-none-any.whl

arctrl/py/Core/Helper/date_time.py

@@ -0,0 +1,26 @@
+from __future__ import annotations
+from typing import Any
+from ...fable_modules.fable_library.date import (min_value, try_parse as try_parse_1)
+from ...fable_modules.fable_library.types import FSharpRef
+
+def try_parse(s: str) -> Any | None:
+    match_value: tuple[bool, Any]
+    out_arg: Any = min_value()
+    def _arrow471(__unit: None=None, s: Any=s) -> Any:
+        return out_arg
+
+    def _arrow472(v: Any, s: Any=s) -> None:
+        nonlocal out_arg
+        out_arg = v
+
+    match_value = (try_parse_1(s, FSharpRef(_arrow471, _arrow472)), out_arg)
+    if match_value[0]:
+        return match_value[1]
+
+    else: 
+        return None
+
+
+
+__all__ = ["try_parse"]
+

arctrl/py/Core/Helper/hash_codes.py

@@ -0,0 +1,60 @@
+from typing import (Any, TypeVar)
+from ...fable_modules.fable_library.array_ import fold
+from ...fable_modules.fable_library.date import (year, month, day, hour, minute, second)
+from ...fable_modules.fable_library.option import value as value_1
+from ...fable_modules.fable_library.seq import fold as fold_1
+from ...fable_modules.fable_library.types import Array
+from ...fable_modules.fable_library.util import (identity_hash, number_hash, IEnumerable_1)
+
+__A = TypeVar("__A")
+
+_A = TypeVar("_A")
+
+def merge_hashes(hash1: int, hash2: int) -> int:
+    return ((-1640531527 + hash2) + (hash1 << 6)) + (hash1 >> 2)
+
+
+def hash_date_time(dt: Any) -> int:
+    acc: int = 0
+    acc = merge_hashes(acc, year(dt)) or 0
+    acc = merge_hashes(acc, month(dt)) or 0
+    acc = merge_hashes(acc, day(dt)) or 0
+    acc = merge_hashes(acc, hour(dt)) or 0
+    acc = merge_hashes(acc, minute(dt)) or 0
+    acc = merge_hashes(acc, second(dt)) or 0
+    return acc
+
+
+def hash_1(obj: Any | None=None) -> int:
+    copy_of_struct: __A = obj
+    return identity_hash(copy_of_struct)
+
+
+def box_hash_option(a: Any | None=None) -> Any:
+    def _arrow511(__unit: None=None, a: Any=a) -> int:
+        copy_of_struct: _A = value_1(a)
+        return identity_hash(copy_of_struct)
+
+    def _arrow512(__unit: None=None, a: Any=a) -> int:
+        copy_of_struct_1: int = 0
+        return number_hash(copy_of_struct_1)
+
+    return _arrow511() if (a is not None) else _arrow512()
+
+
+def box_hash_array(a: Array[Any]) -> Any:
+    def folder(acc: int, o: _A, a: Any=a) -> int:
+        return merge_hashes(acc, hash_1(o))
+
+    return fold(folder, 0, a)
+
+
+def box_hash_seq(a: IEnumerable_1[Any]) -> Any:
+    def folder(acc: int, o: _A, a: Any=a) -> int:
+        return merge_hashes(acc, hash_1(o))
+
+    return fold_1(folder, 0, a)
+
+
+__all__ = ["merge_hashes", "hash_date_time", "hash_1", "box_hash_option", "box_hash_array", "box_hash_seq"]
+

arctrl/py/Core/Helper/identifier.py

@@ -0,0 +1,248 @@
+from typing import Any
+from ...fable_modules.fable_library.guid import new_guid
+from ...fable_modules.fable_library.reg_exp import (get_item, groups)
+from ...fable_modules.fable_library.string_ import starts_with_exact
+from ...FileSystem.path import combine_many
+from .regex import ActivePatterns__007CRegex_007C__007C
+
+def try_check_valid_characters(identifier: str) -> bool:
+    if ActivePatterns__007CRegex_007C__007C("^[a-zA-Z0-9_\\- ]+$", identifier) is not None:
+        return True
+
+    else: 
+        return False
+
+
+
+def check_valid_characters(identifier: str) -> None:
+    if try_check_valid_characters(identifier):
+        pass
+
+    else: 
+        raise Exception(("New identifier \"" + identifier) + "\"contains forbidden characters! Allowed characters are: letters, digits, underscore (_), dash (-) and whitespace ( ).")
+
+
+
+def create_missing_identifier(__unit: None=None) -> str:
+    def _arrow510(__unit: None=None) -> str:
+        copy_of_struct: str = new_guid()
+        return str(copy_of_struct)
+
+    return "MISSING_IDENTIFIER_" + _arrow510()
+
+
+def is_missing_identifier(str_1: str) -> bool:
+    return starts_with_exact(str_1, "MISSING_IDENTIFIER_")
+
+
+def remove_missing_identifier(str_1: str) -> str:
+    if starts_with_exact(str_1, "MISSING_IDENTIFIER_"):
+        return ""
+
+    else: 
+        return str_1
+
+
+
+def Assay_identifierFromFileName(file_name: str) -> str:
+    active_pattern_result: Any | None = ActivePatterns__007CRegex_007C__007C("^(assays(\\/|\\\\))?(?<identifier>[a-zA-Z0-9_\\- ]+)((\\/|\\\\)isa.assay.xlsx)?$", file_name)
+    if active_pattern_result is not None:
+        m: Any = active_pattern_result
+        return get_item(groups(m), "identifier") or ""
+
+    else: 
+        raise Exception(("Cannot parse assay identifier from FileName `" + file_name) + "`")
+
+
+
+def Assay_tryIdentifierFromFileName(file_name: str) -> str | None:
+    active_pattern_result: Any | None = ActivePatterns__007CRegex_007C__007C("^(assays(\\/|\\\\))?(?<identifier>[a-zA-Z0-9_\\- ]+)((\\/|\\\\)isa.assay.xlsx)?$", file_name)
+    if active_pattern_result is not None:
+        m: Any = active_pattern_result
+        return get_item(groups(m), "identifier") or ""
+
+    else: 
+        return None
+
+
+
+def Assay_fileNameFromIdentifier(identifier: str) -> str:
+    check_valid_characters(identifier)
+    return combine_many(["assays", identifier, "isa.assay.xlsx"])
+
+
+def Assay_tryFileNameFromIdentifier(identifier: str) -> str | None:
+    if try_check_valid_characters(identifier):
+        return combine_many(["assays", identifier, "isa.assay.xlsx"])
+
+    else: 
+        return None
+
+
+
+def Assay_datamapFileNameFromIdentifier(identifier: str) -> str:
+    check_valid_characters(identifier)
+    return combine_many(["assays", identifier, "isa.datamap.xlsx"])
+
+
+def Assay_tryDatamapFileNameFromIdentifier(identifier: str) -> str | None:
+    if try_check_valid_characters(identifier):
+        return combine_many(["assays", identifier, "isa.datamap.xlsx"])
+
+    else: 
+        return None
+
+
+
+def Study_identifierFromFileName(file_name: str) -> str:
+    active_pattern_result: Any | None = ActivePatterns__007CRegex_007C__007C("^(studies(\\/|\\\\))?(?<identifier>[a-zA-Z0-9_\\- ]+)((\\/|\\\\)isa.study.xlsx)?$", file_name)
+    if active_pattern_result is not None:
+        m: Any = active_pattern_result
+        return get_item(groups(m), "identifier") or ""
+
+    else: 
+        raise Exception(("Cannot parse study identifier from FileName `" + file_name) + "`")
+
+
+
+def Study_tryIdentifierFromFileName(file_name: str) -> str | None:
+    active_pattern_result: Any | None = ActivePatterns__007CRegex_007C__007C("^(studies(\\/|\\\\))?(?<identifier>[a-zA-Z0-9_\\- ]+)((\\/|\\\\)isa.study.xlsx)?$", file_name)
+    if active_pattern_result is not None:
+        m: Any = active_pattern_result
+        return get_item(groups(m), "identifier") or ""
+
+    else: 
+        return None
+
+
+
+def Study_fileNameFromIdentifier(identifier: str) -> str:
+    check_valid_characters(identifier)
+    return combine_many(["studies", identifier, "isa.study.xlsx"])
+
+
+def Study_tryFileNameFromIdentifier(identifier: str) -> str | None:
+    if try_check_valid_characters(identifier):
+        return combine_many(["studies", identifier, "isa.study.xlsx"])
+
+    else: 
+        return None
+
+
+
+def Study_datamapFileNameFromIdentifier(identifier: str) -> str:
+    check_valid_characters(identifier)
+    return combine_many(["studies", identifier, "isa.datamap.xlsx"])
+
+
+def Study_tryDatamapFileNameFromIdentifier(identifier: str) -> str | None:
+    if try_check_valid_characters(identifier):
+        return combine_many(["studies", identifier, "isa.datamap.xlsx"])
+
+    else: 
+        return None
+
+
+
+def Workflow_identifierFromFileName(file_name: str) -> str:
+    active_pattern_result: Any | None = ActivePatterns__007CRegex_007C__007C("^(workflows(\\/|\\\\))?(?<identifier>[a-zA-Z0-9_\\- ]+)((\\/|\\\\)isa.workflow.xlsx)?$", file_name)
+    if active_pattern_result is not None:
+        m: Any = active_pattern_result
+        return get_item(groups(m), "identifier") or ""
+
+    else: 
+        raise Exception(("Cannot parse workflow identifier from FileName `" + file_name) + "`")
+
+
+
+def Workflow_tryIdentifierFromFileName(file_name: str) -> str | None:
+    active_pattern_result: Any | None = ActivePatterns__007CRegex_007C__007C("^(workflows(\\/|\\\\))?(?<identifier>[a-zA-Z0-9_\\- ]+)((\\/|\\\\)isa.workflow.xlsx)?$", file_name)
+    if active_pattern_result is not None:
+        m: Any = active_pattern_result
+        return get_item(groups(m), "identifier") or ""
+
+    else: 
+        return None
+
+
+
+def Workflow_fileNameFromIdentifier(identifier: str) -> str:
+    check_valid_characters(identifier)
+    return combine_many(["workflows", identifier, "isa.workflow.xlsx"])
+
+
+def Workflow_tryFileNameFromIdentifier(identifier: str) -> str | None:
+    if try_check_valid_characters(identifier):
+        return combine_many(["workflows", identifier, "isa.workflow.xlsx"])
+
+    else: 
+        return None
+
+
+
+def Workflow_datamapFileNameFromIdentifier(identifier: str) -> str:
+    check_valid_characters(identifier)
+    return combine_many(["workflows", identifier, "isa.datamap.xlsx"])
+
+
+def Workflow_tryDatamapFileNameFromIdentifier(identifier: str) -> str | None:
+    if try_check_valid_characters(identifier):
+        return combine_many(["workflows", identifier, "isa.datamap.xlsx"])
+
+    else: 
+        return None
+
+
+
+def Run_identifierFromFileName(file_name: str) -> str:
+    active_pattern_result: Any | None = ActivePatterns__007CRegex_007C__007C("^(runs(\\/|\\\\))?(?<identifier>[a-zA-Z0-9_\\- ]+)((\\/|\\\\)isa.run.xlsx)?$", file_name)
+    if active_pattern_result is not None:
+        m: Any = active_pattern_result
+        return get_item(groups(m), "identifier") or ""
+
+    else: 
+        raise Exception(("Cannot parse run identifier from FileName `" + file_name) + "`")
+
+
+
+def Run_tryIdentifierFromFileName(file_name: str) -> str | None:
+    active_pattern_result: Any | None = ActivePatterns__007CRegex_007C__007C("^(runs(\\/|\\\\))?(?<identifier>[a-zA-Z0-9_\\- ]+)((\\/|\\\\)isa.run.xlsx)?$", file_name)
+    if active_pattern_result is not None:
+        m: Any = active_pattern_result
+        return get_item(groups(m), "identifier") or ""
+
+    else: 
+        return None
+
+
+
+def Run_fileNameFromIdentifier(identifier: str) -> str:
+    check_valid_characters(identifier)
+    return combine_many(["runs", identifier, "isa.run.xlsx"])
+
+
+def Run_tryFileNameFromIdentifier(identifier: str) -> str | None:
+    if try_check_valid_characters(identifier):
+        return combine_many(["runs", identifier, "isa.run.xlsx"])
+
+    else: 
+        return None
+
+
+
+def Run_datamapFileNameFromIdentifier(identifier: str) -> str:
+    check_valid_characters(identifier)
+    return combine_many(["runs", identifier, "isa.datamap.xlsx"])
+
+
+def Run_tryDatamapFileNameFromIdentifier(identifier: str) -> str | None:
+    if try_check_valid_characters(identifier):
+        return combine_many(["runs", identifier, "isa.datamap.xlsx"])
+
+    else: 
+        return None
+
+
+
+__all__ = ["try_check_valid_characters", "check_valid_characters", "create_missing_identifier", "is_missing_identifier", "remove_missing_identifier", "Assay_identifierFromFileName", "Assay_tryIdentifierFromFileName", "Assay_fileNameFromIdentifier", "Assay_tryFileNameFromIdentifier", "Assay_datamapFileNameFromIdentifier", "Assay_tryDatamapFileNameFromIdentifier", "Study_identifierFromFileName", "Study_tryIdentifierFromFileName", "Study_fileNameFromIdentifier", "Study_tryFileNameFromIdentifier", "Study_datamapFileNameFromIdentifier", "Study_tryDatamapFileNameFromIdentifier", "Workflow_identifierFromFileName", "Workflow_tryIdentifierFromFileName", "Workflow_fileNameFromIdentifier", "Workflow_tryFileNameFromIdentifier", "Workflow_datamapFileNameFromIdentifier", "Workflow_tryDatamapFileNameFromIdentifier", "Run_identifierFromFileName", "Run_tryIdentifierFromFileName", "Run_fileNameFromIdentifier", "Run_tryFileNameFromIdentifier", "Run_datamapFileNameFromIdentifier", "Run_tryDatamapFileNameFromIdentifier"]
+

arctrl/py/Core/Helper/orcid.py

@@ -0,0 +1,42 @@
+from typing import Any
+from ...fable_modules.fable_library.reg_exp import (create, match)
+from .regex import ActivePatterns__007CRegex_007C__007C
+
+orcid_regex: Any = create("[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]")
+
+def try_get_orcid_number(orcid: str) -> str | None:
+    m: Any = match(orcid_regex, orcid)
+    if m is not None:
+        return m[0]
+
+    else: 
+        return None
+
+
+
+orcid_prefix: str = "http://orcid.org/"
+
+def _007CORCID_007C__007C(input: str) -> str | None:
+    active_pattern_result: Any | None = ActivePatterns__007CRegex_007C__007C("[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]", input)
+    if active_pattern_result is not None:
+        r: Any = active_pattern_result
+        return r[0]
+
+    else: 
+        return None
+
+
+
+def try_get_orcid_url(orcid: str) -> str | None:
+    active_pattern_result: str | None = _007CORCID_007C__007C(orcid)
+    if active_pattern_result is not None:
+        orcid_1: str = active_pattern_result
+        return ((("" + orcid_prefix) + "") + orcid_1) + ""
+
+    else: 
+        return None
+
+
+
+__all__ = ["orcid_regex", "try_get_orcid_number", "orcid_prefix", "_007CORCID_007C__007C", "try_get_orcid_url"]
+

arctrl/py/Core/Helper/printer.py

@@ -0,0 +1,13 @@
+from abc import abstractmethod
+from typing import Protocol
+
+class IISAPrintable(Protocol):
+    @abstractmethod
+    def Print(self) -> str:
+        ...
+
+    @abstractmethod
+    def PrintCompact(self) -> str:
+        ...
+
+