toil 5.12.0__py3-none-any.whl → 6.1.0__py3-none-any.whl

toil/wdl/wdl_types.py

@@ -1,243 +0,0 @@
-from abc import ABC
-from typing import Any, Dict, Optional
-
-from toil.job import Promise
-
-
-class WDLRuntimeError(RuntimeError):
-    pass
-
-
-class WDLType:
-    """
-    Represents a primitive or compound WDL type:
-
-    https://github.com/openwdl/wdl/blob/main/versions/development/SPEC.md#types
-    """
-
-    def __init__(self, optional: bool = False):
-        self.optional = optional
-
-    @property
-    def name(self) -> str:
-        """
-        Type name as string. Used in display messages / 'mappings.out' if dev
-        mode is enabled.
-        """
-        raise NotImplementedError
-
-    @property
-    def default_value(self) -> Optional[str]:
-        """
-        Default value if optional.
-        """
-        return None
-
-    def create(self, value: Any, output: bool = False) -> Any:
-        """
-        Calls at runtime. Returns an instance of the current type. An error may
-        be raised if the value is not in the correct format.
-
-        :param value: a Python object
-        """
-        if value is None:
-            # check if input is in fact an optional.
-            if self.optional:
-                return self.default_value
-            else:
-                raise WDLRuntimeError(f"Required input for '{self.name}' type not specified.")
-
-        if isinstance(value, Promise):
-            return value
-
-        return self._create(value)
-
-    def _create(self, value: Any) -> Any:
-        raise NotImplementedError
-
-    def __eq__(self, other: Any) -> bool:
-        return self.name.__eq__(other)
-
-    def __str__(self) -> str:
-        return self.name.__str__()
-
-    def __repr__(self) -> str:
-        return self.name.__repr__()
-
-
-class WDLCompoundType(WDLType, ABC):
-    """
-    Represents a WDL compound type.
-    """
-
-
-class WDLStringType(WDLType):
-    """ Represents a WDL String primitive type."""
-
-    @property
-    def name(self) -> str:
-        return 'String'
-
-    @property
-    def default_value(self) -> str:
-        return ''
-
-    def _create(self, value: Any) -> Any:
-        return str(value)
-
-
-class WDLIntType(WDLType):
-    """ Represents a WDL Int primitive type."""
-
-    @property
-    def name(self) -> str:
-        return 'Int'
-
-    def _create(self, value: Any) -> Any:
-        return int(value)
-
-
-class WDLFloatType(WDLType):
-    """ Represents a WDL Float primitive type."""
-
-    @property
-    def name(self) -> str:
-        return 'Float'
-
-    def _create(self, value: Any) -> Any:
-        return float(value)
-
-
-class WDLBooleanType(WDLType):
-    """ Represents a WDL Boolean primitive type."""
-
-    @property
-    def name(self) -> str:
-        return 'Boolean'
-
-    def _create(self, value: Any) -> Any:
-        return True if value else False
-
-
-class WDLFileType(WDLType):
-    """ Represents a WDL File primitive type."""
-
-    @property
-    def name(self) -> str:
-        return 'File'
-
-    @property
-    def default_value(self) -> str:
-        return ''
-
-    def _create(self, value: Any) -> Any:
-        if isinstance(value, (WDLFile, Promise)):
-            # return the original file if it's passed from task to task.
-            return value
-
-        return WDLFile(file_path=value, imported=False)
-
-
-class WDLArrayType(WDLCompoundType):
-    """ Represents a WDL Array compound type."""
-
-    def __init__(self, element: WDLType, optional: bool = False):
-        super().__init__(optional)
-        self.element = element
-
-    @property
-    def name(self) -> str:
-        return f'Array[{self.element.name}]'
-
-    def _create(self, value: Any) -> Any:
-        if not isinstance(value, list):
-            raise WDLRuntimeError(f"Expected an array input for Array, but got '{type(value)}'")
-
-        return [self.element.create(val) for val in value]
-
-
-class WDLPairType(WDLCompoundType):
-    """ Represents a WDL Pair compound type."""
-
-    def __init__(self, left: WDLType, right: WDLType, optional: bool = False):
-        super().__init__(optional)
-        self.left = left
-        self.right = right
-
-    @property
-    def name(self) -> str:
-        return f'Pair[{self.left.name}, {self.right.name}]'
-
-    def _create(self, value: Any) -> Any:
-        if isinstance(value, WDLPair):
-            return value
-        elif isinstance(value, tuple):
-            if len(value) != 2:
-                raise WDLRuntimeError('Only support Pair len == 2')
-            left, right = value
-        elif isinstance(value, dict):
-            if 'left' not in value or 'right' not in value:
-                raise WDLRuntimeError('Pair needs \'left\' and \'right\' keys')
-            left = value.get('left')
-            right = value.get('right')
-        else:
-            raise WDLRuntimeError(f"Expected a pair input for Pair, but got '{type(value)}'")
-
-        return WDLPair(self.left.create(left), self.right.create(right))
-
-
-class WDLMapType(WDLCompoundType):
-    """ Represents a WDL Map compound type."""
-
-    def __init__(self, key: WDLType, value: WDLType, optional: bool = False):
-        super().__init__(optional)
-        self.key = key
-        self.value = value
-
-    @property
-    def name(self) -> str:
-        return f'Map[{self.key.name}, {self.value.name}]'
-
-    def _create(self, value: Any) -> Any:
-        if not isinstance(value, dict):
-            raise WDLRuntimeError(f"Expected a map input for Map, but got '{type(value)}'")
-
-        return {self.key.create(k): self.value.create(v) for k, v in value.items()}
-
-
-class WDLFile:
-    """
-    Represents a WDL File.
-    """
-    def __init__(self, file_path: str, file_name: Optional[str] = None, imported: bool = False):
-        """
-        :param file_path: Path to file.
-        :param file_name: Optional. Preserved file name.
-        :param imported: If True, this file has been imported to the fileStore
-                              via fileStore.importFile().
-        """
-        self.file_path = file_path
-        self.file_name = file_name
-        self.imported = imported
-
-
-class WDLPair:
-    """
-    Represents a WDL Pair literal defined at
-    https://github.com/openwdl/wdl/blob/main/versions/development/SPEC.md#pair-literals
-    """
-
-    def __init__(self, left: Any, right: Any):
-        self.left = left
-        self.right = right
-
-    def to_dict(self) -> Dict[str, Any]:
-        return {'left': self.left, 'right': self.right}
-
-    def __eq__(self, other: Any) -> Any:
-        if not isinstance(other, WDLPair):
-            return False
-        return self.left == other.left and self.right == other.right
-
-    def __repr__(self) -> str:
-        return str(self.to_dict())

toil-5.12.0.dist-info/METADATA

@@ -1,118 +0,0 @@
-Metadata-Version: 2.1
-Name: toil
-Version: 5.12.0
-Summary: Pipeline management software for clusters.
-Home-page: https://github.com/DataBiosphere/toil
-Author: Benedict Paten and the Toil community
-Author-email: toil-community@googlegroups.com
-License: Apache License v2.0
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Environment :: Console
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Science/Research
-Classifier: Intended Audience :: Healthcare Industry
-Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Natural Language :: English
-Classifier: Operating System :: MacOS :: MacOS X
-Classifier: Operating System :: POSIX
-Classifier: Operating System :: POSIX :: Linux
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: Scientific/Engineering :: Astronomy
-Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
-Classifier: Topic :: Scientific/Engineering :: Information Analysis
-Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
-Classifier: Topic :: System :: Distributed Computing
-Classifier: Topic :: Utilities
-Requires-Python: >=3.7
-License-File: LICENSE
-Requires-Dist: dill (<0.4,>=0.3.2)
-Requires-Dist: requests (<3,>=2)
-Requires-Dist: docker (<6,>=3.7.2)
-Requires-Dist: urllib3 (<2.0.0,>=1.26.0)
-Requires-Dist: python-dateutil
-Requires-Dist: psutil (<6,>=3.0.1)
-Requires-Dist: py-tes (<1,>=0.4.2)
-Requires-Dist: PyPubSub (<5,>=4.0.3)
-Requires-Dist: addict (<2.5,>=2.2.1)
-Requires-Dist: pytz (>=2012)
-Requires-Dist: enlighten (<2,>=1.5.2)
-Requires-Dist: typing-extensions
-Provides-Extra: all
-Requires-Dist: boto (<3,>=2.48.0) ; extra == 'all'
-Requires-Dist: boto3-stubs[boto3,iam,s3,sdb,sts] (<2,>=1.28.3.post2) ; extra == 'all'
-Requires-Dist: mypy-boto3-iam (<2,>=1.28.3.post2) ; extra == 'all'
-Requires-Dist: moto (<5,>=4.1.11) ; extra == 'all'
-Requires-Dist: cwltool (==3.1.20230601100705) ; extra == 'all'
-Requires-Dist: schema-salad (<9,>=8.4.20230128170514) ; extra == 'all'
-Requires-Dist: galaxy-tool-util ; extra == 'all'
-Requires-Dist: ruamel.yaml (<=0.17.21,>=0.15) ; extra == 'all'
-Requires-Dist: ruamel.yaml.clib (>=0.2.6) ; extra == 'all'
-Requires-Dist: networkx (<2.8.9,>=2) ; extra == 'all'
-Requires-Dist: CacheControl[filecache] ; extra == 'all'
-Requires-Dist: pynacl (<2,>=1.4.0) ; extra == 'all'
-Requires-Dist: apache-libcloud (<3,>=2.2.1) ; extra == 'all'
-Requires-Dist: google-cloud-storage (<=2.8.0,>=2) ; extra == 'all'
-Requires-Dist: google-auth (<3,>=2.18.1) ; extra == 'all'
-Requires-Dist: kubernetes (<22,>=12.0.1) ; extra == 'all'
-Requires-Dist: kubernetes-stubs (==v22.6.0post1) ; extra == 'all'
-Requires-Dist: types-urllib3 ; extra == 'all'
-Requires-Dist: types-PyYAML ; extra == 'all'
-Requires-Dist: idna (>=2) ; extra == 'all'
-Requires-Dist: pymesos (<0.4,>=0.3.15) ; extra == 'all'
-Requires-Dist: miniwdl (==1.10.0) ; extra == 'all'
-Requires-Dist: wdlparse (==0.1.0) ; extra == 'all'
-Requires-Dist: connexion[swagger-ui] (<3,>=2.10.0) ; extra == 'all'
-Requires-Dist: flask (<3,>=2.0) ; extra == 'all'
-Requires-Dist: werkzeug (<3,>=2.0) ; extra == 'all'
-Requires-Dist: flask-cors (==3.0.10) ; extra == 'all'
-Requires-Dist: gunicorn (==20.1.0) ; extra == 'all'
-Requires-Dist: celery (<6,>=5.1.0) ; extra == 'all'
-Requires-Dist: wes-service (<5,>=4.0.0) ; extra == 'all'
-Requires-Dist: ruamel.yaml (<0.17.22,>=0.15) ; extra == 'all'
-Provides-Extra: aws
-Requires-Dist: boto (<3,>=2.48.0) ; extra == 'aws'
-Requires-Dist: boto3-stubs[boto3,iam,s3,sdb,sts] (<2,>=1.28.3.post2) ; extra == 'aws'
-Requires-Dist: mypy-boto3-iam (<2,>=1.28.3.post2) ; extra == 'aws'
-Requires-Dist: moto (<5,>=4.1.11) ; extra == 'aws'
-Provides-Extra: cwl
-Requires-Dist: cwltool (==3.1.20230601100705) ; extra == 'cwl'
-Requires-Dist: schema-salad (<9,>=8.4.20230128170514) ; extra == 'cwl'
-Requires-Dist: galaxy-tool-util ; extra == 'cwl'
-Requires-Dist: ruamel.yaml (<=0.17.21,>=0.15) ; extra == 'cwl'
-Requires-Dist: ruamel.yaml.clib (>=0.2.6) ; extra == 'cwl'
-Requires-Dist: networkx (<2.8.9,>=2) ; extra == 'cwl'
-Requires-Dist: CacheControl[filecache] ; extra == 'cwl'
-Provides-Extra: encryption
-Requires-Dist: pynacl (<2,>=1.4.0) ; extra == 'encryption'
-Provides-Extra: google
-Requires-Dist: apache-libcloud (<3,>=2.2.1) ; extra == 'google'
-Requires-Dist: google-cloud-storage (<=2.8.0,>=2) ; extra == 'google'
-Requires-Dist: google-auth (<3,>=2.18.1) ; extra == 'google'
-Provides-Extra: htcondor
-Requires-Dist: htcondor (<11,>=10.2.0.post1) ; (sys_platform!="darwin") and extra == 'htcondor'
-Provides-Extra: kubernetes
-Requires-Dist: kubernetes (<22,>=12.0.1) ; extra == 'kubernetes'
-Requires-Dist: kubernetes-stubs (==v22.6.0post1) ; extra == 'kubernetes'
-Requires-Dist: types-urllib3 ; extra == 'kubernetes'
-Requires-Dist: types-PyYAML ; extra == 'kubernetes'
-Requires-Dist: idna (>=2) ; extra == 'kubernetes'
-Provides-Extra: mesos
-Requires-Dist: pymesos (<0.4,>=0.3.15) ; extra == 'mesos'
-Provides-Extra: server
-Requires-Dist: connexion[swagger-ui] (<3,>=2.10.0) ; extra == 'server'
-Requires-Dist: flask (<3,>=2.0) ; extra == 'server'
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-Requires-Dist: wes-service (<5,>=4.0.0) ; extra == 'server'
-Requires-Dist: ruamel.yaml (<0.17.22,>=0.15) ; extra == 'server'
-Provides-Extra: wdl
-Requires-Dist: miniwdl (==1.10.0) ; extra == 'wdl'
-Requires-Dist: wdlparse (==0.1.0) ; extra == 'wdl'
-

toil-5.12.0.dist-info/RECORD

@@ -1,244 +0,0 @@
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