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

toil/wdl/wdl_analysis.py

@@ -1,116 +0,0 @@
-# Copyright (C) 2018-2021 UCSC Computational Genomics Lab
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-import logging
-from collections import OrderedDict
-
-from toil.wdl.wdl_types import (WDLArrayType,
-                                WDLBooleanType,
-                                WDLFileType,
-                                WDLFloatType,
-                                WDLIntType,
-                                WDLMapType,
-                                WDLPairType,
-                                WDLStringType)
-
-logger = logging.getLogger(__name__)
-
-
-class AnalyzeWDL:
-    """
-    An interface to analyze a WDL file. Each version corresponds to a subclass that
-    restructures the WDL document into 2 intermediate data structures (python
-    dictionaries):
-        "workflows_dictionary": containing the parsed workflow information.
-        "tasks_dictionary": containing the parsed task information.
-
-    These are then fed into wdl_synthesis.py which uses them to write a native python
-    script for use with Toil.
-
-    Requires a WDL file.  The WDL file contains ordered commands.
-    """
-    def __init__(self, wdl_file: str):
-        self.wdl_file = wdl_file
-
-        # holds task skeletons from WDL task objects
-        self.tasks_dictionary = OrderedDict()
-
-        # holds workflow structure from WDL workflow objects
-        self.workflows_dictionary = OrderedDict()
-
-        # unique iterator to add to declaration names
-        self.declaration_number = 0
-
-        # unique iterator to add to call names
-        self.call_number = 0
-
-        # unique iterator to add to scatter names
-        self.scatter_number = 0
-
-        # unique iterator to add to if names
-        self.if_number = 0
-
-    @property
-    def version(self) -> str:
-        """
-        Returns the version of the WDL document as a string.
-        """
-        raise NotImplementedError
-
-    def analyze(self):
-        """
-        Analyzes the WDL file passed into the constructor and generates the two
-        intermediate data structures: `self.workflows_dictionary` and
-        `self.tasks_dictionary`.
-
-        :return: Returns nothing.
-        """
-
-    def write_AST(self, out_dir):
-        """
-        Writes a file with the AST for a wdl file in the out_dir.
-        """
-
-    primitive_types = {
-        'String': WDLStringType,
-        'Int': WDLIntType,
-        'Float': WDLFloatType,
-        'Boolean': WDLBooleanType,
-        'File': WDLFileType
-    }
-
-    compound_types = {
-        'Array': WDLArrayType,
-        'Pair': WDLPairType,
-        'Map': WDLMapType
-    }
-
-    def create_wdl_primitive_type(self, key: str, optional: bool = False):
-        """
-        Returns an instance of WDLType.
-        """
-        type_ = self.primitive_types.get(key)
-        if type_:
-            return type_(optional=optional)
-        else:
-            raise RuntimeError(f'Unsupported primitive type: {key}')
-
-    def create_wdl_compound_type(self, key: str, elements: list, optional: bool = False):
-        """
-        Returns an instance of WDLCompoundType.
-        """
-        type_ = self.compound_types.get(key)
-        if type_:
-            return type_(*elements, optional=optional)
-        else:
-            raise RuntimeError(f'Unsupported compound type: {key}')