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

toil/wdl/versions/dev.py

@@ -1,107 +0,0 @@
-# Copyright (C) 2020-2021 Regents of the University of California
-#
-# 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 wdlparse.dev.WdlLexer import FileStream, WdlLexer
-from wdlparse.dev.WdlParser import CommonTokenStream, WdlParser
-
-from toil.wdl.versions.v1 import AnalyzeV1WDL, is_context
-from toil.wdl.wdl_types import WDLType
-
-logger = logging.getLogger(__name__)
-
-
-class AnalyzeDevelopmentWDL(AnalyzeV1WDL):  # extend from 1.0
-    """
-    AnalyzeWDL implementation for the development version using ANTLR4.
-
-    See: https://github.com/openwdl/wdl/blob/main/versions/development/SPEC.md
-         https://github.com/openwdl/wdl/blob/main/versions/development/parsers/antlr4/WdlParser.g4
-    """
-
-    @property
-    def version(self) -> str:
-        return 'development'
-
-    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`.
-        """
-        lexer = WdlLexer(FileStream(self.wdl_file))
-        parser = WdlParser(input=CommonTokenStream(lexer))
-        tree = parser.document()
-        self.visit_document(tree)
-
-    def visit_document(self, ctx: WdlParser.DocumentContext) -> None:
-        """
-        Similar to version 1.0, except the 'workflow' element is included in
-        `ctx.document_element()`.
-        """
-        for element in ctx.document_element():
-            self.visit_document_element(element)
-
-    def visit_document_element(self, ctx: WdlParser.Document_elementContext) -> None:
-        """
-        Similar to version 1.0, except this also contains 'workflow'.
-        """
-        element = ctx.children[0]
-        if is_context(element, 'WorkflowContext'):
-            self.visit_workflow(element)
-        else:
-            # let super take care of the rest.
-            super().visit_document_element(ctx)
-
-    def visit_call(self, ctx: WdlParser.CallContext) -> dict:
-        """
-        Similar to version 1.0, except `ctx.call_afters()` is added.
-        """
-        # TODO: implement call_afters
-        # See: https://github.com/openwdl/wdl/blob/main/versions/development/SPEC.md#call-statement
-        return super().visit_call(ctx)
-
-    def visit_string_expr_part(self, ctx: WdlParser.String_expr_partContext) -> str:
-        """
-        Similar to version 1.0, except `ctx.expression_placeholder_option()`
-        is removed.
-        """
-        # expression placeholder options are removed in development
-        # See: https://github.com/openwdl/wdl/blob/main/versions/development/parsers/antlr4/WdlParser.g4#L55
-
-        return self.visit_expr(ctx.expr())
-
-    def visit_wdl_type(self, ctx: WdlParser.Wdl_typeContext) -> WDLType:
-        """
-        Similar to version 1.0, except Directory type is added.
-        """
-        identifier = ctx.type_base().children[0]
-
-        if identifier == 'Directory':
-            # TODO: implement Directory type
-            raise NotImplementedError('Directory type is not implemented.')
-        else:
-            # let super take care of the rest.
-            return super().visit_wdl_type(ctx)
-
-    def visit_expr_core(self, expr: WdlParser.Expr_coreContext) -> str:
-        """
-        Similar to version 1.0, except struct literal is added.
-        """
-        if is_context(expr, 'Struct_literalContext'):
-            # TODO: implement struct literal
-            raise NotImplementedError(f'WDL struct is not implemented.')
-        else:
-            # let super take care of the rest.
-            return super().visit_expr_core(expr)