toil 5.12.0__py3-none-any.whl → 6.1.0a1__py3-none-any.whl

toil/wdl/versions/draft2.py

@@ -1,980 +0,0 @@
-# Copyright (C) 2018-2020 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
-import os
-from collections import OrderedDict
-
-from wdlparse.draft2 import wdl_parser
-
-from toil.wdl.wdl_analysis import AnalyzeWDL
-
-logger = logging.getLogger(__name__)
-
-
-class AnalyzeDraft2WDL(AnalyzeWDL):
-    """
-    AnalyzeWDL implementation for the draft-2 version.
-    """
-
-    @property
-    def version(self) -> str:
-        return 'draft-2'
-
-    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.
-        """
-        # parse the wdl AST into 2 dictionaries
-        with open(self.wdl_file) as wdl:
-            wdl_string = wdl.read()
-            ast = wdl_parser.parse(wdl_string).ast()
-            self.create_tasks_dict(ast)
-            self.create_workflows_dict(ast)
-
-    def write_AST(self, out_dir=None):
-        """
-        Writes a file with the AST for a wdl file in the out_dir.
-        """
-        if out_dir is None:
-            out_dir = os.getcwd()
-        with open(os.path.join(out_dir, 'AST.out'), 'w') as f:
-            with open(self.wdl_file) as wdl:
-                wdl_string = wdl.read()
-                ast = wdl_parser.parse(wdl_string).ast()
-                f.write(ast.dumps(indent=2))
-
-    def find_asts(self, ast_root, name):
-        """
-        Finds an AST node with the given name and the entire subtree under it.
-        A function borrowed from scottfrazer.  Thank you Scott Frazer!
-
-        :param ast_root: The WDL AST.  The whole thing generally, but really
-                         any portion that you wish to search.
-        :param name: The name of the subtree you're looking for, like "Task".
-        :return: nodes representing the AST subtrees matching the "name" given.
-        """
-        nodes = []
-        if isinstance(ast_root, wdl_parser.AstList):
-            for node in ast_root:
-                nodes.extend(self.find_asts(node, name))
-        elif isinstance(ast_root, wdl_parser.Ast):
-            if ast_root.name == name:
-                nodes.append(ast_root)
-            for attr_name, attr in ast_root.attributes.items():
-                nodes.extend(self.find_asts(attr, name))
-        return nodes
-
-    def create_tasks_dict(self, ast):
-        """
-        Parse each "Task" in the AST.  This will create self.tasks_dictionary,
-        where each task name is a key.
-
-        :return: Creates the self.tasks_dictionary necessary for much of the
-        parser.  Returning it is only necessary for unittests.
-        """
-        tasks = self.find_asts(ast, 'Task')
-        for task in tasks:
-            self.parse_task(task)
-        return self.tasks_dictionary
-
-    def parse_task(self, task):
-        """
-        Parses a WDL task AST subtree.
-
-        Currently looks at and parses 4 sections:
-        1. Declarations (e.g. string x = 'helloworld')
-        2. Commandline (a bash command with dynamic variables inserted)
-        3. Runtime (docker image; disk; CPU; RAM; etc.)
-        4. Outputs (expected return values/files)
-
-        :param task: An AST subtree of a WDL "Task".
-        :return: Returns nothing but adds a task to the self.tasks_dictionary
-        necessary for much of the parser.
-        """
-
-        task_name = task.attributes["name"].source_string
-
-        # task declarations
-        declaration_array = []
-        for declaration_subAST in task.attr("declarations"):
-            declaration_array.append(self.parse_declaration(declaration_subAST))
-            self.tasks_dictionary.setdefault(task_name, OrderedDict())['inputs'] = declaration_array
-
-        for section in task.attr("sections"):
-
-            # task commandline entries section [command(s) to run]
-            if section.name == "RawCommand":
-                command_array = self.parse_task_rawcommand(section)
-                self.tasks_dictionary.setdefault(task_name, OrderedDict())['raw_commandline'] = command_array
-
-            # task runtime section (docker image; disk; CPU; RAM; etc.)
-            if section.name == "Runtime":
-                runtime_dict = self.parse_task_runtime(section.attr("map"))
-                self.tasks_dictionary.setdefault(task_name, OrderedDict())['runtime'] = runtime_dict
-
-            # task output filenames section (expected return values/files)
-            if section.name == "Outputs":
-                output_array = self.parse_task_outputs(section)
-                self.tasks_dictionary.setdefault(task_name, OrderedDict())['outputs'] = output_array
-
-    def parse_task_rawcommand_attributes(self, code_snippet):
-        """
-
-        :param code_snippet:
-        :return:
-        """
-        attr_dict = OrderedDict()
-        if isinstance(code_snippet, wdl_parser.Terminal):
-            raise NotImplementedError
-        if isinstance(code_snippet, wdl_parser.Ast):
-            raise NotImplementedError
-        if isinstance(code_snippet, wdl_parser.AstList):
-            for ast in code_snippet:
-                if ast.name == 'CommandParameterAttr':
-                    # TODO rewrite
-                    if ast.attributes['value'].str == 'string':
-                        attr_dict[ast.attributes['key'].source_string] = "'" + ast.attributes['value'].source_string + "'"
-                    else:
-                        attr_dict[ast.attributes['key'].source_string] = ast.attributes['value'].source_string
-        return attr_dict
-
-    def parse_task_rawcommand(self, rawcommand_subAST):
-        """
-        Parses the rawcommand section of the WDL task AST subtree.
-
-        Task "rawcommands" are divided into many parts.  There are 2 types of
-        parts: normal strings, & variables that can serve as changeable inputs.
-
-        The following example command:
-            'echo ${variable1} ${variable2} > output_file.txt'
-
-        Has 5 parts:
-                     Normal  String: 'echo '
-                     Variable Input: variable1
-                     Normal  String: ' '
-                     Variable Input: variable2
-                     Normal  String: ' > output_file.txt'
-
-        Variables can also have additional conditions, like 'sep', which is like
-        the python ''.join() function and in WDL looks like: ${sep=" -V " GVCFs}
-        and would be translated as: ' -V '.join(GVCFs).
-
-        :param rawcommand_subAST: A subAST representing some bash command.
-        :return: A list=[] of tuples=() representing the parts of the command:
-             e.g. [(command_var, command_type, additional_conditions_list), ...]
-                  Where: command_var = 'GVCFs'
-                         command_type = 'variable'
-                         command_actions = {'sep': ' -V '}
-        """
-        command_array = []
-        for code_snippet in rawcommand_subAST.attributes["parts"]:
-
-            # normal string
-            if isinstance(code_snippet, wdl_parser.Terminal):
-                command_var = "r'''" + code_snippet.source_string + "'''"
-
-            # a variable like ${dinosaurDNA}
-            if isinstance(code_snippet, wdl_parser.Ast):
-                if code_snippet.name == 'CommandParameter':
-                    # change in the future?  seems to be a different parameter but works for all cases it seems?
-                    code_expr = self.parse_declaration_expressn(code_snippet.attr('expr'), es='')
-                    code_attributes = self.parse_task_rawcommand_attributes(code_snippet.attr('attributes'))
-                    command_var = self.modify_cmd_expr_w_attributes(code_expr, code_attributes)
-
-            if isinstance(code_snippet, wdl_parser.AstList):
-                raise NotImplementedError
-            command_array.append(command_var)
-
-        return command_array
-
-    def modify_cmd_expr_w_attributes(self, code_expr, code_attr):
-        """
-
-        :param code_expr:
-        :param code_attr:
-        :return:
-        """
-        for param in code_attr:
-            if param == 'sep':
-                code_expr = f"{code_attr[param]}.join(str(x) for x in {code_expr})"
-            elif param == 'default':
-                code_expr = "{expr} if {expr} else {default}".format(default=code_attr[param], expr=code_expr)
-            else:
-                raise NotImplementedError
-        return code_expr
-
-    def parse_task_runtime_key(self, i):
-        """
-
-        :param runtime_subAST:
-        :return:
-        """
-        if isinstance(i, wdl_parser.Terminal):
-            return i.source_string
-        if isinstance(i, wdl_parser.Ast):
-            raise NotImplementedError
-        if isinstance(i, wdl_parser.AstList):
-            raise NotImplementedError
-
-    def parse_task_runtime(self, runtime_subAST):
-        """
-        Parses the runtime section of the WDL task AST subtree.
-
-        The task "runtime" section currently supports context fields for a
-        docker container, CPU resources, RAM resources, and disk resources.
-
-        :param runtime_subAST: A subAST representing runtime parameters.
-        :return: A list=[] of runtime attributes, for example:
-                 runtime_attributes = [('docker','quay.io/encode-dcc/map:v1.0'),
-                                       ('cpu','2'),
-                                       ('memory','17.1 GB'),
-                                       ('disks','local-disk 420 HDD')]
-        """
-        runtime_attributes = OrderedDict()
-        if isinstance(runtime_subAST, wdl_parser.Terminal):
-            raise NotImplementedError
-        elif isinstance(runtime_subAST, wdl_parser.Ast):
-            raise NotImplementedError
-        elif isinstance(runtime_subAST, wdl_parser.AstList):
-            for ast in runtime_subAST:
-                key = self.parse_task_runtime_key(ast.attr('key'))
-                value = self.parse_declaration_expressn(ast.attr('value'), es='')
-                if value.startswith('"'):
-                    value = self.translate_wdl_string_to_python_string(value[1:-1])
-                runtime_attributes[key] = value
-        return runtime_attributes
-
-    def parse_task_outputs(self, i):
-        """
-        Parse the WDL output section.
-
-        Outputs are like declarations, with a type, name, and value.  Examples:
-
-        ------------
-        Simple Cases
-        ------------
-
-        'Int num = 7'
-            var_name: 'num'
-            var_type: 'Int'
-            var_value: 7
-
-        String idea = 'Lab grown golden eagle burgers.'
-            var_name: 'idea'
-            var_type: 'String'
-            var_value: 'Lab grown golden eagle burgers.'
-
-        File ideaFile = 'goldenEagleStemCellStartUpDisrupt.txt'
-            var_name: 'ideaFile'
-            var_type: 'File'
-            var_value: 'goldenEagleStemCellStartUpDisrupt.txt'
-
-        -------------------
-        More Abstract Cases
-        -------------------
-
-        Array[File] allOfMyTerribleIdeas = glob(*.txt)[0]
-            var_name:      'allOfMyTerribleIdeas'
-            var_type**:    'File'
-            var_value:     [*.txt]
-            var_actions:   {'index_lookup': '0', 'glob': 'None'}
-
-        **toilwdl.py converts 'Array[File]' to 'ArrayFile'
-
-        :return: output_array representing outputs generated by the job/task:
-                e.g. x = [(var_name, var_type, var_value, var_actions), ...]
-        """
-        output_array = []
-        for j in i.attributes['attributes']:
-            if j.name == 'Output':
-                output_array.append(self.parse_declaration(j))
-            else:
-                raise NotImplementedError
-        return output_array
-
-    def translate_wdl_string_to_python_string(self, some_string):
-        """
-        Parses a string representing a given job's output filename into something
-        python can read.  Replaces ${string}'s with normal variables and the rest
-        with normal strings all concatenated with ' + '.
-
-        Will not work with additional parameters, such as:
-        ${default="foo" bar}
-        or
-        ${true="foo" false="bar" Boolean baz}
-
-        This method expects to be passed only strings with some combination of
-        "${abc}" and "abc" blocks.
-
-        :param job: A list such that:
-                        (job priority #, job ID #, Job Skeleton Name, Job Alias)
-        :param some_string: e.g. '${sampleName}.vcf'
-        :return: output_string, e.g. 'sampleName + ".vcf"'
-        """
-
-        try:
-            # add support for 'sep'
-            output_string = ''
-            edited_string = some_string.strip()
-
-            if edited_string.find('${') != -1:
-                continue_loop = True
-                while continue_loop:
-                    index_start = edited_string.find('${')
-                    index_end = edited_string.find('}', index_start)
-
-                    stringword = edited_string[:index_start]
-
-                    if index_start != 0:
-                        output_string = output_string + "'" + stringword + "' + "
-
-                    keyword = edited_string[index_start + 2:index_end]
-                    output_string = output_string + "str(" + keyword + ") + "
-
-                    edited_string = edited_string[index_end + 1:]
-                    if edited_string.find('${') == -1:
-                        continue_loop = False
-                        if edited_string:
-                            output_string = output_string + "'" + edited_string + "' + "
-            else:
-                output_string = "'" + edited_string + "'"
-
-            if output_string.endswith(' + '):
-                output_string = output_string[:-3]
-
-            return output_string
-        except:
-            return ''
-
-    def create_workflows_dict(self, ast):
-        """
-        Parse each "Workflow" in the AST.  This will create self.workflows_dictionary,
-        where each called job is a tuple key of the form: (priority#, job#, name, alias).
-
-        :return: Creates the self.workflows_dictionary necessary for much of the
-        parser.  Returning it is only necessary for unittests.
-        """
-        workflows = self.find_asts(ast, 'Workflow')
-        for workflow in workflows:
-            self.parse_workflow(workflow)
-        return self.workflows_dictionary
-
-    def parse_workflow(self, workflow):
-        """
-        Parses a WDL workflow AST subtree.
-
-        Returns nothing but creates the self.workflows_dictionary necessary for much
-        of the parser.
-
-        :param workflow: An AST subtree of a WDL "Workflow".
-        :return: Returns nothing but adds a workflow to the
-                 self.workflows_dictionary necessary for much of the parser.
-        """
-        workflow_name = workflow.attr('name').source_string
-        self.workflows_dictionary[workflow_name] = self.parse_workflow_body(workflow.attr("body"))
-
-    def parse_workflow_body(self, i):
-        """
-        Currently looks at and parses 3 sections:
-        1. Declarations (e.g. String x = 'helloworld')
-        2. Calls (similar to a python def)
-        3. Scatter (which expects to map to a Call or multiple Calls)
-        4. Conditionals
-        """
-        subworkflow_dict = OrderedDict()
-        if isinstance(i, wdl_parser.Terminal):
-            raise NotImplementedError
-        elif isinstance(i, wdl_parser.Ast):
-            raise NotImplementedError
-        elif isinstance(i, wdl_parser.AstList):
-            for ast in i:
-                if ast.name == "Declaration":
-                    declaration = self.parse_declaration(ast)
-                    subworkflow_dict['declaration' + str(self.declaration_number)] = declaration
-                    self.declaration_number += 1
-
-                elif ast.name == "Scatter":
-                    scattertask = self.parse_workflow_scatter(ast)
-                    subworkflow_dict['scatter' + str(self.scatter_number)] = scattertask
-                    self.scatter_number += 1
-
-                elif ast.name == "Call":
-                    task = self.parse_workflow_call(ast)
-                    subworkflow_dict['call' + str(self.call_number)] = task
-                    self.call_number += 1
-
-                elif ast.name == "If":
-                    task = self.parse_workflow_if(ast)
-                    subworkflow_dict['if' + str(self.if_number)] = task
-                    self.if_number += 1
-        return subworkflow_dict
-
-    def parse_workflow_if(self, ifAST):
-        expression = self.parse_workflow_if_expression(ifAST.attr('expression'))
-        body = self.parse_workflow_body(ifAST.attr('body'))
-        return {'expression': expression, 'body': body}
-
-    def parse_workflow_if_expression(self, i):
-        return self.parse_declaration_expressn(i, es='')
-
-    def parse_workflow_scatter(self, scatterAST):
-        item = self.parse_workflow_scatter_item(scatterAST.attr('item'))
-        collection = self.parse_workflow_scatter_collection(scatterAST.attr('collection'))
-        body = self.parse_workflow_body(scatterAST.attr('body'))
-        return {'item': item, 'collection': collection, 'body': body}
-
-    def parse_workflow_scatter_item(self, i):
-        if isinstance(i, wdl_parser.Terminal):
-            return i.source_string
-        elif isinstance(i, wdl_parser.Ast):
-            raise NotImplementedError
-        elif isinstance(i, wdl_parser.AstList):
-            raise NotImplementedError
-
-    def parse_workflow_scatter_collection(self, i):
-        if isinstance(i, wdl_parser.Terminal):
-            return i.source_string
-        elif isinstance(i, wdl_parser.Ast):
-            return self.parse_declaration_expressn(i, es='')
-        elif isinstance(i, wdl_parser.AstList):
-            raise NotImplementedError
-
-    def parse_declaration(self, ast):
-        """
-        Parses a WDL declaration AST subtree into a Python tuple.
-
-        Examples:
-
-        String my_name
-        String your_name
-        Int two_chains_i_mean_names = 0
-
-        :param ast: Some subAST representing a task declaration like:
-                     'String file_name'
-        :return: var_name, var_type, var_value
-            Example:
-                Input subAST representing:   'String file_name'
-                Output:  var_name='file_name', var_type='String', var_value=None
-        """
-        var_name = self.parse_declaration_name(ast.attr("name"))
-        var_type = self.parse_declaration_type(ast.attr("type"))
-        var_expressn = self.parse_declaration_expressn(ast.attr("expression"), es='')
-
-        return var_name, var_type, var_expressn
-
-    def parse_declaration_name(self, nameAST):
-        """
-        Required.
-
-        Nothing fancy here.  Just the name of the workflow
-        function.  For example: "rnaseqexample" would be the following
-        wdl workflow's name:
-
-        workflow rnaseqexample {File y; call a {inputs: y}; call b;}
-        task a {File y}
-        task b {command{"echo 'ATCG'"}}
-
-        :param nameAST:
-        :return:
-        """
-        if isinstance(nameAST, wdl_parser.Terminal):
-            return nameAST.source_string
-        elif isinstance(nameAST, wdl_parser.Ast):
-            return nameAST.source_string
-        elif isinstance(nameAST, wdl_parser.AstList):
-            raise NotImplementedError
-
-    def parse_declaration_type(self, typeAST):
-        """
-        Required.
-
-        Currently supported:
-        Types are: Boolean, Float, Int, File, String, Array[subtype],
-                    Pair[subtype, subtype], and Map[subtype, subtype].
-        OptionalTypes are: Boolean?, Float?, Int?, File?, String?, Array[subtype]?,
-                            Pair[subtype, subtype]?, and Map[subtype, subtype]?.
-
-        Python is not typed, so we don't need typing except to identify type: "File",
-        which Toil needs to import, so we recursively travel down to the innermost
-        type which will tell us if the variables are files that need importing.
-
-        For Pair and Map compound types, we recursively travel down the subtypes and
-        store them as attributes of a `WDLType` string. This way, the type structure is
-        preserved, which will allow us to import files appropriately.
-
-        :param typeAST:
-        :return: a WDLType instance
-        """
-        if isinstance(typeAST, wdl_parser.Terminal):
-            return self.create_wdl_primitive_type(typeAST.source_string)
-        elif isinstance(typeAST, wdl_parser.Ast):
-            if typeAST.name == 'Type':
-                subtype = typeAST.attr('subtype')
-                optional = False
-            elif typeAST.name == 'OptionalType':
-                subtype = typeAST.attr('innerType')
-                optional = True
-            else:
-                raise NotImplementedError
-
-            if isinstance(subtype, wdl_parser.AstList):
-                # we're looking at a compound type
-                name = typeAST.attr('name').source_string
-                elements = [self.parse_declaration_type(element) for element in subtype]
-                return self.create_wdl_compound_type(name, elements, optional=optional)
-            else:
-                # either a primitive optional type OR deeply recursive types
-                # TODO: add tests #3331
-                wdl_type = self.parse_declaration_type(subtype)
-                wdl_type.optional = optional
-                return wdl_type
-        else:
-            raise NotImplementedError
-
-    def parse_declaration_expressn(self, expressionAST, es):
-        """
-        Expressions are optional.  Workflow declaration valid examples:
-
-        File x
-
-        or
-
-        File x = '/x/x.tmp'
-
-        :param expressionAST:
-        :return:
-        """
-        if not expressionAST:
-            return None
-        else:
-            if isinstance(expressionAST, wdl_parser.Terminal):
-                if expressionAST.str == 'boolean':
-                    if expressionAST.source_string == 'false':
-                        return 'False'
-                    elif expressionAST.source_string == 'true':
-                        return 'True'
-                    else:
-                        raise TypeError('Parsed boolean ({}) must be expressed as "true" or "false".'
-                                        ''.format(expressionAST.source_string))
-                elif expressionAST.str == 'string':
-                    parsed_string = self.translate_wdl_string_to_python_string(expressionAST.source_string)
-                    return f'{parsed_string}'
-                else:
-                    # integers, floats, and variables
-                    return f'{expressionAST.source_string}'
-            elif isinstance(expressionAST, wdl_parser.Ast):
-                if expressionAST.name == 'Add':
-                    es = es + self.parse_declaration_expressn_operator(expressionAST.attr('lhs'),
-                                                                       expressionAST.attr('rhs'),
-                                                                       es,
-                                                                       operator=' + ')
-                elif expressionAST.name == 'Subtract':
-                    es = es + self.parse_declaration_expressn_operator(expressionAST.attr('lhs'),
-                                                                       expressionAST.attr('rhs'),
-                                                                       es,
-                                                                       operator=' - ')
-                elif expressionAST.name == 'Multiply':
-                    es = es + self.parse_declaration_expressn_operator(expressionAST.attr('lhs'),
-                                                                       expressionAST.attr('rhs'),
-                                                                       es,
-                                                                       operator=' * ')
-                elif expressionAST.name == 'Divide':
-                    es = es + self.parse_declaration_expressn_operator(expressionAST.attr('lhs'),
-                                                                       expressionAST.attr('rhs'),
-                                                                       es,
-                                                                       operator=' / ')
-                elif expressionAST.name == 'GreaterThan':
-                    es = es + self.parse_declaration_expressn_operator(expressionAST.attr('lhs'),
-                                                                       expressionAST.attr('rhs'),
-                                                                       es,
-                                                                       operator=' > ')
-                elif expressionAST.name == 'LessThan':
-                    es = es + self.parse_declaration_expressn_operator(expressionAST.attr('lhs'),
-                                                                       expressionAST.attr('rhs'),
-                                                                       es,
-                                                                       operator=' < ')
-                elif expressionAST.name == 'FunctionCall':
-                    es = es + self.parse_declaration_expressn_fncall(expressionAST.attr('name'),
-                                                                     expressionAST.attr('params'),
-                                                                     es)
-                elif expressionAST.name == 'TernaryIf':
-                    es = es + self.parse_declaration_expressn_ternaryif(expressionAST.attr('cond'),
-                                                                        expressionAST.attr('iftrue'),
-                                                                        expressionAST.attr('iffalse'),
-                                                                        es)
-                elif expressionAST.name == 'MemberAccess':
-                    es = es + self.parse_declaration_expressn_memberaccess(expressionAST.attr('lhs'),
-                                                                           expressionAST.attr('rhs'),
-                                                                           es)
-                elif expressionAST.name == 'ArrayLiteral':
-                    es = es + self.parse_declaration_expressn_arrayliteral(expressionAST.attr('values'),
-                                                                           es)
-                elif expressionAST.name == 'TupleLiteral':
-                    es = es + self.parse_declaration_expressn_tupleliteral(expressionAST.attr('values'),
-                                                                           es)
-                elif expressionAST.name == 'ArrayOrMapLookup':
-                    es = es + self.parse_declaration_expressn_arraymaplookup(expressionAST.attr('lhs'),
-                                                                             expressionAST.attr('rhs'),
-                                                                             es)
-                elif expressionAST.name == 'LogicalNot':
-                    es = es + self.parse_declaration_expressn_logicalnot(expressionAST.attr('expression'),
-                                                                         es)
-                else:
-                    raise NotImplementedError
-            elif isinstance(expressionAST, wdl_parser.AstList):
-                raise NotImplementedError
-            return '(' + es + ')'
-
-    def parse_declaration_expressn_logicalnot(self, exprssn, es):
-        if isinstance(exprssn, wdl_parser.Terminal):
-            es = es + exprssn.source_string
-        elif isinstance(exprssn, wdl_parser.Ast):
-            es = es + self.parse_declaration_expressn(exprssn, es='')
-        elif isinstance(exprssn, wdl_parser.AstList):
-            raise NotImplementedError
-        return ' not ' + es
-
-    def parse_declaration_expressn_arraymaplookup(self, lhsAST, rhsAST, es):
-        """
-
-        :param lhsAST:
-        :param rhsAST:
-        :param es:
-        :return:
-        """
-        if isinstance(lhsAST, wdl_parser.Terminal):
-            es = es + lhsAST.source_string
-        elif isinstance(lhsAST, wdl_parser.Ast):
-            # parenthesis must be removed because 'i[0]' works, but '(i)[0]' does not
-            es = es + self.parse_declaration_expressn(lhsAST, es='')[1:-1]
-        elif isinstance(lhsAST, wdl_parser.AstList):
-            raise NotImplementedError
-
-        if isinstance(rhsAST, wdl_parser.Terminal):
-            indexnum = rhsAST.source_string
-        elif isinstance(rhsAST, wdl_parser.Ast):
-            raise NotImplementedError
-        elif isinstance(rhsAST, wdl_parser.AstList):
-            raise NotImplementedError
-
-        return es + f'[{indexnum}]'
-
-    def parse_declaration_expressn_memberaccess(self, lhsAST, rhsAST, es):
-        """
-        Instead of "Class.variablename", use "Class.rv('variablename')".
-
-        :param lhsAST:
-        :param rhsAST:
-        :param es:
-        :return:
-        """
-        if isinstance(lhsAST, wdl_parser.Terminal):
-            es = es + lhsAST.source_string
-        elif isinstance(lhsAST, wdl_parser.Ast):
-            es = es + self.parse_declaration_expressn(lhsAST, es)
-        elif isinstance(lhsAST, wdl_parser.AstList):
-            raise NotImplementedError
-
-        # hack-y way to make sure pair.left and pair.right are parsed correctly.
-        if isinstance(rhsAST, wdl_parser.Terminal) and (
-                rhsAST.source_string == 'left' or rhsAST.source_string == 'right'):
-            es = es + '.'
-        else:
-            es = es + '_'
-
-        if isinstance(rhsAST, wdl_parser.Terminal):
-            es = es + rhsAST.source_string
-        elif isinstance(rhsAST, wdl_parser.Ast):
-            es = es + self.parse_declaration_expressn(rhsAST, es)
-        elif isinstance(rhsAST, wdl_parser.AstList):
-            raise NotImplementedError
-
-        return es
-
-    def parse_declaration_expressn_ternaryif(self, cond, iftrue, iffalse, es):
-        """
-        Classic if statement.  This needs to be rearranged.
-
-        In wdl, this looks like:
-        if <condition> then <iftrue> else <iffalse>
-
-        In python, this needs to be:
-        <iftrue> if <condition> else <iffalse>
-
-        :param cond:
-        :param iftrue:
-        :param iffalse:
-        :param es:
-        :return:
-        """
-        es = es + self.parse_declaration_expressn(iftrue, es='')
-        es = es + ' if ' + self.parse_declaration_expressn(cond, es='')
-        es = es + ' else ' + self.parse_declaration_expressn(iffalse, es='')
-        return es
-
-    def parse_declaration_expressn_tupleliteral(self, values, es):
-        """
-        Same in python.  Just a parenthesis enclosed tuple.
-
-        :param values:
-        :param es:
-        :return:
-        """
-        es = es + '('
-        for ast in values:
-            es = es + self.parse_declaration_expressn(ast, es='') + ', '
-        if es.endswith(', '):
-            es = es[:-2]
-        return es + ')'
-
-    def parse_declaration_expressn_arrayliteral(self, values, es):
-        """
-        Same in python.  Just a square bracket enclosed array.
-
-        :param values:
-        :param es:
-        :return:
-        """
-        es = es + '['
-        for ast in values:
-            es = es + self.parse_declaration_expressn(ast, es='') + ', '
-        if es.endswith(', '):
-            es = es[:-2]
-        return es + ']'
-
-    def parse_declaration_expressn_operator(self, lhsAST, rhsAST, es, operator):
-        """
-        Simply joins the left and right hand arguments lhs and rhs with an operator.
-
-        :param lhsAST:
-        :param rhsAST:
-        :param es:
-        :param operator:
-        :return:
-        """
-        if isinstance(lhsAST, wdl_parser.Terminal):
-            if lhsAST.str == 'string':
-                es = es + f'"{lhsAST.source_string}"'
-            else:
-                es = es + f'{lhsAST.source_string}'
-        elif isinstance(lhsAST, wdl_parser.Ast):
-            es = es + self.parse_declaration_expressn(lhsAST, es='')
-        elif isinstance(lhsAST, wdl_parser.AstList):
-            raise NotImplementedError
-
-        es = es + operator
-
-        if isinstance(rhsAST, wdl_parser.Terminal):
-            if rhsAST.str == 'string':
-                es = es + f'"{rhsAST.source_string}"'
-            else:
-                es = es + f'{rhsAST.source_string}'
-        elif isinstance(rhsAST, wdl_parser.Ast):
-            es = es + self.parse_declaration_expressn(rhsAST, es='')
-        elif isinstance(rhsAST, wdl_parser.AstList):
-            raise NotImplementedError
-        return es
-
-    def parse_declaration_expressn_fncall(self, name, params, es):
-        """
-        Parses out cromwell's built-in function calls.
-
-        Some of these are special and need minor adjustments,
-        for example size() requires a fileStore.
-
-        :param name:
-        :param params:
-        :param es:
-        :return:
-        """
-        # name of the function
-        if isinstance(name, wdl_parser.Terminal):
-            if name.str:
-                if name.source_string == 'stdout':
-                    # let the stdout() function reference the generated stdout file path.
-                    return es + '_toil_wdl_internal__stdout_file'
-                elif name.source_string == 'stderr':
-                    return es + '_toil_wdl_internal__stderr_file'
-                elif name.source_string in ('range', 'zip'):
-                    # replace python built-in functions
-                    es += f'wdl_{name.source_string}('
-                else:
-                    es = es + name.source_string + '('
-            else:
-                raise NotImplementedError
-        elif isinstance(name, wdl_parser.Ast):
-            raise NotImplementedError
-        elif isinstance(name, wdl_parser.AstList):
-            raise NotImplementedError
-
-        es_params = self.parse_declaration_expressn_fncall_normalparams(params)
-
-        if name.source_string == 'glob':
-            return es + es_params + ', tempDir)'
-        elif name.source_string == 'size':
-            return es + (es_params + ', ' if es_params else '') + 'fileStore=fileStore)'
-        elif name.source_string in ('write_lines', 'write_tsv', 'write_json', 'write_map'):
-            return es + es_params + ', temp_dir=tempDir, file_store=fileStore)'
-        else:
-            return es + es_params + ')'
-
-    def parse_declaration_expressn_fncall_normalparams(self, params):
-
-        # arguments passed to the function
-        if isinstance(params, wdl_parser.Terminal):
-            raise NotImplementedError
-        elif isinstance(params, wdl_parser.Ast):
-            raise NotImplementedError
-        elif isinstance(params, wdl_parser.AstList):
-            es_param = ''
-            for ast in params:
-                es_param = es_param + self.parse_declaration_expressn(ast, es='') + ', '
-            if es_param.endswith(', '):
-                es_param = es_param[:-2]
-            return es_param
-
-    def parse_workflow_call_taskname(self, i):
-        """
-        Required.
-
-        :param i:
-        :return:
-        """
-        if isinstance(i, wdl_parser.Terminal):
-            return i.source_string
-        elif isinstance(i, wdl_parser.Ast):
-            raise NotImplementedError
-        elif isinstance(i, wdl_parser.AstList):
-            raise NotImplementedError
-
-    def parse_workflow_call_taskalias(self, i):
-        """
-        Required.
-
-        :param i:
-        :return:
-        """
-        if isinstance(i, wdl_parser.Terminal):
-            return i.source_string
-        elif isinstance(i, wdl_parser.Ast):
-            raise NotImplementedError
-        elif isinstance(i, wdl_parser.AstList):
-            raise NotImplementedError
-
-    def parse_workflow_call_body_declarations(self, i):
-        """
-        Have not seen this used, so expects to return "[]".
-
-        :param i:
-        :return:
-        """
-        declaration_array = []
-        if isinstance(i, wdl_parser.Terminal):
-            declaration_array = [i.source_string]
-        elif isinstance(i, wdl_parser.Ast):
-            raise NotImplementedError
-        elif isinstance(i, wdl_parser.AstList):
-            for ast in i:
-                declaration_array.append(self.parse_declaration(ast))
-
-        # have not seen this used so raise to check
-        if declaration_array:
-            raise NotImplementedError
-
-        return declaration_array
-
-    def parse_workflow_call_body_io(self, i):
-        """
-        Required.
-
-        :param i:
-        :return:
-        """
-        if isinstance(i, wdl_parser.Terminal):
-            raise NotImplementedError
-        elif isinstance(i, wdl_parser.Ast):
-            raise NotImplementedError
-        elif isinstance(i, wdl_parser.AstList):
-            for ast in i:
-                assert len(i) == 1
-                if ast.name == 'Inputs':
-                    return self.parse_workflow_call_body_io_map(ast.attr('map'))
-                else:
-                    raise NotImplementedError
-
-    def parse_workflow_call_body_io_map(self, i):
-        """
-        Required.
-
-        :param i:
-        :return:
-        """
-        io_map = OrderedDict()
-        if isinstance(i, wdl_parser.Terminal):
-            raise NotImplementedError
-        elif isinstance(i, wdl_parser.Ast):
-            raise NotImplementedError
-        elif isinstance(i, wdl_parser.AstList):
-            for ast in i:
-                if ast.name == 'IOMapping':
-                    key = self.parse_declaration_expressn(ast.attr("key"), es='')
-                    value = self.parse_declaration_expressn(ast.attr("value"), es='')
-                    io_map[key] = value
-                else:
-                    raise NotImplementedError
-        return io_map
-
-    def parse_workflow_call_body(self, i):
-        """
-        Required.
-
-        :param i:
-        :return:
-        """
-        io_map = OrderedDict()
-
-        if isinstance(i, wdl_parser.Terminal):
-            return i.source_string  # no io mappings; represents just a blank call
-        elif isinstance(i, wdl_parser.Ast):
-            if i.name == 'CallBody':
-                declarations = self.parse_workflow_call_body_declarations(i.attr("declarations")) # have not seen this used
-                io_map = self.parse_workflow_call_body_io(i.attr('io'))
-            else:
-                raise NotImplementedError
-        elif isinstance(i, wdl_parser.AstList):
-            raise NotImplementedError
-
-        return io_map
-
-    def parse_workflow_call(self, i):
-        """
-        Parses a WDL workflow call AST subtree to give the variable mappings for
-        that particular job/task "call".
-
-        :param i: WDL workflow job object
-        :return: python dictionary of io mappings for that job call
-        """
-        task_being_called = self.parse_workflow_call_taskname(i.attr("task"))
-        task_alias = self.parse_workflow_call_taskalias(i.attr("alias"))
-        io_map = self.parse_workflow_call_body(i.attr("body"))
-
-        if not task_alias:
-            task_alias = task_being_called
-
-        return {'task': task_being_called, 'alias': task_alias, 'io': io_map}
-