Import dependencies from cwl_utils after code refactoring (#1686)

* Removed sandboxjs and expression from cwltool
* req cwl-utils package; type fixes

Co-authored-by: "Bruno P. Kinoshita" <[email protected]>
Co-authored-by: Michael R. Crusoe <[email protected]>

Author: 3 people

MANIFEST.in

@@ -52,9 +52,6 @@ include cwltool/schemas/v1.2/*.yml
 include cwltool/schemas/v1.2/*.md
 include cwltool/schemas/v1.2/salad/schema_salad/metaschema/*.yml
 include cwltool/schemas/v1.2/salad/schema_salad/metaschema/*.md
-include cwltool/cwlNodeEngine.js
-include cwltool/cwlNodeEngineJSConsole.js
-include cwltool/cwlNodeEngineWithContext.js
 include cwltool/extensions.yml
 include cwltool/extensions-v1.1.yml
 include cwltool/jshint/jshint_wrapper.js

cwltool.Dockerfile

@@ -5,9 +5,7 @@ RUN apk add --no-cache git gcc python3-dev libxml2-dev libxslt-dev libc-dev linu
 WORKDIR /cwltool
 COPY . .
 
-RUN pip install toml -rmypy-requirements.txt "$(grep schema.salad requirements.txt)"
-# schema-salad is needed to be installed (this time as pure Python) for
-# cwltool + mypyc
+RUN pip install toml -rmypy-requirements.txt
 RUN CWLTOOL_USE_MYPYC=1 MYPYPATH=mypy-stubs pip wheel --no-binary schema-salad --wheel-dir=/wheels .[deps]
 RUN rm /wheels/schema_salad*
 RUN pip install black

cwltool/builder.py

@@ -15,6 +15,7 @@
     cast,
 )
 
+from cwl_utils import expression
 from rdflib import Graph, URIRef
 from rdflib.namespace import OWL, RDFS
 from ruamel.yaml.comments import CommentedMap
@@ -25,7 +26,6 @@
 from schema_salad.validate import validate
 from typing_extensions import TYPE_CHECKING, Type  # pylint: disable=unused-import
 
-from . import expression
 from .errors import WorkflowException
 from .loghandler import _logger
 from .mutation import MutationManager