Updated JS imports from cwltool (#121)

JavaScript-related code has been migrated from `cwltool` to the `cwl-utils`
package. This commit backports these changes to StreamFlow 0.1.x.

.github/workflows/cwl-conformance.yaml

@@ -2,7 +2,10 @@ name: "CWL Conformance"
 on:
   push:
     branches:
-      - master
+      - 0.1.x
+  pull_request:
+    branches:
+      - 0.1.x
 jobs:
   test:
     runs-on: ubuntu-20.04

.github/workflows/docker.yaml

@@ -4,7 +4,7 @@ on:
     workflows:
       - "CWL Conformance"
     branches:
-      - master
+      - 0.1.x
     types:
       - completed
 jobs:
@@ -21,7 +21,7 @@ jobs:
       - name: "Get StreamFlow version"
         run: echo "STREAMFLOW_VERSION=$(cat streamflow/version.py | grep -oP '(?<=VERSION = \")(.*)(?=\")')" >> $GITHUB_ENV
       - name: "Check if Docker image already exists"
-        run : echo "NEW_IMAGE=$(DOCKER_CLI_EXPERIMENTAL=enabled docker manifest inspect alphaunito/streamflow:${STREAMFLOW_VERSION}-base > /dev/null 2>&1; echo $?)" >> $GITHUB_ENV
+        run : echo "NEW_IMAGE=$(docker buildx imagetools inspect alphaunito/streamflow:${STREAMFLOW_VERSION} > /dev/null 2>&1; echo $?)" >> $GITHUB_ENV
       - name: "Build base image"
         id: docker-base
         if: ${{ env.NEW_IMAGE }}

.github/workflows/github-release.yaml

@@ -4,7 +4,7 @@ on:
     workflows:
       - "CWL Conformance"
     branches:
-      - master
+      - 0.1.x
     types:
       - completed
 jobs:

.github/workflows/pypi.yaml

@@ -4,7 +4,7 @@ on:
     workflows:
       - "CWL Conformance"
     branches:
-      - master
+      - 0.1.x
     types:
       - completed
 jobs:
@@ -15,12 +15,10 @@ jobs:
       - uses: actions/setup-python@v2
         with:
           python-version: "3.8"
-      - name: "Install pypisearch package"
-        run: python -m pip install pypisearch --user
       - name: "Get StreamFlow version"
         run: echo "STREAMFLOW_VERSION=$(cat streamflow/version.py | grep -oP '(?<=VERSION = \")(.*)(?=\")')" >> $GITHUB_ENV
       - name: "Get PyPI version"
-        run: echo "PYPI_VERSION=$(python -m pypisearch streamflow | grep -oP '(?<=^streamflow \()(.*)(?=\))')" >> $GITHUB_ENV
+        run: echo "PYPI_VERSION=$(pip index versions --pre streamflow | grep streamflow | sed 's/.*(\(.*\))/\1/')" >> $GITHUB_ENV
       - name: "Build Python packages"
         if: ${{ env.STREAMFLOW_VERSION != env.PYPI_VERSION }}
         run: |

streamflow/cwl/expression.py

@@ -5,8 +5,8 @@
 from typing import Optional, MutableMapping, Any, Mapping, MutableSequence, Set
 
 import antlr4
-import cwltool.sandboxjs
-from cwltool.sandboxjs import JavascriptException
+import cwl_utils.sandboxjs
+from cwl_utils.sandboxjs import JavascriptException
 from schema_salad.utils import json_dumps
 
 from streamflow.core.exception import WorkflowDefinitionException, WorkflowExecutionException
@@ -156,7 +156,7 @@ def evaluate(self, expr: str) -> Optional[Any]:
 class DependencyResolver(Evaluator):
 
     def _ecmascript_evaluate(self, expr: str) -> Optional[Any]:
-        code = cwltool.sandboxjs.code_fragment_to_js(expr, self.jslib)
+        code = cwl_utils.sandboxjs.code_fragment_to_js(expr, self.jslib)
         lexer = ECMAScriptLexer(antlr4.InputStream(code))
         parser = ECMAScriptParser(antlr4.CommonTokenStream(lexer))
         listener = CWLDependencyListener()
@@ -184,7 +184,7 @@ def _regex_evaluate(self,
 class RuntimeEvaluator(Evaluator):
 
     def _ecmascript_evaluate(self, expr: str) -> Optional[Any]:
-        return cwltool.sandboxjs.execjs(expr, self.jslib, self.timeout)
+        return cwl_utils.sandboxjs.get_js_engine().eval(expr, self.jslib, timeout=self.timeout)
 
     def _regex_evaluate(self,
                         parsed_string: str,

streamflow/cwl/utils.py

@@ -2,7 +2,7 @@
 
 from typing import TYPE_CHECKING, MutableSequence, Set, MutableMapping
 
-import cwltool.expression
+import cwl_utils.expression
 
 from streamflow.core.exception import WorkflowDefinitionException
 from streamflow.core.utils import get_token_value
@@ -44,7 +44,7 @@ def eval_expression(expression: str,
             expression,
             context,
             full_js=full_js,
-            jslib=cwltool.expression.jshead(expression_lib or [], context) if full_js else "",
+            jslib=cwl_utils.expression.jshead(expression_lib or [], context) if full_js else "",
             strip_whitespace=strip_whitespace,
             timeout=timeout)
     else:
@@ -90,7 +90,7 @@ def resolve_dependencies(expression: str,
             expression,
             context,
             full_js=full_js,
-            jslib=cwltool.expression.jshead(expression_lib or [], context) if full_js else "",
+            jslib=cwl_utils.expression.jshead(expression_lib or [], context) if full_js else "",
             strip_whitespace=strip_whitespace,
             timeout=timeout,
             resolve_dependencies=True)