Fix bugs and print -> _logger.info

- Made JavaScript logging work in workflows
- Made decoded data be inputted into re.findall
- print -> _logger.info, so that js output isn't outputted into stdout and the tests can pick out the information

Author: ThomasHickman

cwltool/sandboxjs.py

@@ -197,10 +197,10 @@ def stdfmt(data):  # type: (Text) -> Text
 
     if js_console:
         if len(stderrdata) > 0:
-            print("Javascript console output:")
-            print("----------------------------------------")
-            print('\n'.join(re.findall(r'^[[](?:log|err)[]].*$', stderrdata, flags=re.MULTILINE)))
-            print("----------------------------------------")
+            _logger.info("Javascript console output:")
+            _logger.info("----------------------------------------")
+            _logger.info('\n'.join(re.findall(r'^[[](?:log|err)[]].*$', stderrdata.decode('utf-8'), flags=re.MULTILINE)))
+            _logger.info("----------------------------------------")
 
     if debug:
         info = u"returncode was: %s\nscript was:\n%s\nstdout was: %s\nstderr was: %s\n" %\

cwltool/workflow.py

@@ -332,8 +332,12 @@ def receive_output(self, step, outputparms, final_output_callback, jobout, proce
         if completed == len(self.steps):
             self.do_output_callback(final_output_callback)
 
-    def try_make_job(self, step, final_output_callback, debug=False, js_console=False, **kwargs):
+    def try_make_job(self, step, final_output_callback, **kwargs):
         # type: (WorkflowJobStep, Callable[[Any, Any], Any], bool, bool, **Any) -> Generator
+
+        js_console = kwargs["js_console"] or False
+        debug = kwargs["debug"] or False
+
         inputparms = step.tool["inputs"]
         outputparms = step.tool["outputs"]