cwltool: use _logger.warning

_logger.warn is deprecated in py3

Author: manu-chroma

cwltool/draft2tool.py

@@ -62,7 +62,7 @@ def run(self, **kwargs):  # type: (**Any) -> None
                 normalizeFilesDirs(ev)
                 self.output_callback(ev, "success")
             except Exception as e:
-                _logger.warn(u"Failed to evaluate expression:\n%s",
+                _logger.warning(u"Failed to evaluate expression:\n%s",
                              e, exc_info=kwargs.get('debug'))
                 self.output_callback({}, "permanentFail")
 
@@ -537,7 +537,7 @@ def collect_output(self, schema, builder, outdir, fs_access, compute_checksum=Tr
                                        "class": "File" if fs_access.isfile(g) else "Directory"}
                                       for g in fs_access.glob(fs_access.join(outdir, gb))])
                         except (OSError, IOError) as e:
-                            _logger.warn(Text(e))
+                            _logger.warning(Text(e))
                         except:
                             _logger.error("Unexpected error from fs_access", exc_info=True)
                             raise

cwltool/job.py

@@ -240,7 +240,7 @@ def _execute(self, runtime, env, rm_tmpdir=True, move_outputs="move"):
             processStatus = "permanentFail"
 
         if processStatus != "success":
-            _logger.warn(u"[job %s] completed %s", self.name, processStatus)
+            _logger.warning(u"[job %s] completed %s", self.name, processStatus)
         else:
             _logger.info(u"[job %s] completed %s", self.name, processStatus)
 

cwltool/load_tool.py

@@ -165,7 +165,7 @@ def validate_document(document_loader,  # type: Loader
             r"^(?:cwl:|https://w3id.org/cwl/cwl#)", "",
             workflowobj["cwlVersion"])
     else:
-        _logger.warn("No cwlVersion found, treating this file as draft-2.")
+        _logger.warning("No cwlVersion found, treating this file as draft-2.")
         workflowobj["cwlVersion"] = "draft-2"
 
     if workflowobj["cwlVersion"] == "draft-2":

cwltool/main.py

@@ -833,7 +833,7 @@ def locToPath(p):
                 stdout.flush()
 
             if status != "success":
-                _logger.warn(u"Final process status is %s", status)
+                _logger.warning(u"Final process status is %s", status)
                 return 1
             else:
                 _logger.info(u"Final process status is %s", status)

cwltool/workflow.py

@@ -314,7 +314,7 @@ def receive_output(self, step, outputparms, final_output_callback, jobout, proce
             if self.processStatus != "permanentFail":
                 self.processStatus = processStatus
 
-            _logger.warn(u"[%s] completed %s", step.name, processStatus)
+            _logger.warning(u"[%s] completed %s", step.name, processStatus)
         else:
             _logger.info(u"[%s] completed %s", step.name, processStatus)
 
@@ -381,7 +381,7 @@ def valueFromFunc(k, v):  # type: (Any, Any) -> Any
                 tot = 1
                 emptyscatter = [shortname(s) for s in scatter if len(inputobj[s]) == 0]
                 if emptyscatter:
-                    _logger.warn(u"[job %s] Notice: scattering over empty input in '%s'.  All outputs will be empty.", step.name, "', '".join(emptyscatter))
+                    _logger.warning(u"[job %s] Notice: scattering over empty input in '%s'.  All outputs will be empty.", step.name, "', '".join(emptyscatter))
 
                 if method == "dotproduct" or method is None:
                     jobs = dotproduct_scatter(step, inputobj, scatter,
@@ -609,8 +609,8 @@ def static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs)
     all_exception_msg = "\n".join(exception_msgs)
 
     if warnings:
-        _logger.warn("Workflow checker warning:")
-        _logger.warn(all_warning_msg)
+        _logger.warning("Workflow checker warning:")
+        _logger.warning(all_warning_msg)
     if exceptions:
         raise validate.ValidationException(all_exception_msg)