more exception tracebacks, when in debug mode

cwltool/command_line_tool.py

@@ -1342,7 +1342,7 @@ def collect_output(
                                 ]
                             )
                         except OSError as e:
-                            _logger.warning(str(e))
+                            _logger.warning(str(e), exc_info=builder.debug)
                         except Exception:
                             _logger.error("Unexpected error from fs_access", exc_info=True)
                             raise

cwltool/cwlprov/provenance_profile.py

@@ -546,7 +546,7 @@ def declare_artefact(self, value: Any) -> ProvEntity:
             # FIXME: list value does not support adding "@id"
             return coll
         except TypeError:
-            _logger.warning("Unrecognized type %s of %r", type(value), value)
+            _logger.warning("Unrecognized type %s of %r", type(value), value, exc_info=True)
             # Let's just fall back to Python repr()
             entity = self.document.entity(uuid.uuid4().urn, {PROV_LABEL: repr(value)})
             self.research_object.add_uri(entity.identifier.uri)

cwltool/executors.py

@@ -326,7 +326,10 @@ def _runner(
             self.exceptions.append(err)
         except Exception as err:  # pylint: disable=broad-except
             _logger.exception(f"Got workflow error: {err}")
-            self.exceptions.append(WorkflowException(str(err)))
+            wf_exc = WorkflowException(str(err))
+            wf_exc.__cause__ = err
+            wf_exc.__suppress_context__ = True
+            self.exceptions.append(wf_exc)
         finally:
             if runtime_context.workflow_eval_lock:
                 with runtime_context.workflow_eval_lock:

cwltool/job.py

@@ -376,17 +376,30 @@ def stderr_stdout_log_path(
         except OSError as e:
             if e.errno == 2:
                 if runtime:
-                    _logger.error("'%s' not found: %s", runtime[0], str(e))
+                    _logger.error(
+                        "'%s' not found: %s", runtime[0], str(e), exc_info=runtimeContext.debug
+                    )
                 else:
-                    _logger.error("'%s' not found: %s", self.command_line[0], str(e))
+                    _logger.error(
+                        "'%s' not found: %s",
+                        self.command_line[0],
+                        str(e),
+                        exc_info=runtimeContext.debug,
+                    )
             else:
-                _logger.exception("Exception while running job")
+                _logger.exception(
+                    "Exception while running job: %s", str(e), exc_info=runtimeContext.debug
+                )
             processStatus = "permanentFail"
         except WorkflowException as err:
-            _logger.error("[job %s] Job error:\n%s", self.name, str(err))
+            _logger.error(
+                "[job %s] Job error:\n%s", self.name, str(err), exc_info=runtimeContext.debug
+            )
             processStatus = "permanentFail"
-        except Exception:
-            _logger.exception("Exception while running job")
+        except Exception as err:
+            _logger.exception(
+                "Exception while running job: %s.", str(err), exc_info=runtimeContext.debug
+            )
             processStatus = "permanentFail"
         if (
             runtimeContext.research_obj is not None
@@ -795,7 +808,7 @@ def run(
                     )
             except Exception as err:
                 container = "Singularity" if runtimeContext.singularity else "Docker"
-                _logger.debug("%s error", container, exc_info=True)
+                _logger.debug("%s error", container, exc_info=runtimeContext.debug)
                 if docker_is_req:
                     raise UnsupportedRequirement(
                         f"{container} is required to run this tool: {str(err)}"

cwltool/main.py

@@ -1289,7 +1289,7 @@ def main(
                 if isinstance(err.code, int):
                     return err.code
                 else:
-                    _logger.debug("Non-integer SystemExit: %s", err.code)
+                    _logger.debug("Non-integer SystemExit: %s", err.code, exc_info=args.debug)
                     return 1
 
             del args.workflow

cwltool/procgenerator.py

@@ -57,7 +57,7 @@ def job(
         except WorkflowException:
             raise
         except Exception as exc:
-            _logger.exception("Unexpected exception")
+            _logger.exception("Unexpected exception", exc_info=runtimeContext.debug)
             raise WorkflowException(str(exc)) from exc
 
 
@@ -80,7 +80,7 @@ def __init__(
                 self.embedded_tool = load_tool(toolpath_object["run"], loadingContext)
         except ValidationException as vexc:
             if loadingContext.debug:
-                _logger.exception("Validation exception")
+                _logger.exception("Validation exception", exc_info=loadingContext.debug)
             raise WorkflowException(
                 "Tool definition %s failed validation:\n%s"
                 % (toolpath_object["run"], indent(str(vexc)))
@@ -108,7 +108,7 @@ def result(
             )
         except ValidationException as vexc:
             if runtimeContext.debug:
-                _logger.exception("Validation exception")
+                _logger.exception("Validation exception", exc_info=runtimeContext.debug)
             raise WorkflowException(
                 "Tool definition %s failed validation:\n%s"
                 % (jobout["runProcess"], indent(str(vexc)))

cwltool/resolver.py

@@ -15,8 +15,8 @@ def resolve_local(document_loader: Optional[Loader], uri: str) -> Optional[str]:
 
     try:
         pathobj = Path(pathpart).resolve()
-    except OSError:
-        _logger.debug("local resolver could not resolve %s", uri)
+    except OSError as exc:
+        _logger.debug("local resolver could not resolve %s due to %s", uri, str(exc))
         return None
 
     if pathobj.is_file():

cwltool/workflow.py

@@ -442,7 +442,9 @@ def job(
                 runtimeContext,
             )
         except WorkflowException:
-            _logger.error("Exception on step '%s'", runtimeContext.name)
+            _logger.error(
+                "Exception on step '%s'", runtimeContext.name, exc_info=runtimeContext.debug
+            )
             raise
         except Exception as exc:
             _logger.exception("Unexpected exception")