Improve error reporting of file format errors. (#711)

Author: tetron

cwltool/builder.py

@@ -76,12 +76,12 @@ def checkFormat(actualFile, inputFormats, ontology):
         if not af:
             continue
         if "format" not in af:
-            raise validate.ValidationException(u"Missing required 'format' for File %s" % af)
+            raise validate.ValidationException(u"File has no 'format' defined: %s" % json.dumps(af, indent=4))
         for inpf in aslist(inputFormats):
             if af["format"] == inpf or formatSubclassOf(af["format"], inpf, ontology, set()):
                 return
         raise validate.ValidationException(
-            u"Incompatible file format, expected format(s) %s but file object is: %s" % (inputFormats, json.dumps(af, indent=4)))
+            u"File has an incompatible format: %s" % json.dumps(af, indent=4))
 
 class Builder(object):
     def __init__(self):  # type: () -> None
@@ -237,7 +237,10 @@ def bind_input(self, schema, datum, lead_pos=None, tail_pos=None, discover_secon
                     normalizeFilesDirs(datum["secondaryFiles"])
 
                 if "format" in schema:
-                    checkFormat(datum, self.do_eval(schema["format"]), self.formatgraph)
+                    try:
+                        checkFormat(datum, self.do_eval(schema["format"]), self.formatgraph)
+                    except validate.ValidationException as ve:
+                        raise WorkflowException("Expected value of '%s' to have format %s but\n  %s" % (schema["name"], schema["format"], ve))
 
                 def _capture_files(f):
                     self.files.append(f)

cwltool/executors.py

@@ -6,6 +6,7 @@
 from abc import ABCMeta, abstractmethod
 
 from typing import Dict, Text, Any, Tuple, Set, List
+from schema_salad.validate import ValidationException
 
 from .builder import Builder
 from .errors import WorkflowException
@@ -14,6 +15,7 @@
 from .process import relocateOutputs, cleanIntermediate, Process
 from . import loghandler
 
+
 _logger = logging.getLogger("cwltool")
 
 class JobExecutor(object):
@@ -107,7 +109,7 @@ def run_jobs(self,
                 else:
                     logger.error("Workflow cannot make any more progress.")
                     break
-        except WorkflowException:
+        except (ValidationException, WorkflowException):
             raise
         except Exception as e:
             logger.exception("Got workflow error")