initial stderr & stdout shortcut implementation

Author: mr-c

cwltool/cwltest.py

@@ -72,8 +72,9 @@ def run_test(args, i, t):  # type: (argparse.Namespace, Any, Dict[str,str]) -> i
                 outdir = tempfile.mkdtemp()
             test_command.extend(["--outdir={}".format(outdir),
                                  "--quiet",
-                                 t["tool"],
-                                 t["job"]])
+                                 t["tool"]])
+            if t["job"] != None:
+                test_command.extend([t["job"]])
             outstr = subprocess.check_output(test_command)
             out = {"output": json.loads(outstr)}
         else:
@@ -82,8 +83,9 @@ def run_test(args, i, t):  # type: (argparse.Namespace, Any, Dict[str,str]) -> i
                             "--basedir=" + args.basedir,
                             "--no-container",
                             "--quiet",
-                            t["tool"],
-                            t["job"]]
+                            t["tool"]]
+            if t["job"] != None:
+                test_command.extend([t["job"]])
 
             outstr = subprocess.check_output(test_command)
             out = yaml.load(outstr)
@@ -100,12 +102,12 @@ def run_test(args, i, t):  # type: (argparse.Namespace, Any, Dict[str,str]) -> i
             _logger.error(t.get("doc"))
             _logger.error("Returned non-zero")
             return 1
-    except yaml.scanner.ScannerError as e:
+    except (yaml.scanner.ScannerError, TypeError) as e:
         _logger.error(u"""Test failed: %s""", " ".join([pipes.quote(tc) for tc in test_command]))
         _logger.error(outstr)
         _logger.error(u"Parse error %s", str(e))
 
-    pwd = os.path.abspath(os.path.dirname(t["job"]))
+    # pwd = os.path.abspath(os.path.dirname(t["job"]))
     # t["args"] = map(lambda x: x.replace("$PWD", pwd), t["args"])
     # if "stdin" in t:
     #     t["stdin"] = t["stdin"].replace("$PWD", pwd)
@@ -118,7 +120,8 @@ def run_test(args, i, t):  # type: (argparse.Namespace, Any, Dict[str,str]) -> i
 
     for key in checkkeys:
         try:
-            compare(t.get(key), out.get(key))
+            if key in t and key in out:
+                compare(t.get(key), out.get(key))
         except CompareFail as ex:
             _logger.warn(u"""Test failed: %s""", " ".join([pipes.quote(tc) for tc in test_command]))
             _logger.warn(t.get("doc"))

cwltool/job.py

@@ -154,7 +154,7 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
                      " \\\n    ".join([shellescape.quote(str(arg)) if shouldquote(str(arg)) else str(arg) for arg in (runtime + self.command_line)]),
                      u' < %s' % (self.stdin) if self.stdin else '',
                      u' > %s' % os.path.join(self.outdir, self.stdout) if self.stdout else '',
-                     u' \2> %s' % os.path.join(self.outdir, self.stderr) if self.stderr else '')
+                     u' 2> %s' % os.path.join(self.outdir, self.stderr) if self.stderr else '')
 
         if dry_run:
             return (self.outdir, {})

cwltool/load_tool.py

@@ -2,6 +2,7 @@
 """Loads a CWL document."""
 
 import os
+import uuid
 import logging
 import re
 import urlparse
@@ -41,6 +42,24 @@ def fetch_document(argsworkflow):
 
     return document_loader, workflowobj, uri
 
+def _convert_stdstreams_to_files(workflowobj):
+    # type: (Union[Dict[unicode, Any], List[Dict[unicode, Any]]) -> None
+
+    if isinstance(workflowobj, dict):
+        if 'outputs' in workflowobj:
+            for out in workflowobj['outputs']:
+                for streamtype in ['stdout', 'stderr']:
+                    if out['type'] == streamtype:
+                        if streamtype in workflowobj:
+                            filename = workflowobj[streamtype]
+                        else:
+                            filename = unicode(uuid.uuid4())
+                            workflowobj[streamtype] = filename
+                        out['type'] = 'File'
+                        out['outputBinding'] = {'glob': filename}
+    else:
+        for entry in workflowobj:
+            _convert_stdstreams_to_files(entry)
 
 def validate_document(document_loader, workflowobj, uri,
                       enable_dev=False, strict=True, preprocess_only=False):
@@ -94,6 +113,8 @@ def validate_document(document_loader, workflowobj, uri,
                    "$schemas": processobj.get("$schemas", []),
                    "cwlVersion": processobj["cwlVersion"]}
 
+    _convert_stdstreams_to_files(workflowobj)
+
     if preprocess_only:
         return document_loader, avsc_names, processobj, metadata, uri