Merge branch 'master' into fix-671

Author: tetron

cwltool/argparser.py

@@ -15,6 +15,9 @@
 
 _logger = logging.getLogger("cwltool")
 
+DEFAULT_TMP_PREFIX = "tmp"
+
+
 def arg_parser():  # type: () -> argparse.ArgumentParser
     parser = argparse.ArgumentParser(description='Reference executor for Common Workflow Language')
     parser.add_argument("--basedir", type=Text)
@@ -71,12 +74,12 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     parser.add_argument("--tmpdir-prefix", type=Text,
                         help="Path prefix for temporary directories",
-                        default="tmp")
+                        default=DEFAULT_TMP_PREFIX)
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--tmp-outdir-prefix", type=Text,
                          help="Path prefix for intermediate output directories",
-                         default="tmp")
+                         default=DEFAULT_TMP_PREFIX)
 
     exgroup.add_argument("--cachedir", type=Text, default="",
                          help="Directory to cache intermediate workflow outputs to avoid recomputing steps.")

cwltool/main.py

@@ -17,11 +17,12 @@
 import ruamel.yaml as yaml
 import schema_salad.validate as validate
 import six
+
 from schema_salad.ref_resolver import Loader, file_uri, uri_file_path
 from schema_salad.sourceline import strip_dup_lineno
 
 from . import draft2tool, workflow
-from .argparser import arg_parser, generate_parser
+from .argparser import arg_parser, generate_parser, DEFAULT_TMP_PREFIX
 from .cwlrdf import printdot, printrdf
 from .errors import UnsupportedRequirement, WorkflowException
 from .executors import SingleJobExecutor, MultithreadedJobExecutor
@@ -529,8 +530,16 @@ def main(argsl=None,  # type: List[str]
         if isinstance(tool, int):
             return tool
 
+        # If on MacOS platform, TMPDIR must be set to be under one of the shared volumes in Docker for Mac
+        # More info: https://dockstore.org/docs/faq
+        if sys.platform == "darwin":
+            tmp_prefix = "tmp_outdir_prefix"
+            default_mac_path = "/private/tmp/docker_tmp"
+            if getattr(args, tmp_prefix) and getattr(args, tmp_prefix) == DEFAULT_TMP_PREFIX:
+                setattr(args, tmp_prefix, default_mac_path)
+
         for dirprefix in ("tmpdir_prefix", "tmp_outdir_prefix", "cachedir"):
-            if getattr(args, dirprefix) and getattr(args, dirprefix) != 'tmp':
+            if getattr(args, dirprefix) and getattr(args, dirprefix) != DEFAULT_TMP_PREFIX:
                 sl = "/" if getattr(args, dirprefix).endswith("/") or dirprefix == "cachedir" else ""
                 setattr(args, dirprefix,
                         os.path.abspath(getattr(args, dirprefix)) + sl)