Merge branch 'master' into node_fix

Author: manu-chroma

cwltool/docker.py

@@ -27,6 +27,17 @@ def get_image(dockerRequirement, pull_image, dry_run=False):
             sp = dockerRequirement["dockerImageId"].split(":")
             if len(sp) == 1:
                 sp.append("latest")
+            elif len(sp) == 2:
+                #  if sp[1] doesn't  match valid tag names, it is a part of repository
+                if not re.match(r'[\w][\w.-]{0,127}', sp[1]):
+                    sp[0] = sp[0] + ":" + sp[1]
+                    sp[1] = "latest"
+            elif len(sp) == 3:
+                if re.match(r'[\w][\w.-]{0,127}', sp[2]):
+                    sp[0] = sp[0] + ":" + sp[1]
+                    sp[1] = sp[2]
+                    del sp[2]
+
             # check for repository:tag match or image id match
             if ((sp[0] == m.group(1) and sp[1] == m.group(2)) or dockerRequirement["dockerImageId"] == m.group(3)):
                 found = True

cwltool/main.py

@@ -431,8 +431,8 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,
     if len(args.job_order) == 1 and args.job_order[0][0] != "-":
         job_order_file = args.job_order[0]
     elif len(args.job_order) == 1 and args.job_order[0] == "-":
-        job_order_object = yaml.load(stdin)
-        job_order_object, _ = loader.resolve_all(job_order_object, "")
+        job_order_object = yaml.round_trip_load(stdin)  # type: ignore
+        job_order_object, _ = loader.resolve_all(job_order_object, file_uri(os.getcwd()) + "/")
     else:
         job_order_file = None
 

setup.py

@@ -8,6 +8,12 @@
 SETUP_DIR = os.path.dirname(__file__)
 README = os.path.join(SETUP_DIR, 'README.rst')
 
+# if python3 runtime and `setup.py install` is called
+if sys.version_info.major == 3 and sys.argv[1] == 'install':
+    print("Aborting installation. CWL Tool doesn't support Python 3 currently.")
+    print("Install using Python 2 pip.")
+    exit(1)
+
 try:
     import gittaggers
 
@@ -64,4 +70,10 @@
       },
       zip_safe=True,
       cmdclass={'egg_info': tagger},
+      classifiers=[
+          'Development Status :: 5 - Production/Stable',
+          'Operating System :: POSIX',
+          'Operating System :: OS Independent',
+          'Programming Language :: Python :: 2 :: Only',
+      ]
       )