Merge branch 'master' into feature-js-console-output

Author: tetron

cwltool/draft2tool.py

@@ -221,10 +221,17 @@ def job(self,
                 cmdline = ["docker", "run", dockerimg] + cmdline
             keydict = {u"cmdline": cmdline}
 
-            for _, f in cachebuilder.pathmapper.items():
+            for location, f in cachebuilder.pathmapper.items():
                 if f.type == "File":
+                    checksum = next((e['checksum'] for e in cachebuilder.files
+                            if 'location' in e and e['location'] == location
+                            and 'checksum' in e
+                            and e['checksum'] != 'sha1$hash'), None)
                     st = os.stat(f.resolved)
-                    keydict[f.resolved] = [st.st_size, int(st.st_mtime * 1000)]
+                    if checksum:
+                        keydict[f.resolved] = [st.st_size, checksum]
+                    else:
+                        keydict[f.resolved] = [st.st_size, int(st.st_mtime * 1000)]
 
             interesting = {"DockerRequirement",
                            "EnvVarRequirement",

cwltool/main.py

@@ -436,7 +436,7 @@ 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.round_trip_load(stdin)  # type: ignore
+        job_order_object = yaml.round_trip_load(stdin)
         job_order_object, _ = loader.resolve_all(job_order_object, file_uri(os.getcwd()) + "/")
     else:
         job_order_file = None

cwltool/workflow.py

@@ -684,7 +684,7 @@ def __init__(self, toolpath_object, pos, **kwargs):
                 for tool_entry in self.embedded_tool.tool[toolfield]:
                     frag = shortname(tool_entry["id"])
                     if frag == shortinputid:
-                        param.update(tool_entry)  # type: ignore
+                        param.update(tool_entry)
                         found = True
                         bound.add(frag)
                         break

mypy.ini

@@ -0,0 +1,5 @@
+[mypy-ruamel.*]
+ignore_errors = True
+
+[mypy-schema_salad.*]
+ignore_errors = True

requirements.txt

@@ -1,7 +1,7 @@
 requests>=1.0
-ruamel.yaml==0.13.7
+ruamel.yaml>=0.12.4,<0.15
 rdflib==4.2.2
 rdflib-jsonld==0.4.0
 shellescape==3.4.1
-schema-salad>=2.5.20170623152720,<3
-typing==3.5.2.2 ; python_version>="2.7"
+schema-salad>=2.6,<3
+typing==3.5.3

setup.py

@@ -55,11 +55,11 @@
       install_requires=[
           'setuptools',
           'requests >= 1.0',
-          'ruamel.yaml >= 0.12.4',
+          'ruamel.yaml >= 0.12.4, < 0.15',
           'rdflib >= 4.2.2, < 4.3.0',
           'shellescape >= 3.4.1, < 3.5',
-          'schema-salad >= 2.5.20170623152720, < 3',
-          'typing >= 3.5.2, < 3.6',
+          'schema-salad >= 2.6, < 3',
+          'typing >= 3.5.3',
           'six >= 1.8.0',
       ],
       setup_requires=[] + pytest_runner,

tests/test_fetch.py

@@ -1,5 +1,7 @@
 import unittest
 
+from six.moves import urllib
+
 import schema_salad.main
 import schema_salad.ref_resolver
 import schema_salad.schema
@@ -32,6 +34,16 @@ def check_exists(self, url):  # type: (unicode) -> bool
                 else:
                     return False
 
+	    def urljoin(self, base, url):
+                urlsp = urllib.parse.urlsplit(url)
+                if urlsp.scheme:
+                    return url
+                basesp = urllib.parse.urlsplit(base)
+
+                if basesp.scheme == "keep":
+                    return base + "/" + url
+                return urllib.parse.urljoin(base, url)
+
         def test_resolver(d, a):
             return "baz:bar/" + a
 

tox.ini

@@ -1,6 +1,6 @@
 [tox]
 #envlist = py27-lint, py27-unit, py27-pipconflictchecker, py33-lint, py33-unit, py34-lint, py34-unit, py35-py2_mypy, py35-mypy, py35-lint, py35-unit, py36-lint, py36-unit  # only when py3 compat is done
-envlist = py27-lint, py27-unit, py27-pipconflictchecker, py36-lint, py35-lint, py34-lint, py33-lint
+envlist = py27-lint, py27-unit, py27-pipconflictchecker, py36-lint, py35-lint, py34-lint, py33-lint, py35-py2_mypy
 skipsdist = True
 
 [travis]