Merge branch 'master' into master

Author: mr-c

.travis.yml

@@ -13,3 +13,6 @@ install:
 script: tox
 notifications:
   email: false
+branches:
+  only:
+    - master

README.rst

@@ -4,6 +4,11 @@ Common workflow language tool description reference implementation
 
 CWL Conformance test: |Build Status|
 
+Travis: |Unix Build Status|
+
+.. |Unix Build Status| image:: https://img.shields.io/travis/common-workflow-language/cwltool/master.svg?label=unix%20build
+   :target: https://travis-ci.org/common-workflow-language/cwltool
+
 This is the reference implementation of the Common Workflow Language.  It is
 intended to be feature complete and provide comprehensive validation of CWL
 files as well as provide other tools related to working with CWL.

cwltool/load_tool.py

@@ -24,6 +24,13 @@
 
 _logger = logging.getLogger("cwltool")
 
+jobloaderctx = {
+    u"cwl": "https://w3id.org/cwl/cwl#",
+    u"path": {u"@type": u"@id"},
+    u"location": {u"@type": u"@id"},
+    u"format": {u"@type": u"@id"},
+    u"id": u"@id"
+}
 
 def fetch_document(argsworkflow,  # type: Union[Text, dict[Text, Any]]
                    resolver=None,  # type: Callable[[Loader, Union[Text, dict[Text, Any]]], Text]
@@ -33,7 +40,7 @@ def fetch_document(argsworkflow,  # type: Union[Text, dict[Text, Any]]
     # type: (...) -> Tuple[Loader, CommentedMap, Text]
     """Retrieve a CWL document."""
 
-    document_loader = Loader({"cwl": "https://w3id.org/cwl/cwl#", "id": "@id"},
+    document_loader = Loader(jobloaderctx,
                              fetcher_constructor=fetcher_constructor)
 
     uri = None  # type: Text

cwltool/main.py

@@ -22,7 +22,7 @@
 from . import draft2tool, workflow
 from .cwlrdf import printdot, printrdf
 from .errors import UnsupportedRequirement, WorkflowException
-from .load_tool import fetch_document, make_tool, validate_document
+from .load_tool import fetch_document, make_tool, validate_document, jobloaderctx
 from .mutation import MutationManager
 from .pack import pack
 from .pathmapper import (adjustDirObjs, adjustFileObjs, get_listing,
@@ -424,13 +424,9 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,
 
     job_order_object = None
 
-    jobloaderctx = {
-        u"path": {u"@type": u"@id"},
-        u"location": {u"@type": u"@id"},
-        u"format": {u"@type": u"@id"},
-        u"id": u"@id"}
-    jobloaderctx.update(t.metadata.get("$namespaces", {}))
-    loader = Loader(jobloaderctx, fetcher_constructor=fetcher_constructor)
+    _jobloaderctx = jobloaderctx.copy()
+    _jobloaderctx.update(t.metadata.get("$namespaces", {}))
+    loader = Loader(_jobloaderctx, fetcher_constructor=fetcher_constructor)
 
     if len(args.job_order) == 1 and args.job_order[0][0] != "-":
         job_order_file = args.job_order[0]

cwltool/pathmapper.py

@@ -77,6 +77,9 @@ def addLocation(d):
         if "basename" not in d:
             d["basename"] = os.path.basename(urllib.request.url2pathname(path))
 
+        if d["class"] == "File":
+            d["nameroot"], d["nameext"] = os.path.splitext(d["basename"])
+
     visit_class(job, ("File", "Directory"), addLocation)
 
 

tests/test_examples.py

@@ -209,12 +209,16 @@ def loadref(base, p):
 
         self.assertEquals([{
             "basename": "bar.cwl",
+            "nameroot": "bar",
             "class": "File",
+            "nameext": ".cwl",
             "location": "file:///example/bar.cwl"
         },
             {
                 "basename": "data.txt",
+                "nameroot": "data",
                 "class": "File",
+                "nameext": ".txt",
                 "location": "file:///example/data.txt"
             },
             {
@@ -223,17 +227,23 @@ def loadref(base, p):
                 "location": "file:///example/data2",
                 "listing": [{
                     "basename": "data3.txt",
+                    "nameroot": "data3",
                     "class": "File",
+                    "nameext": ".txt",
                     "location": "file:///example/data3.txt",
                     "secondaryFiles": [{
                         "class": "File",
                         "basename": "data5.txt",
-                        "location": "file:///example/data5.txt"
+                        "location": "file:///example/data5.txt",
+                        "nameext": ".txt",
+                        "nameroot": "data5"
                     }]
                 }]
             }, {
                 "basename": "data4.txt",
+                "nameroot": "data4",
                 "class": "File",
+                "nameext": ".txt",
                 "location": "file:///example/data4.txt"
             }], sc)
 
@@ -245,7 +255,9 @@ def loadref(base, p):
 
         self.assertEquals([{
             "basename": "bar.cwl",
+            "nameroot": "bar",
             "class": "File",
+            "nameext": ".cwl",
             "location": "file:///example/bar.cwl"
         }], sc)
 

tests/test_ext.py

@@ -124,7 +124,7 @@ def test_updatedir(self):
             shutil.rmtree(tmp)
             shutil.rmtree(out)
 
-    def test_updateval_inplace(self):
+    def test_updatedir_inplace(self):
         try:
             tmp = tempfile.mkdtemp()
             with open(os.path.join(tmp, "value"), "w") as f:

tests/test_pathmapper.py

@@ -26,3 +26,30 @@ def test_strip_trailing(self):
                 "basename": "bar"
             },
             d)
+
+    def test_basename_field_generation(self):
+        base_file = {
+            "class": "File",
+            "location": "/foo/"
+        }
+        # (filename, expected: (nameroot, nameext))
+        testdata = [
+            ("foo.bar",     ("foo",     ".bar")),
+            ("foo",         ("foo",     '')),
+            (".foo",        (".foo",    '')),
+            ("foo.",        ("foo",    '.')),
+            ("foo.bar.baz", ("foo.bar", ".baz"))
+        ]
+
+        for filename, (nameroot, nameext) in testdata:
+            file = dict(base_file)
+            file["location"] = file["location"] + filename
+
+            expected = dict(file)
+            expected["basename"] = filename
+            expected["nameroot"] = nameroot
+            expected["nameext"] = nameext
+
+            normalizeFilesDirs(file)
+            self.assertEqual(file, expected)
+

tests/wf/echo.cwl

@@ -5,8 +5,9 @@ inputs:
   script:
     type: string
     default: |
+      from __future__ import print_function
       import sys
-      print sys.argv[1]
+      print(sys.argv[1])
       if sys.argv[1] == "2":
         exit(1)
       else:
@@ -19,4 +20,4 @@ outputs:
     type: File
     outputBinding:
       glob: foo$(inputs.r).txt
-arguments: [python, -c, $(inputs.script), $(inputs.r)]
+arguments: [python, -c, $(inputs.script), $(inputs.r)]