Generate nameroot and nameext from basename (#420)

* [PATCH 1/3] generating nameroot when not provided explicitely from basename Issue#268

* [PATCH 2/3] Calculate correctly nameroot from basename

Additionally only generate it for Files, not Directories
(following specification). And also generate nameext.

* [PATCH 3/3] Fix existing test to conform to generated fields

* fix: generate nameext when nameroot is not missing

* new: test behaviour of nameroot and nameext generation

* fix: make nameext to conform to specs

* fix: generate values from basename unconditionally

Author: undu

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_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)
+