Merge pull request #121 from common-workflow-language/fsaccess-join

Add path join to fsaccess abstraction.

Author: mr-c

cwltool/draft2tool.py

@@ -24,7 +24,7 @@
 from .pathmapper import PathMapper
 from .job import CommandLineJob
 
-ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._-]+$")
+ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
 
 from .flatten import flatten
 
@@ -92,7 +92,7 @@ def revmap_file(builder, outdir, f):
         f["location"] = revmap_f[1]
         return f
     elif f["path"].startswith(builder.outdir):
-        f["location"] = os.path.join(outdir, f["path"][len(builder.outdir)+1:])
+        f["location"] = builder.fs_access.join(outdir, f["path"][len(builder.outdir)+1:])
         return f
     else:
         raise WorkflowException(u"Output file path %s must be within designated output directory (%s) or an input file pass through." % (f["path"], builder.outdir))
@@ -344,7 +344,7 @@ def collect_output_ports(self, ports, builder, outdir):
         # type: (Set[Dict[str,Any]], Builder, str) -> Dict[unicode, Union[unicode, List[Any], Dict[unicode, Any]]]
         try:
             ret = {}  # type: Dict[unicode, Union[unicode, List[Any], Dict[unicode, Any]]]
-            custom_output = os.path.join(outdir, "cwl.output.json")
+            custom_output = builder.fs_access.join(outdir, "cwl.output.json")
             if builder.fs_access.exists(custom_output):
                 with builder.fs_access.open(custom_output, "r") as f:
                     ret = json.load(f)
@@ -400,7 +400,7 @@ def collect_output(self, schema, builder, outdir):
                     try:
                         r.extend([{"location": g,
                                    "class": "File" if builder.fs_access.isfile(g) else "Directory"}
-                                  for g in builder.fs_access.glob(os.path.join(outdir, gb))])
+                                  for g in builder.fs_access.glob(builder.fs_access.join(outdir, gb))])
                     except (OSError, IOError) as e:
                         _logger.warn(str(e))
 

cwltool/stdfsaccess.py

@@ -29,3 +29,6 @@ def isdir(self, fn):  # type: (unicode) -> bool
 
     def listdir(self, fn):  # type: (unicode) -> List[unicode]
         return [abspath(l, fn) for l in os.listdir(self._abs(fn))]
+
+    def join(self, path, *paths): # type: (unicode, *unicode) -> unicode
+        return os.path.join(path, *paths)