Merge pull request #134 from nsoranzo/fixes

Fixes

galaxy/tools/cwl/cwltool_deps.py

@@ -28,10 +28,9 @@
     pathmapper = None
 
 try:
-    from cwltool.context import LoadingContext, RuntimeContext
+    from cwltool.context import LoadingContext  # Introduced in cwltool 1.0.20180615183820
 except (ImportError, SyntaxError):
     LoadingContext = None
-    RuntimeContext = None
 
 try:
     from cwltool import load_tool
@@ -83,7 +82,6 @@ def ensure_cwltool_available():
     'ref_resolver',
     'load_tool',
     'LoadingContext',
-    'RuntimeContext',
     'workflow',
     'process',
     'pathmapper',

galaxy/tools/cwl/schema.py

@@ -68,7 +68,9 @@ def tool(self, **kwds):
             process_definition = self.process_definition(raw_process_reference)
 
         args = {"strict": self._strict}
+        make_tool = kwds.get("make_tool", default_make_tool)
         if LoadingContext is not None:
+            args["construct_tool_object"] = make_tool
             loading_context = LoadingContext(args)
             tool = load_tool.make_tool(
                 process_definition.document_loader,
@@ -78,7 +80,6 @@ def tool(self, **kwds):
                 loading_context,
             )
         else:
-            make_tool = kwds.get("make_tool", default_make_tool)
             tool = load_tool.make_tool(
                 process_definition.document_loader,
                 process_definition.avsc_names,

galaxy/tools/linters/stdio.py

@@ -32,34 +32,12 @@ def lint_stdio(tool_source, lint_ctx):
 
 
 def _lint_exit_code(child, lint_ctx):
-    for key, value in child.attrib.items():
-        if key == "range":
-            # TODO: validate
-            pass
-        elif key == "level":
-            _lint_level(value, lint_ctx)
-        elif key == "description":
-            pass
-        else:
+    for key in child.attrib.keys():
+        if key not in ["description", "level", "range"]:
             lint_ctx.warn("Unknown attribute [%s] encountered on exit_code tag." % key)
 
 
 def _lint_regex(child, lint_ctx):
-    for key, value in child.attrib.items():
-        if key == "source":
-            if value not in ["stderr", "stdout", "both"]:
-                lint_ctx.error("Unknown error code level encountered [%s]" % value)
-        elif key == "level":
-            _lint_level(value, lint_ctx)
-        elif key == "match":
-            # TODO: validate
-            pass
-        elif key == "description":
-            pass
-        else:
+    for key in child.attrib.keys():
+        if key not in ["description", "level", "match", "source"]:
             lint_ctx.warn("Unknown attribute [%s] encountered on regex tag." % key)
-
-
-def _lint_level(level_value, lint_ctx):
-    if level_value not in ["warning", "fatal", "log"]:
-        lint_ctx.error("Unknown error code level encountered [%s]" % level_value)