Merge pull request #344 from caracal-pipeline/issue-122

Issue 121+122

stimela/backends/flavours/casa.py

@@ -23,11 +23,13 @@ class CasaTaskFlavour(_CallableFlavour):
     kind: str = "casa-task"
     path: Optional[str] = None                       # path to CASA executable
     opts: Optional[List[str]] = EmptyListDefault()   # additional options 
+    wrapper: Optional[str] = None                    # wrapper command (e.g. xvfb-run -a)
 
     def finalize(self, cab: Cab):
         super().finalize(cab)
 
-        err_patt = re.compile("(?P<content>(\tSEVERE\t|ABORTING|\*\*\* Error \*\*\*)(.*))$")
+        # catch CASA error messages, except the MeasTable::dUTC complaints which are all-pervasive
+        err_patt = re.compile("(?P<content>(\tSEVERE\s+(?!MeasTable::dUTC)|ABORTING|\*\*\* Error \*\*\*)(.*))$")
         cab._wranglers.append((
             err_patt, [
                 wranglers.DeclareError(err_patt, "ERROR", message="CASA error: {content}" )
@@ -59,10 +61,14 @@ def get_arguments(self, cab: Cab, params: Dict[str, Any], subst: Dict[str, Any],
                     casa_opts = [context.evaluate(opt, location=["opts"]) for opt in casa_opts]
                 except Exception as exc:
                     raise SubstitutionError(f"error substituting casa options '{casa_opts}'", exc)
-
-        # check for virtual_env
-        if virtual_env and "/" not in command:
-            command = f"{virtual_env}/bin/{command}"
+            wrapper = self.wrapper if self.wrapper is not None else casa_config.get('wrapper', 'xvfb-run -a')
+            if wrapper:
+                try:
+                    wrapper = [context.evaluate(wrapper, location=["wrapper"])]
+                except Exception as exc:
+                    raise SubstitutionError(f"error substituting wrapper '{wrapper}'", exc)
+            else:
+                wrapper = []
 
         self.command_name = command
         pass_params = dict(cab.filter_input_params(params))
@@ -72,7 +78,7 @@ def get_arguments(self, cab: Cab, params: Dict[str, Any], subst: Dict[str, Any],
         # this works for both python 2.7 and 3.x
         code = f"{command}(**{pass_params})"
 
-        args =  casa.strip().split() + list(casa_opts) + ["-c", code]
+        args =  wrapper + casa.strip().split() + list(casa_opts) + ["-c", code]
         return args
 
 

stimela/stimela.conf

@@ -16,4 +16,5 @@ opts:
         casa:
             path: casa
             opts: [--log2term, --nologger, --nologfile]
+            wrapper: xvfb-run -a