Correct the inability of accessing the study output root directory. (#…

…103)

* Fixed a bug with removing of environment variables.

* Add the OUTPUT_PATH to the environment.

* Correction of a logger message.

* Tweak to have StepRecords point to WORKSPACE

* Tweaks to examples to include WORKSPACE keyword.

maestrowf/datastructures/core/executiongraph.py

@@ -46,7 +46,8 @@ def __init__(self, workspace, step, **kwargs):
         tmp_dir: A provided temp directory to write scripts to instead of step
         workspace.
         """
-        self.workspace = Variable("OUTPUT_PATH", workspace)
+        self.workspace = Variable("WORKSPACE", workspace)
+        step.run["cmd"] = self.workspace.substitute(step.run["cmd"])
 
         self.jobid = kwargs.get("jobid", [])
         self.script = kwargs.get("script", "")

maestrowf/datastructures/core/study.py

@@ -421,7 +421,7 @@ def _setup_parameterized(self):
             for ws in used_spaces:
                 if ws not in used_params:
                     msg = "Workspace for '{}' is being used before it would" \
-                          "be generated.".format(ws)
+                          " be generated.".format(ws)
                     logger.error(msg)
                     raise Exception(msg)
 

maestrowf/datastructures/core/studyenvironment.py

@@ -160,16 +160,23 @@ def remove(self, key):
         :returns: The environment object labeled by key.
         """
         logger.debug("Looking to remove '%s'...", key)
+
+        if key not in self._names:
+            return None
+
         _ = self.dependencies.pop(key, None)
         if _ is not None:
+            self._names.remove(key)
             return _
 
         _ = self.substitutions.pop(key, None)
         if _ is not None:
+            self._names.remove(key)
             return _
 
         _ = self.labels.pop(key, None)
         if _ is not None:
+            self._names.remove(key)
             return _
 
         logger.debug("'%s' not found -- \n%s", key, self)

maestrowf/maestro.py

@@ -133,6 +133,7 @@ def run_study(args):
             time.strftime("%Y%m%d-%H%M%S")
         )
         output_path = make_safe_path(out_dir, out_name)
+    environment.add(Variable("OUTPUT_PATH", output_path))
 
     # Now that we know outpath, set up logging.
     setup_logging(args, output_path, spec.name)

samples/lulesh/lulesh_sample1_macosx.yaml

@@ -16,8 +16,8 @@ study:
       run:
           cmd: |
             curl -L -o lulesh.tar $(LULESH_URL)
-            mkdir $(OUTPUT_PATH)/lulesh
-            tar -xf lulesh.tar -C $(OUTPUT_PATH)/lulesh
+            mkdir $(WORKSPACE)/lulesh
+            tar -xf lulesh.tar -C $(WORKSPACE)/lulesh
           depends: []
 
     - name: make-lulesh

samples/lulesh/lulesh_sample1_unix.yaml

@@ -16,8 +16,8 @@ study:
       run:
           cmd: |
             curl -L -o lulesh.tar $(LULESH_URL)
-            mkdir $(OUTPUT_PATH)/lulesh
-            tar -xf lulesh.tar -C $(OUTPUT_PATH)/lulesh
+            mkdir $(WORKSPACE)/lulesh
+            tar -xf lulesh.tar -C $(WORKSPACE)/lulesh
           depends: []
 
     - name: make-lulesh