Allow passing metadata path to data-prep-cubes

cli/medperf/commands/dataset/create.py

@@ -158,6 +158,7 @@ def set_staging_parameters(self):
         self.report_path = os.path.join(out_path, config.report_file)
         self.out_datapath = os.path.join(out_path, "data")
         self.out_labelspath = os.path.join(out_path, "labels")
+        self.metadata_path = os.path.join(out_path, "metadata")
 
         # Check if labels_path is specified
         self.labels_specified = (
@@ -167,6 +168,10 @@ def set_staging_parameters(self):
         self.report_specified = (
             self.cube.get_default_output("prepare", "report_file") is not None
         )
+        # Backwards compatibility. Run a cube as before if no metadata is specified
+        self.metadata_specified = (
+            self.cube.get_default_output("prepare", "metadata_path") is not None
+        )
         logging.debug(f"tmp data preparation output: {out_path}")
         logging.debug(f"tmp data statistics output: {self.out_statistics_path}")
 
@@ -211,6 +216,9 @@ def sigint_handler(sig, frame):
 
         observer = Observer()
 
+        if self.metadata_specified:
+            prepare_params["metadata_path"] = self.metadata_path
+
         if self.report_specified:
             prepare_params["report_file"] = out_report
             metadata = {"execution_status": "started"}
@@ -293,6 +301,12 @@ def run_sanity_check(self):
             # Add the labels parameter
             sanity_params["labels_path"] = out_labelspath
 
+        if self.metadata_specified:
+            sanity_params["metadata_path"] = self.metadata_path
+            sanity_params[
+                "Ptasks.sanity_check.parameters.input.metadata_paths.opts"
+            ] = "ro"
+
         if self.report_specified:
             sanity_params["report_file"] = out_report
             sanity_str_params[
@@ -330,6 +344,12 @@ def run_statistics(self):
             "Ptasks.statistics.parameters.input.data_path.opts": "ro"
         }
 
+        if self.metadata_specified:
+            statistics_params["metadata_path"] = self.metadata_path
+            statistics_params[
+                "Ptasks.statistics.parameters.input.metadata_path.opts"
+            ] = "ro"
+
         self.ui.text = "Generating statistics..."
 
         self.cube.run(