change schema_path to output_schema for pipestat config

pepkit · Nov 20, 2023 · 7d6cc5f · 7d6cc5f
1 parent 0ca9bd1
commit 7d6cc5f
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Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/looper/project.py b/looper/project.py
@@ -545,8 +545,13 @@ def _get_pipestat_configuration(self, sample_name=None, project_level=False):
 
         for piface in pifaces:
             # We must also obtain additional pipestat items from the pipeline author's piface
-            if "schema_path" in piface.data:
-                schema_path = expandpath(piface.data["schema_path"])
+            if "output_schema" in piface.data:
+                schema_path = expandpath(piface.data["output_schema"])
+                if not os.path.isabs(schema_path):
+                    # Get path relative to the pipeline_interface
+                    schema_path = os.path.join(
+                        os.path.dirname(piface.pipe_iface_file), schema_path
+                    )
                 pipestat_config_dict.update({"schema_path": schema_path})
             if "pipeline_name" in piface.data:
                 pipestat_config_dict.update(

diff --git a/tests/data/pipeline_interface1_sample_pipestat.yaml b/tests/data/pipeline_interface1_sample_pipestat.yaml
@@ -1,7 +1,7 @@
 pipeline_name: PIPELINE1
 pipeline_type: sample
 input_schema: https://schema.databio.org/pep/2.0.0.yaml
-schema_path: pipestat_output_schema.yaml
+output_schema: pipestat_output_schema.yaml
 var_templates:
   path: "{looper.piface_dir}/pipelines/pipeline1.py"
 pre_submit: