From ef1ef057bb73e140db9f2cc8e37959c9289677bc Mon Sep 17 00:00:00 2001
From: caufieldjh <j.harry.caufield@gmail.com>
Date: Fri, 16 Aug 2024 17:07:17 -0400
Subject: [PATCH] Adding robot relax

---
 src/kg_bioportal/robot_utils.py |  2 +-
 src/kg_bioportal/transformer.py | 26 ++++++++++++++++++++------
 2 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/src/kg_bioportal/robot_utils.py b/src/kg_bioportal/robot_utils.py
index 5faf807..623bc41 100644
--- a/src/kg_bioportal/robot_utils.py
+++ b/src/kg_bioportal/robot_utils.py
@@ -49,7 +49,7 @@ def initialize_robot(robot_path: str) -> list:
     return [robot_command, env]
 
 
-def relax_ontology(
+def robot_relax(
     robot_path: str, input_path: str, output_path: str, robot_env: dict
 ) -> bool:
     """
diff --git a/src/kg_bioportal/transformer.py b/src/kg_bioportal/transformer.py
index 861b1c0..b0bd42d 100644
--- a/src/kg_bioportal/transformer.py
+++ b/src/kg_bioportal/transformer.py
@@ -5,8 +5,9 @@
 import sys
 
 from kg_bioportal.downloader import ONTOLOGY_LIST_NAME
-from kg_bioportal.robot_utils import initialize_robot, robot_convert
+from kg_bioportal.robot_utils import initialize_robot, robot_convert, robot_relax
 
+# TODO: Don't repeat steps if the products already exist
 
 class Transformer:
 
@@ -66,14 +67,14 @@ def transform_all(self) -> None:
         ]
 
         if len(filepaths) == 0:
-            logging.ERROR(f"No ontologies found in {self.input_dir}.")
+            logging.error(f"No ontologies found in {self.input_dir}.")
             sys.exit()
         else:
             logging.info(f"Found {len(filepaths)} ontologies to transform.")
 
         for filepath in filepaths:
             if not self.transform(filepath):
-                logging.ERROR(f"Error transforming {filepath}.")
+                logging.error(f"Error transforming {filepath}.")
             else:
                 logging.info(f"Transformed {filepath}.")
 
@@ -92,14 +93,27 @@ def transform(self, ontology: str) -> bool:
 
         logging.info(f"Transforming {ontology} to nodes and edges.")
         ontology_name = os.path.splitext(os.path.basename(ontology))[0]
-        output_path = os.path.join(self.output_dir, f"{ontology_name}.json")
+        json_output_path = os.path.join(self.output_dir, f"{ontology_name}.json")
+        
+        # Convert
         if not robot_convert(
             robot_path=self.robot_path,
             input_path=ontology,
-            output_path=output_path,
+            output_path=json_output_path,
             robot_env=self.robot_env,
         ):
             status = False
-        status = True
+
+        # Relax
+        relaxed_outpath = os.path.join(self.output_dir, f"{ontology_name}_relaxed.json")
+        if not robot_relax(
+            robot_path=self.robot_path,
+            input_path=json_output_path,
+            output_path=relaxed_outpath,
+            robot_env=self.robot_env,
+        ):
+            status = False
+        else:
+            status = True
 
         return status