Update transformer, now transforms all to obojson

src/kg_bioportal/cli.py

@@ -153,10 +153,10 @@ def download(
     return None
 
 
-@cli.command()
+@main.command()
 @click.option("input_dir", "-i", default="data/raw", type=click.Path(exists=True))
 @click.option("output_dir", "-o", default="data/transformed")
-def transform(*args, **kwargs) -> None:
+def transform(input_dir, output_dir) -> None:
     """Transforms all ontologies in the input directory to KGX nodes and edges.
 
     Args:

src/kg_bioportal/transformer.py

@@ -2,6 +2,10 @@
 
 import logging
 import os
+import sys
+
+from kg_bioportal.downloader import ONTOLOGY_LIST_NAME
+from kg_bioportal.robot_utils import initialize_robot, robot_convert
 
 
 class Transformer:
@@ -13,6 +17,8 @@ def __init__(
     ) -> None:
         """Initializes the Transformer class.
 
+        Also sets up ROBOT.
+
         Args:
 
             input_dir: A string pointing to the location of the raw data.
@@ -29,6 +35,14 @@ def __init__(
         if not os.path.exists(self.output_dir):
             os.makedirs(self.output_dir)
 
+        # Do ROBOT setup
+        logging.info("Setting up ROBOT...")
+        self.robot_path = os.path.join(os.getcwd(), "robot")
+        self.robot_params = initialize_robot(self.robot_path)
+        logging.info(f"ROBOT path: {self.robot_path}")
+        self.robot_env = self.robot_params[1]
+        logging.info(f"ROBOT evironment variables: {self.robot_env['ROBOT_JAVA_ARGS']}")
+
         return None
 
     def transform_all(self) -> None:
@@ -45,4 +59,47 @@ def transform_all(self) -> None:
             f"Transforming all ontologies in {self.input_dir} to KGX nodes and edges."
         )
 
+        filepaths = [
+            os.path.join(self.input_dir, f)
+            for f in os.listdir(self.input_dir)
+            if not f.endswith(ONTOLOGY_LIST_NAME)
+        ]
+
+        if len(filepaths) == 0:
+            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}.")
+            else:
+                logging.info(f"Transformed {filepath}.")
+
         return None
+
+    def transform(self, ontology: str) -> bool:
+        """Transforms a single ontology to KGX nodes and edges.
+
+        Args:
+            ontology: A string representing the ontology to transform.
+
+        Returns:
+            True if transform was successful, otherwise False.
+        """
+        status = False
+
+        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")
+        if not robot_convert(
+            robot_path=self.robot_path,
+            input_path=ontology,
+            output_path=output_path,
+            robot_env=self.robot_env,
+        ):
+            status = False
+        status = True
+
+        return status