Update from_bioregistry.py

Author: cthoyt

scripts/from_bioregistry.py

@@ -18,6 +18,7 @@
 from tqdm.contrib.logging import logging_redirect_tqdm
 
 import bioontologies
+from bioontologies.robot import ROBOTError
 
 
 @click.command()
@@ -27,19 +28,29 @@ def main() -> None:
         resource.prefix
         for resource in bioregistry.resources()
         if resource.get_download_owl() or resource.get_download_obograph()
-    ][282:]
+    ]
     for prefix in tqdm(prefixes, desc="Parsing OWL ontologies", unit="ontology"):
-        tqdm.write(click.style("\n" + prefix, fg="green"))
+        tqdm.write(click.style(f"\n[{prefix}]", fg="green"))
         with logging_redirect_tqdm():
-            document = bioontologies.get_obograph_by_prefix(prefix, cache=False)
             try:
-                graph = document.squeeze(standardize=True, prefix=prefix)
-            except ValueError:
-                tqdm.write(f"[{prefix}] failed to parse")
-            else:
-                tqdm.write(
-                    click.style(f"[{prefix}] parsed {graph.title} - v{graph.version}", fg="red")
+                document = bioontologies.get_obograph_by_prefix(prefix, cache=False, reason=False)
+            except ROBOTError as e:
+                tqdm.write(click.style(f"[{prefix}] {e}", fg="red"))
+                continue
+
+            try:
+                graph = document.squeeze(
+                    standardize=True, prefix=prefix, tqdm_kwargs={"leave": False}
                 )
+            except ValueError as e:
+                tqdm.write(click.style(f"[{prefix}] failed to parse\n\n{e}", fg="red"))
+            else:
+                if graph.version:
+                    msg = f"[{prefix}] parsed {graph.title} - v{graph.version}"
+                else:
+                    msg = f"[{prefix}] parsed {graph.title}"
+
+                tqdm.write(click.style(msg, fg="green"))
 
 
 if __name__ == "__main__":