Update bio_2_bel_utils.py

SmartDataAnalytics · Nov 20, 2018 · 5551dca · 5551dca
1 parent 26f464c
commit 5551dca
Showing 1 changed file with 13 additions and 9 deletions.
diff --git a/src/biokeen/cli_utils/bio_2_bel_utils.py b/src/biokeen/cli_utils/bio_2_bel_utils.py
@@ -44,43 +44,47 @@ def _import_bio2bel_module(name: str):
 
 def install_bio2bel_module(name, connection, rebuild):
     """Install Bio2BEL module."""
-    bio2bel_module_name = f"bio2bel_{name}"
+    if name == 'compath':  # special case for compath
+        module_name = 'compath_resources'
+    else:
+        module_name = f"bio2bel_{name}"
+
     pykeen_df_path = os.path.join(DATA_DIR, f'{name}.keen.tsv')
     pickle_path = os.path.join(DATA_DIR, f'{name}.bel.pickle')
 
     if os.path.exists(pykeen_df_path) and not rebuild:
-        click.secho(f'{EMOJI} {bio2bel_module_name} has already been retrieved. See: {pykeen_df_path}', bold=True)
+        click.secho(f'{EMOJI} {module_name} has already been retrieved. See: {pykeen_df_path}', bold=True)
         return pykeen_df_path
 
     if os.path.exists(pickle_path):
-        click.secho(f'{EMOJI} loaded {bio2bel_module_name} pickle: {pickle_path}', bold=True)
+        click.secho(f'{EMOJI} loaded {module_name} pickle: {pickle_path}', bold=True)
         graph = from_pickle(pickle_path)
         to_pykeen_file(graph, pykeen_df_path)
         return pykeen_df_path
 
     bio2bel_module = _import_bio2bel_module(name)
-    click.secho(f'{EMOJI} imported {bio2bel_module_name}', bold=True)
+    click.secho(f'{EMOJI} imported {module_name}', bold=True)
 
     manager_cls = bio2bel_module.Manager
 
     if not issubclass(manager_cls, BELManagerMixin):
-        click.secho(f'{EMOJI} {bio2bel_module_name} does not produce BEL', bold=True, fg='red')
+        click.secho(f'{EMOJI} {module_name} does not produce BEL', bold=True, fg='red')
         sys.exit(1)
 
     manager = manager_cls(connection=connection)
 
     if issubclass(manager_cls, AbstractManager):
         if not manager.is_populated():
-            click.secho(f'{EMOJI} populating {bio2bel_module_name}', bold=True)
+            click.secho(f'{EMOJI} populating {module_name}', bold=True)
             manager.populate()
         else:
-            click.secho(f'{EMOJI} {bio2bel_module_name} has already been populated', bold=True)
+            click.secho(f'{EMOJI} {module_name} has already been populated', bold=True)
 
-    click.secho(f'{EMOJI} generating BEL for {bio2bel_module_name}', bold=True)
+    click.secho(f'{EMOJI} generating BEL for {module_name}', bold=True)
     graph = manager.to_bel()
     click.echo(f'Summary: {graph.number_of_nodes()} nodes / {graph.number_of_edges()} edges')
     to_pickle(graph, pickle_path)
-    click.secho(f'{EMOJI} generating PyKEEN TSV for {bio2bel_module_name}', bold=True)
+    click.secho(f'{EMOJI} generating PyKEEN TSV for {module_name}', bold=True)
     to_pykeen_file(graph, pykeen_df_path)
 
     return pykeen_df_path