Add compath resources build

src/biokeen/build.py

@@ -16,6 +16,7 @@
     'iterate_source_paths',
     'ensure_hippie',
     'ensure_drugbank',
+    'ensure_compath',
 ]
 
 logger = logging.getLogger(__name__)
@@ -26,6 +27,9 @@
 drugbank_bel_path = os.path.join(DATA_DIR, 'drugbank.bel.pickle')
 drugbank_keen_path = os.path.join(DATA_DIR, 'drugbank.keen.tsv')
 
+compath_bel_path = os.path.join(DATA_DIR, 'compath.bel.pickle')
+compath_keen_path = os.path.join(DATA_DIR, 'compath.keen.tsv')
+
 
 def get_full_matrix():
     """Get all built data as a matrix."""
@@ -76,3 +80,11 @@ def ensure_drugbank(connection: Optional[str] = None):
         to_pickle(drugbank_graph, drugbank_bel_path)
 
     to_pykeen_file(drugbank_graph, drugbank_keen_path)
+
+
+def ensure_compath():
+    """Ensure the ComPath mappings are retrieved."""
+    import compath_resources
+    graph = compath_resources.get_bel()
+    to_pickle(graph, compath_bel_path)
+    to_pykeen_file(graph, compath_keen_path)

src/biokeen/cli.py

@@ -9,27 +9,20 @@
 
 import pykeen
 from bio2bel.constants import get_global_connection
-from biokeen.build import ensure_drugbank, ensure_hippie, iterate_source_paths
+from biokeen.build import ensure_compath, ensure_drugbank, ensure_hippie, iterate_source_paths
 from biokeen.cli_utils.bio_2_bel_utils import install_bio2bel_module
 from biokeen.cli_utils.cli_print_msg_helper import print_intro, print_welcome_message
 from biokeen.cli_utils.cli_query_helper import select_database
 from pykeen.cli import (
-    _configure_evaluation_specific_parameters,
-    device_prompt,
-    execution_mode_specific_prompt,
-    model_selection_prompt,
-    output_direc_prompt,
-    training_file_prompt,
+    _configure_evaluation_specific_parameters, device_prompt, execution_mode_specific_prompt, model_selection_prompt,
+    output_direc_prompt, training_file_prompt,
 )
 from pykeen.constants import EXECUTION_MODE, HPO_MODE, TRAINING_MODE, TRAINING_SET_PATH
 from pykeen.predict import start_predictions_piepline
 from pykeen.utilities.cli_utils.cli_print_msg_helper import (
-    print_execution_mode_message,
-    print_section_divider,
-    print_training_set_message
+    print_execution_mode_message, print_section_divider, print_training_set_message,
 )
 
-
 connection_option = click.option(
     '-c',
     '--connection',
@@ -171,3 +164,9 @@ def hippie(connection):
 def drugbank(connection):
     """Build DrugBank."""
     ensure_drugbank(connection)
+
+
+@build.command()
+def compath():
+    """Build ComPath."""
+    ensure_compath()