Refactor

src/biokeen/cli.py

@@ -2,17 +2,13 @@
 
 """A command line interface for BioKEEN."""
 
+import json
 import logging
 from collections import OrderedDict
 
 import click
-
 import pykeen
 from bio2bel.constants import get_global_connection
-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,
@@ -23,6 +19,11 @@
     print_execution_mode_message, print_section_divider, print_training_set_message,
 )
 
+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
+
 connection_option = click.option(
     '-c',
     '--connection',
@@ -94,13 +95,16 @@ def main():  # noqa: D401
 
 
 @main.command()
-@click.option('-c', '--config', type=click.File())
 @connection_option
+@click.option('-f', '--config', type=click.File())
 @click.option('-r', '--rebuild', is_flag=True)
 def start(config, connection, rebuild):
     """Start BioKEEN pipeline."""
+
     if config is None:
         config = prompt_config(connection, rebuild)
+    else:
+        config = json.load(config)
 
     pykeen.run(config)
 

src/biokeen/cli_utils/cli_query_helper.py

@@ -9,7 +9,7 @@
 
 def select_database():
     """Select database."""
-    click.secho("Current Step: Please select the embedding model you want to train:", fg='blue')
+    click.secho("Current Step: Please select the database you want to train on:", fg='blue')
     for model, model_id in sorted(ID_TO_DATABASE_MAPPING.items()):
         click.echo(f'{model}: {model_id}')
 

src/biokeen/constants.py

@@ -15,23 +15,25 @@
 EMOJI = '🍩'
 
 # Available databases
-DRUGBANK_NAME = 'drugbank'
+COMPATH_NAME = 'compath'
 HIPPE_NAME = 'hippie'
+KEGG_NAME = 'kegg'
 MIRTARBASE_NAME = 'mirtarbase'
-WIKIPATHWAYS_NAME = 'wikipathways'
 MSIG_NAME = 'msig'
-KEGG_NAME = 'kegg'
 REACTOME_NAME = 'reactome'
+WIKIPATHWAYS_NAME = 'wikipathways'
+DRUGBANK_NAME = 'drugbank'
 
 # ToDo: Add databases
 DATABASES = [
-    MIRTARBASE_NAME,
-    DRUGBANK_NAME,
-    WIKIPATHWAYS_NAME,
+    COMPATH_NAME,
     HIPPE_NAME,
-    MSIG_NAME,
     KEGG_NAME,
+    MIRTARBASE_NAME,
+    MSIG_NAME,
     REACTOME_NAME,
+    WIKIPATHWAYS_NAME,
+    DRUGBANK_NAME,
 ]
 
 ID_TO_DATABASE_MAPPING = dict(enumerate(DATABASES, start=1))