Merge pull request #4 from BiomedSciAI/reactome_task_cli

Changed the Reactome cli

scripts/tasks_retrival/Reactome_tasks_creation.py

@@ -81,11 +81,10 @@ def dump_to_task(task_dir, outcomes_df):
  default="Pathways",
 )
 @click.option(
- "--use-local-files",
- "-l",
+ "--allow-downloads",
  type=click.BOOL,
  help="If false data files will be downloaded directly from HGNC and reactome, set to true only if you trust the urls above",
- default=True,
+ default=False,
 )
 @click.option(
  "--pathways-file",
@@ -100,17 +99,17 @@ def dump_to_task(task_dir, outcomes_df):
  default="",
 )
 def main(
- main_task_directory, task_name, use_local_files, pathways_file, top_pathways_file
+ main_task_directory, task_name, allow_downloads, pathways_file, top_pathways_file
 ):
- if use_local_files:
- df_path = pd.read_csv(pathways_file)
- top_level = pd.read_csv(top_pathways_file)
- else:
+ if allow_downloads:
  symb_list = get_symbol_list()
  token = get_token(symb_list)
  url = f"https://reactome.org/AnalysisService/download/{token}/pathways/TOTAL/result.csv"
  df_path = pd.read_csv(url, index_col="Pathway identifier")
  top_level = get_top_level_pathway()
+ else:
+ df_path = pd.read_csv(pathways_file)
+ top_level = pd.read_csv(top_pathways_file)
 
  top_in_file_paths = top_level.intersection(set(df_path.index))
  df_path_top = df_path.loc[list(top_in_file_paths), :]