generalized target data generation to both flu and covid

src/hub_predtimechart/app/generate_target_json_files.py

@@ -20,33 +20,46 @@
 @click.argument('ptc_config_file', type=click.Path(file_okay=True, exists=False))
 @click.argument('target_out_dir', type=click.Path(file_okay=False, exists=True))
 def main(hub_dir, ptc_config_file, target_out_dir):
-    '''
+    """
     Generates the target data json files used by https://github.com/reichlab/predtimechart to
-    visualize a hub's forecasts.
+    visualize a hub's forecasts. Handles missing input target data in two ways, depending on the error. 1) If the
+    `target_data_file_name` entry in the hub config file is missing, then the program will exit with no messages.
+    2) If the entry is present but the file it points to does not exist, then the program will exit with an error
+    message, but won't actually raise a Python exception.
 
     HUB_DIR: (input) a directory Path of a https://hubverse.io hub to generate target data json files from
 
+    PTC_CONFIG_FILE: (input) a file Path to a `predtimechart-config.yaml` file that specifies how to process `hub_dir`
+    to get predtimechart output
+
     TARGET_OUT_DIR: (output) a directory Path to output the viz target data json files to
     \f
     :param hub_dir: (input) a directory Path of a https://hubverse.io hub to generate target data json files from
+    :param ptc_config_file: (input) a file Path to a `predtimechart-config.yaml` file that specifies how to process
+        `hub_dir` to get predtimechart output
     :param target_out_dir: (output) a directory Path to output the viz target data json files to
-
-    '''
+    """
     logger.info(f'main({hub_dir=}, {target_out_dir=}): entered')
 
     hub_dir = Path(hub_dir)
     hub_config = HubConfig(hub_dir, Path(ptc_config_file))
-    target_out_dir = Path(target_out_dir)
-    target_data_df = get_target_data_df(hub_dir, hub_config.target_data_file_name)
+    if hub_config.target_data_file_name is None:
+        logger.info('No `target_data_file_name` entry found in hub config file. exiting')
+        return
 
-    # for each location,
-    # - generate target data file contents
-    # - save as json
+    # for each location, generate target data file contents and then save as json
     json_files = []
+    try:
+        target_data_df = get_target_data_df(hub_dir, hub_config.target_data_file_name)
+    except FileNotFoundError as error:
+        logger.error(f"target data file not found. {hub_config.target_data_file_name=}, {error=}")
+        return
+
     for loc in target_data_df['location'].unique():
         task_ids_tuple = (loc,)
+        target_out_dir = Path(target_out_dir)
+        file_name = json_file_name(hub_config.fetch_target_id, task_ids_tuple, reference_date_from_today().isoformat())
         location_data_dict = ptc_target_data(target_data_df, task_ids_tuple)
-        file_name = json_file_name('wk inc flu hosp', task_ids_tuple, reference_date_from_today().isoformat())
         json_files.append(target_out_dir / file_name)
         with open(target_out_dir / file_name, 'w') as fp:
             json.dump(location_data_dict, fp, indent=4)