Rename to atdb_csv_gen & log extra files

README.md

 # LDV Utility scripts
 
-## CSV Gen
+## ATDB CSV Gen
 Generates csv input files for the `atdb_load_tasks_from_table` script.
 
 ### Installation
 ```bash
 # Using pipenv (update python version if necessary)
-cd csv_gen
+cd atdb_csv_gen
 pipenv install 
 
 # or using pip (optional, use a virtual env)
-cd csv_gen
+cd atdb_csv_gen
 pip install -r requirements.txt
 
 # or using docker
-docker-build -t ldv-csv-gen csv_gen/
+docker-build -t ldv-atdb-csv-gen csv_gen/
 ```
 
 ### Running
 ```bash
 # copy .env.example to .env and fill in the environment vars (DB credentials)
-cp ./csv_gen/.env.example ./csv_gen/.env
+cp ./atdb_csv_gen/.env.example ./atdb_csv_gen/.env
 
 # run using pipenv
-cd csv_gen
+cd atdb_csv_gen
 pipenv shell    # this will use the .env file to set environment variables
 ./csv_gen.py -v -o out.csv 650273
 
 # run using python (note)
-cd csv_gen
+cd atdb_csv_gen
 export $(cat .env | xargs)  # or export env vars elsewhere
 ./csv_gen.py -v -o out.csv 650273
 
 # run in docker (creates out.csv in outdir)
-docker run -it --rm --env-file csv_gen/.env -v $PWD/outdir:/outdir ldv-csv-gen /app/csv_gen.py -v -o /outdir/out.csv 650273
+docker run -it --rm --env-file atdb_csv_gen/.env -v $PWD/outdir:/outdir ldv-atdb-csv-gen /app/csv_gen.py -v -o /outdir/out.csv 650273
 
 # more info and flags
-docker run -it --rm ldv-csv-gen
+docker run -it --rm ldv-atdb-csv-gen
 ```
 
 ### Caveats

csv_gen/csv_gen.py → atdb_csv_gen/atdb_csv_gen.py

 #!/usr/bin/env python3
+# SPDX-License-Identifier: Apache-2.0
 
 import logging
 import os
 from argparse import ArgumentParser, Namespace
 from sys import version
-from typing import Generator, Iterator, List, Optional, Tuple
+from typing import Iterator, List, Optional, Tuple
 
 from sqlalchemy import create_engine
 from sqlalchemy.engine.base import Connection
@@ -24,6 +25,7 @@ def parse_args() -> Namespace:
     parser = ArgumentParser(description="Generates CSV for atdb_load_tasks_from_table")
     parser.add_argument("obs_id", help="Observation ID (SAS ID)")
     parser.add_argument("-o", help="Output file")
+    parser.add_argument("--save-missing", help="Directory to store csc with missing files")
     parser.add_argument("-v", action="store_true", help="Verbose logging")
     parser.add_argument("-q", action="store_true", help="Quiet logging (only errors)")
     return parser.parse_args()
@@ -82,13 +84,15 @@ def main(obs_id: str, o_file: Optional[str]):
     reg_no_file = reg_data.difference(cra_data)
     if len(reg_no_file) > 0:
         logger.warning("Observation contains %i registered files which are not present on disk",  len(reg_no_file))
-        # TODO: write to csv file?
+        for row in reg_no_file:
+            logger.warning(row)
 
     # File found, not registered
     file_no_reg = cra_data.difference(reg_data)
     if len(file_no_reg) > 0:
         logger.warning("Observation contains %i files on disk which are not registered in the LTA", len(file_no_reg))
-        # TODO: write to csv file?
+        for row in file_no_reg:
+            logger.warning(row)
 
 
     inter = reg_data.intersection(cra_data)