diff --git a/.gitignore b/.gitignore
index 2eea525d885d5148108f6f3a9a8613863f783d36..50888c086fb33538c9f18b6b76e4103d6bf6e512 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,3 @@
-.env
\ No newline at end of file
+.env
+*.egg-info
+*.pyc
\ No newline at end of file
diff --git a/README.md b/README.md
index 0c5e160e1199428023afc615cb65e274bc7bfb12..670d61a7253ce7ea2a885566b97f2599cf48b1c2 100644
--- a/README.md
+++ b/README.md
@@ -5,16 +5,8 @@ Generates csv input files for the `atdb_load_tasks_from_table` script.
### Installation
```bash
-# Using pipenv (update python version if necessary)
-cd atdb_csv_gen
-pipenv install
-
-# or using pip (optional, use a virtual env)
-cd atdb_csv_gen
-pip install -r requirements.txt
-
-# or using docker
-docker-build -t ldv-atdb-csv-gen csv_gen/
+# Using pip install (requires valid ssh key, until the repo is set to public)
+pip install pip install -e "git+https://git.astron.nl/ldv/ldv_utils.git#egg=atdb-csv-gen&subdirectory=atdb_csv_gen"
```
### Running
@@ -22,21 +14,12 @@ docker-build -t ldv-atdb-csv-gen csv_gen/
# copy .env.example to .env and fill in the environment vars (DB credentials)
cp ./atdb_csv_gen/.env.example ./atdb_csv_gen/.env
-# run using pipenv
-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 atdb_csv_gen
+# run using python
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 atdb_csv_gen/.env -v $PWD/outdir:/outdir ldv-atdb-csv-gen /app/csv_gen.py -v -o /outdir/out.csv 650273
+atdb_csv_gen -v -o out.csv 650273
-# more info and flags
-docker run -it --rm ldv-atdb-csv-gen
+# More info and flags
+atdb_csv_gen -h
```
### Caveats
diff --git a/atdb_csv_gen/.env.example b/atdb_csv_gen/.env.example
index 194c3b2227682891ced96414df30291f65ecb33d..6563cfa65afa3f3178a04bb4933678a661e20a26 100644
--- a/atdb_csv_gen/.env.example
+++ b/atdb_csv_gen/.env.example
@@ -1,4 +1,4 @@
DB_USERNAME=
DB_PASSWORD=
DB_DATABASE=
-DB_HOST=sdc-db.astron.nl
\ No newline at end of file
+DB_HOST=
\ No newline at end of file
diff --git a/atdb_csv_gen/Dockerfile b/atdb_csv_gen/Dockerfile
deleted file mode 100644
index 5a2351b03643c9562ec69e0067bee1281188a27b..0000000000000000000000000000000000000000
--- a/atdb_csv_gen/Dockerfile
+++ /dev/null
@@ -1,10 +0,0 @@
-FROM python:3.10-slim
-
-RUN pip --no-cache-dir install pipenv
-
-WORKDIR /app
-COPY Pipfile* /app/
-RUN pipenv lock -r > requirements.txt && pip install -r requirements.txt
-
-COPY csv_gen.py /app/
-CMD [ "/app/csv_gen.py", "-h" ]
\ No newline at end of file
diff --git a/atdb_csv_gen/Pipfile b/atdb_csv_gen/Pipfile
deleted file mode 100644
index fdcc203c34d6efb3c1c3e9cadc7960146269bf81..0000000000000000000000000000000000000000
--- a/atdb_csv_gen/Pipfile
+++ /dev/null
@@ -1,18 +0,0 @@
-[[source]]
-url = "https://pypi.org/simple"
-verify_ssl = true
-name = "pypi"
-
-[packages]
-psycopg2-binary = "*"
-sqlalchemy = "*"
-
-[dev-packages]
-flake8 = "*"
-black = "*"
-
-[requires]
-python_version = "3.10"
-
-[pipenv]
-allow_prereleases = true
diff --git a/atdb_csv_gen/Pipfile.lock b/atdb_csv_gen/Pipfile.lock
deleted file mode 100644
index 98a2927925f5dd99b70e1769907f15b56ca46f5e..0000000000000000000000000000000000000000
--- a/atdb_csv_gen/Pipfile.lock
+++ /dev/null
@@ -1,286 +0,0 @@
-{
- "_meta": {
- "hash": {
- "sha256": "6f0f652bc369fdd2d56890d91ca935b9973a50f4d398ca19d1d456010eb804f8"
- },
- "pipfile-spec": 6,
- "requires": {
- "python_version": "3.10"
- },
- "sources": [
- {
- "name": "pypi",
- "url": "https://pypi.org/simple",
- "verify_ssl": true
- }
- ]
- },
- "default": {
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diff --git a/atdb_csv_gen/atdb_csv_gen/__init__.py b/atdb_csv_gen/atdb_csv_gen/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..81aab313eddd2f4cfe046e7c331f1968a8f8e2c7
--- /dev/null
+++ b/atdb_csv_gen/atdb_csv_gen/__init__.py
@@ -0,0 +1 @@
+from .csv_gen import gen_csv, main
\ No newline at end of file
diff --git a/atdb_csv_gen/atdb_csv_gen.py b/atdb_csv_gen/atdb_csv_gen/csv_gen.py
similarity index 71%
rename from atdb_csv_gen/atdb_csv_gen.py
rename to atdb_csv_gen/atdb_csv_gen/csv_gen.py
index 627ad3a109d7b453b1676c505f2ff3f8065a297e..8a1ad36c252e2301dfd48c0c21d0c7f125b7727b 100755
--- a/atdb_csv_gen/atdb_csv_gen.py
+++ b/atdb_csv_gen/atdb_csv_gen/csv_gen.py
@@ -3,6 +3,7 @@
import logging
import os
+import sys
from argparse import ArgumentParser, Namespace
from sys import version
from typing import Iterator, List, Optional, Tuple
@@ -22,10 +23,15 @@ logger = logging.getLogger(__name__)
def parse_args() -> Namespace:
""" Parse CLI arguments """
- 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 = ArgumentParser(description="Generates CSV for atdb_load_tasks_from_table\n"
+ "Requires the following env vars:\n"
+ "\tDB_USERNAME, DB_PASSWORD, DB_DATABASE and optionally:\n"
+ "\tDB_HOST (localhost by default) and DB_PORT (5432, postgres default)"
+ )
+ parser.add_argument("obs_id", type=str, help="Observation ID (SAS ID)")
+ parser.add_argument("-o", type=str, help="Output file")
+ parser.add_argument("--save-missing", type=str, help="Directory to store csv 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()
@@ -64,7 +70,23 @@ def write_output(csv_data: str, output: Optional[str]):
else:
print(csv_data)
-def main(obs_id: str, o_file: Optional[str]):
+def gen_csv(obs_id: str, o_file: Optional[str] = None, save_missing:Optional[str] = None):
+ """ Generate CSV file for ATDB
+
+ Parameters
+ ----------
+ obs_id : string
+ observation id
+ o_file : string, optional
+ File to write the output to (by default to stdout)
+ save_missing : string, optional
+ Directory to write missing files output to (by default only shows warnings!)
+ """
+
+ if not all([USER, PASSWORD, DATABASE, HOST, PORT]):
+ raise RuntimeError("Missing DB credentials in env vars.\n"
+ "Did you export the .env file?")
+
engine = create_engine(f"postgresql://{USER}:{PASSWORD}@{HOST}:{PORT}/{DATABASE}")
logger.debug("Connected to %s:%s", HOST, PORT)
@@ -86,6 +108,8 @@ def main(obs_id: str, o_file: Optional[str]):
logger.warning("Observation contains %i registered files which are not present on disk", len(reg_no_file))
for row in reg_no_file:
logger.warning(row)
+ if save_missing:
+ write_output("\n".join(reg_no_file), os.path.join(save_missing, "reg_no_file.csv"))
# File found, not registered
file_no_reg = cra_data.difference(reg_data)
@@ -93,6 +117,8 @@ def main(obs_id: str, o_file: Optional[str]):
logger.warning("Observation contains %i files on disk which are not registered in the LTA", len(file_no_reg))
for row in file_no_reg:
logger.warning(row)
+ if save_missing:
+ write_output("\n".join(file_no_reg), os.path.join(save_missing, "file_no_reg.csv"))
inter = reg_data.intersection(cra_data)
@@ -102,7 +128,7 @@ def main(obs_id: str, o_file: Optional[str]):
logger.info("Done")
-if __name__ == "__main__":
+def main():
args = parse_args()
if args.v:
@@ -112,4 +138,7 @@ if __name__ == "__main__":
else:
logging.basicConfig(level=logging.INFO)
- main(obs_id=args.obs_id,o_file=args.o)
+ gen_csv(obs_id=args.obs_id,o_file=args.o, save_missing=args.save_missing)
+
+if __name__ == "__main__":
+ main()
diff --git a/atdb_csv_gen/bin/atdb_csv_gen b/atdb_csv_gen/bin/atdb_csv_gen
new file mode 100644
index 0000000000000000000000000000000000000000..3d2351126093b50220d348354a42249817526087
--- /dev/null
+++ b/atdb_csv_gen/bin/atdb_csv_gen
@@ -0,0 +1,4 @@
+#!/usr/bin/env python3
+
+import atdb_csv_gen
+atdb_csv_gen.main()
\ No newline at end of file
diff --git a/atdb_csv_gen/requirements.txt b/atdb_csv_gen/requirements.txt
index 4e812e590066faf3b9840aeb6bae5701f48a065d..41d60dfb716af2546848fa88f99d90c4a543682e 100644
--- a/atdb_csv_gen/requirements.txt
+++ b/atdb_csv_gen/requirements.txt
@@ -1,11 +1,2 @@
-#
-# These requirements were autogenerated by pipenv
-# To regenerate from the project's Pipfile, run:
-#
-# pipenv lock --requirements
-#
-
--i https://pypi.org/simple
-greenlet==1.1.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-psycopg2-binary==2.9.1
-sqlalchemy==1.4.26
+psycopg2-binary>=2.9.1
+sqlalchemy>=1.4.26
diff --git a/atdb_csv_gen/setup.py b/atdb_csv_gen/setup.py
new file mode 100644
index 0000000000000000000000000000000000000000..07cc9eb3fa5f9f718ea953707cd5cf407e532ce0
--- /dev/null
+++ b/atdb_csv_gen/setup.py
@@ -0,0 +1,21 @@
+# SPDX-License-Identifier: Apache-2.0
+
+from setuptools import setup
+
+
+def get_requirements() -> str:
+ with open("requirements.txt") as reqs:
+ return reqs.read().split("\n")
+
+setup(
+ name="atdb-csv-gen",
+ version="1.0.0",
+ description="Tool to generate csv files for ATDB",
+ author="ASTRON",
+ packages=["atdb_csv_gen"],
+ install_requires=get_requirements(),
+ scripts=["bin/atdb_csv_gen"],
+ license="Apache License, Version 2.0",
+ zip=False,
+ python_requires=">=3.7"
+)