refactor: arguments

Author: rmfranken

.gitignore

@@ -33,3 +33,6 @@
 
 # Python cache
 __pycache__/
+
+# Generated turtle files
+*.ttl

justfile

@@ -57,7 +57,8 @@ test *args:
 
 # Run an executable.
 run *args:
-    uv run --env-file=.env cli "$@"
+    # uv run --env-file=.env cli "$@"
+    uv run --env-file=.env cli2 "$@"
 
 # Run the Jupyter notebook.
 notebook *args:

pyproject.toml

@@ -23,6 +23,7 @@ dev = [
 
 [project.scripts]
 cli = 'strings2things.cli:main'
+cli2 = 'strings2things.cli2:main'
 
 [build-system]
 requires = ["hatchling"]

src/strings2things/cli2.py

@@ -2,7 +2,7 @@
 import glob
 import argparse
 import rdflib
-from config import args
+from strings2things.config import args
 from strings2things.sparql import (
     strings_to_things_query,
     things_to_strings_query
@@ -36,7 +36,7 @@ def initialize_graphs(ontology_path, kg_path, ontology_uri, kg_uri):
     return dataset
 
 
-def strings_to_things(dataset, output_file="subgraph.ttl"):
+def strings_to_things(dataset, output_file=args.output):
     """
     Replace human-readable strings in the KG with ontology IRIs based on matches.
     """
@@ -50,7 +50,7 @@ def strings_to_things(dataset, output_file="subgraph.ttl"):
     print(f"Strings replaced with IRIs and written to {output_file} ({len(new_graph)} triples).")
 
 
-def things_to_strings(dataset, output_file="output.ttl"):
+def things_to_strings(dataset, output_file=args.output):
     """
     Replace IRIs in the KG with human-readable labels using the ontology.
     """
@@ -65,14 +65,6 @@ def things_to_strings(dataset, output_file="output.ttl"):
 
 
 def main():
-    parser = argparse.ArgumentParser(description="Convert between strings and ontology terms.")
-    parser.add_argument("direction", choices=["string2thing", "thing2string"], help="Conversion direction")
-    parser.add_argument("--ontology", required=True, help="Path to ontology files directory")
-    parser.add_argument("--kg", required=True, help="Path to knowledge graph files directory")
-    parser.add_argument("--ontology-uri", default="https://imaging-plaza.epfl.ch/ontology#", help="Named graph URI for ontology")
-    parser.add_argument("--kg-uri", default="https://imaging-plaza.epfl.ch/finalGraph", help="Named graph URI for knowledge graph")
-    args = parser.parse_args()
-
     dataset = initialize_graphs(args.ontology, args.kg, args.ontology_uri, args.kg_uri)
 
     if args.direction == "string2thing":

src/strings2things/config.py

@@ -6,4 +6,5 @@
 parser.add_argument("--kg", required=True, help="Path to knowledge graph files directory")
 parser.add_argument("--ontology-uri", default="https://imaging-plaza.epfl.ch/ontology#", help="Named graph URI for ontology")
 parser.add_argument("--kg-uri", default="https://imaging-plaza.epfl.ch/finalGraph", help="Named graph URI for knowledge graph")
+parser.add_argument("-o", "--output", default="output.ttl", help="Output file for the converted graph")
 args = parser.parse_args()

src/strings2things/sparql.py

@@ -1,6 +1,5 @@
-import os
 from dotenv import load_dotenv
-from config import args
+from strings2things.config import args
 
 # Load environment variables from the .env file
 load_dotenv()