Merge pull request #11 from aledlie/main

refactor: replace manual argv parsing with argparse

scientific-skills/uniprot-database/scripts/uniprot_client.py

@@ -22,6 +22,7 @@ Usage examples:
 """
 
 import requests
+import sys
 import time
 import json
 from typing import List, Dict, Optional, Generator
@@ -229,28 +230,112 @@ def get_id_mapping_databases() -> Dict:
     return response.json()
 
 
-# Example usage
+def main():
-if __name__ == "__main__":
+    """Command-line interface for UniProt database queries."""
-    # Example 1: Search for human insulin proteins
+    import argparse
-    print("Searching for human insulin proteins...")
-    results = search_proteins(
-        "insulin AND organism_name:human AND reviewed:true",
-        format="json",
-        fields=["accession", "id", "gene_names", "protein_name"],
-        size=5
-    )
-    print(json.dumps(results, indent=2))
 
-    # Example 2: Get a specific protein in FASTA format
+    parser = argparse.ArgumentParser(
-    print("\nRetrieving protein P01308 (human insulin)...")
+        description='Query UniProt database using REST API',
-    protein = get_protein("P01308", format="fasta")
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  # Search for proteins
+  %(prog)s --search "insulin AND organism_name:human" --format json
+
+  # Get a specific protein
+  %(prog)s --get P01308 --format fasta
+
+  # Map IDs from UniProt to PDB
+  %(prog)s --map P01308,P04637 --from UniProtKB_AC-ID --to PDB
+
+  # Stream large results
+  %(prog)s --stream "taxonomy_id:9606 AND reviewed:true" --format fasta
+
+  # List available fields
+  %(prog)s --list-fields
+
+  # List mapping databases
+  %(prog)s --list-databases
+        """
+    )
+
+    # Main operation arguments (mutually exclusive)
+    group = parser.add_mutually_exclusive_group(required=True)
+    group.add_argument('--search', '-s', help='Search query string')
+    group.add_argument('--get', '-g', help='Get protein by accession number')
+    group.add_argument('--map', '-m', help='Map IDs (comma-separated)')
+    group.add_argument('--stream', help='Stream large result sets')
+    group.add_argument('--list-fields', action='store_true',
+                      help='List all available query fields')
+    group.add_argument('--list-databases', action='store_true',
+                      help='List all ID mapping databases')
+
+    # Format options
+    parser.add_argument('--format', '-f', default='json',
+                       help='Output format (json, tsv, xlsx, xml, fasta, txt, rdf)')
+
+    # Search-specific options
+    parser.add_argument('--fields', help='Comma-separated list of fields to return')
+    parser.add_argument('--size', type=int, default=25,
+                       help='Number of results (default: 25, max: 500)')
+
+    # Mapping-specific options
+    parser.add_argument('--from', dest='from_db',
+                       help='Source database for ID mapping')
+    parser.add_argument('--to', dest='to_db',
+                       help='Target database for ID mapping')
+
+    args = parser.parse_args()
+
+    try:
+        if args.list_fields:
+            fields = get_available_fields()
+            print(json.dumps(fields, indent=2))
+
+        elif args.list_databases:
+            databases = get_id_mapping_databases()
+            print(json.dumps(databases, indent=2))
+
+        elif args.search:
+            fields_list = args.fields.split(',') if args.fields else None
+            results = search_proteins(
+                args.search,
+                format=args.format,
+                fields=fields_list,
+                size=args.size
+            )
+            if args.format == 'json':
+                print(json.dumps(results, indent=2))
+            else:
+                print(results)
+
+        elif args.get:
+            protein = get_protein(args.get, format=args.format)
+            if args.format == 'json':
+                print(json.dumps(protein, indent=2))
+            else:
                 print(protein)
 
-    # Example 3: Map UniProt IDs to PDB IDs
+        elif args.map:
-    print("\nMapping UniProt IDs to PDB...")
+            if not args.from_db or not args.to_db:
-    mapping = map_ids(
+                parser.error("--map requires --from and --to arguments")
-        ["P01308", "P04637"],
+
-        from_db="UniProtKB_AC-ID",
+            ids = [id.strip() for id in args.map.split(',')]
-        to_db="PDB"
+            mapping = map_ids(ids, args.from_db, args.to_db, format=args.format)
-    )
+            if args.format == 'json':
                 print(json.dumps(mapping, indent=2))
+            else:
+                print(mapping)
+
+        elif args.stream:
+            fields_list = args.fields.split(',') if args.fields else None
+            for chunk in stream_results(args.stream, format=args.format, fields=fields_list):
+                print(chunk, end='')
+
+    except Exception as e:
+        print(f"Error: {e}", file=sys.stderr)
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()

scientific-skills/uspto-database/scripts/peds_client.py

@@ -213,30 +213,62 @@ class PEDSHelper:
 
 def main():
     """Command-line interface for PEDS data."""
-    if len(sys.argv) < 2:
+    import argparse
-        print("Usage:")
+
-        print("  python peds_client.py <application_number>")
+    parser = argparse.ArgumentParser(
-        print("  python peds_client.py --patent <patent_number>")
+        description='Query USPTO Patent Examination Data System (PEDS)',
-        print("  python peds_client.py --status <application_number>")
+        formatter_class=argparse.RawDescriptionHelpFormatter,
-        print("  python peds_client.py --analyze <application_number>")
+        epilog="""
-        sys.exit(1)
+Examples:
+  # Get application data by application number
+  %(prog)s --application 16123456
+
+  # Get patent data by patent number
+  %(prog)s --patent 11234567
+
+  # Get status summary
+  %(prog)s --status 16123456
+
+  # Analyze prosecution history
+  %(prog)s --analyze 16123456
+
+  # Get transaction history
+  %(prog)s --transactions 16123456
+
+  # Get office actions
+  %(prog)s --office-actions 16123456
+        """
+    )
 
     if not HAS_USPTO_LIB:
-        print("Error: uspto-opendata-python library not installed")
+        parser.error("uspto-opendata-python library not installed. Install with: pip install uspto-opendata-python")
-        print("Install with: pip install uspto-opendata-python")
-        sys.exit(1)
 
-    helper = PEDSHelper()
+    # Main operation arguments (mutually exclusive)
+    group = parser.add_mutually_exclusive_group(required=True)
+    group.add_argument('--application', '-a', help='Get application by application number')
+    group.add_argument('--patent', '-p', help='Get patent by patent number')
+    group.add_argument('--status', '-s', help='Get status summary for application')
+    group.add_argument('--analyze', help='Analyze prosecution history for application')
+    group.add_argument('--transactions', '-t', help='Get transaction history for application')
+    group.add_argument('--office-actions', '-o', help='Get office actions for application')
+
+    args = parser.parse_args()
 
     try:
-        if sys.argv[1] == "--patent":
+        helper = PEDSHelper()
-            result = helper.get_patent(sys.argv[2])
+
-        elif sys.argv[1] == "--status":
+        if args.application:
-            result = helper.get_status_summary(sys.argv[2])
+            result = helper.get_application(args.application)
-        elif sys.argv[1] == "--analyze":
+        elif args.patent:
-            result = helper.analyze_prosecution(sys.argv[2])
+            result = helper.get_patent(args.patent)
-        else:
+        elif args.status:
-            result = helper.get_application(sys.argv[1])
+            result = helper.get_status_summary(args.status)
+        elif args.analyze:
+            result = helper.analyze_prosecution(args.analyze)
+        elif args.transactions:
+            result = helper.get_transaction_history(args.transactions)
+        elif args.office_actions:
+            result = helper.get_office_actions(args.office_actions)
 
         if result:
             print(json.dumps(result, indent=2))

scientific-skills/uspto-database/scripts/trademark_client.py

@@ -225,35 +225,83 @@ class TrademarkClient:
 
 def main():
     """Command-line interface for trademark search."""
-    if len(sys.argv) < 2:
+    import argparse
-        print("Usage:")
-        print("  python trademark_client.py <serial_or_registration_number>")
-        print("  python trademark_client.py --status <number>")
-        print("  python trademark_client.py --health <number>")
-        print("  python trademark_client.py --goods <number>")
-        sys.exit(1)
 
-    client = TrademarkClient()
+    parser = argparse.ArgumentParser(
+        description='Query USPTO Trademark Status & Document Retrieval (TSDR) API',
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  # Get trademark by serial number
+  %(prog)s --serial 87654321
+
+  # Get trademark by registration number
+  %(prog)s --registration 5678901
+
+  # Get status summary
+  %(prog)s --status 87654321
+
+  # Check trademark health
+  %(prog)s --health 87654321
+
+  # Get goods and services
+  %(prog)s --goods 87654321
+
+  # Get owner information
+  %(prog)s --owner 87654321
+
+  # Get prosecution history
+  %(prog)s --prosecution 87654321
+
+Environment:
+  Set USPTO_API_KEY environment variable with your API key from:
+  https://account.uspto.gov/api-manager/
+        """
+    )
+
+    # Main operation arguments (mutually exclusive)
+    group = parser.add_mutually_exclusive_group(required=True)
+    group.add_argument('--serial', '-s', help='Get trademark by serial number')
+    group.add_argument('--registration', '-r', help='Get trademark by registration number')
+    group.add_argument('--status', help='Get status summary (serial or registration number)')
+    group.add_argument('--health', help='Check trademark health (serial or registration number)')
+    group.add_argument('--goods', '-g', help='Get goods and services (serial or registration number)')
+    group.add_argument('--owner', '-o', help='Get owner information (serial or registration number)')
+    group.add_argument('--prosecution', '-p', help='Get prosecution history (serial or registration number)')
+
+    # API key option
+    parser.add_argument('--api-key', '-k', help='USPTO API key (overrides USPTO_API_KEY env var)')
+
+    args = parser.parse_args()
 
     try:
-        if sys.argv[1] == "--status":
+        client = TrademarkClient(api_key=args.api_key)
-            result = client.get_trademark_status(sys.argv[2])
+
-        elif sys.argv[1] == "--health":
+        if args.serial:
-            result = client.check_trademark_health(sys.argv[2])
+            result = client.get_trademark_by_serial(args.serial)
-        elif sys.argv[1] == "--goods":
+        elif args.registration:
-            result = client.get_goods_and_services(sys.argv[2])
+            result = client.get_trademark_by_registration(args.registration)
-        else:
+        elif args.status:
-            # Get full trademark data
+            result = client.get_trademark_status(args.status)
-            result = client.get_trademark_by_serial(sys.argv[1])
+        elif args.health:
-            if not result:
+            result = client.check_trademark_health(args.health)
-                result = client.get_trademark_by_registration(sys.argv[1])
+        elif args.goods:
+            result = client.get_goods_and_services(args.goods)
+        elif args.owner:
+            result = client.get_owner_info(args.owner)
+        elif args.prosecution:
+            result = client.get_prosecution_history(args.prosecution)
 
         if result:
             print(json.dumps(result, indent=2))
         else:
-            print(f"Trademark {sys.argv[1]} not found", file=sys.stderr)
+            number = (args.serial or args.registration or args.status or
+                     args.health or args.goods or args.owner or args.prosecution)
+            print(f"Trademark {number} not found", file=sys.stderr)
             sys.exit(1)
 
+    except ValueError as e:
+        parser.error(str(e))
     except Exception as e:
         print(f"Error: {e}", file=sys.stderr)
         sys.exit(1)