diff save_to_db.py @ 0:034686b5bc15 draft

planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/save_to_db.py	Thu Apr 24 09:56:36 2025 +0000
@@ -0,0 +1,195 @@
+import subprocess
+import time
+import argparse
+import socket
+import os
+import re
+import pandas as pd
+from sqlalchemy import create_engine, inspect
+from sqlalchemy.sql import text
+from sqlalchemy.engine.url import make_url
+from sqlalchemy.exc import OperationalError
+
+def fix_db_uri(uri):
+    """Replace __at__ with @ in the URI if needed."""
+    return uri.replace("__at__", "@")
+
+def is_port_in_use(port):
+    """Check if a TCP port is already in use on localhost."""
+    with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+        return s.connect_ex(('localhost', port)) == 0
+
+def extract_db_name(uri):
+    """Extract the database name from the SQLAlchemy URI."""
+    url = make_url(uri)
+    return url.database
+
+def start_postgres_container(db_name):
+    """Start a PostgreSQL container with the given database name as the container name."""
+    container_name = db_name
+
+    # Check if container is already running
+    container_running = subprocess.run(
+        f"docker ps -q -f name={container_name}", shell=True, capture_output=True, text=True
+    )
+
+    if container_running.stdout.strip():
+        print(f"Container '{container_name}' is already running.")
+        return  
+
+    # Check if container exists (stopped)
+    container_exists = subprocess.run(
+        f"docker ps -a -q -f name={container_name}", shell=True, capture_output=True, text=True
+    )
+
+    if container_exists.stdout.strip():
+        print(f"Starting existing container '{container_name}'...")
+        subprocess.run(f"docker start {container_name}", shell=True)
+        print(f"PostgreSQL Docker container '{container_name}' activated.")
+        return  
+
+    # If container does not exist, create and start a new one
+    port = 5432 if not is_port_in_use(5432) else 5433
+    postgres_password = os.getenv("POSTGRES_PASSWORD", "RK17")
+
+    start_command = [
+        "docker", "run", "--name", container_name,
+        "-e", f"POSTGRES_PASSWORD={postgres_password}",
+        "-p", f"{port}:5432",
+        "-d", "postgres"
+    ]
+
+    try:
+        subprocess.run(start_command, check=True)
+        print(f"PostgreSQL Docker container '{container_name}' started on port {port}.")
+    except subprocess.CalledProcessError as e:
+        print(f"Failed to start Docker container: {e}")
+
+def wait_for_db(uri, timeout=60):
+    """Try connecting to the DB until it works or timeout."""
+    engine = create_engine(uri)
+    start_time = time.time()
+    while time.time() - start_time < timeout:
+        try:
+            with engine.connect():
+                print("Connected to database.")
+                return
+        except OperationalError:
+            print("Database not ready, retrying...")
+            time.sleep(2)
+    raise Exception("Database connection failed after timeout.")
+
+def push_gb_annotations(gb_files, sequence_column, annotation_column, db_uri, table_name, fragment_column_name, output, file_name_mapping):
+    """Push GenBank file content into the database if the fragment is not already present."""
+    db_uri = fix_db_uri(db_uri)
+    engine = create_engine(db_uri)
+    inserted_fragments = []
+
+    try:
+        # Parse the file_name_mapping string into a dictionary {base_file_name: fragment_name}
+        file_name_mapping_dict = {
+            os.path.basename(path): os.path.splitext(fragment_name)[0]
+            for mapping in file_name_mapping.split(",")
+            for path, fragment_name in [mapping.split(":")]
+        }
+
+        #print("File name mapping dictionary:")
+        #print(file_name_mapping_dict)  # Debugging: Print the mapping dictionary
+
+        with engine.begin() as connection:
+            inspector = inspect(engine)
+            columns = [col['name'] for col in inspector.get_columns(table_name)]
+
+            if fragment_column_name not in columns:
+                raise ValueError(f"Fragment column '{fragment_column_name}' not found in table '{table_name}'.")
+
+            # Get existing fragments
+            all_rows = connection.execute(text(f"SELECT {fragment_column_name} FROM {table_name}")).fetchall()
+            existing_fragments = {row[0] for row in all_rows}
+
+            insert_rows = []
+
+            for gb_file in gb_files:
+                # Extract base file name (just the file name, not the full path)
+                real_file_name = os.path.basename(gb_file)
+
+                print(f"Processing file: {real_file_name}")  # Debugging: Log the current file
+
+                # Get the corresponding fragment name from the mapping
+                fragment_name = file_name_mapping_dict.get(real_file_name)
+
+                if not fragment_name:
+                    raise ValueError(f"Fragment name not found for file '{real_file_name}' in file_name_mapping.")
+
+                # If the fragment is already in the DB, raise an error and stop the process
+                if fragment_name in existing_fragments:
+                    raise RuntimeError(f"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.")
+
+                with open(gb_file, "r") as f:
+                    content = f.read()
+
+                origin_match = re.search(r"^ORIGIN.*$", content, flags=re.MULTILINE)
+                if not origin_match:
+                    raise ValueError(f"ORIGIN section not found in file: {gb_file}")
+
+                origin_start = origin_match.start()
+                annotation_text = content[:origin_start].strip()
+                sequence_text = content[origin_start:].strip()
+
+                values = {}
+                values[fragment_column_name] = fragment_name
+                values[annotation_column] = annotation_text
+                values[sequence_column] = sequence_text
+
+                insert_rows.append(values)
+                inserted_fragments.append(fragment_name)
+
+            # Insert the rows into the database
+            for values in insert_rows:
+                col_names = ", ".join(values.keys())
+                placeholders = ", ".join([f":{key}" for key in values.keys()])
+                insert_stmt = text(f"INSERT INTO {table_name} ({col_names}) VALUES ({placeholders})")
+
+                #print(f"Inserting into DB: {values}")  # Debugging print statement
+                result = connection.execute(insert_stmt, values)
+
+                #print(f"Insert result: {result.rowcount if hasattr(result, 'rowcount') else 'N/A'}")  # Debugging the row count
+
+            print(f"Inserted {len(insert_rows)} fragments.")
+
+            # Write inserted fragment names to a text file
+            with open(output, "w") as log_file:
+                for frag in inserted_fragments:
+                    log_file.write(f"{frag}\n")
+            print(f"Fragment names written to '{output}'.")
+
+    except Exception as e:
+        print(f"Error during GB file insertion: {e}")
+        raise
+
+def main():
+    parser = argparse.ArgumentParser(description="Fetch annotations from PostgreSQL database and save as JSON.")
+    parser.add_argument("--input", required=True, help="Input gb files")
+    parser.add_argument("--sequence_column", required=True, help="DB column contains sequence for ganbank file")
+    parser.add_argument("--annotation_column", required=True, help="DB column contains head for ganbank file")
+    parser.add_argument("--db_uri", required=True, help="Database URI connection string")
+    parser.add_argument("--table", required=True, help="Table name in the database")
+    parser.add_argument("--fragment_column", required=True, help="Fragment column name in the database")
+    parser.add_argument("--output", required=True, help="Text report")
+    parser.add_argument("--file_name_mapping", required=True, help="real fragments names")
+    args = parser.parse_args()
+
+    # Start the Docker container (if not already running)
+    gb_file_list = [f.strip() for f in args.input.split(",") if f.strip()]
+    db_uri = fix_db_uri(args.db_uri)
+    db_name = extract_db_name(db_uri)
+    start_postgres_container(db_name)
+
+    # Wait until the database is ready
+    wait_for_db(db_uri)
+
+    # Fetch annotations from the database and save as gb
+    push_gb_annotations(gb_file_list, args.sequence_column, args.annotation_column, db_uri, args.table, args.fragment_column, args.output, args.file_name_mapping)
+
+if __name__ == "__main__":
+    main()