Goci 2607 tw remove bkgd trait links

trait-representation-migration/remove_background_trait_links.py

@@ -0,0 +1,213 @@
+# Activate Python venv for the script - uncomment to run script on commandline
+# activate_this_file = "/path/to/bin/activate_this.py"
+# execfile(activate_this_file, dict(__file__ = activate_this_file))
+
+import cx_Oracle
+import contextlib
+import argparse
+import sys
+from tqdm import tqdm
+import csv
+import os.path
+
+sys.path.insert(0, '/path/to/gwas_data_sources')
+import gwas_data_sources
+
+import datetime
+
+
+def read_file(filename):
+    '''
+    Read file.
+
+    Args:
+        filename: Name of file provided as a commandline argument.
+
+    Returns:
+        data_map: Dictionary with the STUDY_ID as the key and a 
+        list of EFO_IDs as the dictionary value.
+    '''
+
+    with open(filename, 'r') as file:
+        lines = file.readlines()[1:]
+
+    return lines
+
+
+def process_file_contents(file_data, efo_map, cursor):
+    '''
+    Extract fields of interest from the file and clean-up values.
+
+    Args:
+        file_data: Contents of the file.
+    '''
+
+    count = 0
+
+    for line in file_data:
+        formatted_line = line.split('\t')
+
+        study_accession = formatted_line[2].strip()
+        study_id = _get_study_id(study_accession)
+
+        background_column = formatted_line[4].strip()
+
+        delimiter = '||'
+
+        if not background_column == '':
+            count += 1
+            # print('\nCount: {} StudyID: {} Accession: {}'.format(count, study_id, study_accession))
+
+            if delimiter in background_column:
+                background_column = background_column.split(delimiter)
+
+                for background_trait in background_column:
+                    # Get the EFO_ID
+                    background_trait_id = efo_map[background_trait.strip().lower()]
+                    # print('TID: {}'.format(background_trait_id))
+                    _execute_delete_query(cursor, study_id, background_trait_id)
+            else:
+                # Get the EFO_ID
+                background_trait_id = efo_map[background_column.strip().lower()]
+                # print('TID: {}'.format(background_trait_id))
+                _execute_delete_query(cursor, study_id, background_trait_id)
+
+
+def database_connection(DATABASE_NAME):
+    '''
+    Connect to the database and returns a cursor object.
+
+    Args:
+        database_name (str): The name of the database.
+
+    Raises:
+        DatabaseError: Error reponse if unable to connect to the database.
+
+    Returns:
+        cursor: Database cursor object.
+    '''
+
+    try:
+        ip, port, sid, username, password = gwas_data_sources.get_db_properties(DATABASE_NAME)
+        dsn_tns = cx_Oracle.makedsn(ip, port, sid)
+        connection = cx_Oracle.connect(username, password, dsn_tns)
+
+        cursor = connection.cursor()
+
+        return connection, cursor
+
+    except cx_Oracle.DatabaseError, exception:
+        print exception
+
+
+def get_efo_id_map(cursor):
+    '''
+    Get mapping of term labels to EFO IDs. 
+
+    Args: 
+        cursor (object): Database cursor object.
+
+
+    Returns:
+        efo_map: A mapping of term labels to it's EFO ID
+    '''
+    efo_map = {}
+
+    efo_sql = '''
+        SELECT ID, LOWER(TRAIT)
+        FROM EFO_TRAIT
+    '''
+
+    cursor.execute(efo_sql)
+    efo_data = cursor.fetchall()
+
+    for row in tqdm(efo_data, desc='Build EFO map'):
+        # Key is Trait, Value is ID
+        efo_map[row[1]] = row[0]
+
+    return efo_map
+
+
+def _get_study_id(accession):
+    '''
+    Query the STUDY table with the accession to get the Study ID.
+
+    Args: 
+        accession (str): study accession parsed from input file
+
+    Returns:
+        study_id (int): STUDY.ID, the primary key for the row with the study accession.
+    '''
+
+    study_sql = '''
+        SELECT ID
+        FROM STUDY
+        WHERE ACCESSION_ID = '{}'
+    '''.format(accession)
+
+    cursor.execute(study_sql)
+    study_id = cursor.fetchone()
+
+    return study_id[0]
+
+
+
+def _execute_delete_query(cursor, study_id, efo_trait_id):
+    '''
+    Delete row from STUDY_EFO_TRAIT table.
+
+    Args: 
+        query (str): The query to run.
+
+    Raises:
+    '''
+
+    study_efo_trait_delete_sql = '''
+        DELETE FROM STUDY_EFO_TRAIT
+        WHERE STUDY_ID = '{}' AND EFO_TRAIT_ID = '{}'
+    '''.format(study_id, efo_trait_id)
+
+    cursor.execute(study_efo_trait_delete_sql)
+
+    # commit or rollback changes
+    if args.mode == 'production':
+        cursor.execute('COMMIT')
+    else:
+        cursor.execute('ROLLBACK')
+
+
+if __name__ == '__main__':
+    '''
+    Remove background trait link to Studies.
+    '''
+
+    # Commandline arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--filename', default='study_background_traits-ALL.txt', 
+                        help='Name of data file (default: study_background_traits).')
+    parser.add_argument('--database', default='DEV3', choices=['DEV3', 'SPOTPRO'], 
+                        help='Run as (default: DEV3).')
+    parser.add_argument('--mode', default='debug', choices=['debug', 'production'], 
+                        help='Run as (default: debug).')
+    args = parser.parse_args()
+
+    global DATABASE_NAME
+    DATABASE_NAME = args.database
+
+    # Get database connection
+    conn, cursor = database_connection(args.database)
+
+    # Create map of Trait labels and EFO_IDs
+    efo_map = get_efo_id_map(cursor)
+
+    # Read data file
+    data = read_file(args.filename)
+
+    # Format column values and remove STUDY_EFO_TRAIT link
+    process_file_contents(data, efo_map, cursor)
+
+    # Close database connection
+    conn.close()
+
+
+