TUTORIAL

Create MySQL database

First create a database (f.e. test) as root/admin (mysql -u root -p):

CREATE DATABASE test;
GRANT ALL PRIVILEGES ON test.* TO 'giovanni'@'localhost';
FLUSH PRIVILEGES;

then, as a user, use this code (in bash):

cd tests/data/example/sql/
cat allowed_values.sql subjects.sql protocols.sql sessions.sql runs.sql channels.sql electrodes.sql recordings.sql files.sql extra_sessions.sql extra_runs.sql extra_recordings.sql > full.sql
mysql -u giovanni -p test' < full.sql

Connect to the database

To connect to the database, you need to specify the DATABASE_NAME, the MySQL USERNAME and the MySQL PASSWORD.

from xelo2.database import access_database
db = access_database(DATABASE_NAME, USERNAME)

You’ll be prompted for the password.

Open the connection to the MySQL server

If the MySQL database is not stored in the local machine, you need to forward the local port of the remote database:

ssh -L 3306:localhost:3306 -o ServerAliveInterval=240 user@remote

Another option (if allowed by the mysql server) is to add the host (HOSTNAME) to the command:

from xelo2.database import access_database
db = access_database(DATABASE_NAME, USERNAME, HOSTNAME)

Look up MRI files for one subject

Here you can look up one of the files associated with the T1 of one subject. Specify the subject code in the SUBJECT_CODE as a string.

from xelo2.bids.root import prepare_subset
from xelo2.api import Subject, Run

subj = Subject(db, code=SUBJECT_CODE)

main_search = f"`runs`.`task_name` = 't1_anatomy_scan' AND `subjects`.`id` = {subj.id}"
subset = prepare_subset(db, main_search)

for run_id in subset['runs']:
    run = Run(db, run_id)
    recs = run.list_recordings()
    if len(recs) == 0:
        print('no recordings for this run')
        
    rec = recs[0]
    files = rec.list_files()
    if len(files) == 0:
        print('no files for this run')
    
    file = files[0]
    print(file.path)