diff --git a/.github/workflows/flake8_python_linter.yml b/.github/workflows/flake8_python_linter.yml
index 03f1e1344..8814adc3c 100644
--- a/.github/workflows/flake8_python_linter.yml
+++ b/.github/workflows/flake8_python_linter.yml
@@ -7,36 +7,32 @@ name: Flake8 Linter
 on: pull_request
 
 jobs:
-  
+
   flake8-lint:
     runs-on: ubuntu-latest
-    
+
     steps:
       - name: Check out source repository
         uses: actions/checkout@v2
-      
+
       - name: Set up Python environment
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
-      
+          python-version: "3.11"
+
       - name: Flake8 Lint
         uses: reviewdog/action-flake8@v3
         with:
           # For more flake 8 arguments, visit the link below:
           # https://flake8.pycqa.org/en/latest/user/options.html
           # Currently, flake8 ignores the following;
-          #     W291: Trailing whitespace
-          #     W292: No newline at end of file
-          #     W293: Blank line contains whitespace
           #     E202: Whitespace before ')'
           #     E203: Whitespace before ':'
           #     E221: Multiple spaces before operator
           #     E241: Multiple spaces after ','
           #     E251: Unexpected spaces around keyword / parameter equals
           #     E272: Multiple spaces before keyword
-          flake8_args: "--ignore=W291,W292,W293,W503,E202,E203,E221,E241,E251,E272,E126,E131,E121,E111,E114,E127
+          flake8_args: "--ignore=W503,E202,E203,E221,E241,E251,E272,E126,E131,E121,E111,E114,E127
                         --max-line-length 120
                         --exclude python/react-series-data-viewer/protocol_buffers/"
           github_token: ${{ secrets.GITHUB_TOKEN }}
-
diff --git a/README.md b/README.md
index 49f6ecd2b..05aec1786 100644
--- a/README.md
+++ b/README.md
@@ -3,22 +3,22 @@ This Readme covers release 26.0.* of the LORIS Imaging Insertion Pipeline for Ub
 This repo accompanies the [LORIS neuroimaging data platform main repo](https://github.com/aces/Loris/releases)</b>, release 24.1.*.<br>
 For documentation and detailed setup information, please see the [LORIS-MRI documentation](docs/) for your installed version</b>.
 
-This repo can be installed on the same VM as the main LORIS codebase, or on a different machine such as a designated fileserver where large imaging filesets are to be stored. 
+This repo can be installed on the same VM as the main LORIS codebase, or on a different machine such as a designated fileserver where large imaging filesets are to be stored.
 
 # System Requirements
 
 * Perl
-* Python 3 with pip3 and virtualenv (step 2 below)
+* Python 3.11 with pip3 and venv (step 2 below)
 * MINC toolkit (step 3 below)
 * DICOM toolkit (step 4 below)
 * tpcclib (for HRRT PET only) (step 5 below)
 
-On <u>Ubuntu</u>, DICOM toolkit will be installed by the imaging install script (step 4 below). This script will _apt-get install dcmtk_.   
+On <u>Ubuntu</u>, DICOM toolkit will be installed by the imaging install script (step 4 below). This script will _apt-get install dcmtk_.
 
 For <u>CentOS</u>: The [LORIS wiki](https://github.com/aces/Loris/wiki/Imaging-Database) Imaging setup page (see Section 1, installing codebase) includes links to older transcripts for [CentOS installation](https://github.com/aces/Loris/wiki/CentOS-Imaging-installation-transcript) and notes on dependencies including [DICOM toolkit](https://github.com/aces/Loris/wiki/CentOS-Imaging-installation-transcript#7-install-dicom-toolkit).
 
 The following installation should be run by the `$lorisadmin` user. `sudo` permission is required.
-See [aces/Loris](https://github.com/aces/loris) README.md for further information. 
+See [aces/Loris](https://github.com/aces/loris) README.md for further information.
 
 # Dependencies
 
@@ -54,21 +54,19 @@ sudo chown -R lorisadmin:lorisadmin /opt/$projectname
 cd /opt/$projectname/bin
 ```
 
-Get the code: Download the latest release from the 
-[releases page](https://github.com/aces/Loris-MRI/releases) 
+Get the code: Download the latest release from the
+[releases page](https://github.com/aces/Loris-MRI/releases)
 and extract it to `/opt/$projectname/bin/mri`
 
-#### 2. Install Python 3 with `pip` and `virtualenv`
+#### 2. Install Python 3.11 with `pip` and `venv`
 
 ```bash
-sudo apt install python3 
-sudo apt install python3-dev
+sudo apt install python3.11 python3.11-dev python3.11-venv
 sudo apt install python3-pip
 sudo apt install libmysqlclient-dev
-sudo apt install virtualenv
 ```
 
-#### 3. Install MINC toolkit from http://bic-mni.github.io/ 
+#### 3. Install MINC toolkit from http://bic-mni.github.io/
 
 - Install MINC dependencies:
 
@@ -82,7 +80,7 @@ sudo apt-get install libgl1-mesa-glx libglu1-mesa
 
 - Download the MINC pre-compiled package for your operating system from http://bic-mni.github.io/.
 
-- Then install the MINC toolkit package: 
+- Then install the MINC toolkit package:
 
 ```bash
 # main minc lib
@@ -112,31 +110,31 @@ sudo dpkg -i beast-library-<version>.deb
 
 #### 4. Run installer to set up directories, configure environment, install Perl libraries and DICOM toolkit:
 
-```bash 
+```bash
 cd /opt/$projectname/bin/mri/install/
 bash ./imaging_install.sh
 ```
 
-You will be asked for the following input: 
+You will be asked for the following input:
 
 * What is the database name? $dbname
 * What is the database host? $dbhost
 * What is the MySQL user? $lorisuser [Use the same mysql user from the Loris installation, i.e. _lorisuser_]
-* What is the MySQL password? 
+* What is the MySQL password?
 * What is the Linux user which the installation will be based on? $lorisadmin
 * What is the project name? $projectname
-* What is your email address? 
+* What is your email address?
 * What prod file name would you like to use? default: prod  [leave blank]
 
-If the imaging install script reports errors in creating directories 
-(due to `/data/` mount permissions), review and manually execute 
-`mkdir/chmod/chown` commands starting at 
+If the imaging install script reports errors in creating directories
+(due to `/data/` mount permissions), review and manually execute
+`mkdir/chmod/chown` commands starting at
 [imaging_install.sh:L97](https://github.com/aces/Loris-MRI/blob/main/install/imaging_install.sh#L97)
 
-Note: The installer will allow Apache to write to the `/data/` and `/opt/` directories by 
-adding user `lorisadmin` to the Apache linux group.  To ensure this change takes 
-effect, log out and log back into your terminal session before running the 
-imaging pipeline. The installer will also set Apache group ownership of certain 
+Note: The installer will allow Apache to write to the `/data/` and `/opt/` directories by
+adding user `lorisadmin` to the Apache linux group.  To ensure this change takes
+effect, log out and log back into your terminal session before running the
+imaging pipeline. The installer will also set Apache group ownership of certain
 `/data/` and `/opt/` subdirectories.
 
 #### 5. HRRT PET
@@ -157,7 +155,7 @@ Then source the `.bashrc` file.
 
 **INSTALLATION COMPLETE!**
 
-Please refer to the [Install](docs/02-Install.md) section in the 
+Please refer to the [Install](docs/02-Install.md) section in the
 [LORIS-MRI documentation](docs/) for your installed version for:
 - customizations and protocol configurations ([Section 2.2](docs/02-Install.md#configuration)).
 - verifying that certain fields were correctly populated by `imaging_install.sh`
diff --git a/install/imaging_install.sh b/install/imaging_install.sh
index fbaa7c1c5..adeee58af 100755
--- a/install/imaging_install.sh
+++ b/install/imaging_install.sh
@@ -115,7 +115,7 @@ echo
 echo "Creating loris-mri Python virtualenv in $mridir/python_virtualenvs/loris-mri-python/"
 # create a directory in $mridir that will store python 3 virtualenv
 sudo -S su $USER -c "mkdir -m 770 -p $mridir/python_virtualenvs/loris-mri-python"
-virtualenv $mridir/python_virtualenvs/loris-mri-python -p `which python3`
+python3.11 -m venv $mridir/python_virtualenvs/loris-mri-python
 source $mridir/python_virtualenvs/loris-mri-python/bin/activate
 echo "Installing the Python libraries into the loris-mri virtualenv..."
 pip3 install -r "$mridir/python/requirements.txt"
diff --git a/python/bids_import.py b/python/bids_import.py
index 5f3e73a9f..379aa4c6a 100755
--- a/python/bids_import.py
+++ b/python/bids_import.py
@@ -10,12 +10,12 @@
 import lib.exitcode
 import lib.utilities
 import lib.physiological
-from lib.database   import Database
-from lib.candidate  import Candidate
+from lib.database_lib import Database
+from lib.candidate import Candidate
 from lib.bidsreader import BidsReader
-from lib.session    import Session
-from lib.eeg        import Eeg
-from lib.mri        import Mri
+from lib.session import Session
+from lib.eeg import Eeg
+from lib.mri import Mri
 from lib.database_lib.config import Config
 
 __license__ = "GPLv3"
diff --git a/python/extract_eeg_bids_archive.py b/python/extract_eeg_bids_archive.py
index a5724c624..97a485647 100755
--- a/python/extract_eeg_bids_archive.py
+++ b/python/extract_eeg_bids_archive.py
@@ -7,7 +7,7 @@
 import re
 from lib.lorisgetopt import LorisGetOpt
 from lib.imaging_io import ImagingIO
-from lib.database import Database
+from lib.database_lib import Database
 from lib.database_lib.config import Config
 from lib.exitcode import SUCCESS, BAD_CONFIG_SETTING
 from lib.log import Log
diff --git a/python/ingest_eeg_bids_datasets.py b/python/ingest_eeg_bids_datasets.py
index e62e78d0c..a3922fbb6 100755
--- a/python/ingest_eeg_bids_datasets.py
+++ b/python/ingest_eeg_bids_datasets.py
@@ -5,7 +5,7 @@
 import os
 import sys
 from lib.lorisgetopt import LorisGetOpt
-from lib.database import Database
+from lib.database_lib import Database
 from lib.database_lib.config import Config
 from lib.exitcode import SUCCESS, INVALID_ARG
 import subprocess
@@ -112,7 +112,7 @@ def main():
       if not session_data:
         print('Session ID ' + eeg_dataset['SessionID'] + ' associated with UploadID ' + uploadid + ' does not exist.')
         sys.exit(INVALID_ARG)
-         
+
       candid = session_data[0]['CandID']
       pscid = session_data[0]['PSCID']
       visit = session_data[0]['Visit_label']
@@ -150,13 +150,13 @@ def main():
       # Assume eeg and raw data for now
       eeg_path = os.path.join(path, 'eeg')
       command = 'python ' + script + ' -p ' + profile + ' -d ' + eeg_path + ' --nobidsvalidation --nocopy --type raw'
-      
+
       try:
         result = subprocess.run(command, shell = True, capture_output=True)
 
         if result.stdout:
           print(result.stdout.decode('utf-8'))
-        
+
         if result.stderr:
           print(
             f'ERROR: EEG Dataset with uploadID {uploadid} ingestion log:\n ' + result.stderr.decode('utf-8')
@@ -177,7 +177,7 @@ def main():
         "UPDATE electrophysiology_uploader SET Status = 'Failed Ingestion' WHERE UploadID = %s",
         (uploadid,)
       )
-      
+
     # TODO: reupload of archive after ingestion
     # Delete if already exist
 
diff --git a/python/lib/__init__.py b/python/lib/__init__.py
index d7a393692..c5c77fab3 100644
--- a/python/lib/__init__.py
+++ b/python/lib/__init__.py
@@ -1,4 +1,3 @@
-
 """
 From the documentation at https://docs.python.org/2/tutorial/modules.html#packages
 The __init__.py files are required to make Python treat the directories as
@@ -7,4 +6,4 @@
 the module search path. In the simplest case, __init__.py can just be an empty
 file, but it can also execute initialization code for the package or set the
 __all__ variable, described later.
-"""
\ No newline at end of file
+"""
diff --git a/python/lib/aws_s3.py b/python/lib/aws_s3.py
index baa62d315..eae2a74be 100755
--- a/python/lib/aws_s3.py
+++ b/python/lib/aws_s3.py
@@ -82,9 +82,9 @@ def check_object_content_exists(self, file_path, key):
             etag = lib.utilities.compute_md5_hash(file_path)
             self.s3_client.head_object(Bucket=self.bucket_name, Key=key, IfMatch=etag)
         except ClientError:
-            """            
+            """
             Per Boto3 documentation for S3.Client.head_object IfMatch will:
-            Return the object only if its entity tag (ETag) is the same as the one specified; 
+            Return the object only if its entity tag (ETag) is the same as the one specified;
             otherwise, return a 412 (precondition failed) error.
             """
             return False
diff --git a/python/lib/bidsreader.py b/python/lib/bidsreader.py
index 79ec93e82..688bf628e 100755
--- a/python/lib/bidsreader.py
+++ b/python/lib/bidsreader.py
@@ -97,8 +97,8 @@ def load_bids_data(self, validate):
         # BIDSLayoutIndexer is required for PyBIDS >= 0.12.1
         # bids_pack_version = list(map(int, bids.__version__.split('.')))
         # disabled until is a workaround for https://github.com/bids-standard/pybids/issues/760 is found
-        # [file] bids_import.py 
-        # [function] read_and_insert_bids 
+        # [file] bids_import.py
+        # [function] read_and_insert_bids
         # [line] for modality in row['modalities']: (row['modalities'] is empty)
         # if (bids_pack_version[0] > 0
         #    or bids_pack_version[1] > 12
@@ -147,7 +147,7 @@ def load_candidates_from_bids(self):
         else:
             bids_subjects = self.bids_layout.get_subjects()
             participants_info = [{'participant_id': sub_id} for sub_id in bids_subjects]
-        
+
         if self.verbose:
             print('\t=> List of participants found:')
             for participant in participants_info:
diff --git a/python/lib/candidate.py b/python/lib/candidate.py
index b2bb20c72..e25fce319 100644
--- a/python/lib/candidate.py
+++ b/python/lib/candidate.py
@@ -16,7 +16,7 @@ class Candidate:
     :Example:
 
         from lib.candidate import Candidate
-        from lib.database  import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database.py b/python/lib/database.py
deleted file mode 100644
index fa182d7f3..000000000
--- a/python/lib/database.py
+++ /dev/null
@@ -1,277 +0,0 @@
-"""Allows LORIS database connectivity for LORIS-MRI python code base"""
-
-import MySQLdb
-import sys
-import lib.exitcode
-
-
-__license__ = "GPLv3"
-
-
-class Database:
-    """
-    This class performs common tasks related to database connectivity between
-    the LORIS-MRI python code base and the LORIS backend database.
-
-    :Example:
-
-        from lib.database import Database
-
-        db = Database(config.mysql, verbose)
-
-        db.connect()
-
-        # to select data corresponding to specific parameters
-        results = db.pselect(
-            "SELECT CandID FROM candidate WHERE Active = %s AND Sex = %s",
-            ('Y', 'Male')
-        )
-
-        # to select data without any specific parameter
-        results = db.pselect(
-            "SELECT CandID FROM candidate"
-        ) # args is optional in db.pselect
-
-        # to insert multiple rows
-        db.insert(
-            'media',
-            ('session_id', 'file_name', 'data_dir'),
-            [
-                ('6834', 'bla', 'bndjf'),
-                ('6834', 'blu', 'blui')
-            ]
-        )
-
-        # to insert one row and return the last inserted ID
-        last_id = db.insert(
-            'media',
-            ('session_id', 'file_name', 'data_dir'),
-            [
-                ('6834', 'bla', 'bndjf')
-            ],
-            True
-        ) # get_last_id is default to False in db.insert
-
-        # to update data
-        db.update(
-            "UPDATE media SET file_name = %s WHERE ID = %s,
-            ('filename.txt', '1')
-        )
-
-        db.disconnect()
-    """
-
-    def __init__(self, credentials, verbose):
-        """
-        Constructor method for the Database class.
-
-        :param credentials: LORIS database credentials
-         :type credentials: dict
-        :param verbose    : whether to be verbose or not
-         :type verbose    : bool
-        """
-
-        self.verbose = verbose
-
-        # grep database credentials
-        default_port   = 3306
-        self.db_name   = credentials['database']
-        self.user_name = credentials['username']
-        self.password  = credentials['passwd']
-        self.host_name = credentials['host']
-        port           = credentials['port']
-
-        if not self.user_name:
-            raise Exception("\nUser name cannot be empty string.\n")
-        if not self.db_name:
-            raise Exception("\nDatabase name cannot be empty string.\n")
-        if not self.host_name:
-            raise Exception("\nDatabase host cannot be empty string.\n")
-
-        self.port = int(port) if port else default_port
-
-    def connect(self):
-        """
-        Attempts to connect to the database using the connection parameters
-        passed at construction time. This method will throw a
-        DatabaseException if the connection could not be established.
-        """
-
-        connect_statement = "\nConnecting to:" \
-                            "\n\tdatabase: " + self.db_name   + \
-                            "\n\tusername: " + self.user_name + \
-                            "\n\thostname: " + self.host_name + \
-                            "\n\tport    : " + str(self.port) + '\n'
-        if self.verbose:
-            print(connect_statement)
-
-        try:
-            self.con = MySQLdb.connect(
-                host=self.host_name,
-                user=self.user_name,
-                passwd=self.password,
-                port=self.port,
-                db=self.db_name
-            )
-            # self.cnx.cursor = self.cnx.cursor(prepared=True)
-        except MySQLdb.Error as err:
-            raise Exception("Database connection failure: " + format(err))
-
-    def pselect(self, query, args=None):
-        """
-        Executes a select query on the database. This method will first prepare
-        the statement passed as parameter before sending the request to the
-        database.
-
-        :param query: select query to execute (containing the argument
-                      placeholders if any
-         :type query: str
-        :param args: arguments to replace the placeholders with
-         :type args: tuple
-
-        :return: list of dictionaries with MySQL column header name
-         :rtype: list of dict
-        """
-        if self.verbose:
-            print("\nExecuting query:\n\t" + query + "\n")
-            if args:
-                print("With arguments:\n\t"  + str(args) + "\n")
-
-        try:
-            cursor = self.con.cursor(MySQLdb.cursors.DictCursor)
-            cursor.execute(query, args) if args else cursor.execute(query)
-            results = cursor.fetchall()
-            cursor.close()
-        except MySQLdb.Error as err:
-            raise Exception("Select query failure: " + format(err))
-
-        return results
-
-    def insert(self, table_name, column_names, values, get_last_id=False):
-        """
-        Inserts records in a given database table with the specified column
-        values. This method will raise an exception if the record cannot be
-        inserted.
-
-        :param table_name  : name of the database table to insert into
-         :type table_name  : str
-        :param column_names: name of the table's columns to insert into
-         :type column_names: tuple
-        :param values      : list of values to insert into the table
-         :type values      : list
-
-        :return: the last ID that have been inserted into the database
-         :rtype: int
-        """
-
-        placeholders = ','.join(map(lambda x: '%s', column_names))
-
-        query = "INSERT INTO %s (%s) VALUES (%s)" % (
-            table_name, ', '.join(column_names), placeholders
-        )
-
-        if self.verbose:
-            print("\nExecuting query:\n\t" + query + "\n"
-                  + "With arguments:\n\t" + str(values) + "\n")
-
-        try:
-            cursor = self.con.cursor()
-            if isinstance(values, list):
-                # if values is a list, use cursor.executemany
-                # (to execute multiple inserts at once)
-                cursor.executemany(query, values)
-            else:
-                # else, values is a tuple and want to execute only one insert
-                cursor.execute(query, values)
-            self.con.commit()
-            last_id = cursor.lastrowid
-            cursor.close()
-        except MySQLdb.Error as err:
-            raise Exception("Insert query failure: " + format(err))
-
-        if get_last_id:
-            return last_id
-
-    def update(self, query, args):
-        """
-        Executes an update query on the database. This method will first prepare
-        the statement passed as parameter before sending the request to the
-        database.
-
-        :param query: update query to be run
-         :type query: str
-        :param args : arguments to replace the placeholders with
-         :type args : tuple
-        """
-
-        if self.verbose:
-            print("\nExecuting query:\n\t" + query + "\n"
-                  + "With arguments:\n\t"  + str(args) + "\n")
-
-        try:
-            cursor = self.con.cursor()
-            cursor.execute(query, args)
-            self.con.commit()
-        except MySQLdb.Error as err:
-            raise Exception("Update query failure: " + format(err))
-
-    def grep_id_from_lookup_table(self, id_field_name, table_name, where_field_name,
-                                  where_value, insert_if_not_found=None):
-        """
-        Greps an ID from a given lookup table based on the provided value.
-
-        :param id_field_name      : name of the ID field in the table
-         :type id_field_name      : str
-        :param table_name         : name of the lookup table
-         :type table_name         : str
-        :param where_field_name   : name of the field to use to find the ID
-         :type where_field_name   : str
-        :param where_value        : value of the field to use to find the ID
-         :type where_value        : str
-        :param insert_if_not_found: whether to insert a new row in the lookup table
-                                    if no entry was found for the provided value
-         :type insert_if_not_found: bool
-
-        :return: ID found in the lookup table
-         :rtype: int
-
-        """
-
-        query = "SELECT  " + id_field_name    + " " \
-                "FROM    " + table_name       + " " \
-                "WHERE   " + where_field_name + " = %s"
-
-        result = self.pselect(query=query, args=(where_value,))
-        id     = result[0][id_field_name] if result else None
-
-        if not id and insert_if_not_found:
-            id = self.insert(
-                table_name   = table_name,
-                column_names = (where_field_name,),
-                values       = (where_value,),
-                get_last_id  = True
-            )
-
-        if not id:
-            message = "\nERROR: " + where_value + " " + where_field_name + \
-                      " does not exist in " + table_name + " database table\n"
-            print(message)
-            sys.exit(lib.exitcode.SELECT_FAILURE)
-
-        return id
-
-    def disconnect(self):
-        """
-        Terminates the connection previously instantiated to the database if a
-        connection was previously established.
-        """
-
-        if hasattr(self, 'cnx'):
-            if self.verbose:
-                print("\nDisconnecting from the database")
-
-            try:
-                self.con.close()
-            except MySQLdb.Error as err:
-                message = "Database disconnection failure: " + format(err)
-                raise Exception(message)
diff --git a/python/lib/database_lib/__init__.py b/python/lib/database_lib/__init__.py
index e69de29bb..99dee85b4 100644
--- a/python/lib/database_lib/__init__.py
+++ b/python/lib/database_lib/__init__.py
@@ -0,0 +1,277 @@
+"""Allows LORIS database connectivity for LORIS-MRI python code base"""
+
+import MySQLdb
+import sys
+import lib.exitcode
+
+
+__license__ = "GPLv3"
+
+
+class Database:
+    """
+    This class performs common tasks related to database connectivity between
+    the LORIS-MRI python code base and the LORIS backend database.
+
+    :Example:
+
+        from lib.database_lib import Database
+
+        db = Database(config.mysql, verbose)
+
+        db.connect()
+
+        # to select data corresponding to specific parameters
+        results = db.pselect(
+            "SELECT CandID FROM candidate WHERE Active = %s AND Sex = %s",
+            ('Y', 'Male')
+        )
+
+        # to select data without any specific parameter
+        results = db.pselect(
+            "SELECT CandID FROM candidate"
+        ) # args is optional in db.pselect
+
+        # to insert multiple rows
+        db.insert(
+            'media',
+            ('session_id', 'file_name', 'data_dir'),
+            [
+                ('6834', 'bla', 'bndjf'),
+                ('6834', 'blu', 'blui')
+            ]
+        )
+
+        # to insert one row and return the last inserted ID
+        last_id = db.insert(
+            'media',
+            ('session_id', 'file_name', 'data_dir'),
+            [
+                ('6834', 'bla', 'bndjf')
+            ],
+            True
+        ) # get_last_id is default to False in db.insert
+
+        # to update data
+        db.update(
+            "UPDATE media SET file_name = %s WHERE ID = %s,
+            ('filename.txt', '1')
+        )
+
+        db.disconnect()
+    """
+
+    def __init__(self, credentials, verbose):
+        """
+        Constructor method for the Database class.
+
+        :param credentials: LORIS database credentials
+         :type credentials: dict
+        :param verbose    : whether to be verbose or not
+         :type verbose    : bool
+        """
+
+        self.verbose = verbose
+
+        # grep database credentials
+        default_port   = 3306
+        self.db_name   = credentials['database']
+        self.user_name = credentials['username']
+        self.password  = credentials['passwd']
+        self.host_name = credentials['host']
+        port           = credentials['port']
+
+        if not self.user_name:
+            raise Exception("\nUser name cannot be empty string.\n")
+        if not self.db_name:
+            raise Exception("\nDatabase name cannot be empty string.\n")
+        if not self.host_name:
+            raise Exception("\nDatabase host cannot be empty string.\n")
+
+        self.port = int(port) if port else default_port
+
+    def connect(self):
+        """
+        Attempts to connect to the database using the connection parameters
+        passed at construction time. This method will throw a
+        DatabaseException if the connection could not be established.
+        """
+
+        connect_statement = "\nConnecting to:" \
+                            "\n\tdatabase: " + self.db_name   + \
+                            "\n\tusername: " + self.user_name + \
+                            "\n\thostname: " + self.host_name + \
+                            "\n\tport    : " + str(self.port) + '\n'
+        if self.verbose:
+            print(connect_statement)
+
+        try:
+            self.con = MySQLdb.connect(
+                host=self.host_name,
+                user=self.user_name,
+                passwd=self.password,
+                port=self.port,
+                db=self.db_name
+            )
+            # self.cnx.cursor = self.cnx.cursor(prepared=True)
+        except MySQLdb.Error as err:
+            raise Exception("Database connection failure: " + format(err))
+
+    def pselect(self, query, args=None):
+        """
+        Executes a select query on the database. This method will first prepare
+        the statement passed as parameter before sending the request to the
+        database.
+
+        :param query: select query to execute (containing the argument
+                      placeholders if any
+         :type query: str
+        :param args: arguments to replace the placeholders with
+         :type args: tuple
+
+        :return: list of dictionaries with MySQL column header name
+         :rtype: list of dict
+        """
+        if self.verbose:
+            print("\nExecuting query:\n\t" + query + "\n")
+            if args:
+                print("With arguments:\n\t"  + str(args) + "\n")
+
+        try:
+            cursor = self.con.cursor(MySQLdb.cursors.DictCursor)
+            cursor.execute(query, args) if args else cursor.execute(query)
+            results = cursor.fetchall()
+            cursor.close()
+        except MySQLdb.Error as err:
+            raise Exception("Select query failure: " + format(err))
+
+        return results
+
+    def insert(self, table_name, column_names, values, get_last_id=False):
+        """
+        Inserts records in a given database table with the specified column
+        values. This method will raise an exception if the record cannot be
+        inserted.
+
+        :param table_name  : name of the database table to insert into
+         :type table_name  : str
+        :param column_names: name of the table's columns to insert into
+         :type column_names: tuple
+        :param values      : list of values to insert into the table
+         :type values      : list
+
+        :return: the last ID that have been inserted into the database
+         :rtype: int
+        """
+
+        placeholders = ','.join(map(lambda x: '%s', column_names))
+
+        query = "INSERT INTO %s (%s) VALUES (%s)" % (
+            table_name, ', '.join(column_names), placeholders
+        )
+
+        if self.verbose:
+            print("\nExecuting query:\n\t" + query + "\n"
+                  + "With arguments:\n\t" + str(values) + "\n")
+
+        try:
+            cursor = self.con.cursor()
+            if isinstance(values, list):
+                # if values is a list, use cursor.executemany
+                # (to execute multiple inserts at once)
+                cursor.executemany(query, values)
+            else:
+                # else, values is a tuple and want to execute only one insert
+                cursor.execute(query, values)
+            self.con.commit()
+            last_id = cursor.lastrowid
+            cursor.close()
+        except MySQLdb.Error as err:
+            raise Exception("Insert query failure: " + format(err))
+
+        if get_last_id:
+            return last_id
+
+    def update(self, query, args):
+        """
+        Executes an update query on the database. This method will first prepare
+        the statement passed as parameter before sending the request to the
+        database.
+
+        :param query: update query to be run
+         :type query: str
+        :param args : arguments to replace the placeholders with
+         :type args : tuple
+        """
+
+        if self.verbose:
+            print("\nExecuting query:\n\t" + query + "\n"
+                  + "With arguments:\n\t"  + str(args) + "\n")
+
+        try:
+            cursor = self.con.cursor()
+            cursor.execute(query, args)
+            self.con.commit()
+        except MySQLdb.Error as err:
+            raise Exception("Update query failure: " + format(err))
+
+    def grep_id_from_lookup_table(self, id_field_name, table_name, where_field_name,
+                                  where_value, insert_if_not_found=None):
+        """
+        Greps an ID from a given lookup table based on the provided value.
+
+        :param id_field_name      : name of the ID field in the table
+         :type id_field_name      : str
+        :param table_name         : name of the lookup table
+         :type table_name         : str
+        :param where_field_name   : name of the field to use to find the ID
+         :type where_field_name   : str
+        :param where_value        : value of the field to use to find the ID
+         :type where_value        : str
+        :param insert_if_not_found: whether to insert a new row in the lookup table
+                                    if no entry was found for the provided value
+         :type insert_if_not_found: bool
+
+        :return: ID found in the lookup table
+         :rtype: int
+
+        """
+
+        query = "SELECT  " + id_field_name    + " " \
+                "FROM    " + table_name       + " " \
+                "WHERE   " + where_field_name + " = %s"
+
+        result = self.pselect(query=query, args=(where_value,))
+        id     = result[0][id_field_name] if result else None
+
+        if not id and insert_if_not_found:
+            id = self.insert(
+                table_name   = table_name,
+                column_names = (where_field_name,),
+                values       = (where_value,),
+                get_last_id  = True
+            )
+
+        if not id:
+            message = "\nERROR: " + where_value + " " + where_field_name + \
+                      " does not exist in " + table_name + " database table\n"
+            print(message)
+            sys.exit(lib.exitcode.SELECT_FAILURE)
+
+        return id
+
+    def disconnect(self):
+        """
+        Terminates the connection previously instantiated to the database if a
+        connection was previously established.
+        """
+
+        if hasattr(self, 'cnx'):
+            if self.verbose:
+                print("\nDisconnecting from the database")
+
+            try:
+                self.con.close()
+            except MySQLdb.Error as err:
+                message = "Database disconnection failure: " + format(err)
+                raise Exception(message)
diff --git a/python/lib/database_lib/candidate_db.py b/python/lib/database_lib/candidate_db.py
index bbe4e92d3..958caaf6d 100644
--- a/python/lib/database_lib/candidate_db.py
+++ b/python/lib/database_lib/candidate_db.py
@@ -11,7 +11,7 @@ class CandidateDB:
     :Example:
 
         from lib.database_lib.candidate_db import CandidateDB
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/config.py b/python/lib/database_lib/config.py
index a5030762c..22dd12348 100644
--- a/python/lib/database_lib/config.py
+++ b/python/lib/database_lib/config.py
@@ -11,7 +11,7 @@ class Config:
     :Example:
 
         from lib.database_lib.config import Config
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/files.py b/python/lib/database_lib/files.py
index 4fab37e06..dd5a32e67 100644
--- a/python/lib/database_lib/files.py
+++ b/python/lib/database_lib/files.py
@@ -12,7 +12,7 @@ class Files:
     :Example:
 
         from lib.files import Files
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/mri_candidate_errors.py b/python/lib/database_lib/mri_candidate_errors.py
index 25b70e5e7..eec21fefc 100644
--- a/python/lib/database_lib/mri_candidate_errors.py
+++ b/python/lib/database_lib/mri_candidate_errors.py
@@ -11,7 +11,7 @@ class MriCandidateErrors:
     :Example:
 
         from lib.mri_candidate_errors import MriCandidateErrors
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/mri_protocol.py b/python/lib/database_lib/mri_protocol.py
index 86fa29035..60230b013 100644
--- a/python/lib/database_lib/mri_protocol.py
+++ b/python/lib/database_lib/mri_protocol.py
@@ -11,7 +11,7 @@ class MriProtocol:
     :Example:
 
         from lib.mri_protocol import MriProtocol
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/mri_protocol_checks.py b/python/lib/database_lib/mri_protocol_checks.py
index 1bdd02aac..b6a8dd7c0 100644
--- a/python/lib/database_lib/mri_protocol_checks.py
+++ b/python/lib/database_lib/mri_protocol_checks.py
@@ -11,7 +11,7 @@ class MriProtocolChecks:
     :Example:
 
         from lib.mri_protocol_checks import MriProtocolChecks
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/mri_protocol_violated_scans.py b/python/lib/database_lib/mri_protocol_violated_scans.py
index fd65b55fa..87c9f734c 100644
--- a/python/lib/database_lib/mri_protocol_violated_scans.py
+++ b/python/lib/database_lib/mri_protocol_violated_scans.py
@@ -11,7 +11,7 @@ class MriProtocolViolatedScans:
     :Example:
 
         from lib.mri_protocol_violated_scans import MriProtocolViolatedScans
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/mri_scan_type.py b/python/lib/database_lib/mri_scan_type.py
index 64f4759b6..bf14fb0ee 100644
--- a/python/lib/database_lib/mri_scan_type.py
+++ b/python/lib/database_lib/mri_scan_type.py
@@ -11,7 +11,7 @@ class MriScanType:
     :Example:
 
         from lib.mri_scan_type import MriScanType
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/mri_scanner.py b/python/lib/database_lib/mri_scanner.py
index 7ea0cbc52..edc8a0d2d 100644
--- a/python/lib/database_lib/mri_scanner.py
+++ b/python/lib/database_lib/mri_scanner.py
@@ -13,7 +13,7 @@ class MriScanner:
     :Example:
 
         from lib.mri_scanner import MriScanner
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/mri_upload_db.py b/python/lib/database_lib/mri_upload_db.py
index c636429e2..5bf4a24d3 100644
--- a/python/lib/database_lib/mri_upload_db.py
+++ b/python/lib/database_lib/mri_upload_db.py
@@ -10,7 +10,7 @@ class MriUploadDB:
     :Example:
 
         from lib.mri_upload import MriUploadDB
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/mri_violations_log.py b/python/lib/database_lib/mri_violations_log.py
index 517c97a54..a52950533 100644
--- a/python/lib/database_lib/mri_violations_log.py
+++ b/python/lib/database_lib/mri_violations_log.py
@@ -11,7 +11,7 @@ class MriViolationsLog:
     :Example:
 
         from lib.mri_violations_log import MriViolationsLog
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/notification.py b/python/lib/database_lib/notification.py
index 6c873fa06..33892b6b1 100644
--- a/python/lib/database_lib/notification.py
+++ b/python/lib/database_lib/notification.py
@@ -12,7 +12,7 @@ class Notification:
     :Example:
 
         from lib.notification import Notification
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/parameter_file.py b/python/lib/database_lib/parameter_file.py
index 720431389..603fca396 100644
--- a/python/lib/database_lib/parameter_file.py
+++ b/python/lib/database_lib/parameter_file.py
@@ -10,7 +10,7 @@ class ParameterFile:
     :Example:
 
         from lib.parameter_file import ParameterFile
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/parameter_type.py b/python/lib/database_lib/parameter_type.py
index 421cae4a1..a6c2f60b3 100644
--- a/python/lib/database_lib/parameter_type.py
+++ b/python/lib/database_lib/parameter_type.py
@@ -10,7 +10,7 @@ class ParameterType:
     :Example:
 
         from lib.parameter_type import ParameterType
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/project_cohort_rel.py b/python/lib/database_lib/project_cohort_rel.py
index 06acb9197..c3e3ccde4 100644
--- a/python/lib/database_lib/project_cohort_rel.py
+++ b/python/lib/database_lib/project_cohort_rel.py
@@ -11,7 +11,7 @@ class ProjectCohortRel:
     :Example:
 
         from lib.database_lib.project_cohort_rel import ProjectCohortRel
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/session_db.py b/python/lib/database_lib/session_db.py
index 764015bd1..b95311585 100644
--- a/python/lib/database_lib/session_db.py
+++ b/python/lib/database_lib/session_db.py
@@ -11,7 +11,7 @@ class SessionDB:
     :Example:
 
         from lib.database_lib.session_db import SessionDB
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/site.py b/python/lib/database_lib/site.py
index 192befebd..1af4367bb 100644
--- a/python/lib/database_lib/site.py
+++ b/python/lib/database_lib/site.py
@@ -11,7 +11,7 @@ class Site:
     :Example:
 
         from lib.site import Site
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/tarchive.py b/python/lib/database_lib/tarchive.py
index ec22865a0..f881f6c98 100644
--- a/python/lib/database_lib/tarchive.py
+++ b/python/lib/database_lib/tarchive.py
@@ -11,7 +11,7 @@ class Tarchive:
     :Example:
 
         from lib.tarchive import Tarchive
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/tarchive_series.py b/python/lib/database_lib/tarchive_series.py
index d0f8c5ac0..2586848c8 100644
--- a/python/lib/database_lib/tarchive_series.py
+++ b/python/lib/database_lib/tarchive_series.py
@@ -11,7 +11,7 @@ class TarchiveSeries:
     :Example:
 
         from lib.tarchive_series import TarchiveSeries
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/database_lib/visit_windows.py b/python/lib/database_lib/visit_windows.py
index 14e1636ee..f16ae8930 100644
--- a/python/lib/database_lib/visit_windows.py
+++ b/python/lib/database_lib/visit_windows.py
@@ -11,7 +11,7 @@ class VisitWindows:
     :Example:
 
         from lib.visit_windows import VisitWindows
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/dcm2bids_imaging_pipeline_lib/base_pipeline.py b/python/lib/dcm2bids_imaging_pipeline_lib/base_pipeline.py
index 01176531c..70c3a82c4 100644
--- a/python/lib/dcm2bids_imaging_pipeline_lib/base_pipeline.py
+++ b/python/lib/dcm2bids_imaging_pipeline_lib/base_pipeline.py
@@ -9,7 +9,7 @@
 from lib.database_lib.candidate_db import CandidateDB
 from lib.database_lib.config import Config
 from lib.database_lib.visit_windows import VisitWindows
-from lib.database import Database
+from lib.database_lib import Database
 from lib.dicom_archive import DicomArchive
 from lib.imaging import Imaging
 from lib.log import Log
diff --git a/python/lib/dicom_archive.py b/python/lib/dicom_archive.py
index 47f3b87b4..8497d473c 100644
--- a/python/lib/dicom_archive.py
+++ b/python/lib/dicom_archive.py
@@ -14,7 +14,7 @@ class DicomArchive:
 
     :Example:
 
-        from lib.database import Database
+        from lib.database_lib import Database
         from lib.dicom_archive import DicomArchive
 
         # database connection
diff --git a/python/lib/eeg.py b/python/lib/eeg.py
index 42caa19b1..5baea46d3 100755
--- a/python/lib/eeg.py
+++ b/python/lib/eeg.py
@@ -28,8 +28,8 @@ class Eeg:
     :Example:
 
         from lib.bidsreader import BidsReader
-        from lib.eeg        import Eeg
-        from lib.database   import Database
+        from lib.eeg import Eeg
+        from lib.database_lib import Database
         from lib.database_lib.config import Config
 
         # database connection
@@ -507,7 +507,7 @@ def fetch_and_insert_eeg_files(self, derivatives=False, detect=True):
                 physio_file_id = physiological.insert_physiological_file(
                     eeg_file_info, eeg_file_data
                 )
-            
+
                 if self.loris_bids_root_dir:
                     # If we copy the file in assembly_bids and
                     # if the EEG file was a set file, then update the filename for the .set
@@ -767,7 +767,7 @@ def fetch_and_insert_event_files(
                     event_metadata_path = self.copy_file_to_loris_bids_dir(
                         event_metadata_file.path, derivatives, inheritance
                     )
-                    
+
                     # load json data
                     with open(event_metadata_file.path) as metadata_file:
                         event_metadata = json.load(metadata_file)
@@ -922,7 +922,6 @@ def create_and_insert_archive(self, files_to_archive, archive_rel_name,
         }
         physiological.insert_archive_file(archive_info)
 
-
     def create_and_insert_event_archive(self, files_to_archive, archive_rel_name, eeg_file_id):
         """
         Create an archive with all event files associated to a specific recording
diff --git a/python/lib/imaging.py b/python/lib/imaging.py
index 4a09b7950..420417f9e 100644
--- a/python/lib/imaging.py
+++ b/python/lib/imaging.py
@@ -32,7 +32,7 @@ class Imaging:
     :Example:
 
         from lib.imaging  import Imaging
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
@@ -1110,7 +1110,7 @@ def get_list_of_files_sorted_by_acq_time(self, files_list):
             sorted_files_list = sorted(new_files_list, key=lambda x: x['acq_time'])
         except TypeError:
             return None
-        
+
         return sorted_files_list
 
     def modify_fmap_json_file_to_write_intended_for(self, sorted_fmap_files_list, s3_obj, tmp_dir):
diff --git a/python/lib/imaging_upload.py b/python/lib/imaging_upload.py
index 00e5889cb..f9d28fadf 100644
--- a/python/lib/imaging_upload.py
+++ b/python/lib/imaging_upload.py
@@ -13,7 +13,7 @@ class ImagingUpload:
     :Example:
 
         from lib.imaging_upload  import ImagingUpload
-        from lib.database import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
diff --git a/python/lib/lorisgetopt.py b/python/lib/lorisgetopt.py
index c71740bbb..081f1c18a 100644
--- a/python/lib/lorisgetopt.py
+++ b/python/lib/lorisgetopt.py
@@ -7,7 +7,7 @@
 import sys
 
 from lib.aws_s3 import AwsS3
-from lib.database import Database
+from lib.database_lib import Database
 from lib.database_lib.config import Config
 
 
diff --git a/python/lib/mri.py b/python/lib/mri.py
index 70ee1b533..84fb13353 100644
--- a/python/lib/mri.py
+++ b/python/lib/mri.py
@@ -25,8 +25,8 @@ class Mri:
     :Example:
 
         from lib.bidsreader import BidsReader
-        from lib.mri        import Mri
-        from lib.database   import Database
+        from lib.mri import Mri
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config_file.mysql, verbose)
@@ -130,7 +130,7 @@ def __init__(self, bids_reader, bids_sub_id, bids_ses_id, bids_modality, db,
                 if len(cohort_info) > 0:
                     self.cohort_id = cohort_info[0]['CohortID']
             break
-        
+
         self.session_id      = self.get_loris_session_id()
 
         # grep all the NIfTI files for the modality
@@ -139,7 +139,7 @@ def __init__(self, bids_reader, bids_sub_id, bids_ses_id, bids_modality, db,
         # check if a tsv with acquisition dates or age is available for the subject
         self.scans_file = None
         if self.bids_layout.get(suffix='scans', subject=self.psc_id, return_type='filename'):
-            self.scans_file = self.bids_layout.get(suffix='scans', subject=self.psc_id, 
+            self.scans_file = self.bids_layout.get(suffix='scans', subject=self.psc_id,
                                                    return_type='filename', extension='tsv')[0]
 
         # loop through NIfTI files and register them in the DB
diff --git a/python/lib/physiological.py b/python/lib/physiological.py
index a560b77e2..4b2cbc87a 100755
--- a/python/lib/physiological.py
+++ b/python/lib/physiological.py
@@ -32,7 +32,7 @@ class Physiological:
     :Example:
 
         from lib.physiological import Physiological
-        from lib.database      import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
@@ -386,7 +386,7 @@ def insert_electrode_file(self, electrode_data, electrode_file,
                 row.get('impedance'),
                 electrode_file
             )
-            
+
             inserted_electrode_id = self.db.insert(
                 table_name   = 'physiological_electrode',
                 column_names = electrode_fields,
diff --git a/python/lib/point_3d.py b/python/lib/point_3d.py
index 351b765dd..e1fc8c6ec 100644
--- a/python/lib/point_3d.py
+++ b/python/lib/point_3d.py
@@ -23,4 +23,4 @@ def __init__(self, pid: int, x: float, y: float, z: float):
 
     def __str__(self) -> str:
         """Prints out the point info"""
-        return f"Point [{self.id}] ({self.x}, {self.y}, {self.z})"
\ No newline at end of file
+        return f"Point [{self.id}] ({self.x}, {self.y}, {self.z})"
diff --git a/python/lib/scanstsv.py b/python/lib/scanstsv.py
index 74d6b8456..c4505177a 100644
--- a/python/lib/scanstsv.py
+++ b/python/lib/scanstsv.py
@@ -81,7 +81,7 @@ def get_acquisition_time(self):
                 else:
                     print('More than one or no acquisition time has been found for ', self.acquisition_file)
                     exit()
-            else: 
+            else:
                 eeg_acq_time = self.acquisition_data['acq_time']
 
             if eeg_acq_time == 'n/a':
diff --git a/python/lib/session.py b/python/lib/session.py
index 22729e946..7c91e2c68 100644
--- a/python/lib/session.py
+++ b/python/lib/session.py
@@ -14,15 +14,15 @@ class Session:
 
     :Example:
 
-        from lib.session  import Session
-        from lib.database import Database
+        from lib.session import Session
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)
         db.connect()
 
         session = Session(
-            verbose, cand_id, visit_label, 
+            verbose, cand_id, visit_label,
             center_id, project_id, cohort_id
         )
 
diff --git a/python/mass_electrophysiology_chunking.py b/python/mass_electrophysiology_chunking.py
index baee595b6..e93f7f8a8 100755
--- a/python/mass_electrophysiology_chunking.py
+++ b/python/mass_electrophysiology_chunking.py
@@ -6,7 +6,7 @@
 import sys
 import getopt
 import lib.exitcode
-from lib.database      import Database
+from lib.database_lib import Database
 from lib.physiological import Physiological
 from lib.database_lib.config import Config
 
diff --git a/python/mass_nifti_pic.py b/python/mass_nifti_pic.py
index 589c1ff47..cd8e8b023 100755
--- a/python/mass_nifti_pic.py
+++ b/python/mass_nifti_pic.py
@@ -7,7 +7,7 @@
 import sys
 import getopt
 import lib.exitcode
-from lib.database import Database
+from lib.database_lib import Database
 from lib.imaging  import Imaging
 from lib.database_lib.config import Config
 
diff --git a/python/react-series-data-viewer/chunking.py b/python/react-series-data-viewer/chunking.py
index 7dd94a1eb..596ea0c10 100755
--- a/python/react-series-data-viewer/chunking.py
+++ b/python/react-series-data-viewer/chunking.py
@@ -105,7 +105,7 @@ def write_index_json(
         ('channelMetadata', channel_metadata)
     ])
     create_path_dirs(chunk_dir)
-    
+
     data = None
     try:
         with open(os.path.join(chunk_dir, 'index.json'), 'r+') as index_json:
@@ -206,14 +206,14 @@ def mne_file_to_chunks(path, chunk_size, loader, from_channel_name, channel_coun
     return channel_chunks_list, time_interval, signal_range, channel_names, channel_ranges, valid_samples_in_last_chunk
 
 
-def write_chunk_directory(path, chunk_size, loader, from_channel_index=0, from_channel_name=None, 
+def write_chunk_directory(path, chunk_size, loader, from_channel_index=0, from_channel_name=None,
                           channel_count=None, downsamplings=None, prefix=None, destination=None):
 
     chunk_dir = chunk_dir_path(path, prefix=prefix, destination=destination)
     channel_chunks_list, time_interval, signal_range, \
         channel_names, channel_ranges, valid_samples_in_last_chunk = \
         mne_file_to_chunks(path, chunk_size, loader, from_channel_name, channel_count)
-    
+
     if downsamplings is not None:
         channel_chunks_list = channel_chunks_list[:downsamplings]
 
diff --git a/python/react-series-data-viewer/edf_to_chunks.py b/python/react-series-data-viewer/edf_to_chunks.py
index 58ef541f8..ccbdbb42d 100755
--- a/python/react-series-data-viewer/edf_to_chunks.py
+++ b/python/react-series-data-viewer/edf_to_chunks.py
@@ -60,7 +60,7 @@ def load_channels(exclude):
 
             # check if channel_index is a stim channel
             # to avoid a bug in mne.io.edf.edf
-            # (see issue https://github.com/mne-tools/mne-python/issues/9811) 
+            # (see issue https://github.com/mne-tools/mne-python/issues/9811)
             stim_channel_idxs, _ = mne_edf._check_stim_channel(
                 'auto', [channel_names[channel_index]]
             )
diff --git a/tools/correct_blake2b_and_md5_hashes_in_database.py b/tools/correct_blake2b_and_md5_hashes_in_database.py
index 9b5e45ad4..1ac534bcd 100755
--- a/tools/correct_blake2b_and_md5_hashes_in_database.py
+++ b/tools/correct_blake2b_and_md5_hashes_in_database.py
@@ -6,7 +6,7 @@
 import shutil
 import sys
 
-from lib.database import Database
+from lib.database_lib import Database
 from lib.database_lib.config import Config
 from lib.lorisgetopt import LorisGetOpt
 
diff --git a/tools/correct_lists_incorrectly_saved_in_parameter_file.py b/tools/correct_lists_incorrectly_saved_in_parameter_file.py
index 773d2cece..d9fc98602 100755
--- a/tools/correct_lists_incorrectly_saved_in_parameter_file.py
+++ b/tools/correct_lists_incorrectly_saved_in_parameter_file.py
@@ -2,7 +2,7 @@
 
 import os
 
-from lib.database import Database
+from lib.database_lib import Database
 from lib.lorisgetopt import LorisGetOpt