BRAIN CoGS mini VR rigs

# Database Access

# First steps

# Mount file server volumes

  • There are several xxxxxxxxxxx data files (behavior, imaging & electrophysiology) that are referenced in the database

  • To access these files you should mount PNI file server volumes on your system.

  • There are three main file servers across PNI where data is stored (braininit, Bezos & u19_dj)

# On windows systems

  1. From Windows Explorer, select "Map Network Drive" and enter:
  • \\cup.pni.princeton.edu\braininit\ (for braininit)
  • \\cup.pni.princeton.edu\Bezos-center\ (for Bezos)
  • \\cup.pni.princeton.edu\u19_dj\ (for u19_dj)
  1. Authenticate with your NetID and PU password (NOT your PNI password, which may be different). When prompted for your username, enter PRINCETON\netid (note that PRINCETON can be upper or lower case) where netid is your PU NetID.

# On OS X systems

  1. Select "Go->Connect to Server..." from Finder and enter:
  • smb://cup.pni.princeton.edu/braininit/ (for braininit)
  • smb://cup.pni.princeton.edu/Bezos-center/ (for Bezos)
  • smb://cup.pni.princeton.edu/u19_dj/ (for u19_dj)
  1. Authenticate with your NetID and PU password (NOT your PNI password, which may be different).

# On Linux systems

  1. Follow extra steps depicted in this: link

# DB Access for Python repository

# Prerequisites

Click to expand details

# Install an integrated development environment

  • DataJoint development and use can be done with a plain text editor in the terminal. However, an integrated development environment (IDE) can improve your experience. Several IDEs are available.

  • In this setup example, we will use Microsoft's Visual Studio Code. Installation instructions here. (opens new window)

  • Install the Jupyter extension for VS Code.

# Install a virtual environment

  • A virtual environment allows you to install the packages required for a specific project within an isolated environment on your computer.

  • It is highly recommended to create a virtual environment to run the workflow.

  • Conda and virtualenv are virtual environment managers and you can use either option. Below are the commands for Conda.

  • If you are setting up the pipeline on your local machine follow the instructions below for Conda. If you are using spock.pni.princeton.edu or scotty.pni.princeton.edu, Conda is preinstalled and you can access it by running module load anacondapy/2021.11.

  • We will install Miniconda which is a minimal installer for conda.

  • Select the Miniconda installer link (opens new window) for your operating system and follow the instructions.

    • You may need to add the Miniconda directory to the PATH environment variable

      • First locate the Miniconda directory

      • Then modify and run the following command

        export PATH="<absolute-path-to-miniconda-directory>/bin:$PATH"

    • Create a new conda environment

      • Type the following command into a terminal window

        conda create -n <environment_name> python=<version>

      • Example command to create a conda environment

        conda create -n <environment_name> python=3.9

    • Activate the conda environment

      conda activate <environment_name>

    # Other installs

# First time configuration

  • The following instructions will configure DJ and connect to DB.
conda activate <environment_name>
cd U19-pipeline_python
pip install -e .
python initial_conf.py

(Username and password will be prompted at this moment: Princeton NETiD & NetiD password usually works)

  • The initial_conf.py script will store a local file with credtentials to access DB and configuration variables/filepaths.
  • Now that the virtual modules are created to access the tables in the database, you can query and fetch from the database.

# Connection after configuration

  • The following instructions will load DJ configuration and connect to DB
conda activate <environment_name>
python
from scripts.conf_file_finding import try_find_conf_file
try_find_conf_file()
import datajoint as dj
dj.conn()

# DB Access for MATLAB repository

# Prerequisites

Click to expand details
  • Install DataJoint for MATLAB
  • Utilize MATLAB built-in GUI i.e. Top Ribbon -> Add-Ons -> Get Add-Ons
  • Search, select, and install DataJoint
  • Clone the U19-pipeline-matlab repository

# First time configuration

  • Add this repository to MATLAB Path or cd to this repository folder.
  • Run dj_initial_conf(1)
  • Insert user and password for the DB

Note if you are configuring repository on a public computer, there are two options:

  • Rundj_initial_conf(0) instead, to not store user & pass in configuration file.
  • Rundj_initial_conf(1) and login to the DB with a public user like u19tech.

# Connection after configuration

  • Add this repository to MATLAB Path or cd to this repository folder.
  • connect_datajoint00

# DB Access for MATLAB repository (cluster computing)

# Prerequisites

Click to expand details

# First time configuration

  • Add this repository to MATLAB Path
  • Run startup_virtual_machine.m
  • Run dj_initial_conf(1)
  • Insert user and password for the DB

Note if you are configuring repository on a public computer, there are two options:

  • Rundj_initial_conf(0) instead, to not store user & pass in configuration file.
  • Rundj_initial_conf(1) and login to the DB with a public user like u19tech.

# Connection after configuration

  • Add this repository to MATLAB Path
  • Run startup_virtual_machine.m

# Add researcher to user table

  • This set of instructions only apply for users that will have subjects on his/her supervision:

# Add researcher to user table with MATLAB

  • Connect to DB
  • Run lab.utils.add_researcher_user_table('NETID', 'full name', 'email', 'phone')
  • Note: (All data in function call should be written inside quotes)

# Add researcher to user table with PYTHON

  • Activate conda environment and start a python command line
  • import u19_pipeline.utils.insert_miscelaneous_db as imd imd.add_researcher_user_table('NETID', 'full name', 'email', 'phone')
  • Note: (All data in function call should be written inside quotes)

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