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This tutorial describes how to completely erase all data from an NiDB installation
There exists the possibility that you may need to completely erase all data from an NiDB installation. Maybe you were importing a bunch of test data and now you want to wipe it clean without reinstalling NiDB. Whatever your reason, you want to make an existing installation clean.
This procedure is not part of NiDB and there are no scripts or automated ways to do this because of the possibility of accidents. You may want to completely empty your refrigerator and toss all food in the trash, but you don't want a button available on the side of the fridge to do it.
Truncate all tables except the following
instance
modalities
modules
users
Clear the contents of the following directories. Only delete the files in the directories, do not delete the directories.
There is no need to clear the log files or lock files or any other directories.
NiDB should now be ready to import new data.
Permissions within NiDB are based on project. This probably corresponds an IRB approved project, such that certain personnel should have access to the project.
To give permissions to other users, you must have NiDB Admin permissions.
To add (or remove) a user's permissions to a project
Go to Admin-->User
Click on the username of the user you want to change
If you want to give the user global admin permissions within NiDB, check the NiDB Admin box at the top of the page. This allows the user to assign permissions to other users, and allows users to delete subjects, studies, and series, for the projects they have permissions for
To give permissions to specific projects, check the boxes next to the project name.
Project admin allows them to enroll subjects into that project
View/Edit data/PHI are not clearly separated in their functionality. Just select all of these to allow the user access to the project.
To remove permissions to specific projects, uncheck the appropriate boxes
Click Update at the bottom of the page
System-wide settings are stored in the config file. The default location is /nidb/nidb.cfg.
The NiDB Settings page allows you to edit the configuration file directly. When the page is saved, the config file is updated. But the config file can be edited manually, which is useful when the website is unavailable or you need to edit settings through the command line. To edit the file by hand, start vim from a terminal. (if vim is not be installed on your system, run sudo yum install vim)
This will start vim in the terminal. Within vim:
Use the arrow keys to navigate to the variable you want to edit
Press the [insert] key
Edit as normal
When done editing, press [esc] key
Type :wq which will save the file and quit vim
Some variables can only be changed by editing the config file directly and cannot be changed from the NiDB settings page.
offline - Set to 1 if the website should be unavailable to users, 0 for normal access. Default is 0
debug - Set to 1 if the website should print out every SQL statement, and other debug information. Default is 0
hideerrors - Set to 1 if the website should hide SQL errors from the user. 0 otherwise. Default is 0
NiDB users can have many different permissions, from complete system administration to read-only access. Most users will fall into the project-based permissions. Below are the description of each permission. Protected health information (PHI) and personally identifiable information (PII) are both referred to as PHI below.
| Permission | Description | How to grant |
|---|---|---|
You must be an an NiDB administrator to create projects.
Navigate to the project administration section of NiDB. Admin --> Front-end --> Projects. Click the Create Project button. This will show the new project form.
Fill out the information about the project. There isn't a lot of information required to create a project. Details such as templates, users, etc are created later. Descriptions of the fields:
Once you've fill out the information, click Add and the project will be created. No users will have permissions to access this project. Follow the Adding Users to Projects to add user permissions.
| Field | Description |
|---|---|
Read-only PHI
View lists of subjects/studies in project
View subject PHI
Admin --> Users --> Project permissions
Read-only imaging
All permissions from Read only PHI
Search, view, download imaging
Admin --> Users --> Project permissions
Full PHI
All permissions of Read only PHI
Modify PHI
Create or import assessment (measures, vitals, drugs) data
Admin --> Users --> Project permissions
Full imaging
All permissions of Read only imaging
Download, upload, modify, delete imaging data
Create new imaging studies
Add, modify series notes
Add, modify series ratings
Admin --> Users --> Project permissions
Project admin
All permissions of Full imaging and Full PHI
Enroll subject in project
Move subjects between projects
Move imaging studies between projects
Modify series (rename, move to new study, hide/unhide, reset QC)
Admin --> Users --> Project permissions
NiDB admin
All project-based permissions of Project admin
Manage (add, edit, remove) projects and users
Can view the Admin page
Admin --> Users
Site admin
All non-project based permissions of NiDB admin
Manage system settings
View system status & usage
Manage NiDB modules
Manage QC modules
Mass email
Manage backup
View error logs
Set system messages
View reports
Manage audits
Manage sites
Manage instances
Manage modalities
Access to "Powerful tools" on Projects --> Studies page
Manage all file I/O
All permissions available to NiDB admin
Editing the users table in Mariadb and changing the user_issiteadmin column to 1 for that user
Name
Name displayed throughout NiDB.
Project number
This can be any string of letters or numbers. This is used to uniquely identify the project and is used to automatically archive DICOM series into the correct project. If you don't have an IRB approval or cost-center number, enter a string of the format P1234ABC, where 1234 and ABC are random characters.
Use custom IDs
By default, NiDB IDs (S1234ABC format) are used. If you want to use your own IDs (for example 401, 402, 403, etc) check this box. The NiDB UIDs will still be assigned, but your custom ID will be displayed in place of the UID in most places in the system.
Instance
NiDB can contain multiple instances, or "project groups"
Principle Investigator
The PI for the project. This selection is only used for display purposes and does not create any special permissions,
Administrator
The admin for the project. This selection is also only used for display purposes and does not create any special permissions.
Start date
IRB start-date of the project
End date
IRB end-date of the project
Copy Settings
This option can be used after a project is created. This would copy settings (templates, data dictionary, connections, mappings) from another project.