- Creating Projects
- Security Options
New users are added to TMAJ using this section. Information about
existing users may be modified here.
A group admin is an admin that only has only partial admin
rights. While an admin can change the information on any user,
project, array-block, array-slide, or specimen, a group admin can only
change some of them. Group-admins has more rights than an
ordinary user in that they can grant rights to other people in their
group. Non-admins cannot grant access to resources they own,
while a group admin can. Group admins log onto the admin
application but will only see a subset of the projects, users,
etc. Whatever group-admins can see, they can assign to users in
their group. Group admins are a great way to separate information
in TMAJ if several labs are using the same instance of TMAJ and they do
not want other labs to see their data. A group admin can be set
by setting the AdminApp setting in the Users tab in the Administrator
Passwords assigned in TMAJ must have at least 6 characters, at least 1
letter, and at least 1 number.
Passwords in TMAJ are case-sensitive.
TMAJ does not store a user's actual password, but rather a 1-way hash
of the password, so it is impossible to "lookup" somebody's
Dialog. You may
change any user's password in TMAJ by clicking on the row of the user,
and then clicking the Change Password button.
|Assign Random Password
To assign a randomly-generated password to a new user, highlight the
user's row, and click the Assign Password button.
A protocol is a description of
a scientific experiment that the Internal Review Board has given
permission for a researcher to perform.
The Protocols table is not connected to any other tables in TMAJ, and
is not required to get TMAJ to work. However, following and
keeping track of protocols is important for being HIPPA
A project is a collection of
ArraySlides. ArraySlides are added to a Project in the Projects-ArraySlides tab.
We group ArraySlides into projects so that we can give users access to
only some of the ArraySlides. Generally the only thing you need
to enter a new project is the project name. If you do not wish to
use projects in your version of TMAJ, just create one default project
and assign every arraySlide to it.
|ArraySlides are assigned to
projects in the Projects-ArraySlides tab, as shown to the right.
To add an ArraySlide to a Project:
- Log on to the Admin application
- Click on the Project/ArraySlides Tab
- Locate the Project you want to add an ArraySlide, and then
click on it. The ArraySlides currently in the project will be
displayed on the right side on the panel.
- Click the Add button. A Dialog showing every
ArraySlide in TMAJ will be displayed. Click any ArraySlides you
wish to add to the project.
- Click the Okay Button to close the Add ArraySlides
dialog. You will see the new ArraySlides added.
- Click the Save Button
Tab. This tab is used to add ArraySlides to a project.
In the Images application, security is controlled by giving users only
access to certain projects.
A project, as discussed before is merely a collection of
ArraySlides. Therefore, you limit what ArraySlides a user may
access by assigning users to one o rmore projects. This screen
allows you to assign a user to one or more projects.
Note the rules of Users-Projects do not apply to users who are
administrators. Administrators have access to all projects, no
matter what is assigned on this screen.
The ArrayBuilder application only lets users design ArrayBlocks to
which they have permission. An administrator can set which
ArrayBlocks a user may access by using this tab.
Note#1: If a user is given read-only access to ArrayBuilder, the user
may not change the design of ANY arrayblock. They may only SEE
which arrayblocks they have been assigned in this tabl.
Note#2: If an ArrayBlock has been designated as Final, no user
may modify the ArrayBlock.
Assigning Specimens To Users
An administrator may assign a set of specimens to the user. The UsersSpecimens table
actually keeps track of what specimens to which each user has access.
Note that this does not apply to users who have been given permission
to view all specimens. For them, it does not matter what is in
the UsersSpecimens table. (See SpecimensApp Permission
for details) .
There are 3 ways a user may get permission to view/modify a specimen:
- They have been given "All Access" on the SpecimensApp Permission
so that none of these rules apply.
- An administrator has manually given them access, as described
- The user created the specimen. If you create a specimen,
you automatically get access to it. (On the database level, this
means a record gets added to the UsersSpecimens table.)
to Assign Specimens to Users
Note: You must be an administrator to perform this task.
- Open the specimens application
- Click the search button to search for the specimens you
wish to assign to the user.
Use the Sort/ Filter dialog to filter out any specimens you do not wish
to assign to the user.
- Highlight the specimens you wish to assign to the
user. You can highlight multiple specimens by holding down the
CTRL button. You may select all specimens displayed by clicking
- Click the Assign button. The Assign Specimens To User
dialog will pop up.
- Choose a user
- Click the Assign button in the dialog. The
confirmation message with then pop-up saying you assigned X number of
specimens to the user.
|Specimens Application --
The highlighted specimens are in blue. The Assign Specimens to
Users dialog comes up after the Assign button is clicked.
Summary of Security Options
All 4 of TMAJ's user applications have security options that can be
set in the administator application. These security allow a user
to limit the data a user can view in the respective application.
Meta Data Tab
|This application is used to view
and modify the dynamic meta data in TMAJ.
|a type. In the Specimens
section, a SpecimenType. In the TissueDiagnosis &
ScoredImages Section, a TissueType
|a field. If the dot
is red, it means it has enumerations. If it is black, it means
the field is not enumerated (type-in).
|Meta Data Application
Buttons in the Meta Data Application
Buttons in the Meta Data Application
|Add a type, field, or
enumeration. To add an enumeration, highlight the field to which
you want to add an enumeration. To add a field, highlight the
type you want to add the field to. To add a type, highlight the
section (Specimens, TissueDiagnosis, or ScoredImages) to where you want
to add the type.
Note: TissueDiagnosis & ScoredImages both use the same types
(TissueTypes). So adding, changing, or deleting a type on one is
equivalent to doing it to the other.
|Give the highlighted entry a new
name. The highlighted entry may be either a type, field, or
|Delete the highlighted
entry. The highlighted entry may be either a type, field, or
enumeration. Note that this operation will fail if any data references this entry. Thus
this operation is relatively safe. For example, lets say you are
trying to delete a field called "Prostate Zone". The operation
will fail if the field has any enumerations. You must first
delete all the enumerations. Also, this operation will fail if
any outside data used this field to record some value. For
example, lets say some TissueDiagnosis has ProstateZone recorded and it
is set to "No Zone". There is no way to handle this from the
MetaData application. You must contact a database administrator
to delete these fields.
|Enable the buttons Add, Edit,
and Delete, so that modifications can be made to the Meta Data.
You will be prompted for the application
password. This is not the same as your user
password. Contact a TMAJ administrator to give you this password.
|disable the buttons Add, Edit,
and Delete. No one will be able to modify Dynamic Meta Data until
the Enabled button has been pressed.
|dump a description of the
Dynamic Meta Data in TMAJ to a text file.
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