This topic is under construction for the 18.1 release of LabKey Server. For current documentation of this feature, click here.
The Adjudication Folder Administrator performs these steps to configure the adjudication folder and tools.
Note that the role of folder administrator does not include global permissions within this type of folder, and specifically does not include Adjudication Lab Personnel
permissions. Only adjudicators and designated lab personnel can see and edit the information on role-specific tabs they will use in the process.
Set Up the Adjudication Folder
- Create a new folder of type Adjudication.
- All users with folder read permissions are able to view the Overview tab. The wiki there is intended to be customized with protocol documents or other framing information, but should not reveal anything not intended for all adjudicators and lab personnel.
- The available tabs and which users can see them are shown in the following table:
|Tab Name||Adjudication Roles Granting Access|
|Overview||All users with Read access to the folder.|
|Administrator Dashboard||Administrators, Lab Personnel, Infection Monitors, Data Reviewers|
|Infection Monitor||Administrators, Infection Monitors|
Manage Adjudication Options
The Manage Adjudication
web part on the Manage
tab includes four configuration sections:
Admin SettingsRequired Filename Prefix:
Specify the file prefix used for uploaded cases. Options are:
- Parent Folder Name
- Parent Study Name (requires that the adjudication folder be of type "Study").
- Text: Enter expected text in the box, such as "VTN703" in this example.
The format of a case filename is [PREFIX]_[PTID]_[DATE].txt
- PREFIX often corresponds to the study. It can be generated using a folder name or text, and when specified in this field, is required on any file uploaded. Prefixes are checked for illegal characters, and if you leave the text box blank, the filename is expected to be "_[PTID]_[DATE].txt.
- PTID is the patient ID.
- DATE is specified in the format: DDMMMYYYY. A two digit day, three character month abbreviation, and four digit year.
In our example, the filename is "VTN703_123456782_01Aug2015.txt".Number of Adjudicator Teams:
Select the number of Adjudicator Teams
(from 1 to 5, default is 2).Adjudication Determination Requires:
: Specify what diagnoses are required in this adjudication. Options:
- Both HIV-1 and HIV-2
- HIV-1 only (Default)
- HIV-2 only
Once a case exists in the adjudication folder you will no longer be able to edit the admin settings, so the web part will simply display the selections that apply. Click Save
to save the Admin Settings
Customize Assay Results Table (Case File Format)
The uploaded case file must be named with the correct prefix
, and must include all these columns at a minimum:
- AssayKit (kits must be on the supported list)
Any other columns present in the case file that you want to be able to access within LabKey must also be present in the assay results table. Any columns present in the uploaded case file which are not
included in the assay results table will be ignored. At the time of upload, the user will be warned that the extra columns will not be stored anywhere, but the upload will proceed successfully.
To see current fields or add additional fields to the assay results table, go to the Manage
tab, and in the Manage Adjudication
web part, click Configure Assay Results
. Review or change the list of properties and click Save
Assay values uploaded are both case-insensitive (i.e. GEENIUS, Geenius, geenius are all accepted) and spacing-insensitive (i.e. "Total Nucleic Acid" and TOTALNUCLEICACID are both accepted). Dates within the uploaded data are converted to four digit representations (i.e. '16 will be displayed as 2016).
Set Module Properties
Some administrative settings can be configured as module properties, giving you the ability to make changes after initial case creation in the folder. From the Manage
tab, under Manage Adjudication > Module Propeties
, click Configure Properties
.Property: Protocol/Study Name
: The display name to use in email and case results header pages. Can be specified at the site, project, and/or folder level.
Property: Automatic Reminders
: Use checkboxes to send daily email reminders to adjudicators of cases that are open
for a given scope. Options: Site, project, folder level.
Assign Adjudication Roles and Permissions
In the adjudication process, the objective is adjudication determinations which are reached independently and blinded to each other. Each Adjudicator Team
can be a single person, or may include an additional backup person in case they are unavailable. Both team members are equally empowered to make the determination for the team.
The Adjudication Users
table on the Manage
tab is used to give access and roles to users within this folder. No user can appear twice in the table, and when you insert a new user and grant one of the adjuication roles, you assign the relevant permissions automatically. No explicit setting of folder permissions is required.
You will need to identify at least one member of lab personnel and at least one member of each adjudication team. Additionally, you can assign the other roles for notification and data access purposes. Additional people to be notified may also be specified and carry no distinguishing role.
- Click the Manage tab.
- On the Adjudication Users table, click (Insert New Row)
- Select the user from the dropdown.
- Select the role from the dropdown. Options are:
- Data Reviewer
- Folder Administrator
- Infection Monitor
- Lab Personnel
- To Be Notified
- Click Submit.
- Repeat to add other necessary personnel to fully populate the table.
Assign Adjudicator Team Members
The Adjudicator Team Members
web part is populated with the defined number of teams and pulldowns for eligible users. Users given the role Adjudicator
in the Adjudication Users
web part will be available to select from the team member pulldowns. You must select at least one adjudicator per team. If you select a second, or "backup" adjudicator for one or more teams, no distinction is made between the back-up and primary adjudicator within the tools; either may make the adjudication determination for the team.
Use the Send notifications
checkboxes to select which adjudicators will receive notifications for each team. In circumstances where both adjudicators are available and receiving notifications, they will communicate about who is 'primary' for making decisions. If one is on vacation or otherwise unavailable, unchecking their checkbox will quiet notifications until they are available again.
This screencap shows the two web parts populated using example users assigned to the roles. The Name
column shows the Role Name, not the user name. There is one of each role, plus a total of four adjudicators. Adjudicators 1 and 3 make up team 1, and adjudicators 2 and 4 are team 2.
To change adjudication team assignments, first delete or reassign the current team members using the edit or delete links on the table, then add new users. You can only have two users on each team at any time. When you assign a user to a role in this table, the associated permission is automatically granted; you need not separately set folder permissions. Likewise, when you remove a user from any role in this table, the associated permission is automatically retracted.
Specify Supported Assay Kits
The folder administrator also defines which assays, or assay kits, are expected for the cases. All assay kits available are listed in the Kits
table. The Manage
tab Supported Assay Kits
web part shows kits for this folder. To add a kit to this list:
- Click Insert New Row in the Supported Assay Kits web part.
- Select the desired kit from the pulldown.
Define Assay Types
The administrator also defines the assay types to be made available on the case details page.
- Navigate to the Manage tab.
- In the Assay Types webpart, you will see listed the currently supported assay types.
- To add a new assay type, click (Insert New Row).
- Name (Required): This will match the assay type column in the uploaded case file.
- Label: This label (if provided) will be shown on the adjudication case details page. If no label is provided, the name is used.
- Click Submit.
Deleting values from the Assay Types
list will stop that assay type from appearing the adjudication case file, but the data uploaded will still be stored in the adjudication tables.
The adjudication lab personnel can now use their tools within the folder to initiate a case. See Initiate an Adjudication Case
for the steps they will complete.
If additional columns are necessary, or changes must be made to assigned personnel later in the process, you (or another folder administrator) will need to perform the necessary updates.