Setting up and configuring the specimen repository is a task done by a folder administrator. Even if you will not be acting as the administrator on a production server, you can explore the process by completing these steps as an admin on your own local evaluation server using our sample data. If you do not already have a sample study to work with locally, you can download and import the pre-prepared sample study as described on this page: Set Up the Sample Study
When you import the sample study, it includes a specimen repository with an archive already uploaded. More about importing archives and other administrative tasks can be found in Specimens: Administrator Guide
Select Specimen Repository Settings
Basic options like the type and editability of your repository are covered by the options in the Specimen Repository Settings
section of the manage menu.
Change Repository Type
- Navigate to the home page of the sample study.
- Click the Manage tab.
- Under Specimen Repository Settings, select Change Repository Type.
- Select Advanced (External) Specimen Repository (if it is not already selected). Two advanced options are available:
- Specimen Data options are:
- Read-only: Specimen data is read-only and can only be changed by importing a specimen archive.
- Editable: Specimen data is editable.
- Specimen Requests options are:
- Enabled: The system will allow users with appropriate permissions to request specimens, and will show counts of available specimens.
- Disabled: Specimen request features such as the specimen shopping cart will not appear in the specimen tracking user interface.
- For this tutorial, Advanced Specimen Repository, Read-only, and Enabled should be selected.
- Click Submit.
Edit Specimen Properties
This option allows you to modify the default specimen properties. You can assign custom labels, add new properties, and remove unused ones to best suit your specimen repository. For this tutorial, make no changes. For more information, see Specimen Properties and Rollup Rules
Manage Display and Behavior
- Click the Manage tab.
- Under Specimen Repository Settings, select Manage Display and Behavior.
- Review options available (described below).
- For this tutorial, make no changes.
- Click Cancel to avoid saving accidental changes.
Specimen display settings available:
- Comments and Quality Control:
- Default Mode: The specimen system can function in two modes. Users with appropriate permissions can always manually switch modes.
- Request Mode: Vials are requested and requests are managed.
- Comments Mode: Vial information itself can be modified.
- Manual QC flagging/unflagging: Vials are automatically flagged for QC at time of import if a vial's history contains conflicting information. Enable manual QC flagging/unflagging to allow these states to be changed without updating the underlying specimen data. Once a vial's QC state is set manually, it will no longer be updated automatically during the import process.
- Low Vial Warnings. If enabled, the specimen request system can display warning icons when supplies of any primary specimen are very low (zero or one available). An icon will appear next to all vials of that primary specimen.
- Display one available vial warning: Select whether to show for all users, administrators only, or never.
- Display zero available vial warning: Select whether to show for all users, administrators only, or never.
Configure Specimen Groupings
You can decide which specimen groupings to display by default in the Specimens web part. The default groupings are sufficient for this tutorial. To read about the options available, see Customize Specimens Web Part
Populate the Repository
The administrator loads specimen data into the repository, either from a spreadsheet or from a specimen archive
. For this tutorial, the specimen archive has already been imported with the sample study. For more about uploading data, see Import a Specimen Archive
Assign Specimen Requester and Coordinator Permissions
Specimen data can be made available to others via the usual read or edit permissions within the given study folder. Two additional permission levels are provided to support specimen request tracking:
- Specimen Requester permission is required to place a request or view the status of requests in process.
- Specimen Coordinator permission is offered as an intermediate administrative level for the individual tracking requests through the approval and fulfillment process without requiring full administrative permissions throughout the study.
These specialized roles do not automatically include any other access to resources, so users must also be assigned at least Reader
permission on the folder in order to use them.
To complete the tutorial, you can continue with admin permissions, or choose to explore the other permissions levels using impersonate roles
- Click the Overview tab (so you start on a page that a Reader can view).
- From the pulldown menu for your username (in the top right corner), select Impersonate > Roles.
- In the popup, click the boxes for both Reader and Specimen Coordinator.
- Click Impersonate.
You will now to see your project and folders through the eyes of a user assigned the "Specimen Coordinator" role.
For details about defining users and granting permissions, see Configure Permissions