The
assayRequest module expands the functionality of LabKey's generic
issue tracker, providing a workflow designed especially for the assaying of specimens and samples, providing a collaboration tool that ties together the various elements of the work to be completed in a single trackable ticket.
This topic explains how to set up a new assay request tracker.
General documentation of the issue tracker is available here:
Issue Tracker: Administration.
To set up a new Assay Request tracker, first you define a new issues list (of type Assay Request Tracker), then you add the tracker user interface.
Create a New Issue List Definition
- First, enable the AssayRequest module in your project or folder.
- Go to > Go To Module > Assay Request.
- On the Issue List Definitions page, click (Insert New Row).
- Under Insert Issue List Definitions, enter:
- Label: for example "Assay Jobs"
- Kind: select Assay Request Tracker.
- Click Submit.
- Click Yes, when prompted by the popup dialog titled Create Issue List Definition? to confirm the location of the list creation.
- You will be taken to the administration and configuration page for your assay request tracker.
- Click Save to use the default configuration. You can return to this page later to refine the configuration.
- Now you have defined a new tracker list. Now you can add it to your folder.
Add the Assay Tracker UI to a Folder
- Go to the location where you wish to place the assay jobs list.
- Add the web part Issues List.
- On the Customize Issues List page, on the Issue List Definition dropdown, select the label of the list you entered previously, for example "assayrequests". Notice that your label has been converted to a single lowercase string without whitespace.
- If you like, enter an optional title to use. If you leave this space blank, this web part will be named "Assay Requests List: assayrequests".
- Click Submit.
- Your assay tracker is ready for use.
Administration and Configuration
Administrators can customize the assay request tracker in the following ways:
- Set the available values in dropdowns on the request form, including the priority ratings, the request groupings, and resolution states. (For details, see below.)
- Link assay requests, specimens, and result data for easy navigation. (For details, see below.)
- Select the noun used to identify the request or issue. By default the AssayRequest modules uses "Assay Request", but this can be changed as desired. For details, see Issue Tracker: Item Naming.
- Configure the users who can be assigned requests. For details, see Issue Tracker: Assignment Options.
- Select the default user (if any) to be assigned new requests. For details, see Issue Tracker: Assignment Options.
- Change the display labels for fields, and many other field properties. For details, see Issue Tracker: Administration.
- Customize email notification templates. For details see Customize Email Notifications.
Control Dropdown Values
When a new assay request tracker is created, three lists are created that hold the dropdown values for the following fields: 'Area', 'Priority', 'Resolution'.
An administrator can alter these lists to provide dropdown values that best fit their project. To change these lists, go to
> Manage Lists. Select one of the lists, and update as desired. Note that the list names include the name of your assay request tracker, here "assayrequests".
| Dropdown Field | List Name | Description |
|---|
| Area | list.assayrequests-area-lookup | Holds different groupings of issues/requests, for example, 'HPLC', 'Sequencing', and 'Viability'. |
| Priority | list.assayrequests-priority-lookup | This list holds possible priority rankings for a request/issue. By default, the list includes numbers 1 through 5, where priority 1 is intended to mean highest priority, and priority 5 the lowest priority. |
| Assay | assay.AssayList | Points to the list of assays in scopeof the current folder (i.e., the assay designs that live in the current folder, the current project, and the Shared folder). When creating an assay request, this list is presented to the user as a dropdown used to specify which assay is to be run against the samples. Note that an assay design must have a batch or run level field that is a lookup to the assay request tracker. Once the lookup has been added to an assay design, it will be shown in the dropdown field of assays the requester can select. See "Linking Assay Data to Requests" below for details. |
| Assign To | This dropdown is controlled by pointing to project-level security groups, not an individual list. | For details see Issue Tracker: Administration |
| Resolution | list.assayrequests-resolution-lookup | This list holds possible resolution states for a request. By default three resolution states are included: 'Completed', 'Duplicate', and 'Rejected'. |
Link Assay Data to Requests
Assay data can also link back to the originating request. To provide links from assay data/designs to the request tracker, add a lookup that points to the issue tracker. (Note that this step is necessary for populating the Assay dropdown in the request tracker.)
- Go the Run or Result view on the assay design you wish to modify.
- Open the assay designer. From the Run or Result view of the assay data, select Manage Assay Design > Edit Assay Design.
- In the Assay Designer, scroll down to the Run Fields area and click to expand it.
- Add a new run field by clicking Add Field.
- Name the field "assayRequest" (no spaces) and set the Data Type to 'Lookup'.
- In the Lookup Definitions Options:
- Set the Target Folder to the location of the assay request tracker
- Set the Target Schema to "issues"
- Set the Target Table to "assayrequests(Integer)" (or the name of your assay request tracker).
Once the lookup column has been added, people working with the assay data can point to the originating request when importing the assay runs.
Related Premium Resources
Related Topics
