When you publish a study, a new folder is created to hold the data selected for publication. But what if the data in the original study changes? How do you refresh the data in the published study?

Note that refreshing data is different from reloading data. Refreshing data applies specifically to published and ancillary studies. Reloading data refers to the process of updating study data from source files in the pipeline root. For details on reloading, see Import, Export, and Reload a Study.

Refresh Datasets

To refresh a dataset in the published study, follow the same instructions for refreshing an ancillary study. For details, see Ancillary Studies.

Refresh Specimens

If you want the published specimen data to reflect any changes/updates in the source study, the published study can be set to refresh automatically each day. If you want the published specimen data to remain static, you can specify that a one-time snapshot be made.

You can set the refresh behavior either when you create the published study or after it has been created. To change the refresh behavior after the creation of the published study: go to the published study folder, click the Manage tab, and click the View Settings button. On the Published Study Settings page, use the Refresh Specimens checkbox to indicate whether or not specimens are refreshed nightly.

The specimen refresh occurs as a part of system maintenance, which by default occurs at 2am. To set a different time of day, go to Admin > Site > Admin Console, click System Maintenance, choose a new time from the drop-down list, and click the Save button.

Specimen Refresh: User Credentials

LabKey Server refreshes the specimen data using the security credentials of the user who last modified the specimen refresh settings. The user who initiated the study publication is the initial "modified by" user. If this user is no longer able to refresh specimens (for example, they leave the research organization or their security credentials fall below folder administrator), then subsequent specimen refreshes will fail. In this situation, a different user with at least folder admin permissions in the published study should update the specimen refresh settings:

  • Login as (or impersonate) a user with at least folder permissions
  • Navigate to the published study folder
  • Go to the Published Study Settings page by clicking the Manage tab and then clicking View Settings
  • To perform specimen snapshot updates, LabKey Server uses the account identified in the Modified By field
  • Click Update to update the Modified By field
  • This will change the Modified By field to the current logged in user. LabKey Server will perform future specimen refreshes under this user account.

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