Specimen Queries

The "Specimens" table has been split into two new tables, "Vials" and "Specimens," to enhance query speed. This means that you will need to reference one additional table when you use the raw specimen tables perform a lookup.

Queries that use the raw specimen tables will need to be updated. However, queries that use the special, summary tables (Specimen Detail and Specimen Summary) are unaffected and do not need to be modified.

Example: A 9.1 query would have referenced the PrimaryType of a vial as follows:

SpecimenEvent.SpecimenId.PrimaryType

A 9.2 version of the same query would reference the PrimaryType using "VialId," a column in the new "Vials" table:

SpecimenEvent.VialId.SpecimenId.PrimaryType

The Vial table contains: rowID (of the specimen transaction record), globalUniqueID (of the vial), volume and specimenID. The Specimen table contains: participantID, visit number, date, primary type and rowIDs (of the vials generated from this specimen).

Upgrade Note: If you have changed your specimen database using PgAdmin, you may have problems during upgrade. Please see a member of the LabKey team for assistance if this is the case.

Specimen Import

Specimen import is now more lenient in the conflicts it allows in imported specimen data. Previously, import of the entire specimen archive was disallowed if conflicts were detected between transaction records for any individual vial. In 9.2, all fields with conflicts between vials are marked "NULL" and the upload is allowed to complete.

Use a saved, custom view that filters for vials with the "Quality Control Flag" marked "True" in order to identify and manage vials that imported with conflicts.

Example: In 9.1, a vial with a single globalUniqueSpecimenID was required to have the same type (blood, saliva, etc.) for all transactions. Vials that listed different types in different reaction records prevented upload of the entire archive. In 9.2, the conflicting type fields would be marked "NULL" such that these vials and their problematic fields can be reviewed and corrected after upload.

PostgreSQL 8.3

PostgreSQL 8.2 and 8.1 are unsupported on LabKey Server 9.2 and beyond, so you will need to upgrade.

Security Model

Extensive changes have been made to the security model in LabKey Server 9.2. Please see the Permissions and Roles spreadsheet for a detailed mapping of permissions under the old model to permissions under the new.

View Management

For 9.2, the "Manage Views" page is accessible to admins only. This means that nonadmins cannot delete or rename views of their own creation, as they could previously. Delete/rename ability will be restored for nonadmins in a future milestone.

MS2 Metadata Collection

The metadata collection process for mass spec files has been replaced. It is now based on the assay framework.

Wiki Attachments

Authors of wiki pages now have the option to show or hide the list of attachments that is displayed at the end of a wiki page. If displayed, the list of attachments will now appear under a bar that reads "File Attachments." This bar helps distinguish the attachment list from the page list. For portal pages where display of this bar is undesirable, you can use CSS to hide the bar.

Quality Control (QC)

The "QC Indicator" field is now called the "Missing Value" field.

Folder/Project Administration UI

The "Manage Project" menu under the "Admin" dropdown on the upper right (and on the left navigation bar) has changed. The new menu options available under "Manage Project" are:

  • Permissions (For the folder or project-- you can navigate around the project/folder tree after you get there)
  • Project Users (Equivalent to the old "Project Members" option)
  • Folders (Same as the current "Manage Folders," focused on current folder)
  • Project Settings (Same as existing option of the same name, always available for the project)
  • Folder Settings (Available if the container of interest is a folder. Equivalent to the old "Customize Folder." Allows you to set the folder type and choose missing value indicators)

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