This page covers changes in 9.3 that may alter the behavior of LabKey server in ways such that your team will wish to update its usage of LabKey Server. In particular, those who write custom code or scripts on LabKey Server will benefit from reviewing these changes.

Table Schemas

Cohorts. Advanced cohort support allows participants to change cohorts over time. Changes to the study schema are minor:

  • Cohort (a foreign key to study.Cohort) has been added to ParticipantVisit.
  • InitialCohort (a foreign key to study.Cohort) has been added to Participant.
NAb. The built-in NAb assay schema has been enhanced to allow the use of advanced "Area Under the Curve" calculations. The schema has been augmented as follows:
  • Unchanged data columns:
    • Point IC<CUTOFF>. Point-based titer. <CUTOFF> represents the cutoff percentage specified for the run. Since the user can choose multiple cutoffs, a column will be produced for each cutoff chosen.
    • Curve IC<CUTOFF>. Curve-based titer, using selected Curve Fit Method
  • Enhanced run column:
    • CurveFitMethod. In addition to 4PL and 5PL, this can now be Polynomial
  • New data columns:
    • Curve IC<CUTOFF> 4PL. 4PL curve-based titer
    • Curve IC<CUTOFF> 5PL. 5PL curve-based titer
    • Curve IC<CUTOFF> Poly. Polynomial curve-based titer
    • AUC_4PL. Area under the 4PL curve fit
    • AUC_5PL. Area under the 5PL curve fit
    • AUC_Poly. Area under the Polynomial curve fit

XML Schemas

Study import/export. The new “isMvEnabled” boolean element in tableInfo.xsd is now used by datasets_metadata.xml. The “mvColumnName” attribute has been deprecated because “isMvEnabled” better matches the schema.tsv property.

R Column Names

Some column names for labkey.data have changed, so you may need to update your scripts. Some names have gotten longer because additional characters were necessary to guarantee that names were unique. You can see the new names by calling names(labkey.data) at the start of your script. To avoid the potential need to update column names in the future, it may be helpful to simply set the names of labkey.data's columns to predictable values at the start of each script.

Java Remote API

Please use the newest version of the Java API jar (v9.3). This jar will work against both new and older servers. It fixes a problem with parsing dates that do not include at time zone.

Deprecated Components

The following components have been deprecated for some time and are no longer available in LabKey Server 9.3:

  • Postgres 8.1. Please upgrade to Postgres 8.3. It is now required.
  • Perl Cluster Pipeline. Please move to the Enterprise Pipeline.

Automatic Upgrades for External Components

Tomcat v5.5.27. Tomcat v5.5.27 is installed automatically with the LabKey v9.3 installer for new installations of LabKey Server. Upgrading an existing LabKey installation to v9.3 will not upgrade the Tomcat version automatically. If you wish to upgrade Tomcat from v5.5.20 to v5.5.27 for an existing LabKey installation, you will need to do it manually.

JRE v1.6.0-10. Upgrading an existing LabKey Server to v9.3 will upgrade the JRE from 1.5 to 1.6 automatically if and only if the JRE 1.5 was installed by the LabKey installer. In other words, if you are running a JRE 1.5 that you installed yourself, external to the LabKey installer, you will be on your own to upgrade it if you wish to do so. An upgrade to the 1.6 JRE isn't required for LabKey v9.3, but likely will be for LabKey v10.1 or v10.2.

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