Install SAS/SHARE for Integration with LabKey Server

Documentation

Overview

Publishing SAS datasets to your LabKey Server provides secure, dynamic access to datasets residing in a SAS repository. Published SAS data sets appear on the LabKey Server as directly accessible datasets. They are dynamic, meaning that LabKey treats the SAS repository as a live database; any modifications to the underlying data set in SAS are immediately viewable on LabKey. The data sets are visible only to those who are authorized to see them.

Authorized users view published data sets using the familiar, easy-to-use grid user interface used throughout LabKey. They can customize their views with filters, sorts, and column lists. They can use the data sets in custom queries and reports. They can export the data in Excel, web query, or TSV formats. They can access the data sets from JavaScript, SAS, R, and Java client libraries.

Several layers keep the data secure. SAS administrators expose selected SAS libraries to LabKey. LabKey administrators then selectively expose SAS libraries as schemas available within a specific folder. The folder is protected using standard LabKey security; only users who have been granted permission to that folder can view the published data sets.

SAS Setup

Before SAS datasets can be published to LabKey, an administrator needs to do three things:

  • Set up the SAS/SHARE service on the SAS installation
  • Set up the SAS/SHARE JDBC driver on the LabKey web server
  • Define SAS libraries as external schemas within LabKey
Set up the SAS/SHARE server. This server runs as part of the SAS installation (it does not run on the LabKey server itself). SAS/SHARE allows LabKey to retrieve SAS data sets over an internal corporate network. The SAS/SHARE server must be configured and maintained as part of the SAS installation. The LabKey installation must be able to connect to SAS/SHARE; it requires high-speed network connectivity and authentication credentials. SAS/SHARE must be configured to predefine all data set libraries that the LabKey installation needs to access.

Set up the SAS/SHARE JDBC driver. This driver allows LabKey to connect to SAS/SHARE and treat SAS data sets as if they were tables in a relational database. The SAS/SHARE JDBC driver must be installed on the LabKey installation. This requires copying two .jar files into the tomcat/lib directory on LabKey. It also requires adding a new DataSource entry in the labkey.xml file on LabKey containing several connection settings (e.g., SAS/SHARE URL and credentials). See External SAS Data Sources.

Define SAS libraries as external schemas within LabKey. A folder administrator chooses which SAS libraries to publish in a LabKey Server folder via the Schema Administration user interface. If a SAS data source is defined in the labkey.xml file, the "Data Source" drop-down list contains the name of this data source as an option. After selecting the data source, the administrator selects the schema (library) name to publish. After clicking the “Create” button, all data sets in that library are published; in other words, they can be viewed by anyone with read permissions in the folder.

For further instructions on how to choose an external schema, see Set Up an External Schema.

Usage

Once defined via the Schema Administration page, a SAS library can be treated like any other database schema (with a couple important exceptions listed below). The query schema browser lists all its data sets as “built-in tables.” A query web part can be added to the folder’s home page to display links to a library’s data sets. Links to key data sets can be added to wiki pages, posted on message boards, or published via email. Clicking any of these links displays the data set in the standard LabKey grid with filtering, sorting, exporting, paging, customizing views, etc. all enabled. Queries that operate on these datasets can be written. The data sets can be retrieved using client APIs (Java, JavaScript, R, and SAS).

Limitations

The two major limitations with SAS data sets are currently:
  • SAS data sets can be joined to each other but not joined to data in the LabKey database. Any attempt to join between different databases (e.g., a table in PostgreSQL with a data set in SAS) results in an error message.
  • The SAS/SHARE JDBC driver provides read-only access to SAS data sets. You cannot insert, update, or delete data in SAS data sets from LabKey.

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