1. © 2011 LabKey Software www.labkey.com LabKey Server Release 11.3 Atlas Developers Meeting 11/16/2011 Adam Rauch adam@labkey.com

2. © 2011 LabKey Software 11.2 Changes: Feedback or Usage?  New SQL Editor  ExtJS 4.0  Python API  Large external data sources  Oracle 2

3. © 2011 LabKey Software Significant Changes in 11.3  @RequiresPermissions(int perms) removed  Annotation on controller action classes  Bitmask-based permissions were replaced by class- based system two years ago  @RequiresPermissionsClass annotation only option now  Column caption generation for looked-up columns  Now, only the caption of the last column is shown  e.g., "Label" instead of “Participant Visit Cohort Label"  Affects export (Excel, TSV, and Rlabkey, but not R reports) so external tools may be impacted 3

4. © 2011 LabKey Software Client-Side JavaScript  JavaScript API:  LABKEY.Utils.getDateAltFormats()  Utils.js misc helpers: onError(), isEmptyObj(), roundNumber(), padString(), caseInsensitiveEquals()  Bug fixes, documentation  Ext JS  Upgraded to Ext 4.0.7... use Ext 4 for all new dev  Added Ext4 Store, FormPanel, GridPanel, et al  We’re migrating all our code to Ext 4; Ext 3 is now deprecated and will be removed eventually 4

5. © 2011 LabKey Software Other Scripting Languages  No real changes to Java, R, SAS, or Perl libraries  A few Perl API bug fixes  Reminder: new Python client library  Assay transform scripts  Scripts can run before inferring types: trim white space, replace “-” or “NA” with null, etc. 5

6. © 2011 LabKey Software Other Potential Areas of Interest  Support for building on JDK 7 & running on JRE 7  Nested security groups  Data browser, thumbnails, etc.  Header locking  Support for ancillary studies  Quick participant group create from any dataset  Time chart: visit map, means, multiple groups 6

7. © 2011 LabKey Software Table Layer  Table.java provides access to database tables  Hides grungy details of JDBC  Provides ORM – mapping Java objects to/from tables  Supports select, execute, insert, update, delete  Table “interface” is straightforward but inflexible  100+ static methods that munge query source, modifiers, and output formats into one parameter list  Results in telescoping parameters, method explosion  Every method throws checked SQLException, which callers can rarely handle  Also, static methods don’t share implementation well, resulting in duplication and inconsistencies 7

8. © 2011 LabKey Software New Approach: JdbcCommand  Allows much more flexible composition  Can specify Exception framework per call  Spring runtime DataAccessExceptions (default)  RuntimeSQLException  Checked SQLException (for backward compatibility)  Plan  JdbcCommand (Selector & Executor) available in 11.3  Table layer being rewritten as calls to JdbcCommands  Will extend Selector & add Update, Insert, Delete (12.1?)  Will deprecate Table layer and migrate our code away 8

9. © 2011 LabKey Software Questions? 9

10. © 2011 LabKey Software ExtJS 4.0 Example https://www.labkey.org/wiki/home/Documentation/page.view?name=ext4 LABKEY.requiresExt4Sandbox(); // Ext4 runs in sandbox mode for now Ext4.onReady(function(){ var store = Ext4.create('Ext.data.JsonStore', { fields: ['name', 'data1', 'data2', 'data3', 'data4'], data: [ {'name':'metric one', 'data1':10, 'data2':12, 'data3':14, 'data4':8}, {'name':'metric two', 'data1':7, 'data2':8, 'data3':16, 'data4':10}, {'name':'metric three', 'data1':5, 'data2':2, 'data3':14, 'data4':12}, {'name':'metric four', 'data1':2, 'data2':14, 'data3':6, 'data4':1}, {'name':'metric five', 'data1':27, 'data2':38, 'data3':36, 'data4':13} ] }); Ext4.create('Ext.chart.Chart', { renderTo: 'chartDiv', width: 500, height: 300, store: store, [... Other config params... ] }); 10