Summary of tranSMART 16-2 changes in i2b2/TM 18.1-beta

New features for i2b2/tranSMART

optional support for Auth0 authentication
- new optional plugin
simplify access to current username, user id, roles, etc. via new SecurityService
added simple Spring Security role hierarchy
removed passing AuthUser to methods that always work on the current authenticated user, moving the lookup to where it's used
button added to Dataset Explorer to display samples are available for a given cohort in the Sample Explorer

These changes will be included in the next tranSMART release 16.4 later in 2018.

upgraded to Grails 2.5, Servlet API 3, Java 8
tests cleanup, converted to Spock
deleted many lib directory jars and replaced with BuildConfig dependencies
removed many unused methods, some unused classes, org.json source classes, duplicate classes (e.g. many in both transmartApp and transmart-java)
code formatting and consistency
updated logging to use Slf4j wrapper and parameterized logging for performance and to help with Grails 3 Logback migration
converted most Config lookups to use Spring's @Value annotation
use "private @Autowired" for dependency injection to reduce API pollution
replaced many uses of 'def' with actual types, particularly in method signatures
converted many cases of copy/paste to use methods
domain class cleanup, removed many unnecessary declarations
converted controller closures to methods
controller params simplifications
some removal of logic in GSPs, moving to controller/services (much more needed)
updated sql queries to include schema+table instead of adding many db synonyms
deleted deprecated AccessLog class and changed to use AccessLogEntry and AccessLogService
where possible annotated classes and methods with @CompileStatic for performance
StringBuffer -> StringBuilder
split transmart-extensions into three projects, split out transmart-core-db-tests
moved filters classes from grails-app/conf to grails-app/filters
some SQL injection fixes
some conversion of simple Java classes to CompileStatic Groovy