Allow usage of @Autowired in the CLI definitions since they are loaded
as beans.

Deprecate most of the AbstractSpringAwareCLI logic since it can now be
done via annotations.

Use ApplicationContext in GemmaCLI and SpringContextUtil so that we can
reuse the component scan logic via getBeansOfType.

Merge workerContext with cliContext as we don't need to make
distinctions between the two.

Unfortunately, it appears that this error arises when there is high
contention on this specific call.

Inline removeForExperiment() to make sure that findByInvestigation() and
remove() happens in a single transaction.

…gent transaction isolation level

This essentially locks the database to prevent dirty read. It's not
ideal, but it fixes the problem in a definite manner.

Revert some changes in 4cfb329 since we
don't need to deal with StaleStateException anymore.

Relates to #400.

Use a finally block to close the scrollable results.

Replace two unnecessary usage of scroll() that should be simplified by
a more efficient list() call.

update home page slide show to show only database stats
hide diff ex and coex search from home page
hide some features from navigation menus
gene page some tabs and some details hidden
remove social media link
update copyright date
refer to #154

Only include tests marked by the UnitTest category for
maven-sure-fire-plugin.

Include all test ending with Test.java and exclude those marked by the
UnitTest category for integration tests.

Use integration-test and verify goals for maven-jasmin-plugin as it
require a fake browser.

…egration-tests

Use maven-failsafe-plugin to handle integration tests

Only retain the taxon-based constructor that lookups the configuration.

Move commons-io to the root pom

Related to #259 although we haven't changed the package naming yet.

Fix typo in PubMedSearchTest test name.

Make it an error to pass -testing/--testing in the command arguments.

Add an option in Gemma.properties to make a more stringent check on
boot.

Use package-level annotations.

Fix all mis-annotated depending APIs by adding @nullable or fixing cases
where null should be handled.

Usage of HibernateDaoSupport is currently the only thing blocking us
from moving to Hibernate 4 while remaining with Spring 3 as this
configuration only support the SessionFactory injection.

Inject a SessionFactory wherever a HibernateDaoSupport is used and
replace calls with equivalent calls.

Replace a few list().iterator().next() approaches with uniqueResult().

Replace doInHibernate() with a @Transactional-annotated method.

Replace convertHibernateAccessException() usages to direct call as the
majority of code does.

…crete class

…332)

Emit a warning when the password is masked.

Allow reflective JDK access to java.lang.

This warning is irrelevant only in a test environment where the database
usage does not reflect reality.

The hashCode() definition was based on @EqualsAndHashCode(callSuper=true),
which does not merely invoke the super.hashCode(), but also include all
the fields in the annotated class.

…fix for surefire

…ExperimentCount()

… refreshed

Fix cases where the method was used on a non-unique property.

Add missing @repository annotations for implementations of BaseDao.

Eliminate states in the persister which is absolutely not thread-safe
and creates problems when rolling back. Instead, pass around a new
AbstractDao. Caches object that holds caches that various persister
implementations can reuse.

Have unique implementations for persist() and persistOrUpdate() and a
protected doPersist and doPersistOrUpdate hierarchy.

Remove redundant null-checks and fix all cases where a null can be
passed.

Hide as many implementation details as possible by marking specific
persisters as protected or private.

Remove isTransient() in favour of getId() != null check.

With the persist() in AbstractDao, there is no need to check if the
entity is already persistent before invoking AbstractDao.create().
Incorrect usage will result in a detached entity exception.

Add basic tracing in AbstractDao.

The upcoming gsec release organizes its resources under gemma.gsec
package.

Only apply retries on transactional service method or method explicitly
annotated with @retryable.

Remove RetryExceptionCauseClassifier and RetryPolicy in favour of the
default ones from Spring Retry. For the policy, there was already a flag
for walking up the causes.

Add tests for applying the retry policy in various scenarios.

This allows testing a CLI as we authenticate in the setup phase.