v1.4.3

Fix hideGenelist accessor in the user profile template, which resulted in an error. For now on, property names will be used across all templates, and Thymeleaf will be tasked with inferring the right accessor.

Before running this migration, ensure that no email is duplicated. You can list users with duplicated email with the following SQL query:

select *
from user
where email in (select email
                from user
                group by email
                having count(email) > 1);

You should then take action by removing or merging those users. We recommend removing those with the latest user_id fields, but this is ultimately at your discretion.

v1.4.2

Restore rdp.site.shortname and rdp.site.fullname in application.properties since they're still being used in the
user FAQ.

Fix missing TaskExecutor when using an HTTP proxy. It now uses native-Dhttp.proxyHost and -Dhttp.proxyPort JVM
flags; the proxy settings in SiteSettings and InternationalSearchSetings have been simply removed.

Interpolate shortname and URLs in messages.

Move all email text into messages.properties, so they can be adjusted and translated

Fix missing flash messages after confirming registration and contact email.

Fix /api/users API endpoint for registries that are not using gene-level privacy. In this case, the gene privacy level
is always set to null and the value in the profile must be used instead as a fallback.

Require MySQL 5.7+ and add instructions for using MySQL 5.6 and prior. This is due to a index size limit that is busted
with access and verification token when 4-bytes character encoding is used (i.e. utf8mb4).

Fix incorrect primary key for researcher categories that resulted in the impossibility of adding more than one category
to a given user profile.

v1.4.1

This patch release addresses some issues encountered while running the 1.4.0 in a production setup.

Defaults for the Ehcache have been vastly improved, allowing more users and genes to be cached.

Fix URLs encoding which posed an issue since random token can contain '+' signs.

Fix regression when parsing TierType values. The ANY has been inadvertently changed to TIER_ANY, and TIERS1_2 to TIER1_2.

Validate the database schema on startup. If you are getting error from Hibernate validation with this release, please get in touch with our dev team to adjust your database.

Hide the FAQ menu option if rdp.settings.faq-file is undefined.

If you are still running RDP from the 1.3 series, you must update to 1.3.4 to operate with a 1.4 registry. This is due to the unfortunate default behaviour of Jackson to choke on unknown properties when deserializing JSON.

v1.3.4

This release addresses an issue with Jackson deserialization to allow communication with a 1.4 registry and beyond.

v1.4.0

Service accounts

Service accounts are special kind of users that are used to authenticate external services that
integrate with RDP.

Extensions to the user profile

Users can pick a researcher position to indicate if they are a Principal Investigator.

User profiles now feature researcher categories, allowing search results to be narrowed by a specific kind of expertise.
These categories include in vivo, in vitro and in silico denominations.

Organ systems

Users can select a set of organ systems they focus their research on. These organs are based
on Uberon multi-species anatomy ontology
and a set of icons kindly provided by Shinya Yamamoto Lab in
Houston.

Gene privacy levels

User now have more granularity in how they pick the privacy levels of their individual TIER1 and TIER2 genes. They can
either choose to have it tied to the profile.

Anonymized search results and match request

Search results that are not available to a given user for privacy reasons can be anonymized. A new feature called
"Request Access" allow the user to reach out to the researcher.

More robust security

RDP now fully integrates Spring Security features with its privacy levels making sure that no information leaks in the
wrong hands.

Up-to-date cached data

Cached data (including gene information, orthologs, GO terms, etc...) and their corresponding user associations are
updated monthly and don't impede the boot time (except for GO terms and gene2go annotations).

Gene information are stored in the database, allowing very efficient queries of orthologs.

Database improvements

Complete integration of Flyway to manage production database migrations.

Initial data is part of the migration process.

Eliminate eager fetching of model relationships in favour of more selective optimized fetch join queries where it is
truly needed.

Orthologs are now a proper many-to-many relationship that uses efficient SQL jointures.

Canonical search URLs

Search feature not produces canonical URLs that can be shared.

Dependencies updates

• move to Spring Boot to 1.5.22 (the latest stable release of the 1.5 series)
• use jQuery 3.2.1 consistently
• use external resources from CDN

v1.3.2

 - add Flyway for performing database migration
 - fix type of modification_date in gene table

v1.3.1

This release fix a bug with date parsing from NCBI gene info format.

v1.3.0

Added configuration allowing re-configuration of proxy server for the international search.

Using a proxy server for international search

Configure by adding the follow application.properties configuration.

### Proxy settings (optional) ### 
rdp.settings.isearch.host=
rdp.settings.isearch.port=

Where rdp.settings.isearch.host is the proxy host address, and rdp.settings.isearch.port is the required proxy port. No change is required if not using a proxy server.

pre-release_v1.2.10

Development version allowing re-configuration of proxy for the international search.

v1.2.10

Updated embedded tomcat version to version 8.5.41 via the pom.xml file.