Release Notes

Release notes are now available from GitHub. Those here are kept for historical reasons.

1.4.6

This release has a few fixes that provide better user feedback during registration and while updating the user profile.

Fix deletion of user in the administrative section. Its associated tokens were somehow set to NULL by Hibernate before being deleted.

Hide research focus in the user profile if nothing has been entered.

1.4.5

This release resolves an issue with slow SMTP servers causing a proxy timeout by sending emails asynchronously.

Cleanup usage of @Transactional annotations in the service layer and reorganize email logic in the services instead of controllers. This way, we ensure that the email is sent whenever the transaction that involve creating a token — or whichever relevant entity — is committed.

1.4.4

Use the build version for the OpenAPI specification so that it is always up-to-date.

Fix calculation of human gene coverage, the orthologs were commented out and the SQL query has been added.

Fix field length in the profile to use the value previously set in profile.css. The CSS code it contains as well as other files have been merged in common.css. A flexbox is used for the email since it needs to also account for the verify button.

1.4.3

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.

Since these users are not valid, you will have to remove the verification token that was generated at registration before removing the user itself:

delete from verification_token where user_id = ?;
delete from user where user_id = ?;

1.4.2

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.

1.4.1

This patch release fix 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.

1.4.0

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