v1.5.9

This patch release contains a fix for a critical bug affecting ontology updates and other minor improvements.

• fix a bug when parsing ontologies that contain foreign terms without names
• add links to profile website and phone
• display emails for remote profiles

v1.5.8

This release adds two important features for preventing bots from registering: a reCAPTCHA challenge on registration and a mechanism for administrators to restrict which email providers can be used for creating new accounts. To accommodate registries outside North America, we added support for internationalized domain names. Read more about this feature here.

We also addressed numerous bugs with the GO term recommendation feature. It is now more reliable and provides feedback to the user when terms cannot be recommended. It can detect cases where, for example, there are no GO terms available for a given model organism.

A few more issues were resolved:

• fix a bug when creating or revoking an access token from the admin section: the session was inadvertently set to read-only
• reduce memory usage when parsing the gene2go file by ignoring irrelevant lines
• fix display of non-grouping terms on the public profile: it now reflects the user selection instead of enumerating all the options
• limit which fields can be set when registering or creating a service account
• update yauaa to 7.24.0
• ignore TIER3 genes from GO terms with more than 50 associated genes; the term can be added but its genes won't

v1.5.7

This release addresses an issue with password reset and verification tokens that can be consumed by a third-party (i.e. an anti-virus software that analyses emails) by adding a minimal User-Agent-based challenge.

• implement a challenge for validating password reset and verification tokens
• redirect to the login page if a token was already used
• strip authentication token when logging errors in RemoteResourceService
• allow service accounts to be used as remote search user
• set the User-Agent header with rdp/{version} when communicating with partner registries
• use the production mode when bundling resources with Webpack
• update Spring Boot to 2.6.15
• update frontend dependencies

v1.5.6

• ensure that pending emails are sent on shutdown
• fix email configuration shadowing (regression from 1.5.5)
• rename "Organ Systems" to "Human Organ Systems"
• fix incorrect attribute name for taxon title message

v1.5.5

• customize your taxon appearance in messages.properties
• rename "Model Organism" to "Model System" to encompass biological systems that are not organisms
• update Spring Boot to 2.6.14
• update frontend dependencies
• restrict manual tiers to those enabled in the configuration

v1.5.4

• add support for MariaDB 10.6 LTS
• add testing support for MySQL 5.6
• fix JPA auditing for creation and modification timestamps
• add explicit default values for timestamps
• add User ID to the Google Analytics integration
• fix ordering of users lacking origin URL
• support ordering FAQ entries
• add a workaround when synonyms case change in ontologies

v1.5.3

• Fix counting of genes by tier in the public profile, the wrong column was referenced
• Always use configured API URLs to generate links to partner registries (see #342)
• Fix missing genes on public profiles from partner registries
• Add support for requesting access to anonymized results from partner registries (see #150)

v1.5.2

This release address a few minor issues.

• fix glitchy GO term tooltip placement, which was falling in a scroll box smaller than the tooltip size
• add missing admin.js bundle which prevented the "Refresh Messages" button to work properly

v1.5.1

This is a follow-up release to the 1.5.0 which address a few minor issues.

• better summary for ontology availability
• consistent capitalization of taxon common name
• Spring Boot and Springdoc update to 2.6.12 and 1.6.11 respectively
• fix moving inactive ontologies in the admin section
• numerous fixes suggested by SonarQube static analyzer
• use the user timezone for generating the date: field in OBO format, this field is not complying with ISO 8601, so it is the best assumption we can make in this case, we will eventually support the creation_date field in a future release #318
• add missing rollbackFor for checked exceptions

v1.5.0

The Pavlidis Lab team is proud to announce the completion of approximately four months of development on this new RDP release, the software that powers registries part of the RDMM Network. Please read carefully RDP 1.4 to 1.5 Migration Documentation before performing this update.

This new release brings a system for managing custom profile-associated terms and performing ontology inference for searching researchers.

This might take a while to explain in a few words, so brace yourself!

Overview

• ontology-based system for providing custom profile categories
  • import any ontology from OBO Foundry or any OBO-formatted ontology
  • import Reactome Pathways
  • manage simple categories of at most 20 terms with a simple editor
  • manage complex ontologies by activating/deactivating specific subtrees
  • terms are included when searching by research interests
  • powerful autocompletion interface for finding relevant terms
    • topological sorting of terms to recommend the broadest possible terms first
    • full-text matching on definitions, synonyms, names, etc.
  • resolvers for linking terms to Ontobee or OLS
• revamped administrative features
  • view and manage users more easily
    • users are now paginated
    • roles can be granted or revoked
    • date & time of account verification is displayed if known
• improved search user interface
  • sticky search bar so that you never have to scroll back up to click on the "Search" button
  • summarize the query that is performed
  • display which ontologies and terms are available in partner registries
• improved profile and model organism pages
  • sticky title bar with the "Save" button
• keep track of when users registered and last modified their profiles
• faster startup (< 7 secs)
• dependencies update
  • Spring Boot 2.6
  • Hibernate 5
• static assets are now bundled with Webpack 5
• better accessibility
  • "Skip to man content" (try it by pressing TAB)
  • improved semantic HTML 5 with ARIA roles
  • only feedback requiring immediate attention have the ARIA "alert" or "alertdialog" role
  • improved mobile experience
• tons of bugfixes and small QoL improvements
  • time for querying all partner registries cannot exceed the read timeout #305
  • thorough configuration validation at startup

Highlights

Search Interface

The search user interface has been substantially improved to accommodate ontology-based filters. In particular, the important search elements such as the "Search" button or the "Gene Symbol" and "Taxon" sticks on the top of the viewport so that it is always visible.

Search filters alternate between a white and light grey background. This helps convey which terms are grouped together.

The search also understands which tab to display based on the query, but also a fragment. Try adding #by-gene-search or #by-researcher-search to the URL. In addition, it is now possible to configure which search tab appear and in which order.

Profile Categories

This is by far the most considerable change of this release. By adding the ability to add and manage custom profile categories, we empower registry administrators with the mean to adapt RDP to their needs.

We support two kinds of categories: simple and ontology-based. For simple categories, one may include icons and grouping terms.

Administrators can import OBO-formatted ontologies from a file or by providing a remote source URL, or rely on our simple category editor to manage small ontologies.

Reactome

Reactome does not provide OBO format for their pathways, so we implemented a service for importing and keeping them up-to-date.

Webpack 5

This is a significant change that brings many benefits to the frontend development of RDP. Using Webpack 5, we can now post-process and bundle our sources to support a broader range of Web browsers. It also means that we do not rely on CDN anymore to deliver Bootstrap and jQuery.

This new set of tools will help us get rid of jQuery as a dependency and migrate a future version of RDP to Bootstrap 5.