Breaking news from ggKbase.
After running on Elasticsearch 6.8 for the past so many years, we have finally upgraded it to Elasticsearch 8.7. There were some very minor changes in the API, but for the most part, it did not affect the code base too much. We had to re-index all the feature annotations, and it took 1.5 day…
In keeping with the latest minor upgrade of Rails, we have upgrade Rails from 7.0 to 7.1. For the detailed changes in the Rails system, you can find it in the release notes here: https://edgeguides.rubyonrails.org/7_1_release_notes.html. There is no significant changes to the way ggKbase behaves as a result of this upgrade. The major upgrade coming…
The front end code upgrade was a massive project that involved examining/studying, cleaning out, and modifying the entire front end code base as the following actions were taken: Motivations for these changes:
Rails 7.0 has has transitioned the frontend development away from Webpack, a more tightly coupled packaging environment, to jsbundling, a more loosely connected packaging environment. On top of that, it introduces one of the native ActiveRecord methods that I have been longing for: bulk insert to the database. This would allow me to move away…
After stably running on Rails 5.2 for about 2 years and living on Bootstrap 3 for a long time, ggKbase is long overdue for getting up to speed with the latest code base both on the server end as well as on the front end. So, we take the plunge and went for this major…
In this upgrade of ggKbase, we replaced the listed_features table (which is the core component that supports lists, genome summaries, and binning) with the Elasticsearch search engine. Is this a big deal? It’s HUGE! Lists are automatically updated to all projects, even the newly added ones. No need to update lists when you are adding more projects…
The lists system is a useful tool in ggKbase – it allows users to categorize genes on associated annotation. As the number of lists has increased from the contribution of our users as well as by adding the HMM lists, we have realized the need to be able to access and edit lists more easily.…
Building on the agile permission framework that was adopted at the end of last year, ggKbase 5.3 brings more granular control over memberships and permissions to the owner of the resources on ggKbase. For this rollout, project owners now can not only add members to their projects, but also provide their members fine-grained control over…
Genome Summary, an important tool in ggKbase, has been significantly upgraded in its user interface (UI), user experience (UX) and system performance. For the UI/UX improvement, the Project Selection page has been removed. Instead there is now a Project Selection menu, similar to the Organism Selection and List Selection menus you are already familiar with. This change…
We have developed the Batch Rebin from File web page, located at the project-slug/organisms, to enable users to upload a tab-delimited scaffolds-to-bins file and proceed to batch rebin a project. Users can also dissolve all the bins within the project before batch rebinning. The structure of the file is required to be like the following…
