This release was made to coincide with the InterMine 4.2.0 release, which included many updates to webservices important to BlueGenes. While BlueGenes aims to retain backward compatibility with InterMine instances all the way back to API version 27, (appropriate messages are displayed if your instance doesn’t support a feature) many new features are dependent on being up-to-date with InterMine releases.
We are still working towards the production release of BlueGenes, at which point we can recommend it for future deployments over the legacy user interface. This recent year has brought with it a plethora of necessary technical improvements and bug fixes, along with new additions to bring the user interface towards feature parity with the current webapp. The following details the most visible changes to BlueGenes in the last release, which you can explore by updating your local instance or using the public BlueGenes instance.
Visualization tools
- New version of Tool API to allow list and query results page tools that use IDs from multiple classes
- Tools on list and query results page should work properly for all classes now
- Tools on list and query results page now update when editing im-table
- Initialisation of tools has been made more performant
- CovidMine visualization for Cases
im-tables
- Better selection of constraint operation when creating filter
- Filter manager for adding and modifying constraints and logic
- Overly wide table contents are now hidden behind a scrollbar
- Helpful messages and options when something goes wrong
- Histogram in numeric column summary has been fixed and more features added
- Calendar for Date type constraints
- Searchable dropdown for single and multiple value constraints
Query builder page
- Build queries with outer join and sorting
- Save queries to your account
- Load recently run queries from your current session
- Data browser for selecting the root class
- Import query from XML
Profile page (new)
- Change your password or preferences
- Delete your account
- Register a new account for a mine
Lists
- Folder hierarchy for your lists in My Data
- Add and edit list descriptions
Interactive tool store
- Currently placed in the developer page, but we intend to move it to an admin page in the future
- Manage the installation, updating and removal of BlueGenes visualization tools using a web interface
- Rich information on each tool, where they’ll be visible, and any compatibility issues with the currently active mine
- All Tool API compliant npm packages with the bluegenes-intermine-tool tag are shown (only tools under the @intermine scope are installed by default)
- Only superusers are allowed to make changes
Report page
- Show FASTA information on report page when available (we intend to make drastic changes to the current report page in the near future)
Technical
- Much improved handling of mines that are unresponsive or have erroneous web services
- Java 11 support and a docker container
Previous minor releases
There have been some notable changes in prior minor releases. As they haven’t been mentioned in a blog post, we will include them here.
- Dynamic page titles (the text displayed in the tab or window title) based on the current page and its contents
- Improvements to the keyword search page
- Filters should work as expected when applied
- Multiple filter support
- Endlessly display more results by scrolling down
- Restoration of scroll position when returning to search page
- Reworked routing
- New and improved URL paths
- Deep linking to pages of specific mines
- Stability improvements to mine switching and initialising
- HTTPS support
InterMine 