14.0.0 MINERVA Release#
9 Oct 2019#
New features:#
Security layer has been redesigned - the users privileges types and scope have been changed.
The logging mechanism log4j has been replaced with log4j2.
In debian package database is installed using dbconfig-commons.
The connection pool manager C3P0 has been replaced with the better maintained Hikari. Thus, the restart of PostgreSQL database does not require restart of tomcat.
Feature removal:#
Biocompendium annotator is removed.
Support for tomcat7 is removed.
Small improvement:#
Debian package can be installed on debian:buster.
The info window (after clicking on an element) contains information about overlay No.
In Administrator panel sorting columns by Edit and Remove is disabled.
The version of MINERVA is visible in the left panel in User view.
In select annotators dialog there is added small information on how to display annotator’s details.
CellDesigner layers are always visualized as pathways. Previously, the layers were visible only in Pathway and compartments view.
The notification email content is broaden out with MINERVA name and id of the affected project.
There is new column Created by in the list of projects. It provides the information on person who uploaded the project.
The tab with the list of glyphs is displayed when adding a project with glyphs.
BackgroundColor parameter should be assigned using “:” character. Previously BackgroundColor parameter used “=”.
Anonymous login is no longer required - each API query outside session is authorized with anonymous user privileges.
bcrypt is used for the password encryption.
Caching data is active by default for the new users when uploading project.
During removing an overlay in Administrator panel there is displayed a confirmation dialog.
Providing the overlay name is obligatory during overlay upload.
The list of projects in Administrator panel contains new column Created with the date of project upload.
The hyperlinks in the list of publications are opened in a new tab.
The target gene in the search panel contains also information about the type of database that identifies the target.
Redundant references field in gene variants data overlay is now deprecated.
Information about deprecated columns in data overlay is visible now in the overlay list in the left panel.
The publications list dialog is resizable.
The users list in the Edit project dialog is sortable now.
Fixed:#
The exported SBML file passes online SBML validation now.
Currently, the user is allowed to remove own comments.
Validation of the project name length is provided during project upload.
The list of Copy from elements in Select valid annotations dialog is shortened to use bio entity types.
The version of the project is limited to 20 characters.
Export to CellDesigner could misalign reaction lines that were imported from the formats which did not require the reaction line to be attached to the species.
There was a problem with uploading data overlays which included TYPE in header.
Work on Firefox private window mode could cause logout or raised an error when opening new tab with MINERVA.
Fetching list of miRnas resulted sometimes in “Internal Server Error”.
Edit project dialog verifies organism id (against Taxonomy id).
All colors of lines in boolean reaction (from CellDesigner) are processed properly.
The dotted lines for unknown modification boolean reaction are drawn correctly on the whole reaction.
Creating project with too long name hung upload. Now, project name length has been restricted to 256 characters.
Adding a user with too long login threw an error. Currently, login must be shorter than 256 characters.
When uploading generic data overlay, the type was not updated in case the type was not specified in the input file.
The list of types when copying from annotators contains only types that are selectable in the dialog.
The name for data overlay in element’s info window is trimmed.
In general overlay list the long overlay’s name is wrapped.
After the genome is removed, the list of genomes is refreshed.
REST API bioEntities:search method did not limit results to the submodel id.
Empty general overlay colors were not preserved during exporting map to CellDesigner.
Problem with unloading plugin is properly handled.
Upload of the invalid plugin does not add it to the plugin tab and the list of loaded plugins.
Some layout information was skipped during exporting to CellDesigner the reaction with two modifiers connected with boolean operator.
In SBGNML file format, the reaction containing two products was improperly drawn.
CellDesigner file exported from MINERVA was not fully compliant with SBML standard.
MiRNA targets are limited only to the organism associated with the map.
Search drug by target element did not return values when this element was annotated automatically.