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.



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