16.1.0 MINERVA Release

3 Feb 2022


Improvement:

  • Possibility to register the map in MINERVA-NET.


Small improvement:

  • The list of reaction types in Info Tab > EXPORT > NETWORK is now simplified.

  • Export as image allows to define the size of an image.

  • The progress bar on a project upload is changed into more verbose statements.

  • AVOGADRO unit type from SBML format is parsed properly.

  • Data overlays have automatically generated legend.

  • The list of users is upgraded with information about currently logged in users.

  • Possibility to provide the image coords for Show overview as json file.

  • Possibility to show reaction’s name.

  • Export to SBML provides information about parent-child complex relation using multi package.

  • API converter is case insensitive for the name of a file.

  • Modification residues can use different color then species if format allows (SBGN, SBML).

  • Element id is shown in search results in the left panel.

  • There is possibility to provide custom CSS style in Configuration: Legend and Logo.

  • API provides information about modifier type.

  • map file for JavaScript is properly referenced.

  • Z-index for modification residues and structural states is imported from SBML file if available.

  • Debian installation creates db.properties file that is readable only by tomcat user

  • Import/export of the text objects in SBML is supported.

  • CellDesigner texts inside Layer Text with the name “text” are visible on the map and not transformed into pathways.

  • When free space on device drops under 10MB images will not be generated to prevent using all space on HDD.

  • Additional validation to REST input added.

  • Validation for projectId added when creating project using API.

  • Additional SBGN-ML glyphs are supported: biological activity, outcome, entity, observable, interaction.

  • Additional SBGN-ML reactions are supported: interaction, positive influence, negative influence, unknown influence, absolute stimulation, absolute inhibition.

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Fixed:

  • API endpoints were exposed without ‘api’ prefix.

  • Anonymous user could upload file using API.

  • When passing JSON in patch/post methods contentType was not checked.

  • API does not allow to create plugin with wrong md5 hash.

  • Currently, when exporting to CellDesigner make sure that layer id is numeric.

  • Pathway name was not drawn if there was an element with the same name contained inside that pathway.

  • Help dialog is closed automatically after Add Project dialog is closed.

  • Minerva root url must be valid url pointing to Minerva instance.

  • There were missing lines when exporting truncation and dissociation reaction to GPML.

  • Some SBML files were recognized as CellDesigner files during upload.

  • The middle of any reaction line was not highlighted.

  • When accessing data from cache in parallel, sometimes an unexpected exception was thrown.

  • Transcription factor color is set to black in background Empty.

  • Modifier line end points were not modified when importing from SBGN, there was a gap displayed between line end point and process box.

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