17.0.0 MINERVA Release

02 Apr 2024


Backward incompatibility:

  • Tomcat dependency removed
  • Functionality of String Annotator moved to Uniprot Annotator as they were using the same source database
  • Generating of pdf does not use itext
  • Select mode removed
  • Split semantic zoom removed
  • Support for TransparencyZoomLevelVisibility removed (SemanticZoomLevelTransparency should be used)
  • “don’t care” residues are renamed to “unspecified”
  • After uploading data overlay the summary email will not be sent anymore
  • CAN_CREATE_OVERLAYS permission removed - every user has possibility to create accounts
  • Functionality of Stitch Annotator moved to Chebi Annotator as they were using the same source database
  • Merge API endpoint clears bioEntity notes by default, there is possibility to override this behaviour by using custom header: “X-MINERVA-KEEP-NOTES: true”


Improvement:

  • Login via orcid ID oauth2 is supported
  • User registration is added
  • Possibility to archive project
  • Minerva is compatible with java 17
  • Cached data is automatically refreshed after information is expired, for example information from drug db
  • inchi and inchikey in chemicals are represented as annotation
  • When exporting to SBGN provide dimension of the map
  • In admin panel changing details of user are reflected automatically in the list of user
  • Export to sbgn provide map id
  • Export/import to GPML supports map name
  • Project API provides info if the project is defined as default in config
  • Border width from source file (like CellDesigner) is used when drawing elements
  • When minerva shutdowns unexpectedly try to restart minerva for at most 3 times within 10 minutes
  • JAVA_ARGS in /etc/minerva/minerva.properties are used when starting minerva


Fixed:

  • When importing from CellDesigner coordinates of coding region in a gene were incorrectly computed
  • Export to SBML did not provide text label for CodingRegion and RegulatoryRegion
  • Export as pdf map with some glyphs was broken
  • HGNC changed url format - all identifiers.org links must be refreshed
  • When browsing map without background guest user was able to click add overlay button
  • Invalid columns were marked as sortable in user list panel
  • Refresh of DAPI data did not work properly
  • Download genomes stopped working (http://hgdownload.cse.ucsc.edu/ is down)
  • Upload of invalid javascript plugin was throwing exception
  • UCSC changed the way that data is accessed and genomics download stopped working
  • Export to CellDesigner should not put notes in Antisense RNA, Gene and RNA - the notes are already in Species
  • Adding new project format *.sbml did not change Type in Add project window
  • Reactions imported from CellDesigner and attached to the corner of drug were misaligned