MINERVA: MINERVA 17.0.0

17.0.0 MINERVA Release#

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