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  • v13.0.0
    2fff2388 · ci adapted for the new debian dependencies ·
    Release v13.0.0
    • Bug fix: Since Oracle Java cannot be installed as debian dependency we use openjdk-8. Due to this dependency minerva can be no longer installed on Ubuntu-14 (#223)
  • v12.2.3
    7e538e36 · Merge branch '792-remove-button' into 'devel_12.2.x' ·
    Release v12.2.3
    • Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
    • Bug fix: searching of chemicals stopped working due to expired SSL certificate on https://ctdbase.org/
    • Bug fix: remove button is disabled after starting removing of the data overlay (#791)
    • Bug fix: search autocomplete hint could be initially hidden (#793)
    • Bug fix: updating terms of use could crash when list of users was removed in separate tab or by another user (#797)
    • Bug fix: name of the checkbox in ADD PROJECT window adjusted (#799)
    • Bug fix: when user didn't have privileges to remove comments the button was active on pages other than page 1 (#792)
    • Bug fix: export of reaction to SBML didn't work when lines on the map were too short (#805)
  • v12.2.2
    d78cd97a · Merge branch '783-internet-explorer' into 'devel_12.2.x' ·
    Release v12.2.2
    • Bug fix: downloading overlays didn't work from admin panel when project with different id than default map was accessed
    • Bug fix: change of owner of the data overlay in admin panel incorrectly ordered overlays (#777)
    • Bug fix: chemical search didn't use updated disease identifier, original disease id from project upload was used instead (#779)
    • Bug fix: user login with special characters (like '@') could cause problems in admin panel (#780)
    • Bug fix: removing project without full control in the system (but with enough privileges to remove project) caused "Not enough privileges" error (#778)
    • Bug fix: export of custom properties (like synonyms) are properly encoded in CellDesigner xml (#785)
    • Bug fix: notification about not supported version in IE 11 fixed (#783)
  • v12.2.1
    e6d4b196 · Merge branch '766-delete-comments-without-privileges' into 'devel_12.2.x' ·
    Release v12.2.1
    • Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can read colors properly) (#744)
    • Bug fix: removing active plugin didn't switch plugin tab to the next loaded plugin (#757)
    • Bug fix: closed submap will not be reopened after page refresh (#763)
    • Bug fix: comment remove button is disabled for users without proper privileges (#766)
    • Bug fix: invalid pubmed identifier could break clicking on element containing it (#764, #765, #769)
    • Bug fix: cache for API queries is explicitly disabled - some queries could be mistakenly cached and the system behaviour might get unstable (#771)
  • v12.2.0
    31199bb0 · Merge branch 'v12.2-release' into 'devel_12.2.x' ·
    Release v12.2.0
    • Feature: bug report utility
    • Feature: url GET parameters support all kind of search and selected overlays highlight
    • Feature: user can create custom logging configuration in file /etc/minerva/log4j.properties
    • Feature: plugin panel in admin allows to configure set of available plugins
    • Feature: import export from SBML supports RENDER package
    • Feature: import export from SBML supports MULTI package
    • Feature: API tool providing possibility to transform different types of file formats
    • Feature: current state of the browsed map is reflected in the url (position, zoom, overlays, search queries, etc.)
    • Small improvement: highlighting table rows in admin panel uses better contrast color (#706)
    • Small improvement: list of publication can be filtered by submap (#614)
    • Small improvement: size of add overlay window adjusted to show more data without scrollbars (#657)
    • Small improvement: all popup dialogs in the application have dialog specific css class names (#665)
    • Small improvement: JS plugin can create listener that is triggered on search results focus change
    • Small improvement: export to SBML includes unit factors
    • Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
    • Small improvement: genetics information allows to provide information about modification on peptide level that could be visualized in MolArt
    • Small improvement: allow to control the background and font color of areas drawn from text areas in CellDesigner "layers"
    • Small improvement: config logo location is relative to the root minerva deployment directory
    • Small improvement: there is branding minerva logo in the left panel
    • Small improvement: there is possibility to download part of the map limited to set of reactions/elements
    • Small improvement: allow admin to configure parameters displayed in the left panel
    • Small improvement: arrows for Transcription Starting Sites looks more like in CellDesigner
    • Small improvement: popup window appear with info about exceeding max number of search results when necessary
    • Small improvement: plugins can define default width of the container tab
    • Small improvement: new miriam type is handled: ClinicalTrials.gov
    • Small improvement: click on the border of compartment select the compartment
    • Small improvement: there is max size of the map in configuration panel that disables upload of too big files
    • Small improvement: hitting enter on login page logs in the user (no need to click on the login button)
    • Small improvement: refresh button in overlays panel (useful when data overlays are uploaded separately in using API calls)
    • Small improvement: list of publications is downloadable
    • Small improvement: export of reactions support filtering by reaction type
    • Small improvement: 'BACK TO MAP' link is available only when guest account has proper access level
    • Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact email account is provided
    • Small improvement: Plugin API allows to show/hide data overlays
    • Bug fix: Icons were sometimes not properly loaded on Safari (#661)
    • Bug fix: migration scripts are compatibile with postgres 9.3 version that is default on Ubuntu 14 (#762)
    • Bug fix: update/remove button is disabled when user has no privileges for managing overlays (#742)
    • Bug fix: when user cannot manage users information in overlays and users tab in edit project dialog is provided instead of hiding tabs (#756)
    • Bug fix: removing comments in a project asked for confirmation twice after edit project dialog for specific project was opened; closed and opened again (#697)
    • Bug fix: editing/removing project requires Map Management privilege (#681)
    • Bug fix: when removeAllListeners is called list of registered listeners is cleaned (#687)
    • Bug fix: when plugin is removed the html elements associated with it are removed as well (#686)
    • Bug fix: when creating new user default privileges are set properly (#692)
    • Bug fix: plugin can be added after plugin has been removed in admin plugin panel (#686)
    • Bug fix: too many annotations (>=100) caused misaligning in the left panel (#708)
    • Bug fix: export to svg contains viewBox info (#716)
    • Bug fix: overlays added via API couldn't be visualized after refresh (#718)
    • Bug fix: Safari sometimes cached server responses and used wrong data, for example in admin panel configuration tab (#719)
    • Bug fix: description of transcription site is centered (#720)
    • Bug fix: selecting too few parameters in export doesn't throw reportable error (#721)
    • Bug fix: providing invalid overlay id in url could break minerva (#726)
    • Bug fix: removing project that doesn't exist doesn't cause 500 error (#723)
    • Bug fix: opening map with invalid id shows proper error message (#724)
    • Bug fix: Fixing an issue where search panel was not properly resized on expansion (#682)
    • Bug fix: loading icon is not overlapping input in the search panel (#404)
    • Bug fix: position of transcription sites in genes are computed properly (#553)
    • Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid (#626)
    • Bug fix: working with too many maps within the single session could crash connection to server (#651)
    • Bug fix: drawing corrupted heterodimer association in CellDesigner could crash map upload (#673)
    • Bug fix: export to CellDesigner align inhibition reaction properly
    • Bug fix: export/import to/from SBML handles Heterodimer Association reaction properly
    • Bug fix: logo doesn't need to be square
    • Bug fix: when clicking on a search link (in overview window), input in the left tab was not modified
    • Bug fix: in admin panel changing of genome version is blocking interface until data about url is retrieved
    • Bug fix: export of species inside complex into CellDesigner was causing problems when reading the file in CellDesigner
    • Bug fix: export to SBGN did not export compartments
    • Bug fix: export of complex states to SBGN did not work
    • Bug fix: type of the data overlay can be defined in the file content (useful when uploading genetic variants)
    • Bug fix: CLEAR button clears comment checkbox if necessary
    • Bug fix: minerva install problem on ubuntu 18 fixed
  • v12.2.0-beta.3
    ad58b81d · Merge branch 'patch-1' into 'devel_12.2.x' ·
  • v12.2.0-beta.2
    840e56b6 · Merge branch '684-overlay-order' into 'devel_12.2.x' ·
  • v12.1.8
    bb8865c3 · Merge branch '659-updateUser-fix-final' into 'devel_12.1.x' ·
    Release v12.1.8
    • Bug fix: add a project reset users custom overlays limit to default (#679)
    • Bug fix: edit/remove project button was disabled based on Configuration Manage Privilege, but should be based on Project Manage Privilege (#681)
    • Bug fix: another minor problem with updating privileges introduced in 12.1.6 fixed (#659)
  • v12.2.0-beta.1
    6e5a023f · Merge branch 'typo' into 'devel_12.2.x' ·
  • v12.1.7
    69929e66 · Merge branch 'changelog' into 'devel_12.1.x' ·
    Release v12.1.7
    • Bug fix: problems with updating privileges introduced in 12.1.6 fixed
  • v12.1.6
    0f014818 · Merge branch 'drug-issue' into 'devel_12.1.x' ·
    Release v12.1.6
    • Bug fix: logo on login page was broken with image link being full url
    • Bug fix: plugin API had sometimes problems with fetching reactions properly
    • Bug fix: upload of data overlays without privileges triggers proper error message also in situation when user cannot create projects
    • Bug fix: first login on website when there is Term of use to accept raised error for regular users
    • Bug fix: fetching some drugs via API could cause 500
  • v12.2.0-beta.0
    4c526d14 · timestamp fixed ·
  • v12.2.0-alpha.1
    f625c195 · changelog updated ·
  • v12.2.0-alpha.0
    4d63509e · Merge branch 'gitlab-ci-fix' into 'master' ·
  • v12.1.5
    57d429dd · Merge branch '611-custom-overlays' into 'devel_12.1.x' ·
    Release v12.1.5
    • Bug fix: Drugbank changed output format which crashed drug connector
    • Bug fix: word wrapping fixed in overlay table for long overlay names in Firefox browser
  • v12.1.4
    34fbf66d · Merge branch '621-cannot-interact-with-overlay-with-long-filename' into 'devel_12.1.x' ·
    Release v12.1.4
    • Bug fix: no check for limit on custom data overlays fixed
    • Bug fix: error message improved when there is privilege problem during data overlay upload
    • Bug fix: upload of data overlay from admin panel didn't work
    • Bug fix: add project button is disabled when user doesn't have proper privileges ("Add project" privilege)
    • Bug fix: there are no more extra markers due to map wrapping
    • Bug fix: upload of the project failed when another project was removed during upload
    • Bug fix: word wrapping fixed in overlay table for long overlay names
  • v12.1.3
    05305712 · Merge branch 'changelog' into 'devel_12.1.x' ·
    Release v12.1.3
    • Bug fix: add project button is disabled when user has no privileges
    • Bug fix: projectId was missing in the edit window
    • Bug fix: user could provide invalid mesh ID that caused errors when browsing map
    • Bug fix: user created from LDAP connection doesn't have a password stored in the database
  • v12.1.2
    e1e932c0 · Merge branch 'gitlab-ci-fix' into 'devel_12.1.x' ·
    Release v12.1.2
    • Bug fix: vmh annotations should be properly matching id entered in the input
    • Bug fix: opacity was not working when highliting objects in plugins
    • Bug fix: integer configurtion options (like SMTP_PORT) are properly validated before saving
    • Bug fix: inside of reaction box wasn't properly aligned
    • Bug fix: too long data overlay name disturbed size of the map div and interaction with the map
    • Bug fix: search for some drugs resulted in internal server error
    • Bug fix: LDAP login is case insensitive
    • Bug fix: adding user could end up with error in the frontend
  • v12.1.1
    bbedfd12 · Merge branch 'changelog' into 'devel_12.1.x' ·
    Release v12.1.1
    • Bug fix: lineWidth in data overlays was ignored
    • Bug fix: legend was blinking after using controls
    • Bug fix: comment header was missing
    • Bug fix: click on drug target zooms to the results
    • Bug fix: export columns return proper value types
    • Bug fix: partial zooming is disabled
  • v12.1.0
    9aa4bf2d · changelog for v12.1.0 ·
    Release v12.1.0
    • Small improvement: default privilege value for 'Custom overlays' added
    • Small improvement: explicit logging of successful and unsuccessful logins
    • Small improvement: clicking on search result icon (on the map) change tab to the corresponding search results
    • Small improvement: option to remove additional overlays generated by custom semantic zoom
    • Small improvement: 'Reduced modulation' edge was displayed differently in CellDesigner and Minerva
    • Small improvement: user-friendly documentation for plugin URL field
    • Small improvement: plugins have to access information about active submap
    • Feature: genome browser with gene variants
    • Feature: support of all CellDesigner element modifications
    • Feature: ldap authentication
    • Feature: multicolored anchors for data overlays
    • Feature: minerva is distributed using rpm packages
    • Small improvement: annotations from RHEA are handled
    • Small improvement: changing of Terms of Service url allows admin to reset the status of ToS acceptance for all users
    • Small improvement: description of a grouped results in improved
    • Small improvement: selection of required annotation on map upload improved
    • Bug fix: annotations for elements with mutation in name (like "BID (p15)") weren't provided properly
    • Bug fix: passwords in the configuration tab are hidden with '*'
    • Bug fix: user has access to transparency level when creating custom semantic view (without this parametere functionality was very difficult to use)
    • Bug fix: loading invalid plugin doesn't render empty div anymore
    • Bug fix: sorting of custom overlays was broken when description of overlay was present
    • Bug fix: when there is a problem with adjusting font in complexes (because the font should be smaller than 1pt) description is not drawn anymore
    • Bug fix: going to export page and back was breaking a map
    • Bug fix: coordinates of selected area wasn't processed properly when they exceeded canvas
    • Bug fix: postgres migration script fixed to work with new docker compose
    • Bug fix: double click on user add button disabled
    • Bug fix: privileges are mirrored correctly across different popups
    • Bug fix: plugin tab css fixed
    • Bug fix: uploading sbml file with no ids in glyphs returned error that could not be easily understand
    • Bug fix: ds_store files in subfolders crashed zip upload
    • Bug fix: when creating new user default privileges were not filled