12.2.0 MINERVA Release#

27 Mar 2019#

New:#

• Bugs report utility - allows for a quick reporting on bug’s occurrence

• The Plugin section in Administrator panel - allows to configure the settings of available plugins

• Current state of the browsed map is reflected in the browser url (position, zoom, overlays, search queries, etc.)

Feature enhancements:#

• API: API tool provides the possibility to convert types of file formats. For more details see API MINERVA Manual

• The user can create a custom logging configuration in the file /etc/minerva/log4j.properties

• SBML: import and export from SBML supports RENDER package

• SBML: import and export from SBML supports MULTI package

Small improvements:#

• The table rows in the Administrator panel are highlighted with more contrasting color

• The list of the project publication can be filtered by a submap

• The size of the Add Overlay window is adjusted to display more data at once, thus the need to scroll is reduced

• All popup windows in the MINERVA have the dialog specific CSS class names

• JS plugin can create the listener that is triggered on the search results focus change

• Export to SBML includes also a unit factor (defined by a user in CellDesigner file)

• The MeSH identifiers are resolved to meshb.nlm.nih.gov url

• The genetics information allows to provide details about modification on peptide level which are visualized in the MolArt

• The user control the background and the font color of the areas drawn from the layers in CellDesigner

• The configuration logo location is relative to the root MINERVA deployment directory

• There is the branding MINERVA logo in the bottom part of the left panel

• API: There is a possibility to download a part of the map limited to by a set of reactions or elements

• The administrator can configure which parameters are displayed in the left panel

• The arrows for Transcription Starting Sites are visualized similarly to CellDesigner ones

• There is a popup window that informs about exceeding the max number of the search results

• Plugin API: The plugins can define the default width of the container tab

• A new MIRIAM type is handled now: ClinicalTrials.gov

• A click on the border of the compartment selects the compartment and display its details in the left panel

• There is a max size of the map in the configuration panel that prevents uploading too big files

• Hitting enter on the login page logs the user in (there is no need to click on the login button)

• There is a refresh button in the Overlays panel (it is useful when the data overlays are uploaded separately via API calls)

• The list of the project’s publications is downloadable

• The export of the reactions is supported by filtering by a reaction types

• BACK TO MAP link, on the login page, is available only when the guest account has a proper access level

• REQUEST AN ACCOUNT link, on the login page, is available only if the contact email is provided in the MINERVA configuration

• Plugin API The plugin API allows to show and hide data overlays

Bugs fixed:#

• The icons were not properly loaded in some cases on Safari browser

• The migration scripts are compatible with postgres 9.3 version that is the default on Ubuntu 14

• The Update button and Remove button are now disabled if a user has no Manage overlays privilege

• The appropriate dialog is provided in case a user is not allowed to manage the users information in the Edit project section. Previously, the tabs Overlays and Users were hidden, to avoid editing them

• The user was asked twice for confirmation before removing a comment in case the Edit project dialog for specific project was opened. Currently, that confirmation dialog is displayed only one time

• Editing or removing a project was possible even if a user did not have Map management privilege. Now, if user is not granted with Map management, he cannot remove or edit the project

• Plugin API: When removeAllListeners is called the list of registered listeners is cleaned

• Plugin API: The HTML elements associated with a plugin are removed along with the plugin. Previously, these elements were just hidden what might cause problems for some plugins

• A new user privileges were not set according to the MINERVA default privileges for a new user, in case the administrator did not have Manage configuration privilege

• Plugin API: Adding a plugin directly after removing it from the Administrator’s Plugin panel works correctly now. Previously, that plugin API was recognized as an existing one, thus adding it was denied

• Too many annotations (>=100) caused incorrect aligning of the search results in the left panel

• Currently, the export to SVG contains viewBox info

• The refresh button did not refresh the list of overlays added via API in the left panel

• Safari sometimes cached server responses and used wrong data, for example in the Administrator panel configuration tab (some tabs were missing)

• The position of the Transcription Site description is centred now

• Selecting too few parameters in Export window did not throw a proper error dialog

• Providing an invalid overlay ID in url could break MINERVA

• An attempt to remove a project that has already been removed threw 500 error, now there is a dialog displayed

• Opening a map with an invalid ID shows the proper error message

• The search results were hidden in the left panel in case the left panel was hidden and then shown again

• The loading icon in the left panel overlapped the input filed in the search panel. It decreased the clarity of date in the left panel

• Position of the Transcription Sites in genes are computed properly

• Currently, REQUEST AN ACCOUNT link on the login page is disabled if an associated email is invalid

• Working with too many maps within the single session could crash the connection to the server

• Drawing the corrupted Heterodimer Association in CellDesigner might crash an upload of a map

• Export to CellDesigner aligns the arrows of inhibition reaction correctly

• Export and import to/from SBML handles Heterodimer Association reaction properly

• Currently, the logo does not have to be only square size

• When clicking on a search link (in the Overview window), the input in the left tab was not modified accordingly to the search results

• Changing of the genome version in Administrator panel blocks the interface, until the genome url is retrieved

• The export of the species inside the complex into CellDesigner caused problems when reading the file in CellDesigner

• The compartments were not exported to SBGN format at all

• The export of the complex states to SBGN format works now properly

• Type of the data overlay can be defined in the file content (it is useful when uploading genetic variants)

• CLEAR button uncheck the Comment checkbox if necessary, so the comments and search results are cleared simultaneously

• Installation of MINERVA on Ubuntu 18 is fixed