minerva (12.1.4) stable; urgency=medium
* 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
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 28 Dec 2018 14:00:00 +0200
minerva (12.1.3) stable; urgency=medium
* 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
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 14 Dec 2018 14:00:00 +0200
minerva (12.1.2) stable; urgency=medium
* 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
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 12 Dec 2018 16:00:00 +0200
minerva (12.1.1) stable; urgency=medium
* 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
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 2 Nov 2018 13:00:00 +0200
minerva (12.1.0) stable; urgency=medium
* 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
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 29 Oct 2018 13:00:00 +0200
minerva (12.0.4) stable; urgency=medium
* Bug fix: CellDesigner modifications that are drawn as reaction are handled
properly (like catalysis)
* Bug fix: Removing of guest (anonymous) account is forbidden - system is
unstable after removing such user
* Bug fix: Tair database moved to https
* Bug fix: Taxnomy database changed html output that resulted in problems
with resolving species name to the id
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 12 Sep 2018 17:00:00 +0200
minerva (12.0.3) stable; urgency=medium
* Bug fix: SBML model annotations caused errors on upload
* Bug fix: Export of some models to SBML didn't work properly
* Bug fix: zip files weren't processed properly
* Bug fix: required annotations were always required for some types
* Bug fix: user cannot remove default map anymore
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 27 Aug 2018 11:00:00 +0200
minerva (12.0.2) stable; urgency=medium
* Bug fix: data overlay by annotation type fixed
* Bug fix: [plugin] getting reactions with set of id larger than 100 elements
works properly
* Bug fix: name of commented protein was remembered for the new comment
* Bug fix: setting zoom level wasn't ranged and validated
* Bug fix: when uploading data overlay there is a warning regarding mixed new
line characters when necessary
* Performance: tomcat inside docker image by default can use 3G of memory
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 31 Jul 2018 13:00:00 +0200
minerva (12.0.1) stable; urgency=medium
* Bug fix: setting default zoom level on submap
* Bug fix: opened submap had different background then current selection
* Bug fix: clicking on comments was difficult in OpenLayers
* Bug fix: general map comment didn't display coordinates properly
* Bug fix: opening map could crash when CellDesigner file contained duplicate
reaction id
* Bug fix: map is repositioned when info window is outside of current view in
OpenLayers library
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 24 Jul 2018 10:00:00 +0200
minerva (12.0.0) stable; urgency=medium
* Feature: There is alternative OpenLayers map engine available
* Feature: database connection configuration (login, password, host, etc)
can be modified using /etc/minerva/db.properties file
* Feature: searching for elements in submap gives marker on top map
indicating the submap connection
* Feature: similar search results are merged
* Feature: visualization of protein structures by MolArt
* Feature: reordering of data overlays is supported
* Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA annotators
* Feature: annotations contain info about source (there is difference
between manual and automatically added annotations)
* Feature: default permission for new projects are configurable
* Feature: SBML support (with and without layout extension)
* Feature: kinetics support
* Feature: plugin API
* Feature: all functionalities are provided via REST API
* Feature: visualization of two (or more) overlaying results (like drug
target, mirna target) is highlighted with different icon
* Small improvement: email for account request contain configurable text
* Small improvement: transparency level for data overlays is configurable
* Small improvement: CellDesigner reactions of Modifier type are acceptable
* Small improvement: performance improved for overlays identified by
annotation identifiers
* Small improvement: Legend is always on top
* Small improvement: When email content is too big it's compressed
* Small improvement: Description of chemical panel refers to the disease
connected to the map
* Small improvement: Confirm button when removing data overlay
* Small improvement: Clicking on data overlayed element behaves in the same
way as clicking on not overlayed element
* Small improvement: Title of list of submaps doesn't contain UNKNOWN tag
* Small improvement: DOI is supported as miriam type
* Small improvement: When loading data in search tab there is "LOADING" icon
* Small improvement: Data overlays can use source element identifiers for
filtering
* Small improvement: Data overlays can submap column to differentiate between
maps
* Small improvement: search by chemical names is possible
* Small improvement: auto complete functionality for drugs, mirnas and
chemicals
* Small improvement: columns value and type are not mutually exclusive in
data overlays
* Small improvement: column type is case insensitive in data overlays
* Small improvement: every submap contains default center position and zoom
level to customize default view when entering map for the first time
* Small improvement: data overlays color scale contains configurable default
middle color (for 0 values)
* Small improvement: opening data overlay switch to empty background
* Small improvement: multiple x-frame domains are allowed
* Small improvement: No duration of the text notification in overlay tab
* Small improvement: JS plugin API allows to store data on server side
* Small improvement: submap reference in publication list
* Small improvement: size of connection to database reduced to 90 (so default
connection pool to postgres is not completely filled with minerva)
* Small improvement: visualization of sbml function improved (lambda
expression removed from the definition)
* Small improvement: handling of additional miriam types from BiGG ontology
* Small improvement: configuration options are grouped in categories
* Bug fix: searching with two queries sometimes resulted in one complex
instead of two queries
* Bug fix: uploaded submaps didn't have hierarchical masking
* Bug fix: uploading of zip files created by mac doesn't crash due to
.DS_Store folder
* Bug fix: auto complete is case insensitive
* Bug fix: google maps API 404 errors for non existing tiles are removed
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 16 Jul 2018 12:00:00 +0200
minerva (11.1.3) stable; urgency=medium
* Bug fix RPM: remove directory with contents of unpacked war file
when uninstalling
* Bug fix: don't append Google API key to Google maps javascript URL
when it is not set
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 23 Jul 2018 12:00:00 +0200
minerva (11.1.2) stable; urgency=medium
* Bug fix: Searching for chemicals with invalid mesh ID crashed
* Bug fix: opening map that was removed and re-uploaded could crash
* warning message due to lack of google consent improved
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 04 Jul 2018 16:00:00 +0200
minerva (11.1.1) stable; urgency=medium
* Bug fix: Updating privileges takes much less time
* Bug fix: Concurent update on privileges shouldn't crash anymore
* Bug fix: Search by element id crashed when submaps were available
* Bug fix: GO connector uses new API, because the old one was turned off
and stopped working
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 27 Jun 2018 15:00:00 +0200
minerva (11.1.0) stable; urgency=high
* User can provide Google Maps API key that must be registered in google
cloud account
* User data overlays must be Google Maps API terms of use compliant
* Terms of Use added
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 05 Jun 2018 9:00:00 +0200
minerva (11.0.10) stable; urgency=medium
* Bug fix: link from overview image to search result was broken
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 16 Apr 2018 15:00:00 +0200
minerva (11.0.9) stable; urgency=medium
* Bug fix: some comment couldn't be loaded
* Bug fix: when adding comment it didn't appear on map immediately
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 21 Feb 2018 18:00:00 +0200
minerva (11.0.8) stable; urgency=medium
* Bug fix: XSS vulnerability
* Bug fix: "java.lang.IllegalStateException: getWriter()" exceptions
in logs
* Bug fix: crash for uploading and caching chemical data
* Bug fix: disappearing tiles in submodels
* Bug fix: max number of results is properly taken from configuration
* Bug fix: overlay cannot be hidden before process of fetching data
during opening is finished
* Bug fix: redirection to login page when session expired and access to
export page is requested
* Bug fix: sometimes overlays couldn't be hidden in submaps
* Bug fix: comments on submaps are visualized properly
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 05 Feb 2018 18:00:00 +0200
minerva (11.0.7) stable; urgency=medium
* Bug fix: redirection added when anonymous tries to access secured map
* Bug fix: loading time of custom overlays is reduced
* Bug fix: there should be no problem with symlink when upgrading debian
package
* Bug fix: number of services changed API address to https: pmceurope
(pubmed), uniprot, ensembl, hgnc, recon, ctd database
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 18 Jan 2018 16:00:00 +0200
minerva (11.0.6) stable; urgency=medium
* Bug fix: fix a bug when entering invalid mirna id
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 14 Dec 2017 16:00:00 +0200
minerva (11.0.5) stable; urgency=medium
* Bug fix: fix on connection to drugbank database
* Bug fix: posttranslational modification data was sometimes unavailable
in search results panel
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 30 Nov 2017 16:00:00 +0200
minerva (11.0.4) stable; urgency=medium
* Bug fix: fix on connection to taxonomy database
* Bug fix: color coding for reactions (wrong color was chosen)
* Bug fix: overlays with many reactions did not work properly
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 09 Nov 2017 14:50:00 +0200
minerva (11.0.3) stable; urgency=medium
* Bug fix: removing empty project removed images from all projects
* Bug fix: clicking on map when left panel was hidden threw error
* Bug fix: links to invalid annotations were opening invalid web page
* Bug fix: service resolving miriam resources doesn't work over http
anymore
* Bug fix: chebi annotator doesn't work over http anymore
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 19 Oct 2017 13:50:00 +0200
minerva (11.0.2) stable; urgency=medium
* Bug fix: login issues when default page is in secure area
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 25 Sep 2017 12:00:00 +0200
minerva (11.0.1) stable; urgency=medium
* Bug fix: logout caused issues with session data
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 08 Sep 2017 12:00:00 +0200
minerva (11.0.0) stable; urgency=medium
* Bug fix: security issue - access to specific map can be restricted
by the user login
* Bug fix: sbgn import
* Bug fix: mesh connector
* Rest API (documentation can be found here:
https://git-r3lab.uni.lu/piotr.gawron/minerva/blob/master/README.md)
* Selecting an element on the map shows info about it in the bottom left
corner (when Search tab is not open)
* Upload of data overlays allows to upload just names of the proteins
(or other elements), it can be done via file or just by typing in the
proper text box
* Layout changes: the main one is that there are only 3 tab panels
(search, overlay, info), so it should be easier to navigate
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 28 Aug 2017 12:00:00 +0200
minerva (10.0.5) stable; urgency=medium
* Bug fix: interacting drugs can be found for RNAs
* Bug fix: error handling improved on map upload
* Bug fix: taxonomy ncbi server switched to https
* Overlay presents description field if possible
-- Piotr Gawron <piotr.gawron@uni.lu> Sat, 04 Mar 2017 12:00:00 +0200
minerva (10.0.4) stable; urgency=medium
* Bug fix: overlays colors are centered in white (not black)
* Bug fix: export to CellDesigner fixed
* Bug fix: DrugBank connector updated due to change in DrugBank website
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 29 Dec 2016 17:01:16 +0200
minerva (10.0.3) stable; urgency=medium
* Bug fix: login cannot contain whitespace
* Bug fix: search for multiple drugs will not return more drugs than
queried for
* Bug fix: drug list for some proteins (like RHOA) hung webpage
* Bug fix: comments on submaps issue
* Bug fix: link to submap from comment panel
* Overlay coloring can be defined in Configuration
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 15 Dec 2016 15:01:16 +0200
minerva (10.0.2) stable; urgency=medium
* Bug fix: markers for mirna targets visibility
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 29 Sep 2016 10:01:16 +0200
minerva (10.0.1) stable; urgency=medium
* Bug fix: export to image
* Bug fix: trigger reaction and physical stimulation reactions are no
longer allowed (CellDesigner data model issue)
* Bug fix: clicking on reactions in submaps
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 21 Sep 2016 13:01:16 +0200
minerva (10) stable; urgency=medium
* Project info tab available for users
* Management of overlays in admin panel
* Bug fix: Visualization of text mining
* Bug fix: Exception when accessing non-existing project
* Bug fix: Zooming issue when searching for results on submaps
* Bug fix: Out of memory when caching a lot of data
* Bug fix: Corrupted drug names
* Bug fix: Unexpected errors when uploading layouts
* Bug fix: Coordinates in url
* Bug fix: Hiding left panel
* Bug fix: CellDesigner font size is processed properly
* Bug fix: Search by reaction id is not case sensitive
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 22 Aug 2016 13:01:16 +0200
minerva (9) stable; urgency=medium
* Fix on install script of version 8 that crashed some new installations
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 29 Jun 2016 09:58:34 +0200
minerva (8) stable; urgency=medium
* Micro RNA interface
* Toxic chemicals interface
* Data sets (layouts) visualized dynamically in the browser
* Reverse query for drugs, chemicals, micro RNAs interfaces
* Small bug fixes
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 14 Apr 2016 13:03:55 +0200
minerva (7) stable; urgency=low
* Uploaded datasets are available for download
* Entrez annotator
* Ensembl annotator
* Valid/required annotations and used annotations saved in user profile
* Export to pdf/png/jpg/svg
* New web interface
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 3 Dec 2015 22:00:00 +0200
minerva (6) stable; urgency=low
* Searching by annotations
* Errors from parsing data forwarded to client
* Notification email system added
* Warnings are downloadable
* Complex map (composed from many small maps)
* Visualization of Recon specific annotations
* Versioning system
* Galaxy connector
* Miriam types report
* Advanced annotation options
* Uniprot annotation module
* Customized validation of miriam annotations
* Recon annotation service
* Bug fix: Data autofill problem in user management
* Bug fix: User privileges for adding project
* Bug fix: Problem with some miriam entries in RDF format
* Bug fix: Reporting of drawing problems
* Bug fix: Visualization of posttranslationa modification
* Bug fix: Drugbank problem after update of Drugbank interface
* Bug fix: Session scope fixed (browsing many maps at the same time)
* Bug fix: Asynchronous removing/adding maps
* Bug fix: Export to CellDesigner rarely produced corrupted CellDesigner file
* Bug fix: Recon annotations of reactions
* Bug fix: Login problem when browsing not default map
* Bug fix: Multimers are available for every element
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 21 Jul 2015 22:00:00 +0200
minerva (5) stable; urgency=low
* Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
* Popup window in admin panel that list warnings
* Information about build
* Parsing and annotation warnings for models in admin panel
* Custom reaction visualization in upload overlay
* Bug fix: Problem with touch interface on Windows 8.1
* Bug fix: Google Maps API problem with floating bubbles
* Bug fix: Error handling in admin panel
* Bug fix: Reaction color in CellDesigner file
* Bug fix: Reaction line width
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 18 Dec 2014 22:00:00 +0200
minerva (4) stable; urgency=low
* Export of the part of the map into CellDesigner file
* Logo files managable via config webpage
* Import data from GO
* Custom overlay upload
* Additional structural information imported from annotation service
* Bug fix: Fonts and lines in hierarchical view
* Bug fix: Visualization of residues in rna, antisense rna, proteins
* Bug fix: Problem with touching bubbles on touch interface
* Bug fix: Problem with special UTF-8 characters in CellDesigner file
* Bug fix: Problem with users and session expire
* Bug fix: Export problem
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 11 Sep 2014 22:00:00 +0200
minerva (3) stable; urgency=low
* Drug targeting interface
* Export to CellDesigner
* Status page of all dependent services
* Configuration page
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 5 Jun 2014 22:00:00 +0200
minerva (2) stable; urgency=low
* Upload of the CellDesigner map
* Bug fix: Problem with touch interface after update of browsers engine
* Bug fix: Problem in Safari when searching for elements
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 2 Apr 2014 22:00:00 +0200
minerva (1) stable; urgency=low
* Initial release
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 4 Dec 2013 22:00:00 +0200