CHANGELOG

minerva (12.1.8) stable; urgency=medium
  * Bug fix: add a project reset users custom overlays limit to default (#679)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 8 Feb 2019 15:30:00 +0200

minerva (12.1.7) stable; urgency=medium
  * Bug fix: problems with updating privileges introduced in 12.1.6 fixed

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 6 Feb 2019 15:30:00 +0200

minerva (12.1.6) stable; urgency=medium
  * 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

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Jan 2019 16:00:00 +0200

minerva (12.1.5) stable; urgency=medium
  * 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

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 10 Jan 2019 14:00:00 +0200

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