CHANGELOG

minerva (14.0.3) stable; urgency=medium
  * Bug fix: sbml parser had sometimes problems with combining layout and multi
    packages (#966)
  * Bug fix: parsing of CellDesigner files that contained substanceUnits could
    crash the upload (#985)
  * Bug fix: verificatin of version length added when uploading project
    implemented (#978)
  * Bug fix: CLEAR button disappeard when plugin tab used to much space (#976)
  * Bug fix: removing data overlay refreshes list of overlays in info window
    (#974)
  * Bug fix: general overlays are always on top of data overlays in info window
    (#975)
  * Bug fix: refresh button in overlay panel synchronise list of general and
    user provided data overlays (#975)
  * Bug fix: changing order of data overlays is reflected in info window
  * Bug fix: opening map with no available background crashed (#964)
  * Bug fix: uploading SBGN file that does not pass xsd validation provides a
    warning, but does not fail upload (#937)
  * Bug fix: export of the map to SBML that was imported with older version
    (below 14.0.0) didn't produce valid SBML (#970)
  * Bug fix: fields in add project window are reinitialized after each open
    (#963)
  * Bug fix: filename case in uploaded zip files is preserved (#964)
  * Bug fix: +/- buttons were misaligned in genemove browser (#942)
  * Bug fix: color of links in the left panel was unintentionally changed 
    (#990)
  * Bug fix: minerva logo in left panel is centered properly

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Oct 2019 9:00:00 +0200

minerva (14.0.2) stable; urgency=medium
  * Bug fix: Genetic data overlay uploaded prior to 14.0.0 crashed maps (#988)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 15 Oct 2019 11:00:00 +0200

minerva (14.0.1) stable; urgency=medium
  * Bug fix: maps that were annotated using old Biocompendium annotator could
    not load properly (#986)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 15 Oct 2019 9:00:00 +0200

minerva (14.0.0) stable; urgency=medium
  * Feature removal: BioCompendium annotator removed (#32)
  * Feature removal: support for tomcat7 removed (#828)
  * Feature: security layer redesigned - privilege types and scope changed
    (#636, #624)
  * Feature: log4j is replaced with log4j2 logging mechanism (#291)
  * Feature: database installed via debian package is done via dbconfig-commons
    (#469)
  * Feature: Replaced connection pool manager C3P0 with better maintained
    Hikari - restart of postgresql database doesn't require restart of tomcat
    (#564)
  * Small improvement: debian package can be installed on debian:buster (#879)
  * Small improvement: info window contains information about overlay No (#919)
  * Small improvement: sorting by columns that doesn't make sense in admin
    panel is disabled (#895)
  * Small improvement: version of minerva is visible in map browser panel
  * Small improvement: small info about annotator details is available in
    select annotators dialog (#923)
  * Small improvement: CellDesigner layers are always visualized as pathways
    (#813)
  * Small improvement: notification email uses minerva name and id of affected
    project (#926)
  * Small improvement: information about person who uploaded project is visible
    in list of projects (#927)
  * Small improvement: tab with list of glyphs is available when adding project
    with glyphs (#925)
  * Small improvement: BackgroundColor parameter should be assigned using ":"
    character (#929)
  * Small improvement: anonymous login is no longer required - each API query
    outside session is authorized with anonymous user privileges (#629)
  * Small improvement: bcrypt is used for password encryption (#387)
  * Small improvement: caching is active by default for new users when
    uploading project (#202)
  * Small improvement: when removing overlay in admin panel there is a
    confirmation dialog (#696)
  * Small improvement: overlay name is obligatory (#698)
  * Small improvement: list of projects in admin panel contains creation date
    (#447)
  * Small improvement: links in list of publications open in new tab (#447)
  * Small improvement: target gene in search panel contains also information
    about type of database that identifies the target (#66)
  * Small improvement: redundant 'references' field in gene variants data
    overlay is now deprecated (#850)
  * Small improvement: information about deprecated columns in data overlay is
    visible in overlay list (#838)
  * Small improvement: publication list is resizeable (#740)
  * Small improvement: user list on project edit dialog is sortable (#808)
  * Bug fix: exported SBML passes online validation (#831)
  * Bug fix: allow user to remove own comments (#931)
  * Bug fix: validation of project name length is provided (#950)
  * Bug fix: list of "Copy from" elements in "Select valid annotations" dialog 
    is shortened to used bio entity types (#911)
  * Bug fix: version of the project is limited to 20 characters (#951)
  * Bug fix: export to CD could misalign reaction lines that were imported from
    format that didn't require reaction line to be attached to the species (#933)
  * Bug fix: problem with uploading data_overlays with type included in header
    (#936)
  * Bug fix: work on FF Private Window mode could cause logout or raise an
    error on when opening new tab with minerva (#892)
  * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server
    Error" (#889)
  * Bug fix: edit project dialog verifies organism id  (#914)
  * Bug fix: all colors in boolean reaction (from CellDesigner) are processed
    properly (#907)
  * Bug fix: proper line type for boolean reaction is used on the whole
    reaction (#908)
  * Bug fix: creating project with too long name hung upload (#916)
  * Bug fix: too long user login threw an error (#915)
  * Bug fix: when uploading generic data overlay the type was not updated in
    case the type was not specified in the input file (#906)
  * Bug fix: list of types when copying from annotators contains only types
    that are selectable in the dialog (#911)
  * Bug fix: too long name for data overlay in info window is trimmed (#919)
  * Bug fix: too long name in general overlay list is wrapped (#857)
  * Bug fix: after genome is removed list of genomes is refreshed (#922)
  * Bug fix: REST API bioEntities:search method didn't limit results to the
    submodel id (#860)
  * Bug fix: Empty Overlay colours were not preserved during export to
    CellDesigner (#714)
  * Bug fix: problem with unloading plugin is properly handled (#884)
  * Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of
    loaded plugins (#885)
  * Bug fix: export to CellDesigner of reaction with two modifiers connected
    with boolean operator resulted was skipping some layout information
  * Bug fix: reaction in SBGNML file containing two products was improperly
    drawn
  * Bug fix: color handling in CellDesigner did not work properly for modifiers
    inside boolean gateway
  * Bug fix: CellDesigner file exported from minerva was not fully compliant
    with SBML standard (#831)
  * Bug fix: MiRNA targets are limited only to the organism associated with the
    map (#66)
  * Bug fix: Search drug by target element did not return values when this
    element was annotated automatically (#216)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 09 Oct 2019 12:00:00 +0200

minerva (13.2.0) stable; urgency=medium
  * Small improvement: MolArt v1.4 is used which provide information from
    PredictProtein (#913)
  * Bug fix: search by drugs didn't check synonyms in chembl database
  * Bug fix: verification of overlay type added (#917)
  * Bug fix: opening edit project/user dialog returned list of users/projects
    to the 1st page (#909)
  * Bug fix: show element title option wasn't influencing title visibility
    (#910)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 29 Aug 2019 17:00:00 +0200

minerva (13.1.3) stable; urgency=medium
  * Bug fix: refreshing list of projects or list of users doesn't change active
    page (#870)
  * Bug fix: submap list must be selected to export from every submap (#874)
  * Bug fix: export map as image properly uses bottom limit (#875)
  * Bug fix: reaction info window wasn't closed on CLEAR (#876)
  * Bug fix: name of the uploaded file is displayed when adding overlay (#849)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 14 Aug 2019 17:00:00 +0200

minerva (13.1.2) stable; urgency=medium
  * Bug fix: Information about problematic zip file is more specific (#865)
  * Bug fix: Url didn't contain list of opened plugins and they weren't reload
    automatically on refresh (#866)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Jul 2019 17:00:00 +0200

minerva (13.1.1) stable; urgency=medium
  * Bug fix: adding gene mapping before the genome caused an error (#835)
  * Bug fix: "Terms of Use" change to "Terms of Service" in all places (#843)
  * Bug fix: upgrade to 13.1.0 crashed on machines where every element was
    inside compartment (#856)
  * Bug fix: searching for some drugs in chembl didn't provide any results even
    though that data exists, for instance 'DORLIMOMAB ARITOX' (#842)
  * Bug fix: user wasn't logged out in all tabs when the log out event appeard
    in only one of them (#847)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue,  2 Jul 2019 19:00:00 +0200

minerva (13.1.0) stable; urgency=medium
  * Feature: annotators are more flexible - you can define set of input and
    outputs used by annotator (#617)
  * Feature: changes in admin panel doesn't require saving - they are saved
    automatically (#676)
  * Feature: elements can have custom glyphs used for visualization (#487)
  * Small improvement: model_name renamed to map_name in data overlay columns
    (#827)
  * Small improvement: name, type, reference_genome_type and
    reference_genome_version column in genetic variant data overlay are
    deprecated (#827)
  * Small improvement: all bio entities have z-index associated with them
    (#487)
  * Small improvement: validation of the organism and disease id on map upload
    added (#618)
  * Small improvement: added current username next to logout button in admin
    panel (#660)
  * Small improvement: New comment dialog does not contain content of previous
    comment dialog (#680)
  * Small improvement: Left logo is configurable (#731)
  * Small improvement: list of element types in choose annotator dialog is
    sorted (#798)
  * Small improvement: Plugin API provides list of overview images (#702)
  * Small improvement: Plugin API allows to show/hide overview images (#702)
  * Small improvement: Plugin API allows to trigger search on the map (#702)
  * Small improvement: Plugin API allows to clear search results on map (#702)
  * Small improvement: edit/remove project button is disabled until project is
    uploaded (#683)
  * Small improvement: warning about capslock is visible on login page when
    necessary (#658)
  * Small improvement: names of columns in data overlay are unified: no
    whitespace, "_" used as separator (#596)
  * Small improvement: list of references in drug panel contains PUBMED prefix
    (#666)
  * Small improvement: list of projects is auto refreshed every 5 seconds if at
    least one of the project is uploading/removing (#610)
  * Small improvement: passwords to email account and ldap are not sent over
    API (#732)
  * Small improvement: reactant/product/modifier specific colors are parsed
    properly from CellDesigner file (#597)
  * Small improvement: Info tab contains information about disease and
    organism when info is provided
  * Small improvement: Info tab provides information about model annotations
    and submap tabs provide information about submaps annotations if applicable
    (#591)
  * Small improvement: uploading sbml file should automatically discover a file
    type (#784)
  * Small improvement: when plugin listeners crash the system notifies user
    about problem with a plugin (#767)
  * Small improvement: when exporting reaction and elements there is
    possibility to filter by (sub)map (#615)
  * Small improvement: during first opening of a map, the zoom level is
    automatically computed if no default information is provided (#776)
  * Small improvement: when adding new project columns "Root map", "Mapping
    file" and "Map type" are merged (#700)
  * Small improvement: allow admin to disable CORS check (#802)
  * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
    SemanticZoomLevelTransparency (#801)
  * Small improvement: export/import from SBML support z-index in LAYOUT
    extension
  * Bug fix: due to blocking of our requests from ctdbase the autocomplete for
    this database is disabled
  * Bug fix: deprecated columns in data overlay are not visible to the end user
    (#827)
  * Bug fix: invalid color in data overlay provides proper feedback to the user
    (#822)
  * Bug fix: genetic variant overlay without name caused problems (#832)
  * Bug fix: tair locus identifiers were used improperly - instead of id the
    name was used
  * Bug fix: plugin tab header wasn't properly resized after adding plugins
    that introduced second line for tab selection (#758)
  * Bug fix: invisible layer shouldn't be shown on the map (#813)
  * Bug fix: list of availbale annotators is sorted alphabetically (#815)
  * Bug fix: redirect url from export panel is fixed (#819)
  * Bug fix: allow to reupload the same file without closing add overlay dialog
    (#833)
  * Bug fix: gene_name column is allowed only in the genetic variant data
    overlay
  * Bug fix: protein types are sorted properly in "Select valid annotations"
    dialog (#815)
  * Bug fix: if there is a description of (sub)map then it is available in
    info/submap panel (#824)
  * Bug fix: empty type for data overlay is allowed (#827)
  * Bug fix: genetic variants data overlay was ignoring color parameter (#827)
  * Bug fix: asynchronous calls on showing/hiding data overlays might cause
    problems due to network latency (#830)
  * Bug fix: progress bar of gene genome mapping upload is refreshing properly
    (#728)
  * Bug fix: when editing project Disease and Organism could not be removed
    (#616)
  * Bug fix: dashed line partially wasn't dashed in "Unknown Catalysis" and
    "Unknown Inhibition" reactions (#664)
  * Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is
    slightly separated from target phenotype (#664)
  * Bug fix: order of genomes in admin panel doesn't change after refreshing
    list of genomes (#761)
  * Bug fix: fixing situation when Molart started with variation overlay not
    having the aa change information
  * Bug fix: plugin contect element width is adjusted when link to tabs are
    wrapped in more than one line (#758)
  * Bug fix: export to CellDesigner preserve font size (#798)
  * Bug fix: layout data was ignored for some reactions when importing from
    SBML (#812)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 27 Jun 2019 14:00:00 +0200

minerva (13.0.0) stable; urgency=medium
  * 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)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 6 May 2019 18:00:00 +0200

minerva (12.2.3) stable; urgency=medium
  * 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)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 24 Apr 2019 17:00:00 +0200

minerva (12.2.2) stable; urgency=medium
  * 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)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 9 Apr 2019 17:00:00 +0200

minerva (12.2.1) stable; urgency=medium
  * 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)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 1 Apr 2019 17:00:00 +0200

minerva (12.2.0) stable; urgency=medium
  * 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

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 25 Mar 2019 17:00:00 +0200

minerva (12.1.8) stable; urgency=medium
  * 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)

 -- 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>  Thu, 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