minerva (12.3.1~beta.1) unstable; urgency=low
* 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)
* 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 in the on th 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: when changing data in edit user dialog there was a need to click
close button twice (#818)
* Bug fix: empty type for data overlay is allowed (#827)
* Bug fix: genetic variants data overlay was ignoring color parameter (#827)
* Bug fix: pathways can be drawn using glyphs (#825)
* Bug fix: empty background overlay doesn't show glyphs, instead standard
visualization is used (#826)
* Bug fix: asynchronous cals on showing/hiding data overlays might cause
problems due to network latency (#830)
minerva (13.1.0~beta.0) unstable; urgency=low
* 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: 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: 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> Mon, 13 May 2019 19:00:00 +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
-- 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