CHANGELOG

minerva (15.0.0~beta.5) unstable; urgency=medium
  * Backward incompatible: truncation/association/dissocation points are
    represented as a dot in all new images/uploaded maps (#1265)
  * Bug fix: export to GPML uses proper arrow types (#1262)
  * Bug fix: export to GPML uses dashed lines in reactions when possible
    (#1262)
  * Bug fix: pathways are visualized in image converter (#1266)
  * Bug fix: there is a bug in PathVisio that breaks short segments being the
    end of catalist therefore short segments are removed from export (#1263) 
  * Bug fix: conversion of file containing BOM did not work (#1264)
  * Bug fix: dashed elements imported from GPML are treated as hypothetical
    (#1268)
  * Bug fix: hypothetical elements exported to GPML are drawn with dashed line
    (#1268)
  * Bug fix: proper color is parsed from CellDesigner species marked as 'brief'
    (#1268)
  * Bug fix: export to CellDesigner replace unsupported bqmodel:isDerivedFrom
    types with something readable by CellDesigner (#1281)
  * Bug fix: unknown elements are exported to 'Unknown' data nodes in GPML
    (#1274)
  * Bug fix: uploading map with elements having identifiers like "artX" could
    break upload (#1273)
  * Bug fix: export from minerva does not include SemanticZoom terms for text
    notes (#1287)
  * Bug fix: import from GPML introduces space between inhibition and process
    (#1270)
  * Bug fix: map cantaining kinetic equations exported to CellDesigner was not
    a valid SBML file (#1271)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 2 Jun 2020 16:00:00 +0200

minerva (15.0.0~beta.4) unstable; urgency=medium
  * Backward incompatible: and/split points are represented as a dot in all new
    images/uploaded maps (#1253)
  * Backward incompatible: reation will be on top of elements in maps uploaded
    from formats that does not contain z-index (#1251)
  * Small improvement: "bqbiol:occursIn" and "bqmodel:isDerivedFrom" and
    handled in annotations (#1190),
  * Small improvement: 3DMET, Evidence Code Ontology, Kegg Glycan, LipidBank,
    Chemical Component Dictionary annotations are supported (#1190)
  * Small improvement: SWISS-model annotations are supported (#1249),
  * Small improvement: small css improvement in info tab (#1104)
  * Bug fix: upload of SBGN files didn't process unicode characters properly
    when server was running with encoding different than UTF-8 (#1142)
  * Bug fix: export unknown species to GPML caused pathvisio to crash (#1215)
  * Bug fix: annotations in CD 2.5 caused import to crash (#1125)
  * Bug fix: complex reaction with two required reactants in CD 2.5 caused
    import to crash (#1125)
  * Bug fix: kinetic equation in reaction that referenced complex (instead of
    target species) crashed CellDesigner upload (#1212)
  * Bug fix: transcription-translation should be turned into StateTransition
    reaction when importing GPML (#1236)
  * Bug fix: species graphical shape is taken as secondary indication to
    species type when importing GPML (#1237)
  * Bug fix: name is assigned to complexes when second complex is defined in it
    in GPML (#1238)
  * Bug fix: kinetic equation in SBML that used speciesReference id crashed
    upload (#1190)
  * Bug fix: layout reaction with duplicated reaction element crashed SBML
    upload (#1190)
  * Bug fix: conversion from SBML to CellDesigner escaped "<" twice (#1228)
  * Bug fix: graphical elements imported from GPML have border color and
    background color defined properly (#1259)
  * Bug fix: export/import to GPML properly handles degradation (#1241)
  * Bug fix: Select annotation dialog width is at least 840px (#1210)
  * Bug fix: modifiers joined by operator were exported to SBML without line
    corresponding to the operator (#1199)
  * Bug fix: first state variable that does not match modification residue is
    translated to structural state when importing from SBGNML  (#1088)
  * Bug fix: list of database releases is always updated on DAPI credentials
    change (#1128)
  * Bug fix: proper error is returned when trying to sign up to DAPI with
    exisitng account (#1158)
  * Bug fix: session mixed chemical and drug queries when refreshing webpage
    (#1161)
  * Bug fix: caching data for map with entrez ID crashed
  * Bug fix: not all data were cached about drugs/chemicals/mirnas when "cache
    data" was checked on project upload
  * Bug fix: when invalid password is provided proper warning is raised (#1159)
  * Bug fix: when no release is accepted in admin panel user is notified that
    not all databases will be used in search queries (#1159)
  * Bug fix: when exporting to GPML line ends are aligned to new shapes (#1242)
  * Bug fix: when exporting to GPML proper shapes are used for species
  * Bug fix: export of modifications to GPML generated invalid GPML file
    (#1257)
  * Bug fix: caching file with protin name containing new line character
    crashed
  * Bug fix: when caching the data on project upload list hint list for mirna,
    drugs, chemicals were not cached (#1163)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 2 Jun 2020 16:00:00 +0200

minerva (15.0.0~beta.3) unstable; urgency=medium
  * Improvement: API allows to merge files (#1208)
  * Bug fix: exported SBML was not compliant with the standard when element
    name was empty (#1147)
  * Bug fix: flybase and pato annotations from CellDesigner were not picked
    (#1113)
  * Bug fix: invalid data overlays in uploaded zip file created "valid" project
    that could not be opened (#1086)
  * Bug fix: export to GPML preserves font color of compartments (#1111)
  * Bug fix: export to GPML preserves information about hypotetical complexes
    (#1111)
  * Bug fix: export to GPML preserves complex name (#1111)
  * Bug fix: export to GPML preserves reaction color (#1111)
  * Bug fix: modification residues are exported to gpml (#1111)
  * Bug fix: information about reaction reversibility is exported to gpml
    (#1111)
  * Bug fix: cardinality in SBGN-like view is drawn in separate unit (#1157)
  * Bug fix: notes from SBML are parsed with all html tags (#1196)
  * Bug fix: converter API append conversion warnings to generated output notes

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 3 Apr 2020 15:00:00 +0200

minerva (15.0.0~beta.2) unstable; urgency=medium
  * Small Improvement: SBO annotation support added (#1194)
  * Small Improvement: additional annotation uri qualifiers added: hasProperty,
    isPropertyOf (#1193)
  * Small Improvement: default color of complexes imported from gpml changed to
    the one used by wikipathways (#1107)
  * Bug fix: newt use incorrect attributes when exporting render information
    that could not be parsed by minevra (#1127)
  * Bug fix: catalysis to protein was not parsed from SBGN file (#1116)
  * Bug fix: upload logs for SBGN parser were not translated properly to new
    structured log form
  * Bug fix: antisenseRNA shape is infered from SBGN when antisenseRNA text is
    present in glyph label (#1114)
  * Bug fix: export to SBGN sometimes crashed due to concurrency issues (#1126)
  * Bug fix: CellDesigner models where start and end point of reaction was the
    same were not handled properly (#1131)
  * Bug fix: exporting map to CellDesigner from GPML file created not-editable
    compartments (#1146)
  * Bug fix: some CellDesigner 2.5 files could not be parsed (#1125)
  * Bug fix: more than one authors in CellDesigner file were not parsed
    properly (#1156)
  * Bug fix: pathways imported from gpml persist fill color (#1107)
  * Bug fix: some reversible reactions in gpml were not imported as reversible
    (#1107)
  * Bug fix: colors of reactants/products/modifiers were not imported from gpml
    (#1107)
  * Bug fix: border color of species imported from gpml is preserved (#1107)
  * Bug fix: coordinates of complex name from GPML file is preserved (#1107)
  * Bug fix: element name for general shapes imported from GPML does not
    contain ShapeType if feasible (#1107)
  * Bug fix: z-index of rectangles and some complexes imported from GPML was
    not assigned properly (#1107)
  * Bug fix: new line in label text does not split he text into name and
    desciption (#1107)
  * Bug fix: label omim href with "www" prefix are parsed properly
  * Bug fix: modification position imported from GPML file is preserved (#1107)
  * Bug fix: SBGN reaction with no reactants crashed map upload (#1148)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Mar 2020 14:00:00 +0200

minerva (15.0.0~beta.1) unstable; urgency=medium
  * Bug fix: conflict on libraries caused some features to stop working in
    production (like parsing text notes of species, regresion in
    15.0.0~alpha.1, #1139)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 26 Feb 2020 13:00:00 +0200

minerva (15.0.0~beta.0) unstable; urgency=medium
  * Feature removal: old connection to CTD is removed and replaced with
    new Data-API interface that closely check license compliance
  * Feature removal: some custom fields (like transparency zoom level) are not
    exported to CellDesigner file (#1071)
  * Improvement: export to SBGN/SBML/GPML format provides popup with list of
    warnings occurred in the translation process (#713)
  * Small improvement: autocomplete for chemical searches is enabled (#841)
  * Small improvement: import/export to SBML of unit of information obtained
    from SBGN source is supported (#1088)
  * Small improvement: rounded rectangle is used to visualize Simple chemicals
    in SBGN-like view according to the newest SBGN specification (#1094)
  * Small improvement: after removing project is confirmed the system enforce
    waiting until remove status is confirmed (#1106)
  * Bug fix: import from SBGN assigned invalid name to species that didn't have
    label defined (#1093)
  * Bug fix: drawing protein in SBGN-like style didn't handle properly
    dimension of the species for multimers bigger than 2 (#1091)
  * Bug fix: drawing of structural state in SBGN-like style uses
    RoundedRectangle instead of Ellipse which was not SBGN-compliant (#1095)
  * Bug fix: export to GPML provided invalid font size and pathviosio could not
    open it (#1108)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 28 Jan 2020 13:00:00 +0200

minerva (15.0.0~alpha.2) unstable; urgency=medium
  * Feature removal: old connection to DrugBank is removed and replaced with
    new Data-API interface that closely check license compliance
  * Small improvement: when typing drug, list of autocomplete drugs should be
    available limited to the drugs targetting something on the map (#641)
  * Small improvement: data not compliant with database constraints (for
    instance too long species identifiers) will be automatically adjust instead
    of crashing project upload (#1041)
  * Small improvement: reaction lines in SBML files without layout are set
    outside of the species (not in the center, #1023)
  * Bug fix: import from CellDesigner rounded alias dimension to integer
  * Bug fix: old project with structural state couldn't be removed (regression
    15.0.0~alpha.1, #1021)
  * Bug fix: processing sbgn file with render information was breaking sometimes
    (regression 15.0.0~alpha.1, #1020)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 22 Jan 2020 13:00:00 +0200

minerva (15.0.0~alpha.1) unstable; urgency=medium
  * Feature removal: when uploading complex map with submap there is no
    possibility to change submap name (#947)
  * Improvement: support for rendering colors in SBGNML added (#1009)
  * Small improvement: sort order of tables in admin panel is preserved among
    sessions (#836)
  * Small improvement: simple molecules in sbgn compliant view are drawn as
    ellipses not circles (#796)
  * Small improvement: uploaded map is automatically cached (#983)
  * Small improvement: molart updated to version 1.5.0: Ability to show
    unobserved structure regions in the sequence view.
  * Small improvement: list of genomes is automatically refreshed during genome
    upload (#820)
  * Small improvement: items in context menu are reorganized (#787)
  * Small improvement: CellDesigner files from version 2.5 should be parseable
  * Small improvement: plugins in admin panel can be revalidated to update info
    about the plugins (name, version)
  * Small improvement: there is possibility to define default plugins loaded
    with every opening of a map (#967)
  * Small improvement: support for annotations added: ChemIDplus, EcoGene,
    FlyBase, GeneDB, Intact, Kegg Drug, KNApSAcK, LIPID MAPS, NCBI Protein,
    PATO, RGD, SPIKE, TTD Drug, ZFIN BioEntity
  * Bug fix: compartments limited by corner (left-top corner compartment, etc)
    are parsed properly from CellDesigner files
  * Bug fix: structural states of proteins are imported properly from SBGNML PD
    (#995)
  * Bug fix: clear button icon, refresh comments button and show overview
    button icons were missing (regression 15.0.0~alpha.0)
  * Bug fix: export to CellDesigner names with new line is properly handled
    (#930)
  * Bug fix: layout of the exported reactome pathways is fixed when reactome
    exporter violates SBGN specification (#707)
  * Bug fix: unknown catalysis boolean gate modifiers in CellDesigner are
    visualized with proper line type across all included modifiers (#957)
  * Bug fix: dimension of the modifications is the same as in minerva when
    exporting to SBGNML-PD (#554)

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

minerva (15.0.0~alpha.0) unstable; urgency=medium
  * Improvement: logs provided for validation data model are structurized (#325)
  * Improvement: import/export of GPML implemented
  * Small improvement: compartments in not layouted SBML file are more
    scattered (#326)
  * Small improvement: when downloading a map results in too big file (>1MB)
    the content is compressed and returned as a zip file (#348)
  * Small improvement: confirmation dialog when removing "general view"
    overlays contain proper warning  (#809)
  * Small improvement: CellDesigner text area object can have "BorderColor"
    property defined (#806)
  * Small improvement: list of submaps is sorted alphabetically (#962)
  * Small improvement: notification about new releases of minerva added in
    admin panel (#961)
  * Small improvement: font awesome upgraded to 5.1 (new icon styles)
  * Small improvement: header contains login/logout button and access admin
    panel button (#982)
  * Bug fix: position of structural state is preserved on upload CellDesigner
    file (#671)
  * Bug fix: problematic notes doesn't crash CellDesigner upload (#968)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 4 Nov 2019 11:00:00 +0200

minerva (14.0.13) stable; urgency=medium
  * Bug fix: chrome modified default css and service looked ugly in chrome
    (#1260)
  * Bug fix: uploaded HGNC identifiers that looks like "HGNC:HGNC:1234" are
    changed to "HGNC:1234" (#1252)
  * Bug fix: creating comment with too long name/email resulted in Internal
    Server Error - now the proper error message is returned (#1245)
  * Bug fix: user cannot put too long name in a comment dialog (#1245)
  * Bug fix: when url contained invalid submap id unhandled error was raised
    (#1243)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 3 Jun 2020 17:00:00 +0200

minerva (14.0.12) stable; urgency=medium
  * Bug fix: comments on submaps were not visible (#1230)
  * Bug fix: removing comment from submap did not work
  * Bug fix: reaction name containing "<" character was exported inproperly to
    CellDesigner (#1227)
  * Bug fix: doi annotation was inproperly parsed from CellDesigner file and
    resulted in not clickable link (#1231)
  * Bug fix: when plugin data was too big 500 error was returned (#1232)
  * Bug fix: removing plugin in admin panel removes it from server permanently
    (#1211)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 11 May 2020 17:00:00 +0200

minerva (14.0.11) stable; urgency=medium
  * Bug fix: complex with no border was inproperly imported from CellDesigner
    (#1198)
  * Bug fix: export to CellDesigner deal with CellDesigner issue that does not
    allow compartment species alias to be shorter than 2 characters (#1204)
  * Bug fix: kinetic parameters with INFINITY values could not be uploaded to
    minerva (#1202)
  * Bug fix: infinity value in kinetic parameter could not be parsed from
    CellDesigner file minerva (#1203)
  * Bug fix: author list inproperly presented author data when some fields were
    missing (#1201)
  * Bug fix: refreshing minerva page with more than one plugin opened might
    led to an error due to race condition (#1197)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 31 Mar 2020 09:00:00 +0200

minerva (14.0.10) stable; urgency=medium
  * Bug fix: reaction without ports in SBGN crashed upload (#1065)
  * Bug fix: annotations using newer identifiers.org uri schema were truncated
    by one character (#1191)
  * Bug fix: long annotation string broke listing of annotations (#1155)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Mar 2020 14:00:00 +0200

minerva (14.0.9) stable; urgency=medium
  * Bug fix: simultanous export to SBML of more than one file could result in
    500 Internal Server Error (#1110)
  * Bug fix: refresh data overlay did not hide data overlays that were removed
    and selected (#1097)
  * Bug fix: transparent complexes are shown with wrong color (#1103)
  * Bug fix: CellDesigner sometimes marked reduced notation reaction as
    reversible even though they were not visualized so (#1109)
  * Bug fix: when data overlay was being removed user could request to remove
    overlay second time and an error was thrown (#1121)
  * Bug fix: when data overlay name in zip uploaded zip file is not present the
    name of a file is used as overlay name (#1065)
  * Bug fix: uploading empty data overlay resulted in an error (#1123)
  * Bug fix: exporting map with glyphs crashed (#1130)
  * Bug fix: transcription factor on black&white gene are drawn in black
    (#1132)
  * Bug fix: when SBGN file contained consumption starting in process minerva
    crashed (#1063)
  * Bug fix: when SBGN file contained reaction where every node started in the
    same process port minerva crashed crashed (#1063)
  * Bug fix: activity flow reaction inside SBGN PD caused upload of map to
    crash
  * Bug fix: reaction without product in SBGN crashed upload of map
  * Bug fix: when SBGN production pointed directly to process instead of
    process port upload crashed
  * Bug fix: handle properly corrupted cached chembl drug data (#1140)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 25 Feb 2020 15:00:00 +0200

minerva (14.0.8) stable; urgency=medium
  * Bug fix: API didn't allow to upload plugins with local url (#1084,
    regression 14.0.7)
  * Bug fix: upload of data overlay with two entries having different uniprot
    identifier but pointing to the same gene crashed (#1083)
  * Bug fix: don't allow to remove plugin twice (#1081)
  * Bug fix: upload of SBML file with very short reaction length could produce
    a map that couldn't be exported to SBML anymore (#1078)
  * Bug fix: import of structural state from SBGN-ML PD that cannot be
    normalized to residue is changed into structural state without losing
    information (#1062)
  * Bug fix: import of stimulation modifiers from SBGN-ML crashed converter
    (#1063)
  * Bug fix: export to SBGN files created from newt source produced corrupted
    disconnected reactions
  * Bug fix: upload from zip file allowed empty overlay name (#1065)
  * Bug fix: genome browser slider didn't work properly in Safari on
    non-default Browser zoom level (#1048)
  * Bug fix: project without background overlay but with some custom data
    overlays crashed with an error (#1066)
  * Bug fix: when session expires updating options in configuration panel threw
    unhandled error (#1068)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 28 Jan 2020 11:00:00 +0200

minerva (14.0.7) stable; urgency=high
  * Bug fix: API allowed to provide malformed plugin url that could be used for
    xss attack (#1073)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 14 Jan 2020 17:00:00 +0200

minerva (14.0.6) stable; urgency=medium
  * Bug fix: opening map with no background overlays and search request in url
    provides proper error message (#1046)
  * Bug fix: search by identifier didn't consider identifiers added by
    annotators (#1047)
  * Bug fix: if map has SHOW OVERVIEW, the legend/comment/clear were not
    displayed at all (regresion 14.0.5, #1045)
  * Bug fix: when there is a problem with database during removing project,
    project removal doesn't hang (#1058)
  * Bug fix: coloring of the reaction wasn't applied to center of reaction
    (regression 14.0.0, #1057)
  * Bug fix: genetic variant overlay improperly processed elements identified
    by miriam identifiers, like uniprot (#1059)
  * Bug fix: invalid information was provided for genetic variants overlay when
    map organism was defined (#1060)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 19 Dec 2019 13:00:00 +0200

minerva (14.0.5) stable; urgency=medium
  * Bug fix: copy-paste of genetic-variant data overlay into Add overlay
    content dialog could crash upload (#1040)
  * Bug fix: some annotators (like Cazy) were crashing on old installations
    (#1029)
  * Bug fix: uploading a map that breaks postgres constraints hung upload of
    the project (#1028)
  * Bug fix: uploading of the page with low internet connection speed could
    produce empty screen for several seconds/minutes - now the loading icon is
    present (#1025)
  * Bug fix: search for NADH drug resulted in drug with empty name (#1018)
  * Bug fix: export to SBML didn't handle properly arrows (#1015)
  * Bug fix: Font colour of text area was preserved in Empty view (#1014)
  * Bug fix: exported sbml file always contain model identifier (#1013)
  * Bug fix: typo allel reverted to allele in overlay data (regression 14.0.0,
    #1012)
  * Bug fix: after loading/removing too many plugins it was impossible to load
    new plugins (#1011)
  * Bug fix: CLEAR button disappears after legend, comment checkboxes when
    plugin tab used to much space (#976)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 03 Dec 2019 12:00:00 +0200

minerva (14.0.4) stable; urgency=high
  * Bug fix: some SBGN files uploaded to minerva could not be exported to SBML
    due to problems with identifiers used by SBGN (#1006)
  * Bug fix: upload of data overlay with conflicting overlay types caused error
    (#998)
  * Bug fix: upload of sbml file with protein modifications inside complex
    crashed visualization (#966)
  * Bug fix: list of overlays for admin and curator included also other people
    overlays (regression 14.0.3, #1008)
  * Bug fix: refresh button did not refresh overlay list after overlay was
    removed over API (#997)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 07 Nov 2019 11:00:00 +0200

minerva (14.0.3) stable; urgency=medium
  * Bug fix: default zoom level on main map works even when x or y are
    undefined (#993)
  * 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: verification of version length added when uploading project
    implemented (#978)
  * Bug fix: CLEAR button disappeared 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 genome browser (#942)
  * Bug fix: color of links in the left panel was unintentionally changed 
    (#990)
  * Bug fix: minerva logo in left panel is centred properly
  * Bug fix: width of search button icon was too big

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 18 Oct 2019 15:00:00 +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)