CHANGELOG

minerva (16.0.0~beta.1) stable; urgency=medium
  * Backward incompatibility: layout parameter in minerva url is not supported
    anymore
  * Small improvement: info about background and data overlays is separated in
    edit project panel (#1515)
  * Bug fix: there was issue with updating data overlay in admin panel "Unknown
    parameter: defaultOverlay" (#1489)
  * Bug fix: data overlays uploaded in complex map were not processed properly
    (#1485)
  * Bug fix: sort of the overlays in General Overlays in the left panel was
    wrong (#1486)
  * Bug fix: overlay owner must be defined (#1488)
  * Bug fix: there was issue when upgrading backgrounds in admin panel (#1514)
  * Bug fix: there was issue when editing and saving data overlay (#1494)
  * Bug fix: problem with adding comments (#1495)
  * Bug fix: project with invalid data might cause problem on
    create/update/delete (#1509)
  * Bug fix: exporting part of map as image caused removing not drawn species
    from the database (#1508)
  * Bug fix: adding user with already existing login and changing his
    privileges occured with error (#1507)
  * Bug fix: export model as model could cause an issue (#1500, #1502)
  * Bug fix: problem with export as image with data overlays (#1503, #1498,
    #1496)
  * Bug fix: chrome autofill is disabled for "Search: " in admin panel tables
  * Bug fix: top map was not selected properly sometimes (#1487)
  * Bug fix: data overlays in comlex upload prevented error to be propagated
    to user (#1499)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 9 Jun 2021 15:00:00 +0200

minerva (16.0.0~beta.0) stable; urgency=medium
  * Backward incompatibility: debian package cannot be upgraded from version
    prior to 12.1.0 (#1464)
  * Small improvement: artifitial source and sink is created separately for
    each uncomplete reaction (#1475)
  * Small improvement: homomultimer information is provided in API (#1468)
  * Small improvement: missing info about species for SBML parsing warning
    (#1472)
  * Small improvement: information about dimer in sbgn is provided only once
    if the information is duplicated in sbgn data (#1358)
  * Small improvement: glyph quality is improved (#1458)
  * Small improvement: search results are group by diagram (#1451)
  * Small improvement: "Failed to fetch" errors are reported in a way that
    suggest retrying before submitting error report (#738)
  * Small improvement: reverse search pop-up reorganized (#1366)
  * Bug fix: arrows without a "process" box had an irregular empty space in
    their lines (#1471)
  * Bug fix: when selecting drug in the alias window the input text is updated
    (#1365)
  * Bug fix: zoom slider was not updated when clicking on +/- in genome browser
    (#1064)
  * Bug fix: there was no possibility to see gene variants
    (regression 16.0.0~alpha.1)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 30 Apr 2021 16:30:00 +0200

minerva (16.0.0~alpha.1) stable; urgency=medium
  * Backward incompatibility: deprecated columns in data overlays are no longer
    supported (#958)
  * Backward incompatibility: comment does not contain name anymore (#1070)
  * Backward incompatibility: publication pagination API slightly changed
    (#1007)
  * Backward incompatibility: elements in data overlay are returned differently
    when using data overlay API (#1007)
  * Improvement: performance improved - map is available immediatelly after
    tomcat starts (#1007)
  * Improvement: minerva does not require huge amounts of memory anymore
    (#1007)
  * Improvement: data overlay allows for multiple hits per element (#1007)
  * Small improvement: "dbSNP", "IMGT HLA", "PMC", "Complex Portal" identifiers
    are supported (#1452, #1450, #1420)
  * Small improvement: information about perfect search are stored in the url
    (#1376)
  * Small improvement: context menu exporting map is more precise about scope
    (#1447)
  * Small improvement: styling of GENERIC search tab title improved (#1364)
  * Small improvement: SBML render contains information about species shapes
    (#1055)
  * Small improvement: SBML render contains information about modification
    residues (#1456)
  * Small improvement: SBML render contains information about structural states
    (#1456)
  * Small improvement: SBML render contains process rectangle for reactions
    (#1457)
  * Bug fix: refreshing page after removing last project on the page redirect to
    proper page (#1051)
  * Bug fix: removing plugin that does not exist anymore does not raise an error
    (#1289)
  * Bug fix: broken overlays crashed minerva upgrade (#1453)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 19 Mar 2021 10:00:00 +0200

minerva (16.0.0~alpha.0) stable; urgency=medium
  * Backward incompatibility: deprecated columns in data overlay table are no
    longer supported: reverseReaction, reaction_identifier, reactionIdentifier,
    reference_genome_type, reference_genome_version, allel_frequency, lineWidth,
    elementIdentifier, references, model_name (#958)
  * Backward incompatibility: information about old search queries removed from
    database (it can be still accessed using proper log managing)
  * Improvement: automatically generated API documentation available in the
    package (#1016)
  * Bug fix: md5 hash function of plugin was not computed properly
  * Bug fix: exported gpml for every compartment contained list of species name
    in the comment section

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 27 Aug 2020 13:00:00 +0200

minerva (15.1.4) stable; urgency=medium
  * Bug fix: structural state information data was not available for complexes
    (#1476)
  * Bug fix: orthogonal reactions to phenotypes from CellDesigner were drawn
    incorrectly (#1454)
  * Bug fix: orthogonal reactions to drugs from CellDesigner were drawn
    incorrectly (#1454)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 30 Apr 2021 18:00:00 +0200

minerva (15.1.3) stable; urgency=medium
  * Bug fix: modifier reactions to phenotype were incorrectly translated to
    Process Description reactions when exporting to SBGN-ML (#1445)
  * Bug fix: AND/OR text was missing when drawing diagram as SBGN (#1428)
  * Bug fix: annotators details changes were not saved in few consecutive
    updates (#1446)
  * Bug fix: SearchListener was not triggered when clicking on highlighted
    elements (#1449)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 9 Feb 2021 09:00:00 +0200

minerva (15.1.2) stable; urgency=medium
  * Bug fix: automatic annotations are sometimes missing after project upload
   (#1434)
  * Bug fix: export to SBML failed if reactant/product line had length=0
  * Bug fix: downloading submap from big project as a map quite often resulted
    in error (#1440)
  * Bug fix: colors for values in exported image were incorrect for
    intermediate values, like 0.5 (#1442)
  * Bug fix: when there is a problem with updating sorting preferences no error
    is raised but silent warning is reported in the console (#1426)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 11 Jan 2021 12:00:00 +0200

minerva (15.1.1) stable; urgency=medium
  * Bug fix: export to CD maps with species containing ":" or "." in species id
    generated files that could not be opened in CellDesigner (#1363) 
  * Bug fix: zoom level change was not reflected in the url when submap was
    opened (#1338)
  * Bug fix: API call returning list of overlays returned for non existing
    project returned access denied status insted Not Found (#1370)
  * Bug fix: results for chembl targetting uniprot without gene name (for
    example P0C2L1)  could crash caching (#1377)
  * Bug fix: removing non-existing project results in warning not an error
    message (#1367)
  * Bug fix: opening map in google maps without background resulted in
    unexpected error (#1416)
  * Bug fix: normal user could not update tos information (#1419)
  * Bug fix: and operator in SBGN-like view was not drawn (#1408)
  * Bug fix: export of overlayed map as an image did not respect overlay colors
   (#1417)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 23 Nov 2020 15:00:00 +0200

minerva (15.1.0) stable; urgency=medium
  * Small improvement: information if species has activity, hypothetical flag
    set is available over REST API for element (#1379)
  * Small improvement: "Human Disease Ontology", "IUPHAR ligand" and "Protein
    Modification Ontology" annotation types are handled (#1359)
  * Small improvement: annotations are exported in SBGN extension that can be
    opened by newt (#1296)
  * Small improvement: plugin API allows to add/remove data overlays (#1153)
  * Small improvement: logged user can change password (#1119)
  * Small improvement: possibility to reset password added (#275)
  * Small improvement: import SBML uses render:fill color for compartment
    (#1254)
  * Small improvement: in SBML render stroke color for glyphs is used for
    defining font color
  * Small improvement: when SBML with layout contains different glyph text and
    species name those two values are assigned to name and full name (#1275)
  * Small improvement: process rectangle can be specified in SBML with reaction
    bounding box (#1292)
  * Small improvement: API allows to remove plugin data entry (#1298)
  * Small improvement: transport/translation/transcription reactions are
    exported to SBGN PD (#1302)
  * Small improvement: Unknown Transition Reaction is exported to GPML as
    CONVERSION (#1300)
  * Small improvement: when uploading complex map with images warnings are
    raised if images are not referenced in coords.txt file (#1308)
  * Small improvement: hitting enter after filling credentials automatically
    tries to log in (#1312)
  * Small improvement: rest API provides information about element glyph and z
    index
  * Small improvement: pathways with glyphs and z index below 0 are not
    clickable (#1314)
  * Small improvement: Modifier Reaction from CellDesigner are exported properly
    to SBGN-ML PD (#1320)
  * Small improvement: SBGN notes are imported properly (#1319)
  * Small improvement: SBGN notes are exported properly (#1319)
  * Small improvement: possibility to customize request account email title
    (#1330)
  * Bug fix: SBML text  labels that were referencing layout aliases using
    layout:graphicalObject attribute were not handled properly (#1356)
  * Bug fix: MolArt version upgraded to handle new protein API syntax (#1399)
  * Bug fix: LDAP connection did not work properly where uid in LDAP/AD
    contained upper case letters (#1404)
  * Bug fix: miriam urls in new format
   (like: https://identifiers.org/kegg.compound:197020) are parsed properly for
    all know identifier types (#1359)
  * Bug fix: in SBGN-like view protein state should be drawn as stadium-shape
    (#1357)
  * Bug fix: export to image from selected polygon contained all elements
    inside rectangle bounded by the polygon coordinates (#1096)
  * Bug fix: continuous refreshing list of project when uploading/removing
    project did not allow to change other project details (#996)
  * Bug fix: when multi extension did not contain species type list import of
    SBML crashed
  * Bug fix: when content of element popover is too wide the scrollbar is
    visible (#1269)
  * Bug fix: problem with accessing mirtarbase data on new instances fixed

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 22 Oct 2020 15:00:00 +0200

minerva (15.0.3) stable; urgency=medium
  * Bug fix: caching chemicals/drug data on big map could cause Out of Memory
    issues (#1315)
  * Bug fix: when there is a problem with minerva deployment on tomcat proper
    warning message is presented in admin panel (#1332)
  * Bug fix: API call updating user preferences did not handle properly
    conflicts on new gui properties (#1326)
  * Bug fix: "bqbiol:hasTaxon" relation type is not supported by CellDedigner
    and is now transformed during export into something readable by
    CellDesigner (#1281)
  * Bug fix: concurrency issue that could happen rarely on first search of the
    map and put the project into "unsearchable" state is fixed (#1333)
  * Bug fix: when edit project buton was clicked on project that was removed in
    another tab there was an error thrown (#1343)
  * Bug fix: chebi and entrez annotations were incorrectly exported to GPML
    (#1349)
  * Bug fix: exporting to GPML sometimes resulted in invalid modification point
    end for catalysis (#1350)
  * Bug fix: elements name were not escaped properly when exporting to GPML
    (#1351)
  * Bug fix: reaction with description and pubmed reference was incorrectly
    exported to GPML (#1352)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 13 Aug 2020 15:00:00 +0200

minerva (15.0.2) stable; urgency=medium
  * Bug fix: annotations using identifiers.org urls sometimes required http and
    sometimes required https url (#1297)
  * Bug fix: map notes were not exported to GPML
  * Bug fix: reaction notes were not imported from GPML
  * Bug fix: export of notes could create invalid GPML file (#1299)
  * Bug fix: there was an issue with exporting color and line type of reaction
    additional reactant/product (#1303)
  * Bug fix: coordinates of children in compact complexes in CellDesigner were
    wrong (#1304)
  * Bug fix: user data overlays were not removed when user was deleted (#1301)
  * Bug fix: kinetic parameters exported to SBML created invalid SBML file
    (#1305)
  * Bug fix: text area were not converted to GPML using conversion API (#1306)
  * Bug fix: name provided by user in comment dialog was not visible in admin
    panel (#1245)
  * Bug fix: bqmodel:isInstanceOf and bqmodel:hasInstance relation types were
    not handled properly (#1281)
  * Bug fix: "bqmodel:isInstanceOf", "bqmodel:hasInstance",
    "bqbiol:hasProperty", "bqbiol:isPropertyOf" relation types are not
    supported by CellDedigner and are now transformed during export into
    something readable by CellDesigner (#1281)
  * Bug fix: at random time points there was an issue with cached data (#1323)
  * Bug fix: connection to DAPI timeouted sometimes which resulted in error
    when checking for all chemicals for specfific protein (#1324)
  * Bug fix: complex/compartment with empty name was incorrectly exported to
    CellDesigner (#1310)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 1 Jul 2020 16:00:00 +0200

minerva (15.0.1) stable; urgency=medium
  * Bug fix: when there was problem with DAPI minerva threw unexpected error
    (#1316)
  * Bug fix: DAPI connection must go over HTTPS (#1316)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 26 Jun 2020 11:00:00 +0200

minerva (15.0.0) stable; urgency=medium
  * Backward incompatible: old connection to CTD is removed and replaced with
    new Data-API interface that closely check license compliance
  * Backward incompatible: old connection to DrugBank is removed and replaced
    with new Data-API interface that closely check license compliance
  * Backward incompatible: some custom fields (like transparency zoom level)
    are not exported to CellDesigner file (#1071)
  * Backward incompatible: truncation/association/dissociation points are
    represented as a dot in all new images/uploaded maps (#1265)
  * Backward incompatible: and/split points are represented as a dot in all new
    images/uploaded maps (#1253)
  * Backward incompatible: reaction will be on top of elements in maps uploaded
    from formats that does not contain z-index (#1251)
  * Backward incompatible: when uploading complex map with submap there is no
    possibility to change submap name (#947)
  * Improvement: logs provided for validation data model are structured (#325)
  * Improvement: import/export of GPML implemented
  * Improvement: API allows to merge files (#1208)
  * Improvement: export to SBGN/SBML/GPML format provides popup with list of
    warnings occurred in the translation process (#713)
  * Improvement: support for rendering colors in SBGNML added (#1009)
  * 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)
  * Small improvement: autocomplete for chemical searches is enabled (#841)
  * 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: SBO annotation support added (#1194)
  * 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
  * Small Improvement: additional annotation uri qualifiers added: hasProperty,
    isPropertyOf (#1193)
  * Small improvement: small css improvement in info tab (#1104)
  * 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)
  * Small improvement: when typing drug, list of autocomplete drugs should be
    available limited to the drugs that target 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)
  * 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)
  * Bug fix: pathways are visualized in image converter (#1266)
  * Bug fix: conversion of file containing BOM did not work (#1264)
  * Bug fix: proper color is parsed from CellDesigner species marked as 'brief'
  * 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: kinetic equation in reaction that referenced complex (instead of
    target species) crashed CellDesigner upload (#1212)
  * 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: 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: exported SBML was not compliant with the standard when element
    name was empty (#1147)
  * Bug fix: invalid data overlays in uploaded zip file created "valid" project
    that could not be opened (#1086)
  * 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
  * Bug fix: newt use incorrect attributes when exporting render information
    that could not be parsed by minerva (#1127)
  * Bug fix: catalysis to protein was not parsed from SBGN file (#1116)
  * Bug fix: antisenseRNA shape is inferred 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: more than one authors in CellDesigner file were not parsed
    properly (#1156)
  * Bug fix: SBGN reaction with no reactants crashed map upload (#1148)
  * 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: import from CellDesigner rounded alias dimension to integer
  * 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: 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)
  * 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>  Mon, 22 Jun 2020 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