CHANGELOG 66.2 KB
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minerva (15.0.3) stable; urgency=medium
  * Bug fix: caching chemicals/drug data on big map could cause Out of Memory
    issues (#1315)
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  * Bug fix: when there is a problem with minerva deployment on tomcat proper
    warning message is presented in admin panel (#1332)
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  * Bug fix: API call updating user preferences did not handle properly
    conflicts on new gui properties (#1326)
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  * Bug fix: "bqbiol:hasTaxon" relation type is not supported by CellDedigner
    and is now transformed during export into something readable by
    CellDesigner (#1281)
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  * Bug fix: concurrency issue that could happen rarely on first search of the
    map and put the project into "unsearchable" state is fixed (#1333)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 8 Jul 2020 16:00:00 +0200

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minerva (15.0.2) stable; urgency=medium
  * Bug fix: annotations using identifiers.org urls sometimes required http and
    sometimes required https url (#1297)
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  * Bug fix: map notes were not exported to GPML
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  * Bug fix: reaction notes were not imported from GPML
  * Bug fix: export of notes could create invalid GPML file (#1299) 
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  * Bug fix: there was an issue with exporting color and line type of reaction
    additional reactant/product (#1303) 
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  * Bug fix: coordinates of children in compact complexes in CellDesigner were
    wrong (#1304) 
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  * Bug fix: user data overlays were not removed when user was deleted (#1301)
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  * Bug fix: kinetic parameters exported to SBML created invalid SBML file
    (#1305)
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  * Bug fix: text area were not converted to GPML using conversion API (#1306)
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  * Bug fix: name provided by user in comment dialog was not visible in admin
    panel (#1245)
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  * Bug fix: bqmodel:isInstanceOf and bqmodel:hasInstance relation types were
    not handled properly (#1281)
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  * Bug fix: "bqmodel:isInstanceOf", "bqmodel:hasInstance",
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    "bqbiol:hasProperty", "bqbiol:isPropertyOf" relation types are not
    supported by CellDedigner and are now transformed during export into
    something readable by CellDesigner (#1281)
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  * Bug fix: at random time points there was an issue with cached data (#1323)
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  * Bug fix: connection to DAPI timeouted sometimes which resulted in error
    when checking for all chemicals for specfific protein (#1324)
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  * Bug fix: complex/compartment with empty name was incorrectly exported to
    CellDesigner (#1310)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 1 Jul 2020 16:00:00 +0200
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minerva (15.0.1) stable; urgency=medium
  * Bug fix: when there was problem with DAPI minerva threw unexpected error
    (#1316) 
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  * Bug fix: DAPI connection must go over HTTPS (#1316)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 26 Jun 2020 11:00:00 +0200

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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
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    represented as a dot in all new images/uploaded maps (#1265)
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  * Backward incompatible: and/split points are represented as a dot in all new
    images/uploaded maps (#1253)
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  * Backward incompatible: reaction will be on top of elements in maps uploaded
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    from formats that does not contain z-index (#1251)
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  * 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)
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  * Small improvement: "bqbiol:occursIn" and "bqmodel:isDerivedFrom" and
    handled in annotations (#1190),
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  * Small improvement: 3DMET, Evidence Code Ontology, Kegg Glycan, LipidBank,
    Chemical Component Dictionary annotations are supported (#1190)
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  * Small improvement: SWISS-model annotations are supported (#1249),
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  * 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)
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  * Small improvement: small css improvement in info tab (#1104)
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  * 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'
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  * Bug fix: upload of SBGN files didn't process unicode characters properly
    when server was running with encoding different than UTF-8 (#1142)
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  * Bug fix: kinetic equation in reaction that referenced complex (instead of
    target species) crashed CellDesigner upload (#1212)
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  * Bug fix: kinetic equation in SBML that used speciesReference id crashed
    upload (#1190)
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  * Bug fix: layout reaction with duplicated reaction element crashed SBML
    upload (#1190)
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  * Bug fix: conversion from SBML to CellDesigner escaped "<" twice (#1228)
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  * Bug fix: Select annotation dialog width is at least 840px (#1210)
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  * Bug fix: modifiers joined by operator were exported to SBML without line
    corresponding to the operator (#1199)
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  * Bug fix: first state variable that does not match modification residue is
    translated to structural state when importing from SBGNML  (#1088)
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  * Bug fix: exported SBML was not compliant with the standard when element
    name was empty (#1147)
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  * Bug fix: invalid data overlays in uploaded zip file created "valid" project
    that could not be opened (#1086)
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  * Bug fix: cardinality in SBGN-like view is drawn in separate unit (#1157)
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  * Bug fix: notes from SBML are parsed with all html tags (#1196)
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  * Bug fix: converter API append conversion warnings to generated output notes
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  * Bug fix: newt use incorrect attributes when exporting render information
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    that could not be parsed by minerva (#1127)
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  * Bug fix: catalysis to protein was not parsed from SBGN file (#1116)
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  * Bug fix: antisenseRNA shape is inferred from SBGN when antisenseRNA text is
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    present in glyph label (#1114)
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  * Bug fix: export to SBGN sometimes crashed due to concurrency issues (#1126)
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  * Bug fix: CellDesigner models where start and end point of reaction was the
    same were not handled properly (#1131)
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  * Bug fix: more than one authors in CellDesigner file were not parsed
    properly (#1156)
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  * Bug fix: SBGN reaction with no reactants crashed map upload (#1148)
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  * Bug fix: import from SBGN assigned invalid name to species that didn't have
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    label defined (#1093)
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  * Bug fix: drawing protein in SBGN-like style didn't handle properly
    dimension of the species for multimers bigger than 2 (#1091)
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  * Bug fix: drawing of structural state in SBGN-like style uses
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    RoundedRectangle instead of Ellipse which was not SBGN-compliant (#1095)
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  * Bug fix: import from CellDesigner rounded alias dimension to integer
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  * Bug fix: compartments limited by corner (left-top corner compartment, etc)
    are parsed properly from CellDesigner files
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  * Bug fix: structural states of proteins are imported properly from SBGNML PD
    (#995)
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  * Bug fix: export to CellDesigner names with new line is properly handled
    (#930)
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  * Bug fix: layout of the exported reactome pathways is fixed when reactome
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    exporter violates SBGN specification (#707)
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  * Bug fix: unknown catalysis boolean gate modifiers in CellDesigner are
    visualized with proper line type across all included modifiers (#957)
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  * Bug fix: dimension of the modifications is the same as in minerva when
    exporting to SBGNML-PD (#554)
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  * Bug fix: position of structural state is preserved on upload CellDesigner
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    file (#671)
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  * Bug fix: problematic notes doesn't crash CellDesigner upload (#968)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Jun 2020 11:00:00 +0200
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minerva (14.0.13) stable; urgency=medium
  * Bug fix: chrome modified default css and service looked ugly in chrome
    (#1260)
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  * Bug fix: uploaded HGNC identifiers that looks like "HGNC:HGNC:1234" are
    changed to "HGNC:1234" (#1252)
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  * 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)
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  * Bug fix: when url contained invalid submap id unhandled error was raised
    (#1243)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 3 Jun 2020 17:00:00 +0200

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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
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  * Bug fix: reaction name containing "<" character was exported inproperly to
    CellDesigner (#1227)
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  * Bug fix: doi annotation was inproperly parsed from CellDesigner file and
    resulted in not clickable link (#1231)
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  * Bug fix: when plugin data was too big 500 error was returned (#1232)
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  * Bug fix: removing plugin in admin panel removes it from server permanently
    (#1211)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 11 May 2020 17:00:00 +0200

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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
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    allow compartment species alias to be shorter than 2 characters (#1204)
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  * 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

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minerva (14.0.10) stable; urgency=medium
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  * Bug fix: reaction without ports in SBGN crashed upload (#1065)
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  * Bug fix: annotations using newer identifiers.org uri schema were truncated
    by one character (#1191)
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  * Bug fix: long annotation string broke listing of annotations (#1155)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Mar 2020 14:00:00 +0200
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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)
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  * Bug fix: refresh data overlay did not hide data overlays that were removed
    and selected (#1097)
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  * Bug fix: transparent complexes are shown with wrong color (#1103)
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  * Bug fix: CellDesigner sometimes marked reduced notation reaction as
    reversible even though they were not visualized so (#1109)
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  * Bug fix: when data overlay was being removed user could request to remove
    overlay second time and an error was thrown (#1121)
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  * 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)
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  * Bug fix: uploading empty data overlay resulted in an error (#1123)
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  * Bug fix: exporting map with glyphs crashed (#1130)
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  * Bug fix: transcription factor on black&white gene are drawn in black
    (#1132)
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  * 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)
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  * 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
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  * Bug fix: when SBGN production pointed directly to process instead of
    process port upload crashed
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  * Bug fix: handle properly corrupted cached chembl drug data (#1140)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 25 Feb 2020 15:00:00 +0200
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minerva (14.0.8) stable; urgency=medium
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  * Bug fix: API didn't allow to upload plugins with local url (#1084,
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    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)
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  * Bug fix: don't allow to remove plugin twice (#1081)
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  * Bug fix: upload of SBML file with very short reaction length could produce
    a map that couldn't be exported to SBML anymore (#1078)
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  * Bug fix: import of structural state from SBGN-ML PD that cannot be
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    normalized to residue is changed into structural state without losing
    information (#1062)
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  * Bug fix: import of stimulation modifiers from SBGN-ML crashed converter
    (#1063)
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  * Bug fix: export to SBGN files created from newt source produced corrupted
    disconnected reactions
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  * Bug fix: upload from zip file allowed empty overlay name (#1065)
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  * Bug fix: genome browser slider didn't work properly in Safari on
    non-default Browser zoom level (#1048)
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  * Bug fix: project without background overlay but with some custom data
    overlays crashed with an error (#1066)
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  * Bug fix: when session expires updating options in configuration panel threw
    unhandled error (#1068)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 28 Jan 2020 11:00:00 +0200
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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

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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)
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  * Bug fix: search by identifier didn't consider identifiers added by
    annotators (#1047)
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  * Bug fix: if map has SHOW OVERVIEW, the legend/comment/clear were not
    displayed at all (regresion 14.0.5, #1045)
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  * Bug fix: when there is a problem with database during removing project,
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    project removal doesn't hang (#1058)
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  * Bug fix: coloring of the reaction wasn't applied to center of reaction
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    (regression 14.0.0, #1057)
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  * Bug fix: genetic variant overlay improperly processed elements identified
    by miriam identifiers, like uniprot (#1059)
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  * Bug fix: invalid information was provided for genetic variants overlay when
    map organism was defined (#1060)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 19 Dec 2019 13:00:00 +0200
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minerva (14.0.5) stable; urgency=medium
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  * Bug fix: copy-paste of genetic-variant data overlay into Add overlay
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    content dialog could crash upload (#1040)
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  * Bug fix: some annotators (like Cazy) were crashing on old installations
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    (#1029)
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  * Bug fix: uploading a map that breaks postgres constraints hung upload of
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    the project (#1028)
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  * Bug fix: uploading of the page with low internet connection speed could
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    produce empty screen for several seconds/minutes - now the loading icon is
    present (#1025)
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  * Bug fix: search for NADH drug resulted in drug with empty name (#1018)
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  * Bug fix: export to SBML didn't handle properly arrows (#1015)
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  * Bug fix: Font colour of text area was preserved in Empty view (#1014)
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  * Bug fix: exported sbml file always contain model identifier (#1013)
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  * Bug fix: typo allel reverted to allele in overlay data (regression 14.0.0,
    #1012)
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  * Bug fix: after loading/removing too many plugins it was impossible to load
    new plugins (#1011)
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  * Bug fix: CLEAR button disappears after legend, comment checkboxes when
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    plugin tab used to much space (#976)

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 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 03 Dec 2019 12:00:00 +0200
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minerva (14.0.4) stable; urgency=high
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  * Bug fix: some SBGN files uploaded to minerva could not be exported to SBML
    due to problems with identifiers used by SBGN (#1006)
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  * Bug fix: upload of data overlay with conflicting overlay types caused error
    (#998)
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  * Bug fix: upload of sbml file with protein modifications inside complex
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    crashed visualization (#966)
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  * Bug fix: list of overlays for admin and curator included also other people
    overlays (regression 14.0.3, #1008)
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  * Bug fix: refresh button did not refresh overlay list after overlay was
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    removed over API (#997)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 07 Nov 2019 11:00:00 +0200
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minerva (14.0.3) stable; urgency=medium
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  * Bug fix: default zoom level on main map works even when x or y are
    undefined (#993)
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  * Bug fix: sbml parser had sometimes problems with combining layout and multi
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    packages (#966)
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  * Bug fix: parsing of CellDesigner files that contained substanceUnits could
    crash the upload (#985)
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  * Bug fix: verification of version length added when uploading project
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    implemented (#978)
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  * Bug fix: CLEAR button disappeared when plugin tab used to much space (#976)
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  * Bug fix: removing data overlay refreshes list of overlays in info window
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    (#974)
  * Bug fix: general overlays are always on top of data overlays in info window
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    (#975)
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  * 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
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  * Bug fix: opening map with no available background crashed (#964)
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  * Bug fix: uploading SBGN file that does not pass xsd validation provides a
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    warning, but does not fail upload (#937)
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  * Bug fix: export of the map to SBML that was imported with older version
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    (below 14.0.0) didn't produce valid SBML (#970)
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  * Bug fix: fields in add project window are reinitialized after each open
    (#963)
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  * Bug fix: filename case in uploaded zip files is preserved (#964)
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  * Bug fix: +/- buttons were misaligned in genome browser (#942)
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  * Bug fix: color of links in the left panel was unintentionally changed 
    (#990)
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  * Bug fix: minerva logo in left panel is centred properly
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  * Bug fix: width of search button icon was too big
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 18 Oct 2019 15:00:00 +0200
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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

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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

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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)
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  * Small improvement: info window contains information about overlay No (#919)
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  * Small improvement: sorting by columns that doesn't make sense in admin
    panel is disabled (#895)
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  * Small improvement: version of minerva is visible in map browser panel
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  * Small improvement: small info about annotator details is available in
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    select annotators dialog (#923)
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  * Small improvement: CellDesigner layers are always visualized as pathways
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    (#813)
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  * Small improvement: notification email uses minerva name and id of affected
    project (#926)
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  * Small improvement: information about person who uploaded project is visible
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    in list of projects (#927)
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  * Small improvement: tab with list of glyphs is available when adding project
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    with glyphs (#925)
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  * Small improvement: BackgroundColor parameter should be assigned using ":"
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    character (#929)
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  * 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)
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  * Bug fix: work on FF Private Window mode could cause logout or raise an
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    error on when opening new tab with minerva (#892)
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  * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server
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    Error" (#889)
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  * Bug fix: edit project dialog verifies organism id  (#914)
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  * Bug fix: all colors in boolean reaction (from CellDesigner) are processed
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    properly (#907)
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  * Bug fix: proper line type for boolean reaction is used on the whole
    reaction (#908)
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  * Bug fix: creating project with too long name hung upload (#916)
  * Bug fix: too long user login threw an error (#915)
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  * Bug fix: when uploading generic data overlay the type was not updated in
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    case the type was not specified in the input file (#906)
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  * Bug fix: list of types when copying from annotators contains only types
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    that are selectable in the dialog (#911)
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  * Bug fix: too long name for data overlay in info window is trimmed (#919)
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  * Bug fix: too long name in general overlay list is wrapped (#857)
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  * Bug fix: after genome is removed list of genomes is refreshed (#922)
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  * Bug fix: REST API bioEntities:search method didn't limit results to the
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    submodel id (#860)
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  * Bug fix: Empty Overlay colours were not preserved during export to
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    CellDesigner (#714)
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  * Bug fix: problem with unloading plugin is properly handled (#884)
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  * Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of
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    loaded plugins (#885)
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  * 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
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    drawn
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  * Bug fix: color handling in CellDesigner did not work properly for modifiers
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    inside boolean gateway
  * Bug fix: CellDesigner file exported from minerva was not fully compliant
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    with SBML standard (#831)
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  * Bug fix: MiRNA targets are limited only to the organism associated with the
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    map (#66)
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  * Bug fix: Search drug by target element did not return values when this
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    element was annotated automatically (#216)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 09 Oct 2019 12:00:00 +0200
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minerva (13.2.0) stable; urgency=medium
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  * Small improvement: MolArt v1.4 is used which provide information from
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    PredictProtein (#913)
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  * 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)
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  * Bug fix: show element title option wasn't influencing title visibility
    (#910)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 29 Aug 2019 17:00:00 +0200
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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)

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 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 14 Aug 2019 17:00:00 +0200
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minerva (13.1.2) stable; urgency=medium
  * Bug fix: Information about problematic zip file is more specific (#865)
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  * Bug fix: Url didn't contain list of opened plugins and they weren't reload
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    automatically on refresh (#866)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Jul 2019 17:00:00 +0200
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minerva (13.1.1) stable; urgency=medium
  * Bug fix: adding gene mapping before the genome caused an error (#835)
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  * Bug fix: "Terms of Use" change to "Terms of Service" in all places (#843)
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  * Bug fix: upgrade to 13.1.0 crashed on machines where every element was
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    inside compartment (#856)
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  * Bug fix: searching for some drugs in chembl didn't provide any results even
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    though that data exists, for instance 'DORLIMOMAB ARITOX' (#842)
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  * Bug fix: user wasn't logged out in all tabs when the log out event appeard
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    in only one of them (#847)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue,  2 Jul 2019 19:00:00 +0200
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minerva (13.1.0) stable; urgency=medium
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  * Feature: annotators are more flexible - you can define set of input and
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    outputs used by annotator (#617)
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  * Feature: changes in admin panel doesn't require saving - they are saved
    automatically (#676)
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  * Feature: elements can have custom glyphs used for visualization (#487)
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  * Small improvement: model_name renamed to map_name in data overlay columns
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    (#827)
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  * Small improvement: name, type, reference_genome_type and
    reference_genome_version column in genetic variant data overlay are
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    deprecated (#827)
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  * Small improvement: all bio entities have z-index associated with them
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    (#487)
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  * Small improvement: validation of the organism and disease id on map upload
    added (#618)
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  * Small improvement: added current username next to logout button in admin
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    panel (#660)
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  * Small improvement: New comment dialog does not contain content of previous
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    comment dialog (#680)
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  * Small improvement: Left logo is configurable (#731)
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  * Small improvement: list of element types in choose annotator dialog is
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    sorted (#798)
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  * Small improvement: Plugin API provides list of overview images (#702)
  * Small improvement: Plugin API allows to show/hide overview images (#702)
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  * Small improvement: Plugin API allows to trigger search on the map (#702)
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  * Small improvement: Plugin API allows to clear search results on map (#702)
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  * Small improvement: edit/remove project button is disabled until project is
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    uploaded (#683)
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  * Small improvement: warning about capslock is visible on login page when
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    necessary (#658)
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  * Small improvement: names of columns in data overlay are unified: no
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    whitespace, "_" used as separator (#596)
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  * Small improvement: list of references in drug panel contains PUBMED prefix
    (#666)
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  * Small improvement: list of projects is auto refreshed every 5 seconds if at
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    least one of the project is uploading/removing (#610)
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  * Small improvement: passwords to email account and ldap are not sent over
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    API (#732)
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  * Small improvement: reactant/product/modifier specific colors are parsed
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    properly from CellDesigner file (#597)
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  * Small improvement: Info tab contains information about disease and
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    organism when info is provided
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  * Small improvement: Info tab provides information about model annotations
    and submap tabs provide information about submaps annotations if applicable
    (#591)
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  * Small improvement: uploading sbml file should automatically discover a file
    type (#784)
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  * Small improvement: when plugin listeners crash the system notifies user
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    about problem with a plugin (#767)
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  * Small improvement: when exporting reaction and elements there is
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    possibility to filter by (sub)map (#615)
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  * Small improvement: during first opening of a map, the zoom level is
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    automatically computed if no default information is provided (#776)
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  * Small improvement: when adding new project columns "Root map", "Mapping
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    file" and "Map type" are merged (#700)
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  * Small improvement: allow admin to disable CORS check (#802)
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  * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
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    SemanticZoomLevelTransparency (#801)
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  * Small improvement: export/import from SBML support z-index in LAYOUT
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    extension
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  * Bug fix: due to blocking of our requests from ctdbase the autocomplete for
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    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
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  * Bug fix: plugin tab header wasn't properly resized after adding plugins
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    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)
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  * Bug fix: gene_name column is allowed only in the genetic variant data
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    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)
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  * Bug fix: asynchronous calls on showing/hiding data overlays might cause
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    problems due to network latency (#830)
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  * Bug fix: progress bar of gene genome mapping upload is refreshing properly
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    (#728)
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  * Bug fix: when editing project Disease and Organism could not be removed
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    (#616)
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  * 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
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    slightly separated from target phenotype (#664)
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  * Bug fix: order of genomes in admin panel doesn't change after refreshing
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    list of genomes (#761)
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  * Bug fix: fixing situation when Molart started with variation overlay not
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    having the aa change information
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  * Bug fix: plugin contect element width is adjusted when link to tabs are
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    wrapped in more than one line (#758)
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  * Bug fix: export to CellDesigner preserve font size (#798)
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  * Bug fix: layout data was ignored for some reactions when importing from
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    SBML (#812)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 27 Jun 2019 14:00:00 +0200
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minerva (13.0.0) stable; urgency=medium
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  * 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
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    Ubuntu-14 (#223)

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

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minerva (12.2.3) stable; urgency=medium
  * Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
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  * Bug fix: searching of chemicals stopped working due to expired SSL
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    certificate on https://ctdbase.org/
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  * Bug fix: remove button is disabled after starting removing of the data
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    overlay (#791)
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  * Bug fix: search autocomplete hint could be initially hidden (#793)
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  * Bug fix: updating terms of use could crash when list of users was removed
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    in separate tab or by another user (#797)
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  * Bug fix: name of the checkbox in ADD PROJECT window adjusted (#799)
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  * Bug fix: when user didn't have privileges to remove comments the button was
    active on pages other than page 1 (#792)
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  * Bug fix: export of reaction to SBML didn't work when lines on the map were
    too short (#805)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 24 Apr 2019 17:00:00 +0200

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minerva (12.2.2) stable; urgency=medium
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  * Bug fix: downloading overlays didn't work from admin panel when project
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    with different id than default map was accessed
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  * Bug fix: change of owner of the data overlay in admin panel incorrectly
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    ordered overlays (#777)
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  * Bug fix: chemical search didn't use updated disease identifier, original
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    disease id from project upload was used instead (#779)
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  * Bug fix: user login with special characters (like '@')  could cause
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    problems in admin panel (#780)
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  * Bug fix: removing project without full control in the system (but with
    enough privileges to remove project) caused "Not enough privileges" error
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    (#778)
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  * Bug fix: export of custom properties (like synonyms) are properly encoded
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    in CellDesigner xml (#785)
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  * 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
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minerva (12.2.1) stable; urgency=medium
  * Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can
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    read colors properly) (#744)
  * Bug fix: removing active plugin didn't switch plugin tab to the next loaded
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    plugin (#757)
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  * Bug fix: closed submap will not be reopened after page refresh (#763)
  * Bug fix: comment remove button is disabled for users without proper
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    privileges (#766)
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  * Bug fix: invalid pubmed identifier could break clicking on element
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    containing it (#764, #765, #769)
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  * Bug fix: cache for API queries is explicitly disabled - some queries could
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    be mistakenly cached and the system behaviour might get unstable (#771)
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 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 1 Apr 2019 17:00:00 +0200

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minerva (12.2.0) stable; urgency=medium
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  * Feature: bug report utility
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  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
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  * Feature: user can create custom logging configuration in file
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    /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
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  * Feature: API tool providing possibility to transform different types of
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    file formats
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  * Feature: current state of the browsed map is reflected in the url (position,
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    zoom, overlays, search queries, etc.)
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  * 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)
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  * Small improvement: all popup dialogs in the application have dialog
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    specific css class names (#665)
  * Small improvement: JS plugin can create listener that is triggered on
    search results focus change
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  * Small improvement: export to SBML includes unit factors
  * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
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  * Small improvement: genetics information allows to provide information about
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    modification on peptide level that could be visualized in MolArt
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  * Small improvement: allow to control the background and font color of areas
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    drawn from text areas in CellDesigner "layers"
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  * Small improvement: config logo location is relative to the root minerva
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    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
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  * 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
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  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
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  * Small improvement: hitting enter on login page logs in the user (no need to
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    click on the login button)
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  * Small improvement: refresh button in overlays panel (useful when data
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    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
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  * Small improvement: 'BACK TO MAP' link is available only when guest account
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    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
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    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
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  * Bug fix: Icons were sometimes not properly loaded on Safari (#661)
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  * Bug fix: migration scripts are compatibile with postgres 9.3 version that
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    is default on Ubuntu 14 (#762)
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  * Bug fix: update/remove button is disabled when user has no privileges for
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    managing overlays (#742)
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  * Bug fix: when user cannot manage users information in overlays and users
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    tab in edit project dialog is provided instead of hiding tabs (#756)
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  * Bug fix: removing comments in a project asked for confirmation twice after
    edit project dialog for specific project was opened; closed and opened
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    again (#697)
  * Bug fix: editing/removing project requires Map Management privilege (#681)
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  * Bug fix: when removeAllListeners is called list of registered listeners is
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    cleaned (#687)
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  * Bug fix: when plugin is removed the html elements associated with it are
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    removed as well (#686)
  * Bug fix: when creating new user default privileges are set properly (#692)
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  * Bug fix: plugin can be added after plugin has been removed in admin plugin
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    panel (#686)
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  * Bug fix: too many annotations (>=100) caused misaligning in the left panel
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    (#708)
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  * 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
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    example in admin panel configuration tab (#719)
  * Bug fix: description of transcription site is centered (#720)
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  * Bug fix: selecting too few parameters in export doesn't throw reportable
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    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