Commit 8faf57c2 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

chagelog updated for 15.0.0 release

parent 61cc24c2
Pipeline #28983 passed with stage
in 15 minutes and 17 seconds
minerva (15.0.0~beta.5) unstable; urgency=medium
* Backward incompatible: truncation/association/dissocation points are
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)
* Bug fix: export to GPML uses proper arrow types (#1262)
* Bug fix: export to GPML uses dashed lines in reactions when possible
(#1262)
* Bug fix: pathways are visualized in image converter (#1266)
* Bug fix: there is a bug in PathVisio that breaks short segments being the
end of catalist therefore short segments are removed from export (#1263)
* Bug fix: conversion of file containing BOM did not work (#1264)
* Bug fix: dashed elements imported from GPML are treated as hypothetical
(#1268)
* Bug fix: hypothetical elements exported to GPML are drawn with dashed line
(#1268)
* Bug fix: proper color is parsed from CellDesigner species marked as 'brief'
(#1268)
* Bug fix: unknown elements are exported to 'Unknown' data nodes in GPML
(#1273)
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 2 Jun 2020 16:00:00 +0200
minerva (15.0.0~beta.4) unstable; urgency=medium
* Backward incompatible: and/split points are represented as a dot in all new
images/uploaded maps (#1253)
* Backward incompatible: reation will be on top of elements in maps uploaded
* 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: export unknown species to GPML caused pathvisio to crash (#1215)
* Bug fix: annotations in CD 2.5 caused import to crash (#1125)
* Bug fix: complex reaction with two required reactants in CD 2.5 caused
import to crash (#1125)
* Bug fix: kinetic equation in reaction that referenced complex (instead of
target species) crashed CellDesigner upload (#1212)
* Bug fix: transcription-translation should be turned into StateTransition
reaction when importing GPML (#1236)
* Bug fix: species graphical shape is taken as secondary indication to
species type when importing GPML (#1237)
* Bug fix: name is assigned to complexes when second complex is defined in it
in GPML (#1238)
* Bug fix: kinetic equation in SBML that used speciesReference id crashed
upload (#1190)
* Bug fix: layout reaction with duplicated reaction element crashed SBML
upload (#1190)
* Bug fix: conversion from SBML to CellDesigner escaped "<" twice (#1228)
* Bug fix: graphical elements imported from GPML have border color and
background color defined properly (#1259)
* Bug fix: export/import to GPML properly handles degradation (#1241)
* Bug fix: Select annotation dialog width is at least 840px (#1210)
* Bug fix: modifiers joined by operator were exported to SBML without line
corresponding to the operator (#1199)
* Bug fix: first state variable that does not match modification residue is
translated to structural state when importing from SBGNML (#1088)
* Bug fix: list of database releases is always updated on DAPI credentials
change (#1128)
* Bug fix: proper error is returned when trying to sign up to DAPI with
exisitng account (#1158)
* Bug fix: session mixed chemical and drug queries when refreshing webpage
(#1161)
* Bug fix: caching data for map with entrez ID crashed
* Bug fix: not all data were cached about drugs/chemicals/mirnas when "cache
data" was checked on project upload
* Bug fix: when invalid password is provided proper warning is raised (#1159)
* Bug fix: when no release is accepted in admin panel user is notified that
not all databases will be used in search queries (#1159)
* Bug fix: when exporting to GPML line ends are aligned to new shapes (#1242)
* Bug fix: when exporting to GPML proper shapes are used for species
* Bug fix: export of modifications to GPML generated invalid GPML file
(#1257)
* Bug fix: caching file with protin name containing new line character
crashed
* Bug fix: when caching the data on project upload list hint list for mirna,
drugs, chemicals were not cached (#1163)
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 2 Jun 2020 16:00:00 +0200
minerva (15.0.0~beta.3) unstable; urgency=medium
* Improvement: API allows to merge files (#1208)
* Bug fix: exported SBML was not compliant with the standard when element
name was empty (#1147)
* Bug fix: flybase and pato annotations from CellDesigner were not picked
(#1113)
* Bug fix: invalid data overlays in uploaded zip file created "valid" project
that could not be opened (#1086)
* Bug fix: export to GPML preserves font color of compartments (#1111)
* Bug fix: export to GPML preserves information about hypotetical complexes
(#1111)
* Bug fix: export to GPML preserves complex name (#1111)
* Bug fix: export to GPML preserves reaction color (#1111)
* Bug fix: modification residues are exported to gpml (#1111)
* Bug fix: information about reaction reversibility is exported to gpml
(#1111)
* Bug fix: cardinality in SBGN-like view is drawn in separate unit (#1157)
* Bug fix: notes from SBML are parsed with all html tags (#1196)
* Bug fix: converter API append conversion warnings to generated output notes
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 3 Apr 2020 15:00:00 +0200
minerva (15.0.0~beta.2) unstable; urgency=medium
* Small Improvement: SBO annotation support added (#1194)
* Small Improvement: additional annotation uri qualifiers added: hasProperty,
isPropertyOf (#1193)
* Small Improvement: default color of complexes imported from gpml changed to
the one used by wikipathways (#1107)
* Bug fix: newt use incorrect attributes when exporting render information
that could not be parsed by minevra (#1127)
that could not be parsed by minerva (#1127)
* Bug fix: catalysis to protein was not parsed from SBGN file (#1116)
* Bug fix: upload logs for SBGN parser were not translated properly to new
structured log form
* Bug fix: antisenseRNA shape is infered from SBGN when antisenseRNA text is
* 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: exporting map to CellDesigner from GPML file created not-editable
compartments (#1146)
* Bug fix: some CellDesigner 2.5 files could not be parsed (#1125)
* Bug fix: more than one authors in CellDesigner file were not parsed
properly (#1156)
* Bug fix: pathways imported from gpml persist fill color (#1107)
* Bug fix: some reversible reactions in gpml were not imported as reversible
(#1107)
* Bug fix: colors of reactants/products/modifiers were not imported from gpml
(#1107)
* Bug fix: border color of species imported from gpml is preserved (#1107)
* Bug fix: coordinates of complex name from GPML file is preserved (#1107)
* Bug fix: element name for general shapes imported from GPML does not
contain ShapeType if feasible (#1107)
* Bug fix: z-index of rectangles and some complexes imported from GPML was
not assigned properly (#1107)
* Bug fix: new line in label text does not split he text into name and
desciption (#1107)
* Bug fix: label omim href with "www" prefix are parsed properly
* Bug fix: modification position imported from GPML file is preserved (#1107)
* Bug fix: SBGN reaction with no reactants crashed map upload (#1148)
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 31 Mar 2020 14:00:00 +0200
minerva (15.0.0~beta.1) unstable; urgency=medium
* Bug fix: conflict on libraries caused some features to stop working in
production (like parsing text notes of species, regresion in
15.0.0~alpha.1, #1139)
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 26 Feb 2020 13:00:00 +0200
minerva (15.0.0~beta.0) unstable; urgency=medium
* Feature removal: old connection to CTD is removed and replaced with
new Data-API interface that closely check license compliance
* Feature removal: some custom fields (like transparency zoom level) are not
exported to CellDesigner file (#1071)
* Improvement: export to SBGN/SBML/GPML format provides popup with list of
warnings occurred in the translation process (#713)
* Small improvement: autocomplete for chemical searches is enabled (#841)
* Small improvement: import/export to SBML of unit of information obtained
from SBGN source is supported (#1088)
* Small improvement: rounded rectangle is used to visualize Simple chemicals
in SBGN-like view according to the newest SBGN specification (#1094)
* Small improvement: after removing project is confirmed the system enforce
waiting until remove status is confirmed (#1106)
* Bug fix: import from SBGN assigned invalid name to species that didn't have
label defined (#1093)
* Bug fix: drawing protein in SBGN-like style didn't handle properly
dimension of the species for multimers bigger than 2 (#1091)
* Bug fix: drawing of structural state in SBGN-like style uses
RoundedRectangle instead of Ellipse which was not SBGN-compliant (#1095)
* Bug fix: export to GPML provided invalid font size and pathviosio could not
open it (#1108)
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 28 Jan 2020 13:00:00 +0200
minerva (15.0.0~alpha.2) unstable; urgency=medium
* Feature removal: old connection to DrugBank is removed and replaced with
new Data-API interface that closely check license compliance
* Small improvement: when typing drug, list of autocomplete drugs should be
available limited to the drugs targetting something on the map (#641)
* Small improvement: data not compliant with database constraints (for
instance too long species identifiers) will be automatically adjust instead
of crashing project upload (#1041)
* Small improvement: reaction lines in SBML files without layout are set
outside of the species (not in the center, #1023)
* Bug fix: import from CellDesigner rounded alias dimension to integer
* Bug fix: old project with structural state couldn't be removed (regression
15.0.0~alpha.1, #1021)
* Bug fix: processing sbgn file with render information was breaking sometimes
(regression 15.0.0~alpha.1, #1020)
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 22 Jan 2020 13:00:00 +0200
minerva (15.0.0~alpha.1) unstable; urgency=medium
* Feature removal: when uploading complex map with submap there is no
possibility to change submap name (#947)
* Improvement: support for rendering colors in SBGNML added (#1009)
* Small improvement: sort order of tables in admin panel is preserved among
sessions (#836)
* Small improvement: simple molecules in sbgn compliant view are drawn as
ellipses not circles (#796)
* Small improvement: uploaded map is automatically cached (#983)
* Small improvement: molart updated to version 1.5.0: Ability to show
unobserved structure regions in the sequence view.
* Small improvement: list of genomes is automatically refreshed during genome
upload (#820)
* Small improvement: items in context menu are reorganized (#787)
* Small improvement: CellDesigner files from version 2.5 should be parseable
* Small improvement: plugins in admin panel can be revalidated to update info
about the plugins (name, version)
* Small improvement: there is possibility to define default plugins loaded
with every opening of a map (#967)
* Small improvement: support for annotations added: ChemIDplus, EcoGene,
FlyBase, GeneDB, Intact, Kegg Drug, KNApSAcK, LIPID MAPS, NCBI Protein,
PATO, RGD, SPIKE, TTD Drug, ZFIN BioEntity
* Bug fix: compartments limited by corner (left-top corner compartment, etc)
are parsed properly from CellDesigner files
* Bug fix: structural states of proteins are imported properly from SBGNML PD
(#995)
* Bug fix: clear button icon, refresh comments button and show overview
button icons were missing (regression 15.0.0~alpha.0)
* Bug fix: export to CellDesigner names with new line is properly handled
(#930)
* Bug fix: layout of the exported reactome pathways is fixed when reactome
......@@ -228,31 +128,11 @@ minerva (15.0.0~alpha.1) unstable; urgency=medium
visualized with proper line type across all included modifiers (#957)
* Bug fix: dimension of the modifications is the same as in minerva when
exporting to SBGNML-PD (#554)
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 15 Nov 2019 9:00:00 +0200
minerva (15.0.0~alpha.0) unstable; urgency=medium
* Improvement: logs provided for validation data model are structurized (#325)
* Improvement: import/export of GPML implemented
* Small improvement: compartments in not layouted SBML file are more
scattered (#326)
* Small improvement: when downloading a map results in too big file (>1MB)
the content is compressed and returned as a zip file (#348)
* Small improvement: confirmation dialog when removing "general view"
overlays contain proper warning (#809)
* Small improvement: CellDesigner text area object can have "BorderColor"
property defined (#806)
* Small improvement: list of submaps is sorted alphabetically (#962)
* Small improvement: notification about new releases of minerva added in
admin panel (#961)
* Small improvement: font awesome upgraded to 5.1 (new icon styles)
* Small improvement: header contains login/logout button and access admin
panel button (#982)
* Bug fix: position of structural state is preserved on upload CellDesigner
file (#671)
* Bug fix: problematic notes doesn't crash CellDesigner upload (#968)
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 4 Nov 2019 11:00:00 +0200
-- 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
......
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