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minerva
core
Commits
b2d45f06
Commit
b2d45f06
authored
Jun 27, 2019
by
Piotr Gawron
Browse files
Merge remote-tracking branch 'origin/devel_13.1.x' into merge-13.1.0
parents
ea956483
b2b9808d
Pipeline
#11171
passed with stage
in 9 minutes and 34 seconds
Changes
3
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1
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CHANGELOG
View file @
b2d45f06
...
...
@@ -5,12 +5,12 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
*
Feature
:
Replaced
connection
pool
manager
C3P0
with
better
maintained
Hikari
(#
564
)
*
Feature
removal
:
BioCompendium
annotator
removed
(#
32
)
*
Small
improvement
:
caching
is
active
by
default
for
new
users
when
*
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
*
Small
improvement
:
when
removing
overlay
in
admin
panel
there
is
a
confirmation
dialog
(#
696
)
*
Small
improvement
:
overlay
name
is
obligatory
(#
698
)
*
Small
improvement
:
target
gene
in
search
panel
contains
also
information
*
Small
improvement
:
target
gene
in
search
panel
contains
also
information
about
type
of
database
that
identifies
the
target
(#
66
)
*
Bug
fix
:
export
to
CellDesigner
of
reaction
with
two
modifiers
connected
with
boolean
operator
resulted
was
skipping
some
layout
information
...
...
@@ -20,57 +20,24 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
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
*
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
*
Bug
fix
:
Search
drug
by
target
element
did
not
return
values
when
this
element
was
annotated
automatically
(#
216
)
--
Sascha
Herzinger
<
sascha
.
herzinger
@
uni
.
lu
>
Wed
,
22
May
2019
10
:
30
:
00
+
0200
minerva
(
13.1.0
~
beta
.1
)
unstable
;
urgency
=
low
*
Small
improvement
:
model_name
renamed
to
map_name
in
data
overlay
columns
(#
827
)
*
Small
improvement
:
name
,
type
,
reference_genome_type
and
reference_genome_version
column
in
genetic
variant
data
overlay
are
deprecated
(#
827
)
*
Bug
fix
:
deprecated
columns
in
data
overlay
are
not
visible
to
the
end
user
(#
827
)
*
Bug
fix
:
invalid
color
in
data
overlay
provides
proper
feedback
to
the
user
(#
822
)
*
Bug
fix
:
genetic
variant
overlay
without
name
caused
problems
(#
832
)
*
Bug
fix
:
tair
locus
identifiers
were
used
improperly
-
instead
of
id
the
name
was
used
*
Bug
fix
:
plugin
tab
header
wasn
't properly resized after adding plugins
that introduced second line for tab selection (#758)
* Bug fix: invisible layer shouldn'
t
be
shown
in
the
on
th
map
(#
813
)
*
Bug
fix
:
list
of
availbale
annotators
is
sorted
alphabetically
(#
815
)
*
Bug
fix
:
redirect
url
from
export
panel
is
fixed
(#
819
)
*
Bug
fix
:
allow
to
reupload
the
same
file
without
closing
add
overlay
dialog
(#
833
)
*
Bug
fix
:
gene_name
column
is
allowed
only
in
the
genetic
variant
data
overlay
*
Bug
fix
:
protein
types
are
sorted
properly
in
"Select valid annotations"
dialog
(#
815
)
*
Bug
fix
:
if
there
is
a
description
of
(
sub
)
map
then
it
is
available
in
info
/
submap
panel
(#
824
)
*
Bug
fix
:
when
changing
data
in
edit
user
dialog
there
was
a
need
to
click
close
button
twice
(#
818
)
*
Bug
fix
:
empty
type
for
data
overlay
is
allowed
(#
827
)
*
Bug
fix
:
genetic
variants
data
overlay
was
ignoring
color
parameter
(#
827
)
*
Bug
fix
:
pathways
can
be
drawn
using
glyphs
(#
825
)
*
Bug
fix
:
empty
background
overlay
doesn
't show glyphs, instead standard
visualization is used (#826)
* Bug fix: asynchronous cals on showing/hiding data overlays might cause
problems due to network latency (#830)
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 7 Jun 2019 17:00:00 +0200
minerva (13.1.0~beta.0) unstable; urgency=low
minerva
(
13.1.0
)
stable
;
urgency
=
medium
*
Feature
:
annotators
are
more
flexible
-
you
can
define
set
of
input
and
outputs
used
by
annotator
(#
617
)
*
Feature
:
changes
in
admin
panel
doesn
't require saving - they are saved
automatically (#676)
* Feature: elements can have custom glyphs used for visualization (#487)
* Small improvement: model_name renamed to map_name in data overlay columns
(#827)
* Small improvement: name, type, reference_genome_type and
reference_genome_version column in genetic variant data overlay are
deprecated (#827)
* Small improvement: all bio entities have z-index associated with them
(#487)
* Small improvement: validation of the organism and disease id on map upload
...
...
@@ -120,6 +87,32 @@ minerva (13.1.0~beta.0) unstable; urgency=low
SemanticZoomLevelTransparency (#801)
* Small improvement: export/import from SBML support z-index in LAYOUT
extension
* Bug fix: due to blocking of our requests from ctdbase the autocomplete for
this database is disabled
* Bug fix: deprecated columns in data overlay are not visible to the end user
(#827)
* Bug fix: invalid color in data overlay provides proper feedback to the user
(#822)
* Bug fix: genetic variant overlay without name caused problems (#832)
* Bug fix: tair locus identifiers were used improperly - instead of id the
name was used
* Bug fix: plugin tab header wasn'
t
properly
resized
after
adding
plugins
that
introduced
second
line
for
tab
selection
(#
758
)
*
Bug
fix
:
invisible
layer
shouldn
't be shown on the map (#813)
* Bug fix: list of availbale annotators is sorted alphabetically (#815)
* Bug fix: redirect url from export panel is fixed (#819)
* Bug fix: allow to reupload the same file without closing add overlay dialog
(#833)
* Bug fix: gene_name column is allowed only in the genetic variant data
overlay
* Bug fix: protein types are sorted properly in "Select valid annotations"
dialog (#815)
* Bug fix: if there is a description of (sub)map then it is available in
info/submap panel (#824)
* Bug fix: empty type for data overlay is allowed (#827)
* Bug fix: genetic variants data overlay was ignoring color parameter (#827)
* Bug fix: asynchronous calls on showing/hiding data overlays might cause
problems due to network latency (#830)
* Bug fix: progress bar of gene genome mapping upload is refreshing properly
(#728)
* Bug fix: when editing project Disease and Organism could not be removed
...
...
@@ -138,7 +131,7 @@ minerva (13.1.0~beta.0) unstable; urgency=low
* Bug fix: layout data was ignored for some reactions when importing from
SBML (#812)
--
Piotr
Gawron
<
piotr
.
gawron
@
uni
.
lu
>
Mon
,
13
May
2019
1
9
:
00
:
00
+
0200
-- Piotr Gawron <piotr.gawron@uni.lu>
Thu, 27 Jun
2019 1
4
:00:00 +0200
minerva (13.0.0) stable; urgency=medium
* Bug fix: Since Oracle Java cannot be installed as debian dependency we use
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
View file @
b2d45f06
...
...
@@ -687,7 +687,8 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
String
cachedData
=
getCacheValue
(
cacheQuery
);
List
<
String
>
result
;
if
(
cachedData
==
null
)
{
result
=
getSuggestedQueryListWithoutCache
(
project
,
diseaseMiriam
);
// result = getSuggestedQueryListWithoutCache(project, diseaseMiriam);
result
=
new
ArrayList
<>();
cachedData
=
StringUtils
.
join
(
result
,
"\n"
);
setCacheValue
(
cacheQuery
,
cachedData
);
}
else
{
...
...
service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
View file @
b2d45f06
...
...
@@ -863,13 +863,15 @@ public class ProjectService implements IProjectService {
updateProjectStatus
(
originalModel
.
getProject
(),
ProjectStatus
.
CACHING_MIRIAM
,
progress
,
params
);
}
});
chemicalService
.
cacheDataForModel
(
originalModel
,
new
IProgressUpdater
()
{
@Override
public
void
setProgress
(
double
progress
)
{
updateProjectStatus
(
originalModel
.
getProject
(),
ProjectStatus
.
CACHING_CHEMICAL
,
progress
,
params
);
}
});
logger
.
warn
(
"Cache of chemicals data is disabled"
);
// chemicalService.cacheDataForModel(originalModel, new IProgressUpdater() {
// @Override
// public void setProgress(double progress) {
// updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_CHEMICAL, progress, params);
// }
// });
drugService
.
cacheDataForModel
(
originalModel
,
new
IProgressUpdater
()
{
@Override
...
...
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