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minerva
core
Commits
17a8bf77
Commit
17a8bf77
authored
Aug 29, 2019
by
Piotr Gawron
Browse files
Merge remote-tracking branch 'origin/devel_13.2.x' into merge-13.2.0
parents
e9f40baa
3e5f3475
Pipeline
#13392
failed with stage
in 9 minutes and 50 seconds
Changes
10
Pipelines
1
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CHANGELOG
View file @
17a8bf77
...
...
@@ -2,40 +2,40 @@ minerva (14.0.0~beta.0) unstable; urgency=low
*
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
* Small improvement: small info about annotator details is available in
select anntoators dialog (#923)
* Small improvement: CellDesigner layers are always visualized as pathways
* Small improvement: CellDesigner layers are always visualized as pathways
(#813)
* Small improvement: setting "Modify project| checkbox automatically select
"View project" checkbox when editing privileges (#920)
* Small improvement: notification email uses minerva name and id of affected
project (#926)
* Small improvement: information about person who uploaded project is visible
* Small improvement: information about person who uploaded project is visible
in list of projects (#927)
* Small improvement: user role introduced in edit user dialog (#924)
* Small improvement: tab with list of glyps is available when adding project
with glyphs (#925)
* Small improvement: BackgroundColor parameter should be assigned using ":"
* Small improvement: BackgroundColor parameter should be assigned using ":"
character (#929)
* 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
* Bug fix: fetching list of miRnas resulted sometimes in "Internal Server
Error" (#889)
* Bug fix: user without admin right can accept terms of service (#893)
* Bug fix: edit project dialog verifies organism id (#914)
* Bug fix: user without admin or curator privileges shouldn'
t
be
able
to
* Bug fix: user without admin or curator privileges shouldn'
t
be
able
to
check
logs
(#
894
)
*
Bug
fix
:
user
without
admin
or
curator
privileges
had
issues
with
accesing
and
removing
data
overlays
(#
897
,
#
898
,
#
899
,
#
903
)
*
Bug
fix
:
privilege
checking
on
updating
privileges
,
data
overlays
were
not
*
Bug
fix
:
privilege
checking
on
updating
privileges
,
data
overlays
were
not
sufficient
and
could
lead
to
access
escalation
*
Bug
fix
:
user
without
privileges
had
edit
map
input
options
enabled
*
Bug
fix
:
user
without
privileges
had
edit
map
input
options
for
managing
*
Bug
fix
:
user
without
privileges
had
edit
map
input
options
for
managing
project
users
*
Bug
fix
:
curator
couldn
't update data overlay in some situations (#905)
* Bug fix: alignment of tabs fixed for dialogs: "Add Project", "Edit Genome",
* Bug fix: alignment of tabs fixed for dialogs: "Add Project", "Edit Genome",
"Edit Project", "Edit User" (#881)
* Bug fix: all colors in boolean reaction (from CellDesigner) are processed
* 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)
...
...
@@ -48,7 +48,7 @@ minerva (14.0.0~beta.0) unstable; urgency=low
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: remove of data overlay didn'
t
update
numbering
of
data
overlays
* Bug fix: remove of data overlay didn'
t
update
numbering
of
data
overlays
that
are
still
in
the
system
(#
918
)
*
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
)
...
...
@@ -122,10 +122,17 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
--
Piotr
Gawron
<
piotr
.
gawron
@
uni
.
lu
>
Fri
,
09
Aug
2019
10
:
00
:
00
+
0200
minerva
(
13.1.4
)
stable
;
urgency
=
medium
*
Bug
fix
:
search
by
drugs
didn
't check synonyms in chembl database
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>
Wed,
2
1
Aug 2019 17:00:00 +0200
--
Piotr
Gawron
<
piotr
.
gawron
@
uni
.
lu
>
Thu
,
2
9
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
...
...
@@ -135,7 +142,7 @@ minerva (13.1.3) stable; urgency=medium
* 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
--
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
)
...
...
frontend-js/package.json
View file @
17a8bf77
...
...
@@ -31,7 +31,7 @@
"mkdirp"
:
"^0.5.1"
,
"mocha"
:
"^3.5.3"
,
"mock-local-storage"
:
"^1.1.8"
,
"molart"
:
"1.
3.2
"
,
"molart"
:
"1.
4.0
"
,
"stream-to-blob"
:
"^1.0.1"
,
"uglifyjs"
:
"^2.4.10"
},
...
...
frontend-js/src/main/js/gui/AddOverlayDialog.js
View file @
17a8bf77
...
...
@@ -164,6 +164,9 @@ AddOverlayDialog.prototype.processFile = function (file) {
}
if
(
overlay
.
getType
()
!==
undefined
)
{
if
(
$
(
"
option[value='
"
+
overlay
.
getType
()
+
"
']
"
,
typeSelect
).
length
===
0
)
{
GuiConnector
.
warn
(
"
Invalid type:
"
+
overlay
.
getType
());
}
self
.
setType
(
overlay
.
getType
());
}
else
{
self
.
setType
(
"
GENERIC
"
);
...
...
frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
View file @
17a8bf77
...
...
@@ -376,7 +376,7 @@ MapsAdminPanel.prototype.addUpdateListener = function (project) {
self
.
projectToTableRow
(
project
,
data
,
user
);
var
page
=
dataTable
.
page
();
row
.
data
(
data
).
draw
();
dataTable
.
page
(
page
);
dataTable
.
page
(
page
)
.
draw
(
false
)
;
}
}
});
...
...
frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
View file @
17a8bf77
...
...
@@ -311,7 +311,7 @@ UsersAdminPanel.prototype.addUpdateListener = function (user, dataTableRow) {
if
(
row
.
length
>
0
)
{
var
page
=
dataTable
.
page
();
row
.
data
(
dataTableRow
).
draw
();
dataTable
.
page
(
page
);
dataTable
.
page
(
page
)
.
draw
(
false
)
;
}
};
listener
.
listenerName
=
listenerName
;
...
...
frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
View file @
17a8bf77
...
...
@@ -823,9 +823,17 @@ GuiUtils.prototype.createAliasElement = function (params) {
}));
}
div
.
appendChild
(
this
.
createParamLine
({
label
:
alias
.
getType
()
+
"
:
"
,
value
:
alias
.
getName
()}));
div
.
appendChild
(
this
.
createParamLine
({
label
:
alias
.
getType
()
+
"
:
"
,
className
:
self
.
_configurationOptionToClassName
(
ConfigurationType
.
SHOW_ELEMENT_TITLE
),
value
:
alias
.
getName
()
}));
if
(
alias
.
getModelId
()
!==
self
.
getMap
().
getId
())
{
div
.
appendChild
(
self
.
createSubMapLink
({
label
:
"
In submap:
"
,
mapId
:
alias
.
getModelId
()}));
div
.
appendChild
(
self
.
createSubMapLink
({
label
:
"
In submap:
"
,
className
:
self
.
_configurationOptionToClassName
(
ConfigurationType
.
SHOW_ELEMENT_TITLE
),
mapId
:
alias
.
getModelId
()
}));
}
}
div
.
appendChild
(
self
.
createSubMapLink
({
...
...
service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
View file @
17a8bf77
...
...
@@ -85,7 +85,14 @@ public class ColorSchemaReader {
return
readGenericColorSchema
(
colorInputStream
);
}
}
else
{
ColorSchemaType
type
=
ColorSchemaType
.
valueOf
(
params
.
get
(
ZipEntryFileFactory
.
LAYOUT_HEADER_PARAM_TYPE
));
ColorSchemaType
type
=
null
;
try
{
type
=
ColorSchemaType
.
valueOf
(
params
.
get
(
ZipEntryFileFactory
.
LAYOUT_HEADER_PARAM_TYPE
));
}
catch
(
IllegalArgumentException
e
)
{
String
options
=
StringUtils
.
join
(
ColorSchemaType
.
values
(),
", "
);
throw
new
InvalidColorSchemaException
(
"Invalid overlay type: "
+
params
.
get
(
ZipEntryFileFactory
.
LAYOUT_HEADER_PARAM_TYPE
)
+
". Allowed options: "
+
options
);
}
if
(
type
==
null
)
{
logger
.
warn
(
"Unknown type of layout file: "
+
params
.
get
(
ZipEntryFileFactory
.
LAYOUT_HEADER_PARAM_TYPE
));
return
readGenericColorSchema
(
colorInputStream
);
...
...
service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java
View file @
17a8bf77
...
...
@@ -53,6 +53,17 @@ public class DrugServiceTest extends ServiceTestFunctions {
}
}
@Test
public
void
testGetIstodax
()
throws
Exception
{
try
{
Drug
drug
=
drugService
.
getByName
(
"istodax"
,
new
DbSearchCriteria
());
assertEquals
(
2
,
drug
.
getSources
().
size
());
}
catch
(
Exception
e
)
{
e
.
printStackTrace
();
throw
e
;
}
}
@Test
public
void
testGetTargets
()
throws
Exception
{
long
count
=
searchHistoryDao
.
getCount
();
...
...
service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
View file @
17a8bf77
...
...
@@ -367,4 +367,13 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
overlay
.
setInputData
(
file
);
assertEquals
(
0
,
reader
.
getDeprecatedColumns
(
overlay
).
size
());
}
@Test
(
expected
=
InvalidColorSchemaException
.
class
)
public
void
testReadColorSchemaWithInvalidType
()
throws
Exception
{
FileInputStream
fis
=
new
FileInputStream
(
"testFiles/coloring/invalidType.txt"
);
FileInputStream
fis2
=
new
FileInputStream
(
"testFiles/coloring/invalidType.txt"
);
ColorSchemaReader
reader
=
new
ColorSchemaReader
();
reader
.
readColorSchema
(
fis
,
TextFileUtils
.
getHeaderParametersFromFile
(
fis2
));
}
}
service/testFiles/coloring/invalidType.txt
0 → 100644
View file @
17a8bf77
#TYPE=gen
value identifier Chebi
-0,943978048 HGNC:11138
-0,941309505 CHEBI:15377
1 CHEBI:15376
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