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minerva
core
Commits
f4281908
Commit
f4281908
authored
Oct 16, 2019
by
Piotr Gawron
Browse files
comparison against null filxed
parent
e701559a
Pipeline
#15142
passed with stage
in 18 minutes and 36 seconds
Changes
4
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1
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CHANGELOG
View file @
f4281908
minerva
(
14.0.3
)
stable
;
urgency
=
medium
*
Bug
fix
:
sbml
parser
had
sometimes
problems
with
combining
layout
and
multi
packages
(#
966
)
*
Bug
fix
:
parsing
of
CellDesigner
files
that
contained
substanceUnits
could
crash
the
upload
(#
985
)
*
Bug
fix
:
verificatin
of
version
length
added
when
uploading
project
...
...
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
View file @
f4281908
...
...
@@ -13,6 +13,8 @@ import org.sbml.jsbml.ext.layout.*;
import
org.sbml.jsbml.ext.multi.*
;
import
org.sbml.jsbml.ext.render.LocalStyle
;
import
com.google.common.base.Objects
;
import
lcsb.mapviewer.common.Pair
;
import
lcsb.mapviewer.common.exception.InvalidStateException
;
import
lcsb.mapviewer.converter.InvalidInputDataExecption
;
...
...
@@ -317,7 +319,8 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
if
(((
GeneralGlyph
)
graphicalObject
).
getListOfReferenceGlyphs
().
size
()
>
0
)
{
// find a reference to the alias in layout, so we know it's the proper value
ReferenceGlyph
referenceGlyph
=
((
GeneralGlyph
)
graphicalObject
).
getListOfReferenceGlyphs
().
get
(
0
);
if
(
referenceGlyph
.
getGlyph
().
equals
(
mr
.
getSpecies
().
getElementId
()))
{
if
(
Objects
.
equal
(
referenceGlyph
.
getGlyph
(),
mr
.
getSpecies
().
getElementId
()))
{
// if (referenceGlyph.getGlyph().equals(mr.getSpecies().getElementId())) {
residueGlyph
=
(
GeneralGlyph
)
graphicalObject
;
}
}
else
{
...
...
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
View file @
f4281908
...
...
@@ -62,6 +62,13 @@ public class SbmlParserTest extends SbmlTestFunctions {
assertEquals
(
2
,
model
.
getMiriamData
().
size
());
}
@Test
public
void
testParseProblematicMultiLayout
()
throws
FileNotFoundException
,
InvalidInputDataExecption
{
Model
model
=
parser
.
createModel
(
new
ConverterParams
().
filename
(
"testFiles/small/problematic_inflamation_sbml_layout.xml"
));
assertNotNull
(
model
);
}
@Test
public
void
testParseKinetics
()
throws
FileNotFoundException
,
InvalidInputDataExecption
{
Model
model
=
parser
.
createModel
(
new
ConverterParams
().
filename
(
"testFiles/layoutExample/SBML.xml"
));
...
...
converter-sbml/testFiles/small/problematic_inflamation_sbml_layout.xml
0 → 100644
View file @
f4281908
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