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minerva
core
Commits
41725e7d
Commit
41725e7d
authored
Mar 30, 2020
by
Piotr Gawron
Browse files
import of complex with no border fixed
parent
221794ab
Pipeline
#23754
failed with stage
in 49 minutes and 59 seconds
Changes
4
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1
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CHANGELOG
View file @
41725e7d
minerva
(
14.0.11
)
stable
;
urgency
=
medium
*
Bug
fix
:
miRTarBase
was
down
and
targetting
by
miRNA
stopped
working
on
new
installations
(#
1207
)
*
Bug
fix
:
complex
with
no
border
was
inproperly
imported
from
CellDesigner
(#
1198
)
--
Piotr
Gawron
<
piotr
.
gawron
@
uni
.
lu
>
Mon
,
30
Mar
2020
10
:
00
:
00
+
0200
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
View file @
41725e7d
...
...
@@ -20,6 +20,7 @@ import lcsb.mapviewer.model.map.model.Model;
import
lcsb.mapviewer.model.map.model.ModelData
;
import
lcsb.mapviewer.model.map.species.Complex
;
import
lcsb.mapviewer.model.map.species.Species
;
import
lcsb.mapviewer.modelutils.map.ElementUtils
;
/**
* Parser of CellDesigner xml used for parsing complex aliases. Important: Only
...
...
@@ -132,9 +133,13 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
if
(
state
.
equalsIgnoreCase
(
"usual"
))
{
view
=
usualView
;
}
else
if
(
state
.
equalsIgnoreCase
(
"brief"
))
{
view
=
briefView
;
view
=
usualView
;
}
else
if
(
state
.
equalsIgnoreCase
(
"complexnoborder"
))
{
view
=
usualView
;
}
else
if
(
state
.
equalsIgnoreCase
(
"complexparentbrief"
))
{
view
=
briefView
;
}
else
{
throw
new
InvalidXmlSchemaException
(
new
ElementUtils
().
getElementTag
(
result
)+
"Don't know how to process state: "
+
state
);
}
if
(
view
!=
null
)
{
...
...
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
View file @
41725e7d
...
...
@@ -2,10 +2,9 @@ package lcsb.mapviewer.converter.model.celldesigner;
import
static
org
.
junit
.
Assert
.*;
import
java.awt.
*
;
import
java.awt.
Color
;
import
java.io.ByteArrayInputStream
;
import
java.util.*
;
import
java.util.List
;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
...
...
@@ -317,4 +316,12 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
testXmlSerialization
(
model
);
}
@Test
public
void
testComplexNoBorder
()
throws
Exception
{
CellDesignerXmlParser
parser
=
new
CellDesignerXmlParser
();
Model
model
=
parser
.
createModel
(
new
ConverterParams
().
filename
(
"testFiles/problematic/complex_no_border.xml"
));
assertTrue
(
model
.
getElementByElementId
(
"csa1"
).
getWidth
()
>
0
);
testXmlSerialization
(
model
);
}
}
converter-CellDesigner/testFiles/problematic/complex_no_border.xml
0 → 100644
View file @
41725e7d
<?xml version="1.0" encoding="UTF-8"?>
<sbml
xmlns=
"http://www.sbml.org/sbml/level2/version4"
xmlns:celldesigner=
"http://www.sbml.org/2001/ns/celldesigner"
level=
"2"
version=
"4"
>
<model
metaid=
"untitled"
id=
"untitled"
>
<annotation>
<celldesigner:extension>
<celldesigner:modelVersion>
4.0
</celldesigner:modelVersion>
<celldesigner:modelDisplay
sizeX=
"600"
sizeY=
"400"
/>
<celldesigner:listOfIncludedSpecies>
<celldesigner:species
id=
"s2"
name=
"s2"
>
<celldesigner:notes>
<html
xmlns=
"http://www.w3.org/1999/xhtml"
>
<head>
<title/>
</head>
<body/>
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>
s1
</celldesigner:complexSpecies>
<celldesigner:speciesIdentity>
<celldesigner:class>
PROTEIN
</celldesigner:class>
<celldesigner:proteinReference>
pr1
</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
</celldesigner:listOfIncludedSpecies>
<celldesigner:listOfCompartmentAliases/>
<celldesigner:listOfComplexSpeciesAliases>
<celldesigner:complexSpeciesAlias
id=
"csa1"
species=
"s1"
>
<celldesigner:activity>
inactive
</celldesigner:activity>
<celldesigner:bounds
x=
"171.0"
y=
"79.0"
w=
"100.0"
h=
"120.0"
/>
<celldesigner:font
size=
"12"
/>
<celldesigner:view
state=
"complexnoborder"
/>
<celldesigner:backupSize
w=
"0.0"
h=
"0.0"
/>
<celldesigner:backupView
state=
"none"
/>
<celldesigner:usualView>
<celldesigner:innerPosition
x=
"0.0"
y=
"0.0"
/>
<celldesigner:boxSize
width=
"100.0"
height=
"120.0"
/>
<celldesigner:singleLine
width=
"2.0"
/>
<celldesigner:paint
color=
"fff7f7f7"
scheme=
"Color"
/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition
x=
"0.0"
y=
"0.0"
/>
<celldesigner:boxSize
width=
"80.0"
height=
"60.0"
/>
<celldesigner:singleLine
width=
"2.0"
/>
<celldesigner:paint
color=
"fff7f7f7"
scheme=
"Color"
/>
</celldesigner:briefView>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
</celldesigner:complexSpeciesAlias>
</celldesigner:listOfComplexSpeciesAliases>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias
id=
"sa1"
species=
"s2"
complexSpeciesAlias=
"csa1"
>
<celldesigner:activity>
inactive
</celldesigner:activity>
<celldesigner:bounds
x=
"183.0"
y=
"91.0"
w=
"80.0"
h=
"40.0"
/>
<celldesigner:font
size=
"12"
/>
<celldesigner:view
state=
"usual"
/>
<celldesigner:usualView>
<celldesigner:innerPosition
x=
"12.0"
y=
"12.0"
/>
<celldesigner:boxSize
width=
"80.0"
height=
"40.0"
/>
<celldesigner:singleLine
width=
"1.0"
/>
<celldesigner:paint
color=
"ffccffcc"
scheme=
"Color"
/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition
x=
"0.0"
y=
"0.0"
/>
<celldesigner:boxSize
width=
"80.0"
height=
"60.0"
/>
<celldesigner:singleLine
width=
"0.0"
/>
<celldesigner:paint
color=
"3fff0000"
scheme=
"Color"
/>
</celldesigner:briefView>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
<celldesigner:listOfProteins>
<celldesigner:protein
id=
"pr1"
name=
"s2"
type=
"GENERIC"
/>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
<celldesigner:listOfLayers/>
<celldesigner:listOfBlockDiagrams/>
</celldesigner:extension>
</annotation>
<listOfUnitDefinitions>
<unitDefinition
metaid=
"substance"
id=
"substance"
name=
"substance"
>
<listOfUnits>
<unit
metaid=
"CDMT00001"
kind=
"mole"
/>
</listOfUnits>
</unitDefinition>
<unitDefinition
metaid=
"volume"
id=
"volume"
name=
"volume"
>
<listOfUnits>
<unit
metaid=
"CDMT00002"
kind=
"litre"
/>
</listOfUnits>
</unitDefinition>
<unitDefinition
metaid=
"area"
id=
"area"
name=
"area"
>
<listOfUnits>
<unit
metaid=
"CDMT00003"
kind=
"metre"
exponent=
"2"
/>
</listOfUnits>
</unitDefinition>
<unitDefinition
metaid=
"length"
id=
"length"
name=
"length"
>
<listOfUnits>
<unit
metaid=
"CDMT00004"
kind=
"metre"
/>
</listOfUnits>
</unitDefinition>
<unitDefinition
metaid=
"time"
id=
"time"
name=
"time"
>
<listOfUnits>
<unit
metaid=
"CDMT00005"
kind=
"second"
/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment
metaid=
"default"
id=
"default"
size=
"1"
units=
"volume"
/>
</listOfCompartments>
<listOfSpecies>
<species
metaid=
"s1"
id=
"s1"
name=
"s1"
compartment=
"default"
initialAmount=
"0"
>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>
inside
</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>
COMPLEX
</celldesigner:class>
<celldesigner:name>
s1
</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
</model>
</sbml>
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