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minerva
core
Commits
0bc2881e
Commit
0bc2881e
authored
May 08, 2019
by
Piotr Gawron
Browse files
unit tests fixed
parent
beb2f312
Pipeline
#10160
failed with stage
in 10 minutes and 55 seconds
Changes
7
Pipelines
1
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Side-by-side
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
View file @
0bc2881e
...
...
@@ -44,6 +44,7 @@ import lcsb.mapviewer.common.EventStorageLoggerAppender;
import
lcsb.mapviewer.common.exception.InvalidXmlSchemaException
;
import
lcsb.mapviewer.converter.ConverterParams
;
import
lcsb.mapviewer.converter.InvalidInputDataExecption
;
import
lcsb.mapviewer.model.map.BioEntity
;
import
lcsb.mapviewer.model.map.InconsistentModelException
;
import
lcsb.mapviewer.model.map.model.Model
;
import
lcsb.mapviewer.model.map.model.ModelComparator
;
...
...
@@ -234,14 +235,30 @@ public abstract class CellDesignerTestFunctions {
protected
void
testXmlSerialization
(
Model
model
)
throws
InconsistentModelException
,
UnsupportedEncodingException
,
InvalidInputDataExecption
{
CellDesignerXmlParser
parser
=
new
CellDesignerXmlParser
();
String
xml
=
parser
.
model2String
(
model
);
InputStream
is
=
new
ByteArrayInputStream
(
xml
.
getBytes
(
"UTF-8"
));
Model
model2
=
parser
.
createModel
(
new
ConverterParams
().
inputStream
(
is
).
sizeAutoAdjust
(
false
));
for
(
BioEntity
bioEntity
:
model
.
getBioEntities
())
{
bioEntity
.
setZ
(
null
);
}
Model
model2
=
serializeModel
(
model
);
model
.
setName
(
null
);
ModelComparator
comparator
=
new
ModelComparator
();
assertEquals
(
0
,
comparator
.
compare
(
model
,
model2
));
}
protected
Model
serializeModel
(
Model
model
)
throws
InconsistentModelException
,
UnsupportedEncodingException
,
InvalidInputDataExecption
{
CellDesignerXmlParser
parser
=
new
CellDesignerXmlParser
();
String
xmlString
=
parser
.
model2String
(
model
);
InputStream
is
=
new
ByteArrayInputStream
(
xmlString
.
getBytes
(
"UTF-8"
));
Model
model2
=
parser
.
createModel
(
new
ConverterParams
().
inputStream
(
is
).
sizeAutoAdjust
(
false
));
for
(
BioEntity
bioEntity
:
model2
.
getBioEntities
())
{
bioEntity
.
setZ
(
null
);
}
return
model2
;
}
}
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
View file @
0bc2881e
...
...
@@ -470,11 +470,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
alias2
.
setName
(
"PDK2"
);
model
.
addElement
(
alias2
);
CellDesignerXmlParser
parser
=
new
CellDesignerXmlParser
();
String
xmlString
=
parser
.
model2String
(
model
);
InputStream
is
=
new
ByteArrayInputStream
(
xmlString
.
getBytes
());
Model
model2
=
parser
.
createModel
(
new
ConverterParams
().
inputStream
(
is
).
sizeAutoAdjust
(
false
));
Model
model2
=
serializeModel
(
model
);
assertEquals
(
0
,
modelComparator
.
compare
(
model
,
model2
));
...
...
@@ -1078,11 +1074,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
protein
.
addSynonym
(
"&"
);
model
.
addElement
(
protein
);
CellDesignerXmlParser
parser
=
new
CellDesignerXmlParser
();
String
xmlString
=
parser
.
model2String
(
model
);
InputStream
is
=
new
ByteArrayInputStream
(
xmlString
.
getBytes
(
"UTF-8"
));
Model
model2
=
parser
.
createModel
(
new
ConverterParams
().
inputStream
(
is
));
Model
model2
=
serializeModel
(
model
);
assertEquals
(
0
,
modelComparator
.
compare
(
model
,
model2
));
...
...
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
View file @
0bc2881e
...
...
@@ -7,8 +7,6 @@ import static org.junit.Assert.assertTrue;
import
java.awt.Color
;
import
java.io.ByteArrayInputStream
;
import
java.io.InputStream
;
import
java.nio.charset.StandardCharsets
;
import
java.util.ArrayList
;
import
java.util.HashSet
;
import
java.util.List
;
...
...
@@ -98,7 +96,6 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
}
}
@Test
public
void
testParseTextWithBackground
()
throws
Exception
{
try
{
...
...
@@ -413,14 +410,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
alias
.
setName
(
"name & no-name"
);
model
.
addElement
(
alias
);
CellDesignerXmlParser
parser
=
new
CellDesignerXmlParser
();
String
string
=
parser
.
model2String
(
model
);
InputStream
stream
=
new
ByteArrayInputStream
(
string
.
getBytes
(
StandardCharsets
.
UTF_8
));
ConverterParams
params
=
new
ConverterParams
().
inputStream
(
stream
).
sizeAutoAdjust
(
false
);
Model
model2
=
parser
.
createModel
(
params
);
Model
model2
=
serializeModel
(
model
);
ModelComparator
comparator
=
new
ModelComparator
();
...
...
@@ -443,14 +433,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
alias
.
setName
(
"name\rno-name"
);
model
.
addElement
(
alias
);
CellDesignerXmlParser
parser
=
new
CellDesignerXmlParser
();
String
string
=
parser
.
model2String
(
model
);
InputStream
stream
=
new
ByteArrayInputStream
(
string
.
getBytes
(
StandardCharsets
.
UTF_8
));
ConverterParams
params
=
new
ConverterParams
().
inputStream
(
stream
).
sizeAutoAdjust
(
false
);
Model
model2
=
parser
.
createModel
(
params
);
Model
model2
=
serializeModel
(
model
);
ModelComparator
comparator
=
new
ModelComparator
();
...
...
@@ -485,5 +468,4 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
}
}
}
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
View file @
0bc2881e
...
...
@@ -26,6 +26,7 @@ import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import
lcsb.mapviewer.converter.graphics.NormalImageGenerator
;
import
lcsb.mapviewer.converter.graphics.PngImageGenerator
;
import
lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser
;
import
lcsb.mapviewer.model.map.BioEntity
;
import
lcsb.mapviewer.model.map.model.Model
;
import
lcsb.mapviewer.model.map.model.ModelComparator
;
...
...
@@ -91,11 +92,16 @@ public class GenericSbmlParserTest {
assertNotNull
(
model2
);
ModelComparator
comparator
=
new
ModelComparator
(
1.0
);
for
(
BioEntity
bioEntity:
model
.
getBioEntities
())
{
bioEntity
.
setZ
(
null
);
}
for
(
BioEntity
bioEntity:
model2
.
getBioEntities
())
{
bioEntity
.
setZ
(
null
);
}
assertEquals
(
0
,
comparator
.
compare
(
model
,
model2
));
FileUtils
.
deleteDirectory
(
new
File
(
dir
));
}
catch
(
Exception
e
)
{
// TODO Auto-generated catch block
e
.
printStackTrace
();
throw
e
;
}
...
...
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlTestFunctions.java
View file @
0bc2881e
...
...
@@ -4,6 +4,7 @@ import java.awt.Desktop;
import
java.awt.geom.Point2D
;
import
java.io.ByteArrayInputStream
;
import
java.io.File
;
import
java.io.InputStream
;
import
java.nio.file.Files
;
import
java.util.List
;
...
...
@@ -17,7 +18,9 @@ import lcsb.mapviewer.converter.ConverterParams;
import
lcsb.mapviewer.converter.graphics.AbstractImageGenerator
;
import
lcsb.mapviewer.converter.graphics.NormalImageGenerator
;
import
lcsb.mapviewer.converter.graphics.PngImageGenerator
;
import
lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser
;
import
lcsb.mapviewer.model.graphics.PolylineData
;
import
lcsb.mapviewer.model.map.BioEntity
;
import
lcsb.mapviewer.model.map.compartment.Compartment
;
import
lcsb.mapviewer.model.map.model.Model
;
import
lcsb.mapviewer.model.map.reaction.Product
;
...
...
@@ -117,6 +120,21 @@ public class SbmlTestFunctions {
// showImage(result);
return
result
;
}
protected
Model
getModelAfterCellDEsignerSerializing
(
Model
model
)
throws
Exception
{
CellDesignerXmlParser
parser
=
new
CellDesignerXmlParser
();
String
xmlString
=
parser
.
model2String
(
model
);
InputStream
is
=
new
ByteArrayInputStream
(
xmlString
.
getBytes
(
"UTF-8"
));
Model
model2
=
parser
.
createModel
(
new
ConverterParams
().
inputStream
(
is
).
sizeAutoAdjust
(
false
));
for
(
BioEntity
bioEntity
:
model2
.
getBioEntities
())
{
bioEntity
.
setZ
(
null
);
}
for
(
BioEntity
bioEntity
:
model
.
getBioEntities
())
{
bioEntity
.
setZ
(
null
);
}
return
model2
;
}
...
...
model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
View file @
0bc2881e
...
...
@@ -385,6 +385,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
assertEquals
(
"test"
,
pathway
.
getName
());
assertEquals
(
"5"
,
pathway
.
getVisibilityLevel
());
assertEquals
((
Integer
)
11
,
pathway
.
getZ
());
}
catch
(
Exception
e
)
{
e
.
printStackTrace
();
...
...
model-command/testFiles/layer_text_with_notes.xml
View file @
0bc2881e
...
...
@@ -42,6 +42,7 @@
<celldesigner:layerNotes>
test
SemanticZoomLevelVisibility: 5
Z-Index: 11
</celldesigner:layerNotes>
<celldesigner:bounds
x=
"140.0"
y=
"173.0"
w=
"242.0"
h=
"178.0"
/>
<celldesigner:paint
color=
"ff000000"
/>
...
...
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