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minerva
core
Commits
50633d74
Commit
50633d74
authored
Oct 17, 2019
by
Piotr Gawron
Browse files
validation failure produces a warning instead of exception
parent
a32f0b65
Pipeline
#15158
passed with stage
in 13 minutes and 4 seconds
Changes
5
Pipelines
1
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CHANGELOG
View file @
50633d74
...
...
@@ -14,6 +14,8 @@ minerva (14.0.3) stable; urgency=medium
user
provided
data
overlays
(#
975
)
*
Bug
fix
:
changing
order
of
data
overlays
is
reflected
in
info
window
*
Bug
fix
:
opening
map
with
no
available
background
crashed
(#
964
)
*
Bug
fix
:
uploading
SBGN
file
that
does
not
pass
xsd
validation
provides
a
warning
,
but
does
not
fail
upload
(#
937
)
--
Piotr
Gawron
<
piotr
.
gawron
@
uni
.
lu
>
Wed
,
16
Oct
2019
9
:
00
:
00
+
0200
...
...
converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
View file @
50633d74
...
...
@@ -95,13 +95,11 @@ public class SbgnmlXmlParser {
// Check if input file has valid SBGN-ML data
try
{
if
(!
SbgnUtil
.
isValid
(
inputSbgnmlFile
))
{
throw
new
InvalidInputDataExecptio
n
(
"Given input is not a valid SBGN-ML file."
);
logger
.
war
n
(
"Given input is not a valid SBGN-ML file."
);
}
// Read data from file
sbgnData
=
SbgnUtil
.
readFromFile
(
inputSbgnmlFile
);
}
catch
(
InvalidInputDataExecption
ex
)
{
throw
ex
;
}
catch
(
Exception
ex
)
{
throw
new
InvalidInputDataExecption
(
"Unable to read given file."
,
ex
);
}
...
...
converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
View file @
50633d74
package
lcsb.mapviewer.converter.model.sbgnml
;
import
java.awt.
*
;
import
java.awt.
Desktop
;
import
java.io.File
;
import
java.nio.file.Files
;
import
java.util.List
;
import
org.junit.Rule
;
import
org.apache.logging.log4j.core.LogEvent
;
import
org.junit.*
;
import
lcsb.mapviewer.common.MinervaLoggerAppender
;
import
lcsb.mapviewer.common.UnitTestFailedWatcher
;
import
lcsb.mapviewer.converter.graphics.*
;
import
lcsb.mapviewer.model.map.model.Model
;
...
...
@@ -15,6 +18,23 @@ public class SbgnmlTestFunctions {
@Rule
public
UnitTestFailedWatcher
unitTestFailedWatcher
=
new
UnitTestFailedWatcher
();
private
MinervaLoggerAppender
appender
;
@Before
public
final
void
_setUp
()
throws
Exception
{
MinervaLoggerAppender
.
unregisterLogEventStorage
(
appender
);
appender
=
MinervaLoggerAppender
.
createAppender
();
}
@After
public
final
void
_tearDown
()
throws
Exception
{
MinervaLoggerAppender
.
unregisterLogEventStorage
(
appender
);
}
protected
List
<
LogEvent
>
getWarnings
()
{
return
appender
.
getWarnings
();
}
protected
void
showImage
(
Model
model
)
throws
Exception
{
String
dir
=
Files
.
createTempDirectory
(
"sbml-temp-images-dir"
).
toFile
().
getAbsolutePath
();
AbstractImageGenerator
.
Params
params
=
new
AbstractImageGenerator
.
Params
().
height
(
model
.
getHeight
())
...
...
converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
View file @
50633d74
...
...
@@ -55,6 +55,14 @@ public class SbgnmlXmlParserTest2 extends SbgnmlTestFunctions {
assertNull
(
"Top compartment has not null compartment"
,
compartment
.
getCompartment
());
}
@Test
public
void
parseModelWithXSDProblems
()
throws
Exception
{
Converter
converter
=
new
SbgnmlXmlConverter
();
converter
.
createModel
(
new
ConverterParams
().
filename
(
"testFiles/file_that_does_not_pass_xsd.sbgn"
));
assertEquals
(
1
,
getWarnings
().
size
());
}
@Test
public
void
createModelWithZIndex
()
throws
Exception
{
Converter
converter
=
new
SbgnmlXmlConverter
();
...
...
converter-SBGNML/testFiles/file_that_does_not_pass_xsd.sbgn
0 → 100644
View file @
50633d74
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn
xmlns=
"http://sbgn.org/libsbgn/0.2"
>
<map
language=
"process description"
>
<extension>
<renderInformation
xmlns=
"http://www.sbml.org/sbml/level3/version1/render/version1"
backgroundColor=
"#ffffff"
id=
"renderInformation"
programName=
"graphml2sbgn"
programVersion=
"0.1"
>
<listOfColorDefinitions>
<colorDefinition
id=
"color_1"
value=
"#F2F4F8"
/>
<colorDefinition
id=
"color_2"
value=
"#FFFFFF7F"
/>
<colorDefinition
id=
"color_3"
value=
"#333333"
/>
<colorDefinition
id=
"color_4"
value=
"#E4EAC4"
/>
<colorDefinition
id=
"color_5"
value=
"#FFFFFF"
/>
<colorDefinition
id=
"color_6"
value=
"#000000"
/>
<colorDefinition
id=
"color_7"
value=
"#C2D4ED"
/>
</listOfColorDefinitions>
<listOfStyles>
<style
id=
"style_1.0FFFFFF7F14.0333333"
idList=
"n13"
>
<g
fill=
"color_2"
fontSize=
"14.0"
stroke=
"color_3"
strokeWidth=
"1.0"
/>
</style>
<style
id=
"style_1.0FFFFFF14.0000000"
idList=
"n26 n30 n21 n23 n22"
>
<g
fill=
"color_5"
fontSize=
"14.0"
stroke=
"color_6"
strokeWidth=
"1.0"
/>
</style>
<style
id=
"style_1.0C2D4ED14.0333333"
idList=
"n24::n1 n2 n24::n0 n28::n0 n29::n1 n28::n1 n29::n0 n10 n31 n33::n0 n12 n11 n14 n25 n16 n15 n17 n27::n0"
>
<g
fill=
"color_7"
fontSize=
"14.0"
stroke=
"color_3"
strokeWidth=
"1.0"
/>
</style>
<style
id=
"style_1.0F2F4F812.0000000"
idList=
"n24 n27 n29 n28 n33"
>
<g
fill=
"color_1"
fontSize=
"12.0"
stroke=
"color_6"
strokeWidth=
"1.0"
/>
</style>
<style
id=
"style_1.0FFFFFF14.0333333"
idList=
"n18 n5 n19 n6 n8 n9"
>
<g
fill=
"color_5"
fontSize=
"14.0"
stroke=
"color_3"
strokeWidth=
"1.0"
/>
</style>
<style
id=
"style_1.0C2D4ED14.0000000"
idList=
"n27::n1 n32 n20 n33::n1"
>
<g
fill=
"color_7"
fontSize=
"14.0"
stroke=
"color_6"
strokeWidth=
"1.0"
/>
</style>
<style
id=
"style_1.0E4EAC414.0333333"
idList=
"n0 n1 n3 n4 n7"
>
<g
fill=
"color_4"
fontSize=
"14.0"
stroke=
"color_3"
strokeWidth=
"1.0"
/>
</style>
<style
id=
"style_1.0000000"
idList=
"e31 e30 e11 e33 e10 e32 e13 e35 e12 e34 e15 e14 e17 e16 e19 e18 e20 e22 e21 e24 e23 e26 e25 e28 e0 e27 e1 e2 e29 e3 e4 e5 e6 e7 e8 e9"
>
<g
fill=
"color_6"
fontSize=
"10.0"
stroke=
"color_6"
strokeWidth=
"1.0"
/>
</style>
</listOfStyles>
</renderInformation>
</extension>
<glyph
class=
"complex"
id=
"n24"
>
<bbox
w=
"100.65368"
h=
"126.69954"
x=
"173.66068"
y=
"134.19138"
/>
<glyph
class=
"macromolecule"
id=
"n24::n0"
>
<extension>
<annotation
xmlns:ns2=
"http://sbgn.org/libsbgn/0.2"
xmlns=
""
>
<rdf:RDF
xmlns:rdf=
"http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>
https://www.uniprot.org/uniprot/P01133#PRO_0000007541
</rdf:RDF>
</annotation>
</extension>
<label
text=
"EGF"
/>
<bbox
w=
"80.0"
h=
"40.0"
x=
"184.31435"
y=
"148.19138"
/>
</glyph>
<glyph
class=
"macromolecule"
id=
"n24::n1"
>
<extension>
<annotation
xmlns:ns2=
"http://sbgn.org/libsbgn/0.2"
xmlns=
""
>
<rdf:RDF
xmlns:rdf=
"http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>
https://www.uniprot.org/uniprot/P00533
</rdf:RDF>
</annotation>
</extension>
<label
text=
"EGFR"
/>
<bbox
w=
"80.0"
h=
"40.0"
x=
"184.31435"
y=
"198.39093"
/>
<glyph
class=
"state variable"
id=
"3"
>
<state
value=
""
variable=
"Y"
/>
<bbox
w=
"36.091797"
h=
"15.0"
x=
"222.24153"
y=
"1195.1536"
/>
</glyph>
</glyph>
</glyph>
</map>
</sbgn>
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