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minerva
core
Commits
c7034c9b
Commit
c7034c9b
authored
Apr 15, 2021
by
Piotr Gawron
Browse files
element info added to modifier warnings: Don't know how to handle SBOTerm
parent
74f87ef3
Changes
6
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converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlModelUtils.java
View file @
c7034c9b
...
...
@@ -4,12 +4,15 @@ import java.awt.Color;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
import
org.sbml.jsbml.AbstractNamedSBase
;
import
org.sbml.jsbml.Model
;
import
org.sbml.jsbml.ext.SBasePlugin
;
import
org.sbml.jsbml.ext.layout.*
;
import
org.sbml.jsbml.ext.render.*
;
import
lcsb.mapviewer.common.XmlParser
;
import
lcsb.mapviewer.model.LogMarker
;
import
lcsb.mapviewer.model.ProjectLogEntryType
;
import
lcsb.mapviewer.model.graphics.ArrowType
;
public
class
SbmlModelUtils
{
...
...
@@ -247,4 +250,14 @@ public class SbmlModelUtils {
return
result
;
}
public
static
LogMarker
createMarker
(
ProjectLogEntryType
type
,
AbstractNamedSBase
element
)
{
if
(
element
==
null
)
{
return
new
LogMarker
(
type
,
""
,
"N/A"
,
"N/A"
);
}
else
if
(
element
.
getModel
()
==
null
)
{
return
new
LogMarker
(
type
,
element
.
getClass
().
getSimpleName
(),
element
.
getId
(),
""
);
}
else
{
return
new
LogMarker
(
type
,
element
.
getClass
().
getSimpleName
(),
element
.
getId
(),
element
.
getModel
().
getName
());
}
}
}
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java
View file @
c7034c9b
...
...
@@ -5,7 +5,10 @@ import java.util.List;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
import
org.sbml.jsbml.ModifierSpeciesReference
;
import
lcsb.mapviewer.converter.model.sbml.SbmlModelUtils
;
import
lcsb.mapviewer.model.ProjectLogEntryType
;
import
lcsb.mapviewer.model.map.modifier.*
;
import
lcsb.mapviewer.model.map.reaction.Modifier
;
...
...
@@ -31,7 +34,8 @@ public enum SBOTermModifierType {
}
}
public
static
Class
<?
extends
Modifier
>
getTypeSBOTerm
(
String
sboTerm
)
{
public
static
Class
<?
extends
Modifier
>
getTypeSBOTerm
(
ModifierSpeciesReference
modifier
)
{
String
sboTerm
=
modifier
.
getSBOTermID
();
if
(
sboTerm
==
null
||
sboTerm
.
isEmpty
())
{
return
Modifier
.
class
;
}
...
...
@@ -43,8 +47,10 @@ public enum SBOTermModifierType {
}
}
}
if
(
result
==
null
)
{
logger
.
warn
(
"Don't know how to handle SBOTerm "
+
sboTerm
+
" for modifier"
);
logger
.
warn
(
SbmlModelUtils
.
createMarker
(
ProjectLogEntryType
.
PARSING_ISSUE
,
modifier
),
"Don't know how to handle SBOTerm "
+
sboTerm
+
" for modifier"
);
result
=
Modifier
.
class
;
}
return
result
;
...
...
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
View file @
c7034c9b
...
...
@@ -707,7 +707,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
for
(
ModifierSpeciesReference
modifier
:
sbmlReaction
.
getListOfModifiers
())
{
Species
element
=
getMinervaModel
().
getElementByElementId
(
modifier
.
getSpecies
());
Class
<?
extends
Modifier
>
nodeClass
=
SBOTermModifierType
.
getTypeSBOTerm
(
modifier
.
getSBOTermID
()
);
Class
<?
extends
Modifier
>
nodeClass
=
SBOTermModifierType
.
getTypeSBOTerm
(
modifier
);
try
{
Modifier
newNode
=
nodeClass
.
getConstructor
(
Element
.
class
).
newInstance
(
element
);
reaction
.
addModifier
(
newNode
);
...
...
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java
View file @
c7034c9b
...
...
@@ -8,7 +8,8 @@ import org.junit.runners.Suite.SuiteClasses;
@SuiteClasses
({
SbmlReactionExportArrowType
.
class
,
SbmlReactionExporterTest
.
class
,
SbmlReactionParserTest
.
class
,
SbmlReactionParserExtractCurveTest
.
class
SbmlReactionParserExtractCurveTest
.
class
,
SBOTermModifierTypeTest
.
class
})
public
class
AllSbmlReactionParserTests
{
...
...
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierTypeTest.java
0 → 100644
View file @
c7034c9b
package
lcsb.mapviewer.converter.model.sbml.reaction
;
import
static
org
.
junit
.
Assert
.
assertEquals
;
import
static
org
.
junit
.
Assert
.
assertNotNull
;
import
org.junit.Test
;
import
org.sbml.jsbml.ModifierSpeciesReference
;
import
lcsb.mapviewer.converter.model.sbml.SbmlTestFunctions
;
import
lcsb.mapviewer.model.map.reaction.Modifier
;
public
class
SBOTermModifierTypeTest
extends
SbmlTestFunctions
{
@Test
public
void
testUnknownId
()
{
ModifierSpeciesReference
reference
=
new
ModifierSpeciesReference
(
3
,
2
);
reference
.
setSBOTerm
(
"SBO:0000000"
);
Class
<?
extends
Modifier
>
clazz
=
SBOTermModifierType
.
getTypeSBOTerm
(
reference
);
assertNotNull
(
clazz
);
assertEquals
(
1
,
super
.
getWarnings
().
size
());
assertNotNull
(
super
.
getWarnings
().
get
(
0
).
getMarker
());
}
}
frontend-js/package-lock.json
View file @
c7034c9b
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