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minerva
core
Commits
8e4031af
Commit
8e4031af
authored
Sep 03, 2021
by
Piotr Gawron
Browse files
Merge branch '1540-export-error' into 'devel_16.0.x'
Resolve "MINERVANET - Error Report 326" See merge request
!1335
parents
6122571d
b09b2cc4
Pipeline
#46523
passed with stage
in 15 minutes and 37 seconds
Changes
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CHANGELOG
View file @
8e4031af
minerva
(
16.0.0
~
beta
.2
)
stable
;
urgency
=
medium
*
Bug
fix
:
problem
with
export
map
with
submaps
fixed
(#
1540
)
--
Piotr
Gawron
<
piotr
.
gawron
@
uni
.
lu
>
Fri
,
3
Sep
2021
11
:
00
:
00
+
0200
minerva
(
16.0.0
~
beta
.1
)
stable
;
urgency
=
medium
*
Backward
incompatibility
:
layout
parameter
in
minerva
url
is
not
supported
anymore
...
...
CellDesigner-plugin/pom.xml
View file @
8e4031af
...
...
@@ -5,7 +5,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
CellDesigner-plugin
</artifactId>
<!-- dependency from the MapViewer model -->
...
...
@@ -50,19 +50,19 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
commons
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-CellDesigner
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
...
...
annotation/pom.xml
View file @
8e4031af
...
...
@@ -5,7 +5,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
annotation
</artifactId>
<name>
Annotation module
</name>
...
...
@@ -18,7 +18,7 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- dependency from the MapViewer dao -->
...
...
@@ -26,7 +26,7 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
persist
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser (we need access
...
...
@@ -34,13 +34,13 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-CellDesigner
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- Log4J2 -->
...
...
commons/pom.xml
View file @
8e4031af
...
...
@@ -5,7 +5,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
commons
</artifactId>
<name>
Mapviewer commons
</name>
...
...
converter-CellDesigner/pom.xml
View file @
8e4031af
...
...
@@ -5,7 +5,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
converter-CellDesigner
</artifactId>
<name>
CellDesigner converter
</name>
...
...
@@ -17,13 +17,13 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- Log4J2 -->
...
...
converter-SBGNML/pom.xml
View file @
8e4031af
...
...
@@ -5,7 +5,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
converter-SBGNML
</artifactId>
...
...
@@ -20,26 +20,26 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
persist
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-CellDesigner
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-graphics
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
...
...
converter-graphics/pom.xml
View file @
8e4031af
...
...
@@ -5,7 +5,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
converter-graphics
</artifactId>
<name>
MapViewer graphics converter
</name>
...
...
@@ -18,13 +18,13 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model-command
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- Log4J2-->
...
...
converter-sbml/pom.xml
View file @
8e4031af
...
...
@@ -7,7 +7,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
converter-sbml
</artifactId>
<name>
converter-sbml
</name>
...
...
@@ -40,22 +40,22 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model-command
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-CellDesigner
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- Log4J2 -->
...
...
@@ -154,7 +154,7 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-graphics
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
<scope>
test
</scope>
</dependency>
...
...
converter/pom.xml
View file @
8e4031af
...
...
@@ -5,7 +5,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
converter
</artifactId>
...
...
@@ -15,7 +15,7 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
xerces
</groupId>
...
...
frontend-js/pom.xml
View file @
8e4031af
...
...
@@ -7,7 +7,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
frontend-js
</artifactId>
<name>
frontend-js
</name>
...
...
model-command/pom.xml
View file @
8e4031af
...
...
@@ -3,7 +3,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
model-command
</artifactId>
<name>
Model commands
</name>
...
...
@@ -16,7 +16,7 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
...
...
@@ -24,7 +24,7 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-CellDesigner
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- Log4J2-->
...
...
model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
View file @
8e4031af
...
...
@@ -142,7 +142,9 @@ public class CopyCommand extends NewModelCommand {
original
=
connection
.
getParentModel
();
copy
=
copies
.
get
(
original
);
if
(
copy
==
null
)
{
throw
new
InvalidModelException
(
"Original model contain reference to model that wasn't copied"
);
if
(!
original
.
equals
(
modelCopy
))
{
throw
new
InvalidModelException
(
"Original model contain reference to model that wasn't copied"
);
}
}
else
{
connection
.
setParentModel
(
copy
);
}
...
...
model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
View file @
8e4031af
package
lcsb.mapviewer.commands
;
import
static
org
.
junit
.
Assert
.*;
import
static
org
.
junit
.
Assert
.
assertEquals
;
import
static
org
.
junit
.
Assert
.
assertFalse
;
import
static
org
.
junit
.
Assert
.
assertNotEquals
;
import
static
org
.
junit
.
Assert
.
assertNotNull
;
import
static
org
.
junit
.
Assert
.
assertTrue
;
import
java.awt.geom.Point2D
;
import
java.util.*
;
import
java.util.ArrayList
;
import
java.util.Calendar
;
import
java.util.List
;
import
org.apache.commons.lang3.mutable.MutableBoolean
;
import
org.junit.*
;
import
org.junit.After
;
import
org.junit.Before
;
import
org.junit.Test
;
import
lcsb.mapviewer.common.exception.InvalidArgumentException
;
import
lcsb.mapviewer.model.Project
;
import
lcsb.mapviewer.model.graphics.PolylineData
;
import
lcsb.mapviewer.model.map.MiriamData
;
...
...
@@ -17,11 +24,22 @@ import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import
lcsb.mapviewer.model.map.kinetics.SbmlFunction
;
import
lcsb.mapviewer.model.map.kinetics.SbmlParameter
;
import
lcsb.mapviewer.model.map.layout.graphics.Layer
;
import
lcsb.mapviewer.model.map.model.*
;
import
lcsb.mapviewer.model.map.reaction.*
;
import
lcsb.mapviewer.model.map.model.Author
;
import
lcsb.mapviewer.model.map.model.ElementSubmodelConnection
;
import
lcsb.mapviewer.model.map.model.Model
;
import
lcsb.mapviewer.model.map.model.ModelComparator
;
import
lcsb.mapviewer.model.map.model.ModelFullIndexed
;
import
lcsb.mapviewer.model.map.model.ModelSubmodelConnection
;
import
lcsb.mapviewer.model.map.model.SubmodelType
;
import
lcsb.mapviewer.model.map.reaction.AbstractNode
;
import
lcsb.mapviewer.model.map.reaction.Product
;
import
lcsb.mapviewer.model.map.reaction.Reactant
;
import
lcsb.mapviewer.model.map.reaction.Reaction
;
import
lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction
;
import
lcsb.mapviewer.model.map.reaction.type.TransportReaction
;
import
lcsb.mapviewer.model.map.species.*
;
import
lcsb.mapviewer.model.map.species.Complex
;
import
lcsb.mapviewer.model.map.species.Element
;
import
lcsb.mapviewer.model.map.species.GenericProtein
;
public
class
CopyCommandTest
extends
CommandTestFunctions
{
...
...
@@ -219,17 +237,6 @@ public class CopyCommandTest extends CommandTestFunctions {
assertEquals
(
0
,
comparator
.
compare
(
model
,
copy
));
}
@Test
(
expected
=
InvalidArgumentException
.
class
)
public
void
testCopyModelWithSubmodelsThrowException
()
throws
Exception
{
Model
model
=
getModel
();
Model
model2
=
getModel
();
model2
.
setNotes
(
"ASDSA2"
);
model
.
getElementByElementId
(
"a_id"
)
.
setSubmodel
(
new
ElementSubmodelConnection
(
model2
,
SubmodelType
.
DOWNSTREAM_TARGETS
));
new
CopyCommand
(
model
).
execute
();
}
private
Model
getModel
()
{
Model
model
=
new
ModelFullIndexed
(
null
);
model
.
setName
(
"nam"
+
counter
++);
...
...
model/pom.xml
View file @
8e4031af
...
...
@@ -5,7 +5,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
model
</artifactId>
<name>
model MapViewer
</name>
...
...
@@ -15,7 +15,7 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
commons
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- Java xml serialization -->
...
...
pathvisio/pom.xml
View file @
8e4031af
...
...
@@ -5,7 +5,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
pathvisio
</artifactId>
<name>
Pathvisio plugin
</name>
...
...
@@ -77,20 +77,20 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-CellDesigner
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-graphics
</artifactId>
<scope>
test
</scope>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- Log4J2 -->
...
...
persist/pom.xml
View file @
8e4031af
...
...
@@ -7,7 +7,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
persist
</artifactId>
...
...
@@ -27,7 +27,7 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- apache ftp -->
...
...
pom.xml
View file @
8e4031af
...
...
@@ -6,7 +6,7 @@
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
<packaging>
pom
</packaging>
<name>
parent MapViewer
</name>
...
...
rest-api/pom.xml
View file @
8e4031af
...
...
@@ -7,7 +7,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
rest-api
</artifactId>
<name>
rest-api
</name>
...
...
@@ -19,19 +19,19 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
service
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
pathvisio
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
...
...
service/pom.xml
View file @
8e4031af
...
...
@@ -7,7 +7,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
service
</artifactId>
...
...
@@ -20,7 +20,7 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- dependency from the MapViewer dao -->
...
...
@@ -28,47 +28,47 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
persist
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
model-command
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
annotation
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser -->
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-CellDesigner
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- dependency from the MapViewer SBGN-ML parser -->
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-SBGNML
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- dependency from the MapViewer graphics converter -->
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-graphics
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- dependency from the SBML parser -->
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
converter-sbml
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<!-- Log4J2 -->
...
...
web/pom.xml
View file @
8e4031af
...
...
@@ -7,7 +7,7 @@
<parent>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
parent
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</parent>
<artifactId>
web
</artifactId>
<packaging>
war
</packaging>
...
...
@@ -33,19 +33,19 @@
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
service
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
rest-api
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
<groupId>
lcsb.mapviewer
</groupId>
<artifactId>
frontend-js
</artifactId>
<version>
16.0.0~beta.
1
</version>
<version>
16.0.0~beta.
2
</version>
</dependency>
<dependency>
...
...
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