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minerva
core
Commits
8570b8df
Commit
8570b8df
authored
Feb 25, 2020
by
Piotr Gawron
Browse files
problematic consumption and reversed reaction are parsed now
parent
dcf2b8ee
Pipeline
#21446
passed with stage
in 14 minutes and 13 seconds
Changes
4
Pipelines
1
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Inline
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CHANGELOG
View file @
8570b8df
...
...
@@ -14,6 +14,10 @@ minerva (14.0.9) stable; urgency=medium
*
Bug
fix
:
exporting
map
with
glyphs
crashed
(#
1130
)
*
Bug
fix
:
transcription
factor
on
black
&
white
gene
are
drawn
in
black
(#
1132
)
*
Bug
fix
:
when
SBGN
file
contained
consumption
starting
in
process
minerva
crashed
(#
1063
)
*
Bug
fix
:
when
SBGN
file
contained
reaction
where
every
node
started
in
the
same
process
port
minerva
crashed
crashed
(#
1063
)
--
Piotr
Gawron
<
piotr
.
gawron
@
uni
.
lu
>
Mon
,
3
Feb
2020
15
:
00
:
00
+
0200
...
...
converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
View file @
8570b8df
...
...
@@ -395,7 +395,15 @@ public class SbgnmlXmlParser {
private
void
parseArc
(
Arc
a
,
Model
model
)
throws
InvalidInputDataExecption
{
switch
(
ArcClazz
.
fromClazz
(
a
.
getClazz
()))
{
case
CONSUMPTION:
Port
arcTargetPort
=
(
Port
)
a
.
getTarget
();
Port
arcTargetPort
;
if
(
a
.
getTarget
()
instanceof
Port
)
{
arcTargetPort
=
(
Port
)
a
.
getTarget
();
}
else
if
(
a
.
getSource
()
instanceof
Port
)
{
logger
.
warn
(
"["
+
a
.
getId
()
+
"]\tConsumption is going from process"
);
arcTargetPort
=
(
Port
)
a
.
getSource
();
}
else
{
throw
new
InvalidInputDataExecption
(
"["
+
a
.
getId
()
+
"]\tConsumption must be connected to a Port"
);
}
for
(
Process
p
:
processes
)
{
if
(
p
.
getCentralPoint
().
getPort
().
contains
(
arcTargetPort
))
{
p
.
addReagentArc
(
a
);
...
...
@@ -1209,26 +1217,37 @@ public class SbgnmlXmlParser {
}
p
.
setProductsPort
((
Port
)
p
.
getProductArcs
().
get
(
0
).
getSource
());
for
(
Arc
productArc
:
p
.
getProductArcs
())
{
if
(!((
Port
)
productArc
.
getSource
()).
equals
(
p
.
getProductsPort
()))
{
p
.
setReversible
(
true
);
p
.
setReagentsPort
((
Port
)
productArc
.
getSource
());
}
if
(
p
.
getProductArcs
().
size
()
>=
2
&&
p
.
getReagentArcs
().
size
()
==
0
)
{
p
.
setReversible
(
true
);
}
if
(
p
.
getReagentsPort
()
==
null
&&
!
p
.
getReagentArcs
().
isEmpty
())
{
p
.
setReagentsPort
((
Port
)
p
.
getReagentArcs
().
get
(
0
).
getTarget
());
Set
<
Port
>
ports
=
new
HashSet
<>();
for
(
Arc
a
:
p
.
getProductArcs
())
{
ports
.
add
(
getTargetPort
(
a
));
}
for
(
Arc
a
:
p
.
getReagentArcs
())
{
ports
.
add
(
getSourcePort
(
a
));
}
if
(
ports
.
size
()
<
2
)
{
logger
.
warn
(
"There is only one port used in process: "
+
p
.
getProductsPort
().
getId
());
}
if
((
p
.
getReagentArcs
().
isEmpty
()
&&
!
p
.
isReversible
())
||
(
p
.
getRevReagentArcs
().
isEmpty
()
&&
p
.
isReversible
()))
{
throw
new
InvalidArgumentException
(
p
.
getCentralPoint
().
getId
()
+
": The process must have at least one incoming arc."
);
if
(
p
.
getReagentsPort
()
==
null
&&
!
p
.
getReagentArcs
().
isEmpty
())
{
Port
port
;
if
(
p
.
getReagentArcs
().
get
(
0
).
getTarget
()
instanceof
Port
)
{
port
=
(
Port
)
p
.
getReagentArcs
().
get
(
0
).
getTarget
();
}
else
if
(
p
.
getReagentArcs
().
get
(
0
).
getSource
()
instanceof
Port
)
{
port
=
(
Port
)
p
.
getReagentArcs
().
get
(
0
).
getSource
();
}
else
{
throw
new
InvalidArgumentException
(
"Cannot find proces for arc: "
+
p
.
getReagentArcs
().
get
(
0
).
getId
());
}
p
.
setReagentsPort
(
port
);
}
Reaction
reaction
;
if
(
p
.
getCentralPoint
()
==
null
)
{
throw
new
InvalidArgumentException
(
"Process has no central point."
);
}
reaction
=
getReactionFromProcessGlyphClazz
(
p
.
getCentralPoint
().
getClazz
());
Reaction
reaction
=
getReactionFromProcessGlyphClazz
(
p
.
getCentralPoint
().
getClazz
());
reaction
.
setIdReaction
(
p
.
getCentralPoint
().
getId
());
reaction
.
setModel
(
model
);
...
...
@@ -1243,8 +1262,7 @@ public class SbgnmlXmlParser {
// If there are multiple outputs, add Split operator
SplitOperator
splitOperator
=
null
;
if
((
p
.
getProductArcs
().
size
()
>
1
&&
!
p
.
isReversible
())
||
(
p
.
isReversible
()
&&
p
.
getRevProductArcs
().
size
()
>
1
))
{
if
((
p
.
getProductArcs
().
size
()
>
1
&&
!
p
.
isReversible
())
||
(
p
.
getProductArcs
().
size
()
>
2
))
{
splitOperator
=
getReactionPortSplitOperator
(
p
);
reaction
.
addNode
(
splitOperator
);
}
...
...
@@ -1252,7 +1270,7 @@ public class SbgnmlXmlParser {
for
(
Arc
a
:
p
.
getReagentArcs
())
{
Reactant
reactant
=
new
Reactant
();
reactant
.
setReaction
(
reaction
);
Glyph
source
=
(
Glyph
)
a
.
getSource
(
);
Glyph
source
=
getSource
Glyph
(
a
);
reactant
.
setElement
(
model
.
getElementByElementId
(
source
.
getId
()));
List
<
Point2D
>
pointList
=
getLinePoints
(
a
);
PolylineData
line
=
parseLine
(
a
,
pointList
);
...
...
@@ -1265,7 +1283,7 @@ public class SbgnmlXmlParser {
}
for
(
Arc
a
:
p
.
getProductArcs
())
{
if
(
((
Port
)
a
.
getSource
()
).
equals
(
p
.
getProductsPort
()))
{
if
(
getSource
Port
(
a
).
equals
(
p
.
getProductsPort
())
&&
ports
.
size
()
==
2
||
reaction
.
getProducts
().
size
()
==
0
)
{
Product
product
=
new
Product
();
product
.
setReaction
(
reaction
);
Glyph
target
=
(
Glyph
)
a
.
getTarget
();
...
...
@@ -1290,7 +1308,6 @@ public class SbgnmlXmlParser {
if
(
andOperator
!=
null
)
{
andOperator
.
addInput
(
reactant
);
}
reaction
.
addReactant
(
reactant
);
}
}
...
...
@@ -1347,6 +1364,36 @@ public class SbgnmlXmlParser {
model
.
addReaction
(
reaction
);
}
private
Port
getTargetPort
(
Arc
a
)
{
if
(
a
.
getTarget
()
instanceof
Port
)
{
return
(
Port
)
a
.
getTarget
();
}
else
if
(
a
.
getSource
()
instanceof
Port
)
{
return
(
Port
)
a
.
getSource
();
}
else
{
throw
new
InvalidArgumentException
(
"Arc is not connected to glyph: "
+
a
.
getId
());
}
}
private
Port
getSourcePort
(
Arc
a
)
{
if
(
a
.
getSource
()
instanceof
Port
)
{
return
(
Port
)
a
.
getSource
();
}
else
if
(
a
.
getTarget
()
instanceof
Port
)
{
return
(
Port
)
a
.
getTarget
();
}
else
{
throw
new
InvalidArgumentException
(
"Arc is not connected to glyph: "
+
a
.
getId
());
}
}
private
Glyph
getSourceGlyph
(
Arc
a
)
{
if
(
a
.
getSource
()
instanceof
Glyph
)
{
return
(
Glyph
)
a
.
getSource
();
}
else
if
(
a
.
getTarget
()
instanceof
Glyph
)
{
return
(
Glyph
)
a
.
getTarget
();
}
else
{
throw
new
InvalidArgumentException
(
"Arc is not connected to glyph: "
+
a
.
getId
());
}
}
/**
* Returns {@link ArrowTypeData} based on given {@link ArcClazz}.
*
...
...
converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/problematic_consumption.sbgn
0 → 100644
View file @
8570b8df
<?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"
id=
"renderInformation"
program-name=
"sbgnviz"
program-version=
"5.0.0"
background-color=
"#00000000"
>
<listOfColorDefinitions>
<colorDefinition
id=
"color_1"
value=
"#ffffffff"
/>
<colorDefinition
id=
"color_2"
value=
"#838383"
/>
<colorDefinition
id=
"color_3"
value=
"#555555"
/>
<colorDefinition
id=
"color_4"
value=
"#ffffff"
/>
<colorDefinition
id=
"color_5"
value=
"#000000"
/>
</listOfColorDefinitions>
<listOfBackgroundImages>
<backgroundImage
id=
"image_1"
value=
"http://newteditor.org/color-scheme-images/rb3_3d.png"
/>
<backgroundImage
id=
"image_2"
value=
"http://newteditor.org/color-scheme-images/pg5_3d.png"
/>
<backgroundImage
id=
"image_3"
value=
"http://newteditor.org/color-scheme-images/bw1_3d.png"
/>
</listOfBackgroundImages>
<listOfStyles>
<style
id=
"nodeffffff18383833.2514normalnormalHelvetica000image_1none5050100100"
id-list=
"nwtN_3ab42db3-7946-4642-a215-98b2f74f5061 nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815"
>
<g
font-size=
"14"
font-family=
"Helvetica"
font-weight=
"normal"
font-style=
"normal"
font-color=
"#000"
stroke=
"color_2"
stroke-width=
"3.25"
fill=
"color_1"
background-image=
"image_1"
background-fit=
"none"
background-pos-x=
"50%"
background-pos-y=
"50%"
background-width=
"100%"
background-height=
"100%"
/>
</style>
<style
id=
"nodeffffff15555551.2518normalnormalHelvetica000image_2none5050100100"
id-list=
"2f567801-fc2c-e128-f352-1dfab2f0dbce 35a3e0be-6e00-7a99-fca5-18ed65c2fac1"
>
<g
font-size=
"18"
font-family=
"Helvetica"
font-weight=
"normal"
font-style=
"normal"
font-color=
"#000"
stroke=
"color_3"
stroke-width=
"1.25"
fill=
"color_1"
background-image=
"image_2"
background-fit=
"none"
background-pos-x=
"50%"
background-pos-y=
"50%"
background-width=
"100%"
background-height=
"100%"
/>
</style>
<style
id=
"infoboxffffff5555552.259normalnormalArial0f0f0fstadium"
id-list=
"2f567801-fc2c-e128-f352-1dfab2f0dbce_0 35a3e0be-6e00-7a99-fca5-18ed65c2fac1_0"
>
<g
font-size=
"9"
font-family=
"Arial"
font-weight=
"normal"
font-style=
"normal"
font-color=
"#0f0f0f"
stroke=
"color_3"
stroke-width=
"2.25"
fill=
"color_4"
shape-name=
"stadium"
/>
</style>
<style
id=
"nodeffffff15555551.25image_3none5050100100"
id-list=
"d6a6f52d-8036-ba76-8a3e-dfa5dcd6d57e 6507b78f-2da9-659a-4d3f-d78d84be17ed"
>
<g
stroke=
"color_3"
stroke-width=
"1.25"
fill=
"color_1"
background-image=
"image_3"
background-fit=
"none"
background-pos-x=
"50%"
background-pos-y=
"50%"
background-width=
"100%"
background-height=
"100%"
/>
</style>
<style
id=
"nodeffffff10000001.25image_3none5050100100"
id-list=
"nwtN_af68cdcd-f3e3-4438-9be7-e8feb28bb2e8"
>
<g
stroke=
"color_5"
stroke-width=
"1.25"
fill=
"color_1"
background-image=
"image_3"
background-fit=
"none"
background-pos-x=
"50%"
background-pos-y=
"50%"
background-width=
"100%"
background-height=
"100%"
/>
</style>
<style
id=
"nodeffffff15555551.2511normalnormalHelvetica000image_1none5050100100"
id-list=
"e342a729-472c-3bbf-78da-d20caa7b1c03 0088e5e3-506d-b360-cc23-6ca191128211"
>
<g
font-size=
"11"
font-family=
"Helvetica"
font-weight=
"normal"
font-style=
"normal"
font-color=
"#000"
stroke=
"color_3"
stroke-width=
"1.25"
fill=
"color_1"
background-image=
"image_1"
background-fit=
"none"
background-pos-x=
"50%"
background-pos-y=
"50%"
background-width=
"100%"
background-height=
"100%"
/>
</style>
<style
id=
"edge5555551.25"
id-list=
"01a1302c-8279-8a9d-3025-b640251301f6 cc9b0b19-5606-60a6-4325-45883e217e2f b88e5a04-bd6f-2617-8c80-8bb7aeaf724b f5c88b0d-d0f6-110a-6964-35337c5b66a9 nwtE_6b731a56-0e87-49ea-8425-136bf3b6b18f nwtE_00484b84-815f-4ecb-b309-b3fe9c02b2b1"
>
<g
stroke=
"color_3"
stroke-width=
"1.25"
/>
</style>
</listOfStyles>
</renderInformation>
<mapProperties>
<compoundPadding>
20
</compoundPadding>
<extraCompartmentPadding>
14
</extraCompartmentPadding>
<extraComplexPadding>
10
</extraComplexPadding>
<arrowScale>
1.25
</arrowScale>
<showComplexName>
true
</showComplexName>
<dynamicLabelSize>
regular
</dynamicLabelSize>
<inferNestingOnLoad>
false
</inferNestingOnLoad>
<fitLabelsToNodes>
false
</fitLabelsToNodes>
<fitLabelsToInfoboxes>
false
</fitLabelsToInfoboxes>
<recalculateLayoutOnComplexityManagement>
true
</recalculateLayoutOnComplexityManagement>
<rearrangeOnComplexityManagement>
true
</rearrangeOnComplexityManagement>
<animateOnDrawingChanges>
true
</animateOnDrawingChanges>
<adjustNodeLabelFontSizeAutomatically>
false
</adjustNodeLabelFontSizeAutomatically>
<enablePorts>
false
</enablePorts>
<enableSIFTopologyGrouping>
false
</enableSIFTopologyGrouping>
<allowCompoundNodeResize>
false
</allowCompoundNodeResize>
<mapColorScheme>
opposed_purple_green
</mapColorScheme>
<mapColorSchemeStyle>
3D
</mapColorSchemeStyle>
<mapName>
PD map of the Drosophila cell cycle
</mapName>
<mapDescription>
doi:10.1371/journal.pcbi.1005740
</mapDescription>
<defaultInfoboxHeight>
12
</defaultInfoboxHeight>
<defaultInfoboxWidth>
8
</defaultInfoboxWidth>
<rearrangeAfterExpandCollapse>
true
</rearrangeAfterExpandCollapse>
</mapProperties>
</extension>
<glyph
id=
"nwtN_3ab42db3-7946-4642-a215-98b2f74f5061"
class=
"compartment"
>
<label
text=
"Cytoplasm"
/>
<bbox
x=
"456.79999999999995"
y=
"491.17499999999995"
w=
"210.40000000000003"
h=
"166.7"
/>
</glyph>
<glyph
id=
"nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815"
class=
"compartment"
compartmentRef=
"nwtN_3ab42db3-7946-4642-a215-98b2f74f5061"
>
<label
text=
"Nucleus"
/>
<bbox
x=
"478.625"
y=
"513"
w=
"166.75"
h=
"44.875"
/>
</glyph>
<glyph
id=
"35a3e0be-6e00-7a99-fca5-18ed65c2fac1"
class=
"macromolecule"
compartmentRef=
"nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815"
>
<label
text=
"String"
/>
<bbox
x=
"573.75"
y=
"521.25"
w=
"70"
h=
"35"
/>
<glyph
id=
"35a3e0be-6e00-7a99-fca5-18ed65c2fac1_0"
class=
"state variable"
>
<state
value=
"p"
/>
<bbox
x=
"609.85"
y=
"515.25"
w=
"16"
h=
"12"
/>
</glyph>
</glyph>
<glyph
id=
"0088e5e3-506d-b360-cc23-6ca191128211"
class=
"source and sink"
compartmentRef=
"nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815"
>
<bbox
x=
"480.25"
y=
"526.25"
w=
"25"
h=
"25"
/>
</glyph>
<glyph
id=
"d6a6f52d-8036-ba76-8a3e-dfa5dcd6d57e"
class=
"process"
compartmentRef=
"nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815"
>
<bbox
x=
"535.6056851311953"
y=
"535.1056851311953"
w=
"7.288629737609365"
h=
"7.288629737609365"
/>
<port
id=
"d6a6f52d-8036-ba76-8a3e-dfa5dcd6d57e.1"
x=
"534.1479591836735"
y=
"538.75"
/>
<port
id=
"d6a6f52d-8036-ba76-8a3e-dfa5dcd6d57e.2"
x=
"544.3520408163265"
y=
"538.75"
/>
</glyph>
<glyph
id=
"2f567801-fc2c-e128-f352-1dfab2f0dbce"
class=
"macromolecule"
compartmentRef=
"nwtN_3ab42db3-7946-4642-a215-98b2f74f5061"
>
<label
text=
"String"
/>
<bbox
x=
"573.75"
y=
"621.25"
w=
"70"
h=
"35"
/>
<glyph
id=
"2f567801-fc2c-e128-f352-1dfab2f0dbce_0"
class=
"state variable"
>
<state
value=
"p"
/>
<bbox
x=
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