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metexplore
MetExploreViz
Commits
88d8e224
Commit
88d8e224
authored
May 03, 2021
by
Jean-Clement Gallardo
Browse files
Finish hotfix/MappingInJSON
parents
d580f11e
67c4f86e
Changes
3
Hide whitespace changes
Inline
Side-by-side
resources/lib/functions/GraphMapping.js
View file @
88d8e224
...
...
@@ -23,7 +23,7 @@ metExploreD3.GraphMapping = {
mapNodeDataFile
:
function
(
mapping
,
objects
)
{
var
session
=
_metExploreViz
.
getSessionById
(
'
viz
'
);
var
force
=
session
.
getForce
();
force
.
stop
();
force
.
stop
();
var
myMask
=
metExploreD3
.
createLoadMask
(
"
Mapping in progress...
"
,
'
graphPanel
'
);
if
(
myMask
!=
undefined
){
metExploreD3
.
showMask
(
myMask
);
...
...
@@ -168,7 +168,7 @@ metExploreD3.GraphMapping = {
try
{
var
session
=
_metExploreViz
.
getSessionById
(
'
viz
'
);
var
force
=
session
.
getForce
();
force
.
stop
();
force
.
stop
();
var
networkData
=
session
.
getD3Data
();
var
conditions
=
mapping
.
getConditions
().
filter
(
function
(
c
)
{
return
c
!==
"
PathwayCoverage
"
&&
c
!==
"
PathwayEnrichment
"
...
...
@@ -284,10 +284,10 @@ metExploreD3.GraphMapping = {
* @throws error in function
*/
reloadMapping
:
function
(
mapping
)
{
var
session
=
_metExploreViz
.
getSessionById
(
'
viz
'
);
var
force
=
session
.
getForce
();
force
.
stop
();
force
.
stop
();
var
myMask
=
metExploreD3
.
createLoadMask
(
"
Mapping in progress...
"
,
'
graphPanel
'
);
if
(
myMask
!=
undefined
){
...
...
@@ -305,35 +305,35 @@ metExploreD3.GraphMapping = {
switch
(
mapping
.
getTargetLabel
())
{
case
"
reactionDBIdentifier
"
:
mapping
.
getData
().
forEach
(
function
(
map
)
{
if
(
typeof
map
.
getNode
()
==
"
object
"
)
node
=
networkData
.
getNodeByDbIdentifier
(
map
.
getNode
().
getDbIdentifier
()
);
if
(
typeof
map
==
"
object
"
)
node
=
networkData
.
getNodeByDbIdentifier
(
map
.
node
);
else
node
=
networkData
.
getNodeByDbIdentifier
(
map
.
getNode
()
);
node
=
networkData
.
getNodeByDbIdentifier
(
map
);
if
(
node
!=
undefined
)
{
var
mapNode
=
new
MappingData
(
node
,
mapping
.
get
Name
()
,
map
.
getC
onditionName
()
,
map
.
getM
apValue
()
);
var
mapNode
=
new
MappingData
(
node
,
map
.
map
pingName
,
map
.
c
onditionName
,
map
.
m
apValue
);
node
.
addMappingData
(
mapNode
);
links
=
networkData
.
getLinkByDBIdReaction
(
node
.
getDbIdentifier
()
);
links
=
networkData
.
getLinkByDBIdReaction
(
map
.
node
);
links
.
forEach
(
function
(
link
)
{
link
.
addMappingData
(
mapNode
);
})
})
;
}
});
break
;
case
"
reactionId
"
:
mapping
.
getData
().
forEach
(
function
(
map
)
{
if
(
typeof
map
.
getNode
()
==
"
object
"
)
var
node
=
networkData
.
getNodeById
(
map
.
getNode
().
getId
()
);
if
(
typeof
map
==
"
object
"
)
var
node
=
networkData
.
getNodeById
(
map
.
node
);
else
var
node
=
networkData
.
getNodeById
(
map
.
getNode
()
);
var
node
=
networkData
.
getNodeById
(
map
);
if
(
node
!=
undefined
)
{
var
mapNode
=
new
MappingData
(
node
,
mapping
.
get
Name
()
,
map
.
getC
onditionName
()
,
map
.
getM
apValue
()
);
var
mapNode
=
new
MappingData
(
node
,
map
.
map
pingName
,
map
.
c
onditionName
,
map
.
m
apValue
);
node
.
addMappingData
(
mapNode
);
links
=
networkData
.
getLinkByDBIdReaction
(
node
.
getDbIdentifier
()
);
links
=
networkData
.
getLinkByDBIdReaction
(
map
.
node
);
links
.
forEach
(
function
(
link
)
{
link
.
addMappingData
(
mapNode
);
})
...
...
@@ -343,13 +343,13 @@ metExploreD3.GraphMapping = {
case
"
metaboliteId
"
:
mapping
.
getData
().
forEach
(
function
(
map
)
{
if
(
typeof
map
.
getNode
()
==
"
object
"
)
var
node
=
networkData
.
getNodeById
(
map
.
getNode
().
getId
()
);
if
(
typeof
map
==
"
object
"
)
var
node
=
networkData
.
getNodeById
(
map
.
node
);
else
var
node
=
networkData
.
getNodeById
(
map
.
getNode
()
);
var
node
=
networkData
.
getNodeById
(
map
);
if
(
node
!=
undefined
)
{
var
mapNode
=
new
MappingData
(
node
,
mapping
.
get
Name
()
,
map
.
getC
onditionName
()
,
map
.
getM
apValue
()
);
var
mapNode
=
new
MappingData
(
node
,
map
.
map
pingName
,
map
.
c
onditionName
,
map
.
m
apValue
);
node
.
addMappingData
(
mapNode
);
}
});
...
...
@@ -357,13 +357,13 @@ metExploreD3.GraphMapping = {
case
"
metaboliteDBIdentifier
"
:
mapping
.
getData
().
forEach
(
function
(
map
)
{
if
(
typeof
map
.
getNode
()
==
"
object
"
)
var
node
=
networkData
.
getNodeByDbIdentifier
(
map
.
getNode
().
getDbIdentifier
()
);
if
(
typeof
map
==
"
object
"
)
var
node
=
networkData
.
getNodeByDbIdentifier
(
map
.
node
);
else
var
node
=
networkData
.
getNodeByDbIdentifier
(
map
.
getNode
()
);
var
node
=
networkData
.
getNodeByDbIdentifier
(
map
);
if
(
node
!=
undefined
)
{
var
mapNode
=
new
MappingData
(
node
,
mapping
.
get
Name
()
,
map
.
getC
onditionName
()
,
map
.
getM
apValue
()
);
var
mapNode
=
new
MappingData
(
node
,
map
.
map
pingName
,
map
.
c
onditionName
,
map
.
m
apValue
);
node
.
addMappingData
(
mapNode
);
}
});
...
...
@@ -400,6 +400,124 @@ metExploreD3.GraphMapping = {
},
1
);
}
},
// Initial function reloadMapping
// reloadMapping : function(mapping) {
//
// var session = _metExploreViz.getSessionById('viz');
// var force = session.getForce();
// force.stop();
// var myMask = metExploreD3.createLoadMask("Mapping in progress...", 'graphPanel');
// if(myMask!= undefined){
//
// metExploreD3.showMask(myMask);
// setTimeout(
// function() {
// try {
// var session = _metExploreViz.getSessionById('viz');
// var networkData = session.getD3Data();
// var conditions = mapping.getConditions().filter(function (c) {
// return c !== "PathwayCoverage" && c !== "PathwayEnrichment"
// });
// var node = undefined;
// var links = undefined;
// switch (mapping.getTargetLabel()) {
// case "reactionDBIdentifier":
// mapping.getData().forEach(function (map) {
// if (typeof map.getNode() == "object")
// node = networkData.getNodeByDbIdentifier(map.getNode().getDbIdentifier());
// else
// node = networkData.getNodeByDbIdentifier(map.getNode());
//
// if (node != undefined) {
// var mapNode = new MappingData(node, mapping.getName(), map.getConditionName(), map.getMapValue());
// node.addMappingData(mapNode);
//
// links = networkData.getLinkByDBIdReaction(node.getDbIdentifier());
// links.forEach(function (link) {
// link.addMappingData(mapNode);
// })
// }
// });
// break;
//
// case "reactionId":
// mapping.getData().forEach(function (map) {
// if (typeof map.getNode() == "object")
// var node = networkData.getNodeById(map.getNode().getId());
// else
// var node = networkData.getNodeById(map.getNode());
//
// if (node != undefined) {
// var mapNode = new MappingData(node, mapping.getName(), map.getConditionName(), map.getMapValue());
// node.addMappingData(mapNode);
//
// links = networkData.getLinkByDBIdReaction(node.getDbIdentifier());
// links.forEach(function (link) {
// link.addMappingData(mapNode);
// })
// }
// });
// break;
//
// case "metaboliteId":
// mapping.getData().forEach(function (map) {
// if (typeof map.getNode() == "object")
// var node = networkData.getNodeById(map.getNode().getId());
// else
// var node = networkData.getNodeById(map.getNode());
//
// if (node != undefined) {
// var mapNode = new MappingData(node, mapping.getName(), map.getConditionName(), map.getMapValue());
// node.addMappingData(mapNode);
// }
// });
// break;
//
// case "metaboliteDBIdentifier":
// mapping.getData().forEach(function (map) {
// if (typeof map.getNode() == "object")
// var node = networkData.getNodeByDbIdentifier(map.getNode().getDbIdentifier());
// else
// var node = networkData.getNodeByDbIdentifier(map.getNode());
//
// if (node != undefined) {
// var mapNode = new MappingData(node, mapping.getName(), map.getConditionName(), map.getMapValue());
// node.addMappingData(mapNode);
// }
// });
// break;
// case "inchi":
// // Blah
// break;
// default:
// metExploreD3.displayMessage("Warning", 'The type of node "' + mapping.getTargetLabel() + '" isn\'t know.')
// }
//
// metExploreD3.hideMask(myMask);
//
// var anim = session.isAnimated("viz");
// if (anim) {
// var force = session.getForce();
//
// force.alpha(force.alpha()).restart();
// }
// }
// catch (e) {
// e.functionUsed="reloadMapping";
// metExploreD3.hideMask(myMask);
//
// var anim=session.isAnimated("viz");
// if (anim) {
// var session = _metExploreViz.getSessionById('viz');
// var force = session.getForce();
//
// force.alpha(force.alpha()).restart();
// }
// throw e;
// }
// }, 1);
// }
// },
/***********************************************
* Mapping to discrete data
* This function will look at metabolites that have data
...
...
@@ -896,7 +1014,7 @@ metExploreD3.GraphMapping = {
return
"
translate(
"
+
d
.
x
+
"
,
"
+
d
.
y
+
"
) scale(1)
"
;
})
.
style
(
"
fill
"
,
"
white
"
);
vis
.
selectAll
(
"
g.node
"
)
.
filter
(
function
(
d
){
if
(
this
.
getAttribute
(
"
mapped
"
)
==
undefined
||
this
.
getAttribute
(
"
mapped
"
)
==
false
||
this
.
getAttribute
(
"
mapped
"
)
==
"
false
"
)
return
false
;
...
...
@@ -904,7 +1022,7 @@ metExploreD3.GraphMapping = {
})
.
attr
(
"
mapped
"
,
"
false
"
)
.
selectAll
(
"
rect.stroke
"
)
.
remove
();
.
remove
();
},
/***********************************************
...
...
@@ -954,14 +1072,14 @@ metExploreD3.GraphMapping = {
* @param {Function} func Callback function
*/
launchAfterMappingFunction
:
function
(
mappingId
,
func
)
{
var
mapping
=
_metExploreViz
.
getMappingById
(
mappingId
);
var
mapping
=
_metExploreViz
.
getMappingById
(
mappingId
);
if
(
mapping
!==
null
)
{
// the variable is defined
func
(
mapping
);
return
;
}
var
that
=
this
;
setTimeout
(
function
(){
that
.
launchAfterMappingFunction
(
mappingId
,
func
);},
100
);
setTimeout
(
function
(){
that
.
launchAfterMappingFunction
(
mappingId
,
func
);},
100
);
},
/***********************************************
...
...
@@ -996,7 +1114,7 @@ metExploreD3.GraphMapping = {
if
(
mappingJSON
){
var
session
=
_metExploreViz
.
getSessionById
(
'
viz
'
);
var
force
=
session
.
getForce
();
force
.
stop
();
force
.
stop
();
var
myMask
=
metExploreD3
.
createLoadMask
(
"
Mapping in progress...
"
,
'
graphPanel
'
);
if
(
myMask
!=
undefined
){
...
...
@@ -1052,7 +1170,7 @@ metExploreD3.GraphMapping = {
loadDataTSV
:
function
(
url
,
func
)
{
var
session
=
_metExploreViz
.
getSessionById
(
'
viz
'
);
var
force
=
session
.
getForce
();
force
.
stop
();
force
.
stop
();
var
myMask
=
metExploreD3
.
createLoadMask
(
"
Mapping in progress...
"
,
'
graphPanel
'
);
if
(
myMask
!=
undefined
){
...
...
@@ -1071,8 +1189,8 @@ metExploreD3.GraphMapping = {
var
array
=
[];
var
mapping
=
new
Mapping
(
title
,
arrayAttr
,
targetName
,
array
);
_metExploreViz
.
addMapping
(
mapping
);
_metExploreViz
.
addMapping
(
mapping
);
metExploreD3
.
GraphMapping
.
mapNodeDataFile
(
mapping
,
data
);
metExploreD3
.
fireEventArg
(
'
buttonMap
'
,
"
jsonmapping
"
,
mapping
);
...
...
@@ -1085,7 +1203,7 @@ metExploreD3.GraphMapping = {
var
force
=
session
.
getForce
();
force
.
alpha
(
force
.
alpha
()).
restart
();
}
}
});
}
},
...
...
@@ -2937,4 +3055,4 @@ metExploreD3.GraphMapping = {
}
});
}
};
\ No newline at end of file
};
resources/lib/functions/GraphPanel.js
View file @
88d8e224
...
...
@@ -348,7 +348,8 @@ metExploreD3.GraphPanel = {
if
(
jsonParsed
.
mappings
)
{
jsonParsed
.
mappings
.
forEach
(
function
(
mapping
){
var
mapping
=
new
Mapping
(
mapping
.
name
,
mapping
.
conditions
,
mapping
.
targetLabel
);
var
mapping
=
new
Mapping
(
mapping
.
name
,
mapping
.
conditions
,
mapping
.
targetLabel
,
mapping
.
data
);
mapping
.
data
=
mapping
.
id
;
_metExploreViz
.
addMapping
(
mapping
);
});
}
...
...
resources/lib/functions/GraphUtils.js
View file @
88d8e224
...
...
@@ -1356,6 +1356,7 @@ metExploreD3.GraphUtils = {
networkJSON
+=
"
,
\n\"
metaboliteStyle
\"
:
"
+
JSON
.
stringify
(
metExploreD3
.
getMetaboliteStyle
());
networkJSON
+=
"
,
\n\"
comparedPanels
\"
:
"
+
JSON
.
stringify
(
_metExploreViz
.
comparedPanels
);
networkJSON
+=
"
,
\n\"
linkedByTypeOfMetabolite
\"
:
"
+
JSON
.
stringify
(
_metExploreViz
.
linkedByTypeOfMetabolite
);
networkJSON
+=
"
,
\n\"
mappings
\"
:
"
+
JSON
.
stringify
(
_metExploreViz
.
mappings
);
networkJSON
+=
"
,
\n\"
sessions
\"
:{
"
;
...
...
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