Commit b08b7d5d authored by Jean-Clement Gallardo's avatar Jean-Clement Gallardo
Browse files

Fix GRID vs JSON network and sideCompounds bug

parent 2b9a0222
...@@ -75,6 +75,7 @@ Ext.define('metExploreViz.view.form.girForm.GirFormController', { ...@@ -75,6 +75,7 @@ Ext.define('metExploreViz.view.form.girForm.GirFormController', {
if (extract){ if (extract){
view.lookupReference('launchGIR').setText("launch GIR"); view.lookupReference('launchGIR').setText("launch GIR");
view.lookupReference('extractNQuit').disable(); view.lookupReference('extractNQuit').disable();
view.lookupReference('loadRankFile').enable();
metExploreD3.GraphRank.launchGIR = false; metExploreD3.GraphRank.launchGIR = false;
} }
......
...@@ -460,6 +460,9 @@ metExploreD3.GraphRank = { ...@@ -460,6 +460,9 @@ metExploreD3.GraphRank = {
if (link.source === react && link.target.duplicated === true){ if (link.source === react && link.target.duplicated === true){
networkData.removeNode(link.target); networkData.removeNode(link.target);
} }
if (link.source.duplicated === true && link.target === react){
networkData.removeNode(link.source);
}
}); });
react.sideCompoundsHidden = true; react.sideCompoundsHidden = true;
...@@ -639,16 +642,23 @@ metExploreD3.GraphRank = { ...@@ -639,16 +642,23 @@ metExploreD3.GraphRank = {
* @param {String} identifier node identifier * @param {String} identifier node identifier
*/ */
getIdentifier: function(identifier) { getIdentifier: function(identifier) {
if (identifier.slice(-2, -1) === "_"){ var session = _metExploreViz.getSessionById("viz");
return identifier.slice(0,-2); var networkData = session.getD3Data();
var node = networkData.getNodeByDbIdentifier(identifier);
if (node.getCompartment() !== "metaComp") {
if (identifier.slice(-2, -1) === "_"){
return identifier.slice(0,-2);
}
} }
else { if (node.getCompartment() === "metaComp") {
return identifier.slice(0, -1); return identifier;
} }
}, },
/******************************************* /*******************************************
* According to node identifier, get nodes from all compartments * According to node identifier, get nodes from all compartments if they exist
* @param {String} dbID node identifier * @param {String} dbID node identifier
*/ */
nodeForAll: function(dbID){ nodeForAll: function(dbID){
...@@ -665,7 +675,13 @@ metExploreD3.GraphRank = { ...@@ -665,7 +675,13 @@ metExploreD3.GraphRank = {
listIdentifier.push(identifier); listIdentifier.push(identifier);
} }
}); });
return listIdentifier; if (listIdentifier.length === 0){
listIdentifier.push(dbID);
return listIdentifier;
}
else {
return listIdentifier;
}
}, },
/******************************************* /*******************************************
...@@ -696,6 +712,32 @@ metExploreD3.GraphRank = { ...@@ -696,6 +712,32 @@ metExploreD3.GraphRank = {
} }
}, },
// side compounds functions
/*******************************************
* Set as side compounds nodes in the list
*/
setSideCompound: function(){
var session = _metExploreViz.getSessionById("viz");
var networkData = session.getD3Data();
var sideCompounds = ["M_h", "M_h2o", "M_atp", "M_pi", "M_adp", "M_nadp", "M_ppi", "M_nad", "M_nadph", "M_nadh",
"M_co2", "M_ACP", "M_amp", "M_glyc3p", "M_PGPm1", "M_apoACP", "M_biomass", "M_malACP", "M_nh4", "M_hco3",
"M_fe3", "M_o2", "M_cu2", "M_so4", "M_fe2", "M_mg2", "M_k", "M_mn2", "M_so3", "M_PGP", "M_zn2", "M_palmACP",
"M_ca2", "M_h2o2", "M_cobalt2", "M_cl", "M_h2s", "M_pppi", "M_rnatrans", "M_proteinsynth", "M_dnarep", "M_na1",
"M_pb", "M_hg2", "M_cd2", "M_seln", "M_aso4", "M_o2s", "M_aso3"];
sideCompounds.forEach(function(sideNode){
var listIdentifier = metExploreD3.GraphRank.nodeForAll(sideNode);
if (listIdentifier !== []){
listIdentifier.map(function(identifier){
var node = networkData.getNodeByDbIdentifier(identifier);
if (node !== undefined){
node.setIsSideCompound(true);
}
});
}
});
},
// rank style functions // rank style functions
/******************************************* /*******************************************
* Display style according to rank score of the node * Display style according to rank score of the node
...@@ -849,30 +891,6 @@ metExploreD3.GraphRank = { ...@@ -849,30 +891,6 @@ metExploreD3.GraphRank = {
}); });
}, },
// side compounds functions
/*******************************************
* Set as side compounds nodes in the list
*/
setSideCompound: function(){
var session = _metExploreViz.getSessionById("viz");
var networkData = session.getD3Data();
var sideCompounds = ["M_h", "M_h2o", "M_atp", "M_pi", "M_adp", "M_nadp", "M_ppi", "M_nad", "M_nadph", "M_nadh",
"M_co2", "M_ACP", "M_amp", "M_glyc3p", "M_PGPm1", "M_apoACP", "M_biomass", "M_malACP", "M_nh4", "M_hco3",
"M_fe3", "M_o2", "M_cu2", "M_so4", "M_fe2", "M_mg2", "M_k", "M_mn2", "M_so3", "M_PGP", "M_zn2", "M_palmACP",
"M_ca2", "M_h2o2", "M_cobalt2", "M_cl", "M_h2s", "M_pppi", "M_rnatrans", "M_proteinsynth", "M_dnarep", "M_na1",
"M_pb", "M_hg2", "M_cd2", "M_seln", "M_aso4", "M_o2s", "M_aso3"];
sideCompounds.forEach(function(sideNode){
var listIdentifier = metExploreD3.GraphRank.nodeForAll(sideNode);
if (listIdentifier !== []){
listIdentifier.map(function(identifier){
var node = networkData.getNodeByDbIdentifier(identifier);
node.setIsSideCompound(true);
});
}
});
},
// get nb hidden link // get nb hidden link
/******************************************* /*******************************************
* Check how many reaction is hidden from the node * Check how many reaction is hidden from the node
......
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