Merge pull request #1198 from JamesJeffryes/struct_to_image

Struct to image
kbase · Nov 3, 2017 · 7379868 · 7379868
2 parents ca1a111 + c29b94a
commit 7379868
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Showing 5 changed files with 37 additions and 13 deletions.
diff --git a/kbase-extension/static/kbase/js/widgets/function_output/modeling/KBModeling.js b/kbase-extension/static/kbase/js/widgets/function_output/modeling/KBModeling.js
@@ -44,7 +44,7 @@ function KBModeling(token) {
             method = 'fbaModelServices.'+method;
             return call_ajax(url, method, params)
         } else if (service == 'biochem') {
-            s_url = 'https://kbase.us/services/service_wizard';
+            s_url = window.kbconfig.urls.service_wizard || 'https://ci.kbase.us/services/service_wizard';
             s_params = {'module_name' : "BiochemistryAPI", 'version' : 'beta'};
             s_method = 'ServiceWizard.get_service_status';
             callback = function(service_status_ret) {

diff --git a/kbase-extension/static/kbase/js/widgets/function_output/modeling/KBaseBiochem.Media.js b/kbase-extension/static/kbase/js/widgets/function_output/modeling/KBaseBiochem.Media.js
@@ -35,6 +35,7 @@ function KBaseBiochem_Media(tabwidget) {
 
                         for (var i=0; i< self.mediacompounds.length; i++) {
                             var cpd = self.mediacompounds[i];
+                            cpd.img = tabwidget.compoundImage(cpd.id);
                             cpd.name = cpds[i].name;
                             cpd.formula = cpds[i].formula;
                             cpd.charge = cpds[i].charge;
@@ -54,6 +55,9 @@ function KBaseBiochem_Media(tabwidget) {
         return [{
             "label": "Compound",
             "data": cpd.id,
+        }, {
+        "label": "Image",
+            "data": cpd.img
         }, {
             "label": "Name",
             "data": cpd.name

diff --git a/kbase-extension/static/kbase/js/widgets/function_output/modeling/KBaseFBA.FBAModel.js b/kbase-extension/static/kbase/js/widgets/function_output/modeling/KBaseFBA.FBAModel.js
@@ -276,8 +276,6 @@ function KBaseFBA_FBAModel(modeltabs) {
 			console.log(rxn.rxnkbid);
 			var p = self.modeltabs.kbapi('biochem', 'get_reactions', {
 				reactions: [rxn.rxnkbid],
-				biochemistry: self.biochem,
-    			biochemistry_workspace: "kbase",
 			}).then(function(data) {
 				if ("deltaG" in data[0]) {
 					output.push({
@@ -331,27 +329,46 @@ function KBaseFBA_FBAModel(modeltabs) {
 
     this.CompoundTab = function (info) {
         var cpd = self.cpdhash[info.id];
+        console.log(cpd)
 		var output = [{
 			"label": "Compound",
 			"data": cpd.dispid,
-		}, {
+		},{
+            "label": "Image",
+            "data":  self.modeltabs.compoundImage(cpd.id) //"<img src=http://minedatabase.mcs.anl.gov/compound_images/ModelSEED/"+cpd.id.split("_")[0]+".png style='height:300px !important;'>"
+        }, {
 			"label": "Name",
 			"data": cpd.name
 		 }, {
 			"label": "Formula",
 			"data": cpd.formula
+		}, {
+            "label": "InChIKey",
+			"data": cpd.inchikey
+		}, {
+		    "label": "SMILES",
+			"data": cpd.smiles
 		}, {
 			"label": "Charge",
 			"data": cpd.charge
 		}, {
 			"label": "Compartment",
 			"data": self.cmphash[cpd.cmpkbid].name+" "+self.cmphash[cpd.cmpkbid].compartmentIndex,
 		}];
+		if (cpd.smiles && cpd.cpdkbid == "cpd00000") {
+		    var p = self.modeltabs.kbapi('biochem', 'depict_compounds', {structures: [cpd.smiles]
+		    }).then(function(data) {
+                    output[1] = {
+						"label": "Image",
+						"data": data[0]
+					};
+					return output;
+                });
+            return p;
+		}
 		if (cpd.cpdkbid != "cpd00000") {
 			var p = self.modeltabs.kbapi('biochem', 'get_compounds', {
 				compounds: [cpd.cpdkbid],
-				biochemistry: self.biochem,
-    			biochemistry_workspace: "kbase",
 			}).then(function(data) {
 				if ("deltaG" in data[0]) {
 					output.push({

diff --git a/kbase-extension/static/kbase/js/widgets/function_output/modeling/kbaseTabTable.js b/kbase-extension/static/kbase/js/widgets/function_output/modeling/kbaseTabTable.js
@@ -1,7 +1,7 @@
 'use strict';
 
-define(['kbwidget', 'jquery', 'bootstrap', 'kbaseAuthenticatedWidget', 'kbaseTabTableTabs', 'kbasePathways'],
-function(KBWidget, $, bootstrap, kbaseAuthenticatedWidget, kbaseTabTableTabs, kbasePathways) {
+define(['kbwidget', 'jquery', 'bootstrap', 'kbaseAuthenticatedWidget', 'kbaseTabTableTabs', 'kbasePathways', 'narrativeConfig'],
+function(KBWidget, $, bootstrap, kbaseAuthenticatedWidget, kbaseTabTableTabs, kbasePathways, Config) {
 return KBWidget({
     name: "kbaseTabTable",
     parent : kbaseAuthenticatedWidget,
@@ -409,18 +409,17 @@ return KBWidget({
         this.getBiochemCompounds = function(ids) {
             return self.kbapi('biochem', 'get_compounds', {compounds: ids})
         };
-
+        var imageURL = Config.url('compound_img_url');
         this.compoundImage = function(id) {
-            return 'http://bioseed.mcs.anl.gov/~chenry/jpeg/'+id+'.jpeg';
+            return "<img src="+imageURL+id.split("_")[0]+".png style='height:300px !important;'>"
         };
 
-        var imageURL = "http://bioseed.mcs.anl.gov/~chenry/jpeg/";
         this.pictureEquation = function(eq) {
             var cpds = get_cpds(eq);
 
             for (var i =0; i < cpds.left.length; i++) {
                 var cpd = cpds.left[i];
-                var img_url =  imageURL+cpd+'.jpeg';
+                var img_url =  imageURL+cpd+'.png';
                 panel.append('<div class="pull-left text-center">\
                                     <img src="'+img_url+'" width=150 ><br>\
                                     <div class="cpd-id" data-cpd="'+cpd+'">'+cpd+'</div>\
@@ -456,7 +455,7 @@ return KBWidget({
 
 
             var cpd_ids = cpds.left.concat(cpds.right);
-            var prom = self.kbapi('fba', 'get_compounds', {compounds: cpd_ids})
+            var prom = self.kbapi('biochem', 'get_compounds', {compounds: cpd_ids})
             $.when(prom).done(function(d){
                 var map = {};
                 for (var i in d) {

diff --git a/src/config.json b/src/config.json
@@ -33,6 +33,7 @@
         "awe": "https://appdev.kbase.us/services/awe-api",
         "catalog": "https://appdev.kbase.us/services/catalog",
         "cdn": "https://appdev.kbase.us/cdn/files",
+        "compound_img_url": "http://minedatabase.mcs.anl.gov/compound_images/ModelSEED/",
         "data_import_export": "https://appdev.kbase.us/services/data_import_export",
         "data_panel_sources": "/data_source_config.json",
         "fba": "https://appdev.kbase.us/services/KBaseFBAModeling/",
@@ -74,6 +75,7 @@
         "awe": "https://ci.kbase.us/services/awe-api",
         "catalog": "https://ci.kbase.us/services/catalog",
         "cdn": "https://ci.kbase.us/cdn/files",
+        "compound_img_url": "http://minedatabase.mcs.anl.gov/compound_images/ModelSEED/",
         "data_import_export": "https://ci.kbase.us/services/data_import_export",
         "data_panel_sources": "/data_source_config.json",
         "fba": "https://ci.kbase.us/services/KBaseFBAModeling/",
@@ -151,6 +153,7 @@
         "awe": "https://next.kbase.us/services/awe-api",
         "catalog": "https://next.kbase.us/services/catalog",
         "cdn": "https://next.kbase.us/cdn/files",
+        "compound_img_url": "http://minedatabase.mcs.anl.gov/compound_images/ModelSEED/",
         "data_import_export": "https://next.kbase.us/services/data_import_export",
         "data_panel_sources": "/data_source_config.json",
         "fba": "https://next.kbase.us/services/KBaseFBAModeling/",
@@ -192,6 +195,7 @@
         "awe": "https://kbase.us/services/awe-api",
         "catalog": "https://kbase.us/services/catalog",
         "cdn": "https://kbase.us/cdn/files",
+        "compound_img_url": "http://minedatabase.mcs.anl.gov/compound_images/ModelSEED/",
         "data_import_export": "https://kbase.us/services/data_import_export",
         "data_panel_sources": "/data_source_config.json",
         "fba": "https://kbase.us/services/KBaseFBAModeling/",