From 9bb9cb84c1a30c909dbcc6273e685daece08abf1 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 11 Apr 2017 13:12:20 +0200
Subject: [PATCH] list of publications contain also information about element
---
.../src/main/js/gui/PublicationListDialog.js | 78 +++++++++++++------
.../src/test/js/gui/ProjectInfoPanel-test.js | 12 +--
.../test/js/gui/PublicationListDialog-test.js | 26 ++++---
...9171&projectId=sample&token=MOCK_TOKEN_ID& | 1 +
.../projectId=sample&token=MOCK_TOKEN_ID& | 2 +-
...3508&projectId=sample&token=MOCK_TOKEN_ID& | 1 +
6 files changed, 77 insertions(+), 43 deletions(-)
create mode 100644 frontend-js/testFiles/apiCalls/project/getElements/columns=&id=329166,329171&projectId=sample&token=MOCK_TOKEN_ID&
create mode 100644 frontend-js/testFiles/apiCalls/project/getReactions/columns=&id=153508&projectId=sample&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/src/main/js/gui/PublicationListDialog.js b/frontend-js/src/main/js/gui/PublicationListDialog.js
index e77cde3e39..a377671f60 100644
--- a/frontend-js/src/main/js/gui/PublicationListDialog.js
+++ b/frontend-js/src/main/js/gui/PublicationListDialog.js
@@ -1,9 +1,14 @@
"use strict";
+var Promise = require("bluebird");
+
/* exported logger */
var AbstractGuiElement = require('./AbstractGuiElement');
+var Alias = require('../map/data/Alias');
var GuiConnector = require('../GuiConnector');
+var IdentifiedElement = require('../map/data/IdentifiedElement');
+var Reaction = require('../map/data/Reaction');
var Functions = require('../functions');
var logger = require('../logger');
@@ -15,6 +20,8 @@ function PublicationListDialog(params) {
$(self.getElement()).dialog({
autoOpen : false,
resizable : false,
+ width : window.innerWidth / 2,
+ height : window.innerHeight / 2,
});
}
@@ -49,34 +56,55 @@ PublicationListDialog.prototype.createPublicationListDialogGui = function() {
};
PublicationListDialog.prototype._dataTableAjaxCall = function(data, callback, settings) {
- logger.debug(data);
+ var self = this;
return ServerConnector.getPublications({
start : data.start,
length : data.length
- }).then(function(publicationList) {
- var out = [];
- console.log(publicationList);
- for (var i=0;i<publicationList.data.length;i++) {
- var publication = publicationList.data[i].publication;
-
- var row = [];
- row[0] = "<a href='"+publication.link+"'>"+publication.id+"</a>";
- row[1] = publication.title;
- row[2] = publication.authors.join();
- row[3] = publication.journal;
- row[4] = publication.year;
- row[5] = "xxx";
- out.push(row);
- }
- logger.debug(out);
- callback({
- draw : data.draw,
- recordsTotal : publicationList.totalSize,
- recordsFiltered : publicationList.totalSize,
- data : out,
- });
- return null;
- });
+ })
+ .then(
+ function(publicationList) {
+ var out = [];
+ var allElements = [];
+ for (var i = 0; i < publicationList.data.length; i++) {
+ var publication = publicationList.data[i].publication;
+ var elements = publicationList.data[i].elements;
+
+ var row = [];
+ row[0] = "<a href='" + publication.link + "'>" + publication.id + "</a>";
+ row[1] = publication.title;
+ row[2] = publication.authors.join();
+ row[3] = publication.journal;
+ row[4] = publication.year;
+ row[5] = "<div>";
+ for (var j = 0; j < elements.length; j++) {
+ row[5] += "<a name='" + elements[j].id + "' href='#'>" + elements[j].type + ":" + elements[j].id
+ + "</a>, ";
+ allElements.push(new IdentifiedElement(elements[j]));
+ }
+ row[5] += "</div>";
+ out.push(row);
+ }
+ callback({
+ draw : data.draw,
+ recordsTotal : publicationList.totalSize,
+ recordsFiltered : publicationList.totalSize,
+ data : out,
+ });
+ var promises = [];
+ allElements.forEach(function(element) {
+ promises.push(self.getMap().getSubmodelById(element.getModelId()).getModel().getByIdentifiedElement(
+ element, true).then(function(elementData) {
+ var name = null
+ if (elementData instanceof Alias) {
+ name = elementData.getName();
+ } else if (elementData instanceof Reaction) {
+ name = elementData.getReactionId();
+ }
+ $("a[name=" + elementData.getId() + "]", $(self.getElement())).html(name);
+ }));
+ });
+ return Promise.all(promises);
+ });
};
PublicationListDialog.prototype.show = function() {
diff --git a/frontend-js/src/test/js/gui/ProjectInfoPanel-test.js b/frontend-js/src/test/js/gui/ProjectInfoPanel-test.js
index c1b6ac5cff..38661467d0 100644
--- a/frontend-js/src/test/js/gui/ProjectInfoPanel-test.js
+++ b/frontend-js/src/test/js/gui/ProjectInfoPanel-test.js
@@ -50,12 +50,14 @@ describe('ProjectInfoPanel', function() {
});
it('show publication list', function() {
- var div = testDiv;
- var panel = new ProjectInfoPanel({
- element : div,
- customMap : helper.createCustomMap(),
+ return ServerConnector.getProject().then(function(project) {
+ var div = testDiv;
+ var panel = new ProjectInfoPanel({
+ element : div,
+ customMap : helper.createCustomMap(project),
+ });
+ return panel.showPublicationListDialog();
});
- return panel.showPublicationListDialog();
});
});
diff --git a/frontend-js/src/test/js/gui/PublicationListDialog-test.js b/frontend-js/src/test/js/gui/PublicationListDialog-test.js
index da0de3e546..cdbf05695c 100644
--- a/frontend-js/src/test/js/gui/PublicationListDialog-test.js
+++ b/frontend-js/src/test/js/gui/PublicationListDialog-test.js
@@ -27,22 +27,24 @@ describe('PublicationListDialog', function() {
customMap : map
});
assert.equal(logger.getWarnings().length, 0);
-
+
dialog.destroy();
});
it('_dataTableAjaxCall', function() {
- var div = testDiv;
- var dialog = new PublicationListDialog({
- element : div,
- customMap : helper.createCustomMap(),
- });
- return dialog._dataTableAjaxCall({
- start : 0,
- length : 10
- }, function() {
- }, {}).then(function(){
- dialog.destroy();
+ return ServerConnector.getProject().then(function(project) {
+ var div = testDiv;
+ var dialog = new PublicationListDialog({
+ element : div,
+ customMap : helper.createCustomMap(project),
+ });
+ return dialog._dataTableAjaxCall({
+ start : 0,
+ length : 10
+ }, function() {
+ }, {}).then(function() {
+ dialog.destroy();
+ });
});
});
diff --git a/frontend-js/testFiles/apiCalls/project/getElements/columns=&id=329166,329171&projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/project/getElements/columns=&id=329166,329171&projectId=sample&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..5ddb6b2880
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/project/getElements/columns=&id=329166,329171&projectId=sample&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"formerSymbols":[],"references":[],"modelId":15781,"synonyms":[],"description":"","type":"Protein","name":"gfsdhj","bounds":{"x":160.0,"y":332.0,"width":119.0,"height":63.0},"id":329171},{"symbol":"CNC","formerSymbols":[],"references":[{"name":"REACT_20130","type":"Reactome","link":"http://www.reactome.org/PathwayBrowser/#REACT_20130","idObject":860342},{"name":"2141","type":"HGNC","link":"http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id\u003d2141","idObject":860343},{"name":"6546","type":"Kegg Genes","idObject":860344},{"name":"NP_001106272.1","type":"RefSeq","link":"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val\u003dNP_001106272.1","idObject":860345},{"name":"NP_001106271.1","type":"RefSeq","link":"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val\u003dNP_001106271.1","idObject":860346},{"name":"NP_001106273.1","type":"RefSeq","link":"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val\u003dNP_001106273.1","idObject":860347},{"name":"NP_001239553.1","type":"RefSeq","link":"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val\u003dNP_001239553.1","idObject":860348},{"name":"PA314","type":"PharmGKB Pathways","link":"http://www.pharmgkb.org/pathway/PA314","idObject":860349},{"name":"NP_066920.1","type":"RefSeq","link":"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val\u003dNP_066920.1","idObject":860350},{"name":"6546","type":"Entrez Gene","link":"http://www.ncbi.nlm.nih.gov/gene/6546","idObject":860351}],"modelId":15781,"synonyms":["CNC","NCX1"],"description":"ymbol: CNC\r\nghfjkghfdjkghkdf\r\nfdghjkfdhgjkdfgjhdf\r\njdsfkljsdklfjsdf\r\nsjdkfjsdklfjkl\r\ndsjfkjl\r\nsdfkkjfskldjfkls\r\n\nRecName: Full\u003dSodium/calcium exchanger 1; AltName: Full\u003dNa(+)/Ca(2+)-exchange protein 1; Flags: Precursor;","fullName":"Carney complex, multiple neoplasia and lentiginosis","type":"Protein","name":"CNC","bounds":{"x":11.0,"y":236.0,"width":118.0,"height":66.0},"id":329166}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/project/getMetaData/projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/project/getMetaData/projectId=sample&token=MOCK_TOKEN_ID&
index fa052d1df6..4a62ac3988 100644
--- a/frontend-js/testFiles/apiCalls/project/getMetaData/projectId=sample&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/project/getMetaData/projectId=sample&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"version":"0","idObject":14898,"name":"UNKNOWN DISEASE MAP","projectId":"sample","description":"","map":{"name":"UNKNOWN DISEASE MAP2","idObject":15781,"tileSize":256,"width":1305,"height":473,"minZoom":2,"maxZoom":5,"layouts":[{"modelId":15781,"name":"Pathways and compartments","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_nested0","creator":"","inputDataAvailable":"false","idObject":14081},{"modelId":15781,"name":"Network","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_normal0","creator":"","inputDataAvailable":"false","idObject":14082},{"modelId":15781,"name":"Empty","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_empty0","creator":"","inputDataAvailable":"false","idObject":14083}],"submodels":[],"centerLatLng":{"lat":79.18277721779353,"lng":-135.06093781915757},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":81.26928406550978,"lng":-90.0}},"overviewImageViews":[]}
\ No newline at end of file
+{"version":"0","idObject":15781,"name":"UNKNOWN DISEASE MAP","projectId":"sample","description":"","map":{"name":"UNKNOWN DISEASE MAP2","idObject":15781,"tileSize":256,"width":1305,"height":473,"minZoom":2,"maxZoom":5,"layouts":[{"modelId":15781,"name":"Pathways and compartments","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_nested0","creator":"","inputDataAvailable":"false","idObject":14081},{"modelId":15781,"name":"Network","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_normal0","creator":"","inputDataAvailable":"false","idObject":14082},{"modelId":15781,"name":"Empty","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_empty0","creator":"","inputDataAvailable":"false","idObject":14083}],"submodels":[],"centerLatLng":{"lat":79.18277721779353,"lng":-135.06093781915757},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":81.26928406550978,"lng":-90.0}},"overviewImageViews":[]}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/project/getReactions/columns=&id=153508&projectId=sample&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/project/getReactions/columns=&id=153508&projectId=sample&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..3ecad6cdb4
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/project/getReactions/columns=&id=153508&projectId=sample&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"modelId":15781,"reactants":"329166","reactionId":"re21","id":153508,"type":"State transition","lines":[{"start":{"x":129.00000000000003,"y":269.9853478599471},"end":{"x":217.3857151822324,"y":271.4614610007049},"type":"START"},{"start":{"x":217.3857151822324,"y":271.4614610007049},"end":{"x":217.98919008325365,"y":297.73178548394236},"type":"MIDDLE"},{"start":{"x":218.17291548409574,"y":305.7296755167626},"end":{"x":218.77639038511697,"y":332.0},"type":"END"}],"modifiers":"","centerPoint":{"x":218.0810527836747,"y":301.7307305003525},"products":"329171"}]
\ No newline at end of file
--
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