diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
index 4c2ea656faff5c2618285c743db096871c2f513f..f676f785ac447eb4f5549b45c52c0f65367738f5 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
@@ -10,6 +10,7 @@ import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
+import org.apache.commons.lang3.SerializationException;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.w3c.dom.Document;
@@ -116,7 +117,12 @@ public class PubmedParser extends CachableInterface implements IExternalService
*/
public Article getPubmedArticleById(Integer id) throws PubmedSearchException {
String queryString = "pubmed: " + id;
- Article result = articleSerializer.xmlToObject(getCacheNode(queryString));
+ Article result = null;
+ try {
+ result = articleSerializer.xmlToObject(getCacheNode(queryString));
+ } catch (SerializationException e) {
+ logger.warn("Problem with deserialization of the string: " + queryString);
+ }
if (result != null && result.getTitle() != null) {
return result;
} else {
diff --git a/frontend-js/src/main/css/global.css b/frontend-js/src/main/css/global.css
index da6f6288d13d1ecb9948cdb7a16e460282b43f28..a6b0e2f6d94be4f0e6995bf0b30db9e2390124ec 100644
--- a/frontend-js/src/main/css/global.css
+++ b/frontend-js/src/main/css/global.css
@@ -377,4 +377,8 @@ table.mapInfoBoxResultsTable, table.mapInfoBoxResultsTable th, table.mapInfoBoxR
.minerva-export-dual-listbox-container {
padding: 10px;
float: left;
+}
+
+table.minerva-publication-table td {
+ padding: 0px;
}
\ No newline at end of file
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index a12a922ce8834f4d06e74adb9de0a6f3340cdfd9..d109546174ff8b7e09a06f24c7edd84f22e9c184 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -1248,6 +1248,9 @@ ServerConnector.getPublications = function(params) {
var filterParams = {
start : params.start,
length : params.length,
+ sortColumn : params.sortColumn,
+ sortOrder : params.sortOrder,
+ search : params.search,
};
return self.getProjectId(params.projectId).then(function(result) {
queryParams.projectId = result;
diff --git a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
index 20b4711ee337120bb3e09d63a96e818d00fcc471..1ea977520e95076a6e0c62e6dedc77373e222afa 100644
--- a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
+++ b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
@@ -17,10 +17,11 @@ function PublicationListDialog(params) {
var self = this;
self.createPublicationListDialogGui();
$(self.getElement()).dialog({
+ title : "Publication list",
autoOpen : false,
resizable : false,
- width : window.innerWidth / 2,
- height : window.innerHeight / 2,
+ width : Math.max(window.innerWidth / 2, window.innerWidth - 100),
+ height : Math.max(window.innerHeight / 2, window.innerHeight - 100),
});
}
@@ -44,6 +45,7 @@ PublicationListDialog.prototype.createPublicationListDialogGui = function() {
});
var tableElement = Functions.createElement({
type : "table",
+ className : "minerva-publication-table",
style : "width: 100%",
});
@@ -56,9 +58,13 @@ PublicationListDialog.prototype.createPublicationListDialogGui = function() {
PublicationListDialog.prototype._dataTableAjaxCall = function(data, callback) {
var self = this;
+ logger.info(data);
return ServerConnector.getPublications({
start : data.start,
length : data.length,
+ sortColumn : self.getColumnsDefinition()[data.order[0].column].name,
+ sortOrder : data.order[0].dir,
+ search : data.search.value,
})
.then(
function(publicationList) {
@@ -114,11 +120,12 @@ PublicationListDialog.prototype.show = function() {
return new Promise(function(resolve) {
$(self.tableElement).dataTable({
serverSide : true,
- ordering : false,
- searching : false,
+ ordering : true,
+ searching : true,
ajax : function(data, callback, settings) {
resolve(self._dataTableAjaxCall(data, callback, settings));
},
+ columns : self.getColumnsDefinition(),
});
});
} else {
@@ -127,6 +134,22 @@ PublicationListDialog.prototype.show = function() {
};
+PublicationListDialog.prototype.getColumnsDefinition = function() {
+ return [ {
+ name : "pubmedId"
+ }, {
+ name : "authors"
+ }, {
+ name : "journal"
+ }, {
+ name : "year"
+ }, {
+ orderable : false,
+ searchable : false,
+ name : "elemnts"
+ } ]
+};
+
PublicationListDialog.prototype.destroy = function() {
$(this.getElement()).dialog("destroy");
};
diff --git a/frontend-js/src/test/js/gui/leftPanel/PublicationListDialog-test.js b/frontend-js/src/test/js/gui/leftPanel/PublicationListDialog-test.js
index 7810667ba34218ff4e271aeb29df707bfbec4e54..33f51cd8446f7f16b583b0bd5f3ceca8a91ac0ed 100644
--- a/frontend-js/src/test/js/gui/leftPanel/PublicationListDialog-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/PublicationListDialog-test.js
@@ -36,7 +36,9 @@ describe('PublicationListDialog', function() {
});
return dialog._dataTableAjaxCall({
start : 0,
- length : 10
+ length : 10,
+ order: [ { column: 0, dir: 'asc' } ],
+ search: { value: '', regex: false }
}, function(){
callbackCalled = true;
});
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/publications/length=10&sortColumn=pubmedId&sortOrder=asc&start=0&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/publications/length=10&sortColumn=pubmedId&sortOrder=asc&start=0&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..c4097f530ab19da4e3edd91af4671cbefe2bf98b
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/all/publications/length=10&sortColumn=pubmedId&sortOrder=asc&start=0&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+{"totalSize":1,"data":[{"elements":[{"modelId":15781,"id":153508,"type":"REACTION"}],"publication":{"resource":"123","link":"http://www.ncbi.nlm.nih.gov/pubmed/123","id":860355,"type":"PUBMED","article":{"title":"The importance of an innervated and intact antrum and pylorus in preventing postoperative duodenogastric reflux and gastritis.","authors":["Keighley MR"," Asquith P"," Edwards JA"," Alexander-Williams J."],"journal":"The British journal of surgery","year":1975,"link":"http://www.ncbi.nlm.nih.gov/pubmed/123","id":"123","citationCount":12,"stringAuthors":"Keighley MR, Asquith P, Edwards JA, Alexander-Williams J."}}}],"start":0,"length":1}
\ No newline at end of file