Merge pull request #388 from Rothamsted/20190722_mdjuly2019

fixes to #371 #374 #311
Rothamsted · Jul 31, 2019 · 00aef32 · 00aef32
2 parents 21a5820 + 71720b1
commit 00aef32
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Showing 4 changed files with 29 additions and 5 deletions.
diff --git a/common/client-base/src/main/webapp/html/css/style.css b/common/client-base/src/main/webapp/html/css/style.css
@@ -410,6 +410,9 @@ table.tablesorter thead tr .header {
 	background-repeat: no-repeat;
 	background-position: center right;
 	cursor: pointer;
+        position: sticky;
+        top: 0;
+        z-index: 999;
 }
 table.tablesorter tbody td {
 	color:#3D3D3D;
@@ -912,4 +915,4 @@ a.contact-button :hover {
 
 #genemap {
 	height: 620px;/*450px;*/
-}
+}
diff --git a/common/server-base/src/main/webapp/WEB-INF/views/evidencepage.jsp b/common/server-base/src/main/webapp/WEB-INF/views/evidencepage.jsp
@@ -1,3 +1,8 @@
+<%
+// added to overcome double quotes issue
+String keywords = request.getParameter("keyword");
+keywords = keywords.replaceAll("^\"|\"$", "###");
+%>
 <html>
 <head>
 <link rel="stylesheet" type="text/css" href="https://knetminer.rothamsted.ac.uk/KnetMaps/dist/css/knetmaps.css"/>
@@ -17,7 +22,7 @@
             },
             dataType: "json",
             data: JSON.stringify({
-                keyword: "${keyword}",
+                keyword: "<%=keywords%>",
                 list: ${list}
             })
         }).success(function (data) {

diff --git a/common/server-base/src/main/webapp/WEB-INF/views/genepage.jsp b/common/server-base/src/main/webapp/WEB-INF/views/genepage.jsp
@@ -1,3 +1,8 @@
+<%
+// added to overcome double quotes issue
+String keywords = request.getParameter("keyword");
+keywords = keywords.replaceAll("^\"|\"$", "###");
+%>
 <html>
 <head>
 <link rel="stylesheet" type="text/css" href="https://knetminer.rothamsted.ac.uk/KnetMaps/dist/css/knetmaps.css"/>
@@ -17,7 +22,7 @@
             },
             dataType: "json",
             data: JSON.stringify({
-                keyword: "${keyword}",
+                keyword: "<%=keywords%>",
                 list: ${list}
             })
         }).success(function (data) {

diff --git a/...e-ondexlocal/src/main/java/rres/knetminer/datasource/ondexlocal/OndexServiceProvider.java b/...e-ondexlocal/src/main/java/rres/knetminer/datasource/ondexlocal/OndexServiceProvider.java
@@ -644,6 +644,12 @@ public HashMap<ONDEXConcept, Float> searchLucene(String keywords, Collection<OND
 
         String keyword = keywords;
 
+        //added to overcome double quotes issue
+        //if changing this, need to change genepage.jsp and evidencepage.jsp
+        keyword = keyword.replaceAll("^###|###$", "\"");
+        log.debug("Keyword is:"+ keyword);
+
+
         // creates the NOT list (list of all the forbidden documents)
         String NOTQuery = createsNotList(keyword);
         String crossTypesNotQuery = "";
@@ -1349,12 +1355,12 @@ public int compare(String o1, String o2) {
             }
             //For each conceptName of the update list deletes and creates a new conceptName
             for (String ntc : namesToCreate.keySet()) {
-                if (!ntc.contains("</span>")) {
+//                if (!ntc.contains("</span>")) {
                     String newName = p.matcher(ntc).replaceAll(highlighter);
                     boolean isPref = namesToCreate.get(ntc);
                     concept.deleteConceptName(ntc);
                     concept.createConceptName(newName, isPref);
-                }
+//                }
             }
 
             // search in concept attributes
@@ -1402,6 +1408,11 @@ public ONDEXGraph findSemanticMotifs(Set<ONDEXConcept> seed, String keyword) {
         Set<ONDEXConcept> keywordConcepts = new HashSet<ONDEXConcept>();
         Set<EvidencePathNode> pathSet = new HashSet<EvidencePathNode>();
 
+
+        //added to overcome double quotes issue
+        //if changing this, need to change genepage.jsp and evidencepage.jsp
+        keyword = keyword.replaceAll("^###|###$", "\"");
+
         log.info("Keyword is: " + keyword);
         Set<String> keywords = "".equals(keyword) ? Collections.EMPTY_SET : this.parseKeywordIntoSetOfWords(keyword);
         Map<String, String> keywordColourMap = new HashMap<String, String>();