migrate code to use JsonUtil and JavaScriptFragment (#728)

LabKey · Feb 2, 2024 · e01e2f6 · e01e2f6
1 parent 5322bcf
commit e01e2f6
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Showing 8 changed files with 22 additions and 17 deletions.
diff --git a/flow/src/org/labkey/flow/controllers/editscript/CompensationCalculationPage.java b/flow/src/org/labkey/flow/controllers/editscript/CompensationCalculationPage.java
@@ -18,7 +18,9 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.fhcrc.cpas.flow.script.xml.*;
+import org.json.JSONArray;
 import org.labkey.api.query.FieldKey;
+import org.labkey.api.util.JavaScriptFragment;
 import org.labkey.flow.analysis.model.Analysis;
 import org.labkey.flow.analysis.model.AutoCompensationScript;
 import org.labkey.flow.analysis.model.Population;
@@ -217,11 +219,9 @@ public String javascriptArray(List<String> strings)
         return "['" + StringUtils.join(strings, "',\n'") + "']";
     }
 
-    public String javascriptArray(String... strings)
+    public JSONArray javascriptArray(String... strings)
     {
-        if (strings.length == 0)
-            return "[]";
-        return "['" + StringUtils.join(strings, "',\n'") + "']";
+        return new JSONArray(strings);
     }
 
     public String option(String value, String display, String currentValue)

diff --git a/flow/src/org/labkey/flow/controllers/editscript/editCompensationCalculation.jsp b/flow/src/org/labkey/flow/controllers/editscript/editCompensationCalculation.jsp
@@ -33,7 +33,7 @@
 <%=getScriptTag("/Flow/editCompensationCalculation.js")%>
 <script type="text/javascript" nonce="<%=getScriptNonce()%>">
 function o() { var o = {}; for (var i = 0; i < arguments.length; i += 2) o[arguments[i]] = arguments[i + 1]; return o; }
-var parameters = <%=text(javascriptArray(form.parameters))%>
+var parameters = <%= javascriptArray(form.parameters) %>
 var AutoComp = {};
 <%
     boolean hasAutoCompScripts = form.workspace.getAutoCompensationScripts().size() > 0;
@@ -45,7 +45,7 @@ var AutoComp = {};
         AutoCompensationScript.MatchingCriteria criteria = autoComp.getCriteria();
         if (criteria != null)
         {
-        %>'criteria' : <%=text(javascriptArray(criteria.getPrimaryKeyword(), criteria.getSecondaryKeyword(), criteria.getSecondaryValue()))%>,
+        %>'criteria' : <%=javascriptArray(criteria.getPrimaryKeyword(), criteria.getSecondaryKeyword(), criteria.getSecondaryValue())%>,
         <%
         }
 
@@ -54,8 +54,8 @@ var AutoComp = {};
         String and = "\n";
         for (AutoCompensationScript.ParameterDefinition param : autoComp.getParameters().values())
         {
-            %><%=text(and)%><%=q(param.getParameterName())%> : <%=text(javascriptArray(
-                param.getSearchKeyword(), param.getSearchValue(), param.getPositiveGate(), param.getNegativeGate()))%><%
+            %><%=text(and)%><%=q(param.getParameterName())%> : <%=javascriptArray(
+                param.getSearchKeyword(), param.getSearchValue(), param.getPositiveGate(), param.getNegativeGate())%><%
             and = ",\n";
         }
         %>}

diff --git a/flow/src/org/labkey/flow/controllers/run/StatusJsonHelper.java b/flow/src/org/labkey/flow/controllers/run/StatusJsonHelper.java
@@ -19,6 +19,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.Assert;
 import org.junit.Test;
+import org.labkey.api.util.JsonUtil;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -53,7 +54,7 @@ protected static String getStatusUrl(List<String> lines)
          }
          if(stringBuilder.length() > 0)
          {
-             ObjectMapper mapper = new ObjectMapper();
+             ObjectMapper mapper = JsonUtil.createDefaultMapper();
              mapper.configure(JsonParser.Feature.ALLOW_SINGLE_QUOTES, true);
              try
              {

diff --git a/flow/src/org/labkey/flow/controllers/well/showWell.jsp b/flow/src/org/labkey/flow/controllers/well/showWell.jsp
@@ -58,6 +58,7 @@
 <%@ page import="java.util.Map" %>
 <%@ page import="java.util.regex.Matcher" %>
 <%@ page import="java.util.regex.Pattern" %>
+<%@ page import="org.labkey.api.util.JavaScriptFragment" %>
 <%@ page extends="org.labkey.flow.controllers.well.WellController.Page" %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%!
@@ -346,10 +347,10 @@ Ext.onReady(function()
     }
 });
 
-var statistics = <%=unsafe(jsonStats.toString())%>;
+var statistics = <%=JavaScriptFragment.unsafe(jsonStats.toString())%>;
 var treeData;
 var stats;
-var keywords = <%=unsafe(jsonKeywords.toString())%>;
+var keywords = <%=JavaScriptFragment.unsafe(jsonKeywords.toString())%>;
 </script>
 <table class="lk-fields-table"><%
 

diff --git a/flow/src/org/labkey/flow/reports/statPicker.jsp b/flow/src/org/labkey/flow/reports/statPicker.jsp
@@ -30,6 +30,7 @@
 <%@ page import="java.util.Collection" %>
 <%@ page import="java.util.Map" %>
 <%@ page import="java.util.stream.Stream" %>
+<%@ page import="org.labkey.api.util.JavaScriptFragment" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%!
     @Override
@@ -379,7 +380,7 @@ function createStatStore(stats)
 
 let FlowPropertySet = {};
 FlowPropertySet.keywords = <%=toJsonArray(fps.getVisibleKeywords())%>;
-FlowPropertySet.statistics = <%=unsafe(jsonStats.toString())%>;
+FlowPropertySet.statistics = <%=JavaScriptFragment.unsafe(jsonStats.toString())%>;
 
 let SampleType = {};
 SampleType.properties = <%=toJsonArray(sampleTypeProperties)%>;

diff --git a/flow/src/org/labkey/flow/view/ExportAnalysisManifest.java b/flow/src/org/labkey/flow/view/ExportAnalysisManifest.java
@@ -25,6 +25,7 @@
 import org.json.JSONObject;
 import org.junit.Assert;
 import org.junit.Test;
+import org.labkey.api.util.JsonUtil;
 import org.labkey.flow.analysis.model.SampleIdMap;
 
 import java.io.IOException;
@@ -136,7 +137,7 @@ public String toJSON()
         {
             StringWriter sw = new StringWriter();
             JsonGenerator jsonGen = new JsonFactory().createGenerator(sw);
-            ObjectMapper oc = new ObjectMapper();
+            ObjectMapper oc = JsonUtil.createDefaultMapper();
             String dateFormat = "yyyy-MM-dd HH:mm:ss";
             DateFormat df = new SimpleDateFormat(dateFormat);
             oc.setDateFormat(df);

diff --git a/flow/src/org/labkey/flow/view/setComment.jsp b/flow/src/org/labkey/flow/view/setComment.jsp
@@ -69,7 +69,7 @@ LABKEY.requiresExt3(function() {
 
                 this.statusMessage('loading', "Updating...");
                 Ext.Ajax.request({
-                    url: "<%=unsafe(setFlagUrl.toString())%>&comment=" + encodeURIComponent(textField.getValue()),
+                    url: <%=q(setFlagUrl + "&comment=")%> + encodeURIComponent(textField.getValue()),
                     method : 'POST',
                     success: function (response) {
                         this.statusMessage('success', "Comment updated");

diff --git a/nab/src/org/labkey/nab/view/nabQC.jsp b/nab/src/org/labkey/nab/view/nabQC.jsp
@@ -31,6 +31,8 @@
 <%@ page import="static org.labkey.api.util.DOM.cl" %>
 <%@ page import="static org.labkey.api.util.DOM.DIV" %>
 <%@ page import="static org.labkey.api.util.DOM.createHtml" %>
+<%@ page import="org.labkey.api.util.JsonUtil" %>
+<%@ page import="org.labkey.api.util.JavaScriptFragment" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%!
     @Override
@@ -43,7 +45,6 @@
     JspView<NabAssayController.NabQCForm> me = (JspView<NabAssayController.NabQCForm>) HttpView.currentView();
     NabAssayController.NabQCForm bean = me.getModelBean();
     DilutionAssayRun assay = bean.getAssay();
-    ObjectMapper jsonMapper = new ObjectMapper();
     HtmlString errorMsg = HtmlString.EMPTY_STRING;
 
     // run properties array
@@ -95,8 +96,8 @@
                 runId       : <%=bean.getRunId()%>,
                 returnUrl   : <%=q(bean.getReturnUrl(getContainer()))%>,
                 runName     : <%=q(assay.getRunName())%>,
-                runProperties : <%=unsafe(jsonMapper.writeValueAsString(runProperties))%>,
-                controlProperties : <%=unsafe(jsonMapper.writeValueAsString(controlProperties))%>
+                runProperties : <%=JavaScriptFragment.asJson(runProperties)%>,
+                controlProperties : <%=JavaScriptFragment.asJson(controlProperties)%>
             });
         });
 </script><%