Issue 53306: Some LKS forms don't distinguish between fields properly

elispotassay/src/org/labkey/elispot/query/ElispotRunDataTable.java

@@ -170,7 +170,7 @@ public List<FieldKey> getDefaultVisibleColumns()
         FieldKey runPropFieldKey = FieldKey.fromParts("Run");
         fieldKeys.add(FieldKey.fromParts(runPropFieldKey, FieldKey.fromString("ProtocolName")));
         fieldKeys.add(FieldKey.fromParts(runPropFieldKey, FieldKey.fromString("PlateReader")));
-        fieldKeys.add(FieldKey.fromParts(runPropFieldKey,  FieldKey.fromString("Batch"), FieldKey.fromString("TargetStudy")));
+        fieldKeys.add(FieldKey.fromParts(runPropFieldKey,  FieldKey.fromString("Batch"), FieldKey.fromString(AbstractAssayProvider.TARGET_STUDY_PROPERTY_NAME)));
         return fieldKeys;
     }
 

flow/src/org/labkey/flow/controllers/executescript/confirmRunsToImport.jsp

@@ -30,6 +30,7 @@
 <%@ page import="java.util.LinkedHashMap" %>
 <%@ page import="java.util.Map" %>
 <%@ page import="java.util.Set" %>
+<%@ page import="org.labkey.api.assay.AbstractAssayProvider" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
     JspView<ImportRunsForm> me = HttpView.currentView();
@@ -86,8 +87,8 @@
                 to look up specimen information from the target study's specimen repository.
             </p>
             <p class="labkey-indented">
-                <label for="targetStudy">Optionally, choose a target study folder:</label><br>
-                <select id="targetStudy" name="targetStudy">
+                <label for="<%= h(AbstractAssayProvider.TARGET_STUDY_PROPERTY_NAME)%>">Optionally, choose a target study folder:</label><br>
+                <select id="<%= h(AbstractAssayProvider.TARGET_STUDY_PROPERTY_NAME)%>" name="<%= h(AbstractAssayProvider.TARGET_STUDY_PROPERTY_NAME)%>">
                     <labkey:options value="<%=unsafe(form.getTargetStudy())%>" map="<%=targetStudies%>"/>
                 </select>
             </p>

flow/src/org/labkey/flow/controllers/executescript/importAnalysisChooseAnalysis.jsp

@@ -36,6 +36,7 @@
 <%@ page import="java.util.List" %>
 <%@ page import="java.util.Map" %>
 <%@ page import="java.util.Set" %>
+<%@ page import="org.labkey.api.assay.AbstractAssayProvider" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%
@@ -233,11 +234,8 @@ if (form.getKeywordDir() != null && form.getKeywordDir().length > 0 && StudyPubl
         <div style="padding-left: 2em; padding-bottom: 1em;">
             <br>
             Choose a target study folder:<br>
-            <%=select().name("targetStudy").className(null).addOptions(targetStudies).selected(unsafe(form.getTargetStudy())).onChange("document.getElementById('studyChanged').value = true;")
+            <%=select().name(AbstractAssayProvider.TARGET_STUDY_PROPERTY_NAME).className(null).addOptions(targetStudies).selected(unsafe(form.getTargetStudy())).onChange("document.getElementById('studyChanged').value = true;")
             %>
-<%--            <select id="targetStudy" name="targetStudy">--%>
-<%--                <labkey:options value="<%=text(form.getTargetStudy())%>" map="<%=targetStudies%>"/>--%>
-<%--            </select>--%>
             <br><br>
         </div>
         <%

flow/src/org/labkey/flow/controllers/executescript/importAnalysisConfirm.jsp

@@ -42,6 +42,7 @@
 <%@ page import="java.util.Map" %>
 <%@ page import="java.util.Set" %>
 <%@ page import="static org.labkey.flow.controllers.executescript.AnalysisScriptController.BACK_BUTTON_ACTION" %>
+<%@ page import="org.labkey.api.assay.AbstractAssayProvider" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
     ImportAnalysisForm form = (ImportAnalysisForm)getModelBean();
@@ -93,7 +94,7 @@
 <input type="hidden" name="existingAnalysisId" id="existingAnalysisId" value="<%=form.getExistingAnalysisId()%>">
 <% } %>
 
-<input type="hidden" name="targetStudy" id="targetStudy" value="<%=h(form.getTargetStudy())%>">
+<input type="hidden" name="<%= h(AbstractAssayProvider.TARGET_STUDY_PROPERTY_NAME)%>" id="<%= h(AbstractAssayProvider.TARGET_STUDY_PROPERTY_NAME)%>" value="<%=h(form.getTargetStudy())%>">
 
 <p>You are about to import the analysis from the workspace with the following settings:</p>
 <%

flow/src/org/labkey/flow/data/FlowProperty.java

@@ -16,6 +16,7 @@
 
 package org.labkey.flow.data;
 
+import org.labkey.api.assay.AbstractAssayProvider;
 import org.labkey.api.exp.PropertyType;
 import org.labkey.api.exp.property.SystemProperty;
 
@@ -35,7 +36,7 @@ abstract public class FlowProperty
     static public final SystemProperty AnalysisEngine = new SystemProperty(PROPERTY_BASE + "AnalysisEngine", PropertyType.STRING);
 
     // Property on FlowRun ExpRun object: container id of target study
-    static public final SystemProperty TargetStudy = new SystemProperty(PROPERTY_BASE + "TargetStudy", PropertyType.STRING);
+    static public final SystemProperty TargetStudy = new SystemProperty(PROPERTY_BASE + AbstractAssayProvider.TARGET_STUDY_PROPERTY_NAME, PropertyType.STRING);
 
     // Property on FlowFCSFile ExpData object: true when the FlowFCSFile was created from an external analysis (extracted from FlowJo workspace or analysis archive)
     //static public final SystemProperty ExtraKeywordsFCSFile = new SystemProperty(PROPERTY_BASE + "ExtraKeywordsFCSFile", PropertyType.BOOLEAN);

flow/src/org/labkey/flow/query/FCSFileCoalescingColumn.java

@@ -16,6 +16,7 @@
 package org.labkey.flow.query;
 
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.assay.AbstractAssayProvider;
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.JdbcType;
 import org.labkey.api.data.SQLFragment;
@@ -74,7 +75,7 @@ public FCSFileCoalescingColumn(TableInfo parent, FieldKey key, JdbcType type, @N
                 _dateFieldKeys = Pair.of(dateFieldKey, FlowSchema.rewriteAsOriginalFCSFile(dateFieldKey));
         }
 
-        FieldKey targetStudyFieldKey = relativeFromFCSFile ? FieldKey.fromParts("Run", "TargetStudy") : FieldKey.fromParts("FCSFile", "Run", "TargetStudy");
+        FieldKey targetStudyFieldKey = relativeFromFCSFile ? FieldKey.fromParts("Run", AbstractAssayProvider.TARGET_STUDY_PROPERTY_NAME) : FieldKey.fromParts("FCSFile", "Run", "TargetStudy");
         _targetStudyFieldKeys = Pair.of(targetStudyFieldKey, FlowSchema.rewriteAsOriginalFCSFile(targetStudyFieldKey));
     }
 

flow/src/org/labkey/flow/reports/FilterFlowReport.java

@@ -197,7 +197,7 @@ void addScriptProlog(ViewContext context, StringBuffer sb)
     private String oldLegalName(FieldKey fkey)
     {
         String r = AliasManager.makeLegalName(StringUtils.join(fkey.getParts(), "_"), FlowManager.get().getSchema().getSqlDialect(), false);
-        return ColumnInfo.propNameFromName(r).toLowerCase();
+        return ColumnInfo.legalNameFromName(r).toLowerCase();
     }
 
     protected void convertDateColumn(CachedResultSet rs, String fromCol, String toCol) throws SQLException

luminex/src/org/labkey/luminex/LuminexDataHandler.java

@@ -141,7 +141,7 @@ public class LuminexDataHandler extends AbstractExperimentDataHandler implements
     public static final String QC_FLAG_SINGLE_POINT_CONTROL_ID = "SinglePointControlId";   // Column name to use in createQCFlagEnabledSQLFragment
     public static final String POSITIVITY_THRESHOLD_COLUMN_NAME = "PositivityThreshold";
     public static final String POSITIVITY_THRESHOLD_DISPLAY_NAME = "Positivity Threshold";
-    public static final String CALCULATE_POSITIVITY_COLUMN_NAME = "calculatePositivity";
+    public static final String CALCULATE_POSITIVITY_COLUMN_NAME = "CalculatePositivity";
     public static final String NEGATIVE_CONTROL_COLUMN_NAME = "NegativeControl";
     public static final String NEGATIVE_BEAD_COLUMN_NAME = "NegativeBead";
     public static final String NEGATIVE_BEAD_DISPLAY_NAME = "Subtract Negative Bead";

luminex/src/org/labkey/luminex/LuminexRunUploadForm.java

@@ -268,7 +268,7 @@ public List<Titration> getTitrations() throws ExperimentException
             titration.setName(titrationName);
             for (Titration.Type type : Titration.Type.values())
             {
-                String propertyName = LuminexUploadWizardAction.getTitrationTypeCheckboxName(type, titration);
+                String propertyName = LuminexUploadWizardAction.getTitrationTypeCheckboxNameAndId(type, titration);
                 if (getViewContext().getRequest().getParameter(propertyName) != null)
                 {
                     String hiddenValue = getViewContext().getRequest().getParameter(propertyName);
@@ -293,7 +293,7 @@ public List<SinglePointControl> getSinglePointControls() throws ExperimentExcept
         {
             SinglePointControl singlePointControl = new SinglePointControl();
             singlePointControl.setName(singlePointControlName);
-            String propertyName = LuminexUploadWizardAction.getSinglePointControlCheckboxName(singlePointControlName);
+            String propertyName = LuminexUploadWizardAction.getSinglePointControlCheckboxNameAndId(singlePointControlName);
             if (StringUtils.isNotBlank(getViewContext().getRequest().getParameter(propertyName)))
             {
                 result.add(singlePointControl);

luminex/src/org/labkey/luminex/LuminexUploadWizardAction.java

@@ -60,6 +60,7 @@
 import org.labkey.api.view.JspView;
 import org.labkey.api.view.VBox;
 import org.labkey.api.view.ViewServlet;
+import org.labkey.api.view.template.PageConfig;
 import org.labkey.api.writer.HtmlWriter;
 import org.labkey.luminex.model.Analyte;
 import org.labkey.luminex.model.SinglePointControl;
@@ -324,7 +325,7 @@ else if (analyteDefaultValue != null)
             }
 
             Titration existingTitration = existingTitrations.get(titrationEntry.getKey());
-            String propertyName = getTitrationTypeCheckboxName(Titration.Type.standard, titrationEntry.getValue());
+            String propertyName = getTitrationTypeCheckboxNameAndId(Titration.Type.standard, titrationEntry.getValue());
             // If we have an existing titration as a baseline from the run we're replacing, use its value
             String defVal = existingTitration == null ? defaultWellRoleValues.get(propertyName) : Boolean.toString(existingTitration.isStandard());
 
@@ -359,7 +360,7 @@ else if (titrationEntry.getValue().isStandard())
 
             if (!titrationEntry.getValue().isUnknown())
             {
-                propertyName = getTitrationTypeCheckboxName(Titration.Type.standard, titrationEntry.getValue());
+                propertyName = getTitrationTypeCheckboxNameAndId(Titration.Type.standard, titrationEntry.getValue());
                 // If we have an existing titration as a baseline from the run we're replacing, use its value
                 defVal = existingTitration == null ? defaultWellRoleValues.get(propertyName) : Boolean.toString(existingTitration.isStandard());
                 value = setInitialTitrationInput(errorReshow, propertyName, defVal, titrationEntry.getValue().isStandard()) ? "true" : "";
@@ -369,21 +370,21 @@ else if (titrationEntry.getValue().isStandard())
                 value = toShowStandardCheckboxColumn(errorReshow, standardTitrations, titrationEntry.getValue()) ? "true" : "";
                 view.getDataRegion().addHiddenFormField(getShowStandardCheckboxColumnName(titrationEntry.getValue()), value);
 
-                propertyName = getTitrationTypeCheckboxName(Titration.Type.qccontrol, titrationEntry.getValue());
+                propertyName = getTitrationTypeCheckboxNameAndId(Titration.Type.qccontrol, titrationEntry.getValue());
                 // If we have an existing titration as a baseline from the run we're replacing, use its value
                 defVal = existingTitration == null ? defaultWellRoleValues.get(propertyName) : Boolean.toString(existingTitration.isQcControl());
                 value = setInitialTitrationInput(errorReshow, propertyName, defVal, titrationEntry.getValue().isQcControl()) ? "true" : "";
                 view.getDataRegion().addHiddenFormField(propertyName, value);
 
-                propertyName = getTitrationTypeCheckboxName(Titration.Type.othercontrol, titrationEntry.getValue());
+                propertyName = getTitrationTypeCheckboxNameAndId(Titration.Type.othercontrol, titrationEntry.getValue());
                 // If we have an existing titration as a baseline from the run we're replacing, use its value
                 defVal = existingTitration == null ? defaultWellRoleValues.get(propertyName) : Boolean.toString(existingTitration.isOtherControl());
                 value = setInitialTitrationInput(errorReshow, propertyName, defVal, titrationEntry.getValue().isOtherControl()) ? "true" : "";
                 view.getDataRegion().addHiddenFormField(propertyName, value);
             }
             else
             {
-                propertyName = getTitrationTypeCheckboxName(Titration.Type.unknown, titrationEntry.getValue());
+                propertyName = getTitrationTypeCheckboxNameAndId(Titration.Type.unknown, titrationEntry.getValue());
                 // If we have an existing titration as a baseline from the run we're replacing, use its value
                 defVal = existingTitration == null ? defaultWellRoleValues.get(propertyName) : Boolean.toString(existingTitration.isUnknown());
                 value = setInitialTitrationInput(errorReshow, propertyName, defVal, titrationEntry.getValue().isUnknown()) ? "true" : "";
@@ -400,7 +401,7 @@ else if (titrationEntry.getValue().isStandard())
 
             boolean existingSinglePointControl = existingSinglePointControls.contains(singlePointControl);
 
-            propertyName = getSinglePointControlCheckboxName(singlePointControl);
+            propertyName = getSinglePointControlCheckboxNameAndId(singlePointControl);
             // If we have an existing singlePointControl as a baseline from the run we're replacing, use its value
             defVal = existingSinglePointControl ? "true" : defaultWellRoleValues.get(propertyName);
             value = setInitialSinglePointControlInput(errorReshow, propertyName, defVal) ? "true" : "";
@@ -431,8 +432,9 @@ else if (titrationEntry.getValue().isStandard())
                 @Override
                 public void writeSameCheckboxCell(RenderContext ctx, HtmlWriter out)
                 {
-                    String titrationCellName = PageFlowUtil.filter(getTitrationColumnCellName(titrationEntry.getValue().getName()));
-                    String groupName = ColumnInfo.propNameFromName(getColumns().get(0).getFormFieldName(ctx));
+                    String titrationCellName = PageFlowUtil.filter(getTitrationColumnCellNameAndId(titrationEntry.getValue().getName()));
+                    // DOM ids and JS function names can't have spaces
+                    String groupName = PageConfig.makeIdFromName(getColumns().get(0).getFormFieldName(ctx));
                     String id = groupName + "CheckBox";
 
                     TD(
@@ -453,7 +455,8 @@ public void writeSameCheckboxCell(RenderContext ctx, HtmlWriter out)
                 @Override
                 public void writeCopyableJavaScript(RenderContext ctx, Writer out) throws IOException
                 {
-                    String groupName = ColumnInfo.propNameFromName(getColumns().get(0).getFormFieldName(ctx));
+                    // DOM ids and JS function names can't have spaces
+                    String groupName = PageConfig.makeIdFromName(getColumns().get(0).getFormFieldName(ctx));
                     out.write("function " + groupName + "Updated() {\n");
                     out.write("  if (document.getElementById('" + groupName + "CheckBox') != null && document.getElementById('" + groupName + "CheckBox').checked) {\n");
                     out.write("    var v = document.getElementsByName('" + getColumns().get(0).getFormFieldName(ctx) + "')[0].checked;\n");
@@ -550,7 +553,7 @@ private JspView<LuminexRunUploadForm> addExclusionWarning(LuminexRunUploadForm f
 
     private String getShowStandardCheckboxColumnName(Titration standard)
     {
-        String titrationCheckboxName = getTitrationTypeCheckboxName(Titration.Type.standard, standard);
+        String titrationCheckboxName = getTitrationTypeCheckboxNameAndId(Titration.Type.standard, standard);
         return titrationCheckboxName + "_showcol";
     }
 
@@ -691,19 +694,22 @@ protected RunStepHandler getRunStepHandler()
         return new LuminexRunStepHandler();
     }
 
-    public static String getTitrationTypeCheckboxName(Titration.Type type, Titration titration)
+    public static String getTitrationTypeCheckboxNameAndId(Titration.Type type, Titration titration)
     {
-        return ColumnInfo.propNameFromName("_titrationRole_" + type + "_" + titration.getName());
+        // DOM ids and JS function names can't have spaces
+        return PageConfig.makeIdFromName("_titrationRole_" + type + "_" + titration.getName());
     }
 
-    public static String getSinglePointControlCheckboxName(String singlePointControl)
+    public static String getSinglePointControlCheckboxNameAndId(String singlePointControl)
     {
-        return ColumnInfo.propNameFromName("_singlePointControl_" + singlePointControl);
+        // DOM ids and JS function names can't have spaces
+        return PageConfig.makeIdFromName("_singlePointControl_" + singlePointControl);
     }
 
-    public static String getTitrationColumnCellName(String titrationName)
+    public static String getTitrationColumnCellNameAndId(String titrationName)
     {
-        return ColumnInfo.propNameFromName("_titrationcell_" + titrationName);
+        // DOM ids and JS function names can't have spaces
+        return PageConfig.makeIdFromName("_titrationcell_" + titrationName);
     }
 
     protected class LuminexRunStepHandler extends RunStepHandler
@@ -806,21 +812,21 @@ public boolean executeStep(LuminexRunUploadForm form, BindException errors) thro
                     // add the name/value pairs for the titration well role definition section
                     if (!titrationEntry.getValue().isUnknown())
                     {
-                        propertyName = getTitrationTypeCheckboxName(Titration.Type.standard, titrationEntry.getValue());
+                        propertyName = getTitrationTypeCheckboxNameAndId(Titration.Type.standard, titrationEntry.getValue());
                         value = getViewContext().getRequest().getParameter(propertyName).equals("true");
                         defaultWellRoleValues.put(propertyName, Boolean.toString(value));
 
-                        propertyName = getTitrationTypeCheckboxName(Titration.Type.qccontrol, titrationEntry.getValue());
+                        propertyName = getTitrationTypeCheckboxNameAndId(Titration.Type.qccontrol, titrationEntry.getValue());
                         value = getViewContext().getRequest().getParameter(propertyName).equals("true");
                         defaultWellRoleValues.put(propertyName, Boolean.toString(value));
 
-                        propertyName = getTitrationTypeCheckboxName(Titration.Type.othercontrol, titrationEntry.getValue());
+                        propertyName = getTitrationTypeCheckboxNameAndId(Titration.Type.othercontrol, titrationEntry.getValue());
                         value = getViewContext().getRequest().getParameter(propertyName).equals("true");
                         defaultWellRoleValues.put(propertyName, Boolean.toString(value));
                     }
                     else
                     {
-                        propertyName = getTitrationTypeCheckboxName(Titration.Type.unknown, titrationEntry.getValue());
+                        propertyName = getTitrationTypeCheckboxNameAndId(Titration.Type.unknown, titrationEntry.getValue());
                         value = getViewContext().getRequest().getParameter(propertyName).equals("true");
                         defaultWellRoleValues.put(propertyName, Boolean.toString(value));
                     }
@@ -845,7 +851,7 @@ public boolean executeStep(LuminexRunUploadForm form, BindException errors) thro
                 for (String singlePointControl : form.getParser().getSinglePointControls())
                 {
                     // add the name/value pairs for the singlePointControl well role definition section
-                    String propertyName = getSinglePointControlCheckboxName(singlePointControl);
+                    String propertyName = getSinglePointControlCheckboxNameAndId(singlePointControl);
                     boolean value = getViewContext().getRequest().getParameter(propertyName).equals("true");
                     defaultWellRoleValues.put(propertyName, Boolean.toString(value));
                 }