Merge pull request #197 from bimberlabinternal/25.7_fb_htmldecoding

Manually decode form parameters

Author: bbimber

GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java

@@ -16,6 +16,7 @@
 
 package org.labkey.genotypeassays;
 
+import org.apache.commons.text.StringEscapeUtils;
 import org.json.JSONArray;
 import org.labkey.api.action.ApiResponse;
 import org.labkey.api.action.ApiSimpleResponse;
@@ -37,6 +38,7 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -130,7 +132,8 @@ public ApiResponse execute(CacheAnalysesForm form, BindException errors)
                         return null;
                     }
 
-                    Pair<List<Integer>, List<Integer>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), protocol, form.getAlleleNames());
+                    String[] alleleNames = Arrays.stream(form.getAlleleNames()).map(StringEscapeUtils::unescapeHtml4).toArray(String[]::new);
+                    Pair<List<Integer>, List<Integer>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), protocol, alleleNames);
                     resultProperties.put("runsCreated", ret.first);
                     resultProperties.put("runsDeleted", ret.second);
                 }

GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java

@@ -60,6 +60,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.concurrent.atomic.AtomicInteger;
 
 public class GenotypeAssaysManager
 {
@@ -121,13 +122,15 @@ public Pair<List<Integer>, List<Integer>> cacheAnalyses(final ViewContext ctx, f
             final Map<Integer, List<Map<String, Object>>> rowHash = new HashMap<>();
             final Map<Integer, Set<Integer>> toDeleteByAnalysis = new HashMap<>();
 
+            AtomicInteger records = new AtomicInteger();
             TableSelector tsAlignments = new TableSelector(tableAlignments, cols.values(), new SimpleFilter(FieldKey.fromString("key"), Arrays.asList(pks), CompareType.IN), null);
             tsAlignments.forEach(new Selector.ForEachBlock<ResultSet>()
             {
                 @Override
                 public void exec(ResultSet object) throws SQLException
                 {
                     Results rs = new ResultsImpl(object, cols);
+                    records.getAndIncrement();
 
                     int analysisId = rs.getInt(FieldKey.fromString("analysis_id"));
                     String lineages = rs.getString(FieldKey.fromString("lineages"));
@@ -167,6 +170,11 @@ public void exec(ResultSet object) throws SQLException
                 }
             });
 
+            if (records.get() != pks.length)
+            {
+                throw new IllegalStateException("The number of records found did not match the number supplied. This indicates a problem with the import.");
+            }
+
             if (!rowHash.isEmpty())
             {
                 processSet(SBT_LINEAGE_ASSAY_TYPE, rowHash, assayDataTable, u, ctx, toDeleteByAnalysis, ap, protocol, runsCreated);