Merge 25.7 to develop

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<Long>, List<Long>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), protocol, form.getAlleleNames());
+                    String[] alleleNames = Arrays.stream(form.getAlleleNames()).map(StringEscapeUtils::unescapeHtml4).toArray(String[]::new);
+                    Pair<List<Long>, List<Long>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), protocol, alleleNames);
                     resultProperties.put("runsCreated", ret.first);
                     resultProperties.put("runsDeleted", ret.second);
                 }

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

@@ -62,6 +62,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.concurrent.atomic.AtomicInteger;
 
 public class GenotypeAssaysManager
 {
@@ -123,13 +124,15 @@ public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final E
             final Map<Integer, List<Map<String, Object>>> rowHash = new IntHashMap<>();
             final Map<Integer, Set<Integer>> toDeleteByAnalysis = new IntHashMap<>();
 
+            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"));
@@ -169,6 +172,11 @@ 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);

mGAP/resources/views/login.html

@@ -66,6 +66,6 @@
     </div>
 </form>
 <div class="otherLoginMechanismsSection" hidden>
-    <div class="auth-header">Users from these institutions can use their existing logins (after registration):</div>
+    <div class="auth-header">Registered users from the following institutions can log in using their home institution's credentials below:</div>
     <div class="otherLoginMechanismsContent"></div>
 </div>

mcc/src/client/RequestReview/components/RabReviewForm.tsx

@@ -124,8 +124,8 @@ export default function RabReviewForm(props: {requestId: string}) {
             <TableRow>
                 <TableCell>
                     <FormControl>
-                        <InputLabel id={"review-input-label"}>Enter review...</InputLabel>
-                        <Select id={"review"} variant={"outlined"} name={"review"} aria-label="Review" label={"Review"} error={hasSubmitted && !recordData[0].review} onChange={handleChange} required={true} value={recordData[0].review ?? ''} fullWidth={true} displayEmpty={true}>
+                        <InputLabel id={"review-input-label"}>Review</InputLabel>
+                        <Select id={"review"} variant={"outlined"} name={"review"} aria-label="Review" label={"Review"} labelId={"review-input-label"} error={hasSubmitted && !recordData[0].review} onChange={handleChange} required={true} value={recordData[0].review ?? ''} fullWidth={true} displayEmpty={true}>
                             <MenuItem value={""}>Not Decided</MenuItem>
                             <MenuItem value={"I recommend this proposal"}>I recommend this proposal</MenuItem>
                             <MenuItem value={"I recommend this proposal with conditions"}>I recommend this proposal with conditions</MenuItem>

mcc/src/org/labkey/mcc/MccManager.java

@@ -56,10 +56,10 @@ public enum RequestStatus
         Fulfilled(8, "Fulfilled", MccRequestAdminPermission.class),
         Withdrawn(9, "Withdrawn", MccRequestorPermission.class);
 
-        int sortOrder;
-        String label;
-        Class<? extends Permission> updatePermission;
-        Class<? extends Permission> insertPermission;
+        final int sortOrder;
+        final String label;
+        final Class<? extends Permission> updatePermission;
+        final Class<? extends Permission> insertPermission;
 
         RequestStatus(int sortOrder, String label, Class<? extends Permission> editPermission)
         {

mcc/src/org/labkey/mcc/query/MccRequestCustomizer.java

@@ -58,15 +58,15 @@ public boolean isSortable()
 
             ti.addColumn(newCol);
 
-            SQLFragment sql2 = new SQLFragment("(SELECT COALESCE(sum(CASE WHEN r.review IS NULL THEN 1 ELSE 0 END), -1) as expr FROM mcc.requestReviews r WHERE r.requestId = " + ExprColumn.STR_TABLE_ALIAS + ".requestId)");
+            SQLFragment sql2 = new SQLFragment("(SELECT COALESCE(sum(CASE WHEN r.review IS NULL THEN 1 ELSE 0 END), -1) as expr FROM mcc.requestReviews r WHERE CAST(r.requestId AS VARCHAR(36)) = CAST(" + ExprColumn.STR_TABLE_ALIAS + ".requestId AS VARCHAR(36)))");
             ExprColumn newCol2 = new ExprColumn(ti, "pendingRabReviews", sql2, JdbcType.INTEGER, ti.getColumn("requestId"));
             newCol2.setLabel("Pending RAB Reviews");
             ti.addColumn(newCol2);
         }
 
         if (ti.getColumn("numAnimalsRequested") == null)
         {
-            SQLFragment sql = new SQLFragment("(SELECT SUM(rc.numberofanimals) as expr FROM mcc." + MccSchema.TABLE_REQUEST_COHORTS + " rc WHERE rc.requestId = " + ExprColumn.STR_TABLE_ALIAS + ".requestId)");
+            SQLFragment sql = new SQLFragment("(SELECT SUM(rc.numberofanimals) as expr FROM mcc." + MccSchema.TABLE_REQUEST_COHORTS + " rc WHERE CAST(rc.requestId AS VARCHAR(36)) = CAST(" + ExprColumn.STR_TABLE_ALIAS + ".requestId AS VARCHAR(36)))");
             ExprColumn newCol = new ExprColumn(ti, "numAnimalsRequested", sql, JdbcType.INTEGER, ti.getColumn("requestId"));
             newCol.setLabel("# Animals Requested");
             newCol.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=mcc&query.queryName=" + MccSchema.TABLE_REQUEST_COHORTS + "&query.requestId~eq=${requestId}"));
@@ -98,7 +98,7 @@ public boolean isSortable()
                         append(" as expr FROM ").
                         append(" mcc." + MccSchema.TABLE_ANIMAL_REQUESTS + " ar JOIN studydataset.").append(dti.getName()).
                         append(" d ON (d.mccRequestId = ar.rowId)").
-                        append(" WHERE ar.objectid = " + ExprColumn.STR_TABLE_ALIAS + ".requestId)");
+                        append(" WHERE CAST(ar.objectid AS VARCHAR(36)) = CAST(" + ExprColumn.STR_TABLE_ALIAS + ".requestId AS VARCHAR(36)))");
 
                 ExprColumn newCol = new ExprColumn(ti, "transferIds", sql, JdbcType.VARCHAR, ti.getColumn("requestId"));
                 newCol.setLabel("Animal ID(s)");

primeseq/src/org/labkey/primeseq/pipeline/BismarkWrapper.java

@@ -297,6 +297,9 @@ public Provider()
                         put("minValue", 0);
                         put("maxValue", 1);
                     }}, 1),
+                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--score_min"), "score_min", "Score Min", "Sets a function governing the minimum alignment score needed for an alignment to be considered \"valid\" (i.e. good enough to report). This is a function of read length. For instance, specifying L,0,-0.2 sets the minimum-score function f to f(x) = 0 + -0.2 * x, where x is the read length", "textfield", new JSONObject(){{
+
+                    }}, null),
                     ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--local"), "local", "Local Alignment", "In this mode, it is not required that the entire read aligns from one end to the other. Rather, some characters may be omitted (“soft-clipped”) from the ends in order to achieve the greatest possible alignment score. For Bowtie 2, the match bonus --ma (default: 2) is used in this mode, and the best possible alignment score is equal to the match bonus (--ma) times the length of the read. This is mutually exclusive with end-to-end alignments.", "checkbox", new JSONObject(){{
 
                     }}, false),