Augment seurat prototype description field

Author: bbimber

singlecell/src/org/labkey/singlecell/SingleCellController.java

@@ -79,6 +79,7 @@
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -592,6 +593,7 @@ public ModelAndView getConfirmView(Object form, BindException errors) throws Exc
         public boolean handlePost(Object form, BindException errors) throws Exception
         {
             UserSchema sa = QueryService.get().getUserSchema(getUser(), getContainer(), SingleCellSchema.SEQUENCE_SCHEMA_NAME);
+            List<Map<String, Object>> toUpdate = new ArrayList<>();
             new TableSelector(sa.getTable("outputfiles"), PageFlowUtil.set("rowid"), new SimpleFilter(FieldKey.fromString("category"), "Seurat Object Prototype"), null).forEach(Integer.class, rowId -> {
                 SequenceOutputFile so = SequenceOutputFile.getForId(rowId);
                 if (so == null)
@@ -642,17 +644,34 @@ public boolean handlePost(Object form, BindException errors) throws Exception
                     }
 
                     String description = AbstractSingleCellHandler.getOutputDescription(params, _log, so.getFile(), null);
-                    so.setDescription(description);
-
-                    _log.info(rowId);
-                    _log.info(description);
+                    toUpdate.add(new CaseInsensitiveHashMap<>(Map.of("rowid", so.getRowid(), "description", description)));
                 }
                 catch (PipelineJobException e)
                 {
                     _log.error("Error generating description for: " + rowId, e);
                 }
             });
 
+            if (!toUpdate.isEmpty())
+            {
+                try
+                {
+                    BatchValidationException bve = new BatchValidationException();
+                    List<Map<String, Object>> oldKeys = toUpdate.stream().map(row -> Map.of("rowid", row.get("rowid"))).toList();
+                    sa.getTable("outputfiles").getUpdateService().updateRows(getUser(), getContainer(), toUpdate, oldKeys, bve, null, null);
+
+                    if (bve.hasErrors())
+                    {
+                        throw bve;
+                    }
+                }
+                catch (SQLException | BatchValidationException e)
+                {
+                    _log.error("Unable to update outputfiles", e);
+                    return false;
+                }
+            }
+
             return true;
         }
     }

singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java

@@ -1026,6 +1026,7 @@ public static String getOutputDescription(JSONObject jsonParams, Logger log, Fil
                 int cellsWithTRB = 0;
                 int cellsWithTRD = 0;
                 int cellsWithTRG = 0;
+                int cellsLackingCDR3 = 0;
                 while ((line = reader.readNext()) != null)
                 {
                     // This will test whether this is the first line or not
@@ -1084,13 +1085,15 @@ else if ("NotUsed".equals(val))
                         {
                             if ("T_NK".equals(line[riraIdx]))
                             {
+                                boolean hasCDR3 = false;
                                 totalTNK++;
                                 if (traIdx >= 0)
                                 {
                                     String tra = StringUtils.trimToNull(line[traIdx]);
                                     if (tra != null && !"NA".equals(tra))
                                     {
                                         cellsWithTRA++;
+                                        hasCDR3 = true;
                                     }
                                 }
 
@@ -1100,6 +1103,7 @@ else if ("NotUsed".equals(val))
                                     if (trb != null && !"NA".equals(trb))
                                     {
                                         cellsWithTRB++;
+                                        hasCDR3 = true;
                                     }
                                 }
 
@@ -1109,6 +1113,7 @@ else if ("NotUsed".equals(val))
                                     if (trd != null && !"NA".equals(trd))
                                     {
                                         cellsWithTRD++;
+                                        hasCDR3 = true;
                                     }
                                 }
 
@@ -1118,8 +1123,14 @@ else if ("NotUsed".equals(val))
                                     if (trg != null && !"NA".equals(trg))
                                     {
                                         cellsWithTRG++;
+                                        hasCDR3 = true;
                                     }
                                 }
+
+                                if (!hasCDR3)
+                                {
+                                    cellsLackingCDR3++;
+                                }
                             }
                         }
                     }
@@ -1157,6 +1168,7 @@ else if ("NotUsed".equals(val))
                     descriptions.add("% T/NK Cells with TRB: " + pf.format(cellsWithTRB / (double)totalTNK));
                     descriptions.add("% T/NK Cells with TRD: " + pf.format(cellsWithTRD / (double)totalTNK));
                     descriptions.add("% T/NK Cells with TRG: " + pf.format(cellsWithTRG / (double)totalTNK));
+                    descriptions.add("% T/NK Cells without TCR: " + pf.format(cellsLackingCDR3 / (double)totalTNK));
                 }
                 else if (riraIdx == -1 || traIdx == -1)
                 {