Fix sql scripts, add natural sorting

Author: bbimber

singlecell/resources/schemas/dbscripts/postgresql/singlecell-20.002-20.003.sql

@@ -2,7 +2,6 @@ CREATE TABLE singlecell.hashing_labels (
   rowid serial,
   name varchar(100),
   groupName varchar(100),
-  markerLabel varchar(100),
   adaptersequence varchar(4000),
   barcodePattern varchar(100),
 

singlecell/resources/schemas/dbscripts/postgresql/singlecell-20.003-20.004.sql

@@ -0,0 +1 @@
+;

singlecell/resources/schemas/dbscripts/sqlserver/singlecell-20.002-20.003.sql

@@ -2,7 +2,6 @@ CREATE TABLE singlecell.hashing_labels (
   rowid int IDENTITY(1,1),
   name nvarchar(100),
   groupName nvarchar(100),
-  markerLabel nvarchar(100),
   adaptersequence nvarchar(4000),
   barcodePattern nvarchar(100),
 

singlecell/resources/schemas/dbscripts/sqlserver/singlecell-20.003-20.004.sql

@@ -0,0 +1,2 @@
+--Accidentally deployed:
+EXEC core.fn_dropifexists 'hashing_labels', 'singlecell', 'COLUMN', 'markerLabel';

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -110,7 +110,7 @@ public void prepareHashingAndCiteSeqFilesIfNeeded(File sourceDir, PipelineJob jo
                 FieldKey.fromString("sortId/sampleId/stim"),
                 FieldKey.fromString("sortId/population"),
                 FieldKey.fromString("sortId/hto"),
-                FieldKey.fromString("sortId/hto/sequence"),
+                FieldKey.fromString("sortId/hto/adaptersequence"),
                 FieldKey.fromString("hashingReadsetId"),
                 FieldKey.fromString("hashingReadsetId/totalFiles"),
                 FieldKey.fromString("citeseqReadsetId"),
@@ -153,7 +153,7 @@ public void prepareHashingAndCiteSeqFilesIfNeeded(File sourceDir, PipelineJob jo
                             String.valueOf(results.getObject(FieldKey.fromString("hashingReadsetId")) == null ? "" : results.getInt(FieldKey.fromString("hashingReadsetId"))),
                             String.valueOf(results.getObject(FieldKey.fromString("hashingReadsetId/totalFiles")) != null && results.getInt(FieldKey.fromString("hashingReadsetId/totalFiles")) > 0),
                             results.getString(FieldKey.fromString("sortId/hto")),
-                            results.getString(FieldKey.fromString("sortId/hto/sequence")),
+                            results.getString(FieldKey.fromString("sortId/hto/adaptersequence")),
                             String.valueOf(results.getObject(FieldKey.fromString("citeseqReadsetId")) == null ? "" : results.getInt(FieldKey.fromString("citeseqReadsetId"))),
                             String.valueOf(results.getObject(FieldKey.fromString("citeseqReadsetId/totalFiles")) != null && results.getInt(FieldKey.fromString("citeseqReadsetId/totalFiles")) > 0),
                             results.getString(FieldKey.fromString("citeseqPanel"))
@@ -173,14 +173,14 @@ public void prepareHashingAndCiteSeqFilesIfNeeded(File sourceDir, PipelineJob jo
                         {
                             readsetToHashingMap.put(rs.getReadsetId(), results.getInt(FieldKey.fromString("hashingReadsetId")));
 
-                            String hto = results.getString(FieldKey.fromString("sortId/hto")) + "<>" + results.getString(FieldKey.fromString("sortId/hto/sequence"));
-                            if (!distinctHTOs.contains(hto) && !StringUtils.isEmpty(results.getString(FieldKey.fromString("sortId/hto/sequence"))))
+                            String hto = results.getString(FieldKey.fromString("sortId/hto")) + "<>" + results.getString(FieldKey.fromString("sortId/hto/adaptersequence"));
+                            if (!distinctHTOs.contains(hto) && !StringUtils.isEmpty(results.getString(FieldKey.fromString("sortId/hto/adaptersequence"))))
                             {
                                 distinctHTOs.add(hto);
-                                bcWriter.writeNext(new String[]{results.getString(FieldKey.fromString("sortId/hto/sequence")), results.getString(FieldKey.fromString("sortId/hto"))});
+                                bcWriter.writeNext(new String[]{results.getString(FieldKey.fromString("sortId/hto/adaptersequence")), results.getString(FieldKey.fromString("sortId/hto"))});
                             }
 
-                            if (results.getObject(FieldKey.fromString("sortId/hto/sequence")) == null)
+                            if (results.getObject(FieldKey.fromString("sortId/hto/adaptersequence")) == null)
                             {
                                 job.getLogger().error("Unable to find sequence for HTO: " + results.getString(FieldKey.fromString("sortId/hto")));
                                 hasError.set(true);

singlecell/src/org/labkey/singlecell/SingleCellModule.java

@@ -57,7 +57,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 20.003;
+        return 20.004;
     }
 
     @Override

singlecell/src/org/labkey/singlecell/SingleCellTableCustomizer.java

@@ -36,6 +36,14 @@ else if (matches(ti, SingleCellSchema.NAME, SingleCellSchema.TABLE_CDNAS))
             {
                 customizeCdnas(ti);
             }
+            else if (matches(ti, SingleCellSchema.NAME, SingleCellSchema.TABLE_HASHING_LABELS))
+            {
+                LDKService.get().applyNaturalSort(ti, "name");
+            }
+            else if (matches(ti, SingleCellSchema.NAME, SingleCellSchema.TABLE_CITE_SEQ_ANTIBODIES))
+            {
+                LDKService.get().applyNaturalSort(ti, "antibodyName");
+            }
         }
     }