revert to support the recently added remove case

Author: Baunsgaard

src/main/java/org/apache/sysds/runtime/transform/encode/ColumnEncoder.java

@@ -425,14 +425,6 @@ public List<DependencyTask<?>> getApplyTasks(CacheBlock<?> in, MatrixBlock out,
 		return new ColumnApplyTask<>(this, in, out, outputCol, startRow, blk);
 	}
 
-	// public Set<Integer> getSparseRowsWZeros(){
-	// 	if (_sparseRowsWZeros != null) {
-	// 		return new HashSet<>(_sparseRowsWZeros);
-	// 	}
-	// 	else
-	// 		return null;
-	// }
-
 	protected void addSparseRowsWZeros(List<Integer> sparseRowsWZeros){
 		synchronized (this){
 			if(_sparseRowsWZeros == null)
@@ -441,13 +433,6 @@ protected void addSparseRowsWZeros(List<Integer> sparseRowsWZeros){
 		}
 
 	}
-	// protected void addSparseRowsWZeros(ArrayList<Integer> sparseRowsWZeros){
-	// 	synchronized (this){
-	// 		if(_sparseRowsWZeros == null)
-	// 			_sparseRowsWZeros = new ArrayList<>();
-	// 		_sparseRowsWZeros.addAll(sparseRowsWZeros);
-	// 	}
-	// }
 
 	protected boolean containsZeroOut(){
 		return containsZeroOut;

src/main/java/org/apache/sysds/runtime/transform/encode/ColumnEncoderComposite.java

@@ -423,15 +423,6 @@ public void shiftCol(int columnOffset) {
 		_columnEncoders.forEach(e -> e.shiftCol(columnOffset));
 	}
 
-	// @Override
-	// public Set<Integer> getSparseRowsWZeros(){
-	// 	return _columnEncoders.stream().map(ColumnEncoder::getSparseRowsWZeros).flatMap(l -> {
-	// 				if(l == null)
-	// 					return null;
-	// 				return l.stream();
-	// 			}).collect(Collectors.toSet());
-	// }
-
 	protected boolean containsZeroOut(){
 		for(int i = 0; i < _columnEncoders.size(); i++)
 			if(_columnEncoders.get(i).containsZeroOut())

src/main/java/org/apache/sysds/runtime/transform/encode/ColumnEncoderPassThrough.java

@@ -82,39 +82,6 @@ protected double[] getCodeCol(CacheBlock<?> in, int startInd, int endInd, double
 	}
 
 	protected void applySparse(CacheBlock<?> in, MatrixBlock out, int outputCol, int rowStart, int blk){
-		//Set<Integer> sparseRowsWZeros = null;
-		// ArrayList<Integer> sparseRowsWZeros = null;
-		// boolean mcsr = MatrixBlock.DEFAULT_SPARSEBLOCK == SparseBlock.Type.MCSR;
-		// mcsr = false; //force CSR for transformencode
-		// int index = _colID - 1;
-		// // Apply loop tiling to exploit CPU caches
-		// int rowEnd = getEndIndex(in.getNumRows(), rowStart, blk);
-		// double[] codes = getCodeCol(in, rowStart, rowEnd, null);
-		// int B = 32; //tile size
-		// for(int i = rowStart; i < rowEnd; i+=B) {
-		// 	int lim = Math.min(i+B, rowEnd);
-		// 	for (int ii=i; ii<lim; ii++) {
-		// 		double v = codes[ii-rowStart];
-		// 		if(v == 0) {
-		// 			if(sparseRowsWZeros == null)
-		// 				sparseRowsWZeros = new ArrayList<>();
-		// 			sparseRowsWZeros.add(ii);
-		// 		}
-		// 		int indexWithOffset = sparseRowPointerOffset != null ? sparseRowPointerOffset[ii] - 1 + index : index;
-		// 		if (mcsr) {
-		// 			SparseRowVector row = (SparseRowVector) out.getSparseBlock().get(ii);
-		// 			row.values()[indexWithOffset] = v;
-		// 			row.indexes()[indexWithOffset] = outputCol;
-		// 		}
-		// 		else { //csr
-		// 			// Manually fill the column-indexes and values array
-		// 			SparseBlockCSR csrblock = (SparseBlockCSR)out.getSparseBlock();
-		// 			int rptr[] = csrblock.rowPointers();
-		// 			csrblock.indexes()[rptr[ii]+indexWithOffset] = outputCol;
-		// 			csrblock.values()[rptr[ii]+indexWithOffset] = codes[ii-rowStart];
-		// 		}
-		// 	}
-		
 		final SparseBlock sb = out.getSparseBlock();
 		final boolean mcsr = sb instanceof SparseBlockMCSR;
 		final int index = _colID - 1;

src/main/java/org/apache/sysds/runtime/transform/encode/EncoderFactory.java

@@ -132,10 +132,10 @@ public static MultiColumnEncoder createEncoder(String spec, String[] colnames, i
 
 			// List<Integer> ptIDs = except(except(except(UtilFunctions.getSeqList(1, clen, 1), unionDistinct(rcIDs, haIDs)), binIDs), weIDs);
 
-			List<Integer> oIDs = Arrays.asList(ArrayUtils
-					.toObject(TfMetaUtils.parseJsonIDList(jSpec, colnames, TfMethod.OMIT.toString(), minCol, maxCol)));
-			List<Integer> mvIDs = Arrays.asList(ArrayUtils.toObject(
-					TfMetaUtils.parseJsonObjectIDList(jSpec, colnames, TfMethod.IMPUTE.toString(), minCol, maxCol)));
+			List<Integer> oIDs = new ArrayList<>(Arrays.asList(ArrayUtils
+				.toObject(TfMetaUtils.parseJsonIDList(jSpec, colnames, TfMethod.OMIT.toString(), minCol, maxCol))));
+			List<Integer> mvIDs = new ArrayList<>(Arrays.asList(ArrayUtils.toObject(
+				TfMetaUtils.parseJsonObjectIDList(jSpec, colnames, TfMethod.IMPUTE.toString(), minCol, maxCol))));
 			List<Integer> udfIDs = TfMetaUtils.parseUDFColIDs(jSpec, colnames, minCol, maxCol);
 
 			// robustness for transformencode specs w/ non-existing columns (so far, endless loops)