refactor(loader): move UDF0 contract from Loader to capability mix-ins

src/main/java/com/atgenomix/seqslab/piper/plugin/api/loader/Loader.java

@@ -19,11 +19,8 @@
 import com.atgenomix.seqslab.piper.plugin.api.DataSource;
 import com.atgenomix.seqslab.piper.plugin.api.Operator;
 import com.atgenomix.seqslab.piper.tags.DeveloperApi;
-import org.apache.spark.sql.Row;
-import org.apache.spark.sql.api.java.UDF0;
 import org.apache.spark.sql.types.StructType;
 
-import java.util.Iterator;
 
 /**
  * The operator responsible for loading (reading) a dataset into in-memory DataFrame or copying to local host
@@ -48,7 +45,7 @@
  * @see SupportsScanPartitions
  */
 @DeveloperApi
-public interface Loader extends Operator, UDF0<Iterator<Row>> {
+public interface Loader extends Operator {
 
     /**
      * Initializes this operator with a specific data source.

src/main/java/com/atgenomix/seqslab/piper/plugin/api/loader/SupportsCopyToLocal.java

@@ -18,6 +18,7 @@
 
 import com.atgenomix.seqslab.piper.tags.DeveloperApi;
 import com.atgenomix.seqslab.piper.tags.FeatureBeforeCall;
+import org.apache.spark.sql.api.java.UDF0;
 
 /**
  * A mix-in interface for {@link Loader}. Dataset loaders can implement this interface to support
@@ -28,7 +29,7 @@
  */
 @DeveloperApi
 @FeatureBeforeCall
-public interface SupportsCopyToLocal extends Loader {
+public interface SupportsCopyToLocal extends Loader, UDF0<Void> {
 
     /**
      * Sets the local destination path where the datasets will be saved.

src/main/java/com/atgenomix/seqslab/piper/plugin/api/loader/SupportsInMemoryLoading.java

@@ -0,0 +1,35 @@
+/*
+ * Copyright (c) 2021-2022, ATGENOMIX INCORPORATED.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package com.atgenomix.seqslab.piper.plugin.api.loader;
+
+import com.atgenomix.seqslab.piper.tags.DeveloperApi;
+import com.atgenomix.seqslab.piper.tags.FeatureBeforeCall;
+import org.apache.spark.sql.api.java.UDF0;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Row;
+
+/**
+ * A mix-in interface for {@link Loader}. Dataset loaders can implement this interface to support
+ * copying storage files or directories directly to local file system.
+ * Loaders supporting this interface typically localize datasets that do not require
+ * in-memory processing optimization, e.g. reference files.
+ * This feature is invoked before calling operator function.
+ */
+@DeveloperApi
+@FeatureBeforeCall
+public interface SupportsInMemoryLoading extends Loader, UDF0<Dataset<Row>> {
+}

src/main/java/com/atgenomix/seqslab/piper/plugin/api/loader/SupportsReadPartitions.java

@@ -18,6 +18,10 @@
 
 import com.atgenomix.seqslab.piper.tags.DeveloperApi;
 import com.atgenomix.seqslab.piper.tags.FeatureBeforeCall;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.api.java.UDF0;
+
+import java.util.Iterator;
 
 /**
  * A mix-in interface for {@link Loader}. Dataset loaders can implement this interface to support
@@ -27,7 +31,7 @@
  */
 @DeveloperApi
 @FeatureBeforeCall
-public interface SupportsReadPartitions extends Loader {
+public interface SupportsReadPartitions extends Loader, UDF0<Iterator<Row>> {
 
     /**
      * Get the number of partitions in the data source.

src/main/java/com/atgenomix/seqslab/piper/plugin/api/loader/SupportsScanPartitions.java

@@ -19,16 +19,18 @@
 import com.atgenomix.seqslab.piper.tags.DeveloperApi;
 import com.atgenomix.seqslab.piper.tags.FeatureBeforeCall;
 import org.apache.spark.sql.Row;
+import org.apache.spark.sql.api.java.UDF0;
 
 import java.util.Iterator;
 
+
 /**
  * A mix-in interface for {@link Loader}. Dataset loaders can implement this interface to support
  * transformation of partitioned datasets read by SeqsLab.
  */
 @DeveloperApi
 @FeatureBeforeCall
-public interface SupportsScanPartitions extends Loader {
+public interface SupportsScanPartitions extends Loader, UDF0<Iterator<Row>>  {
 
     /**
      * Set the partition loaded by SeqsLab for applying Loader's call function.