Checkpoint on adding Daffodil to Drill

Depends on a mbeckerle-specific 3.7.0-SNAPSHOT fork of
Daffodil.

New format-daffodil module created

A basic unit test of DFDL schema with a single int field
works in that drill metadata is created by traversing the
schema, then data is populated using drill's row-set-writer
being drivn by a Daffodil InfosetOutputter from a
Daffodil parse.

Still uses absolute paths for the schemaFileURI.
(which is cheating. Wouldn't work in a true distributed
drill environment.)

We have yet to work out how to enable Drill to provide
access for DFDL schemas in XML form with include/import
to be resolved.

The input data stream is, however, being accessed in the
proper Drill manner. Gunzip happened automatically. Nice.

Note: Fix boxed Boolean vs. boolean problem. Don't use
boxed primitives in Format config objects.

https://github.com/apache/drill/issues/2835ssues/2835

contrib/format-daffodil/.gitignore

@@ -0,0 +1,2 @@
+# Directory to store oauth tokens for testing Googlesheets Storage plugin
+/src/test/resources/logback-test.xml

contrib/format-daffodil/README.md

@@ -0,0 +1,41 @@
+# Daffodil 'Format' Reader
+This plugin enables Drill to read DFDL-described data by way of the Apache Daffodil DFDL implementation.
+
+## Configuration
+ * ?? src/main/resources/bootstrap-format-plugins.json
+ * ?? src/main/resources/drill-module.conf
+
+TBD - how to enable/disable validation by Daffodil?
+Note that this should be per sql query that reads data.
+
+Note that schemas should be able to be loaded once in the config file and then referenced from queries.
+
+The query should include whether to validate (daffodil 'limited' is the only option) or not.
+
+## Data Types
+
+TBD
+
+## Provided Schema
+The Daffodil Format Reader supports pre-compiled DFDL schemas.
+
+TBD example query, data, and schema
+```sql
+SELECT * FROM dfs.`/tmp/data.dat`(type => 'daffodil',
+    schema => "schema_identifier_from_config");
+```
+
+## Limitations:  TBD
+
+This version of the daffodil interface only supports data querying, there is no ability to output (aka unparse in DFDL terminology).
+
+The data is parsed fully from its native form into a Drill data structure held in memory.
+No attempt is made to avoid access to parts of the DFDL-described data that are not needed to answer the query.
+
+If the data is not well-formed, an error occurs and the query fails.
+
+If the data is invalid, and validity checking by Daffodil is enabled, then an error occurs and the query fails.
+
+## Future Functionality
+
+* TBD

contrib/format-daffodil/pom.xml

@@ -0,0 +1,94 @@
+<?xml version="1.0"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you 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.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <parent>
+    <artifactId>drill-contrib-parent</artifactId>
+    <groupId>org.apache.drill.contrib</groupId>
+    <version>1.22.0-SNAPSHOT</version>
+  </parent>
+
+  <artifactId>drill-format-daffodil</artifactId>
+  <name>Drill : Contrib : Format : Daffodil</name>
+
+  <dependencies>
+    <dependency>
+      <groupId>org.apache.drill.exec</groupId>
+      <artifactId>drill-java-exec</artifactId>
+      <version>${project.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.daffodil</groupId>
+      <artifactId>daffodil-japi_2.12</artifactId>
+      <version>3.7.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.daffodil</groupId>
+      <artifactId>daffodil-runtime1_2.12</artifactId>
+      <version>3.7.0-SNAPSHOT</version>
+    </dependency>
+    <!-- Test dependencies -->
+    <dependency>
+      <groupId>org.apache.drill.exec</groupId>
+      <artifactId>drill-java-exec</artifactId>
+      <classifier>tests</classifier>
+      <version>${project.version}</version>
+      <scope>test</scope>
+    </dependency>
+
+    <dependency>
+      <groupId>org.apache.drill</groupId>
+      <artifactId>drill-common</artifactId>
+      <classifier>tests</classifier>
+      <version>${project.version}</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+
+  <build>
+    <plugins>
+      <plugin>
+        <artifactId>maven-resources-plugin</artifactId>
+        <executions>
+          <execution>
+            <id>copy-java-sources</id>
+            <phase>process-sources</phase>
+            <goals>
+              <goal>copy-resources</goal>
+            </goals>
+            <configuration>
+              <outputDirectory>${basedir}/target/classes/org/apache/drill/exec/store/daffodil
+              </outputDirectory>
+              <resources>
+                <resource>
+                  <directory>src/main/java/org/apache/drill/exec/store/daffodil</directory>
+                  <filtering>true</filtering>
+                </resource>
+              </resources>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+</project>

contrib/format-daffodil/src/main/java/org/apache/drill/exec/store/daffodil/DaffodilBatchReader.java

@@ -0,0 +1,184 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 org.apache.drill.exec.store.daffodil;
+
+import java.io.InputStream;
+import java.net.URI;
+import java.net.URISyntaxException;
+
+import org.apache.daffodil.japi.DataProcessor;
+import org.apache.drill.common.AutoCloseables;
+import org.apache.drill.common.exceptions.CustomErrorContext;
+import org.apache.drill.common.exceptions.UserException;
+import org.apache.drill.exec.physical.impl.scan.v3.ManagedReader;
+import org.apache.drill.exec.physical.impl.scan.v3.file.FileDescrip;
+import org.apache.drill.exec.physical.impl.scan.v3.file.FileSchemaNegotiator;
+import org.apache.drill.exec.physical.resultSet.RowSetLoader;
+import org.apache.drill.exec.record.metadata.TupleMetadata;
+import org.apache.drill.exec.store.daffodil.schema.DaffodilDataProcessorFactory;
+import org.apache.drill.exec.store.dfs.DrillFileSystem;
+import org.apache.drill.exec.store.dfs.easy.EasySubScan;
+import org.apache.hadoop.fs.Path;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static org.apache.drill.exec.store.daffodil.schema.DrillDaffodilSchemaUtils.daffodilDataProcessorToDrillSchema;
+
+
+public class DaffodilBatchReader implements ManagedReader {
+
+  private static final Logger logger = LoggerFactory.getLogger(DaffodilBatchReader.class);
+  private final DaffodilFormatConfig dafConfig;
+  private final RowSetLoader rowSetLoader;
+  private final CustomErrorContext errorContext;
+  private final DaffodilMessageParser dafParser;
+  private final InputStream dataInputStream;
+
+  static class DaffodilReaderConfig {
+    final DaffodilFormatPlugin plugin;
+    DaffodilReaderConfig(DaffodilFormatPlugin plugin) {
+      this.plugin = plugin;
+    }
+  }
+
+  public DaffodilBatchReader (DaffodilReaderConfig readerConfig, EasySubScan scan, FileSchemaNegotiator negotiator) {
+
+    errorContext = negotiator.parentErrorContext();
+    this.dafConfig = readerConfig.plugin.getConfig();
+
+    String schemaURIString = dafConfig.getSchemaURI(); // "schema/complexArray1.dfdl.xsd";
+    String rootName = dafConfig.getRootName();
+    String rootNamespace = dafConfig.getRootNamespace();
+    Boolean validationMode = dafConfig.getValidationMode();
+
+    URI dfdlSchemaURI;
+    try {
+      dfdlSchemaURI = new URI(schemaURIString);
+    } catch (URISyntaxException e) {
+      throw UserException.validationError(e)
+          .build(logger);
+    }
+
+    FileDescrip file = negotiator.file();
+    DrillFileSystem fs = file.fileSystem();
+    URI fsSchemaURI = fs.getUri().resolve(dfdlSchemaURI);
+
+
+    DaffodilDataProcessorFactory dpf = new DaffodilDataProcessorFactory();
+    DataProcessor dp;
+    try {
+      dp = dpf.getDataProcessor(fsSchemaURI, validationMode, rootName, rootNamespace);
+    } catch (Exception e) {
+      throw UserException.dataReadError(e)
+          .message(String.format("Failed to get Daffodil DFDL processor for: %s", fsSchemaURI))
+          .addContext(errorContext).addContext(e.getMessage()).build(logger);
+    }
+    // Create the corresponding Drill schema.
+    // Note: this could be a very large schema. Think of a large complex RDBMS schema,
+    // all of it, hundreds of tables, but all part of the same metadata tree.
+    TupleMetadata drillSchema = daffodilDataProcessorToDrillSchema(dp);
+    // Inform Drill about the schema
+    negotiator.tableSchema(drillSchema, true);
+
+    //
+    // DATA TIME: Next we construct the runtime objects, and open files.
+    //
+    // We get the DaffodilMessageParser, which is a stateful driver for daffodil that
+    // actually does the parsing.
+    rowSetLoader = negotiator.build().writer();
+
+    // We construct the Daffodil InfosetOutputter which the daffodil parser uses to
+    // convert infoset event calls to fill in a Drill row via a rowSetLoader.
+    DaffodilDrillInfosetOutputter outputter = new DaffodilDrillInfosetOutputter(rowSetLoader);
+
+    // Now we can setup the dafParser with the outputter it will drive with
+    // the parser-produced infoset.
+    dafParser = new DaffodilMessageParser(dp); // needs further initialization after this.
+    dafParser.setInfosetOutputter(outputter);
+
+    Path dataPath = file.split().getPath();
+    // Lastly, we open the data stream
+    try {
+      dataInputStream = fs.openPossiblyCompressedStream(dataPath);
+    } catch (Exception e) {
+      throw UserException.dataReadError(e)
+          .message(String.format("Failed to open input file: %s", dataPath.toString()))
+          .addContext(errorContext).addContext(e.getMessage()).build(logger);
+    }
+    // And lastly,... tell daffodil the input data stream.
+    dafParser.setInputStream(dataInputStream);
+  }
+
+
+  /**
+   * This is the core of actual processing - data movement from Daffodil to Drill.
+   *
+   * If there is space in the batch, and there is data available to parse
+   * then this calls the daffodil parser, which parses data, delivering it to the rowWriter
+   * by way of the infoset outputter.
+   * <p>
+   * Repeats until the rowWriter is full (a batch is full), or there is no more data, or
+   * a parse error ends execution with a throw.
+   * <p>
+   * Validation errors and other warnings are not errors and are logged but do not cause
+   * parsing to fail/throw.
+   * @return true if there are rows retrieved, false if no rows were retrieved, which means
+   * no more will ever be retrieved (end of data).
+   * @throws RuntimeException on parse errors.
+   */
+  @Override
+  public boolean next() {
+    // Check assumed invariants
+    // We don't know if there is data or not. This could be called on an empty data file.
+    // We DO know that this won't be called if there is no space in the batch for even 1
+    // row.
+    if (dafParser.isEOF()) {
+      return false; // return without even checking for more rows or trying to parse.
+    }
+    while (rowSetLoader.start() && !dafParser.isEOF()) { // we never zero-trip this loop.
+      // the predicate is always true once.
+      try {
+        dafParser.parse();
+        if (dafParser.isProcessingError()) {
+          throw UserException.dataReadError().message(dafParser.getDiagnosticsAsString())
+              .addContext(errorContext).build(logger);
+        }
+        if (dafParser.isValidationError()) {
+          logger.warn(dafParser.getDiagnosticsAsString());
+          // Note that even if daffodil is set to not validate, validation errors may still occur
+          // from DFDL's "recoverableError" assertions.
+        }
+      } catch (Exception e) {
+        throw UserException.dataReadError(e).message("Error parsing file: " + e.getMessage())
+            .addContext(errorContext).build(logger);
+      }
+      // success! We have parsed data and populated a row.
+      rowSetLoader.save();
+    }
+    int nRows = rowSetLoader.rowCount();
+    assert nRows > 0; // This cannot be zero. If the parse failed we will have already thrown out of here.
+    return true;
+  }
+
+  @Override
+  public void close() {
+    if (dataInputStream != null)
+       AutoCloseables.closeSilently(dataInputStream);
+  }
+}