cgivre commented on a change in pull request #2359: URL: https://github.com/apache/drill/pull/2359#discussion_r769004049
########## File path: contrib/format-pdf/src/main/java/org/apache/drill/exec/store/pdf/PdfBatchReader.java ########## @@ -0,0 +1,549 @@ +/* + * 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.pdf; + +import org.apache.drill.common.types.TypeProtos.DataMode; +import org.apache.drill.exec.record.MaterializedField; +import org.apache.drill.shaded.guava.com.google.common.base.Strings; +import org.apache.drill.common.AutoCloseables; +import org.apache.drill.common.exceptions.CustomErrorContext; +import org.apache.drill.common.exceptions.UserException; +import org.apache.drill.common.types.TypeProtos; +import org.apache.drill.common.types.TypeProtos.MinorType; +import org.apache.drill.exec.physical.impl.scan.file.FileScanFramework; +import org.apache.drill.exec.physical.impl.scan.framework.ManagedReader; +import org.apache.drill.exec.physical.resultSet.ResultSetLoader; +import org.apache.drill.exec.physical.resultSet.RowSetLoader; +import org.apache.drill.exec.record.metadata.ColumnMetadata; +import org.apache.drill.exec.record.metadata.MetadataUtils; +import org.apache.drill.exec.record.metadata.SchemaBuilder; +import org.apache.drill.exec.record.metadata.TupleMetadata; +import org.apache.drill.exec.vector.accessor.ScalarWriter; +import org.apache.drill.exec.vector.accessor.TupleWriter; +import org.apache.hadoop.mapred.FileSplit; +import org.apache.pdfbox.pdmodel.PDDocument; +import org.apache.pdfbox.pdmodel.PDDocumentInformation; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import technology.tabula.RectangularTextContainer; +import technology.tabula.Table; + +import java.io.InputStream; +import java.text.ParseException; +import java.text.SimpleDateFormat; +import java.time.Instant; +import java.time.LocalDate; +import java.time.LocalTime; +import java.time.format.DateTimeFormatter; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.List; + +public class PdfBatchReader implements ManagedReader<FileScanFramework.FileSchemaNegotiator> { + + private static final Logger logger = LoggerFactory.getLogger(PdfBatchReader.class); + private static final String NEW_FIELD_PREFIX = "field_"; + private final int maxRecords; + + private final List<PdfColumnWriter> writers; + private FileSplit split; + private CustomErrorContext errorContext; + private RowSetLoader rowWriter; + private InputStream fsStream; + private PDDocument document; + private PdfReaderConfig config; + + private SchemaBuilder builder; + private List<String> columnHeaders; + private int currentRowIndex; + private Table currentTable; + private int currentTableIndex; + private int startingTableIndex; + private FileScanFramework.FileSchemaNegotiator negotiator; + + // Document Metadata Fields + private int pageCount; + private String title; + private String author; + private String subject; + private String keywords; + private String creator; + private String producer; + private Calendar creationDate; + private Calendar modificationDate; + private String trapped; + private int unregisteredColumnCount; + private int columns; + private int tableCount; + private int rows; + private int metadataIndex; + + + // Tables + private List<Table> tables; + + + static class PdfReaderConfig { + final PdfFormatPlugin plugin; + + PdfReaderConfig(PdfFormatPlugin plugin) { + this.plugin = plugin; + } + } + + public PdfBatchReader(PdfReaderConfig readerConfig, int maxRecords) { + this.maxRecords = maxRecords; + this.unregisteredColumnCount = 0; + this.writers = new ArrayList<>(); + this.config = readerConfig; + this.startingTableIndex = readerConfig.plugin.getConfig().getDefaultTableIndex() < 0 ? 0 : readerConfig.plugin.getConfig().getDefaultTableIndex(); + this.currentTableIndex = this.startingTableIndex; + this.columnHeaders = new ArrayList<>(); + } + + @Override + public boolean open(FileScanFramework.FileSchemaNegotiator negotiator) { + System.setProperty("java.awt.headless", "true"); + this.negotiator = negotiator; + + split = negotiator.split(); + errorContext = negotiator.parentErrorContext(); + builder = new SchemaBuilder(); + + openFile(); + + // Get the tables + tables = Utils.extractTablesFromPDF(document); + populateMetadata(); + logger.debug("Found {} tables", tables.size()); + + // Support provided schema + TupleMetadata schema = null; + if (this.negotiator.hasProvidedSchema()) { + schema = this.negotiator.providedSchema(); + this.negotiator.tableSchema(schema, false); + } else { + this.negotiator.tableSchema(buildSchema(), false); + } + ResultSetLoader loader = this.negotiator.build(); + rowWriter = loader.writer(); + + if (negotiator.hasProvidedSchema()) { + buildWriterListFromProvidedSchema(schema); + } else { + buildWriterList(); + } + addImplicitColumnsToSchema(); + + // Prepare for reading + currentRowIndex = 1; // Skip the first line if there are headers + currentTable = tables.get(startingTableIndex); + + return true; + } + + @Override + public boolean next() { + System.setProperty("java.awt.headless", "true"); + + while(!rowWriter.isFull()) { + // Check to see if the limit has been reached + if (rowWriter.limitReached(maxRecords)) { + return false; + } else if (currentRowIndex >= currentTable.getRows().size() && + currentTableIndex < tables.size() && + config.plugin.getConfig().getCombinePages()) { + currentRowIndex = 0; + currentTable = tables.get(currentTableIndex++); + } else if (currentRowIndex >= currentTable.getRows().size()) { + return false; + } + + // Process the row + processRow(currentTable.getRows().get(currentRowIndex)); + currentRowIndex++; + } + return true; + } + + private void processRow(List<RectangularTextContainer> row) { + if (row == null || row.size() == 0) { + return; + } + + String value; + rowWriter.start(); + for (int i = 0; i < row.size(); i++) { + value = row.get(i).getText(); + + if (Strings.isNullOrEmpty(value)) { + continue; + } + writers.get(i).load(row.get(i)); + } + writeMetadata(); + rowWriter.save(); + } + + @Override + public void close() { + if (fsStream != null) { + AutoCloseables.closeSilently(fsStream); + fsStream = null; + } + + if (document != null) { + AutoCloseables.closeSilently(document.getDocument()); + AutoCloseables.closeSilently(document); + document = null; + } + } + + /** + * This method opens the PDF file, and finds the tables + */ + private void openFile() { + try { + fsStream = negotiator.fileSystem().openPossiblyCompressedStream(split.getPath()); + document = PDDocument.load(fsStream); + } catch (Exception e) { + throw UserException + .dataReadError(e) + .message("Failed to open open input file: %s", split.getPath().toString()) + .addContext(e.getMessage()) + .addContext(errorContext) + .build(logger); + } + } + + /** + * Metadata fields are calculated once when the file is opened. This function populates + * the metadata fields so that these are only calculated once. + */ + private void populateMetadata() { + PDDocumentInformation info = document.getDocumentInformation(); + pageCount = document.getNumberOfPages(); + title = info.getTitle(); + author = info.getAuthor(); + subject = info.getSubject(); + keywords = info.getKeywords(); + creator = info.getCreator(); + producer = info.getProducer(); + creationDate = info.getCreationDate(); + modificationDate = info.getModificationDate(); + trapped = info.getTrapped(); + tableCount = tables.size(); + } + + private void addImplicitColumnsToSchema() { + metadataIndex = columns; + // Add to schema + addMetadataColumnToSchema("_page_count", MinorType.INT); + addMetadataColumnToSchema("_title", MinorType.VARCHAR); + addMetadataColumnToSchema("_author", MinorType.VARCHAR); + addMetadataColumnToSchema("_subject", MinorType.VARCHAR); + addMetadataColumnToSchema("_keywords", MinorType.VARCHAR); + addMetadataColumnToSchema("_creator", MinorType.VARCHAR); + addMetadataColumnToSchema("_producer", MinorType.VARCHAR); + addMetadataColumnToSchema("_creation_date", MinorType.TIMESTAMP); + addMetadataColumnToSchema("_modification_date", MinorType.TIMESTAMP); + addMetadataColumnToSchema("_trapped", MinorType.VARCHAR); + addMetadataColumnToSchema("_table_count", MinorType.INT); + } + + private void addMetadataColumnToSchema(String columnName, MinorType dataType) { + int index = rowWriter.tupleSchema().index(columnName); + if (index == -1) { + ColumnMetadata colSchema = MetadataUtils.newScalar(columnName, dataType, DataMode.OPTIONAL); + + // Exclude from wildcard queries + colSchema.setBooleanProperty(ColumnMetadata.EXCLUDE_FROM_WILDCARD, true); + metadataIndex++; + + index = rowWriter.addColumn(colSchema); + } + + writers.add(new StringPdfColumnWriter(index, columnName, rowWriter)); + } + + private void writeMetadata() { + int startingIndex = columnHeaders.size(); + writers.get(startingIndex).getWriter().setInt(pageCount); + writeStringMetadataField(title, startingIndex+1); + writeStringMetadataField(author, startingIndex+2); + writeStringMetadataField(subject, startingIndex+3); + writeStringMetadataField(keywords, startingIndex+4); + writeStringMetadataField(creator, startingIndex+5); + writeStringMetadataField(producer, startingIndex+6); + writeTimestampMetadataField(creationDate, startingIndex+7); + writeTimestampMetadataField(modificationDate, startingIndex+8); + writeStringMetadataField(trapped, startingIndex+9); + writers.get(startingIndex+10).getWriter().setInt(tableCount); + } + + private void writeStringMetadataField(String value, int index) { + if (value == null) { + return; + } + writers.get(index).getWriter().setString(value); + } + + private void writeTimestampMetadataField(Calendar dateValue, int index) { + if (dateValue == null) { + return; + } + + writers.get(index).getWriter().setTimestamp(Instant.ofEpochMilli(dateValue.getTimeInMillis())); + } + + private void addUnknownColumnToSchemaAndCreateWriter (TupleWriter rowWriter, String name) { + int index = rowWriter.tupleSchema().index(name); + if (index == -1) { + ColumnMetadata colSchema = MetadataUtils.newScalar(name, TypeProtos.MinorType.VARCHAR, TypeProtos.DataMode.OPTIONAL); + index = rowWriter.addColumn(colSchema); + } + ScalarWriter colWriter = rowWriter.scalar(index); + + // Create a new column name which will be field_n + String newColumnName = NEW_FIELD_PREFIX + unregisteredColumnCount; + unregisteredColumnCount++; + + // Add a new writer. Since we want the metadata always to be at the end of the schema, we must track the metadata + // index and add this before the metadata, so that the column index tracks with the writer index. + writers.add(metadataIndex, new StringPdfColumnWriter(1, newColumnName, (RowSetLoader) rowWriter)); + + // Increment the metadata index + metadataIndex++; + } + + private TupleMetadata buildSchema() { + Table table = tables.get(startingTableIndex); + columns = table.getColCount(); + rows = table.getRowCount(); + + // Get column header names + columnHeaders = Utils.extractRowValues(table); + + // Add columns to table + int index = 0; + for (String columnName : columnHeaders) { + if (Strings.isNullOrEmpty(columnName)) { + columnName = NEW_FIELD_PREFIX + unregisteredColumnCount; + columnHeaders.set(index, columnName); + unregisteredColumnCount++; + } + builder.addNullable(columnName, MinorType.VARCHAR); + index++; + } + + return builder.buildSchema(); + } + + private void buildWriterList() { + for (String header : columnHeaders) { + writers.add(new StringPdfColumnWriter(columnHeaders.indexOf(header), header, rowWriter)); + } + } + + private void buildWriterListFromProvidedSchema(TupleMetadata schema) { + if (schema == null) { + buildWriterList(); + return; + } + int counter = 0; + for (MaterializedField field: schema.toFieldList()) { + String fieldName = field.getName(); + MinorType type = field.getType().getMinorType(); + columnHeaders.add(fieldName); + + switch (type) { + case VARCHAR: + writers.add(new StringPdfColumnWriter(counter, fieldName, rowWriter)); + break; + case SMALLINT: + case TINYINT: + case INT: + writers.add(new IntPdfColumnWriter(counter, fieldName, rowWriter)); + break; + case BIGINT: + writers.add(new BigIntPdfColumnWriter(counter, fieldName, rowWriter)); + break; + case FLOAT4: + case FLOAT8: + writers.add(new DoublePdfColumnWriter(counter, fieldName, rowWriter)); + break; + case DATE: + writers.add(new DatePdfColumnWriter(counter, fieldName, rowWriter, negotiator)); + break; + case TIME: + writers.add(new TimePdfColumnWriter(counter, fieldName, rowWriter, negotiator)); + break; + case TIMESTAMP: + writers.add(new TimestampPdfColumnWriter(counter, fieldName, rowWriter, negotiator)); + break; + default: + throw UserException.unsupportedError() + .message("PDF Reader with provided schema does not support " + type.name() + " data type.") + .addContext(errorContext) + .build(logger); + } + } + } + + public abstract static class PdfColumnWriter { + final String columnName; + final ScalarWriter writer; + final int columnIndex; + + public PdfColumnWriter(int columnIndex, String columnName, ScalarWriter writer) { + this.columnIndex = columnIndex; + this.columnName = columnName; + this.writer = writer; + } + + public abstract void load (RectangularTextContainer<?> cell); + + public ScalarWriter getWriter() { + return writer; + } + } + + public static class IntPdfColumnWriter extends PdfColumnWriter { + IntPdfColumnWriter (int columnIndex, String columnName, RowSetLoader rowWriter) { + super(columnIndex, columnName, rowWriter.scalar(columnName)); + } + + @Override + public void load(RectangularTextContainer<?> cell) { + writer.setInt(Integer.parseInt(cell.getText())); + } + } + + public static class BigIntPdfColumnWriter extends PdfColumnWriter { + BigIntPdfColumnWriter (int columnIndex, String columnName, RowSetLoader rowWriter) { + super(columnIndex, columnName, rowWriter.scalar(columnName)); + } + + @Override + public void load(RectangularTextContainer<?> cell) { + writer.setLong(Long.parseLong(cell.getText())); + } + } + + public static class DoublePdfColumnWriter extends PdfColumnWriter { + DoublePdfColumnWriter (int columnIndex, String columnName, RowSetLoader rowWriter) { + super(columnIndex, columnName, rowWriter.scalar(columnName)); + } + + @Override + public void load(RectangularTextContainer<?> cell) { + writer.setDouble(Double.parseDouble(cell.getText())); + } + } + + public static class StringPdfColumnWriter extends PdfColumnWriter { + StringPdfColumnWriter (int columnIndex, String columnName, RowSetLoader rowWriter) { + super(columnIndex, columnName, rowWriter.scalar(columnName)); + } + + @Override + public void load(RectangularTextContainer<?> cell) { + writer.setString(cell.getText()); + } + } + + public static class DatePdfColumnWriter extends PdfColumnWriter { + private String dateFormat; + + DatePdfColumnWriter (int columnIndex, String columnName, RowSetLoader rowWriter, FileScanFramework.FileSchemaNegotiator negotiator) { + super(columnIndex, columnName, rowWriter.scalar(columnName)); + + ColumnMetadata metadata = negotiator.providedSchema().metadata(columnName); + if (metadata != null) { + this.dateFormat = metadata.property("drill.format"); + } + } + + @Override + public void load(RectangularTextContainer<?> cell) { + LocalDate localDate; + if (Strings.isNullOrEmpty(this.dateFormat)) { + localDate = LocalDate.parse(cell.getText()); Review comment: Fixed -- This is an automated message from the Apache Git Service. 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