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Posted to dev@drill.apache.org by GitBox <gi...@apache.org> on 2020/03/13 00:02:12 UTC
[GitHub] [drill] cgivre opened a new pull request #2024: DRILL-7641 Convert
Excel Reader to use Streaming Reader
cgivre opened a new pull request #2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024
# [DRILL-7641](https://issues.apache.org/jira/browse/DRILL-7641): Convert Excel Reader to use Streaming Reader
## Description
The current implementation of the Excel reader uses the Apache POI reader, which uses excessive amounts of memory. As a result, attempting to read large Excel files will cause out of memory errors.
This PR converts the format plugin to use a streaming reader, based still on the POI library. The documentation for the streaming reader can be found here. [1]. This library was billed as a drop in replacement for the POI reader, however I had to make some minor changes to the batch reader to get this to work. Minor code cleanup as well.
[1]: https://github.com/pjfanning/excel-streaming-reader
## Documentation
No user visible changes.
## Testing
All unit tests from the original plugin pass. Additionally, I tested this with large Excel files on my local machine and Drill was able to query them whereas before this PR, Drill would run out of memory.
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[GitHub] [drill] arina-ielchiieva commented on a change in pull request
#2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
arina-ielchiieva commented on a change in pull request #2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399234204
##########
File path: contrib/format-excel/pom.xml
##########
@@ -64,6 +64,11 @@
<version>${project.version}</version>
<scope>test</scope>
</dependency>
+ <dependency>
+ <groupId>com.github.pjfanning</groupId>
+ <artifactId>excel-streaming-reader</artifactId>
+ <version>2.3.1</version>
Review comment:
Please use the latest version of the reader: https://mvnrepository.com/artifact/com.github.pjfanning/excel-streaming-reader
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[GitHub] [drill] arina-ielchiieva commented on a change in pull request
#2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
arina-ielchiieva commented on a change in pull request #2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399250290
##########
File path: contrib/format-excel/src/main/java/org/apache/drill/exec/store/excel/ExcelBatchReader.java
##########
@@ -134,121 +131,131 @@ public ExcelBatchReader(ExcelReaderConfig readerConfig) {
@Override
public boolean open(FileSchemaNegotiator negotiator) {
split = negotiator.split();
- loader = negotiator.build();
+ ResultSetLoader loader = negotiator.build();
rowWriter = loader.writer();
openFile(negotiator);
defineSchema();
return true;
}
+ /**
+ * This method opens the Excel file, initializes the Streaming Excel Reader, and initializes the sheet variable.
+ * @param negotiator The Drill file negotiator object that represents the file system
+ */
private void openFile(FileScanFramework.FileSchemaNegotiator negotiator) {
try {
fsStream = negotiator.fileSystem().openPossiblyCompressedStream(split.getPath());
- workbook = new XSSFWorkbook(fsStream);
+
+ // Open streaming reader
+ workbook = StreamingReader.builder()
+ .rowCacheSize(ROW_CACHE_SIZE)
+ .bufferSize(BUFFER_SIZE)
+ .open(fsStream);
} catch (Exception e) {
throw UserException
.dataReadError(e)
.message("Failed to open open input file: %s", split.getPath().toString())
- .message(e.getMessage())
+ .addContext(e.getMessage())
.build(logger);
}
-
- // Evaluate formulae
- evaluator = workbook.getCreationHelper().createFormulaEvaluator();
-
- workbook.setMissingCellPolicy(Row.MissingCellPolicy.CREATE_NULL_AS_BLANK);
sheet = getSheet();
}
/**
* This function defines the schema from the header row.
- * @return TupleMedata of the discovered schema
*/
- private TupleMetadata defineSchema() {
+ private void defineSchema() {
SchemaBuilder builder = new SchemaBuilder();
- return getColumnHeaders(builder);
+ getColumnHeaders(builder);
}
- private TupleMetadata getColumnHeaders(SchemaBuilder builder) {
+ private void getColumnHeaders(SchemaBuilder builder) {
//Get the field names
- int columnCount = 0;
+ int columnCount;
- // Case for empty sheet.
- if (sheet.getFirstRowNum() == 0 && sheet.getLastRowNum() == 0) {
- return builder.buildSchema();
+ // Case for empty sheet
+ if (sheet.getLastRowNum() == 0) {
+ builder.buildSchema();
+ return;
}
+ rowIterator = sheet.iterator();
+
// Get the number of columns.
columnCount = getColumnCount();
- excelFieldNames = new ArrayList<>(columnCount);
- cellWriterArray = new ArrayList<>(columnCount);
- rowIterator = sheet.iterator();
+ excelFieldNames = new ArrayList<>();
+ cellWriterArray = new ArrayList<>();
//If there are no headers, create columns names of field_n
if (readerConfig.headerRow == -1) {
String missingFieldName;
- for (int i = 0; i < columnCount; i++) {
+ int i = 0;
+
+ for(Cell c : currentRow) {
Review comment:
```suggestion
for (Cell c : currentRow) {
```
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[GitHub] [drill] arina-ielchiieva commented on a change in pull request
#2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
arina-ielchiieva commented on a change in pull request #2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399237321
##########
File path: contrib/format-excel/src/main/java/org/apache/drill/exec/store/excel/ExcelBatchReader.java
##########
@@ -134,121 +126,131 @@ public ExcelBatchReader(ExcelReaderConfig readerConfig) {
@Override
public boolean open(FileSchemaNegotiator negotiator) {
split = negotiator.split();
- loader = negotiator.build();
+ ResultSetLoader loader = negotiator.build();
rowWriter = loader.writer();
openFile(negotiator);
defineSchema();
return true;
}
+ /**
+ * This method opens the Excel file, initializes the Streaming Excel Reader, and initializes the sheet variable.
+ * @param negotiator The Drill file negotiator object that represents the file system
+ */
private void openFile(FileScanFramework.FileSchemaNegotiator negotiator) {
try {
fsStream = negotiator.fileSystem().openPossiblyCompressedStream(split.getPath());
- workbook = new XSSFWorkbook(fsStream);
+
+ // Open streaming reader
+ workbook = StreamingReader.builder()
+ .rowCacheSize(100) // Possible configuration option?
+ .bufferSize(4096) // Possible configuration option?
+ .open(fsStream);
} catch (Exception e) {
throw UserException
.dataReadError(e)
.message("Failed to open open input file: %s", split.getPath().toString())
.message(e.getMessage())
Review comment:
Can't have two messages, use addContext for the second message instead.
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[GitHub] [drill] cgivre commented on issue #2024: DRILL-7641: Convert Excel
Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
cgivre commented on issue #2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#issuecomment-604989138
@arina-ielchiieva
Thank you for the review. I addressed all your comments and rebased to latest master.
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[GitHub] [drill] asfgit closed pull request #2024: DRILL-7641: Convert Excel
Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
asfgit closed pull request #2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024
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[GitHub] [drill] arina-ielchiieva commented on a change in pull request
#2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
arina-ielchiieva commented on a change in pull request #2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399237699
##########
File path: contrib/format-excel/src/main/java/org/apache/drill/exec/store/excel/ExcelBatchReader.java
##########
@@ -134,121 +126,131 @@ public ExcelBatchReader(ExcelReaderConfig readerConfig) {
@Override
public boolean open(FileSchemaNegotiator negotiator) {
split = negotiator.split();
- loader = negotiator.build();
+ ResultSetLoader loader = negotiator.build();
rowWriter = loader.writer();
openFile(negotiator);
defineSchema();
return true;
}
+ /**
+ * This method opens the Excel file, initializes the Streaming Excel Reader, and initializes the sheet variable.
+ * @param negotiator The Drill file negotiator object that represents the file system
+ */
private void openFile(FileScanFramework.FileSchemaNegotiator negotiator) {
try {
fsStream = negotiator.fileSystem().openPossiblyCompressedStream(split.getPath());
- workbook = new XSSFWorkbook(fsStream);
+
+ // Open streaming reader
+ workbook = StreamingReader.builder()
+ .rowCacheSize(100) // Possible configuration option?
Review comment:
Please either make values as conf options or create constants.
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[GitHub] [drill] cgivre commented on a change in pull request #2024:
DRILL-7641: Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
cgivre commented on a change in pull request #2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399246672
##########
File path: contrib/format-excel/src/test/java/org/apache/drill/exec/store/excel/TestExcelFormat.java
##########
@@ -339,11 +339,12 @@ public void testInconsistentDataQuery() throws Exception {
testBuilder()
.sqlQuery(sql)
- .ordered().baselineColumns("col1", "col2")
- .baselineValues("1.0", "Bob")
- .baselineValues("2.0", "Steve")
- .baselineValues("3.0", "Anne")
- .baselineValues("Bob", "3.0")
+ .ordered()
Review comment:
Fixed
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[GitHub] [drill] arina-ielchiieva commented on a change in pull request
#2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
arina-ielchiieva commented on a change in pull request #2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399236022
##########
File path: contrib/format-excel/src/test/java/org/apache/drill/exec/store/excel/TestExcelFormat.java
##########
@@ -339,11 +339,12 @@ public void testInconsistentDataQuery() throws Exception {
testBuilder()
.sqlQuery(sql)
- .ordered().baselineColumns("col1", "col2")
- .baselineValues("1.0", "Bob")
- .baselineValues("2.0", "Steve")
- .baselineValues("3.0", "Anne")
- .baselineValues("Bob", "3.0")
+ .ordered()
Review comment:
Your test does not include order by thus returned result order is unpredictable. Please change to unordered here and in other tests above.
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[GitHub] [drill] cgivre commented on a change in pull request #2024:
DRILL-7641: Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
cgivre commented on a change in pull request #2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399246616
##########
File path: contrib/format-excel/src/main/java/org/apache/drill/exec/store/excel/ExcelBatchReader.java
##########
@@ -68,20 +66,18 @@
private final ExcelReaderConfig readerConfig;
- private XSSFSheet sheet;
+ private Sheet sheet;
- private XSSFWorkbook workbook;
+ private Row currentRow;
- private InputStream fsStream;
+ private Workbook workbook;
- private FormulaEvaluator evaluator;
+ private InputStream fsStream;
private ArrayList<String> excelFieldNames;
Review comment:
Fixed
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[GitHub] [drill] arina-ielchiieva commented on issue #2024: DRILL-7641:
Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
arina-ielchiieva commented on issue #2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#issuecomment-604996784
+1, LGTM
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[GitHub] [drill] arina-ielchiieva commented on a change in pull request
#2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
arina-ielchiieva commented on a change in pull request #2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399236555
##########
File path: contrib/format-excel/src/main/java/org/apache/drill/exec/store/excel/ExcelBatchReader.java
##########
@@ -289,83 +298,78 @@ public boolean next() {
}
private boolean nextLine(RowSetLoader rowWriter) {
- if( sheet.getFirstRowNum() == 0 && sheet.getLastRowNum() == 0) {
+ if(sheet.getLastRowNum() == 0) {
Review comment:
```suggestion
if (sheet.getLastRowNum() == 0) {
```
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[GitHub] [drill] cgivre commented on a change in pull request #2024:
DRILL-7641: Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
cgivre commented on a change in pull request #2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399254035
##########
File path: contrib/format-excel/src/main/java/org/apache/drill/exec/store/excel/ExcelBatchReader.java
##########
@@ -134,121 +131,131 @@ public ExcelBatchReader(ExcelReaderConfig readerConfig) {
@Override
public boolean open(FileSchemaNegotiator negotiator) {
split = negotiator.split();
- loader = negotiator.build();
+ ResultSetLoader loader = negotiator.build();
rowWriter = loader.writer();
openFile(negotiator);
defineSchema();
return true;
}
+ /**
+ * This method opens the Excel file, initializes the Streaming Excel Reader, and initializes the sheet variable.
+ * @param negotiator The Drill file negotiator object that represents the file system
+ */
private void openFile(FileScanFramework.FileSchemaNegotiator negotiator) {
try {
fsStream = negotiator.fileSystem().openPossiblyCompressedStream(split.getPath());
- workbook = new XSSFWorkbook(fsStream);
+
+ // Open streaming reader
+ workbook = StreamingReader.builder()
+ .rowCacheSize(ROW_CACHE_SIZE)
+ .bufferSize(BUFFER_SIZE)
+ .open(fsStream);
} catch (Exception e) {
throw UserException
.dataReadError(e)
.message("Failed to open open input file: %s", split.getPath().toString())
- .message(e.getMessage())
+ .addContext(e.getMessage())
.build(logger);
}
-
- // Evaluate formulae
- evaluator = workbook.getCreationHelper().createFormulaEvaluator();
-
- workbook.setMissingCellPolicy(Row.MissingCellPolicy.CREATE_NULL_AS_BLANK);
sheet = getSheet();
}
/**
* This function defines the schema from the header row.
- * @return TupleMedata of the discovered schema
*/
- private TupleMetadata defineSchema() {
+ private void defineSchema() {
SchemaBuilder builder = new SchemaBuilder();
- return getColumnHeaders(builder);
+ getColumnHeaders(builder);
}
- private TupleMetadata getColumnHeaders(SchemaBuilder builder) {
+ private void getColumnHeaders(SchemaBuilder builder) {
//Get the field names
- int columnCount = 0;
+ int columnCount;
- // Case for empty sheet.
- if (sheet.getFirstRowNum() == 0 && sheet.getLastRowNum() == 0) {
- return builder.buildSchema();
+ // Case for empty sheet
+ if (sheet.getLastRowNum() == 0) {
+ builder.buildSchema();
+ return;
}
+ rowIterator = sheet.iterator();
+
// Get the number of columns.
columnCount = getColumnCount();
- excelFieldNames = new ArrayList<>(columnCount);
- cellWriterArray = new ArrayList<>(columnCount);
- rowIterator = sheet.iterator();
+ excelFieldNames = new ArrayList<>();
+ cellWriterArray = new ArrayList<>();
//If there are no headers, create columns names of field_n
if (readerConfig.headerRow == -1) {
String missingFieldName;
- for (int i = 0; i < columnCount; i++) {
+ int i = 0;
+
+ for(Cell c : currentRow) {
Review comment:
Fixed
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[GitHub] [drill] cgivre commented on a change in pull request #2024:
DRILL-7641: Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
cgivre commented on a change in pull request #2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399247726
##########
File path: contrib/format-excel/src/main/java/org/apache/drill/exec/store/excel/ExcelBatchReader.java
##########
@@ -134,121 +126,131 @@ public ExcelBatchReader(ExcelReaderConfig readerConfig) {
@Override
public boolean open(FileSchemaNegotiator negotiator) {
split = negotiator.split();
- loader = negotiator.build();
+ ResultSetLoader loader = negotiator.build();
rowWriter = loader.writer();
openFile(negotiator);
defineSchema();
return true;
}
+ /**
+ * This method opens the Excel file, initializes the Streaming Excel Reader, and initializes the sheet variable.
+ * @param negotiator The Drill file negotiator object that represents the file system
+ */
private void openFile(FileScanFramework.FileSchemaNegotiator negotiator) {
try {
fsStream = negotiator.fileSystem().openPossiblyCompressedStream(split.getPath());
- workbook = new XSSFWorkbook(fsStream);
+
+ // Open streaming reader
+ workbook = StreamingReader.builder()
+ .rowCacheSize(100) // Possible configuration option?
Review comment:
Converted to constants.
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[GitHub] [drill] cgivre commented on a change in pull request #2024:
DRILL-7641: Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
cgivre commented on a change in pull request #2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399246903
##########
File path: contrib/format-excel/src/main/java/org/apache/drill/exec/store/excel/ExcelBatchReader.java
##########
@@ -134,121 +126,131 @@ public ExcelBatchReader(ExcelReaderConfig readerConfig) {
@Override
public boolean open(FileSchemaNegotiator negotiator) {
split = negotiator.split();
- loader = negotiator.build();
+ ResultSetLoader loader = negotiator.build();
rowWriter = loader.writer();
openFile(negotiator);
defineSchema();
return true;
}
+ /**
+ * This method opens the Excel file, initializes the Streaming Excel Reader, and initializes the sheet variable.
+ * @param negotiator The Drill file negotiator object that represents the file system
+ */
private void openFile(FileScanFramework.FileSchemaNegotiator negotiator) {
try {
fsStream = negotiator.fileSystem().openPossiblyCompressedStream(split.getPath());
- workbook = new XSSFWorkbook(fsStream);
+
+ // Open streaming reader
+ workbook = StreamingReader.builder()
+ .rowCacheSize(100) // Possible configuration option?
+ .bufferSize(4096) // Possible configuration option?
+ .open(fsStream);
} catch (Exception e) {
throw UserException
.dataReadError(e)
.message("Failed to open open input file: %s", split.getPath().toString())
.message(e.getMessage())
Review comment:
Changed to addContext()
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[GitHub] [drill] arina-ielchiieva commented on a change in pull request
#2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
arina-ielchiieva commented on a change in pull request #2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399236600
##########
File path: contrib/format-excel/src/main/java/org/apache/drill/exec/store/excel/ExcelBatchReader.java
##########
@@ -267,14 +269,21 @@ private XSSFSheet getSheet() {
/**
* Returns the column count. There are a few gotchas here in that we have to know the header row and count the physical number of cells
- * in that row. Since the user can define the header row,
+ * in that row. This function also has to move the rowIterator object to the first row of data.
* @return The number of actual columns
*/
private int getColumnCount() {
+ // Initialize
+ currentRow = rowIterator.next();
int rowNumber = readerConfig.headerRow > 0 ? sheet.getFirstRowNum() : 0;
- XSSFRow sheetRow = sheet.getRow(rowNumber);
- return sheetRow != null ? sheetRow.getPhysicalNumberOfCells() : 0;
+ // If the headerRow is greater than zero, advance the iterator to the first row of data
+ // This is unfortunately necessary since the streaming reader eliminated the getRow() method.
+ for(int i = 1; i < rowNumber; i++) {
Review comment:
```suggestion
for (int i = 1; i < rowNumber; i++) {
```
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[GitHub] [drill] cgivre commented on issue #2024: DRILL-7641: Convert Excel
Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
cgivre commented on issue #2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#issuecomment-604993669
@arina-ielchiieva
Thanks for the review. Commits squashed.
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[GitHub] [drill] arina-ielchiieva commented on a change in pull request
#2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
arina-ielchiieva commented on a change in pull request #2024: DRILL-7641 Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399234441
##########
File path: contrib/format-excel/src/main/java/org/apache/drill/exec/store/excel/ExcelBatchReader.java
##########
@@ -68,20 +66,18 @@
private final ExcelReaderConfig readerConfig;
- private XSSFSheet sheet;
+ private Sheet sheet;
- private XSSFWorkbook workbook;
+ private Row currentRow;
- private InputStream fsStream;
+ private Workbook workbook;
- private FormulaEvaluator evaluator;
+ private InputStream fsStream;
private ArrayList<String> excelFieldNames;
Review comment:
Use List instead of ArrayList here and in other fields below.
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[GitHub] [drill] cgivre commented on a change in pull request #2024:
DRILL-7641: Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
cgivre commented on a change in pull request #2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399246726
##########
File path: contrib/format-excel/src/main/java/org/apache/drill/exec/store/excel/ExcelBatchReader.java
##########
@@ -289,83 +298,78 @@ public boolean next() {
}
private boolean nextLine(RowSetLoader rowWriter) {
- if( sheet.getFirstRowNum() == 0 && sheet.getLastRowNum() == 0) {
+ if(sheet.getLastRowNum() == 0) {
Review comment:
Fixed
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[GitHub] [drill] cgivre commented on a change in pull request #2024:
DRILL-7641: Convert Excel Reader to use Streaming Reader
Posted by GitBox <gi...@apache.org>.
cgivre commented on a change in pull request #2024: DRILL-7641: Convert Excel Reader to use Streaming Reader
URL: https://github.com/apache/drill/pull/2024#discussion_r399246782
##########
File path: contrib/format-excel/src/main/java/org/apache/drill/exec/store/excel/ExcelBatchReader.java
##########
@@ -267,14 +269,21 @@ private XSSFSheet getSheet() {
/**
* Returns the column count. There are a few gotchas here in that we have to know the header row and count the physical number of cells
- * in that row. Since the user can define the header row,
+ * in that row. This function also has to move the rowIterator object to the first row of data.
* @return The number of actual columns
*/
private int getColumnCount() {
+ // Initialize
+ currentRow = rowIterator.next();
int rowNumber = readerConfig.headerRow > 0 ? sheet.getFirstRowNum() : 0;
- XSSFRow sheetRow = sheet.getRow(rowNumber);
- return sheetRow != null ? sheetRow.getPhysicalNumberOfCells() : 0;
+ // If the headerRow is greater than zero, advance the iterator to the first row of data
+ // This is unfortunately necessary since the streaming reader eliminated the getRow() method.
+ for(int i = 1; i < rowNumber; i++) {
Review comment:
Fixed
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