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Merge pull request #537 from broadinstitute/cw_duplicatevcfcheck_66084436 

Added command line checks for duplicate files in ROD lists
This commit is contained in:
cwhelan 2014-02-27 13:39:09 -05:00
parent 4395d25726 e61ba8b340
commit 523eeecc15
2 changed files with 74 additions and 2 deletions
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54
public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -455,6 +455,8 @@ public abstract class ArgumentTypeDescriptor {
/**
* Retrieve and parse a collection of RodBindings from the given file.
*
* If the file contains duplicate entries or is empty, an exception will be thrown.
*
* @param file the source file
* @param parsingEngine the engine responsible for parsing
* @param parameterType the Tribble Feature parameter type
@ -471,6 +473,9 @@ public abstract class ArgumentTypeDescriptor {
final String fieldName) throws IOException {
final List<RodBinding> bindings = new ArrayList<>();
// Keep track of the files in this list so that we can check for duplicates and empty files
final Set<String> fileValues = new HashSet<>();
// parse each line separately using the given Tags if none are provided on each line
for ( final String line: FileUtils.readLines(file) ) {
final String[] tokens = line.split("\\s+");
@ -481,14 +486,15 @@ public abstract class ArgumentTypeDescriptor {
}
// use the default tags if none are provided for this binding
else if ( tokens.length == 1 ) {
final ArgumentMatchValue value = new ArgumentMatchStringValue(tokens[0]);
final ArgumentMatchValue value = parseAndValidateArgumentMatchValue(tokens[0], fileValues, fieldName, file.getName());
binding = (RodBinding)parseBinding(value, parameterType, RodBinding.class, bindingName, defaultTags, fieldName);
parsingEngine.addTags(binding, defaultTags);
}
// use the new tags if provided
else if ( tokens.length == 2 ) {
final Tags tags = ParsingMethod.parseTags(fieldName, tokens[0]);
final ArgumentMatchValue value = new ArgumentMatchStringValue(tokens[1]);
final ArgumentMatchValue value = parseAndValidateArgumentMatchValue(tokens[1], fileValues, fieldName, file.getName());
binding = (RodBinding)parseBinding(value, parameterType, RodBinding.class, bindingName, tags, fieldName);
parsingEngine.addTags(binding, tags);
} else {
@ -499,8 +505,52 @@ public abstract class ArgumentTypeDescriptor {
parsingEngine.addRodBinding(binding);
}
if (fileValues.isEmpty()) {
throw new UserException.BadArgumentValue(fieldName, "The input list " + file.getName() + " is empty.");
}
return RodBindingCollection.createRodBindingCollectionOfType(parameterType, bindings);
}
/**
* Validates the resource file name and constructs an ArgumentMatchValue from it.
*
* If the list name has already been processed in the current list, throws a UserException, otherwise
* creates an ArgumentMatchValue to represent the list.
*
* @param token Name of the ROD resource file.
* @param fileValues Set of names of ROD files that have already been processed.
* @param fieldName Name of the argument field being populated.
* @param listFileName Name of the list file being processed.
* @return
*/
private static ArgumentMatchValue parseAndValidateArgumentMatchValue(final String token, final Set<String> fileValues, final String fieldName,
final String listFileName) {
checkForDuplicateFileName(token, fileValues, fieldName, listFileName);
return new ArgumentMatchStringValue(token);
}
/**
* Checks to make sure that the current file name to be processed has not already been processed.
*
* Checks the name of the current file against the names that have already been processed, throwing
* an informative BadArgumentValue exception if it has already been seen. As a side effect adds the
* current file name to the set of filenames that have already been processed.
*
* @param currentFile Name of the current file to process
* @param processedFiles Set of file names that have already been processed
* @param fieldName Name of the argument that is being populated
* @param listName Filename of the list that is being processed
*/
protected static void checkForDuplicateFileName(final String currentFile, final Set<String> processedFiles,
final String fieldName, final String listName) {
if (processedFiles.contains(currentFile)) {
throw new UserException.BadArgumentValue(fieldName, "The input list " + listName + " contains file " + currentFile +
" multiple times, which isn't allowed. If you are intentionally trying to " +
"include the same file more than once, you will need to specify it in separate file lists.");
}
processedFiles.add(currentFile);
}
}
/**

22
public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingCollectionUnitTest.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.testng.Assert;
import org.testng.annotations.BeforeMethod;
@ -105,6 +106,27 @@ public class RodBindingCollectionUnitTest extends BaseTest {
Assert.assertEquals(parsingEngine.getTags(binding), mytags);
}
@Test(expectedExceptions = UserException.BadArgumentValue.class)
public void testDuplicateEntriesInFile() throws IOException {
final File testFile = File.createTempFile("RodBindingCollectionUnitTest.variantListWithDuplicates", ".list");
testFile.deleteOnExit();
final FileWriter writer = new FileWriter(testFile);
writer.write(testVCFFileName + "\n");
writer.write(testVCFFileName + "\n");
writer.close();
ArgumentTypeDescriptor.getRodBindingsCollection(testFile, parsingEngine, VariantContext.class, "foo", mytags, "input");
}
@Test(expectedExceptions = UserException.BadArgumentValue.class)
public void testValidateEmptyFile() throws IOException {
final File testFile = File.createTempFile("RodBindingCollectionUnitTest.emptyVCFList", ".list");
testFile.deleteOnExit();
ArgumentTypeDescriptor.getRodBindingsCollection(testFile, parsingEngine, VariantContext.class, "foo", mytags, "input");
}
@Test
public void testOverrideTagsInFile() throws IOException {
final File testFile = File.createTempFile("RodBindingCollectionUnitTest.overrideTags", ".list");