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Addressed forgotten TODO.
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@LeeTL1220
LeeTL1220 committed Jun 6, 2018
1 parent 52ef45b commit 76178df
Showing 1 changed file with 21 additions and 35 deletions.
56 changes: 21 additions & 35 deletions src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotationMapUnitTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -280,76 +280,64 @@ private static List<GencodeFuncotation> createGencodeFuncotations(final String c
.map(f -> (GencodeFuncotation) f).collect(Collectors.toList());
}


//TODO: Duplicate code
private List<String> createFieldValuesFromNameList(final String prefix, final List<String> baseFieldList, final int fieldSize) {
final List<String> outList = new ArrayList<>(baseFieldList.size());

for ( int i = 0; i < baseFieldList.size() ; ++i ) {
final String formatString = "%s%0" +
((fieldSize - prefix.length()) > 0 ? fieldSize - prefix.length() : "") +
"d";
outList.add(String.format(formatString, prefix, i+1));
}

return outList;
private List<String> createFieldValuesFromNameList(final String prefix, final List<String> baseFieldList) {
return baseFieldList.stream().map(f -> prefix + f + "value").collect(Collectors.toList());
}

@DataProvider
public Object[][] provideTableFuncotations() {
final List<String> baseFieldNameList = Arrays.asList("FOO", "BAR");
final int fieldSize = 10;
return new Object[][]{
// NOTE: The data field names must match data sources that are checked in for this to work in an expected way:
{
Collections.singletonList(
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("A", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("A", baseFieldNameList),
Allele.create("T"),
GencodeFuncotationFactory.DEFAULT_NAME
)
)},{
Collections.singletonList(
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("B", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("B", baseFieldNameList),
Allele.create("C"),
GencodeFuncotationFactory.DEFAULT_NAME
)
)},{
Collections.singletonList(
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("C", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("C", baseFieldNameList),
Allele.create("GG"),
GencodeFuncotationFactory.DEFAULT_NAME
)
)},{
Collections.singletonList(
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("D", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("D", baseFieldNameList),
Allele.create("T"),
"TestDataSource4"
)
)},{
Arrays.asList(
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("E", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("E", baseFieldNameList),
Allele.create("A"),
"TestDataSource5"
),
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("F", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("F", baseFieldNameList),
Allele.create("AG"),
"TestDataSource5"
),
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("G", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("G", baseFieldNameList),
Allele.create("AT"),
"TestDataSource5"
)
Expand All @@ -363,8 +351,6 @@ public Object[][] provideTableFuncotations() {
@DataProvider
public Object[][] provideTestAdd() {
final List<String> baseFieldNameList = Arrays.asList("TESTFIELD1", "TESTADD");
final int fieldSize = 10;

return new Object[][]{
{"chr3", 178916538, 178916538, "G", "C", FuncotatorReferenceTestUtils.retrieveHg19Chr3Ref(),
ReferenceDataSource.of( IOUtils.getPath(FuncotatorReferenceTestUtils.retrieveHg19Chr3Ref())),
Expand All @@ -373,19 +359,19 @@ public Object[][] provideTestAdd() {
Arrays.asList(
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("E", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("E", baseFieldNameList),
Allele.create("A"),
"TestDataSource5"
),
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("F", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("F", baseFieldNameList),
Allele.create("AG"),
"TestDataSource5"
),
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("G", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("G", baseFieldNameList),
Allele.create("AT"),
"TestDataSource5"
)
Expand All @@ -397,19 +383,19 @@ public Object[][] provideTestAdd() {
Arrays.asList(
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("E", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("E", baseFieldNameList),
Allele.create("A"),
"TestDataSource5"
),
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("F", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("F", baseFieldNameList),
Allele.create("AG"),
"TestDataSource5"
),
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("G", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("G", baseFieldNameList),
Allele.create("AT"),
"TestDataSource5"
)
Expand All @@ -421,19 +407,19 @@ public Object[][] provideTestAdd() {
Arrays.asList(
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("E", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("E", baseFieldNameList),
Allele.create("A"),
"TestDataSource5"
),
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("F", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("F", baseFieldNameList),
Allele.create("AG"),
"TestDataSource5"
),
new TableFuncotation(
baseFieldNameList,
createFieldValuesFromNameList("G", baseFieldNameList, fieldSize),
createFieldValuesFromNameList("G", baseFieldNameList),
Allele.create("AT"),
"TestDataSource5"
)
Expand Down Expand Up @@ -492,19 +478,19 @@ public void testAddingGencodeFuncotationToFuncotationMap() {
// Create a funcotationMap with some pre-made funcotations. Content does not really matter.
final FuncotationMap funcotationMap = FuncotationMap.createNoTranscriptInfo(Arrays.asList(new TableFuncotation(
Arrays.asList("TESTFIELD1", "TESTADD1"),
createFieldValuesFromNameList("E", Arrays.asList("TESTFIELD1", "TESTADD1"), 20),
createFieldValuesFromNameList("E", Arrays.asList("TESTFIELD1", "TESTADD1")),
Allele.create("A"),
"TestDataSource5"
),
new TableFuncotation(
Arrays.asList("TESTFIELD2", "TESTADD2"),
createFieldValuesFromNameList("F", Arrays.asList("TESTFIELD2", "TESTADD2"), 20),
createFieldValuesFromNameList("F", Arrays.asList("TESTFIELD2", "TESTADD2")),
Allele.create("AG"),
"TestDataSource5"
),
new TableFuncotation(
Arrays.asList("TESTFIELD3", "TESTADD3"),
createFieldValuesFromNameList("G", Arrays.asList("TESTFIELD3", "TESTADD3"), 20),
createFieldValuesFromNameList("G", Arrays.asList("TESTFIELD3", "TESTADD3")),
Allele.create("AT"),
"TestDataSource5"
)));
Expand Down

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