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Convert Parameter test to junit 5 format
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@zhx828
zhx828 committed Sep 18, 2024
1 parent d54b6c1 commit 94418a5
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20 changes: 0 additions & 20 deletions src/test/java/org/mskcc/oncokb/curation/TestHelper.java
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102 changes: 17 additions & 85 deletions src/test/java/org/mskcc/oncokb/curation/test/ParseProteinChangeParameterizedTest.java
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package org.mskcc.oncokb.curation.test;

import static org.junit.Assert.assertEquals;
import static org.mskcc.oncokb.curation.TestHelper.getTestFileBufferedReader;
import static org.mskcc.oncokb.curation.util.AlterationUtils.parseProteinChange;

import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.*;
import org.apache.commons.lang3.StringUtils;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.CsvFileSource;
import org.mskcc.oncokb.curation.domain.Alteration;
import org.mskcc.oncokb.curation.domain.AlterationAnnotationStatus;
import org.mskcc.oncokb.curation.domain.EntityStatus;

@RunWith(Parameterized.class)
public class ParseProteinChangeParameterizedTest {

private static String TEST_FILE_PATH = "src/test/resources/data/test_parse_protein_change.tsv";

private String proteinChange;
private String expectedConsequence;
private String expectedRefAllele;
private String expectedVarAllele;
private String expectedProteinStart;
private String expectedProteinEnd;

public ParseProteinChangeParameterizedTest(
@ParameterizedTest
@CsvFileSource(files = "src/test/resources/data/test_parse_protein_change.csv", numLinesToSkip = 1)
public void test(
String proteinChange,
String expectedConsequence,
String expectedRefAllele,
String expectedVarAllele,
String expectedProteinStart,
String expectedProteinEnd
) {
this.proteinChange = proteinChange;
this.expectedConsequence = expectedConsequence;
this.expectedRefAllele = expectedRefAllele;
this.expectedVarAllele = expectedVarAllele;
this.expectedProteinStart = expectedProteinStart;
this.expectedProteinEnd = expectedProteinEnd;
}

@Parameterized.Parameters
public static Collection<String[]> getParameters() throws IOException {
return importer();
}

private static List<String[]> importer() throws IOException {
BufferedReader buf = getTestFileBufferedReader(TEST_FILE_PATH);
String line = buf.readLine();
EntityStatus<Alteration> alterationEntityStatus = new AlterationAnnotationStatus();

List<String[]> queries = new ArrayList<>();
int count = 0;
while (line != null) {
if (!line.startsWith("#") && line.trim().length() > 0) {
try {
String parts[] = line.split("\t");
if (parts.length < 1) {
throw new IllegalArgumentException("Test case should have at least protein change. Current case: " + line);
}
String proteinChange = parts[0];
String expectedConsequence = parts.length > 1 ? parts[1].toUpperCase() : "";
String expectedRefAllele = parts.length > 2 ? parts[2] : "";
String expectedVarAllele = parts.length > 3 ? parts[3] : "";
String expectedProteinStart = parts.length > 4 ? parts[4] : "";
String expectedProteinEnd = parts.length > 5 ? parts[5] : "";
String[] query = {
proteinChange,
expectedConsequence,
expectedRefAllele,
expectedVarAllele,
expectedProteinStart,
expectedProteinEnd,
};
queries.add(query);
count++;
} catch (Exception e) {
System.err.println("Could not add line '" + line + "'. " + e);
}
}
line = buf.readLine();
}
System.err.println("Contains " + count + " queries.");
System.err.println("Done.");
parseProteinChange(alterationEntityStatus, proteinChange);

return queries;
testSuite(
alterationEntityStatus.getEntity(),
proteinChange,
Optional.ofNullable(expectedConsequence).orElse("").toUpperCase(),
Optional.ofNullable(expectedRefAllele).orElse(""),
Optional.ofNullable(expectedVarAllele).orElse(""),
Optional.ofNullable(expectedProteinStart).orElse(""),
Optional.ofNullable(expectedProteinEnd).orElse("")
);
}

private void testSuite(
Expand Down Expand Up @@ -126,19 +73,4 @@ private void testSuite(
annotatedAlteration.getEnd() == null ? "" : Integer.toString(annotatedAlteration.getEnd())
);
}

@Test
public void testSummary() {
EntityStatus<Alteration> alterationEntityStatus = new AlterationAnnotationStatus();
parseProteinChange(alterationEntityStatus, proteinChange);
testSuite(
alterationEntityStatus.getEntity(),
proteinChange,
expectedConsequence,
expectedRefAllele,
expectedVarAllele,
expectedProteinStart,
expectedProteinEnd
);
}
}
92 changes: 92 additions & 0 deletions src/test/resources/data/test_parse_protein_change.csv
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#
# List of alterations for testing. Each line is the following format:
#
# Protein Change,Expected consequence,Expected Reference Allele,Expected Variant Allele,Expected Protein Start,Expected Protein End
#

# missense variants
N505I,missense_variant,N,I,505,505
E323_D324delinsKN,missense_variant,,,323,324
814_852mis,missense_variant,,,814,852
IK744KI,missense_variant,IK,KI,744,745

# inframes
Q58_Q59insL,inframe_insertion,,,58,59
58_Q59insL,inframe_insertion,,,58,59
Q58_59insL,inframe_insertion,,,58,59
58_59insL,inframe_insertion,,,58,59
P68_C77dup,inframe_insertion,,,68,77
P68_77dup,inframe_insertion,,,68,77
68_C77dup,inframe_insertion,,,68,77
68_77dup,inframe_insertion,,,68,77
T599delinsIP,inframe_insertion,T,,599,599
599delinsIP,inframe_insertion,,,599,599
599delins,UNKNOWN,,,599,599
599delins2,UNKNOWN,,,599,599
I744KI,inframe_insertion,I,KI,744,744
M1ext-1,inframe_insertion,,,1,1
1ext-1,inframe_insertion,,,1,1
1ext,inframe_insertion,,,1,1
C359del,inframe_deletion,C,,359,359
359del,inframe_deletion,,,359,359
IK744A,inframe_deletion,IK,A,744,745
1459_1468del,inframe_deletion,,,1459,1468
A1459_D1468del,inframe_deletion,,,1459,1468
1459_D1468del,inframe_deletion,,,1459,1468
A1459_1468del,inframe_deletion,,,1459,1468
D1161_S1172delinsE,inframe_deletion,,,1161,1172
D1161_1172delinsE,inframe_deletion,,,1161,1172
1161_S1172delinsE,inframe_deletion,,,1161,1172
1161_1172delinsE,inframe_deletion,,,1161,1172

# frame shifts
S859Afs*12,frameshift_variant,S,,859,859
859Afs*12,frameshift_variant,,,859,859
S859fs*12,frameshift_variant,S,,859,859
G314fs,frameshift_variant,G,,314,314
314fs,frameshift_variant,,,314,314
S330_S352fs,frameshift_variant,,,330,352
330_S352fs,frameshift_variant,,,330,352
S330_352fs,frameshift_variant,,,330,352
330_352fs,frameshift_variant,,,330,352

# truncating mutations
W143_A314trunc,feature_truncation,,,143,314
W143_314trunc,feature_truncation,,,143,314
143_A314trunc,feature_truncation,,,143,314
422_605trunc,feature_truncation,,,422,605
Truncating Mutations,feature_truncation,,,,

# splice variants
596_619splice,splice_region_variant,,,596,619
X1429_splice,splice_region_variant,,,1429,1429
1429_splice,splice_region_variant,,,1429,1429
M1I,start_lost,M,I,1,1
1I,start_lost,,I,1,1
M1?,start_lost,M,?,1,1
A149*,stop_gained,A,*,149,149
149*,stop_gained,,*,149,149
*149*,stop_lost,*,*,149,149

# extension
*757Kext*36,stop_lost,*,,757,757
757Kext*36,stop_lost,*,,757,757
*757ext*36,stop_lost,*,,757,757
*757Kext*,stop_lost,*,,757,757
*757Kext*?,stop_lost,*,,757,757

# synonymous variants
K24K,synonymous_variant,K,K,24,24

# any
449_514mut,any,,,449,514

# Unknown variants
D399,NA,D,,399,399
MCUR1-AKT1 fusion,UNKNOWN,,,,
Fusions,UNKNOWN,,,,
Deletion,UNKNOWN,,,,
Amplification,UNKNOWN,,,,
Oncogenic Mutations,UNKNOWN,,,,
Oncogenic Mutations {excluding V600},UNKNOWN,,,,

92 changes: 0 additions & 92 deletions src/test/resources/data/test_parse_protein_change.tsv
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