OverlapPipelineCommandITCase.java

package edu.mayo.bior.cli.func;

import static org.junit.Assert.assertEquals;

import java.io.File;
import java.io.IOException;

import org.junit.Test;

import com.jayway.jsonpath.JsonPath;

public class OverlapPipelineCommandITCase extends BaseFunctionalTest
{

	@Test
	public void testNoMatch() throws IOException, InterruptedException
	{
		String catRelativePath = "src/test/resources/overlapCatalog.tsv.bgz";
		String catCanonicalPath = (new File(catRelativePath)).getCanonicalPath();

		String stdin = 
				"##fileformat=VCFv4.0\n" +
				"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tJUNIT_JSON\n" +
				"BADCHR\t999\trs116645811X\tX\tY\t.\t.\t.\t{\"CHROM\":\"BADCHR\",\"POS\":\"999\",\"ID\":\"rs116645811X\",\"REF\":\"X\",\"ALT\":\"Y\",\"QUAL\":\".\",\"FILTER\":\".\",\"_id\":\"rs116645811X\",\"_type\":\"variant\",\"_landmark\":\"BADCHR\",\"_refAllele\":\"X\",\"_altAlleles\":[\"Y\"],\"_minBP\":999,\"_maxBP\":999}";

		CommandOutput out = executeScript("bior_overlap", stdin, "-d", catRelativePath);

		assertEquals(out.stderr, 0, out.exit);
		assertEquals("", out.stderr);

		String header = getHeader(out.stdout);
		String[] headerLines = header.split("\n");
		assertEquals(3, headerLines.length);
		assertEquals("##fileformat=VCFv4.0", headerLines[0]);
		assertEquals(String.format("##BIOR=<ID=\"bior.overlapCatalog\",Operation=\"bior_overlap\",DataType=\"JSON\",ShortUniqueName=\"overlapCatalog\",Path=\"%s\">", catCanonicalPath), headerLines[1]);
		assertEquals("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tJUNIT_JSON\tbior.overlapCatalog", headerLines[2]);

		// pull out just data rows
		String data = out.stdout.replace(header, "");
		String[] cols = data.split("\t");

		// If variant is not found, results in empty json string
		assertEquals("{}", cols[9].trim());
	}

	@Test
	public void testMatch() throws IOException, InterruptedException {
		String catRelativePath = "src/test/resources/overlapCatalog.tsv.bgz";
		String catCanonicalPath = (new File(catRelativePath)).getCanonicalPath();

		String stdin = 
				"##fileformat=VCFv4.0\n" +
				"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tJUNIT_JSON\n" +
				"21\t26960070\trs116645811\tG\tA\t.\t.\t.\t{\"CHROM\":\"21\",\"POS\":\"26960070\",\"ID\":\"rs116645811\",\"REF\":\"A\",\"ALT\":\"T\",\"QUAL\":\".\",\"FILTER\":\".\",\"_id\":\"rs116645811\",\"_type\":\"variant\",\"_landmark\":\"21\",\"_refAllele\":\"G\",\"_altAlleles\":[\"A\"],\"_minBP\":26960070,\"_maxBP\":26960070}";
		CommandOutput out = executeScript("bior_overlap", stdin, "-d", catRelativePath);

		assertEquals(out.stderr, 0, out.exit);
		assertEquals("", out.stderr);

		String header = getHeader(out.stdout);
		String[] headerLines = header.split("\n");
		assertEquals(3, headerLines.length);
		assertEquals("##fileformat=VCFv4.0", headerLines[0]);
		assertEquals(String.format("##BIOR=<ID=\"bior.overlapCatalog\",Operation=\"bior_overlap\",DataType=\"JSON\",ShortUniqueName=\"overlapCatalog\",Path=\"%s\">", catCanonicalPath), headerLines[1]);
		assertEquals("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tJUNIT_JSON\tbior.overlapCatalog", headerLines[2]);

		// pull out just data rows
		String data = out.stdout.replace(header, "");
		String[] cols = data.split("\t");

		// If variant is not found, results in empty json string
		// System.out.println(cols.length + cols[9]);
		assertEquals(10, cols.length);
		String json = cols[cols.length - 1];
		assertEquals("21", JsonPath.compile("CHROM").read(json));
	}

	@Test
	public void testCatalogWithProps() throws IOException, InterruptedException {
		String catRelativePath = "src/test/resources/metadata/00-All_GRCh37.tsv.bgz";
		String catCanonicalPath = (new File(catRelativePath))
				.getCanonicalPath();

		String stdin = 
				"##fileformat=VCFv4.0\n" +
				"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tJUNIT_JSON\n" +
				"1\t10144\trs144773400\tTA\tT\t.\t.\t.\t{\"CHROM\":\"1\",\"POS\":\"10144\",\"ID\":\"rs144773400\",\"REF\":\"TA\",\"ALT\":\"T\",\"QUAL\":\".\",\"FILTER\":\".\",\"_id\":\"rs144773400\",\"_type\":\"variant\",\"_landmark\":\"BADCHR\",\"_refAllele\":\"TA\",\"_altAlleles\":[\"T\"],\"_minBP\":10144,\"_maxBP\":10144}";

		CommandOutput out = executeScript("bior_overlap", stdin, "-d", catRelativePath);

		assertEquals(out.stderr, 0, out.exit);
		assertEquals("", out.stderr);

		String header = getHeader(out.stdout);
		String[] headerLines = header.split("\n");
		assertEquals(3, headerLines.length);
		assertEquals("##fileformat=VCFv4.0", headerLines[0]);
		assertEquals(String.format("##BIOR=<ID=\"bior.dbSNP137\",Operation=\"bior_overlap\",DataType=\"JSON\",ShortUniqueName=\"dbSNP137\",Source=\"dbSNP\",Description=\"dbSNP version 137, Patch 10, Human\",Version=\"137\",Build=\"GRCh37.p10\",Path=\"%s\">", catCanonicalPath), headerLines[1]);
		assertEquals("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tJUNIT_JSON\tbior.dbSNP137", headerLines[2]);
	}

}