Commit e237f749 authored by Michael Menzel's avatar Michael Menzel

fixed tests

parent b92d0fb1
......@@ -33,7 +33,7 @@ public class SingleTrackBackgroundModelTest {
public void generateInGenes() throws Exception {
TrackEntry te = new TrackEntry("Known genes", "desc", "hg19/inout/knownGenes.bed", "inout", "hg19", "", 20, "", 42);
TrackEntry te = new TrackEntry("Known genes", "desc", "hg19/inout/knownGenes.bed", "inout", "hg19", "", 20, "", 42, "", "");
TrackFactory.getInstance().loadTrack(te);
Track t = TrackFactory.getInstance().getTrackByName("Known genes", Genome.Assembly.hg19);
......
package de.thm.genomeData;
import de.thm.genomeData.sql.DBConnector;
import de.thm.genomeData.tracks.InOutTrack;
import de.thm.genomeData.tracks.Track;
import de.thm.genomeData.tracks.TrackFactory;
import de.thm.misc.Genome;
import de.thm.run.BackendServer;
import org.junit.BeforeClass;
import org.junit.Test;
import java.lang.reflect.Field;
import java.io.File;
import java.util.List;
import java.util.stream.Collectors;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.mockito.Mockito.mock;
/**
* Created by menzel on 7/3/17.
......@@ -27,26 +25,18 @@ public class TrackFactoryTest {
@BeforeClass
public static void getTracks() throws Exception {
//reset track factory
Class<?> inner = tf.getClass();
Field instance = inner.getDeclaredField("instance");
instance.setAccessible(true);
instance.set(tf,null);
BackendServer.dbfilepath = "/home/menzel/Desktop/THM/lfba/enhort/stefan.db";
BackendServer.basePath = new File("/home/menzel/Desktop/THM/lfba/enhort/dat/stefan/").toPath();
DBConnector connector = new DBConnector();
connector.connect();
connector.getAllTracks("WHERE (name like 'House%' OR name like 'known%' OR name like 'exons' OR name like 'contigs') AND assembly = 'hg19'").forEach(tf::loadTrack);
List<Track> tmp = tf.getTracks(Genome.Assembly.hg19);
trackCounter = tmp.size();
assertTrue(tmp.size() > 0);
//set track package
//TrackPackage pack = new TrackPackage(tmp, TrackPackage.PackageName.Basic, "basic tracks", Genome.Assembly.hg19, null);
connector.getAllTracks("WHERE (name like 'House%' OR name like 'known%' OR name like 'contigs') AND genome_assembly = 'hg19'")
.forEach(tf::loadTrack);
trackCounter = tf.getTracks(Genome.Assembly.hg19).size();
Field packs = inner.getDeclaredField("trackPackages");
packs.setAccessible(true);
//packs.set(tf, Collections.singletonList(pack));
if (trackCounter < 1)
throw new Exception("No tracks loaded for TrackFactoryTest");
}
@Test
......@@ -71,8 +61,9 @@ public class TrackFactoryTest {
@Test
public void getTracksById() throws Exception {
List<String> ids = tf.getTracks(Genome.Assembly.hg19).stream().map(t -> Integer.toString(t.getUid())).collect(Collectors.toList());
List<String> ids = tf.getTracks(Genome.Assembly.hg19).stream()
.map(t -> Integer.toString(t.getUid()))
.collect(Collectors.toList());
List<Track> tracks = tf.getTracksById(ids);
......@@ -90,17 +81,4 @@ public class TrackFactoryTest {
public void getTrackByNameException() throws Exception {
tf.getTrackByName("notaname", Genome.Assembly.hg19);
}
@Test
public void addAndCountTest() throws Exception {
assertEquals(trackCounter,tf.getTracks(Genome.Assembly.hg19).size());
assertEquals(trackCounter, tf.getTrackCount());
Track track = mock(InOutTrack.class);
int before = tf.getTrackCount();
tf.addTrack(track);
assertEquals(before+1, tf.getTrackCount());
}
}
\ No newline at end of file
......@@ -6,6 +6,7 @@ import de.thm.misc.Genome;
import org.junit.Test;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
......@@ -452,7 +453,7 @@ public class TracksTest {
double[] exp = new double[]{-0.25, -0.1, -0.1, -0.1, 0.22, 0.22, 0.22, 0.22, 0.431, 0.431, 0.431, 0.431, 0.89, 0.89, 0.89, 0.89, 4.0, 4.0, 4.0, 4.0};
ScoredTrack track = Tracks.bin(TrackFactory.getInstance().createScoredTrack(null,null,null,vals,null,null), 5);
ScoredTrack track = Tracks.bin(TrackFactory.getInstance().createScoredTrack(Collections.emptyList(), Collections.emptyList(), Collections.emptyList(), vals, "noname", ""), 5);
assertArrayEquals(exp, track.getIntervalScore(), 0.05);
}
......
package de.thm.genomeData.sql;
import de.thm.misc.ChromosomSizes;
import de.thm.misc.Genome;
import de.thm.run.BackendServer;
import org.junit.Test;
import java.io.File;
import java.util.List;
import java.util.Map;
import java.util.SortedMap;
import static org.junit.Assert.assertEquals;
......@@ -14,22 +16,16 @@ public class DBConnectorTest {
@Test
public void getAllCellLines() throws Exception {
BackendServer.dbfilepath = "/home/menzel/Desktop/THM/lfba/enhort/stefan.db";
BackendServer.basePath = new File("/home/menzel/Desktop/THM/lfba/enhort/dat/stefan/").toPath();
DBConnector connector = new DBConnector();
connector.connect();
SortedMap<String, List<String>> allCellLines = connector.getAllCellLines();
assertNull(allCellLines.get("ACHN"));
assertNull(allCellLines.get("HeLa-S3"));
assertEquals(36, allCellLines.get("GM").size());
}
@Test
public void getAllTracks() throws Exception {
DBConnector connector = new DBConnector();
connector.connect();
assertEquals(481, connector.getAllTracks().size());
assertEquals(481, connector.getAllTracks().size());
assertNull(allCellLines.get("GM12878"));
}
@Test
......@@ -37,10 +33,9 @@ public class DBConnectorTest {
DBConnector connector = new DBConnector();
connector.connect();
Map<Genome.Assembly, Map<String, Integer>> chrSizes = connector.getChrSizes();
assertEquals((long) ChromosomSizes.getInstance().getChrSize(Genome.Assembly.hg19, "chr5"), 180915260);
assertEquals(chrSizes.get(Genome.Assembly.hg19).get("chr5"), (Integer)180915260);
assertEquals(chrSizes.get(Genome.Assembly.hg38).get("chr12"), (Integer)133275309);
assertEquals((long) ChromosomSizes.getInstance().getChrSize(Genome.Assembly.GRCh38, "chr12"), 133275309);
}
......
package de.thm.misc;
import de.thm.misc.Genome;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import org.junit.Test;
......@@ -76,9 +75,9 @@ public class ChromosomSizesTest {
Pair<String, Long> oldPos= new ImmutablePair<>("chrX", 11014L);
ChromosomSizes chrSizes = ChromosomSizes.getInstance();
Long mappedPos = chrSizes.offset(Genome.Assembly.hg38, oldPos.getLeft()) + oldPos.getRight();
Long mappedPos = chrSizes.offset(Genome.Assembly.GRCh38, oldPos.getLeft()) + oldPos.getRight();
Pair<String, Long> newPos = chrSizes.mapToChr(Genome.Assembly.hg38, mappedPos);
Pair<String, Long> newPos = chrSizes.mapToChr(Genome.Assembly.GRCh38, mappedPos);
assertEquals(oldPos.getLeft(), newPos.getLeft());
assertEquals(oldPos.getRight(), newPos.getRight());
......
package de.thm.misc;
import de.thm.genomeData.sql.DBConnector;
import de.thm.genomeData.tracks.Track;
import de.thm.genomeData.tracks.TrackEntry;
import de.thm.genomeData.tracks.TrackFactory;
import de.thm.run.BackendServer;
import org.junit.Test;
import java.io.File;
public class OffsetTest {
@Test
......@@ -12,14 +15,18 @@ public class OffsetTest {
TrackFactory tf = TrackFactory.getInstance();
TrackEntry entry = new TrackEntry("foo", "desc", "hg19/inout/contigs", "inout", "hg19", "", 20, "", 42);
tf.loadTrack(entry);
BackendServer.dbfilepath = "/home/menzel/Desktop/THM/lfba/enhort/stefan.db";
BackendServer.basePath = new File("/home/menzel/Desktop/THM/lfba/enhort/dat/stefan/").toPath();
Track track = tf.getTrackByName("foo", Genome.Assembly.hg19);
DBConnector connector = new DBConnector();
connector.connect();
connector.getAllTracks("WHERE name = 'Contigs' AND genome_assembly = 'hg19'")
.forEach(tf::loadTrack);
Track track = tf.getTrackByName("contigs", Genome.Assembly.hg19);
for(int i = 0; i < track.getStarts().length; i++){
System.out.println(track.getStarts()[i] + "\t" + track.getEnds()[i]);
//TODO System.out.println(track.getStarts()[i] + "\t" + track.getEnds()[i]);
}
}
}
......@@ -5,6 +5,7 @@ import de.thm.genomeData.tracks.TrackFactory;
import de.thm.genomeData.tracks.Tracks;
import org.junit.Test;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.List;
......@@ -90,9 +91,9 @@ public class TrackBuilderTest {
start3.add(4L);
end3.add(42L);
Track interval1 = mockTrack(start1, end1);
Track interval2 = mockTrack(start2, end2);
Track interval3 = mockTrack(start3, end3);
Track interval1 = mockTrack(start1, end1, 41);
Track interval2 = mockTrack(start2, end2, 42);
Track interval3 = mockTrack(start3, end3, 43);
tracks = new ArrayList<>();
......@@ -104,10 +105,21 @@ public class TrackBuilderTest {
return tracks;
}
private Track mockTrack(List<Long> start, List<Long> end) {
private Track mockTrack(List<Long> start, List<Long> end, int uid) {
Track track = TrackFactory.getInstance().createInOutTrack(start, end,"name", "desc", Genome.Assembly.hg19);
Class<?> inner = track.getClass();
try {
Field id = inner.getSuperclass().getDeclaredField("id");
id.setAccessible(true);
id.setInt(track, uid);
} catch (Exception e) {
e.printStackTrace();
}
TrackFactory.getInstance().addTrack(track);
return track;
......
......@@ -39,7 +39,7 @@ public class SiteFactoryTest {
DBConnector connector = new DBConnector();
connector.connect();
connector.getAllTracks("WHERE name like 'known genes' AND assembly = 'hg19'").forEach(TrackFactory.getInstance()::loadTrack);
connector.getAllTracks("WHERE name like 'known genes' AND genome_assembly = 'hg19'").forEach(TrackFactory.getInstance()::loadTrack);
//mock contigs track
Track contigs = mock(InOutTrack.class);
......
......@@ -8,6 +8,7 @@ import org.junit.Test;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import static org.junit.Assert.assertEquals;
......@@ -34,7 +35,7 @@ public class IndependenceTestTest {
IndependenceTest tester = new IndependenceTest();
ScoredTrack track = mockTrack(null,null, null,null);
ScoredTrack track = mockTrack(Collections.emptyList(), Collections.emptyList(), Collections.emptyList(), Collections.emptyList());
// get expected value
KolmogorovSmirnovTest kolmo = new KolmogorovSmirnovTest();
......
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