[med-svn] [Git][med-team/igv][master] 2 commits: * d/p/skip_tests_network.patch: add tests requiring internet
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Mar 8 07:41:23 GMT 2024
Andreas Tille pushed to branch master at Debian Med / igv
Commits:
252de171 by Vladimir Petko at 2024-03-08T19:43:55+13:00
* d/p/skip_tests_network.patch: add tests requiring internet
(Closes: #1065646).
- - - - -
42b0712d by Vladimir Petko at 2024-03-08T19:48:34+13:00
changelog
- - - - -
2 changed files:
- debian/changelog
- debian/patches/skip_tests_network.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+igv (2.17.1+dfsg-2) UNRELEASED; urgency=medium
+
+ * d/p/skip_tests_network.patch: add tests requiring internet
+ (Closes: #1065646).
+
+ -- Vladimir Petko <vladimir.petko at canonical.com> Fri, 08 Mar 2024 19:32:23 +1300
+
igv (2.17.1+dfsg-1) unstable; urgency=medium
* New upstream version 2.17.1+dfsg
=====================================
debian/patches/skip_tests_network.patch
=====================================
@@ -117,13 +117,6 @@ Last-Update: 2021-12-21
@Test
public void testRemoteBaiCram() throws Exception {
-@@ -149,4 +155,4 @@
- return counter;
- }
-
--}
-\ No newline at end of file
-+}
--- a/src/test/java/org/broad/igv/sam/cram/IGVReferenceSourceTest.java
+++ b/src/test/java/org/broad/igv/sam/cram/IGVReferenceSourceTest.java
@@ -28,6 +28,7 @@
@@ -538,13 +531,6 @@ Last-Update: 2021-12-21
@Test
public void testQueryAlignments() throws Exception {
-@@ -69,4 +70,4 @@
- // }
-
-
--}
-\ No newline at end of file
-+}
--- a/src/test/java/org/broad/igv/htsget/HtsgetReaderTest.java
+++ b/src/test/java/org/broad/igv/htsget/HtsgetReaderTest.java
@@ -8,6 +8,7 @@
@@ -563,13 +549,6 @@ Last-Update: 2021-12-21
@Test
public void testReadData() throws Exception {
-@@ -33,4 +35,4 @@
-
- }
-
--}
-\ No newline at end of file
-+}
--- a/src/test/java/org/broad/igv/htsget/HtsgetVariantSourceTest.java
+++ b/src/test/java/org/broad/igv/htsget/HtsgetVariantSourceTest.java
@@ -13,6 +13,7 @@
@@ -588,13 +567,6 @@ Last-Update: 2021-12-21
@Test
public void testReadFeatures() throws Exception {
-@@ -50,4 +52,4 @@
- // (new HtsgetVariantSourceTest()).testReadFeatures();
- // }
-
--}
-\ No newline at end of file
-+}
--- a/src/test/java/org/broad/igv/tools/parsers/TestBEDCodecs.java
+++ b/src/test/java/org/broad/igv/tools/parsers/TestBEDCodecs.java
@@ -41,6 +41,7 @@
@@ -655,10 +627,152 @@ Last-Update: 2021-12-21
@Test
public void testBigWigWig() throws IOException {
-@@ -85,4 +89,4 @@
- }
+--- a/src/test/java/org/broad/igv/ucsc/twobit/TwoBitSequenceTest.java
++++ b/src/test/java/org/broad/igv/ucsc/twobit/TwoBitSequenceTest.java
+@@ -1,6 +1,7 @@
+ package org.broad.igv.ucsc.twobit;
+ import org.broad.igv.util.TestUtils;
++import org.junit.Ignore;
+ import org.junit.Test;
+
+ import java.io.IOException;
+@@ -27,6 +28,7 @@
+ assertEquals(expectedSequence.substring(start, end), seqString);
}
--}
-\ No newline at end of file
-+}
+
++ @Ignore("No network access")
+ @Test
+ public void readSequenceRemote() throws IOException {
+
+--- a/src/test/java/org/broad/igv/feature/genome/load/JsonGenomeLoaderTest.java
++++ b/src/test/java/org/broad/igv/feature/genome/load/JsonGenomeLoaderTest.java
+@@ -4,6 +4,7 @@
+ import org.broad.igv.track.Track;
+ import org.broad.igv.util.ResourceLocator;
+ import org.broad.igv.util.TestUtils;
++import org.junit.Ignore;
+ import org.junit.Test;
+
+ import java.io.IOException;
+@@ -15,6 +16,7 @@
+
+ public class JsonGenomeLoaderTest {
+
++ @Ignore("No network access")
+ @Test
+ public void loadGenome() throws IOException {
+ String path = TestUtils.DATA_DIR + "genomes/json/hg38.json";
+--- a/src/test/java/org/broad/igv/ucsc/bb/BBFeatureSourceTest.java
++++ b/src/test/java/org/broad/igv/ucsc/bb/BBFeatureSourceTest.java
+@@ -5,6 +5,7 @@
+ import org.broad.igv.feature.genome.Genome;
+ import org.broad.igv.ucsc.Trix;
+ import org.broad.igv.util.TestUtils;
++import org.junit.Ignore;
+ import org.junit.Test;
+
+ import java.io.IOException;
+@@ -96,7 +97,7 @@
+
+ }
+
+-
++ @Ignore("No network access")
+ @Test
+ public void testBigGenePred() throws IOException {
+
+@@ -121,6 +122,7 @@
+ assertTrue(count > 0);
+ }
+
++ @Ignore("No network access")
+ @Test
+ public void testBigNarrowpeak() throws IOException {
+
+@@ -145,6 +147,7 @@
+ }
+
+ // NOTE: bigInteract is not yet supported in IGV desktop, bigInteract is treated as a plain bed file.
++ @Ignore("No network access")
+ @Test
+ public void testBigInteract() throws IOException {
+
+@@ -193,6 +196,7 @@
+ // })
+
+ // NOTE: bigInteract is not yet supported in IGV desktop, bigInteract is treated as a plain bed file.
++ @Ignore("No network access")
+ @Test
+ public void testBigRmsk() throws IOException {
+
+--- a/src/test/java/org/broad/igv/tdf/TDFReaderTest.java
++++ b/src/test/java/org/broad/igv/tdf/TDFReaderTest.java
+@@ -26,6 +26,7 @@
+ package org.broad.igv.tdf;
+
+ import org.broad.igv.util.ResourceLocator;
++import org.junit.Ignore;
+ import org.junit.Test;
+
+ import java.util.Set;
+@@ -41,6 +42,7 @@
+ */
+ public class TDFReaderTest {
+
++ @Ignore("No network access")
+ @Test
+ public void testReader() throws Exception {
+ String url = "http://data.broadinstitute.org/igvdata/tutorials/hg18/wgEncodeBroadChipSeqSignalK562H3k4me3.wig.gz.tdf";
+--- a/src/test/java/org/broad/igv/util/blat/BlatClientTest.java
++++ b/src/test/java/org/broad/igv/util/blat/BlatClientTest.java
+@@ -6,6 +6,7 @@
+ import org.broad.igv.prefs.Constants;
+ import org.broad.igv.prefs.PreferencesManager;
+ import org.broad.igv.ui.util.MessageUtils;
++import org.junit.Ignore;
+ import org.junit.Test;
+
+ import java.io.IOException;
+@@ -15,6 +16,7 @@
+
+ public class BlatClientTest extends AbstractHeadlessTest {
+
++ @Ignore("No network access")
+ @Test
+ public void blatGET() throws IOException {
+
+@@ -30,6 +32,7 @@
+ assertEquals(34, results.get(0).getqSize());
+ }
+
++ @Ignore("No network access")
+ @Test
+ public void blatPOST() throws IOException {
+
+@@ -45,6 +48,7 @@
+ assertEquals(34, results.get(0).getqSize());
+ }
+
++ @Ignore("No network access")
+ @Test
+ public void blatTooShort() throws IOException {
+
+--- a/src/test/java/org/broad/igv/sam/mods/BaseModificationCountsTest.java
++++ b/src/test/java/org/broad/igv/sam/mods/BaseModificationCountsTest.java
+@@ -9,6 +9,7 @@
+ import org.broad.igv.util.ResourceLocator;
+ import org.broad.igv.util.TestUtils;
+ import org.junit.Before;
++import org.junit.Ignore;
+ import org.junit.Test;
+
+ import java.io.IOException;
+@@ -55,6 +56,7 @@
+ }
+ }
+
++ @Ignore("No network access")
+ @Test
+ public void incrementCounts2() throws IOException {
+
View it on GitLab: https://salsa.debian.org/med-team/igv/-/compare/a33c71d5800b88bf2a8436529feb915508f71f27...42b0712d9f6bc467f424823e909b11ddb805fd8e
--
View it on GitLab: https://salsa.debian.org/med-team/igv/-/compare/a33c71d5800b88bf2a8436529feb915508f71f27...42b0712d9f6bc467f424823e909b11ddb805fd8e
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