[med-svn] [Git][med-team/snpeff][master] 4 commits: Now build-time tests are conveniently put under src/test instead of src/main, Maven should see them
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Fri Aug 25 13:25:23 BST 2023
Pierre Gruet pushed to branch master at Debian Med / snpeff
Commits:
c97287cc by Pierre Gruet at 2023-08-25T11:25:54+02:00
Now build-time tests are conveniently put under src/test instead of src/main, Maven should see them
- - - - -
5f8d1f10 by Pierre Gruet at 2023-08-25T11:27:19+02:00
Updating changelog
- - - - -
cf47ec9f by Pierre Gruet at 2023-08-25T12:09:34+02:00
Removing now unused Lintian override
- - - - -
683d2dbf by Pierre Gruet at 2023-08-25T12:10:42+02:00
Changing the path to tests in the autopkgtest
- - - - -
7 changed files:
- debian/changelog
- − debian/libsnpeff-java.lintian-overrides
- debian/patches/exclude_tests_with_missing_data.patch
- debian/patches/update_launching_script_and_config_file_for_Debian.patch
- debian/patches/use_fastq_from_biojava6.patch
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,14 @@
snpeff (5.1+f+dfsg-1) UNRELEASED; urgency=medium
- * New upstream version
+ * Alleviating d/rules and correcting paths in the patches as build-time
+ test .java files are now conveniently located under src/test
+ * Removing now unused Lintian override
+
+ [ Andreas Tille ]
+ * New upstream version 5.1+f+dfsg-1
* Remove trailing whitespace in debian/copyright (routine-update)
- -- Andreas Tille <tille at debian.org> Thu, 24 Aug 2023 11:11:53 +0200
+ -- Pierre Gruet <pgt at debian.org> Fri, 25 Aug 2023 11:26:08 +0200
snpeff (5.1+d+dfsg-3) unstable; urgency=medium
=====================================
debian/libsnpeff-java.lintian-overrides deleted
=====================================
@@ -1,3 +0,0 @@
-# The indicated file is the real jar and not a symlink, but this really does
-# not harm.
-bad-jar-name [usr/share/java/snpeff.jar]
=====================================
debian/patches/exclude_tests_with_missing_data.patch
=====================================
@@ -4,8 +4,8 @@ Author: Pierre Gruet <pgt at debian.org>
Forwarded: not-needed
Last-Update: 2022-01-29
---- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesCytoBands.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesCytoBands.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesCytoBands.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesCytoBands.java
@@ -1,5 +1,6 @@
package org.snpeff.snpEffect.testCases.unity;
@@ -29,8 +29,8 @@ Last-Update: 2022-01-29
@Test
public void test02() {
Log.debug("Test");
---- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesGenomicSequences.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesGenomicSequences.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesGenomicSequences.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesGenomicSequences.java
@@ -1,5 +1,6 @@
package org.snpeff.snpEffect.testCases.unity;
@@ -54,8 +54,8 @@ Last-Update: 2022-01-29
@Test
public void test_02() {
Log.debug("Test");
---- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesNmers.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesNmers.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesNmers.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesNmers.java
@@ -1,5 +1,6 @@
package org.snpeff.snpEffect.testCases.unity;
=====================================
debian/patches/update_launching_script_and_config_file_for_Debian.patch
=====================================
@@ -87,7 +87,7 @@ Last-Update: 2022-02-07
snpEffectPredictor = config.getSnpEffectPredictor();
--- a/src/main/java/org/snpeff/SnpEff.java
+++ b/src/main/java/org/snpeff/SnpEff.java
-@@ -163,7 +163,7 @@
+@@ -166,7 +166,7 @@
public SnpEff() {
genomeVer = ""; // Genome version
@@ -151,8 +151,8 @@ Last-Update: 2022-02-07
String proteinFile = "";
Map<String, String> proteinByTrId;
AutoHashMap<String, List<Transcript>> trByChromo;
---- a/src/main/java/org/snpeff/snpEffect/testCases/integration/CompareEffects.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/CompareEffects.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/CompareEffects.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/CompareEffects.java
@@ -42,7 +42,7 @@
this.verbose = verbose;
this.snpEffectPredictor = snpEffectPredictor;
@@ -180,8 +180,8 @@ Last-Update: 2022-02-07
if (snpEffectPredictor == null) {
config.loadSnpEffectPredictor();
---- a/src/main/java/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.java
@@ -57,7 +57,7 @@
public CompareToEnsembl(String genomeName, boolean throwException) {
this.throwException = throwException;
@@ -191,8 +191,8 @@ Last-Update: 2022-02-07
config.loadSnpEffectPredictor();
snpEffectPredictor = config.getSnpEffectPredictor();
genome = config.getGenome();
---- a/src/main/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java
@@ -33,7 +33,7 @@
*/
public void run() {
@@ -202,8 +202,8 @@ Last-Update: 2022-02-07
config.loadSnpEffectPredictor();
for (Gene gint : config.getGenome().getGenes()) {
---- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesHgvsBase.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesHgvsBase.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesHgvsBase.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesHgvsBase.java
@@ -75,7 +75,7 @@
*/
protected void initSnpEffPredictor(boolean addUtrs, boolean onlyPlusStrand) {
@@ -213,8 +213,8 @@ Last-Update: 2022-02-07
// Initialize factory
int maxGeneLen = 1000;
---- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java
@@ -95,7 +95,7 @@
String expectedResult = Gpr.readFile(resultFile).trim();
@@ -242,16 +242,16 @@ Last-Update: 2022-02-07
SnpEffPredictorFactoryGenBank sepfg = new SnpEffPredictorFactoryGenBank(config, genBankFile);
sepfg.setVerbose(verbose);
sepfg.setCircularCorrectLargeGap(circularCorrectlargeGap);
-@@ -158,7 +158,7 @@
+@@ -157,7 +157,7 @@
+ */
public SnpEffectPredictor buildGff3AndCompare(String genome, String gff3File, String resultFile, boolean readSeqs, boolean createRandSequences) {
-
// Build
- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);
+ Config config = new Config(genome, Config.defaultConfigFile());
SnpEffPredictorFactoryGff3 fgff3 = new SnpEffPredictorFactoryGff3(config);
fgff3.setVerbose(verbose);
if (gff3File != null) fgff3.setFileName(gff3File);
-@@ -195,7 +195,7 @@
+@@ -194,7 +194,7 @@
String expectedResult = Gpr.readFile(resultFile).trim();
// Build
@@ -260,8 +260,8 @@ Last-Update: 2022-02-07
SnpEffPredictorFactoryGtf22 fgtf22 = new SnpEffPredictorFactoryGtf22(config);
fgtf22.setFileName(gtf22);
fgtf22.setVerbose(verbose);
---- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationExonFrame.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationExonFrame.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationExonFrame.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationExonFrame.java
@@ -50,7 +50,7 @@
//---
// Load database and check some numbers
@@ -271,8 +271,8 @@ Last-Update: 2022-02-07
Config config = new Config(genomeName, configFile);
if (verbose) Log.info("Loading database");
SnpEffectPredictor snpEffectPredictor = config.loadSnpEffectPredictor();
---- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationLof.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationLof.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationLof.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationLof.java
@@ -281,7 +281,7 @@
// Load database
@@ -282,8 +282,8 @@ Last-Update: 2022-02-07
config.loadSnpEffectPredictor();
config.setTreatAllAsProteinCoding(true); // For historical reasons...
config.getSnpEffectPredictor().buildForest();
---- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationNmd.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationNmd.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationNmd.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationNmd.java
@@ -25,7 +25,7 @@
// Load database
String genomeVer = "testHg3766Chr1";
@@ -293,8 +293,8 @@ Last-Update: 2022-02-07
config.setTreatAllAsProteinCoding(true); // For historical reasons...
config.loadSnpEffectPredictor();
---- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationVariant.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationVariant.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationVariant.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationVariant.java
@@ -225,7 +225,7 @@
@Test
public void test_25_exon_bases() {
@@ -313,8 +313,8 @@ Last-Update: 2022-02-07
SnpEffPredictorFactoryGtf22 fgtf22 = new SnpEffPredictorFactoryGtf22(config);
fgtf22.setFileName(gtfFile);
fgtf22.setReadSequences(false); // Don't read sequences
---- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBase.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBase.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesBase.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesBase.java
@@ -254,7 +254,7 @@
protected void initSnpEffPredictor(Gene[] genesToAdd) {
// Create a config and force out snpPredictor
@@ -324,8 +324,8 @@ Last-Update: 2022-02-07
}
// Initialize factory
---- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBaseApply.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBaseApply.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesBaseApply.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesBaseApply.java
@@ -44,7 +44,7 @@
protected void initSnpEffPredictor() {
// Create a config and force out snpPredictor
@@ -335,8 +335,8 @@ Last-Update: 2022-02-07
}
// Create predictor
---- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBuild.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBuild.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesBuild.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesBuild.java
@@ -30,7 +30,7 @@
};
=====================================
debian/patches/use_fastq_from_biojava6.patch
=====================================
@@ -50,8 +50,8 @@ Last-Update: 2023-01-12
/**
* DnaAndQualitySequence with an ID
---- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaOverlap.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaOverlap.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaOverlap.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaOverlap.java
@@ -10,7 +10,7 @@
import org.snpeff.binseq.coder.DnaCoder;
import org.snpeff.binseq.comparator.DnaQualSubsequenceComparator;
@@ -61,8 +61,8 @@ Last-Update: 2023-01-12
import org.snpeff.util.Gpr;
import org.snpeff.util.Log;
---- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaSequence.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaSequence.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaSequence.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaSequence.java
@@ -5,8 +5,8 @@
import org.snpeff.binseq.DnaSequence;
import org.snpeff.binseq.DnaSequencePe;
@@ -74,8 +74,8 @@ Last-Update: 2023-01-12
import org.snpeff.fileIterator.FastqFileIterator;
import org.snpeff.util.Gpr;
import org.snpeff.util.Log;
---- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesSequenceIndexer.java
-+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesSequenceIndexer.java
+--- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesSequenceIndexer.java
++++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesSequenceIndexer.java
@@ -8,8 +8,8 @@
import org.snpeff.binseq.comparator.SequenceReference;
import org.snpeff.binseq.indexer.SequenceIndexer;
=====================================
debian/rules
=====================================
@@ -12,10 +12,6 @@ export LC_ALL=C.UTF-8
override_dh_auto_clean:
dh_auto_clean
- # Removing the unit tests we copied into a subdirectory of src/test.
- if [ -e src/test/java/org ]; then \
- $(RM) -rf src/test/java/org; \
- fi
# Replacing our modified org/snpeff/SnpEff.java with the original one.
if [ -e SnpEff.java.old ]; then \
mv SnpEff.java.old src/main/java/org/snpeff/SnpEff.java; \
@@ -27,12 +23,3 @@ override_dh_auto_configure:
cp src/main/java/org/snpeff/SnpEff.java SnpEff.java.old
sed "s/Gpr\.compile.*/\"$$(date --utc --date="@$(SOURCE_DATE_EPOCH)" +"%Y-%m-%d %H:%M" )\";/" SnpEff.java.old > src/main/java/org/snpeff/SnpEff.java
dh_auto_configure
-
-override_dh_auto_test:
-ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- # Moving the unit tests into a subdir of src/test so that Maven sees them.
- mkdir -p src/test/java/org/snpeff/snpEffect/testCases
- cp -a src/main/java/org/snpeff/snpEffect/testCases/integration src/test/java/org/snpeff/snpEffect/testCases
- cp -a src/main/java/org/snpeff/snpEffect/testCases/unity src/test/java/org/snpeff/snpEffect/testCases
- dh_auto_test
-endif
=====================================
debian/tests/run-unit-test
=====================================
@@ -21,8 +21,8 @@ mkdir -p ~/.snpEff
cp /etc/snpeff/snpEff.config ~/.snpEff
mkdir -p "${AUTOPKGTEST_TMP}/org/snpeff/snpEffect/testCases/"
-cp -a src/main/java/org/snpeff/snpEffect/testCases/integration "${AUTOPKGTEST_TMP}/org/snpeff/snpEffect/testCases/"
-cp -a src/main/java/org/snpeff/snpEffect/testCases/unity "${AUTOPKGTEST_TMP}/org/snpeff/snpEffect/testCases/"
+cp -a src/test/java/org/snpeff/snpEffect/testCases/integration "${AUTOPKGTEST_TMP}/org/snpeff/snpEffect/testCases/"
+cp -a src/test/java/org/snpeff/snpEffect/testCases/unity "${AUTOPKGTEST_TMP}/org/snpeff/snpEffect/testCases/"
cp -a tests/ "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/compare/f706b932d6cfae7be7654ec779c2814e4dd84084...683d2dbfcf681cc3cfe8048557c4862d1b91d0ab
--
View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/compare/f706b932d6cfae7be7654ec779c2814e4dd84084...683d2dbfcf681cc3cfe8048557c4862d1b91d0ab
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