Pierre Gruet pushed to branch master at Debian Med / libgoby-java
Commits: 229021b1 by Pierre Gruet at 2021-08-09T22:09:44+02:00 Adding autopkgtests - - - - - 01e94515 by Pierre Gruet at 2021-08-09T22:10:34+02:00 Adding the ITP bug number in the changelog - - - - - 4 changed files: - debian/changelog - + debian/tests/control - + debian/tests/test-BZip2ChunkCodec - + debian/tests/test-fasta-to-compact Changes: ===================================== debian/changelog ===================================== @@ -1,13 +1,5 @@ -libgoby-java (3.3.1+dfsg-1) UNRELEASED; urgency=medium +libgoby-java (3.3.1+dfsg1-1) UNRELEASED; urgency=medium - * Initial release (Closes: #<bug>) - TODO: - - Packaging variationanalysis by Campagnelab, needed by goby. - - Go on investigating non-passing tests - (begun in debian/patches/exclude_not_runnable_tests.patch) - - I have put some dependencies in debian/maven.ignoreRules but it may be - wrong. - - See also https://lists.debian.org/debian-med/2013/02/msg00152.html, - although written for a previous upstream version of goby. + * Initial release (Closes: #992044) - -- Pierre Gruet <[email protected]> Fri, 30 Jul 2021 11:48:56 +0200 + -- Pierre Gruet <[email protected]> Mon, 09 Aug 2021 22:10:04 +0200 ===================================== debian/tests/control ===================================== @@ -0,0 +1,7 @@ +Tests: test-fasta-to-compact +Depends: goby-java +Restrictions: allow-stderr + +Tests: test-BZip2ChunkCodec +Depends: libgoby-io-java +Restrictions: allow-stderr ===================================== debian/tests/test-BZip2ChunkCodec ===================================== @@ -0,0 +1,58 @@ +#!/bin/sh +# autopkgtest check: This runs one specific unit test needing only the goby-io +# jar, and also in order to check the patch about Bzip2 is correct. +# (C) 2021 Pierre Gruet. +# Author: Pierre Gruet <[email protected]> +set -e + +pkg=libgoby-java + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + # Double quote below to expand the temporary directory variable now versus + # later is on purpose. + # shellcheck disable=SC2064 + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +# We copy the class of the test inside the temp directory. +mkdir -p "${AUTOPKGTEST_TMP}/org/campagnelab/goby/compression/" +cp goby-distribution/src/test/java/org/campagnelab/goby/compression/TestBZip2ChunkCodec.java ${AUTOPKGTEST_TMP}/org/campagnelab/goby/compression/ + +cd "${AUTOPKGTEST_TMP}" + +# Creating the launcher. +cat <<EOF > Test.java +import org.campagnelab.goby.compression.TestBZip2ChunkCodec; +import java.io.IOException; + +public class Test { + public static void main(String[] args) { + try { + TestBZip2ChunkCodec t = new TestBZip2ChunkCodec(); + t.roundTrip(); + } catch (IOException e) { + System.out.println(e.getMessage()); + System.exit(1); + } + } +} +EOF + +# Removing the junit stuff in the class of the test. +sed -i 's/^import org\.junit\.Test;$//' org/campagnelab/goby/compression/TestBZip2ChunkCodec.java +sed -i 's/^import static junit\.framework\.Assert\.assertNotNull;$//' org/campagnelab/goby/compression/TestBZip2ChunkCodec.java +sed -i 's/@Test//' org/campagnelab/goby/compression/TestBZip2ChunkCodec.java +sed -i 's/assertNotNull(decoded);/if (decoded == null) { System.exit(1); }/' org/campagnelab/goby/compression/TestBZip2ChunkCodec.java + +# Building and running. +javac -cp .:/usr/share/java/goby-io.jar:/usr/share/java/protobuf.jar Test.java org/campagnelab/goby/compression/TestBZip2ChunkCodec.java +java -cp .:/usr/share/java/goby-io.jar:/usr/share/java/protobuf.jar Test + +if [ $? -eq 0 ]; then + echo "Test ran successfully" +else + echo "Test failed to run" + exit 1 +fi ===================================== debian/tests/test-fasta-to-compact ===================================== @@ -0,0 +1,43 @@ +#!/bin/sh +# autopkgtest check: Run goby in fasta-to-compact mode, first with a java call, +# then through the goby shell wrapper. +# (C) 2021 Pierre Gruet. +# Author: Pierre Gruet <[email protected]> +set -e + +pkg=libgoby-java + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + # Double quote below to expand the temporary directory variable now versus + # later is on purpose. + # shellcheck disable=SC2064 + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a test-data/ "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}/test-data/seq-var-test" + +# We launch a command in fasta-to-compact mode without the wrapper. +java -Xmx100m -jar /usr/share/java/goby.jar -m fasta-to-compact -d -o small-synth.compact-reads small-synth.fa | grep "Total logical entries written: 1" + +if [ $? -eq 0 ]; then + echo "Result file correctly outputted by the java invocation" +else + echo "Failed to generate output" + exit 1 +fi + +# Now we delete the output and try to launch a command in fasta-to-compact mode +# by invoking the shell launcher. +rm small-synth.compact-reads +goby 100m fasta-to-compact -d -o small-synth.compact-reads small-synth.fa | grep "Total logical entries written: 1" + +if [ $? -eq 0 ]; then + echo "Result file correctly outputted by the goby call" +else + echo "Failed to generate output" + exit 1 +fi View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/94cb53edc0174d900c2c90aef495ad4209cf37a8...01e9451542b3935c60e20e314dd161e8187214c5 -- View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/94cb53edc0174d900c2c90aef495ad4209cf37a8...01e9451542b3935c60e20e314dd161e8187214c5 You're receiving this email because of your account on salsa.debian.org.
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