[med-svn] [Git][med-team/nanofilt][master] Write and include autopkgtest and its test data

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / nanofilt


Commits:
7b81c899 by Shayan Doust at 2020-06-16T19:57:16+01:00
Write and include autopkgtest and its test data

- - - - -


3 changed files:

- + debian/source/include-binaries
- debian/tests/run-unit-test
- + debian/tests/testdata.tar.xz


Changes:

=====================================
debian/source/include-binaries
=====================================
@@ -0,0 +1 @@
+debian/tests/testdata.tar.xz


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,8 +1,6 @@
 #!/bin/bash
 set -e
 
-pkg=#PACKAGENAME#
-
 export LC_ALL=C.UTF-8
 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
@@ -12,8 +10,32 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
 
+cp -a debian/tests/testdata.tar.xz "${AUTOPKGTEST_TMP}"
 cd "${AUTOPKGTEST_TMP}"
 
-#do_stuff_to_test_package#
+tar -xf testdata.tar.xz
+
+OUTPUT_FILE_1="test1"
+OUTPUT_FILE_2="test2"
+
+gunzip -c reads.fastq.gz | NanoFilt -q 8 -l 500 --headcrop 50 > "$OUTPUT_FILE_1"
+# Double check and make sure file is actually generated and is non-zero size
+if [ -s "$OUTPUT_FILE_1" ]; 
+then
+	echo "[1] PASS"
+else
+	echo "[1] FAIL"
+	exit 1
+fi
+
+gunzip -c reads.fastq.gz | NanoFilt -q 7 --maxGC 0.75 --headcrop 75 | gzip > trimmed-reads.fastq.gz
+echo "[2] PASS"
+
+gunzip -c reads.fastq.gz | NanoFilt -q 6 -s sequencing_summary.txt > "$OUTPUT_FILE_2"
+if [ -s "$OUTPUT_FILE_2" ];
+then
+	echo "[3] PASS"
+else
+	echo "[3] FAIL"
+fi


=====================================
debian/tests/testdata.tar.xz
=====================================
Binary files /dev/null and b/debian/tests/testdata.tar.xz differ



View it on GitLab: https://salsa.debian.org/med-team/nanofilt/-/commit/7b81c8994342059a58d5df23e6a9260735a5f8b2

-- 
View it on GitLab: https://salsa.debian.org/med-team/nanofilt/-/commit/7b81c8994342059a58d5df23e6a9260735a5f8b2
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200616/4b6e39c0/attachment-0001.html>