[med-svn] [Git][med-team/epcr][master] 3 commits: Drop primer data also in data dir

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / epcr


Commits:
b0266fd1 by Andreas Tille at 2019-06-26T16:11:01Z
Drop primer data also in data dir

- - - - -
a3e4c0a4 by Andreas Tille at 2019-06-26T16:26:03Z
No-parallel - otherwise the build might fail

- - - - -
93c20b89 by Andreas Tille at 2019-06-26T16:27:37Z
Add unit test script to help Saira finalising test

- - - - -


8 changed files:

- + debian/README.test
- debian/changelog
- debian/ncbi-epcr.docs
- debian/rules
- + debian/tests/control
- + debian/tests/data/rbcL-primer.txt
- debian/tests/fetch_test_data.py
- + debian/tests/run-unit-test


Changes:

=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+    sh run-unit-test
+
+in order to confirm its integrity.


=====================================
debian/changelog
=====================================
@@ -11,7 +11,7 @@ epcr (2.3.12-1-8) UNRELEASED; urgency=medium
   [ Saira Hussain ]
   * Add script to fetch the required data for testing
 
- -- Vagrant Default User <vagrant at contrib-testing.localdomain>  Mon, 24 Jun 2019 13:23:50 +0000
+ -- Saira Hussain <saira.h0213 at zoho.com>  Mon, 24 Jun 2019 13:23:50 +0000
 
 epcr (2.3.12-1-7) unstable; urgency=medium
 


=====================================
debian/ncbi-epcr.docs
=====================================
@@ -1,3 +1,6 @@
 README.txt
 README.html
 debian/RETIRED_README.txt
+debian/tests/data
+debian/tests/run-unit-test
+debian/README.test


=====================================
debian/rules
=====================================
@@ -14,7 +14,7 @@ CFLAGS += -I. -g2 -DDEALLOCATE=0 -DVERSION=\"$(DEB_VERSION_UPSTREAM)\" -DVER_MAJ
 LDFLAGS += -L.
 
 %:
-	dh $@
+	dh $@ --no-parallel
 
 override_dh_auto_clean:
 	rm -fr epcr


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/data/rbcL-primer.txt
=====================================
@@ -0,0 +1 @@
+rbcL1/rbcLA	 TTGGCAGCATTYCGAGTAACTCC	 CCTTTRTAACGATCAAGRC


=====================================
debian/tests/fetch_test_data.py
=====================================
@@ -34,7 +34,7 @@ def fetch_ids(dbs, qr):
 
 
 def create_primer(pr):
-    pf = open('rbcL-primer.txt', 'w')
+    pf = open('data/rbcL-primer.txt', 'w')
     pf.write(pr)
     pf.write('\n')
     pf.close()


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,18 @@
+#!/bin/bash
+set -e
+
+pkg=ncbi-epcr
+
+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 ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/data/* "${AUTOPKGTEST_TMP}"
+cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
+
+re-PCR -S ginko.hash -n 5 -g 0 -d 100-300 -o rbcL5.rePCR rbcL-primer.txt



View it on GitLab: https://salsa.debian.org/med-team/epcr/compare/d5680fb645bba60dd59ca5477b47eb3a917af9d0...93c20b89742cd0579abe0e363084d06980c95cc1

-- 
View it on GitLab: https://salsa.debian.org/med-team/epcr/compare/d5680fb645bba60dd59ca5477b47eb3a917af9d0...93c20b89742cd0579abe0e363084d06980c95cc1
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