[med-svn] [Git][med-team/ncbi-tools6][master] Autopkgtest: check if NCBI is available to start testing

[Liubov Chuprikova]

Liubov Chuprikova pushed to branch master at Debian Med / ncbi-tools6


Commits:
fac5500e by Liubov Chuprikova at 2018-04-13T18:37:49+00:00
Autopkgtest: check if NCBI is available to start testing

- - - - -


2 changed files:

- debian/tests/control
- debian/tests/run-unit-test


Changes:

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


=====================================
debian/tests/run-unit-test
=====================================
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -113,21 +113,22 @@ end_out="$(grep -c "<Object-id_id>${last_id}</Object-id_id>" dsRNA_viruses.xgs)"
 [ $end_in -eq $end_out ]
 
 
-## _insdseqget_ and _idfetch_ testing requires internet connection.
-## Uncomment the lines below to run the tests provided.
-#grep 'GI:' nc0225.gbk | head | sed 's/.*GI://' > GIs.txt
-###################################################################
-#echo '---insdseqget test---'
-###################################################################
-#/usr/bin/insdseqget -i GIs.txt > insdset.xml
-#[ -s insdset.xml ]
-#check_GI insdset.xml GIs.txt
-###################################################################
-#echo '---idfetch test---'
-###################################################################
-#/usr/bin/idfetch -G GIs.txt -o idfetch.text
-#[ -s idfetch.text ]
-#check_GI idfetch.text GIs.txt
+if nc -z -w 1 www.ncbi.nlm.nih.gov 80; then
+	grep 'GI:' nc0225.gbk | head | sed 's/.*GI://' > GIs.txt
+
+	##################################################################
+	echo '---insdseqget test---'
+	##################################################################
+	/usr/bin/insdseqget -i GIs.txt > insdset.xml
+	[ -s insdset.xml ]
+	check_GI insdset.xml GIs.txt
+	##################################################################
+	echo '---idfetch test---'
+	##################################################################
+	/usr/bin/idfetch -G GIs.txt -o idfetch.text
+	[ -s idfetch.text ]
+	check_GI idfetch.text GIs.txt
+fi
 
 
 ##################################################################



View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/fac5500e8e9b2339d2c9d2a5f534022ba8a0ebe2

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View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/fac5500e8e9b2339d2c9d2a5f534022ba8a0ebe2
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