[med-svn] [Git][med-team/ncbi-tools6][master] Autopkgtest: improved one test, amended README.test

[Liubov Chuprikova]

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


Commits:
474ec7bc by Liubov Chuprikova at 2018-04-12T12:32:51+00:00
Autopkgtest: improved one test, amended README.test

- - - - -


2 changed files:

- debian/README.test
- debian/tests/run-unit-test


Changes:

=====================================
debian/README.test
=====================================
--- a/debian/README.test
+++ b/debian/README.test
@@ -3,6 +3,6 @@ _______________________________________
 
 This package can be tested by execution
 
-	sh run-unit-test
+	bash run-unit-test
 
 in order to confirm its integrity.


=====================================
debian/tests/run-unit-test
=====================================
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -14,6 +14,13 @@ cp /usr/share/ncbi/data/autofix.prt .
 cp /usr/share/ncbi/data/UniVec.* .
 gunzip *.gz
 
+check_GI()
+{
+	while read GI; do
+		grep -q $GI $1
+	done < $2
+}
+
 ##################################################################
 echo '---asn2asn test---'
 ##################################################################
@@ -59,6 +66,15 @@ gbk="$(grep -c "^LOCUS " nc0225.gbk)"
 [ $genes -eq $gbk ]
 
 ##################################################################
+echo '---asn2idx test---'
+##################################################################
+/usr/bin/asn2idx -p . -x .text < nc0225.text
+[ -s nc0225.idx ]
+[ -s master.idx ]
+awk 'NR == 1 || NR % 50 == 0 {print $1}' nc0225.idx | sed 's/\.1//' > indexed_GIs
+check_GI nc0225.text indexed_GIs
+
+##################################################################
 echo '---asn2xml test---'
 ##################################################################
 /usr/bin/asn2xml -i nc0225.text -b F -o nc0225.xml
@@ -100,12 +116,6 @@ end_out="$(grep -c "<Object-id_id>${last_id}</Object-id_id>" dsRNA_viruses.xgs)"
 # _insdseqget_ and _idfetch_ testing requires internet connection.
 # Comment the lines below to skip the testing.
 grep 'GI:' nc0225.gbk | head | sed 's/.*GI://' > GIs.txt
-check_GI()
-{
-	while read GI; do
-		grep -q $GI $1
-	done < $2
-}
 ##################################################################
 echo '---insdseqget test---'
 ##################################################################
@@ -130,11 +140,6 @@ last_out="$(grep ">" vecscreen.output | tail -1 | sed 's/>Vector //' | sed 's/ .
 [ $last_in==$last_out ]
 
 
-echo '---asn2idx test---'
-/usr/bin/asn2idx -p . -x .text < nc0225.text
-[ -s nc0225.idx ]
-[ -s master.idx ]
-
 echo '---asndisc test---'
 /usr/bin/asndisc -i nc0225.text -a t -o nc0225.disc
 [ -s nc0225.disc ]



View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/474ec7bc5c3143d71ae53ead5ba94bdebe96cf46

---
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/474ec7bc5c3143d71ae53ead5ba94bdebe96cf46
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/debian-med-commit/attachments/20180412/6f0b07d7/attachment-0001.html>