[med-svn] [Git][med-team/ncbi-tools6][master] Autopkgtest. More tests, but will be more

[Liubov Chuprikova]

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


Commits:
71bca8b8 by Liubov Chuprikova at 2018-03-28T19:34:58+00:00
Autopkgtest. More tests, but will be more

- - - - -


4 changed files:

- debian/copyright
- debian/source/include-binaries
- debian/tests/run-unit-test
- + debian/tests/test-data/dsRNA_viruses.ags.gz


Changes:

=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -13,12 +13,13 @@ Copyright: 1998-1999 Stephane Bortzmeyer <bortzmeyer at pasteur.fr>
            2001-2017 Aaron M. Ucko <ucko at debian.org>
 License: public_domain
 
-Files: debian/tests/test-data/nc0305.aso.gz
+Files: debian/tests/test-data
 Copyright: 1996-2018 NCBI 
 License: public_domain
 Comment: GenBank Release 224.0
- To dowload the file use:
+ To dowload the files use:
 	wget ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/nc0305.aso.gz
+	wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Viruses/dsRNA_viruses.ags.gz
 
 License: public_domain
  The NCBI toolkit has been put into the public domain, completely unfettered:


=====================================
debian/source/include-binaries
=====================================
--- a/debian/source/include-binaries
+++ b/debian/source/include-binaries
@@ -1 +1,2 @@
 debian/tests/test-data/nc0305.aso.gz
+debian/tests/test-data/dsRNA_viruses.ags.gz


=====================================
debian/tests/run-unit-test
=====================================
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -10,7 +10,7 @@ fi
 
 cd $AUTOPKGTEST_TMP
 
-cp /usr/share/doc/${pkg}/test-data/nc0305.aso.gz .
+cp -a /usr/share/doc/${pkg}/test-data/* .
 gunzip *
 
 echo '---asn2all test---'
@@ -48,3 +48,26 @@ echo '---asnval test---'
 /usr/bin/asnval -i nc0305.aso -b -a t -o nc0305.val
 [ -f nc0305.val ]
 [ ! -s nc0305.val ] # empty
+
+echo '---cleanasn test---'
+/usr/bin/cleanasn -b -a t -D t -i nc0305.aso -o nc0305_cleaned.aso
+[ -s nc0305_cleaned.aso ]
+
+echo '---debruijn test---'
+/usr/bin/debruijn -a ncbistdaa -n 4 > debruijn.output
+[ -s debruijn.output ]
+
+echo '---gene2xml test---'
+/usr/bin/gene2xml -b -i dsRNA_viruses.ags -o dsRNA_viruses.xgs
+[ -s dsRNA_viruses.xgs ]
+
+grep 'GI:' nc0305.gbk | head | sed 's/.*GI://' > GIs.txt
+# insdseqget and idfetch testing requires internet connection. Comment lines below
+# to skip the testing.
+echo '---insdseqget test---'
+/usr/bin/insdseqget -n -i GIs.txt > insdset.xml
+[ -s insdset.xml ]
+echo '---idfetch test---'
+/usr/bin/idfetch -G GIs.txt -t 2 -o idfetch.aso
+[ -s idfetch.aso ]
+


=====================================
debian/tests/test-data/dsRNA_viruses.ags.gz
=====================================
Binary files /dev/null and b/debian/tests/test-data/dsRNA_viruses.ags.gz differ



View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/71bca8b826f3d0d2e28c6116e60fa385435197eb

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View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/71bca8b826f3d0d2e28c6116e60fa385435197eb
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