[med-svn] [Git][med-team/trf][master] 3 commits: tmp

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / trf


Commits:
b982e084 by Nilesh Patra at 2020-07-16T10:38:06+00:00
tmp

- - - - -
9433f83a by Nilesh Patra at 2020-07-16T11:06:05+00:00
Fix exit codes

- - - - -
b6c5733e by Nilesh Patra at 2020-07-16T11:06:27+00:00
Try to diff against results for test check

- - - - -


4 changed files:

- + debian/patches/fix-exit-code.patch
- + debian/patches/series
- debian/tests/control
- debian/tests/run-unit-test


Changes:

=====================================
debian/patches/fix-exit-code.patch
=====================================
@@ -0,0 +1,23 @@
+Author: Nilesh Patra <npatra974 at gmail.com>
+Description: Fix exit return codes on successful completion.
+Last-Changed: Thu July 16, 2020
+--- a/src/trfrun.h
++++ b/src/trfrun.h
+@@ -304,7 +304,7 @@
+ 
+         paramset.endstatus = CTRL_SUCCESS;
+         paramset.running   = 0;
+-        return 1;
++        return 0;
+     }
+     paramset.multisequencefile = 1;
+     paramset.sequenceordinal   = 1;
+@@ -590,7 +590,7 @@
+ 
+     paramset.endstatus = CTRL_SUCCESS;
+     paramset.running   = 0;
+-    return i;
++    return 0;
+ }
+ 
+ /*************************************************


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+fix-exit-code.patch


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
 Tests: run-unit-test
-Depends: @
+Depends: @, html2text, bc
 Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -15,3 +15,44 @@ cd "${AUTOPKGTEST_TMP}"
 gunzip *.gz
 
 trf test_seqs.fasta 2 5 7 80 10 50 2000 -l 10
+
+echo "comparing test results ..."
+html2text test_seqs.fasta.s1.2.5.7.80.10.50.2000.1.html > test.txt
+result=`cat test.txt | grep -A 2 Entropy | grep -Ev 'Entropy|Size'`
+result=${result//_}
+echo "$result"
+
+function check_compare()
+{
+	# $1: result of the command
+	# $2: value to compare result with
+	if (( $(echo "$1 < $2" |bc -l) ))
+	then
+			exit 1
+	fi
+}
+
+IFS='|'
+read -ra ADDR <<< "$result"
+cnt=0
+for i in "${ADDR[@]}";
+do
+	echo $i
+
+	if [ "$cnt" = 2 ]
+	then
+		echo "Compare consensus size"
+		if [ "$i" != 7 ]
+		then
+			exit 1
+		fi
+	fi
+
+	if [ "$cnt" = 12 ]
+	then
+		echo "Comparing extropy"
+		check_compare $i 1.5
+	fi
+	((cnt++))
+done
+



View it on GitLab: https://salsa.debian.org/med-team/trf/-/compare/b6c7bb87829c2a984ba75f1f47e4e09cd1125832...b6c5733e3dc19ca64bf7982253266fe291fa2ba2

-- 
View it on GitLab: https://salsa.debian.org/med-team/trf/-/compare/b6c7bb87829c2a984ba75f1f47e4e09cd1125832...b6c5733e3dc19ca64bf7982253266fe291fa2ba2
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