Rewrote and improved test_amrfinder.sh

- Improved reporting of errors and made it run through all tests even if some fail. - Added color to report - Allowed multiple options including declining to download test data
ncbi · Jan 24, 2025 · a09600e · a09600e
1 parent a26045f
commit a09600e
Showing 1 changed file with 100 additions and 47 deletions.
diff --git a/test_amrfinder.sh b/test_amrfinder.sh
@@ -1,6 +1,40 @@
 #!/bin/bash
 
-if [ "$1" == "path" ]
+AMRFINDER_OPTS=" --plus --print_node --threads 6 "
+path=0
+no_download=0
+print_help=0
+while getopts "pnh" opt; do
+    case $opt in
+        p) path=1 ;;
+        n) no_download=1 ;;
+        h) print_help=1 ;;
+    esac
+done
+
+if [ "$print_help" -gt 0 ]
+then
+    echo "test_amrfinder.sh - Run tests"
+    echo "Options: "
+    echo "    -p Test the amrfinder command in path instead of ./amrfinder"
+    echo "    -n Don't attempt to download fresh test data, use the test data in $PWD"
+    echo "    -h print this help message"
+    exit 1
+fi
+
+# some color macros
+if [ "$TERM" == "" ] || [ "$TERM" == "dumb" ] || [ ! -t 1 ]
+then
+    green='' # no colors
+    red=''
+    reset=''
+else
+    green=`tput setaf 2`  # Set green foreground color (code 2)
+    red=`tput setaf 1`    # Set red foreground color (code 1)
+    reset=`tput sgr0`     # Reset color to default
+fi
+
+if [ "$path" -gt 0 ]
 then
     echo "Testing amrfinder command in your \$PATH"
     which amrfinder
@@ -10,57 +44,76 @@ else
     AMRFINDER=./amrfinder
 fi
 
-echo Downloading fresh test data...
-curl -s -f \
-     -O https://raw.githubusercontent.com/ncbi/amr/master/test_dna.fa \
-     -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.fa \
-     -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.gff \
-     -O https://raw.githubusercontent.com/ncbi/amr/master/test_both.expected \
-     -O https://raw.githubusercontent.com/ncbi/amr/master/test_dna.expected \
-     -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.expected
-
-if [ $? != 0 ]
+if [ "$no_download" -gt 0 ]
 then
-    echo "WARNING: Could not download new test data, test data included with installation may"
-    echo "not match the latest database release"
-fi
+    echo "-n option detected, skipping download of test data"
+else
+    echo Downloading fresh test data...
+    curl -k -s -f \
+         -O https://raw.githubusercontent.com/ncbi/amr/master/test_dna.fa \
+         -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.fa \
+         -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.gff \
+         -O https://raw.githubusercontent.com/ncbi/amr/master/test_both.expected \
+         -O https://raw.githubusercontent.com/ncbi/amr/master/test_dna.expected \
+         -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.expected
 
-if ! $AMRFINDER --plus -p test_prot.fa -g test_prot.gff -O Escherichia --print_node > test_prot.got \
-    || ! diff -q test_prot.expected test_prot.got
-then
-    echo "Test failed: "
-    echo "  $AMRFINDER --plus -p test_prot.fa -g test_prot.gff -O Escherichia --print_node > test_prot.got"
-    echo "  diff test_prot.expected test_prot.got "
-    diff test_prot.expected test_prot.got
-    exit 1
+    if [ $? != 0 ]
+    then
+        echo "WARNING: Could not download new test data."
+        echo "Will attempt to use test data in $PWD."
+        echo "Test data included with installation not match the latest database release."
+    fi
 fi
 
-if ! $AMRFINDER --plus -n test_dna.fa -O Escherichia --mutation_all test_dna_mut_all.got --print_node > test_dna.got \
-    || ! diff -q test_dna.expected test_dna.got
-then 
-    echo "Test failed: "
-    echo "  $AMRFINDER --plus -n test_dna.fa -O Escherichia --mutation_all test_dna_mut_all.got --print_node > test_dna.got"
-    echo "  diff test_dna.expected test_dna.got"
-    diff test_dna.expected test_dna.got
-    exit 1
-fi
-#if ! diff -q test_dna_mut_all.expected test_dna_mut_all.got
-#then
-#        echo "Test failed: "
-#    echo "  $AMRFINDER --plus -n test_dna.fa -O Escherichia --mutation_all test_dna_mut_all.got > test_dna.got"
-#    echo "  diff test_dna_mut_all.expected test_dna_mut_all.got"
-#    diff test_dna_mut_all.expected test_dna_mut_all.got
-#    exit 1
-#fi
+TESTS=0
+TEST_TEXT=""
+FAILURES=0
+
+function test_input_file {
+    local test_base="$1"
+    local options="$2"
+
+    TESTS=$(( $TESTS + 1 ))
 
-if ! $AMRFINDER --plus -n test_dna.fa -p test_prot.fa -g test_prot.gff -O Escherichia --print_node > test_both.got \
-    || ! diff -q test_both.expected test_both.got
+    if ! $AMRFINDER $options $AMRFINDER_OPTS > "$test_base.got"
+    then
+        echo "${red}not ok: $AMRFINDER returned a non-zero exit value indicating a failure of the software${reset}"
+        echo "#   $AMRFINDER $options $AMRFINDER_OPTS > $test_base.got"
+        return 1
+    else
+        if ! diff -q "$test_base.expected" "$test_base.got"
+        then
+            echo "${red}not ok: $AMRFINDER returned output different from expected.${reset}"
+            echo "#   diff $test_base.expected $test_base.got"
+            echo "#   To approve run: "
+            echo "#         mv $test_base.got $test_base.expected"
+            TEST_TEXT="$TEST_TEXT"$'\n'"${red}Failed $test_base${reset}";
+            echo ""
+            return 1
+        else
+            echo "${green}ok:${reset} $test_base"
+            return 0
+        fi
+    fi
+}
+
+test_input_file "test_prot" "-p test_prot.fa -g test_prot.gff -O Escherichia"
+FAILURES=$(( $? + $FAILURES ))
+
+test_input_file "test_dna" "-n test_dna.fa -O Escherichia --mutation_all test_dna_mut_all.got"
+FAILURES=$(( $? + $FAILURES ))
+
+test_input_file "test_both" "-n test_dna.fa -g test_prot.gff -p test_prot.fa -O Escherichia"
+FAILURES=$(( $? + $FAILURES ))
+
+echo "Done."
+echo "$TEST_TEXT"
+echo ""
+if [ "$FAILURES" -gt 0 ]
 then
-    echo "Test failed: "
-    echo "  $AMRFINDER --plus -n test_dna.fa -p test_prot.fa -g test_prot.gff -O Escherichia --print_node > test_both.got" 
-    echo "  diff test_both.expected test_both.got "
-    diff test_both.expected test_both.got
+    PASSED=$(( $TESTS - $FAILURES ))
+    echo "${red}not ok overall: $FAILURES out of $TESTS amrfinder tests failed${reset}"
     exit 1
+else
+    echo "${green}ok: all $TESTS amrfinder tests passed ${reset}"
 fi
-
-echo "Success!"