what a rotten piece of software

ncbi · Jul 7, 2016 · f33890e · f33890e
2 parents 9e5544c + b0f74e2
commit f33890e
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Showing 4 changed files with 79 additions and 9 deletions.
diff --git a/test/fuse/Makefile b/test/fuse/Makefile
@@ -22,7 +22,9 @@
 #
 # ===========================================================================
 
-default: slowtests
+default: runtests
+
+runtests:
 
 TOP ?= $(abspath ../..)
 
@@ -60,11 +62,18 @@ $(TEST_BINDIR)/remote-fuser-test: $(REMOTE_FUSER_TEST_OBJ)
 # slowtests: match output vs sra-pileup
 #
 
-slowtests: runtests
-
-runtests: run-test
+ifeq (linux,$(BUILD_OS))
+    ifneq (Ubuntu,$(OS_DISTRIBUTOR))
+slowtests: run-test
 
 run-test: $(TEST_BINDIR)/remote-fuser-test
 	@$(SRCDIR)/remote_fuser_test.sh standard 180 $(TARGDIR)/bin
 
+    else
+slowtests:
+    endif
+else
+slowtests:
+endif
+
 .PHONY: run-test
diff --git a/test/fuse/remote_fuser_test.sh b/test/fuse/remote_fuser_test.sh
@@ -220,9 +220,15 @@ fi
 ####
 ##  Checking config file data and prepareing environment
 #
-if [ -z "$USER" ]
+EFF_USER=$USER
+if [ -z "$EFF_USER" ]
 then
-    _err_exit "Environment variable \$USER is not set"
+    EFF_USER=`id -n -u`
+    if [ -z "$EFF_USER" ]
+    then
+        EFF_USER="undefined-user"
+        # _err_exit "Environment variable \$USER is not set"
+    fi
 fi
 
 if [ -z "$TEST_DIR" ]
@@ -235,7 +241,7 @@ then
     _err_exit "Can not stat directory '$TEST_DIR'"
 fi
 
-F_TEST_DIR=$TEST_DIR/$USER
+F_TEST_DIR=$TEST_DIR/$EFF_USER
 if [ ! -d "$F_TEST_DIR" ]
 then
     _msg "Creating directory '$F_TEST_DIR'"
@@ -314,6 +320,46 @@ then
     _err_exit "Mount point is in use '$F_MOUNT_DIR'"
 fi
 
+
+##  Here we are clearing old logs
+##
+DAYS_KEEP_LOG=10
+
+SEC_IN_DAY=$(( 60 * 60 * 24 ))
+NOW_DAY=$(( `date +%s` / $SEC_IN_DAY ))
+
+check_remove ()
+{
+    F2R=$1
+
+    if [ -n "$F2R" ]
+    then
+        FILE_DAY=$(( `stat --print="%X" $F2R` / $SEC_IN_DAY ))
+        DALT=$(( $NOW_DAY - $FILE_DAY ))
+        if [ $DAYS_KEEP_LOG -le $DALT ]
+        then
+            _msg Log file is $DALT days old, removing \'$F2R\'
+            echo rm -f $F2R
+            if [ $? -ne 0 ]
+            then
+                _wrn Can not remove file \'$F2R\'
+            fi
+        fi
+    fi
+}
+
+clear_old_logs ()
+{
+    _msg Clearing old logs ...
+
+    for i in `ls $F_LOG_DIR`
+    do
+        check_remove $F_LOG_DIR/$i
+    done
+}
+
+clear_old_logs
+
 ##  Here we are logging and execing
 ##
 F_TIME_STAMP=`date +%Y-%m-%d_%H-%M-%S`

diff --git a/test/kar/kar-test.sh b/test/kar/kar-test.sh
@@ -160,6 +160,7 @@ test_list ()
     echo "Testing test mode..."    
     if ! $KAR -t $ARCHIVE > /dev/null
     then
+        STATUS=$?
         echo "KAR listing failed"
         cleanup
         exit 1
@@ -168,6 +169,7 @@ test_list ()
     echo "   Testing option variation --test ..."
     if ! $KAR --test $ARCHIVE > /dev/null
     then
+        STATUS=$?
         echo "KAR listing failed"
         cleanup
         exit 1
@@ -179,6 +181,7 @@ test_list_options ()
     echo "   Testing longlist: -l mode..."
     if ! $KAR -l -t $ARCHIVE > /dev/null
     then
+        STATUS=$?
         echo "KAR long listing failed"
         cleanup
         exit 1
@@ -191,6 +194,7 @@ test_extract ()
     DIR="extracted"
     if ! $KAR -x $ARCHIVE -d $DIR
     then
+        STATUS=$?
         echo "KAR extraction failed"
         cleanup
         exit 1
@@ -202,6 +206,7 @@ test_extract ()
     DIR="extracted"
     if ! $KAR --extract $ARCHIVE -d $DIR
     then
+        STATUS=$?
         echo "KAR extraction failed"
         cleanup 
         exit 1
@@ -223,20 +228,23 @@ test_cNew_txOld_cmp ()
 
     if ! $OLDKAR -t $ARCHIVE > $RESULT/olist.txt
     then
+        STATUS=$?
         echo "      legacy-KAR could not test the archive...failed"
         cleanup
         exit 1
     fi
 
     if ! $OLDKAR -l -t $ARCHIVE > $RESULT/ollist.txt
     then
+        STATUS=$?
         echo "      legacy-KAR could not test the archive with longlist...failed"
         cleanup
         exit 1
     fi
 
     if ! $OLDKAR -x $ARCHIVE -d $RESULT/o_extracted
     then
+        STATUS=$?
         echo "      legacy-KAR could not extract the archive...failed"
         cleanup
         exit 1
@@ -248,6 +256,7 @@ test_cNew_txOld_cmp ()
     $KAR -t $ARCHIVE > $RESULT/nlist.txt
     if ! diff -w $RESULT/olist.txt $RESULT/nlist.txt > $RESULT/diff.txt
     then
+        STATUS=$?
         echo "      KAR listing differs from legacy...test failed"
         cat $RESULT/diff.txt
         cleanup
@@ -265,6 +274,7 @@ test_cNew_txOld_cmp ()
 
         if [ -s $RESULT/diff.txt ] 
         then
+            STATUS=$?
             echo "      KAR extracting content differs from legacy...test failed"
             cat $RESULT/diff.txt
             cleanup
@@ -293,6 +303,7 @@ test_cOld_txNew_cmp ()
 
     if ! $KAR -t $ARCHIVE > $RESULT/nlist.txt
     then
+        STATUS=$?
         echo "      KAR could not test the archive...failed"
         rm -rf $SS
         cleanup
@@ -301,6 +312,7 @@ test_cOld_txNew_cmp ()
 
     if ! $KAR -l -t $ARCHIVE > $RESULT/nllist.txt
     then
+        STATUS=$?
         echo "      KAR could not test the archive with longlist...failed"
         rm -rf $SS
         cleanup
@@ -309,6 +321,7 @@ test_cOld_txNew_cmp ()
 
     if ! $KAR -x $ARCHIVE -d $RESULT/n_extracted
     then
+        STATUS=$?
         echo "      KAR could not extract the archive...failed"
         rm -rf $SS
         cleanup
@@ -321,6 +334,7 @@ test_cOld_txNew_cmp ()
     $OLDKAR -t $ARCHIVE > $RESULT/olist.txt
     if ! diff -w $RESULT/nlist.txt $RESULT/olist.txt > $RESULT/diff.txt
     then
+        STATUS=$?
         echo "      KAR listing differs from legacy...test failed"
         cat $RESULT/diff.txt
         cleanup
@@ -338,6 +352,7 @@ test_cOld_txNew_cmp ()
 
         if [ -s $RESULT/diff.txt ] 
         then
+            STATUS=$?
             echo "      KAR extracting content differs from legacy...test failed"
             cat $RESULT/diff.txt
             cleanup

diff --git a/tools/bam-loader/loader-imp.c b/tools/bam-loader/loader-imp.c
@@ -2108,12 +2108,12 @@ static rc_t ProcessBAM(char const bamFile[], context_t *ctx, VDatabase *db,
                     else if (rl != clipped_rl) {
                         if (isPrimary) {
                             rc = RC(rcApp, rcFile, rcReading, rcConstraint, rcViolated);
-                            (void)PLOGERR(klogErr, (klogErr, rc, "Primary alignment for '$(name)' has different length ($(len)) then previously recorded secondary alignment. Try to defer secondary alignment processing.",
+                            (void)PLOGERR(klogErr, (klogErr, rc, "Primary alignment for '$(name)' has different length ($(len)) than previously recorded secondary alignment. Try to defer secondary alignment processing.",
                                                     "name=%s,len=%d", name, readlen));
                         }
                         else {
                             rc = SILENT_RC(rcApp, rcFile, rcReading, rcConstraint, rcViolated);
-                            (void)PLOGERR(klogWarn, (klogWarn, rc, "Secondary alignment for '$(name)' has different length ($(len)) then previously recorded primary alignment; discarding secondary alignment.",
+                            (void)PLOGERR(klogWarn, (klogWarn, rc, "Secondary alignment for '$(name)' has different length ($(len)) than previously recorded primary alignment; discarding secondary alignment.",
                                                      "name=%s,len=%d", name, readlen));
                             DISCARD_BAD_SECONDARY;
                             rc = CheckLimitAndLogError();