add nextflow d30e48d

nextflow/tests/checks/run.sh

@@ -0,0 +1,106 @@
+#!/bin/bash 
+set -u 
+trap "exit" INT
+
+NORMAL=$(tput sgr0)
+GREEN=$(tput setaf 2; tput bold)
+YELLOW=$(tput setaf 3)
+RED=$(tput setaf 1)
+
+function echo_red() {
+    echo -e "$RED$*$NORMAL"
+}
+
+function echo_green() {
+    echo -e "$GREEN$*$NORMAL"
+}
+
+function echo_yellow() {
+    echo -e "$YELLOW$*$NORMAL"
+}
+
+
+#
+# Some vars 
+#
+NXF_CMD=${NXF_CMD:-nextflow}
+NXF_SYNTAX_PARSER=${NXF_SYNTAX_PARSER:-v2}
+REPORT=$PWD/.report
+WITH_DOCKER=${WITH_DOCKER:=''}
+
+#
+# Clean scratch dir 
+#
+export NXF_WORK=$PWD/scratch
+rm -rf $NXF_WORK
+
+
+function run_checks() {
+  NXF_SCRIPT="../../$1"
+  NXF_RUN="$NXF_CMD -q run $NXF_SCRIPT"
+  export NXF_SCRIPT
+  export NXF_CMD
+  export NXF_RUN
+  set +e   
+            
+  if [ -f $1/.checks ]; then 
+     cd $basename; 
+     rm -rf *
+     bash -ex .checks &> checks.out
+  else
+     mkdir -p $1
+     cd $1
+     $NXF_RUN > checks.out
+  fi
+  
+  ret=$?
+  set -e
+  if [[ $ret != 0 ]]; then 
+    echo "~ Test '$1' run failed" >> $REPORT
+    # dump error output
+    [[ -s checks.out ]] && cat checks.out | sed 's/^/   /'>> $REPORT  
+    echo '' >> $REPORT 
+    # dump nextflow log file  
+    [[ -f .nextflow.log ]] && cat .nextflow.log >> $REPORT
+    echo '' >> $REPORT   
+    exit 1
+  fi  
+}
+
+
+rm -rf $REPORT
+
+list=${1:-'../*.nf'}
+
+function can_run() {
+    if [[ $(grep -c "$1" .IGNORE) != 0 ]]; then
+        echo 'no'
+    elif [[ ! $WITH_DOCKER && $(grep -c "$1" .IGNORE-DOCKER) != 0 ]]; then
+        echo 'no'
+    elif [[ -f .IGNORE-JAVA-$TEST_JDK && $(grep -c "$1" ".IGNORE-JAVA-$TEST_JDK") != 0 ]]; then
+        echo 'no'
+    elif [[ $NXF_SYNTAX_PARSER == 'v1' && $(grep -c "$1" .IGNORE-PARSER-V2) != 0 ]]; then
+        echo 'no'
+    else
+        echo 'yes'
+    fi
+}
+
+for x in $list; do
+  basename=$(basename $x)
+  if [[ $(can_run $basename) == 'yes' ]]; then
+    echo "> Running test: $basename"
+    ( set -e; 
+      run_checks $basename 
+    )
+  else
+    echo "- Ignoring test: $basename"
+  fi  
+done
+
+if [[ -s $REPORT ]]; then
+  echo -e "$RED"
+  cat $REPORT
+  echo -e "$NORMAL"
+  exit 1
+fi