LMS-1546 screening integration test script

SVN: 16744

integration-tests/test-screening.sh

+#!/bin/sh
+#
+# The integration test scenario for screening workflow.
+#
+
+# --- include external sources ------------------------ 
+
+source common.bash
+
+# --------------------
+
+#WORK=$TARGETS/playground-screening
+DATA_TEMPLATE=$TEMPLATE/data-screening.zip
+MY_DATA=$WORK/data-screening
+IMAGING_DB=imaging_integration_tests
+OPENBIS_SERVER_HCS=$WORK/openBIS-server-screening
+DSS_DIR_NAME=datastore_server_screening
+DSS_INCOMING_PARENT_DIR=$WORK/$DSS_DIR_NAME/data
+SVN_WEB_SRC_HCS=http://svncisd.ethz.ch/repos/cisd/screening/trunk
+OPENBIS_DATABASE_HCS=openbis_screening
+
+# --------------------
+
+# Prepare template incoming data and some destination data structures
+function prepare_data_first_phase {
+		rm -fr $DSS_INCOMING_PARENT_DIR/incoming*
+		unzip $DATA_TEMPLATE -d $DSS_INCOMING_PARENT_DIR -x incoming-analysis-genedata/*
+		mkdir -p $DSS_INCOMING_PARENT_DIR/incoming-analysis-genedata
+    chmod -R 700 $DSS_INCOMING_PARENT_DIR/incoming*
+}
+
+function prepare_data_second_phase {
+		unzip $DATA_TEMPLATE -d $DSS_INCOMING_PARENT_DIR incoming-analysis-genedata/*
+    chmod -R 700 $DSS_INCOMING_PARENT_DIR/incoming*
+}
+
+function build_and_install_components {
+	rm -fr $INSTALL
+	mkdir -p $INSTALL
+	fetch_latest_artifacts_from_cruise_control screening $INSTALL
+}
+
+function install_openbis_server_screening {
+    local install_openbis=$1
+    
+		local openbis_server_dir=$OPENBIS_SERVER_HCS
+		local openbis_server_name=`basename $openbis_server_dir`
+		
+		restore_database $OPENBIS_DATABASE_HCS $TEMPLATE/$openbis_server_name/test_database.sql
+    if [ $install_openbis == "true" ]; then
+        rm -fr $openbis_server_dir
+    
+        unzip -d $openbis_server_dir $INSTALL/openBIS*.zip
+        mv $openbis_server_dir/openBIS-server/* $openbis_server_dir
+				rmdir $openbis_server_dir/openBIS-server
+		
+				$openbis_server_dir/install.sh $PWD/$openbis_server_dir
+				startup_openbis_server $openbis_server_dir
+				wait_for_server
+    else
+        restart_openbis $openbis_server_dir
+    fi
+}
+
+function install_dss_screening {
+		local dss_dest=$WORK/$DSS_DIR_NAME
+		local dss_template=$TEMPLATE/$DSS_DIR_NAME
+
+		rm -fr $dss_dest
+		unzip $INSTALL/datastore_server-screening*.zip -d $dss_dest
+		mv $dss_dest/datastore_server/* $dss_dest
+		rmdir $dss_dest/datastore_server
+
+		# extend distribution configuration
+		cat $dss_template/integration-tests-service.properties >> $dss_dest/etc/service.properties
+		cat $dss_template/genedata-dropboxes-service.properties >> $dss_dest/etc/service.properties
+}
+
+function build_and_install_screening {
+		mkdir -p $WORK
+		install_dss_screening
+		install_openbis_server_screening "true"
+    
+		echo Dropping imaging database: $IMAGING_DB
+		psql_cmd=`run_psql`
+		$psql_cmd -U postgres -c "drop database if exists $IMAGING_DB" 
+}
+
+function check_file_exists {
+    local file=$1
+    if [ -e $marker ]; then echo true; else echo false; fi
+}
+
+function assert_correct_incoming_content {
+	local dir_name=$1
+	local expected_file_count=$2
+	local has_error_marker=$3
+	
+	local dir=$MY_DATA/incoming/$dir_name
+	assert_dir_exists $dir
+	if [ ! -e $dir ]; then
+		return
+	fi
+	
+	assert_files_number $dir $expected_file_count
+	
+	local marker=$dir/_delete_me_after_correcting_errors
+	local error_log=$dir/error-log.txt
+	if [ "$has_error_marker" = "true" ]; then
+		assert_file_exists $marker
+		assert_file_exists $error_log
+	else
+		assert_file_not_exists $marker
+		assert_file_not_exists $error_log
+	fi
+}
+
+
+function integration_tests_screening {
+		build_and_install_screening
+
+    prepare_data_first_phase
+    switch_dss "on" datastore_server_screening
+		sleep 60
+		prepare_data_second_phase
+  	sleep 20
+	  
+		assert_dir_empty  $DSS_INCOMING_PARENT_DIR/incoming-analysis
+		assert_dir_empty  $DSS_INCOMING_PARENT_DIR/incoming-analysis-genedata
+		assert_dir_empty  $DSS_INCOMING_PARENT_DIR/incoming-images-genedata
+		assert_dir_empty  $DSS_INCOMING_PARENT_DIR/incoming-images-merged-channels
+		assert_dir_empty  $DSS_INCOMING_PARENT_DIR/incoming-images-split-channels
+    
+    switch_dss "off" datastore_server_screening
+    shutdown_openbis_server $OPENBIS_SERVER_HCS
+    exit_if_assertion_failed
+}
+
+function build_and_test {
+	build_and_install_components
+	integration_tests_screening
+}
+
+build_and_test