LMS-2335, LMS-2346 bugfixes in InfectX dropboxes + tests

SVN: 21963

integration-tests/common-screening.bash

+# This code is ment to be common for all screening integration tests,
+# but for now only biozentrum integration tests are using it.
+
+function install_and_run_openbis_server_screening {
+    local install_openbis=$1
+    local local_template_dir=$2
+    
+		local openbis_server_dir=$OPENBIS_SERVER_HCS
+		local openbis_server_name=`basename $openbis_server_dir`
+		
+		restore_database $OPENBIS_DATABASE_HCS $local_template_dir/$openbis_server_name/test_database.sql
+    if [ $install_openbis == "true" ]; then
+        rm -fr $openbis_server_dir
+    
+        unzip -q -d $openbis_server_dir $INSTALL/openBIS*.zip
+        mv $openbis_server_dir/openBIS-server/* $openbis_server_dir
+				rmdir $openbis_server_dir/openBIS-server
+
+				cp -v $local_template_dir/$openbis_server_name/service.properties $openbis_server_dir/service.properties
+				$openbis_server_dir/install.sh $PWD/$openbis_server_dir
+				startup_openbis_server $openbis_server_dir
+    else
+        restart_openbis $openbis_server_dir
+				wait_for_server
+    fi
+}
+
+function install_dss_screening {
+		local local_template_dir=$1
+
+		local dss_dest=$DSS_SERVER_HCS
+		local dss_template=$local_template_dir/$DSS_DIR_NAME
+
+		rm -fr $dss_dest
+		unzip -q $INSTALL/datastore_server-screening*.zip -d $dss_dest
+		mv $dss_dest/datastore_server/* $dss_dest
+		rmdir $dss_dest/datastore_server
+
+		# override default DSS configuration
+		cp -v $dss_template/etc/* $dss_dest/etc
+}
+
+# installs AS and DSS and starts AS
+function install_screening {
+		local local_template=$1
+		
+		# FIXME uncomment !!!!!!!!!!!!!!!!!!!!
+		#rm -fr $INSTALL
+		#fetch_distributions datastore_server
+		#fetch_distributions screening
+
+		echo Dropping imaging database: $IMAGING_DB
+		psql_cmd=`run_psql`
+		$psql_cmd -U postgres -c "drop database if exists $IMAGING_DB" 
+		
+		rm -fr $WORK
+		mkdir -p $WORK
+		install_dss_screening $local_template
+		install_and_run_openbis_server_screening "true" $local_template
+}
+
+function assertFeatureVectorDef {
+    local psql=`run_psql`
+    local result=`$psql -t -U postgres -d $IMAGING_DB \
+       -c "select label from feature_defs where code = '$1'"  \
+       | awk '{gsub(/\|/,";");print}'`
+    echo "Checking feature $1"
+    assert_equals "Feature code and label" " $2" "$result"
+}
+
+# returns 0 on success, 1 otherwise
+function wait_for_file {
+	local file_name=$1
+
+	local timeout=40
+	local total_time=0
+	local check_interval=5	
+	echo -n Waiting for creation of $file_name
+	while [ ! -e $file_name ]; do 
+	  echo -n .
+	  sleep $check_interval
+    total_time=$(( $total_time + $check_interval ))
+	  if [ $total_time -gt $timeout ]; then
+	  	report_error "File $file_name has not been detected after $timeout sec [Error]"
+	  	return 1
+	  fi
+	done
+	echo "  [OK]"
+	return 0
+}

integration-tests/test-biozentrum.sh

+#!/bin/sh
+#
+# The integration test scenario for Biozentrum screening workflow (iBrain2 integration).
+#
+
+# --- include external sources ------------------------ 
+
+source common.bash
+
+ERR_LOG=$WORK/all_err_log.txt
+SVN_WEB_SRC_HCS=http://svncisd.ethz.ch/repos/cisd/screening/trunk
+
+WORK=$TARGETS/playground-screening-ibrain2
+OPENBIS_DATABASE_HCS=openbis_screening_biozentrum_integration_tests
+IMAGING_DB=imaging_biozentrum_integration_tests
+
+# dir which contains AS and DSS configuration and AS core db dump
+LOCAL_TEMPLATE=$TEMPLATE/data-biozentrum
+DATA_TEMPLATE=$LOCAL_TEMPLATE/examples/ibrain2-dropboxes-test
+OPENBIS_SERVER_HCS=$WORK/openBIS-server
+DSS_DIR_NAME=datastore_server
+
+DSS_SERVER_HCS=$WORK/$DSS_DIR_NAME
+DSS_INCOMING_PARENT_DIR=$DSS_SERVER_HCS/data
+
+source common-screening.bash
+
+# --- Specific part -----------------
+
+TEST_ROOT_DIR=$DSS_INCOMING_PARENT_DIR/dropboxes
+INCOMING_ROOT_DIR=$TEST_ROOT_DIR/incoming
+CONFIRMATION_DIR=$TEST_ROOT_DIR/registration-status
+
+function copyDataset {
+  local dropbox_type=$1
+  local name=$2
+
+  local dropbox=$INCOMING_ROOT_DIR/$dropbox_type
+  
+  echo Copy $name to $dropbox as $name
+  if [ -e $dropbox/$name ]; then
+     fatal_error Directory already exits in the dropbox!
+  fi
+  cp -r $DATA_TEMPLATE/$dropbox_type/$name $dropbox/$name
+	clean_svn $dropbox/$name
+}
+
+function submitRawDataset {
+  
+  local dropbox=$INCOMING_ROOT_DIR/$1
+  local name=$2
+  
+  copyDataset $1 $name
+  touch $dropbox/.MARKER_is_finished_$name
+}
+
+function submitDerivedDataset {
+  local dropbox=$INCOMING_ROOT_DIR/$1
+  local name=$2
+	local parent_dataset_code=$3
+	  
+  copyDataset $1 $name
+
+	local key_pattern="storage_provider\.parent\.dataset\.id = "
+	find $dropbox/$name -name "metadata.properties" -exec sed -i "" "s/$key_pattern.*/${key_pattern}${parent_dataset_code}/g" {} \;
+
+  touch $dropbox/.MARKER_is_finished_$name
+}
+
+# returns 0 on success, 1 otherwise
+function wait_for_confirmation_file {
+	local file_name=$1
+	
+	wait_for_file $file_name
+	local ok=$?
+	
+	if [ $ok == 0 ]; then
+		 local succeeded=`cat $file_name | grep STORAGE_SUCCESSFUL`
+		 if [ "$succeeded" == "" ]; then
+		 		report_error `cat $file_name`
+		 		return 1
+		 else
+		 		return 0
+		 fi
+	else
+		return 1
+	fi
+}
+
+function submit_correct_datasets_and_wait {
+	echo Submit raw images dataset
+	submitRawDataset HCS_IMAGE_RAW ibrain2_dataset_id_32
+
+	CONF_FILE=$CONFIRMATION_DIR/ibrain2_dataset_id_32.properties
+	wait_for_confirmation_file $CONF_FILE 
+	
+	# update parent dataset code in all files
+	PARENT_CODE_KEY="storage_provider.dataset.id = "
+	RAW_IMAGE_DATASET_CODE=`cat $CONF_FILE | grep "$PARENT_CODE_KEY" | tr -d "$PARENT_CODE_KEY"`
+	echo Update raw image dataset code: $RAW_IMAGE_DATASET_CODE
+	if [ "$RAW_IMAGE_DATASET_CODE" = "" ]; then
+	   report_error Confirmation with code of raw image dataset has not been found
+	   return
+	fi
+	
+	echo Submit all derived datasets
+	submitDerivedDataset HCS_IMAGE_OVERVIEW ibrain2_dataset_id_48 $RAW_IMAGE_DATASET_CODE 
+	submitDerivedDataset HCS_IMAGE_SEGMENTATION ibrain2_dataset_id_99 $RAW_IMAGE_DATASET_CODE 
+	submitDerivedDataset HCS_ANALYSIS_WELL_QUALITY_SUMMARY ibrain2_dataset_id_47 $RAW_IMAGE_DATASET_CODE
+	submitDerivedDataset HCS_ANALYSIS_WELL_RESULTS_SUMMARIES ibrain2_dataset_id_77 $RAW_IMAGE_DATASET_CODE
+	submitDerivedDataset HCS_ANALYSIS_CELL_FEATURES_CC_MAT ibrain2_dataset_id_58 $RAW_IMAGE_DATASET_CODE
+	
+	wait_for_confirmation_file $CONFIRMATION_DIR/ibrain2_dataset_id_48.properties
+	wait_for_confirmation_file $CONFIRMATION_DIR/ibrain2_dataset_id_99.properties
+	wait_for_confirmation_file $CONFIRMATION_DIR/ibrain2_dataset_id_47.properties
+	wait_for_confirmation_file $CONFIRMATION_DIR/ibrain2_dataset_id_77.properties
+	wait_for_confirmation_file $CONFIRMATION_DIR/ibrain2_dataset_id_58.properties
+}
+
+function getDropboxNamesList {
+	echo "HCS_IMAGE_RAW HCS_IMAGE_OVERVIEW HCS_IMAGE_SEGMENTATION HCS_ANALYSIS_WELL_QUALITY_SUMMARY HCS_ANALYSIS_WELL_RESULTS_SUMMARIES HCS_ANALYSIS_CELL_FEATURES_CC_MAT"
+}
+
+function createEmptyDropoxes {
+		rm -fr $TEST_ROOT_DIR
+		for name in `getDropboxNamesList`; do
+					mkdir -p $INCOMING_ROOT_DIR/$name
+		done
+		cp -r $LOCAL_TEMPLATE/dropboxes/scripts $TEST_ROOT_DIR
+		mkdir $TEST_ROOT_DIR/registration-status
+		mkdir $TEST_ROOT_DIR/tmp
+}
+
+function assert_datasets_in_store_number {
+	local expected_number=$1
+	
+	local datasets=`find $DSS_INCOMING_PARENT_DIR/store -name "original*" | wc -l | tr -d " "`; 
+  assert_equals "Wrong number of registered datasets" $expected_number $datasets
+}
+
+# FIXME: change to False !!!!!!!!!!!!!!!!!!!!!!!!!!
+DEBUG=false
+
+function integration_tests_screening_biozentrum {
+    if [ "$DEBUG" == "false" ]; then 
+			install_screening $LOCAL_TEMPLATE
+		fi
+		createEmptyDropoxes
+    if [ "$DEBUG" == "false" ]; then 
+    	switch_dss "on" $DSS_DIR_NAME
+		fi
+		submit_correct_datasets_and_wait
+	  
+	  for name in `getDropboxNamesList`; do
+					assert_dir_empty $INCOMING_ROOT_DIR/$name
+		done
+	  
+    assert_datasets_in_store_number 6
+
+		# results_summaries dataset    
+    assertFeatureVectorDef INTERPHASEINVASOMEINFECTION_INDEX InterphaseInvasomeInfection_Index
+    assertFeatureVectorDef COUNT_BACTERIA Count_Bacteria
+		# quality_summary dataset    
+    assertFeatureVectorDef FOCUS_SCORE Focus_Score
+
+    if [ "$DEBUG" == "false" ]; then 
+    	switch_dss "off" $DSS_DIR_NAME
+    	shutdown_openbis_server $OPENBIS_SERVER_HCS
+    fi
+    exit_if_assertion_failed
+}
+
+integration_tests_screening_biozentrum
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