From 742ca2d5209bb38238158889cfa4d2c6633e2d9e Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Mon, 4 Jul 2011 13:07:26 +0000
Subject: [PATCH] LMS-2335, LMS-2346 bugfixes in InfectX dropboxes + tests
SVN: 21963
---
integration-tests/common-screening.bash | 90 ++++++++++++
integration-tests/test-biozentrum.sh | 173 ++++++++++++++++++++++++
2 files changed, 263 insertions(+)
create mode 100644 integration-tests/common-screening.bash
create mode 100755 integration-tests/test-biozentrum.sh
diff --git a/integration-tests/common-screening.bash b/integration-tests/common-screening.bash
new file mode 100644
index 00000000000..d33105fb92c
--- /dev/null
+++ b/integration-tests/common-screening.bash
@@ -0,0 +1,90 @@
+# 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 $timeout sec [Error]"
+ return 1
+ fi
+ done
+ echo " [OK]"
+ return 0
+}
diff --git a/integration-tests/test-biozentrum.sh b/integration-tests/test-biozentrum.sh
new file mode 100755
index 00000000000..377d8daa84f
--- /dev/null
+++ b/integration-tests/test-biozentrum.sh
@@ -0,0 +1,173 @@
+#!/bin/sh
+#
+# The integration test scenario for Biozentrum screening workflow (iBrain2 integration).
+#
+
+# --- include external sources ------------------------
+
+source common.bash
+
+ERR_LOG=$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
\ No newline at end of file
--
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