SE-133 YeastX: extend integration tests with db checks

SVN: 12716

integration-tests/common.bash

@@ -529,6 +529,28 @@ function switch_dmv {
     switch_sth $1 $2 "datamover.sh start" "datamover.sh stop" $TRUE
 }
 
+function assert_correct_dataset_content_in_database {
+    local dataset_id=$1
+    local pattern=$2
+    echo ==== assert correct dataset $dataset_id content in database with pattern $pattern ====
+    local psql=`run_psql`
+    local dataset=`$psql -U postgres -d $DATABASE \
+       -c "select d.id, e.code, ds.code, d.code, d.is_placeholder, r.data_id_parent, \
+                  ed.is_complete, d.data_producer_code, d.production_timestamp \
+           from data as d left join data_set_relationships as r on r.data_id_child = d.id \
+                          left join data_stores as ds on ds.id = d.dast_id \
+                          left join external_data as ed on ed.data_id = d.id,
+                experiments as e
+           where d.id = $dataset_id and d.expe_id = e.id"  \
+       | awk '/ +[0-9]+/' \
+       | awk '{gsub(/ /,"");print}' \
+       | awk '{gsub(/\|/,";");print}'`
+    local lines=`echo "$dataset" | grep "$pattern" | wc -l`
+    if [ $lines == 0 ]; then
+        report_error dataset does not match pattern $pattern: $dataset
+    fi 
+}
+
 function assert_dss_registration {
     local dss=$1
     echo ==== assert registration of DSS $dss ====

integration-tests/templates/data-yeastx/incoming-eicml/TEST&TEST_PROJECT&EXP_TEST.20090925182754736-36.eicML

+<?xml version="1.0" encoding="utf-8"?>
+<eicML>
+   <msRun>
+      <filePath>file://IMSB-US-CORTEX/D/CONVERSION robot/dropbox/workinprogress/</filePath>
+      <fileName>NCA4.RAW</fileName>
+      <instrumentType>LC-QQQ</instrumentType>
+      <instrumentManufacturer>Thermo Finnigan</instrumentManufacturer>
+      <instrumentModel>unknown</instrumentModel>
+      <methodIonisation>ESI</methodIonisation>
+      <methodSeparation/>
+      <acquisitionDate/>
+      <chromCount>137</chromCount>
+      <startTime>0.315</startTime>
+      <endTime>1439.66</endTime>
+      <msRunId/>
+   </msRun>
+   <chromatogram>
+      <Q1Mz>87.02</Q1Mz>
+      <Q3LowMz>42.96</Q3LowMz>
+      <Q3HighMz>43.05</Q3HighMz>
+      <label>-EIC 87&gt;43</label>
+      <polarity>-</polarity>
+      <chromData>
+         <RT>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</RT>
+         <INT>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</INT>
+      </chromData>
+   </chromatogram>
+   <chromatogram>
+      <Q1Mz>88.05</Q1Mz>
+      <Q3LowMz>88.01</Q3LowMz>
+      <Q3HighMz>88.1</Q3HighMz>
+      <label>-EIC 88&gt;88</label>
+      <polarity>-</polarity>
+      <chromData>
+         <RT>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</RT>
+         <INT>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</INT>
+      </chromData>
+   </chromatogram>
+</eicML>
\ No newline at end of file

integration-tests/test-3v.sh

@@ -117,28 +117,6 @@ function assert_empty_in_out_folders {
     assert_dir_empty $DATA/analysis-copy
 }
 
-function assert_correct_dataset_content_in_database {
-    local dataset_id=$1
-    local pattern=$2
-    echo ==== assert correct dataset $dataset_id content in database with pattern $pattern ====
-    local psql=`run_psql`
-    local dataset=`$psql -U postgres -d $DATABASE \
-       -c "select d.id, e.code, ds.code, d.code, d.is_placeholder, r.data_id_parent, \
-                  ed.is_complete, d.data_producer_code, d.production_timestamp \
-           from data as d left join data_set_relationships as r on r.data_id_child = d.id \
-                          left join data_stores as ds on ds.id = d.dast_id \
-                          left join external_data as ed on ed.data_id = d.id,
-                experiments as e
-           where d.id = $dataset_id and d.expe_id = e.id"  \
-       | awk '/ +[0-9]+/' \
-       | awk '{gsub(/ /,"");print}' \
-       | awk '{gsub(/\|/,";");print}'`
-    local lines=`echo "$dataset" | grep "$pattern" | wc -l`
-    if [ $lines == 0 ]; then
-        report_error dataset does not match pattern $pattern: $dataset
-    fi 
-}
-
 function assert_correct_content_of_plate_3VCP1_in_store {
     local cell_plate=3VCP1
     echo ==== assert correct content of plate 3VCP1 in store ====

integration-tests/test-yeastx.sh

@@ -117,8 +117,9 @@ function assert_correct_datasets_metabol_database {
     local eicms_runs=`count_db_table_records $METABOL_DB eic_ms_runs`
     local fiams_runs=`count_db_table_records $METABOL_DB fia_ms_runs`
 
-    assert_equals "Wrong number of eic MS runs in the metablomics db" 1 $eicms_runs  
-    assert_equals "Wrong number of fia MS runs in the metablomics db" 1 $fiams_runs
+		# one run comes from the incoming and one from incoming-*ml
+    assert_equals "Wrong number of eic MS runs in the metablomics db" 2 $eicms_runs  
+    assert_equals "Wrong number of fia MS runs in the metablomics db" 2 $fiams_runs
 }
 
 function assert_correct_incoming_contents {
@@ -145,14 +146,30 @@ function assert_correct_incoming_contents {
 	assert_files_number "$MY_DATA/dropbox-eicml/TEST&TEST_PROJECT&EXP_TEST.*.mzXML" 6
 	assert_files_number "$MY_DATA/dropbox-fiaml/TEST&TEST_PROJECT&EXP_TEST.*.mzXML" 2
 
+	local registered_datasets=16
 	# check content of the store	
 	local store=$MY_DATA/store
 	local store_files_count=`find $store -type f | wc -l`
-	assert_equals "Wrong number of files in the store $store" 14 $store_files_count
+	assert_equals "Wrong number of files in the store $store" $registered_datasets $store_files_count
 	
 	assert_correct_datasets_metabol_database
-}
 
+	# check the number of datasets in openbis database	
+	local datasets=`count_db_table_records $DATABASE data`
+	# there will be one additional dataset placeholder for the incoming-*ml files which specify 
+	# the parent code which does not exist
+  assert_equals "Wrong number of datasets in the openbis db" $(($registered_datasets+1)) $datasets
+	
+	# check each dataset in openbis database.
+	# Result set columns are:
+	#   id;experiment_code;data_store_code;code;is_placeholder;data_id_parent;is_complete;data_producer_code;production_timestamp
+	local pattern="[0-9]*;EXP_TEST;DSS1;20[0-9]*-[0-9]*;[ft];[0-9]*;[TFU]*;;.*"
+	local i=2; 
+	while [ $i -lt 18 ]; do 
+		assert_correct_dataset_content_in_database $i $pattern
+		i=$(( $i +1))
+	done
+}
 
 function integration_tests_yeastx {
     local use_local_source=$1