diff --git a/integration-tests/templates/data-yeastx/incoming-quantml/TEST&TEST_PROJECT&EXP_TEST.quantML b/integration-tests/templates/data-yeastx/incoming-quantml/TEST&TEST_PROJECT&EXP_TEST.quantML
new file mode 100644
index 0000000000000000000000000000000000000000..d4dbbc9d50eb82b047f85b33952808495a1f8846
--- /dev/null
+++ b/integration-tests/templates/data-yeastx/incoming-quantml/TEST&TEST_PROJECT&EXP_TEST.quantML
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="utf-8"?>
+<quantML>
+ <msQuantification>
+ <source>msSoft</source>
+ <valid>true</valid>
+ <concentration>
+ <datasetParent>20090925182754736-36</datasetParent>
+ <amount>0.689155</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>939.5</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ <cmpdId>23807</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090925182754736-36</datasetParent>
+ <amount>3.775339</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>922.2</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ </msQuantification>
+</quantML>
\ No newline at end of file
diff --git a/integration-tests/templates/datastore_server_yeastx/etc/service.properties b/integration-tests/templates/datastore_server_yeastx/etc/service.properties
index 56f17f1f748c281ad1adcbd4c7cd9513ae541c23..7490b15f2e905148c2f86138f7aa7cd2a2218fad 100644
--- a/integration-tests/templates/datastore_server_yeastx/etc/service.properties
+++ b/integration-tests/templates/datastore_server_yeastx/etc/service.properties
@@ -96,7 +96,7 @@ dataset-deletion-synchronizer.interval = 60
# ------------------------
-inputs=main-thread, eicml-uploader, fiaml-uploader
+inputs=main-thread, eicml-uploader, fiaml-uploader, quantml-uploader
# Globally used separator character which separates entities in a data set file name
data-set-file-name-entity-separator = .
@@ -225,4 +225,34 @@ fiaml-uploader.storage-processor.unique-experiment-name-property-code = ${experi
fiaml-uploader.storage-processor.database.databaseEngineCode = ${yeastx-databaseEngineCode}
fiaml-uploader.storage-processor.database.basicDatabaseName = ${yeastx-basicDatabaseName}
fiaml-uploader.storage-processor.database.databaseKind = ${yeastx-databaseKind}
-fiaml-uploader.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
\ No newline at end of file
+fiaml-uploader.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+
+# ---------------- plugin properties for the thread which uploads quantML files
+
+# The directory to watch for incoming data.
+quantml-uploader.incoming-dir = ${root}/incoming-quantml
+quantml-uploader.incoming-data-completeness-condition = auto-detection
+quantml-uploader.incoming-dir.format =
+
+# The extractor class to use for code extraction
+quantml-uploader.data-set-info-extractor = ch.systemsx.cisd.yeastx.quant.QuantMLDataSetInfoExtractor
+quantml-uploader.data-set-info-extractor.index-of-experiment-identifier = 0
+quantml-uploader.data-set-info-extractor.sub-entity-separator = &
+# unused but required to be different than sub-entity-separator
+quantml-uploader.data-set-info-extractor.entity-separator = .
+
+# The extractor class to use for type extraction
+quantml-uploader.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+quantml-uploader.type-extractor.file-format-type = XML
+quantml-uploader.type-extractor.locator-type = RELATIVE_LOCATION
+quantml-uploader.type-extractor.data-set-type = UNKNOWN
+quantml-uploader.type-extractor.is-measured = false
+
+# The storage processor which uploads the content of the files to the additional database
+quantml-uploader.storage-processor = ch.systemsx.cisd.yeastx.etl.StorageProcessorWithMLUploader
+quantml-uploader.storage-processor.unique-sample-name-property-code = ${sample-name-property-code}
+quantml-uploader.storage-processor.unique-experiment-name-property-code = ${experiment-name-property-code}
+quantml-uploader.storage-processor.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+quantml-uploader.storage-processor.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+quantml-uploader.storage-processor.database.databaseKind = ${yeastx-databaseKind}
+quantml-uploader.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
\ No newline at end of file
diff --git a/integration-tests/test-yeastx.sh b/integration-tests/test-yeastx.sh
index 2f13ae938c1af20c84bdf4be1790abe3bc79237f..50f2e1ca4d396fc732d277d1bd52513133c9cb73 100755
--- a/integration-tests/test-yeastx.sh
+++ b/integration-tests/test-yeastx.sh
@@ -15,21 +15,6 @@ METABOL_DB=metabol_dev
# --------------------
-# Changes last-modification-time so that the order is the same as the alphabetical order.
-function change_modification_time_alphabetically {
- local dir=$1
-
- local file
- # modification data format: YYYYMMDDhhmm
- local modification_time=200811221122
- for file in `ls -1 $dir | sort`; do
- local full_path=$dir/$file
- # change the modification date format
- touch -t $modification_time $full_path
- modification_time=$(($modification_time+1))
- done
-}
-
# Prepare template incoming data and some destination data structures
function prepare_data {
# Prepare empty incoming data
@@ -40,8 +25,6 @@ function prepare_data {
clean_svn $MY_DATA
chmod -R 700 $MY_DATA/incoming*
- # DSS processes files ordered by modification time, so in this way we make the tests more predictable.
- change_modification_time_alphabetically $MY_DATA/incoming
}
function build_and_install_components {
@@ -151,16 +134,22 @@ function count_db_table_records {
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`
-
+ local quantms_runs=`count_db_table_records $METABOL_DB ms_quantifications`
+ local quantms_concentrations=`count_db_table_records $METABOL_DB ms_quant_concentrations`
+ local quantms_component_ids=`count_db_table_records $METABOL_DB ms_quant_compounds`
+
# 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
+ assert_equals "Wrong number of quantifications in the metablomics db" 1 $quantms_runs
+ assert_equals "Wrong number of quant. concentrations in the metablomics db" 2 $quantms_concentrations
+ assert_equals "Wrong number of quant. component ids in the metablomics db" 3 $quantms_component_ids
}
function assert_correct_incoming_contents {
local incoming_dir=$1
- # check content of incoming directory
+ # check content of incoming directory for faulty or ignored datasets
assert_files_number $incoming_dir 12
assert_correct_incoming_content faulty-duplicated-mapping 4 true
assert_correct_incoming_content faulty-experiment-code 4 true
@@ -180,8 +169,9 @@ function assert_correct_incoming_contents {
# check content of dropboxes
assert_files_number "$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
+ assert_dir_empty $MY_DATA/incoming-quantml
+
+ local registered_datasets=17
# check content of the store
local store=$MY_DATA/store
local store_files_count=`find $store -type f | wc -l`
@@ -200,7 +190,7 @@ function assert_correct_incoming_contents {
# 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
+ while [ $i -lt $(($registered_datasets+2)) ]; do
assert_correct_dataset_content_in_database $i $pattern
i=$(( $i +1))
done