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Commit 312502c7 authored by tpylak's avatar tpylak
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SE-133 YeastX: integration tests (step 1) 

SVN: 12710
parent 758ff4dc
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integration-tests/templates/data-yeastx/incoming/faulty-wrong-conversion/file2.eicML 0 → 100644
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content
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integration-tests/templates/data-yeastx/incoming/faulty-wrong-conversion/file2.fiaML 0 → 100644
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content
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integration-tests/templates/data-yeastx/incoming/faulty-wrong-conversion/file3.mzXML 0 → 100644
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integration-tests/templates/data-yeastx/incoming/faulty-wrong-conversion/file4.mzXML 0 → 100644
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content
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integration-tests/templates/data-yeastx/incoming/faulty-wrong-conversion/index1.tsv 0 → 100644
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# openbis-user@mailinator.pl
file_name sample group conversion
file1.mzXML s32 TEST
file2.eicML s32 TEST fiaML
file2.fiaML s32 TEST eicML
file3.mzXML s32 TEST fiaML
file4.mzXML s32 TEST eicML
integration-tests/templates/data-yeastx/incoming/ignore-no-index/file1.mzXML 0 → 100644
+ 86
− 0
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<?xml version="1.0" encoding="ISO-8859-1"?>
<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.0 http://sashimi.sourceforge.net/schema_revision/mzXML_3.0/mzXML_idx_3.0.xsd" >
<msRun scanCount="73606" startTime="PT0.355S" endTime="PT1440.39S" >
<parentFile fileName="file://IMSB-US-WS02/Y/Boris/09-02-27praktikum/glc1.RAW" fileType="RAWData" fileSha1="5f6d3e83dfc62fd234f6aad9c2bae318f0fd05f7" />
<msInstrument>
<msManufacturer category="msManufacturer" value="Thermo Scientific" />
<msModel category="msModel" value="TSQ Quantum" />
<msIonisation category="msIonisation" value="ESI" />
<msMassAnalyzer category="msMassAnalyzer" value="ITMS" />
<msDetector category="msDetector" value="unknown" />
<software type="acquisition" name="Xcalibur" version="1.5" />
</msInstrument>
<dataProcessing>
<software type="conversion" name="ReAdW" version="4.0.2(build Jul 1 2008 14:23:37)" />
</dataProcessing>
<scan num="1"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 88.050 [88.000-88.100]"
retentionTime="PT0.355S"
lowMz="88.01"
highMz="88.1"
basePeakMz="88.04"
basePeakIntensity="3.67434"
totIonCurrent="31.9056" >
<precursorMz precursorIntensity="0" activationMethod="CID" >88.05</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >QrAFH0A0/HhCsAo+QCzoM0KwD1xAWapiQrAUe0BrKFtCsBmaQFwb0UKwHrlARVUKQrAj10Birq1CsCj2QERSqUKwLhVAQnXvQrAzM0BIVkE=</peaks>
</scan>
<scan num="2"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 91.030 [90.980-91.080]"
retentionTime="PT0.369S"
lowMz="90.99"
highMz="91.08"
basePeakMz="90.99"
basePeakIntensity="3.72983"
totIonCurrent="32.8957" >
<precursorMz precursorIntensity="0" activationMethod="CID" >91.03</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >QrX64UButZpCtgAAQG6SHkK2BR5AZAD4QrYKPUBpvbdCtg9cQFRbbEK2FHtAVdFLQrYZmUAzNxdCth64QDLWCEK2I9dANMWOQrYo9UBJTZA=</peaks>
</scan>
<scan num="3"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 118.100 [99.950-100.050]"
retentionTime="PT0.383S"
lowMz="99.96"
highMz="100.05"
basePeakMz="100"
basePeakIntensity="3.59829"
totIonCurrent="31.9226" >
<precursorMz precursorIntensity="0" activationMethod="CID" >118.1</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >QsfrhUA0gyRCx/CkQEtcnELH9cJAUjHMQsf64UBDfINCyAAAQGZKYkLIBR9AT2vKQsgKPUBMHo5CyA9cQEQSiULIFHtAO3dxQsgZmUBkH34=</peaks>
</scan>
<scan num="4"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 122.000 [103.950-104.050]"
retentionTime="PT0.397S"
lowMz="103.96"
highMz="104.05"
basePeakMz="104.01"
basePeakIntensity="3.5998"
totIonCurrent="29.7796" >
<precursorMz precursorIntensity="0" activationMethod="CID" >122</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >Qs/rhUBKxQpCz/CkQCqSfELP9cJAJkUDQs/64UAj3fdC0AAAQEsP/0LQBR9AZmMQQtAKPUAw1q1C0A9cQFyvNULQFHtARZIwQtAZmUAt3o4=</peaks>
</scan>
</msRun>
\ No newline at end of file
integration-tests/templates/data-yeastx/incoming/real-data-small/description.tsv 0 → 100644
+ 6
− 0
View file @ 312502c7
# openbis-user@mailinator.pl
file_name sample group experiment project conversion
file1.mzXML s32 TEST fiaML
file2.eicML glucose 1 TEST
file3.mzXML glucose 2 TEST Praktikum Metabolic Networks 2009 TEST_PROJECT eicML
file4.fiaML glucose 1 TEST
integration-tests/templates/data-yeastx/incoming/real-data-small/file1.mzXML 0 → 100644
+ 86
− 0
View file @ 312502c7
<?xml version="1.0" encoding="ISO-8859-1"?>
<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.0 http://sashimi.sourceforge.net/schema_revision/mzXML_3.0/mzXML_idx_3.0.xsd" >
<msRun scanCount="73606" startTime="PT0.355S" endTime="PT1440.39S" >
<parentFile fileName="file://IMSB-US-WS02/Y/Boris/09-02-27praktikum/glc1.RAW" fileType="RAWData" fileSha1="5f6d3e83dfc62fd234f6aad9c2bae318f0fd05f7" />
<msInstrument>
<msManufacturer category="msManufacturer" value="Thermo Scientific" />
<msModel category="msModel" value="TSQ Quantum" />
<msIonisation category="msIonisation" value="ESI" />
<msMassAnalyzer category="msMassAnalyzer" value="ITMS" />
<msDetector category="msDetector" value="unknown" />
<software type="acquisition" name="Xcalibur" version="1.5" />
</msInstrument>
<dataProcessing>
<software type="conversion" name="ReAdW" version="4.0.2(build Jul 1 2008 14:23:37)" />
</dataProcessing>
<scan num="1"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 88.050 [88.000-88.100]"
retentionTime="PT0.355S"
lowMz="88.01"
highMz="88.1"
basePeakMz="88.04"
basePeakIntensity="3.67434"
totIonCurrent="31.9056" >
<precursorMz precursorIntensity="0" activationMethod="CID" >88.05</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >QrAFH0A0/HhCsAo+QCzoM0KwD1xAWapiQrAUe0BrKFtCsBmaQFwb0UKwHrlARVUKQrAj10Birq1CsCj2QERSqUKwLhVAQnXvQrAzM0BIVkE=</peaks>
</scan>
<scan num="2"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 91.030 [90.980-91.080]"
retentionTime="PT0.369S"
lowMz="90.99"
highMz="91.08"
basePeakMz="90.99"
basePeakIntensity="3.72983"
totIonCurrent="32.8957" >
<precursorMz precursorIntensity="0" activationMethod="CID" >91.03</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >QrX64UButZpCtgAAQG6SHkK2BR5AZAD4QrYKPUBpvbdCtg9cQFRbbEK2FHtAVdFLQrYZmUAzNxdCth64QDLWCEK2I9dANMWOQrYo9UBJTZA=</peaks>
</scan>
<scan num="3"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 118.100 [99.950-100.050]"
retentionTime="PT0.383S"
lowMz="99.96"
highMz="100.05"
basePeakMz="100"
basePeakIntensity="3.59829"
totIonCurrent="31.9226" >
<precursorMz precursorIntensity="0" activationMethod="CID" >118.1</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >QsfrhUA0gyRCx/CkQEtcnELH9cJAUjHMQsf64UBDfINCyAAAQGZKYkLIBR9AT2vKQsgKPUBMHo5CyA9cQEQSiULIFHtAO3dxQsgZmUBkH34=</peaks>
</scan>
<scan num="4"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 122.000 [103.950-104.050]"
retentionTime="PT0.397S"
lowMz="103.96"
highMz="104.05"
basePeakMz="104.01"
basePeakIntensity="3.5998"
totIonCurrent="29.7796" >
<precursorMz precursorIntensity="0" activationMethod="CID" >122</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >Qs/rhUBKxQpCz/CkQCqSfELP9cJAJkUDQs/64UAj3fdC0AAAQEsP/0LQBR9AZmMQQtAKPUAw1q1C0A9cQFyvNULQFHtARZIwQtAZmUAt3o4=</peaks>
</scan>
</msRun>
\ No newline at end of file
integration-tests/templates/data-yeastx/incoming/real-data-small/file3.mzXML 0 → 100644
+ 86
− 0
View file @ 312502c7
<?xml version="1.0" encoding="ISO-8859-1"?>
<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.0 http://sashimi.sourceforge.net/schema_revision/mzXML_3.0/mzXML_idx_3.0.xsd" >
<msRun scanCount="73606" startTime="PT0.355S" endTime="PT1440.39S" >
<parentFile fileName="file://IMSB-US-WS02/Y/Boris/09-02-27praktikum/glc1.RAW" fileType="RAWData" fileSha1="5f6d3e83dfc62fd234f6aad9c2bae318f0fd05f7" />
<msInstrument>
<msManufacturer category="msManufacturer" value="Thermo Scientific" />
<msModel category="msModel" value="TSQ Quantum" />
<msIonisation category="msIonisation" value="ESI" />
<msMassAnalyzer category="msMassAnalyzer" value="ITMS" />
<msDetector category="msDetector" value="unknown" />
<software type="acquisition" name="Xcalibur" version="1.5" />
</msInstrument>
<dataProcessing>
<software type="conversion" name="ReAdW" version="4.0.2(build Jul 1 2008 14:23:37)" />
</dataProcessing>
<scan num="1"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 88.050 [88.000-88.100]"
retentionTime="PT0.355S"
lowMz="88.01"
highMz="88.1"
basePeakMz="88.04"
basePeakIntensity="3.67434"
totIonCurrent="31.9056" >
<precursorMz precursorIntensity="0" activationMethod="CID" >88.05</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >QrAFH0A0/HhCsAo+QCzoM0KwD1xAWapiQrAUe0BrKFtCsBmaQFwb0UKwHrlARVUKQrAj10Birq1CsCj2QERSqUKwLhVAQnXvQrAzM0BIVkE=</peaks>
</scan>
<scan num="2"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 91.030 [90.980-91.080]"
retentionTime="PT0.369S"
lowMz="90.99"
highMz="91.08"
basePeakMz="90.99"
basePeakIntensity="3.72983"
totIonCurrent="32.8957" >
<precursorMz precursorIntensity="0" activationMethod="CID" >91.03</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >QrX64UButZpCtgAAQG6SHkK2BR5AZAD4QrYKPUBpvbdCtg9cQFRbbEK2FHtAVdFLQrYZmUAzNxdCth64QDLWCEK2I9dANMWOQrYo9UBJTZA=</peaks>
</scan>
<scan num="3"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 118.100 [99.950-100.050]"
retentionTime="PT0.383S"
lowMz="99.96"
highMz="100.05"
basePeakMz="100"
basePeakIntensity="3.59829"
totIonCurrent="31.9226" >
<precursorMz precursorIntensity="0" activationMethod="CID" >118.1</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >QsfrhUA0gyRCx/CkQEtcnELH9cJAUjHMQsf64UBDfINCyAAAQGZKYkLIBR9AT2vKQsgKPUBMHo5CyA9cQEQSiULIFHtAO3dxQsgZmUBkH34=</peaks>
</scan>
<scan num="4"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 122.000 [103.950-104.050]"
retentionTime="PT0.397S"
lowMz="103.96"
highMz="104.05"
basePeakMz="104.01"
basePeakIntensity="3.5998"
totIonCurrent="29.7796" >
<precursorMz precursorIntensity="0" activationMethod="CID" >122</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >Qs/rhUBKxQpCz/CkQCqSfELP9cJAJkUDQs/64UAj3fdC0AAAQEsP/0LQBR9AZmMQQtAKPUAw1q1C0A9cQFyvNULQFHtARZIwQtAZmUAt3o4=</peaks>
</scan>
</msRun>
\ No newline at end of file
integration-tests/templates/data-yeastx/incoming/sample-code-with-experiment/description.tsv 0 → 100644
+ 3
− 0
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# openbis-user@mailinator.pl
file_name sample group experiment project conversion
file1.mzXML s32 TEST Praktikum Metabolic Networks 2009 TEST_PROJECT eicML
\ No newline at end of file
integration-tests/templates/data-yeastx/incoming/sample-code-with-experiment/file1.mzXML 0 → 100644
+ 86
− 0
View file @ 312502c7
<?xml version="1.0" encoding="ISO-8859-1"?>
<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.0 http://sashimi.sourceforge.net/schema_revision/mzXML_3.0/mzXML_idx_3.0.xsd" >
<msRun scanCount="73606" startTime="PT0.355S" endTime="PT1440.39S" >
<parentFile fileName="file://IMSB-US-WS02/Y/Boris/09-02-27praktikum/glc1.RAW" fileType="RAWData" fileSha1="5f6d3e83dfc62fd234f6aad9c2bae318f0fd05f7" />
<msInstrument>
<msManufacturer category="msManufacturer" value="Thermo Scientific" />
<msModel category="msModel" value="TSQ Quantum" />
<msIonisation category="msIonisation" value="ESI" />
<msMassAnalyzer category="msMassAnalyzer" value="ITMS" />
<msDetector category="msDetector" value="unknown" />
<software type="acquisition" name="Xcalibur" version="1.5" />
</msInstrument>
<dataProcessing>
<software type="conversion" name="ReAdW" version="4.0.2(build Jul 1 2008 14:23:37)" />
</dataProcessing>
<scan num="1"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 88.050 [88.000-88.100]"
retentionTime="PT0.355S"
lowMz="88.01"
highMz="88.1"
basePeakMz="88.04"
basePeakIntensity="3.67434"
totIonCurrent="31.9056" >
<precursorMz precursorIntensity="0" activationMethod="CID" >88.05</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >QrAFH0A0/HhCsAo+QCzoM0KwD1xAWapiQrAUe0BrKFtCsBmaQFwb0UKwHrlARVUKQrAj10Birq1CsCj2QERSqUKwLhVAQnXvQrAzM0BIVkE=</peaks>
</scan>
<scan num="2"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 91.030 [90.980-91.080]"
retentionTime="PT0.369S"
lowMz="90.99"
highMz="91.08"
basePeakMz="90.99"
basePeakIntensity="3.72983"
totIonCurrent="32.8957" >
<precursorMz precursorIntensity="0" activationMethod="CID" >91.03</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >QrX64UButZpCtgAAQG6SHkK2BR5AZAD4QrYKPUBpvbdCtg9cQFRbbEK2FHtAVdFLQrYZmUAzNxdCth64QDLWCEK2I9dANMWOQrYo9UBJTZA=</peaks>
</scan>
<scan num="3"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 118.100 [99.950-100.050]"
retentionTime="PT0.383S"
lowMz="99.96"
highMz="100.05"
basePeakMz="100"
basePeakIntensity="3.59829"
totIonCurrent="31.9226" >
<precursorMz precursorIntensity="0" activationMethod="CID" >118.1</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >QsfrhUA0gyRCx/CkQEtcnELH9cJAUjHMQsf64UBDfINCyAAAQGZKYkLIBR9AT2vKQsgKPUBMHo5CyA9cQEQSiULIFHtAO3dxQsgZmUBkH34=</peaks>
</scan>
<scan num="4"
msLevel="2"
peaksCount="10"
polarity="-"
scanType="SRM"
filterLine="- p ESI SRM ms2 122.000 [103.950-104.050]"
retentionTime="PT0.397S"
lowMz="103.96"
highMz="104.05"
basePeakMz="104.01"
basePeakIntensity="3.5998"
totIonCurrent="29.7796" >
<precursorMz precursorIntensity="0" activationMethod="CID" >122</precursorMz>
<peaks precision="32"
byteOrder="network"
pairOrder="m/z-int" >Qs/rhUBKxQpCz/CkQCqSfELP9cJAJkUDQs/64UAj3fdC0AAAQEsP/0LQBR9AZmMQQtAKPUAw1q1C0A9cQFyvNULQFHtARZIwQtAZmUAt3o4=</peaks>
</scan>
</msRun>
\ No newline at end of file
integration-tests/templates/data-yeastx/store/.gitignore 0 → 100644
+ 0
− 0
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integration-tests/templates/datastore_server1/datastore_server.sh deleted 100755 → 0
+ 0
− 3
View file @ 758ff4dc
#! /bin/sh
./shutdown.sh
java -ea -Djavax.net.ssl.trustStore=etc/openBIS.keystore -jar lib/datastore_server.jar "$@" & echo $! > running.pid
\ No newline at end of file
integration-tests/templates/datastore_server1/etc/openBIS.keystore deleted 100644 → 0
+ 0
− 0
View file @ 758ff4dc
File deleted
integration-tests/templates/datastore_server1/shutdown.sh deleted 100755 → 0
+ 0
− 48
View file @ 758ff4dc
#! /bin/sh
# This is an exact copy of datamover.stop
awkBin()
{
# We need a awk that accepts variable assignments with '-v'
case `uname -s` in
"SunOS")
echo "nawk"
return
;;
esac
# default
echo "awk"
}
isPIDRunning()
{
if [ "$1" = "" ]; then
return 0
fi
# This will have a return value of 0 on BSDish systems
isBSD="`ps aux > /dev/null 2>&1; echo $?`"
AWK=`awkBin`
if [ "$isBSD" = "0" ]; then
if [ "`ps aux | $AWK -v PID=$1 '{if ($2==PID) {print "FOUND"}}'`" = "FOUND" ]; then
return 0
else
return 1
fi
else
if [ "`ps -ef | $AWK -v PID=$1 '{if ($2==PID) {print "FOUND"}}'`" = "FOUND" ]; then
return 0
else
return 1
fi
fi
}
if [ -f running.pid ]; then
PID=`cat running.pid`
isPIDRunning $PID
if [ $? -eq 0 ]; then
kill $PID
echo "Previously running program with PID $PID was found and killed"
fi
rm running.pid
fi
integration-tests/templates/datastore_server2/datastore_server.sh deleted 100755 → 0
+ 0
− 3
View file @ 758ff4dc
#! /bin/sh
./shutdown.sh
java -ea -Djavax.net.ssl.trustStore=etc/openBIS.keystore -jar lib/datastore_server.jar "$@" & echo $! > running.pid
\ No newline at end of file
integration-tests/templates/datastore_server2/etc/openBIS.keystore deleted 100644 → 0
+ 0
− 0
View file @ 758ff4dc
File deleted
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