Skip to content
Snippets Groups Projects
Commit bb6a0803 authored by tpylak's avatar tpylak
Browse files

LMS-940 yeastx: resources to support manual tests 

SVN: 11391
parent 1d47c404
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 456 additions and 22 deletions
rtd_yeastx/sourceTest/bash/incoming/faulty-unknown-mapping/index.tsv 0 → 100644
+ 7
− 0
View file @ bb6a0803
# openbis-user@mailinator.pl
file_name sample group experiment project conversion comment
file1.mzXML unknown IMSB_ZAMBONI eicML x
file2.mzXML x IMSB_ZAMBONI unknown unknown eicML x
file3.mzXML x IMSB_ZAMBONI without-proj eicML x
file4.mzXML x IMSB_ZAMBONI without-exp eicML x
file5.mzXML x unknown eicML x
rtd_yeastx/sourceTest/bash/incoming/faulty-wrong-conversion/file1.mzXML 0 → 100644
+ 1
− 0
View file @ bb6a0803
content
\ No newline at end of file
rtd_yeastx/sourceTest/bash/incoming/faulty-wrong-conversion/file2.eicML 0 → 100644
+ 1
− 0
View file @ bb6a0803
content
\ No newline at end of file
rtd_yeastx/sourceTest/bash/incoming/faulty-wrong-conversion/file2.fiaML 0 → 100644
+ 1
− 0
View file @ bb6a0803
content
\ No newline at end of file
rtd_yeastx/sourceTest/bash/incoming/faulty-wrong-conversion/file3.mzXML 0 → 100644
+ 1
− 0
View file @ bb6a0803
content
\ No newline at end of file
rtd_yeastx/sourceTest/bash/incoming/faulty-wrong-conversion/file4.mzXML 0 → 100644
+ 1
− 0
View file @ bb6a0803
content
\ No newline at end of file
rtd_yeastx/sourceTest/bash/incoming/faulty-wrong-conversion/index1.tsv 0 → 100644
+ 7
− 0
View file @ bb6a0803
# openbis-user@mailinator.pl
file_name sample group conversion
file1.mzXML s32 IMSB_ZAMBONI
file2.eicML s32 IMSB_ZAMBONI fiaML
file2.fiaML s32 IMSB_ZAMBONI eicML
file3.mzXML s32 IMSB_ZAMBONI fiaML
file4.mzXML s32 IMSB_ZAMBONI eicML
rtd_yeastx/sourceTest/bash/incoming/real-data-small/description.tsv 0 → 100644
+ 5
− 0
View file @ bb6a0803
# openbis-user@mailinator.pl
file_name sample group experiment project conversion
file1.mzXML s32 IMSB_ZAMBONI fiaML
file2.eicML glucose 1 IMSB_ZAMBONI
file3.mzXML glucose 2 IMSB_ZAMBONI e2 bacteria eicML
rtd_yeastx/sourceTest/bash/incoming/real-data-small/file1.mzXML 0 → 100644
+ 86
− 0
View file @ bb6a0803
<?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
rtd_yeastx/sourceTest/bash/incoming/real-data-small/file2.eicML 0 → 100644
+ 259
− 0
View file @ bb6a0803
Source diff could not be displayed: it is too large. Options to address this: view the blob.
rtd_yeastx/sourceTest/bash/incoming/real-data-small/file3.mzXML 0 → 100644
+ 86
− 0
View file @ bb6a0803
<?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
rtd_yeastx/sourceTest/bash/prepare_tests.sh
+ 1
− 22
View file @ bb6a0803
#!/bin/bash #!/bin/bash
USER=`whoami`
RES=../../../datastore_server/targets
# ----- restore test database ./clean.sh
DB=openbis_yeastx_test
FILE=yeastx-tests-openbis-database.sql
psql -U postgres -c "drop database $DB;"
psql -U postgres -c "create database $DB with owner $USER encoding = 'UNICODE';"
psql -U $USER -d $DB -f $FILE
# ----- clean target directory
rm -rf $RES/incoming
rm -rf $RES/store
rm -rf $RES/dropbox1
rm -rf $RES/dropbox2
mkdir -p $RES/incoming
mkdir -p $RES/store
mkdir -p $RES/dropbox1
mkdir -p $RES/dropbox2
# ----- compile the plugin and copy it to DSS dir # ----- compile the plugin and copy it to DSS dir
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment