diff --git a/eu_basynthec/dist/etc/growth-profiles/data-set-handler.py b/eu_basynthec/dist/etc/growth-profiles/data-set-handler.py
index bc76e78a48d3ca0504b14bb9470e6dedd36dad79..1bffee7cc3e59bc88aeea3cf6e9729c7a67eb378 100644
--- a/eu_basynthec/dist/etc/growth-profiles/data-set-handler.py
+++ b/eu_basynthec/dist/etc/growth-profiles/data-set-handler.py
@@ -1,6 +1,9 @@
from datetime import datetime
from eu.basynthec.cisd.dss import TimeSeriesDataExcel
+def set_data_type(data_set):
+ data_set.setPropertyValue("DATA_TYPE", "OD600")
+
def retrieve_experiment(tr, exp_id):
"""Get the specified experiment form the server. Return the experiment."""
if exp_id is None:
@@ -102,12 +105,15 @@ assign_properties(dataset, metadata)
# Store the original and tsv data in data sets
original_dataset = tr.createNewDataSet("EXCEL_ORIGINAL")
+set_data_type(original_dataset)
store_original_data(tr, original_dataset, "xls")
tsv_dataset = tr.createNewDataSet("TSV_MULTISTRAIN_EXPORT")
+set_data_type(tsv_dataset)
convert_data_to_tsv(tr, tsv_dataset, "tsv-multi")
tsv_split_dataset = tr.createNewDataSet("TSV_EXPORT")
+set_data_type(tsv_split_dataset)
convert_data_to_split_tsv(tr, tsv_split_dataset, "tsv")
# Make the original contain these
diff --git a/eu_basynthec/dist/etc/metabolomics/data-set-handler.py b/eu_basynthec/dist/etc/metabolomics/data-set-handler.py
index 56737bf7a8dc2b5897a402cbc9c9c36daf32056c..eee034223fce52437b99fe1c46bb00d9528060ca 100644
--- a/eu_basynthec/dist/etc/metabolomics/data-set-handler.py
+++ b/eu_basynthec/dist/etc/metabolomics/data-set-handler.py
@@ -1,6 +1,9 @@
from datetime import datetime
from eu.basynthec.cisd.dss import TimeSeriesDataExcel
+def set_data_type(data_set):
+ data_set.setPropertyValue("DATA_TYPE", "METABOLITE_INTENSITIES")
+
def retrieve_experiment(tr, exp_id):
"""Get the specified experiment form the server. Return the experiment."""
if exp_id is None:
@@ -55,9 +58,11 @@ assign_properties(dataset, metadata)
# Store the original and tsv data in data sets
original_dataset = tr.createNewDataSet("EXCEL_ORIGINAL")
+set_data_type(original_dataset)
store_original_data(tr, original_dataset, "xls")
tsv_dataset = tr.createNewDataSet("TSV_EXPORT")
+set_data_type(tsv_dataset)
convert_data_to_tsv(tr, tsv_dataset, "tsv")
# Make the original contain these
diff --git a/eu_basynthec/dist/etc/proteomics/data-set-handler.py b/eu_basynthec/dist/etc/proteomics/data-set-handler.py
index 369cf170b5870c353a48827190526ffa623b8332..81da79a7eda66c1182a2b31d2be4b13436f2918a 100644
--- a/eu_basynthec/dist/etc/proteomics/data-set-handler.py
+++ b/eu_basynthec/dist/etc/proteomics/data-set-handler.py
@@ -1,6 +1,9 @@
from datetime import datetime
from eu.basynthec.cisd.dss import TimeSeriesDataExcel
+def set_data_type(data_set):
+ data_set.setPropertyValue("DATA_TYPE", "PROTEIN_QUANTIFICATIONS")
+
def retrieve_experiment(tr, exp_id):
"""Get the specified experiment form the server. Return the experiment."""
if exp_id is None:
@@ -56,9 +59,11 @@ assign_properties(dataset, metadata)
# Store the original and tsv data in data sets
original_dataset = tr.createNewDataSet("EXCEL_ORIGINAL")
+set_data_type(original_dataset)
store_original_data(tr, original_dataset, "xls")
tsv_dataset = tr.createNewDataSet("TSV_EXPORT")
+set_data_type(tsv_dataset)
convert_data_to_tsv(tr, tsv_dataset, "tsv")
# Make the original contain these
diff --git a/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py b/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
index 81078ecaa8a2dc7718229ae3caf0777084b62f3f..55c20c1e6eb83af819a461a7fe1cf4f1d8b3cb8f 100644
--- a/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
+++ b/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
@@ -2,6 +2,9 @@ from datetime import datetime
from eu.basynthec.cisd.dss import TimeSeriesDataExcel
import re
+def set_data_type(data_set):
+ data_set.setPropertyValue("DATA_TYPE", "TRANSCRIPTOMICS")
+
def getInitialDataRowAndCol(metadata):
"""Extract the initial row and column as specified in the metadata. Returns an array with [row, col]."""
# get the raw value from the map
@@ -169,12 +172,15 @@ assign_properties(dataset, metadata)
# Store the original and tsv data in data sets
original_dataset = tr.createNewDataSet("EXCEL_ORIGINAL")
+set_data_type(original_dataset)
store_original_data(tr, original_dataset, "xls")
tsv_dataset = tr.createNewDataSet("TSV_MULTISTRAIN_EXPORT")
+set_data_type(tsv_dataset)
convert_data_to_tsv(tr, dataStart[0], dataStart[1], tsv_dataset, "tsv-multi")
tsv_split_dataset = tr.createNewDataSet("TSV_EXPORT")
+set_data_type(tsv_split_dataset)
convert_data_to_split_tsv(tr, dataStart[0], dataStart[1], tsv_split_dataset, "tsv")
# Make the original contain these
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java
index 4cf7b8ae70c3b46b8309975e47330f42c1a60b37..3091229a84a9398716d32a9a06aa07e634eb495a 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java
+++ b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java
@@ -35,6 +35,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
@@ -154,4 +155,12 @@ public abstract class AbstractBaSynthecDataSetRegistratorTest extends
return propertyMap;
}
+ protected void checkDataTypeProperty(NewExternalData dataSet, String expectedValue)
+ {
+ HashMap<String, NewProperty> propertyMap =
+ getDataSetPropertiesMap(dataSet.getDataSetProperties());
+ NewProperty property = propertyMap.get("DATA_TYPE");
+ assertEquals(expectedValue, property.getValue());
+ }
+
}
\ No newline at end of file
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600DataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600DataSetRegistratorTest.java
index 8205496cd8ad2dbc1d16644a00b771fd5fccc4bf..91b1e6cfd3fea1fecf9c7502a5ac9631417dcb23 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600DataSetRegistratorTest.java
+++ b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600DataSetRegistratorTest.java
@@ -55,6 +55,13 @@ public class OD600DataSetRegistratorTest extends AbstractBaSynthecDataSetRegistr
assertEquals(4, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
+ checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
+ .get(1), "OD600");
+ checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
+ .get(2), "OD600");
+ checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
+ .get(3), "OD600");
+
NewExternalData dataSet =
atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistratorTest.java
index 641a9ed8277a5b4a25833863cbc93c2959746611..2a233e66a0f4eec08c6bc912bae3fe0a084fc079 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistratorTest.java
+++ b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistratorTest.java
@@ -51,6 +51,11 @@ public class MetabolomicsDataSetRegistratorTest extends AbstractBaSynthecDataSet
assertEquals(3, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
+ checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
+ .get(1), "PROTEIN_QUANTIFICATIONS");
+ checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
+ .get(2), "PROTEIN_QUANTIFICATIONS");
+
NewExternalData dataSet =
atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsDataSetRegistratorTest.java
index 3a71075823435d316ec85aa91a06612189d825c9..6946eace5f1196fe41f915246629aadd19f278fc 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsDataSetRegistratorTest.java
+++ b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsDataSetRegistratorTest.java
@@ -51,6 +51,11 @@ public class ProteomicsDataSetRegistratorTest extends AbstractBaSynthecDataSetRe
assertEquals(3, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
+ checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
+ .get(1), "METABOLITE_INTENSITIES");
+ checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
+ .get(2), "METABOLITE_INTENSITIES");
+
NewExternalData dataSet =
atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java
index 1131553c8023c279f94a6193c0a5c2866871c672..11ea320a123db6cc6bddb150b0fb5d3770d646bd 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java
+++ b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java
@@ -55,6 +55,13 @@ public class TranscriptomicsDataSetRegistratorTest extends AbstractBaSynthecData
assertEquals(4, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
+ checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
+ .get(1), "TRANSCRIPTOMICS");
+ checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
+ .get(2), "TRANSCRIPTOMICS");
+ checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
+ .get(3), "TRANSCRIPTOMICS");
+
NewExternalData dataSet =
atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);