diff --git a/rtd_phosphonetx/etc/service.properties b/rtd_phosphonetx/etc/service.properties
index eb117179b5e342c12edf98be8c9871e20f24995e..1a95363c6578110c3574057c7de101ace7f0ccc8 100644
--- a/rtd_phosphonetx/etc/service.properties
+++ b/rtd_phosphonetx/etc/service.properties
@@ -151,7 +151,7 @@ ms-injection.incoming-dir = targets/playground/data/incoming-ms
ms-injection.incoming-data-completeness-condition = auto-detection
ms-injection.data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection
ms-injection.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-ms-injection.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+ms-injection.type-extractor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.TypeExtractorForMSInjection
# ---------------------------------------------------------------------------
# 'prot-result' thread configuration
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
index 1214c5313ad3d65975a5e5abd1e6e422d7f913d8..45fa5588c6c0923aa6840464feb602b093dabf6d 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
@@ -17,6 +17,9 @@
package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
import java.util.Properties;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
@@ -25,10 +28,14 @@ import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
/**
@@ -40,84 +47,119 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
*/
public class DataSetInfoExtractorForMSInjection extends AbstractDataSetInfoExtractorWithService
{
- static final String MS_INJECTION_PROPERTIES_FILE_KEY = "ms-injection-properties-file";
- static final String DEFAULT_MS_INJECTION_PROPERTIES_FILE = "ms-injection.properties";
+ static final String MS_INJECTION_PROPERTIES_FILE = "ms-injection.properties";
+ static final String DATA_SET_PROPERTIES_FILE = "data-set.properties";
static final String PROJECT_CODE_KEY = "PROJECT_CODE";
static final String EXPERIMENT_CODE_KEY = "EXPERIMENT_CODE";
static final String SAMPLE_CODE_KEY = "SAMPLE_CODE";
static final String USER_KEY = "USER";
+ static final String DATA_SET_TYPE_KEY = "DATA_SET_TYPE";
+ static final String FILE_TYPE_KEY = "FILE_TYPE";
+ static final String PARENT_TYPE_KEY = "PARENT_TYPE";
+
static final String EXPERIMENT_TYPE_CODE = "MS_INJECT";
static final String SAMPLE_TYPE_CODE = "MS_INJECTION";
- private final String msInjectionPropertiesFileName;
-
public DataSetInfoExtractorForMSInjection(Properties properties)
{
- this(properties.getProperty(MS_INJECTION_PROPERTIES_FILE_KEY,
- DEFAULT_MS_INJECTION_PROPERTIES_FILE), ServiceProvider.getOpenBISService());
+ this(ServiceProvider.getOpenBISService());
}
- DataSetInfoExtractorForMSInjection(String msInjectionPropertiesFileName,
- IEncapsulatedOpenBISService service)
+ DataSetInfoExtractorForMSInjection(IEncapsulatedOpenBISService service)
{
super(service);
- this.msInjectionPropertiesFileName = msInjectionPropertiesFileName;
}
public DataSetInformation getDataSetInformation(File incomingDataSetPath,
IEncapsulatedOpenBISService openbisService) throws UserFailureException,
EnvironmentFailureException
{
- Properties properties =
- loadMSInjectionProperties(incomingDataSetPath);
+ Properties sampleProperties =
+ Util.loadPropertiesFile(incomingDataSetPath, MS_INJECTION_PROPERTIES_FILE);
DataSetInformation info = new DataSetInformation();
info.setSpaceCode(Constants.MS_DATA_SPACE);
- info.setSampleCode(PropertyUtils.getMandatoryProperty(properties, SAMPLE_CODE_KEY));
+ info.setSampleCode(PropertyUtils.getMandatoryProperty(sampleProperties, SAMPLE_CODE_KEY));
NewSample sample = new NewSample();
SampleType sampleType = service.getSampleType(SAMPLE_TYPE_CODE);
sample.setSampleType(sampleType);
- sample.setExperimentIdentifier(getOrCreateExperiment(properties));
+ ExperimentIdentifier experimentIdentifier = getExperimentIdentifier(sampleProperties);
+ long experimentID = getOrCreateExperiment(experimentIdentifier);
+ sample.setExperimentIdentifier(experimentIdentifier.toString());
sample.setIdentifier(info.getSampleIdentifier().toString());
- sample.setProperties(Util.getAndCheckProperties(properties, sampleType));
- service.registerSample(sample, properties.getProperty(USER_KEY));
+ sample.setProperties(Util.getAndCheckProperties(sampleProperties, sampleType));
+ service.registerSample(sample, sampleProperties.getProperty(USER_KEY));
+
+ Properties dataSetProperties =
+ Util.loadPropertiesFile(incomingDataSetPath, DATA_SET_PROPERTIES_FILE);
+ String dataSetTypeCode = PropertyUtils.getMandatoryProperty(dataSetProperties, DATA_SET_TYPE_KEY);
+ String parentTypeOrNull = dataSetProperties.getProperty(PARENT_TYPE_KEY);
+ dataSetProperties.remove(DATA_SET_TYPE_KEY);
+ dataSetProperties.remove(FILE_TYPE_KEY);
+ dataSetProperties.remove(PARENT_TYPE_KEY);
+ setDataSetPropertiesFor(info, dataSetProperties, dataSetTypeCode);
+ if (parentTypeOrNull != null)
+ {
+ List<ExternalData> dataSets = service.listDataSetsByExperimentID(experimentID);
+ ExternalData youngestDataSet = null;
+ for (ExternalData dataSet : dataSets)
+ {
+ if (dataSet.getDataSetType().getCode().equals(parentTypeOrNull))
+ {
+ if (youngestDataSet == null || timeStamp(youngestDataSet) < timeStamp(dataSet))
+ {
+ youngestDataSet = dataSet;
+ }
+ }
+ }
+ if (youngestDataSet != null)
+ {
+ info.setParentDataSetCodes(Arrays.asList(youngestDataSet.getCode()));
+ }
+ }
return info;
}
- private String getOrCreateExperiment(Properties msInjectionProperties)
+ private long timeStamp(ExternalData dataSet)
+ {
+ return dataSet.getRegistrationDate().getTime();
+ }
+
+ private void setDataSetPropertiesFor(DataSetInformation info, Properties dataSetProperties,
+ String dataSetTypeCode)
+ {
+ DataSetType dataSetType = service.getDataSetType(dataSetTypeCode).getDataSetType();
+ IEntityProperty[] props = Util.getAndCheckProperties(dataSetProperties, dataSetType);
+ List<NewProperty> properties = new ArrayList<NewProperty>();
+ for (IEntityProperty p : props)
+ {
+ properties.add(new NewProperty(p.getPropertyType().getCode(), p.tryGetAsString()));
+ }
+ info.setDataSetProperties(properties);
+ }
+
+ private long getOrCreateExperiment(ExperimentIdentifier identifier)
{
- String projectCode =
- PropertyUtils.getMandatoryProperty(msInjectionProperties, PROJECT_CODE_KEY);
- String experimentCode =
- PropertyUtils.getMandatoryProperty(msInjectionProperties, EXPERIMENT_CODE_KEY);
- ExperimentIdentifier identifier =
- new ExperimentIdentifier(null, Constants.MS_DATA_SPACE, projectCode, experimentCode);
Experiment experiment = service.tryToGetExperiment(identifier);
if (experiment == null)
{
- service.registerExperiment(new NewExperiment(identifier.toString(),
+ return service.registerExperiment(new NewExperiment(identifier.toString(),
EXPERIMENT_TYPE_CODE));
}
- return identifier.toString();
+ return experiment.getId();
}
- private Properties loadMSInjectionProperties(File incomingDataSetDirectory)
+ private ExperimentIdentifier getExperimentIdentifier(Properties msInjectionProperties)
{
- File msInjectionPropertiesFile =
- new File(incomingDataSetDirectory, msInjectionPropertiesFileName);
- if (msInjectionPropertiesFile.exists() == false)
- {
- throw new UserFailureException("Missing MS injection properties file '"
- + msInjectionPropertiesFileName + "'.");
- }
- if (msInjectionPropertiesFile.isFile() == false)
- {
- throw new UserFailureException("Properties file '" + msInjectionPropertiesFileName
- + "' is a folder.");
- }
- return PropertyUtils.loadProperties(msInjectionPropertiesFile);
+ String projectCode =
+ PropertyUtils.getMandatoryProperty(msInjectionProperties, PROJECT_CODE_KEY);
+ String experimentCode =
+ PropertyUtils.getMandatoryProperty(msInjectionProperties, EXPERIMENT_CODE_KEY);
+ ExperimentIdentifier identifier =
+ new ExperimentIdentifier(null, Constants.MS_DATA_SPACE, projectCode, experimentCode);
+ return identifier;
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/TypeExtractorForMSInjection.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/TypeExtractorForMSInjection.java
new file mode 100644
index 0000000000000000000000000000000000000000..519ad9d7675ec9770a6439ba95b9597c8b75b25b
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/TypeExtractorForMSInjection.java
@@ -0,0 +1,73 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
+
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.DATA_SET_PROPERTIES_FILE;
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.DATA_SET_TYPE_KEY;
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.FILE_TYPE_KEY;
+
+import java.io.File;
+import java.util.Properties;
+
+import ch.systemsx.cisd.common.utilities.PropertyUtils;
+import ch.systemsx.cisd.etlserver.ITypeExtractor;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class TypeExtractorForMSInjection implements ITypeExtractor
+{
+ private static final LocatorType LOCATOR_TYPE = new LocatorType(LocatorType.DEFAULT_LOCATOR_TYPE_CODE);
+
+ public DataSetType getDataSetType(File incomingDataSetPath)
+ {
+ Properties properties = loadProperties(incomingDataSetPath);
+ return new DataSetType(PropertyUtils.getMandatoryProperty(properties, DATA_SET_TYPE_KEY));
+ }
+
+ public FileFormatType getFileFormatType(File incomingDataSetPath)
+ {
+ Properties properties = loadProperties(incomingDataSetPath);
+ return new FileFormatType(PropertyUtils.getMandatoryProperty(properties, FILE_TYPE_KEY));
+ }
+
+ public LocatorType getLocatorType(File incomingDataSetPath)
+ {
+ return LOCATOR_TYPE;
+ }
+
+ public String getProcessorType(File incomingDataSetPath)
+ {
+ return null;
+ }
+
+ public boolean isMeasuredData(File incomingDataSetPath)
+ {
+ return true;
+ }
+
+ private Properties loadProperties(File incomingDataSetPath)
+ {
+ return Util.loadPropertiesFile(incomingDataSetPath, DATA_SET_PROPERTIES_FILE);
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/Util.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/Util.java
index 0b55c3c396492773ee1e1319e8b323d3d562b857..55390e584c1d425a64e5520d7d15c8912179e03b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/Util.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/Util.java
@@ -16,11 +16,13 @@
package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
+import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityTypePropertyType;
@@ -76,4 +78,19 @@ class Util
}
return sampleProperties.toArray(new IEntityProperty[sampleProperties.size()]);
}
+
+ static Properties loadPropertiesFile(File incomingDataSetDirectory, String propertiesFileName)
+ {
+ File propertiesFile = new File(incomingDataSetDirectory, propertiesFileName);
+ if (propertiesFile.exists() == false)
+ {
+ throw new UserFailureException("Missing properties file '" + propertiesFileName + "'.");
+ }
+ if (propertiesFile.isFile() == false)
+ {
+ throw new UserFailureException("Properties file '" + propertiesFileName
+ + "' is a folder.");
+ }
+ return PropertyUtils.loadProperties(propertiesFile);
+ }
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjectionTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjectionTest.java
index 3162ac66e2684ecdeeb56ad9759c32288fc6070e..e371f8055be1cc11b33fb0fac1dc8daaf7e9cfd0 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjectionTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjectionTest.java
@@ -16,9 +16,11 @@
package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
-import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.DEFAULT_MS_INJECTION_PROPERTIES_FILE;
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.DATA_SET_PROPERTIES_FILE;
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.DATA_SET_TYPE_KEY;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.EXPERIMENT_CODE_KEY;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.EXPERIMENT_TYPE_CODE;
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.MS_INJECTION_PROPERTIES_FILE;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.PROJECT_CODE_KEY;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.SAMPLE_CODE_KEY;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.SAMPLE_TYPE_CODE;
@@ -29,6 +31,7 @@ import java.io.FileOutputStream;
import java.io.IOException;
import java.util.Arrays;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import java.util.Properties;
@@ -48,6 +51,9 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypePropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
@@ -55,6 +61,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleTypePropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
@@ -75,6 +82,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + Constants.MS_DATA_SPACE
+ DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + PROJECT_CODE
+ DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + EXPERIMENT_CODE;
+ private static final long EXPERIMENT_ID = 42;
private Mockery context;
private IEncapsulatedOpenBISService service;
@@ -87,8 +95,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
context = new Mockery();
service = context.mock(IEncapsulatedOpenBISService.class);
extractor =
- new DataSetInfoExtractorForMSInjection(DEFAULT_MS_INJECTION_PROPERTIES_FILE,
- service);
+ new DataSetInfoExtractorForMSInjection(service);
dataSet = new File(workingDirectory, "data-set");
dataSet.mkdirs();
}
@@ -110,8 +117,8 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
- assertEquals("Missing MS injection properties file '"
- + DEFAULT_MS_INJECTION_PROPERTIES_FILE + "'.", ex.getMessage());
+ assertEquals("Missing properties file '" + MS_INJECTION_PROPERTIES_FILE + "'.", ex
+ .getMessage());
}
context.assertIsSatisfied();
@@ -120,14 +127,14 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
@Test
public void testPropertiesFileIsAFolder()
{
- new File(dataSet, DEFAULT_MS_INJECTION_PROPERTIES_FILE).mkdir();
+ new File(dataSet, MS_INJECTION_PROPERTIES_FILE).mkdir();
try
{
extractor.getDataSetInformation(dataSet, service);
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
- assertEquals("Properties file '" + DEFAULT_MS_INJECTION_PROPERTIES_FILE
+ assertEquals("Properties file '" + MS_INJECTION_PROPERTIES_FILE
+ "' is a folder.", ex.getMessage());
}
@@ -138,7 +145,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
public void testMissingSampleCode()
{
Properties properties = new Properties();
- save(properties, DEFAULT_MS_INJECTION_PROPERTIES_FILE);
+ save(properties, MS_INJECTION_PROPERTIES_FILE);
try
{
@@ -159,7 +166,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
Properties properties = new Properties();
properties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
- save(properties, DEFAULT_MS_INJECTION_PROPERTIES_FILE);
+ save(properties, MS_INJECTION_PROPERTIES_FILE);
prepareGetSampleType();
try
@@ -181,7 +188,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
Properties properties = new Properties();
properties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
properties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- save(properties, DEFAULT_MS_INJECTION_PROPERTIES_FILE);
+ save(properties, MS_INJECTION_PROPERTIES_FILE);
prepareGetSampleType();
try
@@ -197,64 +204,93 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
context.assertIsSatisfied();
}
+ @Test
+ public void testMissingDataSetPropertiesFile()
+ {
+ Properties sampleProperties = new Properties();
+ sampleProperties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
+ sampleProperties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
+ sampleProperties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
+ sampleProperties.setProperty(USER_KEY, "user1");
+ save(sampleProperties, MS_INJECTION_PROPERTIES_FILE);
+ SampleTypePropertyType pt = createPropertyType(SAMPLE_CODE_KEY, true);
+ prepareGetExperimentAndGetSampleType(true, pt);
+ prepareRegisterSample();
+
+ try
+ {
+ extractor.getDataSetInformation(dataSet, service);
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Missing properties file '" + DATA_SET_PROPERTIES_FILE + "'.", ex.getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testMissingDataSetType()
+ {
+ Properties sampleProperties = new Properties();
+ sampleProperties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
+ sampleProperties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
+ sampleProperties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
+ sampleProperties.setProperty(USER_KEY, "user1");
+ save(sampleProperties, MS_INJECTION_PROPERTIES_FILE);
+ Properties dataSetProperties = new Properties();
+ save(dataSetProperties, DATA_SET_PROPERTIES_FILE);
+ SampleTypePropertyType pt = createPropertyType(SAMPLE_CODE_KEY, true);
+ prepareGetExperimentAndGetSampleType(true, pt);
+ prepareRegisterSample();
+
+ try
+ {
+ extractor.getDataSetInformation(dataSet, service);
+ fail("ConfigurationFailureException expected");
+ } catch (ConfigurationFailureException ex)
+ {
+ assertEquals("Given key '" + DATA_SET_TYPE_KEY + "' not found in properties '[]'", ex
+ .getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
@Test
public void test()
{
- Properties properties = new Properties();
- properties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- properties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
- properties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
- properties.setProperty(USER_KEY, "user1");
- properties.setProperty("TEMPERATURE", "47.11");
- save(properties, DEFAULT_MS_INJECTION_PROPERTIES_FILE);
+ Properties sampleProperties = new Properties();
+ sampleProperties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
+ sampleProperties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
+ sampleProperties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
+ sampleProperties.setProperty(USER_KEY, "user1");
+ sampleProperties.setProperty("TEMPERATURE", "47.11");
+ save(sampleProperties, MS_INJECTION_PROPERTIES_FILE);
+ Properties dataSetProperties = new Properties();
+ dataSetProperties.setProperty(DATA_SET_TYPE_KEY, "MZXML_DATA");
+ dataSetProperties.setProperty("CENTROID", "true");
+ dataSetProperties.setProperty("BLABLA", "blub");
+ save(dataSetProperties, DATA_SET_PROPERTIES_FILE);
SampleTypePropertyType pt1 = createPropertyType(SAMPLE_CODE_KEY, true);
SampleTypePropertyType pt2 = createPropertyType("VOLUME", false);
prepareGetExperimentAndGetSampleType(false, pt1, pt2);
- context.checking(new Expectations()
- {
- {
- one(service).registerSample(with(new BaseMatcher<NewSample>()
- {
- public boolean matches(Object item)
- {
- if (item instanceof NewSample)
- {
- NewSample sample = (NewSample) item;
- assertEquals(SAMPLE_TYPE_CODE, sample.getSampleType().getCode());
- assertEquals(SAMPLE_IDENTIFIER, sample.getIdentifier());
- assertEquals(EXPERIMENT_IDENTIFIER, sample.getExperimentIdentifier());
- IEntityProperty[] sampleProperties = sample.getProperties();
- Map<String, IEntityProperty> map =
- new HashMap<String, IEntityProperty>();
- for (IEntityProperty property : sampleProperties)
- {
- map.put(property.getPropertyType().getCode(), property);
- }
-
- assertEquals(SAMPLE_CODE, map.get(SAMPLE_CODE_KEY).getValue());
- assertEquals(1, map.size());
- return true;
- }
- return false;
- }
-
- public void describeTo(Description description)
- {
- description.appendText(SAMPLE_IDENTIFIER);
- }
- }), with("user1"));
- }
- });
+ prepareRegisterSample();
+ prepareGetDataSetType(createDataSetPropertyType("CENTROID", false));
DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
assertEquals(Constants.MS_DATA_SPACE, info.getSpaceCode());
assertEquals(SAMPLE_CODE, info.getSampleCode());
assertEquals(null, info.getExperimentIdentifier());
+ List<NewProperty> dProps = info.getDataSetProperties();
+ assertEquals(1, dProps.size());
+ assertEquals("CENTROID", dProps.get(0).getPropertyCode());
+ assertEquals("true", dProps.get(0).getValue());
context.assertIsSatisfied();
}
-
+
@Test
public void testMissingMandatoryProperties()
{
@@ -262,7 +298,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
properties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
properties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
properties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
- save(properties, DEFAULT_MS_INJECTION_PROPERTIES_FILE);
+ save(properties, MS_INJECTION_PROPERTIES_FILE);
SampleTypePropertyType pt1 = createPropertyType(SAMPLE_CODE_KEY, true);
SampleTypePropertyType pt2 = createPropertyType("VOLUME", true);
SampleTypePropertyType pt3 = createPropertyType("TEMPERATURE", true);
@@ -287,12 +323,14 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
context.checking(new Expectations()
{
{
- ExperimentIdentifier identifier = new ExperimentIdentifier(null, Constants.MS_DATA_SPACE, PROJECT_CODE,
- EXPERIMENT_CODE);
- one(service).tryToGetExperiment(identifier
- );
- will(returnValue(experimentExists ? new Experiment() : null));
-
+ ExperimentIdentifier identifier =
+ new ExperimentIdentifier(null, Constants.MS_DATA_SPACE, PROJECT_CODE,
+ EXPERIMENT_CODE);
+ one(service).tryToGetExperiment(identifier);
+ Experiment experiment = new Experiment();
+ experiment.setId(EXPERIMENT_ID);
+ will(returnValue(experimentExists ? experiment : null));
+
if (experimentExists == false)
{
one(service).registerExperiment(
@@ -302,19 +340,73 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
});
prepareGetSampleType(sampleTypePropertyTypes);
}
-
+
private void prepareGetSampleType(final SampleTypePropertyType... sampleTypePropertyTypes)
{
context.checking(new Expectations()
- {
{
- one(service).getSampleType(DataSetInfoExtractorForMSInjection.SAMPLE_TYPE_CODE);
- SampleType sampleType = new SampleType();
- sampleType.setCode(DataSetInfoExtractorForMSInjection.SAMPLE_TYPE_CODE);
- sampleType.setSampleTypePropertyTypes(Arrays.asList(sampleTypePropertyTypes));
- will(returnValue(sampleType));
- }
- });
+ {
+ one(service).getSampleType(DataSetInfoExtractorForMSInjection.SAMPLE_TYPE_CODE);
+ SampleType sampleType = new SampleType();
+ sampleType.setCode(DataSetInfoExtractorForMSInjection.SAMPLE_TYPE_CODE);
+ sampleType.setSampleTypePropertyTypes(Arrays.asList(sampleTypePropertyTypes));
+ will(returnValue(sampleType));
+ }
+ });
+ }
+
+ private void prepareGetDataSetType(final DataSetTypePropertyType... types)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(service).getDataSetType("MZXML_DATA");
+ DataSetTypeWithVocabularyTerms result = new DataSetTypeWithVocabularyTerms();
+ DataSetType dataSetType = new DataSetType("MZXML_DATA");
+ dataSetType.setDataSetTypePropertyTypes(Arrays.asList(types));
+ result.setDataSetType(dataSetType);
+ will(returnValue(result));
+ }
+ });
+ }
+
+ private void prepareRegisterSample()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(service).registerSample(with(new BaseMatcher<NewSample>()
+ {
+ public boolean matches(Object item)
+ {
+ if (item instanceof NewSample)
+ {
+ NewSample sample = (NewSample) item;
+ assertEquals(SAMPLE_TYPE_CODE, sample.getSampleType().getCode());
+ assertEquals(SAMPLE_IDENTIFIER, sample.getIdentifier());
+ assertEquals(EXPERIMENT_IDENTIFIER, sample.getExperimentIdentifier());
+ IEntityProperty[] properties = sample.getProperties();
+ Map<String, IEntityProperty> map =
+ new HashMap<String, IEntityProperty>();
+ for (IEntityProperty property : properties)
+ {
+ map.put(property.getPropertyType().getCode(), property);
+ }
+
+ assertEquals(SAMPLE_CODE, map.get(SAMPLE_CODE_KEY).getValue());
+ assertEquals(1, map.size());
+ return true;
+ }
+ return false;
+ }
+
+ public void describeTo(Description description)
+ {
+ description.appendText(SAMPLE_IDENTIFIER);
+ }
+ }), with("user1"));
+ }
+ });
}
private void save(Properties properties, String fileName)
@@ -343,4 +435,14 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
stpt.setPropertyType(propertyType);
return stpt;
}
+
+ private DataSetTypePropertyType createDataSetPropertyType(String key, boolean mandatory)
+ {
+ DataSetTypePropertyType etpt = new DataSetTypePropertyType();
+ etpt.setMandatory(mandatory);
+ PropertyType propertyType = new PropertyType();
+ propertyType.setCode(key);
+ etpt.setPropertyType(propertyType);
+ return etpt;
+ }
}
\ No newline at end of file