From 93380f6ef6492c9f2e34fda1f69a2afed25716d2 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 11 May 2010 06:48:11 +0000
Subject: [PATCH] SE-246 RawDataServiceInternal.processRawData() implemented
SVN: 15881
---
.../server/RawDataServiceInternal.java | 31 ++-----
.../phosphonetx/server/business/Manager.java | 5 +-
.../shared/dto/MsInjectionSample.java | 20 +++--
.../server/RawDataServiceInternalTest.java | 81 ++++++++-----------
4 files changed, 56 insertions(+), 81 deletions(-)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
index def74792eaf..c56856f69e5 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
@@ -26,26 +26,21 @@ import java.util.Set;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.IValidator;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
@@ -106,31 +101,21 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
List<MsInjectionSample> samples = loadAllRawDataSamples(session);
Set<Long> sampleIDs = new HashSet<Long>();
+ List<String> dataSetCodes = new ArrayList<String>();
for (MsInjectionSample sample : samples)
{
if (RAW_DATA_SAMPLE_VALIDATOR.isValid(person, sample))
{
sampleIDs.add(sample.getSample().getId());
+ Map<String, ExternalData> latestDataSets = sample.getLatestDataSets();
+ ExternalData latestDataSet = latestDataSets.get(dataSetType);
+ if (latestDataSet != null)
+ {
+ dataSetCodes.add(latestDataSet.getCode());
+ }
}
}
- ISampleDAO sampleDAO = getDAOFactory().getSampleDAO();
- IExternalDataDAO externalDataDAO = getDAOFactory().getExternalDataDAO();
- List<String> dataSetCodes = new ArrayList<String>();
- for (long id : rawDataSampleIDs)
- {
- if (sampleIDs.contains(id) == false)
- {
- throw new UserFailureException("Invalid or unauthorized access on sample with ID: "
- + id);
- }
- SamplePE sample = sampleDAO.getByTechId(new TechId(id));
- List<ExternalDataPE> dataSets = externalDataDAO.listExternalData(sample);
- for (ExternalDataPE dataSet : dataSets)
- {
- dataSetCodes.add(dataSet.getCode());
- }
- }
String dataStoreServerCode = findDataStoreServer(dataSetProcessingKey);
IExternalDataTable externalDataTable =
businessObjectFactory.createExternalDataTable(session);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/Manager.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/Manager.java
index 944a500d97e..764fa94098e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/Manager.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/Manager.java
@@ -17,7 +17,6 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
import java.util.ArrayList;
-import java.util.Date;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedHashMap;
@@ -69,12 +68,10 @@ public class Manager
Long sampleID = dataSetSampleMap.get(dataSet.getId());
if (sampleID != null)
{
- String code = dataSet.getDataSetType().getCode();
- Date registrationDate = dataSet.getRegistrationDate();
MsInjectionSample sample = samples.get(sampleID);
if (sample != null)
{
- sample.addLatestDataSet(code, registrationDate);
+ sample.addLatestDataSet(dataSet);
}
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/MsInjectionSample.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/MsInjectionSample.java
index 99a8b8fbde3..45ef8105d4a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/MsInjectionSample.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/MsInjectionSample.java
@@ -20,6 +20,7 @@ import java.util.Date;
import java.util.LinkedHashMap;
import java.util.Map;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
/**
@@ -30,7 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
public class MsInjectionSample
{
private final Sample sample;
- private final Map<String, Date> latestRegistrationDates = new LinkedHashMap<String, Date>();
+ private final Map<String, ExternalData> latestDataSets = new LinkedHashMap<String, ExternalData>();
public MsInjectionSample(Sample sample)
{
@@ -42,24 +43,27 @@ public class MsInjectionSample
return sample;
}
- public Map<String, Date> getLatestRegistrationDates()
+ public Map<String, ExternalData> getLatestDataSets()
{
- return latestRegistrationDates;
+ return latestDataSets;
}
- public void addLatestDataSet(String dataSetTypeCode, Date registrationDate)
+ public void addLatestDataSet(ExternalData dataSet)
{
- Date date = latestRegistrationDates.get(dataSetTypeCode);
- if (date == null || date.getTime() < registrationDate.getTime())
+ String dataSetTypeCode = dataSet.getDataSetType().getCode();
+ Date registrationDate = dataSet.getRegistrationDate();
+ ExternalData latestDataSet = latestDataSets.get(dataSetTypeCode);
+ if (latestDataSet == null
+ || latestDataSet.getRegistrationDate().getTime() < registrationDate.getTime())
{
- latestRegistrationDates.put(dataSetTypeCode, registrationDate);
+ latestDataSets.put(dataSetTypeCode, dataSet);
}
}
@Override
public String toString()
{
- return sample.getIdentifier()+":"+latestRegistrationDates;
+ return sample.getIdentifier()+":"+latestDataSets;
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java
index 40ef550f52c..b319f969d5b 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java
@@ -40,15 +40,15 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObject
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
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.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
@@ -98,47 +98,54 @@ public class RawDataServiceInternalTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- for (long id : ids)
- {
- one(sampleDAO).getByTechId(new TechId(id));
- SamplePE sample = new SamplePE();
- sample.setId(id);
- sample.setCode("s" + id);
- will(returnValue(sample));
-
- one(externalDataDAO).listExternalData(sample);
- List<ExternalDataPE> dataSets = new ArrayList<ExternalDataPE>();
- for (int i = 0; i < (int) (id % 3); i++)
- {
- ExternalDataPE dataSet = new ExternalDataPE();
- dataSet.setCode("ds" + id + "." + i);
- dataSets.add(dataSet);
- }
- will(returnValue(dataSets ));
- }
-
one(dataStoreDAO).listDataStores();
- DataStorePE s1 = store("s1", service("a", PROCESSING), service(COPY_PROCESSING_KEY, QUERIES));
+ DataStorePE s1 =
+ store("s1", service("a", PROCESSING), service(COPY_PROCESSING_KEY,
+ QUERIES));
DataStorePE s2 = store("s2", service(COPY_PROCESSING_KEY, PROCESSING));
will(returnValue(Arrays.asList(s1, s2)));
-
+
one(boFactory).createExternalDataTable(SESSION);
will(returnValue(externalDataTable));
-
- List<String> dataSetCodes = Arrays.asList("ds2.0", "ds2.1");
+
+ List<String> dataSetCodes = Arrays.asList("ds-2", "ds-42");
HashMap<String, String> parameterBindings = new HashMap<String, String>();
- one(externalDataTable).processDatasets(COPY_PROCESSING_KEY, "s2", dataSetCodes, parameterBindings);
+ one(externalDataTable).processDatasets(COPY_PROCESSING_KEY, "s2", dataSetCodes,
+ parameterBindings);
}
});
- service.processRawData(SESSION_TOKEN, COPY_PROCESSING_KEY, ids, "");
+ service.processRawData(SESSION_TOKEN, COPY_PROCESSING_KEY, ids, "dt-0");
context.assertIsSatisfied();
}
private void prepareListRawDataSamples(final Long... sampleIDs)
{
+ final List<Sample> samples = new ArrayList<Sample>();
+ final List<ExternalData> dataSets = new ArrayList<ExternalData>();
+ final LinkedHashSet<TechId> experimentIds = new LinkedHashSet<TechId>();
+ for (Long id : sampleIDs)
+ {
+ Sample sample = new Sample();
+ sample.setId(id);
+ sample.setIdentifier("S" + id);
+ Experiment experiment = new Experiment();
+ experiment.setId(id * 10);
+ sample.setExperiment(experiment);
+ Sample parent = new Sample();
+ parent.setId(id * 100);
+ sample.setGeneratedFrom(parent);
+ samples.add(sample);
+ ExternalData dataSet = new ExternalData();
+ dataSet.setId(id * 1000);
+ dataSet.setCode("ds-" + id);
+ dataSet.setDataSetType(new DataSetType("dt-" + id % 2));
+ dataSet.setSample(sample);
+ dataSets.add(dataSet);
+ experimentIds.add(new TechId(id * 10));
+ }
context.checking(new Expectations()
{
{
@@ -178,31 +185,13 @@ public class RawDataServiceInternalTest extends AbstractServerTestCase
description.appendValue(sampleType);
}
}));
- List<Sample> samples = new ArrayList<Sample>();
- for (Long id : sampleIDs)
- {
- Sample sample = new Sample();
- sample.setId(id);
- sample.setIdentifier("S" + id);
- Experiment experiment = new Experiment();
- experiment.setId(id * 10);
- sample.setExperiment(experiment);
- Sample parent = new Sample();
- parent.setId(id * 100);
- sample.setGeneratedFrom(parent);
- samples.add(sample);
- }
will(returnValue(samples));
one(boFactory).createDatasetLister(SESSION, "");
will(returnValue(datasetLister));
- LinkedHashSet<TechId> experimentIds = new LinkedHashSet<TechId>();
- for (Long id : sampleIDs)
- {
- experimentIds.add(new TechId(id * 10));
- }
one(datasetLister).listByExperimentTechIds(experimentIds);
+ will(returnValue(dataSets));
one(datasetLister).listParentIds(Collections.<Long>emptySet());
will(returnValue(Collections.<Long, Set<Long>>emptyMap()));
--
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