From baf469fedd0c3e40179553882aac01cb14f07f3b Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 14 Sep 2009 13:50:30 +0000
Subject: [PATCH] LMS-1165 change method names in DataSetInformation and add
setExperiment()
SVN: 12580
---
.../etlserver/phosphonetx/ResultDataSetUploader.java | 12 +++++++++---
.../cisd/yeastx/etl/ML2DatabaseUploader.java | 6 +++++-
2 files changed, 14 insertions(+), 4 deletions(-)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
index 1aa3b88d088..a4e8829e7f4 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
@@ -79,13 +79,19 @@ class ResultDataSetUploader extends AbstractHandler
{
try
{
- Experiment experiment = getOrCreateExperiment(dataSetInfo.getExperiment().getPermId());
- Sample sample = getOrCreateSample(experiment, dataSetInfo.getSample().getPermId());
+ Experiment experiment = getOrCreateExperiment(dataSetInfo.tryToGetExperiment().getPermId());
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample dataSetInfoSample =
+ dataSetInfo.tryToGetSample();
+ if (dataSetInfoSample == null)
+ {
+ throw new UserFailureException("Missing sample in " + dataSetInfo);
+ }
+ Sample sample = getOrCreateSample(experiment, dataSetInfoSample.getPermId());
String referenceDatabase = summary.getSummaryHeader().getReferenceDatabase();
Database database = getOrGreateDatabase(referenceDatabase);
DataSet ds =
getOrCreateDataSet(experiment, sample, database, dataSetInfo.getDataSetCode());
- addToDatabase(ds, experiment, dataSetInfo.getSample().getGroup(), summary);
+ addToDatabase(ds, experiment, dataSetInfoSample.getGroup(), summary);
if (errorMessages.length() == 0)
{
connection.commit();
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java
index fd08bd1749d..0ade461f3a4 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java
@@ -115,7 +115,11 @@ public class ML2DatabaseUploader implements IDataSetUploader
private DMDataSetDTO createBacklink(DataSetInformation dataSetInformation)
{
String datasetPermId = dataSetInformation.getDataSetCode();
- Sample sample = dataSetInformation.getSample();
+ Sample sample = dataSetInformation.tryToGetSample();
+ if (sample == null)
+ {
+ throw new EnvironmentFailureException("Missing sample in " + dataSetInformation);
+ }
Experiment experiment = sample.getExperiment();
String experimentName = findExperimentName(experiment.getProperties());
String sampleName = findSampleName(sample.getProperties());
--
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