From 4edbaa17cc453848170a6a3966002f71da0fbca7 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Tue, 20 Apr 2010 13:18:02 +0000
Subject: [PATCH] [LMS-1457] minor refactorings
SVN: 15535
---
.../dsu/tracking/dto/TrackingStateDTO.java | 2 +-
.../tracking/main/FileBasedTrackingDAO.java | 6 +-
.../cisd/dsu/tracking/main/TrackingBO.java | 88 +++++++++++--------
3 files changed, 54 insertions(+), 42 deletions(-)
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/dto/TrackingStateDTO.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/dto/TrackingStateDTO.java
index 7abc3bf55d9..c311de09d59 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/dto/TrackingStateDTO.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/dto/TrackingStateDTO.java
@@ -41,7 +41,7 @@ public class TrackingStateDTO
return alreadyTrackedSampleIdsToBeProcessed;
}
- public void setAlreadyTrackedSamplesIdsToBeProcessed(
+ public void setAlreadyTrackedSampleIdsToBeProcessed(
Set<Long> alreadyTrackedSampleIdsToBeProcessed)
{
this.alreadyTrackedSampleIdsToBeProcessed = alreadyTrackedSampleIdsToBeProcessed;
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/FileBasedTrackingDAO.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/FileBasedTrackingDAO.java
index a167891ae03..0050db9caf0 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/FileBasedTrackingDAO.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/FileBasedTrackingDAO.java
@@ -22,9 +22,9 @@ import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
-import java.util.HashSet;
import java.util.List;
import java.util.Set;
+import java.util.TreeSet;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.StringUtils;
@@ -75,7 +75,7 @@ public class FileBasedTrackingDAO implements ITrackingDAO
String[] toBeProcessed = lines.get(1).split("\t");
String[] processed = lines.get(2).split("\t");
state.setLastSeenDatasetId(Integer.parseInt(datasetId[1]));
- state.setAlreadyTrackedSamplesIdsToBeProcessed(parseIds(toBeProcessed));
+ state.setAlreadyTrackedSampleIdsToBeProcessed(parseIds(toBeProcessed));
state.setAlreadyTrackedSampleIdsProcessed(parseIds(processed));
return state;
} catch (Exception e)
@@ -86,7 +86,7 @@ public class FileBasedTrackingDAO implements ITrackingDAO
private static Set<Long> parseIds(String[] array)
{
- Set<Long> ids = new HashSet<Long>();
+ Set<Long> ids = new TreeSet<Long>();
for (int i = 1; i < array.length; i++)
{
ids.add(Long.parseLong(array[i]));
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/TrackingBO.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/TrackingBO.java
index b1fca069bb0..39215b05a55 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/TrackingBO.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/TrackingBO.java
@@ -17,9 +17,9 @@
package ch.ethz.bsse.cisd.dsu.tracking.main;
import java.util.Collections;
-import java.util.HashSet;
import java.util.List;
import java.util.Set;
+import java.util.TreeSet;
import ch.ethz.bsse.cisd.dsu.tracking.dto.TrackedEntities;
import ch.ethz.bsse.cisd.dsu.tracking.dto.TrackingStateDTO;
@@ -33,9 +33,9 @@ import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.openbis.generic.shared.ITrackingServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdentifiable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
/**
@@ -158,45 +158,11 @@ public class TrackingBO
private static void saveTrackingState(TrackingStateDTO prevState,
TrackedEntities changedEntities, ITrackingDAO trackingDAO)
{
- TrackingStateDTO state = calcNewTrackingState(prevState, changedEntities);
+ TrackingStateDTO state =
+ TrackingStateUpdateHelper.calcNewTrackingState(prevState, changedEntities);
trackingDAO.saveTrackingState(state);
}
- private static TrackingStateDTO calcNewTrackingState(TrackingStateDTO prevState,
- TrackedEntities changedEntities)
- {
- TrackingStateDTO state = new TrackingStateDTO();
- Set<Long> sequencingSamplesProcessed =
- new HashSet<Long>(prevState.getAlreadyTrackedSampleIdsProcessed());
- addNewSampleIds(sequencingSamplesProcessed, changedEntities.getSequencingSamplesProcessed());
- state.setAlreadyTrackedSampleIdsProcessed(sequencingSamplesProcessed);
-
- int lastSeenDatasetId =
- calcMaxId(changedEntities.getDataSets(), prevState.getLastSeenDatasetId());
- state.setLastSeenDatasetId(lastSeenDatasetId);
- return state;
- }
-
- private static void addNewSampleIds(Set<Long> alreadyTrackedSampleIdsProcessed,
- List<Sample> sequencingSamplesProcessed)
- {
- for (Sample sample : sequencingSamplesProcessed)
- {
- alreadyTrackedSampleIdsProcessed.add(sample.getId());
- }
- }
-
- private static int calcMaxId(List<? extends IIdentifiable> entities, int initialValue)
- {
- long max = initialValue;
- for (IIdentifiable entity : entities)
- {
- max = Math.max(max, entity.getId());
- }
- // TODO 2009-12-01, Tomasz Pylak: refactor ids to long everywhere
- return (int) max;
- }
-
private static TrackedEntities fetchChangedEntities(TrackingStateDTO trackingState,
ITrackingServer trackingServer, SessionContextDTO session)
{
@@ -226,4 +192,50 @@ public class TrackingBO
Collections.EMPTY_LIST);
return trackingServer.listSamples(session.getSessionToken(), criteria);
}
+
+ public static class TrackingStateUpdateHelper
+ {
+
+ public static TrackingStateDTO calcNewTrackingState(TrackingStateDTO prevState,
+ TrackedEntities changedEntities)
+ {
+ TrackingStateDTO state = new TrackingStateDTO();
+ Set<Long> sequencingSamplesToBeProcessed =
+ new TreeSet<Long>(prevState.getAlreadyTrackedSampleIdsToBeProcessed());
+ addNewSampleIds(sequencingSamplesToBeProcessed, changedEntities
+ .getSequencingSamplesToBeProcessed());
+ state.setAlreadyTrackedSampleIdsToBeProcessed(sequencingSamplesToBeProcessed);
+
+ Set<Long> sequencingSamplesProcessed =
+ new TreeSet<Long>(prevState.getAlreadyTrackedSampleIdsProcessed());
+ addNewSampleIds(sequencingSamplesProcessed, changedEntities
+ .getSequencingSamplesProcessed());
+ state.setAlreadyTrackedSampleIdsProcessed(sequencingSamplesProcessed);
+
+ int lastSeenDatasetId =
+ calcMaxId(changedEntities.getDataSets(), prevState.getLastSeenDatasetId());
+ state.setLastSeenDatasetId(lastSeenDatasetId);
+ return state;
+ }
+
+ private static void addNewSampleIds(Set<Long> alreadyTrackedSampleIdsProcessed,
+ List<Sample> sequencingSamplesProcessed)
+ {
+ for (Sample sample : sequencingSamplesProcessed)
+ {
+ alreadyTrackedSampleIdsProcessed.add(sample.getId());
+ }
+ }
+
+ private static int calcMaxId(List<? extends IIdentifiable> entities, int initialValue)
+ {
+ long max = initialValue;
+ for (IIdentifiable entity : entities)
+ {
+ max = Math.max(max, entity.getId());
+ }
+ // TODO 2009-12-01, Tomasz Pylak: refactor ids to long everywhere
+ return (int) max;
+ }
+ }
}
--
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