diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailGenerator.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailGenerator.java
index 6858c77e5a211c9d9fc01b7c46869f211bd15685..4b38e84081450ce71c8a66c34384b846048dde40 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailGenerator.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailGenerator.java
@@ -132,7 +132,6 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
if (propertyKey.contains("*"))
{
String spacePreffix = propertyKey.substring(0, propertyKey.lastIndexOf("*"));
- System.out.println(spacePreffix);
for (SpaceWithProjectsAndRoleAssignments space : spacesList)
{
if (space.getCode().startsWith(spacePreffix))
@@ -368,7 +367,7 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
HashMap<String, String> parentProperties = propertiesFromParentSample(dataSet, sequencingSamples, Index1, Index2);
- String externalSampleName = parentProperties.get(EXTERNAL_SAMPLE_NAME_PROPERTY_CODE);
+ String externalSampleName = getExternalSampleNamefromDataSet(dataSet);
String contactPersonName = parentProperties.get(CONTACT_PERSON_NAME_PROPERTY_CODE);
String Index = null;
@@ -448,6 +447,22 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
return null;
}
+ private static String getExternalSampleNamefromDataSet(AbstractExternalData dataSet)
+ {
+ List<IEntityProperty> properties = dataSet.getProperties();
+
+ String externalSampleName = null;
+ for (IEntityProperty p : properties)
+ {
+ if (p.getPropertyType().getCode().equals(EXTERNAL_SAMPLE_NAME_PROPERTY_CODE))
+ {
+ externalSampleName = p.getValue();
+ return externalSampleName;
+ }
+ }
+ return null;
+ }
+
private static HashMap<String, String> propertiesFromParentSample(AbstractExternalData dataSet,
Collection<Sample> sequencingSamples, String dsIndex1, String dsIndex2)
{
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 c97ee934c98dfdd20a0d6045502088d5d4ef41e3..54d937f0b19e4593b3cc9342bc50092489fa03c7 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
@@ -19,9 +19,9 @@ package ch.ethz.bsse.cisd.dsu.tracking.main;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
-import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;
@@ -61,12 +61,6 @@ public class TrackingBO
private static final String TRUE = "true";
- // private static final String CL_PARAMETER_LANES = "lanes";
-
- // private static final String CL_PARAMETER_ALL = "all";
-
- // private static final String CL_PARAMETER_CHANGED_LANES = "changed_lanes";
-
private final ITrackingServer trackingServer;
private final IEntityTrackingEmailGenerator emailGenerator;
@@ -97,11 +91,12 @@ public class TrackingBO
commandLineMap.get(TrackingClient.CL_PARAMETER_LANES), session);
} else if (commandLineMap.containsKey(TrackingClient.CL_PARAMETER_ALL))
{
- changedEntities = fetchChangedEntities(prevTrackingState, trackingServer, commandLineMap, session);
+ // changedEntities = fetchChangedEntities(prevTrackingState, trackingServer, commandLineMap, session);
+ System.out.println("This function is deactivated");
}
else if (commandLineMap.containsKey(TrackingClient.CL_PARAMETER_CHANGED_LANES))
{
- Set<String> changed_lanes = fetchChangedLanes(prevTrackingState, trackingServer, session);
+ Map<String, String> changed_lanes = fetchChangedLanes(prevTrackingState, trackingServer, session);
sendEmails = false;
}
@@ -228,7 +223,7 @@ public class TrackingBO
return gatherTrackedEntities(trackingState, trackingServer, session, dataSets, changedTrackingMap);
}
- private static Set<String> fetchChangedLanes(TrackingStateDTO trackingState,
+ private static Map<String, String> fetchChangedLanes(TrackingStateDTO trackingState,
ITrackingServer trackingServer, SessionContextDTO session)
{
long maxDataSetId = getMaxDataSetId(trackingState);
@@ -239,25 +234,32 @@ public class TrackingBO
List<AbstractExternalData> dataSets =
trackingServer.listDataSets(session.getSessionToken(), dataSetCriteria);
- Set<String> changedLanesSet = new HashSet<String>();
+ Map<String, String> changedLanesMap = new HashMap<String, String>();
// Loop over all new data sets
for (AbstractExternalData d : dataSets)
{
Long newDataSetID = d.getId();
- String lanePermId = d.getSample().getPermId();
+ Sample lane = d.getSample();
+ String lanePermId = lane.getPermId();
+ String laneSpace = lane.getSpace().getCode();
Long maxDatasetIdForSample = getMaxDataSetIdForSample(trackingState, lanePermId);
// Check if the given lanes/samples have data sets which are newer than the last seen one (= maxDatasetIdForSample)
if (newDataSetID > maxDatasetIdForSample)
{
SampleIdentifier currentLaneId = new SampleIdentifier(d.getSampleCode());
- changedLanesSet.add(currentLaneId.toString());
+ changedLanesMap.put(currentLaneId.toString().substring(1), laneSpace);
LogUtils.info("DataSetID: " + newDataSetID + " of NEW data Sets > MAX DataSet id for this sample: " + maxDatasetIdForSample);
}
}
- LogUtils.info(changedLanesSet.toString());
- return changedLanesSet;
+ Set<Map.Entry<String, String>> entrySet = changedLanesMap.entrySet();
+ for (Entry<String, String> entry : entrySet)
+ {
+ System.out.println(entry.getKey() + " " + entry.getValue());
+ }
+ LogUtils.info(changedLanesMap.toString());
+ return changedLanesMap;
}
private static TrackedEntities fetchChangedDataSets(TrackingStateDTO trackingState,
@@ -295,6 +297,7 @@ public class TrackingBO
{
LogUtils.info("DataSetID: " + newDataSetID + " of NEW data Sets > MAX DataSet id for this sample: " + maxDatasetIdForSample);
filteredDataSets.add(d);
+ System.out.println("Sending Email for " + newDataSetID + " which is part of " + d.getSampleCode());
addDataSetTo(changedTrackingMap, d);
}
}
@@ -396,13 +399,13 @@ public class TrackingBO
TreeMap<String, Long> newTrackingState = new TreeMap<String, Long>();
HashMap<String, ArrayList<Long>> changedTrackingMap = changedEntities.getChangedTrackingMap();
- System.out.println(changedTrackingMap.toString());
+ // System.out.println(changedTrackingMap.toString());
for (Map.Entry<String, ArrayList<Long>> entry : changedTrackingMap.entrySet())
{
newTrackingState.put(entry.getKey(), Collections.max(entry.getValue()));
}
- System.out.println(newTrackingState.entrySet().toString());
+ // System.out.println(newTrackingState.entrySet().toString());
for (Map.Entry<String, Long> entry : prevState.getLastSeenDataSetIdMap().entrySet())
{
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/TrackingClient.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/TrackingClient.java
index bdf203c31ddc08fd6a51ab6aad4ed7be63cccb14..47d6d046be3bc15b9c4f248f35c3e1154f4d9a81 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/TrackingClient.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/TrackingClient.java
@@ -97,11 +97,11 @@ public class TrackingClient
.withDescription("list of lanes to track")
.create(CL_PARAMETER_LANES);
lanes.setArgs(Option.UNLIMITED_VALUES);
- Option all = new Option(CL_PARAMETER_ALL, "track all lanes, only for testing, never use in production!");
+ // Option all = new Option(CL_PARAMETER_ALL, "track all lanes, only for testing, never use in production!");
Option new_lanes = new Option(CL_PARAMETER_CHANGED_LANES, "only list lanes which have new datasets");
options.addOption(lanes);
- options.addOption(all);
+ // options.addOption(all);
options.addOption(new_lanes);
// automatically generate the help statement
@@ -122,7 +122,9 @@ public class TrackingClient
}
if (line.hasOption(CL_PARAMETER_ALL))
{
- commandLineMap.put(CL_PARAMETER_ALL, null);
+ // commandLineMap.put(CL_PARAMETER_ALL, null);
+ System.out.println("This option is deactivated.");
+
}
if (line.hasOption(CL_PARAMETER_CHANGED_LANES))
{