diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailDataManager.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailDataManager.java
index 86223c97de4b1476fdeb9538102c0dbae79e0712..afce37a6324bfa1212fe06054dd8fa4e39523d3b 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailDataManager.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailDataManager.java
@@ -28,7 +28,6 @@ import ch.systemsx.cisd.common.mail.EMailAddress;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
/**
* Manager that groups data about tracked entities into {@link EntityTrackingEmailData} objects.
@@ -43,8 +42,6 @@ class EntityTrackingEmailDataManager
private final static String PRINCIPAL_INVESTIGATOR_EMAIL = "PRINCIPAL_INVESTIGATOR_EMAIL";
- private final static String MASTER_SAMPLE_TYPE = "MASTER_SAMPLE";
-
private static Map<String, String> recipientsByAffiliation;
public static void initialize(final Map<String, String> recipients)
@@ -125,7 +122,8 @@ class EntityTrackingEmailDataManager
}
/**
- * Returns a set of emails of recipients that should get a tracking information about given <var>sequencingSample</var>.<br>
+ * Returns a set of emails of recipients that should get a tracking information about given
+ * <var>sequencingSample</var>.<br>
*/
// NOTE: Set is needed because one recipient can occur in many roles for one sample
private static Set<EMailAddress> getSequencingSampleTrackingRecipients(
@@ -140,91 +138,58 @@ class EntityTrackingEmailDataManager
recipientPropertyTypeCodes.add(CONTACT_PERSON_EMAIL);
recipientPropertyTypeCodes.add(PRINCIPAL_INVESTIGATOR_EMAIL);
- SampleType masterSampleType = new SampleType();
- masterSampleType.setCode(MASTER_SAMPLE_TYPE);
-
for (Sample sequencingSample : sequencingSamples)
{
-
- findMasterSample(sequencingSample, recipients);
-
- }
- return recipients;
- }
-
- private static void findMasterSample(Sample s, Set<EMailAddress> recipients)
- {
- SampleType masterSampleType = new SampleType();
- masterSampleType.setCode(MASTER_SAMPLE_TYPE);
- // Recipients are taken from properties of the sequencing sample.
- final Set<String> recipientPropertyTypeCodes = new HashSet<String>();
- recipientPropertyTypeCodes.add(CONTACT_PERSON_EMAIL);
- recipientPropertyTypeCodes.add(PRINCIPAL_INVESTIGATOR_EMAIL);
-
- SampleType seqSampleSampleType = s.getSampleType();
- if (seqSampleSampleType.equals(masterSampleType))
- {
- Set<EMailAddress> r = extractProperties(recipientPropertyTypeCodes, s);
- recipients.addAll(r);
- }
- else
- {
- for (Sample parent : s.getParents())
- {
- findMasterSample(parent, recipients);
-
- }
- }
-
- }
-
- private static Set<EMailAddress> extractProperties(final Set<String> recipientPropertyTypeCodes, Sample sequencingSample)
- {
- Set<EMailAddress> recipients = new HashSet<EMailAddress>();
- for (IEntityProperty property : sequencingSample.getProperties())
- {
- final String propertyCode = property.getPropertyType().getCode();
- EMailAddress propertyValue = new EMailAddress(property.tryGetAsString());
- if (recipientPropertyTypeCodes.contains(propertyCode))
+ for (IEntityProperty property : sequencingSample.getProperties())
{
- recipients.add(propertyValue);
- } else
- {
- // add recipient for affiliation if his email was specified in properties
- if (propertyCode.equals(AFFILIATION))
+ final String propertyCode = property.getPropertyType().getCode();
+ final String propertyValue = property.tryGetAsString();
+ if (recipientPropertyTypeCodes.contains(propertyCode))
+ {
+ EMailAddress myEmail = new EMailAddress(propertyValue);
+ recipients.add(myEmail);
+ } else
{
- EMailAddress affiliationRecipientOrNull = new EMailAddress(
- recipientsByAffiliation.get(propertyValue));
- if (affiliationRecipientOrNull != null)
+ // add recipient for affiliation if his email was specified in properties
+ if (propertyCode.equals(AFFILIATION))
{
- recipients.add(affiliationRecipientOrNull);
+ String affiliationRecipientOrNull =
+ recipientsByAffiliation.get(propertyValue);
+ if (affiliationRecipientOrNull != null)
+ {
+ EMailAddress myEmail = new EMailAddress(affiliationRecipientOrNull);
+ recipients.add(myEmail);
+ }
}
}
}
}
+
return recipients;
}
/**
- * Returns a set of emails of recipients that should get a tracking information about given <var>flowLaneSample</var>.
+ * Returns a set of emails of recipients that should get a tracking information about given
+ * <var>flowLaneSample</var>.
*/
- private static Set<EMailAddress> getSampleTrackingRecipients(Sample sample)
+ private static Set<EMailAddress> getFlowLaneSampleTrackingRecipients(Sample flowLaneSample)
{
- // Recipients are taken from properties of master sample
- // that is a parent/grandparent of a library/raw sample
- assert sample != null;
- return getSequencingSampleTrackingRecipients(sample.getParents());
+ // Recipients are taken from properties of sequencing sample
+ // that is a parent of the flow lane sample.
+ assert flowLaneSample != null;
+ return getSequencingSampleTrackingRecipients(flowLaneSample.getParents());
}
/**
- * Returns a set of emails of recipients that should get a tracking information about given <var>dataSet</var>.
+ * Returns a set of emails of recipients that should get a tracking information about given
+ * <var>dataSet</var>.
*/
private static Set<EMailAddress> getDataSetTrackingRecipients(AbstractExternalData dataSet)
{
- // Recipients are taken from properties of master sample
- // that is a parent/grandparent of a library/raw sample connected with the data set.
+ // Recipients are taken from properties of sequencing sample
+ // that is a parent of a flow lane sample connected directly with the data set.
assert dataSet != null;
- return getSampleTrackingRecipients(dataSet.getSample());
+ return getFlowLaneSampleTrackingRecipients(dataSet.getSample());
}
}
\ No newline at end of file
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 35a8e19d03c3b270c413e3386f8c72bb0fc2684b..e0cf1d25a0320fd51480b81cb46596e774817f83 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
@@ -26,7 +26,6 @@ import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Properties;
-import java.util.Set;
import java.util.TreeMap;
import ch.ethz.bsse.cisd.dsu.tracking.dto.TrackedEntities;
@@ -176,11 +175,11 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
private static final String PERMLINK_LABEL = "See details in openBIS";
- private static final String GENERATED_CONTENT_TARGET = "{generated-content}";
+ private static final String GENARATED_CONTENT_TARGET = "{generated-content}";
public static String fillTemplateWithData(String template, EntityTrackingEmailData emailData)
{
- return template.replace(GENERATED_CONTENT_TARGET, generateContent(emailData));
+ return template.replace(GENARATED_CONTENT_TARGET, generateContent(emailData));
}
private static String generateContent(EntityTrackingEmailData emailData)
@@ -192,33 +191,12 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
return sb.toString();
}
- private static String getName(Sample sequencingSample)
- {
- /**
- * We try to get the external sample name recursively in the sample tree. This means we take the first name in the tree. This results in
- * the following precedence: LIBARY -> RAW
- */
-
- String externalSampleName = getExternalSampleName(sequencingSample);
- if (externalSampleName == null || externalSampleName.isEmpty())
- {
- Set<Sample> parents = sequencingSample.getParents();
- for (Sample parent : parents)
- {
- externalSampleName = getName(parent);
- }
- }
-
- return externalSampleName;
-
- }
-
private static void appendSequencingSamplesData(StringBuilder sb,
Collection<Sample> sequencingSamples, boolean processed)
{
for (Sample sequencingSample : sequencingSamples)
{
- String externalSampleName = getName(sequencingSample);
+ final String externalSampleName = getExternalSampleName(sequencingSample);
appendln(sb, SECTION_SEPARATOR_LINE);
appendln(sb, SUBSECTION_SEPARATOR_LINE);
@@ -263,19 +241,18 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
appendln(sb, SUBSECTION_SEPARATOR_LINE);
appendln(sb, "There are new sequencing results available to you.");
appendln(sb, SUBSECTION_SEPARATOR_LINE);
-
+
// Using a TreeMap, so the keys are sorted
TreeMap<String, List<AbstractExternalData>> sampleMap = new TreeMap<String, List<AbstractExternalData>>();
- List<AbstractExternalData> dsList = new ArrayList<AbstractExternalData>();
-
+ List <AbstractExternalData> dsList = new ArrayList<AbstractExternalData>();
+
// we just loop over the data sets and write the connected samples as keys
- // and the data sets as values in a map, so that we can group together as
+ // and the data sets as values in a map, so that we can group together as
// data sets per lane
for (AbstractExternalData dataSet : dataSets)
{
Sample s = dataSet.getSample();
- if (sampleMap.containsKey(s.getIdentifier()))
- {
+ if (sampleMap.containsKey(s.getIdentifier())) {
dsList = sampleMap.get(s.getIdentifier());
}
dsList.add(dataSet);
@@ -285,13 +262,11 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
// now we can write out this per sample
Iterator<Entry<String, List<AbstractExternalData>>> it = sampleMap.entrySet().iterator();
- while (it.hasNext())
- {
- Map.Entry pairs = (Map.Entry) it.next();
+ while (it.hasNext()) {
+ Map.Entry pairs = (Map.Entry)it.next();
appendln(sb, String.format("Results for %s", pairs.getKey()));
dsList = (List<AbstractExternalData>) pairs.getValue();
- for (AbstractExternalData ed : dsList)
- {
+ for (AbstractExternalData ed : dsList) {
appendDataSetDetails(sb, ed);
}
it.remove(); // avoids a ConcurrentModificationException
@@ -307,18 +282,16 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
assert flowLaneSample != null;
sequencingSamples = flowLaneSample.getParents();
assert sequencingSamples != null;
-
+
String Index1 = getIndex1(dataSet);
String Index2 = getIndex2(dataSet);
String externalSampleName = externalSampleNameFromDataSet(dataSet);
String Index = null;
- if (Index1 != null)
- {
+ if (Index1 != null) {
Index = Index1;
}
- if (Index2 != null)
- {
+ if (Index2 != null) {
Index = Index + "-" + Index2;
}
@@ -327,8 +300,7 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
appendln(sb, "Data Set Type: " + dataSet.getDataSetType().toString() +
" Index: " + Index + ", External Sample Name: " + externalSampleName);
}
- else
- {
+ else {
appendln(sb, "Data Set Type: " + dataSet.getDataSetType().toString());
}
appendln(sb, dataSet.getPermlink());
@@ -338,45 +310,33 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
{
String externalSampleName =
tryGetSamplePropertyValue(sequencingSample, EXTERNAL_SAMPLE_NAME_PROPERTY_CODE);
- // assert externalSampleName != null;
- if (externalSampleName == null)
- {
- externalSampleName = "";
- }
+ assert externalSampleName != null;
return externalSampleName;
}
-
- private static String getIndex1(AbstractExternalData dataSet)
- {
+
+ private static String getIndex1(AbstractExternalData dataSet) {
List<IEntityProperty> properties = dataSet.getProperties();
-
- String Index = null;
- for (IEntityProperty p : properties)
- {
- if (p.getPropertyType().getCode().equals(INDEX1_PROPERTY_CODE))
- {
+
+ String Index = null;
+ for (IEntityProperty p : properties) {
+ if (p.getPropertyType().getCode().equals(INDEX1_PROPERTY_CODE)) {
Index = p.getVocabularyTerm().getCode();
- if (!Index.equals("NOINDEX"))
- {
+ if (! Index.equals("NOINDEX")) {
return Index;
}
}
}
return null;
}
-
- private static String getIndex2(AbstractExternalData dataSet)
- {
+
+ private static String getIndex2(AbstractExternalData dataSet) {
List<IEntityProperty> properties = dataSet.getProperties();
-
- String Index = null;
- for (IEntityProperty p : properties)
- {
- if (p.getPropertyType().getCode().equals(INDEX2_PROPERTY_CODE))
- {
+
+ String Index = null;
+ for (IEntityProperty p : properties) {
+ if (p.getPropertyType().getCode().equals(INDEX2_PROPERTY_CODE)) {
Index = p.getVocabularyTerm().getCode();
- if (!Index.equals("NOINDEX"))
- {
+ if (! Index.equals("NOINDEX")) {
return Index;
}
}
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 36b121623cf42207b03b374ccae996574b5fbcff..0305f8bba570bdbc6eddb69fa708da225237f38d 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
@@ -21,7 +21,6 @@ import java.util.Arrays;
import java.util.EnumSet;
import java.util.HashSet;
import java.util.List;
-import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
@@ -35,19 +34,9 @@ import ch.systemsx.cisd.common.collection.CollectionUtils;
import ch.systemsx.cisd.common.mail.EMailAddress;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.openbis.generic.shared.ITrackingServer;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.SearchOperator;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
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.basic.dto.TrackingDataSetCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
@@ -61,38 +50,27 @@ public class TrackingBO
private static final String EXTERNAL_SAMPLE_NAME = "EXTERNAL_SAMPLE_NAME";
- private static final String LIBRARY_SAMPLE_TYPE = "LIBRARY";
+ private static final String SEQUENCING_SAMPLE_TYPE = "ILLUMINA_SEQUENCING";
- private static final String RAW_SAMPLE_TYPE = "RAW_SAMPLE";
+ private static final String FLOW_LANE_SAMPLE_TYPE = "ILLUMINA_FLOW_LANE";
- private static final String DATASET_ATTACHED_TO_SAMPLE_TYPE = "LIBRARY";
-
- private static final String PROCESSING_POSSIBLE_PROPERTY_CODE = "LIBRARY_PROCESSING_POSSIBLE_YES_NO";
+ private static final String PROCESSING_POSSIBLE_PROPERTY_CODE = "LIBRARY_PROCESSING_POSSIBLE";
private static final String PROCESSING_SUCCESSFUL_PROPERTY_CODE =
"LIBRARY_PROCESSING_SUCCESSFUL";
- private final static String CONTACT_PERSON_EMAIL = "CONTACT_PERSON_EMAIL";
-
- private final static String PRINCIPAL_INVESTIGATOR_EMAIL = "PRINCIPAL_INVESTIGATOR_EMAIL";
-
private static final String TRUE = "true";
- private static final String YES = "YES";
-
private final ITrackingServer trackingServer;
- private final IGeneralInformationService gis;
-
private final IEntityTrackingEmailGenerator emailGenerator;
private final IMailClient mailClient;
- public TrackingBO(ITrackingServer trackingServer, IGeneralInformationService gis, IEntityTrackingEmailGenerator emailGenerator,
+ public TrackingBO(ITrackingServer trackingServer, IEntityTrackingEmailGenerator emailGenerator,
IMailClient mailClient)
{
this.trackingServer = trackingServer;
- this.gis = gis;
this.emailGenerator = emailGenerator;
this.mailClient = mailClient;
}
@@ -102,7 +80,7 @@ public class TrackingBO
TrackingStateDTO prevTrackingState = trackingDAO.getTrackingState();
TrackedEntities changedEntities =
- fetchChangedEntities(prevTrackingState, trackingServer, gis, session);
+ fetchChangedEntities(prevTrackingState, trackingServer, session);
List<EmailWithSummary> emailsWithSummary = emailGenerator.generateEmails(changedEntities);
sendEmails(emailsWithSummary, mailClient);
saveTrackingState(prevTrackingState, changedEntities, trackingDAO);
@@ -197,18 +175,17 @@ public class TrackingBO
}
private static TrackedEntities fetchChangedEntities(TrackingStateDTO trackingState,
- ITrackingServer trackingServer, IGeneralInformationService gis, SessionContextDTO session)
+ ITrackingServer trackingServer, SessionContextDTO session)
{
List<Sample> sequencingSamplesToBeProcessed =
- listSequencingSamples(RAW_SAMPLE_TYPE, YES, PROCESSING_POSSIBLE_PROPERTY_CODE, trackingState
- .getAlreadyTrackedSampleIdsToBeProcessed(), trackingServer, gis, session);
-
+ listSequencingSamples(PROCESSING_POSSIBLE_PROPERTY_CODE, trackingState
+ .getAlreadyTrackedSampleIdsToBeProcessed(), trackingServer, session);
List<Sample> sequencingSamplesSuccessfullyProcessed =
- listSequencingSamples(LIBRARY_SAMPLE_TYPE, TRUE, PROCESSING_SUCCESSFUL_PROPERTY_CODE, trackingState
- .getAlreadyTrackedSampleIdsProcessed(), trackingServer, gis, session);
+ listSequencingSamples(PROCESSING_SUCCESSFUL_PROPERTY_CODE, trackingState
+ .getAlreadyTrackedSampleIdsProcessed(), trackingServer, session);
TrackingDataSetCriteria dataSetCriteria =
- new TrackingDataSetCriteria(DATASET_ATTACHED_TO_SAMPLE_TYPE, trackingState
+ new TrackingDataSetCriteria(FLOW_LANE_SAMPLE_TYPE, trackingState
.getLastSeenDatasetId());
List<AbstractExternalData> dataSets =
trackingServer.listDataSets(session.getSessionToken(), dataSetCriteria);
@@ -217,108 +194,22 @@ public class TrackingBO
sequencingSamplesSuccessfullyProcessed, dataSets);
}
- private static List<Sample> listSequencingSamples(String SampleType, String propertyValue, String propertyTypeCode,
- Set<Long> alreadyTrackedSampleIds, ITrackingServer trackingServer, IGeneralInformationService gis,
+ private static List<Sample> listSequencingSamples(String propertyTypeCode,
+ Set<Long> alreadyTrackedSampleIds, ITrackingServer trackingServer,
SessionContextDTO session)
{
- List<Sample> completeList = new ArrayList<Sample>();
-
- for (String sampleType : SEQUENCING_SAMPLE_TYPES)
- {
- completeList.addAll(listSamples(SampleType, propertyTypeCode, propertyValue, alreadyTrackedSampleIds,
- trackingServer, gis, session));
-
- }
- return completeList;
-
+ return listSamples(SEQUENCING_SAMPLE_TYPE, propertyTypeCode, TRUE, alreadyTrackedSampleIds,
+ trackingServer, session);
}
private static List<Sample> listSamples(String sampleType, String propertyTypeCode,
String propertyValue, Set<Long> alreadyTrackedSampleIds,
- ITrackingServer trackingServer, IGeneralInformationService gis, SessionContextDTO session)
+ ITrackingServer trackingServer, SessionContextDTO session)
{
TrackingSampleCriteria criteria =
new TrackingSampleCriteria(sampleType, propertyTypeCode, propertyValue,
alreadyTrackedSampleIds);
- List<Sample> samples = trackingServer.listSamples(session.getSessionToken(), criteria);
-
- for (Sample sample : samples)
- {
- SearchCriteria parentCriteria = new SearchCriteria();
- parentCriteria.setOperator(SearchOperator.MATCH_ANY_CLAUSES);
-
- for (Sample parent : sample.getParents())
- {
- parentCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, parent.getCode()));
- }
-
- List<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample> apiParents =
- gis.searchForSamples(session.getSessionToken(), parentCriteria,
- EnumSet.of(SampleFetchOption.PARENTS, SampleFetchOption.PROPERTIES));
- Set<Sample> dtoParents = new HashSet<Sample>();
-
- for (ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample apiParent : apiParents)
- {
- dtoParents.add(convertSample(apiParent));
- }
- sample.setParents(dtoParents);
- }
-
- return samples;
- }
-
- private static Sample convertSample(ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample apiSample)
- {
- Sample dtoSample = new Sample();
-
- EntityProperty person = new EntityProperty();
- EntityProperty pi = new EntityProperty();
- EntityProperty externalSampleName = new EntityProperty();
-
- List<IEntityProperty> propertyList = new ArrayList<IEntityProperty>();
-
- dtoSample.setCode(apiSample.getCode());
- String sampleTypeCode = apiSample.getSampleTypeCode();
-
- SampleType stc = new SampleType();
- stc.setCode(sampleTypeCode);
-
- dtoSample.setSampleType(stc);
-
- Map<String, String> properties = apiSample.getProperties();
-
- PropertyType personType = new PropertyType();
- PropertyType piType = new PropertyType();
- PropertyType externalSampleNameType = new PropertyType();
-
- personType.setCode(CONTACT_PERSON_EMAIL);
- piType.setCode(PRINCIPAL_INVESTIGATOR_EMAIL);
- externalSampleNameType.setCode(EXTERNAL_SAMPLE_NAME);
-
- person.setPropertyType(personType);
- person.setValue(properties.get(CONTACT_PERSON_EMAIL));
- propertyList.add(person);
-
- pi.setPropertyType(piType);
- pi.setValue(properties.get(PRINCIPAL_INVESTIGATOR_EMAIL));
- propertyList.add(pi);
-
- externalSampleName.setPropertyType(externalSampleNameType);
- externalSampleName.setValue(properties.get(EXTERNAL_SAMPLE_NAME));
- propertyList.add(externalSampleName);
-
- dtoSample.setProperties(propertyList);
-
- if (apiSample.getRetrievedFetchOptions().contains(SampleFetchOption.PARENTS))
- {
- Set<Sample> dtoParents = new HashSet<Sample>();
- for (ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample apiParent : apiSample.getParents())
- {
- dtoParents.add(convertSample(apiParent));
- }
- dtoSample.setParents(dtoParents);
- }
- return dtoSample;
+ return trackingServer.listSamples(session.getSessionToken(), criteria);
}
static class TrackingStateUpdateHelper
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 780ce7375d81fc30334ae52a58a9a9cc7d16a567..bdaf5b9c4d55ecaf08c36fdaa5267e4e777fbd98 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
@@ -38,7 +38,6 @@ import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
import ch.systemsx.cisd.openbis.generic.shared.ITrackingServer;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
/**
@@ -75,11 +74,10 @@ public class TrackingClient
Parameters params = new Parameters(props);
ITrackingServer trackingServer = createOpenBISTrackingServer(params);
- IGeneralInformationService gis = createOpenBISGeneralInformationService(params);
IEntityTrackingEmailGenerator emailGenerator =
new EntityTrackingEmailGenerator(props, retrieveEmailTemplate());
IMailClient mailClient = params.getMailClient();
- TrackingBO trackingBO = new TrackingBO(trackingServer, gis, emailGenerator, mailClient);
+ TrackingBO trackingBO = new TrackingBO(trackingServer, emailGenerator, mailClient);
ITrackingDAO trackingDAO = new FileBasedTrackingDAO(LOCAL_STORAGE_FILE);
@@ -95,13 +93,6 @@ public class TrackingClient
5 * DateUtils.MILLIS_PER_MINUTE);
}
- private static IGeneralInformationService createOpenBISGeneralInformationService(Parameters params)
- {
- String serviceURL = params.getOpenbisServerURL() + IGeneralInformationService.SERVICE_URL;
- return HttpInvokerUtils.createServiceStub(IGeneralInformationService.class, serviceURL,
- 5 * DateUtils.MILLIS_PER_MINUTE);
- }
-
private static SessionContextDTO authentificateInOpenBIS(Parameters params,
ITrackingServer trackingServer)
{