diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/Email.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/Email.java
index f153d20b7aa5c255f2d0637136d77503be668cd2..2d4b6fc9c6c0384d11d9b59bab7c3e5611133dd6 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/Email.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/Email.java
@@ -16,12 +16,12 @@
package ch.ethz.bsse.cisd.dsu.tracking.email;
+import ch.systemsx.cisd.common.mail.EMailAddress;
import ch.systemsx.cisd.common.mail.From;
import ch.systemsx.cisd.common.mail.IMailClient;
/**
- * Simple encapsulation of {@link IMailClient#sendMessage(String, String, String, From, String...)}
- * method parameters.
+ * Simple encapsulation of {@link IMailClient#sendMessage(String, String, String, From, String...)} method parameters.
*
* @author Piotr Buczek
*/
@@ -31,14 +31,14 @@ public class Email
private final String content;
- private final String replyToOrNull;
+ private final EMailAddress replyToOrNull;
- private final From fromOrNull;
+ private final EMailAddress fromOrNull;
- private final String[] recipients;
+ private final EMailAddress[] recipients;
- public Email(String subject, String content, String replyToOrNull, From fromOrNull,
- String... recipients)
+ public Email(String subject, String content, EMailAddress replyToOrNull, EMailAddress fromOrNull,
+ EMailAddress... recipients)
{
super();
this.subject = subject;
@@ -48,10 +48,10 @@ public class Email
this.recipients = recipients;
}
- public Email(String subject, String content, String replyToOrNull, String fromOrNull,
- String... recipients)
+ public Email(String subject, String content, EMailAddress replyToOrNull, String fromOrNull,
+ EMailAddress... recipients)
{
- this(subject, content, replyToOrNull, new From(fromOrNull), recipients);
+ this(subject, content, replyToOrNull, new EMailAddress(fromOrNull), recipients);
}
public String getSubject()
@@ -64,17 +64,17 @@ public class Email
return content;
}
- public String getReplyToOrNull()
+ public EMailAddress getReplyToOrNull()
{
return replyToOrNull;
}
- public From getFromOrNull()
+ public EMailAddress getFromOrNull()
{
return fromOrNull;
}
- public String[] getRecipients()
+ public EMailAddress[] getRecipients()
{
return recipients;
}
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailData.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailData.java
index 4baae2d63089c24acd8f8345a49b867e9fc7f81c..08c7d402190da2d672fbce90c2d6212808f2f68b 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailData.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailData.java
@@ -19,13 +19,13 @@ package ch.ethz.bsse.cisd.dsu.tracking.email;
import java.util.ArrayList;
import java.util.List;
+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.Sample;
/**
- * Structure containing all data about tracked entities that will be used in a single email to an
- * recipient. Its purpose is to group data that will be used to generate content of an email
- * containing merged information about all events that the recipient should be notified about.
+ * Structure containing all data about tracked entities that will be used in a single email to an recipient. Its purpose is to group data that will be
+ * used to generate content of an email containing merged information about all events that the recipient should be notified about.
*
* @author Piotr Buczek
*/
@@ -37,15 +37,15 @@ public class EntityTrackingEmailData
private final List<AbstractExternalData> dataSets = new ArrayList<AbstractExternalData>(0);
- private final String recipient;
+ private final EMailAddress recipient;
/** creates email data for given <var>recipient</var> */
- public EntityTrackingEmailData(String recipient)
+ public EntityTrackingEmailData(EMailAddress recipient)
{
this.recipient = recipient;
}
- public String getRecipient()
+ public EMailAddress getRecipient()
{
return recipient;
}
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 2b83c189661a4fe017d70abd909e2a1267da9c47..86223c97de4b1476fdeb9538102c0dbae79e0712 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
@@ -24,6 +24,7 @@ import java.util.Map;
import java.util.Set;
import ch.ethz.bsse.cisd.dsu.tracking.dto.TrackedEntities;
+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;
@@ -56,8 +57,8 @@ class EntityTrackingEmailDataManager
{
assert recipientsByAffiliation != null : "recipientsByAffiliation not initialized";
// <recipients email, email data>
- final Map<String, EntityTrackingEmailData> dataByRecipient =
- new HashMap<String, EntityTrackingEmailData>();
+ final Map<EMailAddress, EntityTrackingEmailData> dataByRecipient =
+ new HashMap<EMailAddress, EntityTrackingEmailData>();
groupSequencingSamplesToBeProcessed(dataByRecipient, trackedEntities);
groupSequencingSamplesProcessed(dataByRecipient, trackedEntities);
groupDataSetSamples(dataByRecipient, trackedEntities);
@@ -66,11 +67,11 @@ class EntityTrackingEmailDataManager
/** Puts tracked sequencing samples to be processed grouped by recipient into <var>result</var>. */
private static void groupSequencingSamplesToBeProcessed(
- Map<String, EntityTrackingEmailData> result, TrackedEntities trackedEntities)
+ Map<EMailAddress, EntityTrackingEmailData> result, TrackedEntities trackedEntities)
{
for (Sample sequencingSample : trackedEntities.getSequencingSamplesToBeProcessed())
{
- for (String recipient : getSequencingSampleTrackingRecipients(Collections
+ for (EMailAddress recipient : getSequencingSampleTrackingRecipients(Collections
.singleton(sequencingSample)))
{
final EntityTrackingEmailData emailData =
@@ -82,11 +83,11 @@ class EntityTrackingEmailDataManager
/** Puts tracked processed sequencing samples grouped by recipient into <var>result</var>. */
private static void groupSequencingSamplesProcessed(
- Map<String, EntityTrackingEmailData> result, TrackedEntities trackedEntities)
+ Map<EMailAddress, EntityTrackingEmailData> result, TrackedEntities trackedEntities)
{
for (Sample sequencingSample : trackedEntities.getSequencingSamplesProcessed())
{
- for (String recipient : getSequencingSampleTrackingRecipients(Collections
+ for (EMailAddress recipient : getSequencingSampleTrackingRecipients(Collections
.singleton(sequencingSample)))
{
final EntityTrackingEmailData emailData =
@@ -97,12 +98,12 @@ class EntityTrackingEmailDataManager
}
/** Puts tracked data sets grouped by recipient into <var>result</var>. */
- private static void groupDataSetSamples(Map<String, EntityTrackingEmailData> result,
+ private static void groupDataSetSamples(Map<EMailAddress, EntityTrackingEmailData> result,
TrackedEntities trackedEntities)
{
for (AbstractExternalData dataSet : trackedEntities.getDataSets())
{
- for (String recipient : getDataSetTrackingRecipients(dataSet))
+ for (EMailAddress recipient : getDataSetTrackingRecipients(dataSet))
{
final EntityTrackingEmailData emailData =
getOrCreateRecipientEmailData(result, recipient);
@@ -112,7 +113,7 @@ class EntityTrackingEmailDataManager
}
private static EntityTrackingEmailData getOrCreateRecipientEmailData(
- Map<String, EntityTrackingEmailData> dataByRecipient, String recipient)
+ Map<EMailAddress, EntityTrackingEmailData> dataByRecipient, EMailAddress recipient)
{
EntityTrackingEmailData emailDataOrNull = dataByRecipient.get(recipient);
if (emailDataOrNull == null)
@@ -127,12 +128,12 @@ class EntityTrackingEmailDataManager
* 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<String> getSequencingSampleTrackingRecipients(
+ private static Set<EMailAddress> getSequencingSampleTrackingRecipients(
Collection<Sample> sequencingSamples)
{
assert sequencingSamples != null;
- final Set<String> recipients = new HashSet<String>();
+ final Set<EMailAddress> recipients = new HashSet<EMailAddress>();
// Recipients are taken from properties of the sequencing sample.
final Set<String> recipientPropertyTypeCodes = new HashSet<String>();
@@ -147,45 +148,11 @@ class EntityTrackingEmailDataManager
findMasterSample(sequencingSample, recipients);
- // SampleType seqSampleSampleType = sequencingSample.getSampleType();
- // if (seqSampleSampleType.equals(masterSampleType))
- // {
- // Set<String> r = extractProperties(recipientPropertyTypeCodes, sequencingSample);
- // recipients.addAll(r);
- // }
- // else
- // {
- // Set<Sample> parents = sequencingSample.getParents();
- // assert parents != null;
- // for (Sample parent : parents)
- // {
- // SampleType sampleType = parent.getSampleType();
- //
- // if (false == sampleType.equals(masterSampleType))
- // {
- // Set<Sample> grandParents = parent.getParents();
- // for (Sample grandparent : grandParents)
- // {
- // Set<String> r = extractProperties(recipientPropertyTypeCodes, grandparent);
- // recipients.addAll(r);
- // }
- // }
- // else
- // {
- // {
- // Set<String> r = extractProperties(recipientPropertyTypeCodes, sequencingSample);
- // recipients.addAll(r);
- // }
- // }
- //
- // }
- //
- // }
}
return recipients;
}
- private static void findMasterSample(Sample s, Set<String> recipients)
+ private static void findMasterSample(Sample s, Set<EMailAddress> recipients)
{
SampleType masterSampleType = new SampleType();
masterSampleType.setCode(MASTER_SAMPLE_TYPE);
@@ -197,7 +164,7 @@ class EntityTrackingEmailDataManager
SampleType seqSampleSampleType = s.getSampleType();
if (seqSampleSampleType.equals(masterSampleType))
{
- Set<String> r = extractProperties(recipientPropertyTypeCodes, s);
+ Set<EMailAddress> r = extractProperties(recipientPropertyTypeCodes, s);
recipients.addAll(r);
}
else
@@ -211,13 +178,13 @@ class EntityTrackingEmailDataManager
}
- private static Set<String> extractProperties(final Set<String> recipientPropertyTypeCodes, Sample sequencingSample)
+ private static Set<EMailAddress> extractProperties(final Set<String> recipientPropertyTypeCodes, Sample sequencingSample)
{
- Set<String> recipients = new HashSet<String>();
+ Set<EMailAddress> recipients = new HashSet<EMailAddress>();
for (IEntityProperty property : sequencingSample.getProperties())
{
final String propertyCode = property.getPropertyType().getCode();
- final String propertyValue = property.tryGetAsString();
+ EMailAddress propertyValue = new EMailAddress(property.tryGetAsString());
if (recipientPropertyTypeCodes.contains(propertyCode))
{
recipients.add(propertyValue);
@@ -226,8 +193,8 @@ class EntityTrackingEmailDataManager
// add recipient for affiliation if his email was specified in properties
if (propertyCode.equals(AFFILIATION))
{
- String affiliationRecipientOrNull =
- recipientsByAffiliation.get(propertyValue);
+ EMailAddress affiliationRecipientOrNull = new EMailAddress(
+ recipientsByAffiliation.get(propertyValue));
if (affiliationRecipientOrNull != null)
{
recipients.add(affiliationRecipientOrNull);
@@ -241,7 +208,7 @@ class EntityTrackingEmailDataManager
/**
* Returns a set of emails of recipients that should get a tracking information about given <var>flowLaneSample</var>.
*/
- private static Set<String> getSampleTrackingRecipients(Sample sample)
+ private static Set<EMailAddress> getSampleTrackingRecipients(Sample sample)
{
// Recipients are taken from properties of master sample
// that is a parent/grandparent of a library/raw sample
@@ -252,7 +219,7 @@ class EntityTrackingEmailDataManager
/**
* Returns a set of emails of recipients that should get a tracking information about given <var>dataSet</var>.
*/
- private static Set<String> getDataSetTrackingRecipients(AbstractExternalData dataSet)
+ 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.
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 c17eb0b22d69c2cfa2b587ee6eb9157c1610de78..35a8e19d03c3b270c413e3386f8c72bb0fc2684b 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
@@ -30,6 +30,7 @@ import java.util.Set;
import java.util.TreeMap;
import ch.ethz.bsse.cisd.dsu.tracking.dto.TrackedEntities;
+import ch.systemsx.cisd.common.mail.EMailAddress;
import ch.systemsx.cisd.common.properties.PropertyUtils;
import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.lang.StringEscapeUtils;
@@ -52,9 +53,9 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
private static final String AFFILIATION_NOTIFICATION_EMAIL_CONTACT_SUFFIX =
"-affiliation-notification-email-contact";
- private final String from;
+ private final EMailAddress from;
- private final String replyTo;
+ private final EMailAddress replyTo;
private final String subject;
@@ -62,8 +63,8 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
public EntityTrackingEmailGenerator(Properties properties, String template)
{
- this.from = PropertyUtils.getMandatoryProperty(properties, NOTIFICATION_EMAIL_FROM);
- this.replyTo = PropertyUtils.getMandatoryProperty(properties, NOTIFICATION_EMAIL_REPLY_TO);
+ this.from = new EMailAddress(PropertyUtils.getMandatoryProperty(properties, NOTIFICATION_EMAIL_FROM));
+ this.replyTo = new EMailAddress(PropertyUtils.getMandatoryProperty(properties, NOTIFICATION_EMAIL_REPLY_TO));
this.subject = PropertyUtils.getMandatoryProperty(properties, NOTIFICATION_EMAIL_SUBJECT);
this.template = template;
@@ -116,8 +117,19 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
private Email createEmail(EntityTrackingEmailData emailData)
{
String content = EmailContentGenerator.fillTemplateWithData(template, emailData);
- String recipient = emailData.getRecipient();
- return new Email(subject, content, replyTo, from, filterBlanks(recipient.split(",|;| ")));
+ EMailAddress recipients = emailData.getRecipient();
+
+ String[] mailStringArray = filterBlanks(recipients.tryGetEmailAddress().split(",|;| "));
+ EMailAddress[] recipientsArray = new EMailAddress[mailStringArray.length];
+
+ for (int i = 0; i < mailStringArray.length; ++i)
+ {
+ EMailAddress e = new EMailAddress(mailStringArray[i]);
+ recipientsArray[i] = e;
+ }
+
+ return new Email(subject, content, replyTo, from, recipientsArray);
+
}
private static String[] filterBlanks(String[] arr)
@@ -298,6 +310,7 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
String Index1 = getIndex1(dataSet);
String Index2 = getIndex2(dataSet);
+ String externalSampleName = externalSampleNameFromDataSet(dataSet);
String Index = null;
if (Index1 != null)
@@ -309,10 +322,10 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
Index = Index + "-" + Index2;
}
- if (Index != null)
+ if (Index != null && externalSampleName != null)
{
appendln(sb, "Data Set Type: " + dataSet.getDataSetType().toString() +
- " Index: " + Index);
+ " Index: " + Index + ", External Sample Name: " + externalSampleName);
}
else
{
@@ -371,6 +384,25 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
return null;
}
+ private static String externalSampleNameFromDataSet(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();
+ if (!externalSampleName.equals(null))
+ {
+ return externalSampleName;
+ }
+ }
+ }
+ return null;
+ }
+
private static String tryGetSamplePropertyValue(Sample sequencingSample, String propertyCode)
{
String result = null;
@@ -425,11 +457,4 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
}
}
-
- public static void findSampleWithExternalSampleName(Sample sequencingSample)
- {
- // TODO Auto-generated method stub
-
- }
-
}
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 888cf720ab96387b7da2da4033bbff0f9f696fea..36b121623cf42207b03b374ccae996574b5fbcff 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
@@ -17,6 +17,7 @@
package ch.ethz.bsse.cisd.dsu.tracking.main;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.EnumSet;
import java.util.HashSet;
import java.util.List;
@@ -31,7 +32,7 @@ import ch.ethz.bsse.cisd.dsu.tracking.email.EmailWithSummary;
import ch.ethz.bsse.cisd.dsu.tracking.email.IEntityTrackingEmailGenerator;
import ch.ethz.bsse.cisd.dsu.tracking.utils.LogUtils;
import ch.systemsx.cisd.common.collection.CollectionUtils;
-import ch.systemsx.cisd.common.mail.From;
+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;
@@ -56,6 +57,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
*/
public class TrackingBO
{
+ private static final List<String> SEQUENCING_SAMPLE_TYPES = Arrays.asList("ILLUMINA_SEQUENCING", "ILLUMINA_SEQUENCING_NEUROSTEMX");
+
private static final String EXTERNAL_SAMPLE_NAME = "EXTERNAL_SAMPLE_NAME";
private static final String LIBRARY_SAMPLE_TYPE = "LIBRARY";
@@ -168,11 +171,15 @@ public class TrackingBO
{
String subject = email.getSubject();
String content = email.getContent();
- String replyToOrNull = email.getReplyToOrNull();
- From fromOrNull = email.getFromOrNull();
- String[] recipients = email.getRecipients();
+ EMailAddress replyToOrNull = email.getReplyToOrNull();
+ EMailAddress fromOrNull = email.getFromOrNull();
+ EMailAddress[] recipients = email.getRecipients();
+
+ mailClient.sendEmailMessage(subject, content, replyToOrNull, fromOrNull, recipients);
+
+ // sendEmailMessage(String subject, String content, EMailAddress replyToOrNull,
+ // EMailAddress fromOrNull, EMailAddress... recipients)
- mailClient.sendMessage(subject, content, replyToOrNull, fromOrNull, recipients);
}
private static void appendLine(StringBuilder sb, String msg)
@@ -214,8 +221,16 @@ public class TrackingBO
Set<Long> alreadyTrackedSampleIds, ITrackingServer trackingServer, IGeneralInformationService gis,
SessionContextDTO session)
{
- return listSamples(SampleType, propertyTypeCode, propertyValue, alreadyTrackedSampleIds,
- trackingServer, gis, 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;
+
}
private static List<Sample> listSamples(String sampleType, String propertyTypeCode,