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 94315a6abf8f39033875e2b25994b18f6ef31fe1..f153d20b7aa5c255f2d0637136d77503be668cd2 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
@@ -16,11 +16,11 @@
package ch.ethz.bsse.cisd.dsu.tracking.email;
+import ch.systemsx.cisd.common.mail.From;
import ch.systemsx.cisd.common.mail.IMailClient;
/**
- * Simple encapsulation of
- * {@link IMailClient#sendMessage(String, String, String, ch.systemsx.cisd.common.mail.From, String...)}
+ * Simple encapsulation of {@link IMailClient#sendMessage(String, String, String, From, String...)}
* method parameters.
*
* @author Piotr Buczek
@@ -33,11 +33,11 @@ public class Email
private final String replyToOrNull;
- private final String fromOrNull;
+ private final From fromOrNull;
private final String[] recipients;
- public Email(String subject, String content, String replyToOrNull, String fromOrNull,
+ public Email(String subject, String content, String replyToOrNull, From fromOrNull,
String... recipients)
{
super();
@@ -48,6 +48,12 @@ public class Email
this.recipients = recipients;
}
+ public Email(String subject, String content, String replyToOrNull, String fromOrNull,
+ String... recipients)
+ {
+ this(subject, content, replyToOrNull, new From(fromOrNull), recipients);
+ }
+
public String getSubject()
{
return subject;
@@ -63,7 +69,7 @@ public class Email
return replyToOrNull;
}
- public String getFromOrNull()
+ public From getFromOrNull()
{
return fromOrNull;
}
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EmailWithSummary.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EmailWithSummary.java
new file mode 100644
index 0000000000000000000000000000000000000000..ae91239a0c783ab6967cf46800115855f25cfade
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EmailWithSummary.java
@@ -0,0 +1,46 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.ethz.bsse.cisd.dsu.tracking.email;
+
+/**
+ * Encapsulation of {@link Email} with a short summary of its content.
+ *
+ * @author Piotr Buczek
+ */
+public class EmailWithSummary
+{
+ private final Email email;
+
+ private final String summary;
+
+ public EmailWithSummary(Email email, String summary)
+ {
+ this.email = email;
+ this.summary = summary;
+ }
+
+ public Email getEmail()
+ {
+ return email;
+ }
+
+ public String getSummary()
+ {
+ return summary;
+ }
+
+}
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 b95d70da38471faab5d3040581096264d9418906..83c15ecb91602ff4294e15e9422c15c83f6b62aa 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
@@ -71,7 +71,7 @@ public class EntityTrackingEmailData
}
// data grouped by sequencing sample: <sequencing sample id, data>
- private final Map<Long, SequencingSampleData> sequencingSampleData =
+ private final Map<Long, SequencingSampleData> sequencingSampleDataById =
new HashMap<Long, SequencingSampleData>(0);
private final List<ExternalData> dataSets = new ArrayList<ExternalData>(0);
@@ -91,7 +91,7 @@ public class EntityTrackingEmailData
public Collection<SequencingSampleData> getSequencingSamplesData()
{
- return sequencingSampleData.values();
+ return sequencingSampleDataById.values();
}
public List<ExternalData> getDataSets()
@@ -112,7 +112,7 @@ public class EntityTrackingEmailData
final Sample sequencingSample = flowLaneSample.getGeneratedFrom();
assert sequencingSample != null;
- SequencingSampleData infoOrNull = sequencingSampleData.get(sequencingSample.getId());
+ SequencingSampleData infoOrNull = sequencingSampleDataById.get(sequencingSample.getId());
if (infoOrNull == null)
{
// because sequencing samples are processed before flow lane samples
@@ -127,7 +127,7 @@ public class EntityTrackingEmailData
boolean newlyTracked)
{
final SequencingSampleData data = new SequencingSampleData(sequencingSample, newlyTracked);
- sequencingSampleData.put(sequencingSample.getId(), data);
+ sequencingSampleDataById.put(sequencingSample.getId(), data);
return data;
}
@@ -137,4 +137,58 @@ public class EntityTrackingEmailData
dataSets.add(dataSet);
}
+ /** short description of data kept in the structure */
+ public String getDescription()
+ {
+ final StringBuilder sb = new StringBuilder();
+
+ // append info about tracked samples
+ if (getSequencingSamplesData().isEmpty())
+ {
+ sb.append("no new samples tracked");
+ } else
+ {
+ for (SequencingSampleData seqencingSampleData : getSequencingSamplesData())
+ {
+ final int flowLaneSamplesSize = seqencingSampleData.getFlowLaneSamples().size();
+ final String sequencingSampleIdentifier =
+ seqencingSampleData.getSequencingSample().getIdentifier();
+ final boolean newlyTracked = seqencingSampleData.isNewlyTracked();
+ sb.append(String.format(
+ "%sSequencing sample: '%s' with %d new Flow Lane samples tracked",
+ newlyTracked ? "new " : "", sequencingSampleIdentifier,
+ flowLaneSamplesSize, flowLaneSamplesSize > 0 ? ": " : ""));
+ for (Sample flowLaneSample : seqencingSampleData.getFlowLaneSamples())
+ {
+ sb.append(flowLaneSample.getIdentifier() + ", ");
+ }
+ }
+ }
+ sb.append("\n");
+ // append info about tracked data sets
+ if (getDataSets().isEmpty())
+ {
+ sb.append("no new data sets tracked");
+ } else
+ {
+ sb.append(getDataSets().size() + " new data set(s) tracked: ");
+ for (ExternalData dataSet : getDataSets())
+ {
+ sb.append(dataSet.getIdentifier() + ", ");
+ }
+ }
+ sb.append("\n");
+ return sb.toString();
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public String toString()
+ {
+ return getDescription();
+ }
+
}
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 91066093d21e262a657220c6ac5103cc4fe6424d..2a0b97a631fd48e002f0d7a239911f9c29ae0679 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
@@ -86,20 +86,25 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
return result;
}
- public List<Email> generateEmails(TrackedEntities trackedEntities)
+ public List<EmailWithSummary> generateEmails(TrackedEntities trackedEntities)
{
final Collection<EntityTrackingEmailData> emailDataGroupedByRecipient =
EntityTrackingEmailDataManager.groupByRecipient(trackedEntities);
- final List<Email> results = new ArrayList<Email>();
+ final List<EmailWithSummary> results = new ArrayList<EmailWithSummary>();
for (EntityTrackingEmailData emailData : emailDataGroupedByRecipient)
{
- results.add(createEmail(emailData));
+ results.add(createEmailWithSummary(emailData));
}
return results;
}
+ private EmailWithSummary createEmailWithSummary(EntityTrackingEmailData emailData)
+ {
+ return new EmailWithSummary(createEmail(emailData), emailData.getDescription());
+ }
+
private Email createEmail(EntityTrackingEmailData emailData)
{
String content = EmailContentGenerator.fillTemplateWithData(template, emailData);
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/IEntityTrackingEmailGenerator.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/IEntityTrackingEmailGenerator.java
index 812d6168575874908b51ae8b92d8e15be2fd038e..19c650ff288ce64a6cc694a36c5526871d0d9f36 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/IEntityTrackingEmailGenerator.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/IEntityTrackingEmailGenerator.java
@@ -26,10 +26,10 @@ import ch.ethz.bsse.cisd.dsu.tracking.dto.TrackedEntities;
public interface IEntityTrackingEmailGenerator
{
/**
- * Generates all {@link Email}s to be send containing information about
+ * Generates all {@link EmailWithSummary}s to be send containing information about
* <var>trackedEntities</var>.
*
* @param trackedEntities recently tracked entities
*/
- List<Email> generateEmails(TrackedEntities trackedEntities);
+ List<EmailWithSummary> generateEmails(TrackedEntities trackedEntities);
}
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 4a25c9fc885390dfe66b5799b0e682b2c5f698b0..56469105863c73333f0863b8b29257b9a8878dd7 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
@@ -21,6 +21,7 @@ import java.util.List;
import ch.ethz.bsse.cisd.dsu.tracking.dto.TrackedEntities;
import ch.ethz.bsse.cisd.dsu.tracking.dto.TrackingStateDTO;
import ch.ethz.bsse.cisd.dsu.tracking.email.Email;
+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.collections.CollectionUtils;
@@ -63,75 +64,87 @@ public class TrackingBO
TrackedEntities changedEntities =
fetchChangedEntities(prevTrackingState, trackingServer, session);
- List<Email> emails = emailGenerator.generateEmails(changedEntities);
- sendEmails(emails, mailClient);
+ List<EmailWithSummary> emailsWithSummary = emailGenerator.generateEmails(changedEntities);
+ sendEmails(emailsWithSummary, mailClient);
saveTrackingState(changedEntities, trackingDAO);
}
- private static void sendEmails(List<Email> emails, IMailClient mailClient)
+ private static void sendEmails(List<EmailWithSummary> emailsWithSummary, IMailClient mailClient)
{
- for (Email email : emails)
+ for (EmailWithSummary emailWithSummary : emailsWithSummary)
{
try
{
- From from = tryGetFromField(email);
- String[] recipients = email.getRecipients();
- String content = email.getContent();
- String subject = email.getSubject();
- String replyToOrNull = email.getReplyToOrNull();
- sendMessage(mailClient, subject, content, replyToOrNull, from, recipients);
+ sendMessage(mailClient, emailWithSummary);
} catch (Exception ex)
{
- sendErrorReport(mailClient, ex, email);
+ sendErrorReport(mailClient, ex, emailWithSummary);
}
}
}
- private static From tryGetFromField(Email email)
- {
- return (email.getFromOrNull() == null) ? null : new From(email.getFromOrNull());
- }
-
// This email could not be sent, most probably the recipient addresses were
// incorrect.
// We send the email to the administrator "replyTo' address, the admin should
// forward it to the right recipient.
- private static void sendErrorReport(IMailClient mailClient, Exception exception, Email email)
+ private static void sendErrorReport(IMailClient mailClient, Exception exception,
+ EmailWithSummary emailWithSummary)
{
- StringBuffer errorReportContent = new StringBuffer();
- appendLine(errorReportContent, "Dear openBIS Admin,");
- appendLine(errorReportContent,
+ Email email = emailWithSummary.getEmail();
+
+ StringBuilder errorReportContentBuilder = new StringBuilder();
+ appendLine(errorReportContentBuilder, "Dear openBIS Admin,");
+ appendLine(errorReportContentBuilder,
"This email has been generated automatically from the openBIS Changes Tracking system.");
- appendLine(errorReportContent, "There was a failure while trying to send the email:");
- appendLine(errorReportContent, exception.getMessage());
- appendLine(errorReportContent,
+ appendLine(errorReportContentBuilder, "There was a failure while trying to send the email:");
+ appendLine(errorReportContentBuilder, exception.getMessage());
+ appendLine(errorReportContentBuilder,
"The possible reason is that the recipient address is not valid.");
- appendLine(errorReportContent,
+ appendLine(errorReportContentBuilder,
"If you know the address of the recipient please correct it and forward this email to him.");
- appendLine(errorReportContent,
+ appendLine(errorReportContentBuilder,
"!!! Note that the Tracking System will not try to send this email again !!!");
- appendLine(errorReportContent,
+ appendLine(errorReportContentBuilder,
"Please correct the recipient email address in openBIS to avoid similar problems in future.");
- appendLine(errorReportContent, "");
- appendLine(errorReportContent, "Subject: " + email.getSubject());
- appendLine(errorReportContent, "Recipients: "
+ appendLine(errorReportContentBuilder, "");
+ appendLine(errorReportContentBuilder, "Subject: " + email.getSubject());
+ appendLine(errorReportContentBuilder, "Recipients: "
+ CollectionUtils.abbreviate(email.getRecipients(), -1));
- appendLine(errorReportContent, "");
- appendLine(errorReportContent, "Original content:");
+ appendLine(errorReportContentBuilder, "");
- sendMessage(mailClient, "[Tracking] Sending an email failed",
- errorReportContent.toString(), null, tryGetFromField(email), email
- .getReplyToOrNull());
+ StringBuilder errorReportSummaryBuilder =
+ new StringBuilder(errorReportContentBuilder.toString());
+
+ appendLine(errorReportContentBuilder, "Original content: ");
+ appendLine(errorReportContentBuilder, email.getContent());
+ String errorReportContent = errorReportContentBuilder.toString();
+
+ appendLine(errorReportSummaryBuilder, "Original content summary: ");
+ appendLine(errorReportSummaryBuilder, emailWithSummary.getSummary());
+ String errorReportSummary = errorReportSummaryBuilder.toString();
+
+ Email errorReportEmail =
+ new Email("[Tracking] Sending an email failed", errorReportContent, null, email
+ .getFromOrNull(), email.getReplyToOrNull());
+ sendMessage(mailClient, new EmailWithSummary(errorReportEmail, errorReportSummary));
}
- private static void sendMessage(IMailClient mailClient, String subject, String content,
- String replyToOrNull, From fromOrNull, String... recipients)
+ private static void sendMessage(IMailClient mailClient, EmailWithSummary emailWithSummary)
{
+ Email email = emailWithSummary.getEmail();
+ String summary = emailWithSummary.getSummary();
+
+ String subject = email.getSubject();
+ String content = email.getContent();
+ String replyToOrNull = email.getReplyToOrNull();
+ From fromOrNull = email.getFromOrNull();
+ String[] recipients = email.getRecipients();
mailClient.sendMessage(subject, content, replyToOrNull, fromOrNull, recipients);
- LogUtils.debug("Sending an email [" + subject + "]\n" + content);
+
+ LogUtils.debug("Sending an email [" + subject + "]\n" + summary);
}
- private static void appendLine(StringBuffer sb, String msg)
+ private static void appendLine(StringBuilder sb, String msg)
{
sb.append(msg);
sb.append("\n");