- added Data Set Type to Email

- fixed typo in LogUtils
- changed etc/service.properties property from 'notification-email-from' to 'mail.from'

SVN: 23973

deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/email/EntityTrackingEmailGenerator.java

@@ -37,14 +37,14 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
  */
 public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerator
 {
-    private static final String NOTIFICATION_EMAIL_FROM = "notification-email-from";
+    private static final String NOTIFICATION_EMAIL_FROM = "mail.from";
 
     private static final String NOTIFICATION_EMAIL_REPLY_TO = "notification-email-reply-to";
 
     private static final String NOTIFICATION_EMAIL_SUBJECT = "notification-email-subject";
 
     private static final String AFFILIATION_NOTIFICATION_EMAIL_CONTACT_SUFFIX =
-        "-affiliation-notification-email-contact";
+            "-affiliation-notification-email-contact";
 
     private final String from;
 
@@ -62,7 +62,7 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
         this.template = template;
 
         final Map<String, String> recipientsByAffiliation =
-            retrieveRecipientsByAffiliation(properties);
+                retrieveRecipientsByAffiliation(properties);
         EntityTrackingEmailDataManager.initialize(recipientsByAffiliation);
     }
 
@@ -77,10 +77,10 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
             if (propertyKey.endsWith(AFFILIATION_NOTIFICATION_EMAIL_CONTACT_SUFFIX))
             {
                 final String affiliation =
-                    propertyKey.substring(0, propertyKey.length()
-                            - AFFILIATION_NOTIFICATION_EMAIL_CONTACT_SUFFIX.length());
+                        propertyKey.substring(0, propertyKey.length()
+                                - AFFILIATION_NOTIFICATION_EMAIL_CONTACT_SUFFIX.length());
                 final String affiliationRecipient =
-                    PropertyUtils.getMandatoryProperty(properties, propertyKey);
+                        PropertyUtils.getMandatoryProperty(properties, propertyKey);
                 result.put(affiliation, affiliationRecipient);
             }
         }
@@ -90,7 +90,7 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
     public List<EmailWithSummary> generateEmails(TrackedEntities trackedEntities)
     {
         final Collection<EntityTrackingEmailData> emailDataGroupedByRecipient =
-            EntityTrackingEmailDataManager.groupByRecipient(trackedEntities);
+                EntityTrackingEmailDataManager.groupByRecipient(trackedEntities);
 
         final List<EmailWithSummary> results = new ArrayList<EmailWithSummary>();
         for (EntityTrackingEmailData emailData : emailDataGroupedByRecipient)
@@ -129,10 +129,10 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
         private static final char SUBSECTION_SEPARATOR_CHAR = '-';
 
         private static final String SECTION_SEPARATOR_LINE =
-            createSeparatorLine(SECTION_SEPARATOR_CHAR);
+                createSeparatorLine(SECTION_SEPARATOR_CHAR);
 
         private static final String SUBSECTION_SEPARATOR_LINE =
-            createSeparatorLine(SUBSECTION_SEPARATOR_CHAR);
+                createSeparatorLine(SUBSECTION_SEPARATOR_CHAR);
 
         private final static String EXTERNAL_SAMPLE_NAME_PROPERTY_CODE = "EXTERNAL_SAMPLE_NAME";
 
@@ -167,8 +167,8 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
                 // append Sequencing sample details
                 if (processed)
                 {
-                    appendSampleDetails(sb, String
-                            .format("Library processing of sample '%s' was successful.",
+                    appendSampleDetails(sb,
+                            String.format("Library processing of sample '%s' was successful.",
                                     externalSampleName), sequencingSample);
                     appendln(sb, SUBSECTION_SEPARATOR_LINE);
                 } else
@@ -220,8 +220,8 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
             sequencingSamples = flowLaneSample.getParents();
             assert sequencingSamples != null;
 
-            for (Sample sequencingSample : sequencingSamples) {
-
+            for (Sample sequencingSample : sequencingSamples)
+            {
 
                 String externalSampleName = getExternalSampleName(sequencingSample);
 
@@ -229,23 +229,24 @@ public class EntityTrackingEmailGenerator implements IEntityTrackingEmailGenerat
                 appendAttribute(sb, String.format(
                         "You can download results for external sample named '%s' at",
                         externalSampleName), dataSet.getPermlink());
+                // add which Data set type has been added
+                appendAttribute(sb, "Data Set Type:", dataSet.getDataSetType().toString());
 
                 // data set properties
                 appendProperties(sb, dataSet.getProperties());
 
                 // sequencing sample info
                 appendAttribute(sb, String.format(
-                        "Meta data of Sequencing sample '%s' are available here", externalSampleName),
-                        sequencingSample.getPermlink());
+                        "Meta data of Sequencing sample '%s' are available here",
+                        externalSampleName), sequencingSample.getPermlink());
             }
 
-
         }
 
         private static String getExternalSampleName(Sample sequencingSample)
         {
             String externalSampleName =
-                tryGetSamplePropertyValue(sequencingSample, EXTERNAL_SAMPLE_NAME_PROPERTY_CODE);
+                    tryGetSamplePropertyValue(sequencingSample, EXTERNAL_SAMPLE_NAME_PROPERTY_CODE);
             assert externalSampleName != null;
             return externalSampleName;
         }

deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/main/Parameters.java

@@ -39,7 +39,7 @@ public class Parameters
 
     private static final String TRACKING_ADMIN_EMAIL = "tracking-admin-email";
 
-    private static final String NOTIFICATION_EMAIL_FROM = "notification-email-from";
+    private static final String NOTIFICATION_EMAIL_FROM = "mail.from";
 
     private final String openbisUser;
 

deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/tracking/utils/LogUtils.java

@@ -27,18 +27,18 @@ import ch.systemsx.cisd.common.logging.LogFactory;
  */
 public class LogUtils
 {
-    private static final Logger notificationLog =
-            LogFactory.getLogger(LogCategory.NOTIFY, LogUtils.class);
+    private static final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY,
+            LogUtils.class);
 
-    private static final Logger operationLog =
-            LogFactory.getLogger(LogCategory.OPERATION, LogUtils.class);
+    private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+            LogUtils.class);
 
     public static void notify(EnvironmentFailureException ex)
     {
         String causeMsg =
                 (ex.getCause() == null) ? "" : "Error cause: " + ex.getCause().getMessage();
         String fullMsg =
-                "An environment exception occured why trying to send emails with changes.\n"
+                "An environment exception occured while trying to send emails with changes.\n"
                         + "Check and correct the configuration.\n" + "Error details: "
                         + ex.getMessage() + "\n" + causeMsg;
         notify(ex, fullMsg);

deep_sequencing_unit/tracking/dist/etc/service.properties

@@ -6,21 +6,21 @@ permlink-url = https://<openbis-server-url>:8443/openbis
 # SMTP properties.
 # To test the system and save emails as files instead of sending them, 
 # set the smtp host to file://path-to-directory
-mail.smtp.host = 
+mail.smtp.host = smtp0.ethz.ch
 mail.smtp.user = 
 mail.smtp.password = 
 
 # all emails will be sent from this address
-notification-email-from = openbis-noreply@bsse.ethz.ch
+mail.from = openbis-noreply@bsse.ethz.ch
 # all emails will have this address in the reply-to field
-notification-email-reply-to = <admin@address.ch>
+notification-email-reply-to = manuel.kohler@bsse.ethz.ch
 # subject of all the notification emails
-notification-email-subject = Status report of your sequencing order
+notification-email-subject = BSSE DSU: Status report of your deep sequencing order
 
 # if the tracking client fails an email will be sent out to these recipients
-tracking-admin-email =  <admin1@address.ch>,  <admin2@address.ch>
+tracking-admin-email = kohleman@ethz.ch, gpawel@ethz.ch
 
 # Recipients that will receive notifications when entity connected with sequencing sample 
 # with certain AFFILIATION value. Property key should contain affiliation vocabulary term code
 # with '-affiliation-notification-email-contact' suffix, e.g. for 'FMI' affiliation:
-FMI-affiliation-notification-email-contact = <affiliation-responsible@address.ch>
+FMI-affiliation-notification-email-contact =

deep_sequencing_unit/tracking/etc/service.properties

-openbis-user=kohleman
-openbis-password=xxx
-openbis-server-url = http://localhost:8888/openbis
+openbis-user=tracker
+openbis-password=jadfs8r3jahu12
+openbis-server-url = http://openbis-dsu.bsse.ethz.ch:8080/openbis/openbis
+permlink-url = https://openbis-dsu.bsse.ethz.ch/openbis
 
-
-mail.smtp.host = file://../targets
+mail.smtp.host = file://../targets/playground
 mail.smtp.user = 
 mail.smtp.password = 
 
-notification-email-from = openbis-noreply@bsse.ethz.ch
-notification-email-reply-to = tomasz.pylak@bsse.ethz.ch
-notification-email-subject = Status report of your sequencing order 
-
 FMI-affiliation-notification-email-contact = fmi@bsse.ethz.ch
+
+# all emails will be sent from this address
+mail.from = openbis-noreply@bsse.ethz.ch
+# all emails will have this address in the reply-to field
+notification-email-reply-to = manuel.kohler@bsse.ethz.ch
+# subject of all the notification emails
+notification-email-subject = BSSE DSU (LOCAL TEST): Status report of your deep sequencing order
+
+# if the tracking client fails an email will be sent out to these recipients
+tracking-admin-email = kohleman@ethz.ch, gpawel@ethz.ch
\ No newline at end of file