From 3e763d7c3dc1d9d77abc23f03d5c5584946ebb77 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Fri, 19 Aug 2011 08:28:13 +0000
Subject: [PATCH] [LMS-2445] Allow multiple parent sequencing samples for a
flow lane sample
SVN: 22565
---
.../email/EntityTrackingEmailDataManager.java | 42 +++++++++++--------
1 file changed, 25 insertions(+), 17 deletions(-)
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 05ee3dec3dd..3254a61ccba 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
@@ -17,6 +17,7 @@
package ch.ethz.bsse.cisd.dsu.tracking.email;
import java.util.Collection;
+import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
@@ -66,7 +67,8 @@ class EntityTrackingEmailDataManager
{
for (Sample sequencingSample : trackedEntities.getSequencingSamplesToBeProcessed())
{
- for (String recipient : getSequencingSampleTrackingRecipients(sequencingSample))
+ for (String recipient : getSequencingSampleTrackingRecipients(Collections
+ .singleton(sequencingSample)))
{
final EntityTrackingEmailData emailData =
getOrCreateRecipientEmailData(result, recipient);
@@ -81,7 +83,8 @@ class EntityTrackingEmailDataManager
{
for (Sample sequencingSample : trackedEntities.getSequencingSamplesProcessed())
{
- for (String recipient : getSequencingSampleTrackingRecipients(sequencingSample))
+ for (String recipient : getSequencingSampleTrackingRecipients(Collections
+ .singleton(sequencingSample)))
{
final EntityTrackingEmailData emailData =
getOrCreateRecipientEmailData(result, recipient);
@@ -122,9 +125,10 @@ class EntityTrackingEmailDataManager
* <var>sequencingSample</var>.<br>
*/
// NOTE: Set is needed because one recipient can occur in many roles for one sample
- private static Set<String> getSequencingSampleTrackingRecipients(Sample sequencingSample)
+ private static Set<String> getSequencingSampleTrackingRecipients(
+ Collection<Sample> sequencingSamples)
{
- assert sequencingSample != null;
+ assert sequencingSamples != null;
final Set<String> recipients = new HashSet<String>();
@@ -133,22 +137,26 @@ class EntityTrackingEmailDataManager
recipientPropertyTypeCodes.add(CONTACT_PERSON_EMAIL);
recipientPropertyTypeCodes.add(PRINCIPAL_INVESTIGATOR_EMAIL);
- for (IEntityProperty property : sequencingSample.getProperties())
+ for (Sample sequencingSample : sequencingSamples)
{
- final String propertyCode = property.getPropertyType().getCode();
- final String propertyValue = 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))
+ {
+ recipients.add(propertyValue);
+ } else
{
- String affiliationRecipientOrNull = 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)
+ {
+ recipients.add(affiliationRecipientOrNull);
+ }
}
}
}
@@ -166,7 +174,7 @@ class EntityTrackingEmailDataManager
// Recipients are taken from properties of sequencing sample
// that is a parent of the flow lane sample.
assert flowLaneSample != null;
- return getSequencingSampleTrackingRecipients(flowLaneSample.getGeneratedFrom());
+ return getSequencingSampleTrackingRecipients(flowLaneSample.getParents());
}
/**
--
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