diff --git a/checkstyle.xml b/checkstyle.xml
index 8506a80..408879b 100644
--- a/checkstyle.xml
+++ b/checkstyle.xml
@@ -3,7 +3,7 @@
"https://checkstyle.org/dtds/configuration_1_3.dtd">
-
+
diff --git a/pom.xml b/pom.xml
index 2653971..d8f691b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
org.reactome.release
go-update
- 1.1.1
+ 1.1.2
jar
go-update
@@ -20,9 +20,18 @@
Solomon Shorser
- solomon.shorser@oicr.on.ca
- Reactome
- https://reactome.org
+
+ alumni
+
+ Ontario Institute for Cancer Research
+ https://oicr.on.ca
+
+
+
+ Joel Weiser
+ jweiser@oicr.on.ca
+ Ontario Institute for Cancer Research
+ https://oicr.on.ca
@@ -50,7 +59,7 @@
org.reactome.release
release-common-lib
- 2.0.0-SNAPSHOT
+ 2.0.0
diff --git a/src/main/java/org/reactome/release/goupdate/GoTermsUpdater.java b/src/main/java/org/reactome/release/goupdate/GoTermsUpdater.java
index d45110a..7c7fbbe 100644
--- a/src/main/java/org/reactome/release/goupdate/GoTermsUpdater.java
+++ b/src/main/java/org/reactome/release/goupdate/GoTermsUpdater.java
@@ -373,49 +373,40 @@ private void processObsoleteGOTerm(Map> goTermsFromF
{
StringBuilder attemptToDeleteObsoleteMessage = new StringBuilder();
Map referrersCount = new HashMap<>();
- // Only add instance(s) to deletion list if they have a valid replacement.
- if (goTermsFromFile.get(goID).get(GoUpdateConstants.REPLACED_BY) != null)
- {
- instancesForDeletion.addAll(goInstances);
- attemptToDeleteObsoleteMessage.append(" Replacement Accession: ").append(goTermsFromFile.get(goID).get(GoUpdateConstants.REPLACED_BY));
- }
- else
- {
- // ...or, if an obsolete term has no replacement AND also has no referrers, it can be
- // safely be deleted because nothing will be affected.
- //
- // (Check that the instance has not already been added to instancesForDeletion by some other path)
- goInstances.stream().filter(inst -> !instancesForDeletion.contains(inst)).forEach( inst -> {
- try
+ // If an obsolete term has no replacement AND also has no referrers, it can be
+ // safely be deleted because nothing will be affected.
+ //
+ // (Check that the instance has not already been added to instancesForDeletion by some other path)
+ goInstances.stream().filter(inst -> !instancesForDeletion.contains(inst)).forEach( inst -> {
+ try
+ {
+ referrersCount.putAll( GoTermsUpdater.getReferrerCountsExcludingGOEntities(inst) );
+ if (referrersCount.isEmpty())
{
- referrersCount.putAll( GoTermsUpdater.getReferrerCountsExcludingGOEntities(inst) );
- if (referrersCount.isEmpty())
- {
- instancesForDeletion.add(inst);
- }
- else // if referrers DO exists, log that, with suggestions about REPLACE_BY/CONSIDER terms.
- {
- @SuppressWarnings("unchecked")
- List replaceByList = (List) goTermsFromFile.get(goID).get(GoUpdateConstants.REPLACED_BY);
- @SuppressWarnings("unchecked")
- List considerList = (List) goTermsFromFile.get(goID).get(GoUpdateConstants.CONSIDER);
- String replaceBy = "";
- String consider = "";
- replaceBy = replaceByList != null && !replaceByList.isEmpty() ? "Replace by: " + String.join(", ", replaceByList) : "";
- consider = considerList != null && !considerList.isEmpty() ? "Consider: " + String.join(", ", considerList) : "";
- String replacementTermString = replaceBy + consider;
- replacementTermString = replacementTermString.length() == 0 ? "N/A" : replacementTermString;
- obsoleteAccessionPrinter.printRecord(inst.getDBID(), inst.getSchemClass().getName(), inst.getAttributeValue(ReactomeJavaConstants.accession), "Manual cleanup (referrers exist)", replacementTermString);
- }
+ instancesForDeletion.add(inst);
}
- catch (Exception e)
+ else // if referrers DO exist, log that, with suggestions about REPLACE_BY/CONSIDER terms.
{
- e.printStackTrace();
- obsoleteAccessionLogger.error(e);
- attemptToDeleteObsoleteMessage.append(" An exception occcured while trying to get the number of referrers - this instance will not be deleted. Manual clean up may be necessary.");
+ @SuppressWarnings("unchecked")
+ List replaceByList = (List) goTermsFromFile.get(goID).get(GoUpdateConstants.REPLACED_BY);
+ @SuppressWarnings("unchecked")
+ List considerList = (List) goTermsFromFile.get(goID).get(GoUpdateConstants.CONSIDER);
+ String replaceBy = "";
+ String consider = "";
+ replaceBy = replaceByList != null && !replaceByList.isEmpty() ? "Replace by: " + String.join(", ", replaceByList) : "";
+ consider = considerList != null && !considerList.isEmpty() ? "Consider: " + String.join(", ", considerList) : "";
+ String replacementTermString = replaceBy + consider;
+ replacementTermString = replacementTermString.length() == 0 ? "N/A" : replacementTermString;
+ obsoleteAccessionPrinter.printRecord(inst.getDBID(), inst.getSchemClass().getName(), inst.getAttributeValue(ReactomeJavaConstants.accession), "Manual cleanup (referrers exist)", replacementTermString);
}
- });
- }
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ obsoleteAccessionLogger.error(e);
+ attemptToDeleteObsoleteMessage.append(" An exception occcured while trying to get the number of referrers - this instance will not be deleted. Manual clean up may be necessary.");
+ }
+ });
logger.warn("GO:{} ({}) marked as OBSOLETE!{}",goID, goInstances.toString(), attemptToDeleteObsoleteMessage);
}