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adds deleted stable identifiers for checks if stable id is used #60

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adds deleted stable identifiers for checks if stable id is used #60

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b69def1
adds deleted stable identifiers for checks if stable id is used
Aug 23, 2023
a351624
Merge branch 'main' into feature/st-id-not-used-update
jweiser Jan 27, 2026
f37cf4d
bug fix - adds null check for collections of referrers
jweiser Jan 27, 2026
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126 changes: 66 additions & 60 deletions src/main/java/org/reactome/release/qa/check/StableIdentifierCheck.java
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Original file line number Diff line number Diff line change
@@ -1,10 +1,6 @@
package org.reactome.release.qa.check;

import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.*;

import org.gk.model.GKInstance;
import org.gk.model.ReactomeJavaConstants;
Expand All @@ -23,64 +19,74 @@
public class StableIdentifierCheck extends AbstractQACheck {

public StableIdentifierCheck() {
}
}

@Override
public QAReport executeQACheck() throws Exception {
QAReport report = new QAReport();
report.setColumnHeaders("DBID", "DisplayName", "Issue", "LastAuthor");

Collection<GKInstance> stableIds = dba.fetchInstancesByClass(ReactomeJavaConstants.StableIdentifier);
dba.loadInstanceAttributeValues(stableIds, new String[] {ReactomeJavaConstants.identifier});
Map<String, Set<GKInstance>> idToInsts = new HashMap<>();
for (GKInstance stableId : stableIds) {
if (isEscaped(stableId)) {
continue;
}
String id = (String) stableId.getAttributeValue(ReactomeJavaConstants.identifier);
if (id == null) {
report.addLine(stableId.getDBID().toString(),
stableId.getDisplayName(),
"Missing identifier",
QACheckerHelper.getLastModificationAuthor(stableId));
continue;
}
idToInsts.compute(id, (key, set) -> {
if (set == null)
set = new HashSet<>();
set.add(stableId);
return set;
});
// Check if this stableId is used
Collection<GKInstance> referrers = stableId.getReferers(ReactomeJavaConstants.stableIdentifier);
if (referrers == null || referrers.size() == 0) {
report.addLine(stableId.getDBID().toString(),
stableId.getDisplayName(),
"Not used",
QACheckerHelper.getLastModificationAuthor(stableId));
}
else if (referrers.size() > 1) {
report.addLine(stableId.getDBID().toString(),
stableId.getDisplayName(),
"Referred more than once",
QACheckerHelper.getLastModificationAuthor(stableId));
}
}

for (Collection<GKInstance> instances: idToInsts.values()) {
if (instances.size() != 1) {
for (GKInstance stableId: instances) {
if (!isEscaped(stableId)) {
report.addLine(stableId.getDBID().toString(),
stableId.getDisplayName(),
"Duplicated identifier",
QACheckerHelper.getLastModificationAuthor(stableId));
}
}
}
}

return report;
QAReport report = new QAReport();
report.setColumnHeaders("DBID", "DisplayName", "Issue", "LastAuthor");

Collection<GKInstance> stableIds = dba.fetchInstancesByClass(ReactomeJavaConstants.StableIdentifier);
dba.loadInstanceAttributeValues(stableIds, new String[] {ReactomeJavaConstants.identifier});
Map<String, Set<GKInstance>> idToInsts = new HashMap<>();
for (GKInstance stableId : stableIds) {
if (isEscaped(stableId)) {
continue;
}
String id = (String) stableId.getAttributeValue(ReactomeJavaConstants.identifier);
if (id == null) {
report.addLine(stableId.getDBID().toString(),
stableId.getDisplayName(),
"Missing identifier",
QACheckerHelper.getLastModificationAuthor(stableId));
continue;
}
idToInsts.compute(id, (key, set) -> {
if (set == null)
set = new HashSet<>();
set.add(stableId);
return set;
});
// Check if this stableId is used by an existing instance or a deleted instance
Collection<GKInstance> instanceReferrers = stableId.getReferers(ReactomeJavaConstants.stableIdentifier);
Collection<GKInstance> deletedInstanceReferrers =
stableId.getReferers("deletedStableIdentifier");
Collection<GKInstance> referrers = new ArrayList<>();
if (instanceReferrers != null) {
referrers.addAll(instanceReferrers);
}
if (deletedInstanceReferrers != null) {
referrers.addAll(deletedInstanceReferrers);
}

if (referrers.size() == 0) {
report.addLine(stableId.getDBID().toString(),
stableId.getDisplayName(),
"Not used",
QACheckerHelper.getLastModificationAuthor(stableId));
}
else if (referrers.size() > 1) {
report.addLine(stableId.getDBID().toString(),
stableId.getDisplayName(),
"Referred more than once",
QACheckerHelper.getLastModificationAuthor(stableId));
}
}

for (Collection<GKInstance> instances: idToInsts.values()) {
if (instances.size() != 1) {
for (GKInstance stableId: instances) {
if (!isEscaped(stableId)) {
report.addLine(stableId.getDBID().toString(),
stableId.getDisplayName(),
"Duplicated identifier",
QACheckerHelper.getLastModificationAuthor(stableId));
}
}
}
}

return report;
}

}
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