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updates verifier to need doi if without prefix #13

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Merged
adamjohnwright merged 1 commit into from
Jun 9, 2026
Merged

updates verifier to need doi if without prefix #13

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8 changes: 4 additions & 4 deletions src/main/java/org/reactome/release/updateDOIs/Verifier.java
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,8 @@ public class Verifier {
@Parameter(names ={"--output", "--o"})
private String outputFolder = ".";

private final String REACTOME_DOI_PREFIX = "10.3180";

public static void main(String[] args) throws Exception {
Verifier verifier = new Verifier();
JCommander.newBuilder()
Expand Down Expand Up @@ -176,14 +178,12 @@ private boolean hasExpectedDOI(GKInstance pathway, String expectedDOI) throws Ex
}

private String getCorrectDOI(GKInstance pathway) {
final String reactomeDOIPrefix = "10.3180/";

try {
GKInstance pathwayStableIdInstance = (GKInstance)
pathway.getAttributeValue(ReactomeJavaConstants.stableIdentifier);
String pathwayStableId = pathwayStableIdInstance.getDisplayName();

return reactomeDOIPrefix + pathwayStableId;
return REACTOME_DOI_PREFIX + "/" + pathwayStableId;
} catch (Exception e) {
throw new RuntimeException(e);
}
Expand All @@ -196,7 +196,7 @@ private boolean needsDOI(GKInstance pathway) {
} catch (Exception e) {
throw new RuntimeException("Unable to get doi value from pathway " + pathway, e);
}
return doiValue != null && doiValue.equals("needs DOI");
return doiValue != null && !doiValue.startsWith(REACTOME_DOI_PREFIX);
}

private List<String> getExpectedDOIs() throws IOException {
Expand Down
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