diff --git a/src/main/java/org/reactome/release/updateDOIs/Verifier.java b/src/main/java/org/reactome/release/updateDOIs/Verifier.java index c5c6637..f52b3f5 100644 --- a/src/main/java/org/reactome/release/updateDOIs/Verifier.java +++ b/src/main/java/org/reactome/release/updateDOIs/Verifier.java @@ -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() @@ -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); } @@ -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 getExpectedDOIs() throws IOException {