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Citations - bp:AUTHORS are deleted #198

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larsgw opened this issue Aug 26, 2023 · 0 comments
Open

Citations - bp:AUTHORS are deleted #198

larsgw opened this issue Aug 26, 2023 · 0 comments

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@larsgw
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larsgw commented Aug 26, 2023

I get that the TITLE, YEAR, SOURCE, and AUTHORS are on their way out, but for now, editing GPML 2013a, it seems like bp:AUTHORS elements are always deleted. Looking at the code I see this:

// now sort the generated elements in the order defined by the xsd
Collections.sort(elementList, new ByElementName());
for (Element e : elementList) {
// make sure biopax references are sorted alphabetically by rdf-id
if(e.getName().equals("Biopax")) {
for(Element e3 : e.getChildren()) {
e3.removeChildren("AUTHORS", GpmlFormat.BIOPAX);
}
e.sortChildren(new BiopaxAttributeComparator());
}
root.addContent(e);
}

Removing the inner for loop fixes the issue. Why was this introduced (83b82e4)?

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