Citations - duplicate fields

[AlexanderPico]

In a pathway edited in April 2022, each of the publicationXrefs contained duplicated fields (ID, DB, TITLE, SOURCE and YEAR) two more more times with a single element. Only the AUTHOR fields are unique. For example:

11278778 PubMed The yeast ALG11 gene specifies addition of the terminal alpha 1,2-Man to the Man5GlcNAc2-PP-dolichol N-glycosylation intermediate formed on the cytosolic side of the endoplasmic reticulum. J Biol Chem 2001 11278778 PubMed The yeast ALG11 gene specifies addition of the terminal alpha 1,2-Man to the Man5GlcNAc2-PP-dolichol N-glycosylation intermediate formed on the cytosolic side of the endoplasmic reticulum. J Biol Chem 2001 11278778 PubMed The yeast ALG11 gene specifies addition of the terminal alpha 1,2-Man to the Man5GlcNAc2-PP-dolichol N-glycosylation intermediate formed on the cytosolic side of the endoplasmic reticulum. J Biol Chem 2001 Cipollo JF Trimble RB Chi JH Yan Q Dean N

This doesn't appear to break our current processing pipeline for md and tsv files, but it's probably something we should fix.

[larsgw]

Based on the git history this might have been the case for 10 years but when these properties are set they're technically just added, and the maxCardinality makes sure the old element is removed. Except, they're only removed from the internal representation of the data (line 65), not the org.jdom2.Element (line 70):

https://github.com/PathVisio/pathvisio/blob/33d315b4e0fab46768398773f28b87ad4a829187/modules/org.pathvisio.core/src/org/pathvisio/core/biopax/BiopaxNode.java#L61-L70

Fix should be as easy as calling removeProperty() instead of properties.remove() as it updates wrapped. I'm including a patch in an upcoming PR.

[larsgw]

(but to fix existing GPML, it also needs to delete all occurrences, not just the first.)