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[Treebase-guts] [ treebase-Bugs-3037070 ] Invalid NexML output
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From: SourceForge.net <no...@so...> - 2010-07-30 12:24:01
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Bugs item #3037070, was opened at 2010-07-30 14:24 Message generated for change (Tracker Item Submitted) made by thasso You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3037070&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Thasso Griebel (thasso) Assigned to: Nobody/Anonymous (nobody) Summary: Invalid NexML output Initial Comment: Downloading a Study as NexML can result in an invalid XML file. The Study I tried was 1144 ( http://www.treebase.org/treebase-web/search/study/summary.html?id=1144 ). I tried the online validator and the Java parser and both report the file as invalid. The problem seems to be the OTUs groups and the the tree blocks referencing the OTUs. The file for 1144 contains two OTUs (otus304719 and otus304819) and two tree blocks. The first tree block ( trees306715 ) references the OTUs otus304819, but contains a node that references an OTU ( otu304721 ) from the other OTUs group (otus304719). It should istead reference to otu304821. The essential parts: <nex:nexml> <otus about="#otus304719" id="otus304719" label="TaxonLabelSet11490"> <otu about="#otu304721" id="otu304721" label="Megadyptes antipodes"></otu> </otus> <otus about="#otus304819" id="otus304819" label="TaxonLabelSet11489"> <otu about="#otu304821" id="otu304821" label="Megadyptes antipodes"></otu> </otus> <trees about="#trees306715" id="trees306715" label="Tb6842" otus="otus304819"> <tree> <node about="#node306728" id="node306728" label="Megadyptes antipodes" otu="otu304721"></node> </tree> </trees> <trees about="#trees306934" id="trees306934" label="Tb6843" otus="otus304719"> <tree> <node about="#node306947" id="node306947" label="Megadyptes antipodes" otu="otu304721"></node> </tree> </trees> </nex:nexml> ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3037070&group_id=248804 |
