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Download in Newick format dysfunctional #419

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opentreeapi opened this issue Sep 13, 2018 · 6 comments
Open

Download in Newick format dysfunctional #419

opentreeapi opened this issue Sep 13, 2018 · 6 comments

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@opentreeapi
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@opentreeapi opentreeapi commented Sep 13, 2018

Starting from a few weeks ago, I cannot download a subtree anymore in Newick format. There seems to have been also some change with the download URL recently. I need to download regularly the vertebrate subtree (https://tree.opentreeoflife.org/opentree/default/download_subtree/node-id/ott801601/Vertebrata) and luckily I have an old version of the tree, which works for my script, but it will become outdated with time :-(

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Author mjeltsch
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@mtholder
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@mtholder mtholder commented Sep 13, 2018

hmm that is odd that it changed a few weeks ago. we did change some of the back-end software on Monday. I'll try to figure out what is going on. There is a limit on the number of tips that can be downloaded from the web services. But if you have the entire vertebrate tree via a previous download, that seems like a poor explanation...

@mtholder
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@mtholder mtholder commented Sep 13, 2018

and thanks for the bug report!

@opentreeapi
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@opentreeapi opentreeapi commented Feb 26, 2019

Still gives my nothing when I try to download the vertebrate subtree in newick format :-( Maybe you have changed the limits? I manage with smaller subtrees, but e.g. also the amniota phylum fails. The downlaoded filecontains only the string "NEWICK_NOT_FOUND"

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@jimallman
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@jimallman jimallman commented Feb 26, 2019

Confirmed, this tree won't load, while I'm able to fetch the primate tree as Newick successfully. Could be a problem with larger clades, or perhaps a "poison pill" (funky Unicode taxon name)?

@mjeltsch
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@mjeltsch mjeltsch commented Mar 31, 2020

It's working again, thanks. If I reference this tree in a scientific publication, how should I cite it?

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Author Michael Jeltsch
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@mtholder
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@mtholder mtholder commented Apr 8, 2020

Great. General guidelines for citation of parts of the project are at https://tree.opentreeoflife.org/about/open-tree-of-life
Studies that inform parts of the primate tree can be found in the "Supporting trees" panel for the relevant view of the tree at https://tree.opentreeoflife.org/opentree/argus/opentree12.3@ott913935/Primates if you want to cite the original publications.

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