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REST API cannot retrieve large clades #1

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ethanbass opened this issue Jun 19, 2020 · 1 comment
Closed

REST API cannot retrieve large clades #1

ethanbass opened this issue Jun 19, 2020 · 1 comment

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@ethanbass
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ethanbass commented Jun 19, 2020

Working up the tree from Homininae:

import omadb

# these requests work fine
dendropy_tree = c.taxonomy.dendropy_tree(root='Homininae')
dendropy_tree = c.taxonomy.dendropy_tree(root='Homininae')
dendropy_tree = c.taxonomy.dendropy_tree(root='Hominidae')
dendropy_tree = c.taxonomy.dendropy_tree(root='Hominoidea')
dendropy_tree = c.taxonomy.dendropy_tree(root='Catarrhini')
dendropy_tree = c.taxonomy.dendropy_tree(root='Simiiformes')
dendropy_tree = c.taxonomy.dendropy_tree(root='Primates')
dendropy_tree = c.taxonomy.dendropy_tree(root='Euarchontoglires')

#below this line the API returns a 500 server error:
dendropy_tree = c.taxonomy.dendropy_tree(root='Boreoeutheria')
dendropy_tree = c.taxonomy.dendropy_tree(root='Eutheria')
dendropy_tree = c.taxonomy.dendropy_tree(root='Theria')
dendropy_tree = c.taxonomy.dendropy_tree(root='Amniota')

error:

Traceback (most recent call last):

  File "<ipython-input-60-6c7b6d8ed68f>", line 1, in <module>
    dendropy_tree = c.taxonomy.dendropy_tree(root='Boreoeutheria')

  File "/usr/local/lib/python3.7/site-packages/omadb/OMARestAPI.py", line 1238, in dendropy_tree
    struct = self.read(root)

  File "/usr/local/lib/python3.7/site-packages/omadb/OMARestAPI.py", line 1186, in read
    (format is not 'dictionary')))

  File "/usr/local/lib/python3.7/site-packages/omadb/OMARestAPI.py", line 456, in _request
    raise ClientException(response_status)

ClientException: 500 Server Error: Internal Server Error 

Also, the same problem arises when interacting with the API through the website at this link(https://omabrowser.org/api/docs). E.g. https://omabrowser.org/api/taxonomy/Homininae/ works, but https://omabrowser.org/api/taxonomy/Amniota/ returns the 500 server error.

@alpae
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alpae commented Feb 3, 2021

This has been fixed in the latest omabrowser release. thanks for reporting

@alpae alpae closed this as completed Feb 3, 2021
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