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OpenTreeOfLife / peyotl

python library for interacting with Open Tree of Life resources
BSD 2-Clause "Simplified" License
11 stars 7 forks source link

Error importing from TreeBASE #142

Closed kcranston closed 8 years ago

kcranston commented 8 years ago

We seem to be having problems importing from treebase. The error is traced back to this exception.

Investigating further, but any tips welcome. There is a test for importing from TreeBASE which currently passes, although the test doesn't actually import from TreeBASE - it simply compares the parsing of an already-downloaded treebase xml file to a previously-converted json.

Here is a list of currently-failing treebase IDs (ref gitter): S16424 S18711 S17122 S15345 s9943 s2231 s13995 s1472 S14726 S14112 S10579 S10276 S11453 S1771

kcranston commented 8 years ago

I added a test that downloads from Treebase (see branch) which now fails with a UnicodeEncodeError. Strangely, the treebase study being used for testing (S15515) doesn't actually exist in phylesystem so not sure if this would have ever worked. More soon.