The XML document has moved

[hubner-lab]

Hi,
when i'm using "Fetch" i get this error:

DEBUG The XML I got was

<title>302 Found</title>

Found

The document has moved here.

===2020-01-26 12:56:30,035 - lrt_predict.Fetch.fetch===
DEBUG The XML I got was

<title>302 Found</title>

Found

The document has moved here.

Traceback (most recent call last):
File "/mnt/data/Tools/BAD_Mutations-Python3/BAD_Mutations/BAD_Mutations.py", line 382, in
main()
File "/mnt/data/Tools/BAD_Mutations-Python3/BAD_Mutations/BAD_Mutations.py", line 348, in main
fetch(arguments_valid, loglevel)
File "/mnt/data/Tools/BAD_Mutations-Python3/BAD_Mutations/BAD_Mutations.py", line 110, in fetch
phy.get_xml_urls()
File "/mnt/data/Tools/BAD_Mutations-Python3/BAD_Mutations/lrt_predict/Fetch/phytozome.py", line 168, in get_xml_urls
xml_tree = ElementTree.fromstring(xml)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1311, in XML
parser.feed(text)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1659, in feed
self._raiseerror(v)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1523, in _raiseerror
raise err
xml.etree.ElementTree.ParseError: syntax error: line 1, column 49

i didn't manage to redirect the phytosome.py script to the correct XML, any suggestions?

[conJUSTover]

I had this error too, and couldn't figure out a fix. But if you log into phytozome, you can download all the files from phytozome12 (I would recommend clicking all the files you want, and downloading them as a zipped file). The species list is in the file lrt_predict/Fetch/phytozome_species.py. Then you can use the --convert-only flag in the fetch subcommand.

This is a potential manual way around the bug, and it only took me about half an hour to download the files and organize them correctly.

[dumitru314]

hi, i have too this problem ... you found some solutions ?