tools-iuc: StringIO error in ncbi_eutil_esearch
I’m not a python expert, and I haven’t tried messing with the code (yet), but I think this line:
may be causing this error:
Traceback (most recent call last):
File "/data/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esearch/b88af93de1b7/ncbi_eutils_esearch/esearch.py", line 47, in <module>
history = c.extract_history(results)
File "/data/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esearch/b88af93de1b7/ncbi_eutils_esearch/eutils.py", line 91, in extract_history
parsed_data = Entrez.read(StringIO.StringIO(xml_data))
AttributeError: type object '_io.StringIO' has no attribute 'StringIO'
because StringIO is already imported on this line:
…at least, according the second answer here:
This happens when switching Store results to history server to Yes and searching the Gene database with the query:
genetype rrna[Properties] AND Homo sapiens[Organism] AND (srcdb refseq[Properties] AND alive[prop])
Let me know if I did something wrong that’s causing this error.
About this issue
- Original URL
- State: closed
- Created 4 years ago
- Comments: 29 (29 by maintainers)
Thanks for the clarification.
You’re right, the webenv and key strings are transient, which has implications for partially re-running a workflow. It should be OK if you re-run an entire workflow as that would get a fresh webenv/key.