Hello,
Trying to validate clinical file and it just throws an error. Is there something obvious I'm doing wrong?
f45c89a52ce5:Clinical ramanp$ genie validate clinical data_clinical_supp_CHOP.txt CHOP
INFO:processing_sage.clinical:VALIDATING data_clinical_supp_CHOP.txt
Traceback (most recent call last):
File "/usr/local/bin/genie", line 11, in
sys.exit(main())
File "/usr/local/lib/python2.7/site-packages/processing_sage/__main__.py", line 163, in main
perform_main(syn, args)
File "/usr/local/lib/python2.7/site-packages/processing_sage/__main__.py", line 127, in perform_main
args.func(syn, args)
File "/usr/local/lib/python2.7/site-packages/processing_sage/__main__.py", line 121, in perform_validate
message = validate(syn, args.fileType, args.file, args.center, args.thread, args.oncotreeLink, args.offline, args.uploadToSynapse, args.testing, args.noSymbolCheck)
File "/usr/local/lib/python2.7/site-packages/processing_sage/__main__.py", line 75, in validate
total_error, warning = PROCESS_FILES[fileType](syn, center, threads).validate(filePathList=filePath, oncotreeLink=oncotree_url, testing=testing, noSymbolCheck=noSymbolCheck)
File "/usr/local/lib/python2.7/site-packages/processing_sage/example_filetype_format.py", line 65, in validate
total_error, warning = self.validate_steps(filePathList, **mykwargs)
File "/usr/local/lib/python2.7/site-packages/processing_sage/clinical.py", line 430, in validate_steps
total_error, warning = self.validate_helper(clinicalDF, otherClinicalDF, oncotreeLink)
File "/usr/local/lib/python2.7/site-packages/processing_sage/clinical.py", line 242, in validate_helper
oncotree_mapping = process_functions.get_oncotree_codes(oncotreeLink)
File "/usr/local/lib/python2.7/site-packages/processing_sage/process_functions.py", line 160, in get_oncotree_codes
with requests.get(oncotree_url) as oncotreeUrl:
AttributeError: __exit__
Created by Pichai Raman ramanp1 Dear Pichai,
That is really odd. It should work on python 2.7.12. But can you try in a python environment.
```
import requests
requests.get("http://oncotree.mskcc.org/oncotree/api/tumor_types.txt?version=oncotree_2017_06_21")
Out[1]:
```
I get that output.
Best,
Tom Hi Thomas,
Thanks so much, happy it validates. Yes, I have a network connection and can visit the oncotree site. Oddly when I call the validation python script
```
python validateGENIE.py ...
```
it does validate but when I use
```
genie validate ...
```
it throws the error above. My python environment is Python 2.7.12 ... maybe that's the issue? Not backward compatible?
Cheers,
Pichai
Dear Pichai,
I validated your file locally and it is valid!. When using the validator, do you have network connection?
Are you able to visit this site:
http://oncotree.mskcc.org/oncotree/api/tumor_types.txt?version=oncotree_2017_06_21
May I also ask what version of python you are using?
Best,
Tom