Got Error below when running `validateGENIE.py`
```
python sage_processing/validateGENIE.py -h
Traceback (most recent call last):
File "sage_processing/validateGENIE.py", line 15, in
import processing_functions as process
File "/Users/zhuy/Documents/chopwork/git/genie-chop/bin/Genie/sage_processing/processing_functions.py", line 22, in
syn = synapseclient.login(silent=True)
File "/usr/local/lib/python2.7/site-packages/synapseclient/client.py", line 155, in login
syn.login(*args, **kwargs)
File "/usr/local/lib/python2.7/site-packages/synapseclient/client.py", line 379, in login
raise SynapseNoCredentialsError("No credentials provided.")
synapseclient.exceptions.SynapseNoCredentialsError: No credentials provided.
```
Checked `synapseclient/client.py`, maybe caused by missing `~/.synapseConfig `? [synapseclient/client.py#L103](https://github.com/Sage-Bionetworks/synapsePythonClient/blob/dd44daedc8b8b8458f9c0476b37e6fffe32d897f/synapseclient/client.py#L103), file not exist, not sure how to deal with that.
Created by Yuankun Zhu zhuy Dear all,
Apologies for the delay in response. I have fixed the issue. Please pull down the most recent version of the validator from here:
https://github.com/Sage-Bionetworks/Genie/blob/master/sage_processing/validateGENIE.py
Best,
Tom Think I figured out. Probably should remind people not to skip the synapse login step.
So after [login](http://docs.synapse.org/articles/getting_started.html#logging-into-synapse), it seems working now.
```bash
$ synapse login -u $SYNAPSE_USERNAME -p $SYNAPSE_PASSWORD --rememberMe
Welcome, zhuy!
Logged in as: zhuy (3324011)
$ python sage_processing/validateGENIE.py -h
[####################]100.00% 1/1 Done...
Downloading [####################]100.00% 780.0bytes/780.0bytes (203.6kB/s) Job-45599271862978411271755186.csv Done...
usage: validateGENIE.py [-h] [--thread THREAD] [--offline]
[--uploadToSynapse UPLOADTOSYNAPSE]
{maf,clinical,fusions,cnv,vcf,seg,bed,cbs} file
[file ...]
{JHU,DFCI,GRCC,NKI,MSK,UHN,VICC,MDA,WAKE,YALE,UCSF,VHIO,UCHI,TJU,SWED,NWCC,Northwell,MSCC,IUCC,CORN,CRUK,COLU,CHOP,BCGSC,BordeauxUniCancer,StJude,JEFF,UBCC,VHIO}
Validate GENIE files
positional arguments:
{maf,clinical,fusions,cnv,vcf,seg,bed,cbs}
Filetypes that you are validating.
file File(s) that you are validating. If you validation
your clinical files and you have both sample and
patient files, you must provide both
{JHU,DFCI,GRCC,NKI,MSK,UHN,VICC,MDA,WAKE,YALE,UCSF,VHIO,UCHI,TJU,SWED,NWCC,Northwell,MSCC,IUCC,CORN,CRUK,COLU,CHOP,BCGSC,BordeauxUniCancer,StJude,JEFF,UBCC,VHIO}
Contributing Center
optional arguments:
-h, --help show this help message and exit
--thread THREAD Number of threads used in validation symbols
--offline No validation of filenames
--uploadToSynapse UPLOADTOSYNAPSE
Will upload the file to the synapse directory of users
choice
``` I have this same error when run under python 3. I did try python 2, but the script needs request module which is python 3 only.
My question is why credentials are needed for -h ?
Drop files to upload
`SynapseNoCredentialsError` when run validator script `validateGENIE.py` page is loading…