Error running rxnorm_graph.py

[gpinkham]

Tried to run the rxnorm_graph command but it errors out immediately. Admittedly I'm not a python guy so quite possible it's my environment. But I have requests and graphviz modules installed..

python rxnorm_graph.py 316074
Traceback (most recent call last):
  File "rxnorm_graph.py", line 22, in <module>
    rx = RxNormCUI(rxcui)
  File "/Users/gpinkham/dev/py-umls/rxnorm.py", line 405, in __init__
    super().__init__(rxcui, rxcui)
TypeError: super() takes at least 1 argument (0 given)

I also tried with the CUI you used in the readme. same error..

[p2]

Yes, that's an error occurring in Python 2, you'll have to use Python 3.x.

[gpinkham]

ok I will try that.. I changed the code to: GraphableObject.__init__(self, rxcui, rxcui) which worked for the moment but failed trying to read the rxnconso table (not found).. I will update to python 3 and reset the code and try again.. (and I ran rxnorm.sh to import the rrf's).. thanks!!!

[gpinkham]

thanks.. updating to Python3 fixed that issue. . I still get "no such table: rxnconso" despite running the importer. I even deleted the previous import and reran it.. I have a 1.9gb rxnorm.db file so seems like it has data.. the importer reported "indexing RXNCONSO table".. so seems like it should be there..

[gpinkham]

Figured it out.. running this command: databases/rxnorm.sh ~/Downloads/RxNorm_full_04042016 from the root of the project created the rxnorm.db file in the root of the project but the rxnorm.py code looks for it in the databases directory. I guess the command should be run as ./rxnorm.sh ~/Downloads/RxNorm_full_04042016 inside the databases directory.. still having issues with tables not found (this time va_cache) but I'll close this out and put this aside till later (need to do my day job now).. many thanks! cool tool..