chb / py-umls Goto Github PK

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..

Can you please add a license for this module?

I followed all of the instructions for downloading and unzipping the SNOMED term database and provided the path for database formation and got the following print-outs:
DEBUG:root:Importing SNOMED descriptions into snomed.db...
----- DID IMPORT descriptions
DEBUG:root:1613155 concepts parsed
DEBUG:root:Importing SNOMED relationships into snomed.db...
----- DID IMPORT relationships
DEBUG:root:4863481 concepts parsed

However, when I run the snomed.py command again from command line, I get AssertionError: "315004001" refines "128462008" should return True or the database hasn't been set up properly

Is there a way to further debug this error and find out which step of database set up caused the failure?

I downloaded the most current rxnorm_full file and tried to run "bash rxnorm.sh" against this file. After running for a few minutes, I received a number of errors and ended up with an rxnorm.db of only 48kb. The full error list is posted below:

-> Converting RRF files for SQLite
rxnorm.sh: line 32: cd: too many arguments
basename: extra operand ‘Year’
Try 'basename --help' for more information.
-> Importing
Error: near " ": syntax error
basename: extra operand ‘Year’
Try 'basename --help' for more information.
-> Importing
Error: near " ": syntax error
basename: extra operand ‘Year’
Try 'basename --help' for more information.
-> Importing
Error: near " ": syntax error
basename: extra operand ‘Year’
Try 'basename --help' for more information.
-> Importing
Error: near " ": syntax error
basename: extra operand ‘Year’
Try 'basename --help' for more information.
-> Importing
Error: near " ": syntax error
basename: extra operand ‘Year’
Try 'basename --help' for more information.
-> Importing
Error: near " ": syntax error
basename: extra operand ‘Year’
Try 'basename --help' for more information.
-> Importing
Error: near " ": syntax error
basename: extra operand ‘Year’
Try 'basename --help' for more information.
-> Importing
Error: near " ": syntax error
basename: extra operand ‘Year’
Try 'basename --help' for more information.
-> Importing
Error: near " ": syntax error
-> Creating extra tables
Error: no such table: RXNSAT
-> Indexing NDC table
-> Indexing RXNSAT table
Error: no such table: main.RXNSAT
Error: no such table: main.RXNSAT
-> Indexing RXNREL table
Error: no such table: main.RXNREL
Error: no such table: main.RXNREL
Error: no such table: main.RXNREL
-> Indexing RXNCONSO table
Error: no such table: main.RXNCONSO
Error: no such table: main.RXNCONSO

What did I do wrong? Sorry if this is a dumb question, I am pretty new to python and these databases.