Ensure that the environ variable of database location is used through out. #8
Open
kindofluke wants to merge 10 commits intochb:masterfrom
Open
Ensure that the environ variable of database location is used through out. #8kindofluke wants to merge 10 commits intochb:masterfrom
kindofluke wants to merge 10 commits intochb:masterfrom
Conversation
Adding RREL is a bad idea but the db part is a good idea Adding query to get the cpt desc on one table
Note also reverting a minor change that we use in our environment but maybe not important for everyone.
… the chang being proposed.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Great library!
I know you all haven't worked on this in a little while but I wanted to offer this PR.
In looking at rxnorm_link_run, the db_file location is determined through
os.environ.get('SQLITE_FILE')However, when actually running linkage though rxnorm values are looked up using the
RxNormLookupclass which hardcodes the database to always be indatabasesdirectory.See below from rxnorm.py:
To fix this, I reused the same code from rxnorm_link_run which checks the environment variable first and happily falls back on the
databaseslocation if it is not populated.