Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[Change Request] Remove unused OMOP code #1002

Closed
frankcorneliusmartin opened this issue Jan 23, 2024 · 0 comments · Fixed by #1067
Closed

[Change Request] Remove unused OMOP code #1002

frankcorneliusmartin opened this issue Jan 23, 2024 · 0 comments · Fixed by #1067
Assignees
Labels
change Internal change

Comments

@frankcorneliusmartin
Copy link
Contributor

Description
There are a few sections that should be removed now that we have the OMOP decorator (for connection):

https://github.com/vantage6/vantage6/blob/2da5230e5895a1d23a01a311243dbb3240e912fc/vantage6-algorithm-tools/vantage6/algorithm/tools/wrappers.py#54

elif database_type == "omop":
return load_omop_data

def load_omop_data(database_uri: str, query: str) -> pd.DataFrame:
"""
Load the local privacy-sensitive data from the database.
Parameters
----------
database_uri : str
URI of the OMOP database, supplied by te node
query: str
Query to retrieve the data from the database
Returns
-------
pd.DataFrame
The data from the database
"""
# TODO: replace query by OMOP json and convert to SQL
return pd.read_sql(database_uri, query)

@frankcorneliusmartin frankcorneliusmartin added the change Internal change label Jan 23, 2024
@frankcorneliusmartin frankcorneliusmartin self-assigned this Jan 23, 2024
@github-actions github-actions bot added the New label Jan 23, 2024
@frankcorneliusmartin frankcorneliusmartin linked a pull request Feb 26, 2024 that will close this issue
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
change Internal change
Projects
Status: Done
Development

Successfully merging a pull request may close this issue.

2 participants