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.

Sign up for GitHub

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

Small things to update #68

Draft
wants to merge 4 commits into
base: main
Choose a base branch
from
Draft

Small things to update #68

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
74156cb
add physionet2012 to doc
eroell Nov 26, 2024
95249a9
undo escape % w/ prerelease update duckdb
eroell Nov 26, 2024
d2bf04e
Merge branch 'main' into maintnc/misc-updates
eroell Dec 2, 2024
3fc587c
check push permission
Dec 3, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/ehrdata/test.yaml?branch=main
[badge-docs]: https://img.shields.io/readthedocs/ehrdata

A Python package for EHR data
Python package for EHR data

## Getting started

Expand Down
1 change: 1 addition & 0 deletions docs/api.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@
dt.gibleed_omop
dt.synthea27nj_omop
dt.mimic_ii
dt.physionet2012
```

## Preprocessing
Expand Down
2 changes: 1 addition & 1 deletion src/ehrdata/io/omop/omop.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ def _set_up_duckdb(path: Path, backend_handle: DuckDBPyConnection, prefix: str =
dtype = None

# read raw csv as temporary table
temp_relation = backend_handle.read_csv(path / file_name, dtype=dtype, escapechar="%") # noqa: F841
temp_relation = backend_handle.read_csv(path / file_name, dtype=dtype) # noqa: F841
backend_handle.execute("CREATE OR REPLACE TABLE temp_table AS SELECT * FROM temp_relation")

# make query to create table with lowercase column names
Expand Down
Loading