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

Rgx fix #5

Open
wants to merge 2 commits into
base: main
Choose a base branch
from
Open

Rgx fix #5

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
7c57500
Added cmd-line example in README
PhilAppleby Dec 11, 2024
a1b4ee5
enhancement to rgx ddl parser - allows for lower case table names
PhilAppleby Dec 23, 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
11 changes: 7 additions & 4 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,12 @@ TODO:
Reduction in complexity over the original CaRROT-CDM version for the Transform part of *ETL* - In practice *Extract* is always
performed by Data Partners, *Load* by database bulk-load software.

Statistics
Sample command line:

External libraries imported (approximate)
`carrot-transform run mapstream \
--rulesfile=${DATASETHOME}/rules/mapping.json \
--person-file=${DATASETHOME/input/Demographics.csv \
--omop-version="5.3" \
--output-dir=${DATASETHOME}/output \
${DATASETHOME}/input`

carrot-cdm 61
carrot-transform 12
2 changes: 1 addition & 1 deletion carrottransform/tools/omopcdm.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ def process_ddl(self, fp):
output_dict["date_fields"] = {}

ver_rgx = re.compile(r'^--postgresql.*(\d+\.\d+)$')
start_rgx = re.compile(r'^CREATE\s*TABLE\s*(\@?[a-zA-Z]+\.)?([A-Z_]+)')
start_rgx = re.compile(r'^CREATE\s*TABLE\s*(\@?[a-zA-Z]+\.)?([a-zA-Z_]+)')
datatype_rgx = re.compile(r'^\s*([a-z_]+)\s+([a-zA-Z_]+)')
end_rgx = re.compile(r'.*[)];$')
vermatched = False
Expand Down
Loading