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implement medication administration in dataframer #44

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Jan 22, 2025
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4 changes: 2 additions & 2 deletions etl-job/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,8 @@ COPY ./requirements.txt /root
RUN source venv/bin/activate && pip install -r requirements.txt

# move these out of requirements.txt, so that builds are quicker when we change
RUN source venv/bin/activate && pip install "gen3_tracker==0.0.7rc2"
RUN source venv/bin/activate && pip install "aced-submission==0.0.10rc3"
RUN source venv/bin/activate && pip install "gen3_tracker==0.0.7rc6"
RUN source venv/bin/activate && pip install "aced-submission==0.0.10rc7"
ENV PATH="/usr/local/bin:$PATH"


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3 changes: 2 additions & 1 deletion etl-job/fhir_import_export.py
Original file line number Diff line number Diff line change
Expand Up @@ -205,7 +205,8 @@ def _load_all(program: str,
index_generator_dict = {
'researchsubject': db.flattened_research_subjects,
'specimen': db.flattened_specimens,
'file': db.flattened_document_references
'file': db.flattened_document_references,
"medicationadministration": db.flattened_medication_administrations,
}

# To ensure differences in the dataframer versions do not conflict, clear the project, and reload the project.
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6 changes: 0 additions & 6 deletions etl-job/requirements.txt
Original file line number Diff line number Diff line change
@@ -1,9 +1,3 @@
# moved to docker file
# gen3_util>=0.0.7rc2
# iceberg_tools>=0.0.4
# aced_submission>=0.0.7rc6

psycopg2
boto3
yp
click
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