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added participant/pii tables #3

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added participant/pii tables #3

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57cc4f6
added participant/pii tables
lav-patel Sep 23, 2024
3c183f4
added new tables into export_tables
lav-patel Sep 23, 2024
27718bf
oops .make.export_tables
lav-patel Sep 23, 2024
1e75367
add pii_address to export
lav-patel Sep 30, 2024
155b263
exporting following tables also .make.pii_address
lav-patel Nov 15, 2024
1999c3c
delete old csv and error folder
lav-patel Nov 17, 2024
8a0b28e
provider FORCE_QUOTE
lav-patel Nov 19, 2024
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54 changes: 52 additions & 2 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,9 @@ all: .make.counts
.make.export_tables: .make.person .make.visit_occurrence .make.condition_occurrence .make.drug_exposure
.make.export_tables: .make.measurement .make.procedure_occurrence .make.observation .make.device_exposure
.make.export_tables: .make.death .make.fact_relationship .make.specimen
.make.export_tables: .make.pii_name .make.pii_email .make.pii_phone_number .make.pii_mrn .make.participant_match .make.pii_address
.make.export_tables: .make.care_site .make.location .make.provider .make.note .make.visit_detail

touch $@

.make.person:
Expand All @@ -28,6 +31,7 @@ all: .make.counts
.make.visit_occurrence:
$(psql) -c "\COPY (select * from omop_id_allofus.visit_occurrence) TO '$(csv_path)visit_occurrence.csv' WITH (FORMAT CSV, HEADER);"
touch $@

.make.condition_occurrence:
$(psql) -c "\COPY (select * from omop_id_allofus.condition_occurrence) TO '$(csv_path)condition_occurrence.csv' WITH (FORMAT CSV, HEADER);"
touch $@
Expand Down Expand Up @@ -64,6 +68,50 @@ all: .make.counts
$(psql) -c "\COPY (select * from omop_id_allofus.specimen) TO '$(csv_path)specimen.csv' WITH (FORMAT CSV, HEADER);"
touch $@

.make.pii_name:
$(psql) -c "\COPY (select * from omop_id_allofus.pii_name) TO '$(csv_path)pii_name.csv' WITH (FORMAT CSV, HEADER);"
touch $@

.make.pii_email:
$(psql) -c "\COPY (select * from omop_id_allofus.pii_email) TO '$(csv_path)pii_email.csv' WITH (FORMAT CSV, HEADER);"
touch $@

.make.pii_address:
$(psql) -c "\COPY (select * from omop_id_allofus.pii_address) TO '$(csv_path)pii_address.csv' WITH (FORMAT CSV, HEADER);"
touch $@

.make.pii_phone_number:
$(psql) -c "\COPY (select * from omop_id_allofus.pii_phone_number) TO '$(csv_path)pii_phone_number.csv' WITH (FORMAT CSV, HEADER);"
touch $@

.make.pii_mrn:
$(psql) -c "\COPY (select * from omop_id_allofus.pii_mrn) TO '$(csv_path)pii_mrn.csv' WITH (FORMAT CSV, HEADER);"
touch $@

.make.participant_match:
$(psql) -c "\COPY (select * from omop_id_allofus.participant_match) TO '$(csv_path)participant_match.csv' WITH (FORMAT CSV, HEADER);"
touch $@

.make.care_site:
$(psql) -c "\COPY (select * from omop_id_allofus.care_site) TO '$(csv_path)care_site.csv' WITH (FORMAT CSV, HEADER);"
touch $@

.make.location:
$(psql) -c "\COPY (select * from omop_id_allofus.location) TO '$(csv_path)location.csv' WITH (FORMAT CSV, HEADER);"
touch $@

.make.provider:
$(psql) -c "\COPY (select * from omop_id_allofus.provider) TO '$(csv_path)provider.csv' WITH (FORMAT CSV, HEADER, FORCE_QUOTE *) ;"
touch $@

.make.note:
$(psql) -c "\COPY (select * from omop_id_allofus.note) TO '$(csv_path)note.csv' WITH (FORMAT CSV, HEADER);"
touch $@

.make.visit_detail:
$(psql) -c "\COPY (select * from omop_id_allofus.visit_detail) TO '$(csv_path)visit_detail.csv' WITH (FORMAT CSV, HEADER);"
touch $@

.make.venv:
# create python3 virtual environment
python3 -m pip install --upgrade pip
Expand All @@ -77,5 +125,7 @@ all: .make.counts
touch $@

clean:
rm -rf venv
rm -rf .make.*
rm -rf venv || true
rm -rf .make.* || true
rm -rf $(csv_path)*.csv || true
rm -rf $(csv_path)errors || true