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Switched to RxNorm db for rxnconso #22

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merged 2 commits into from
Aug 1, 2024
Merged

Switched to RxNorm db for rxnconso #22

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f1ea960
Switched to RxNorm db for rxnconso
dogversioning Aug 1, 2024
559bd2d
remove debug commenting
dogversioning Aug 1, 2024
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76 changes: 38 additions & 38 deletions cumulus_library_opioid/manifest.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,44 +7,44 @@ file_names = [
"vocab/additional_rules_builder.py",
]

[sql_config]
file_names = [
"define_dx.sql",
"define_dx_sepsis.sql",
"define_dx_sud.sql",
"define_lab.sql",
"define_rx.sql",
"define_rx_buprenorphine.sql",
"define_rx_naloxone.sql",
"define_rx_opioid.sql",
"table_study_period.sql",
"table_dx.sql",
"table_dx_sepsis.sql",
"table_lab.sql",
"table_rx.sql",
"version.sql"
]
# [sql_config]
# file_names = [
# "define_dx.sql",
# "define_dx_sepsis.sql",
# "define_dx_sud.sql",
# "define_lab.sql",
# "define_rx.sql",
# "define_rx_buprenorphine.sql",
# "define_rx_naloxone.sql",
# "define_rx_opioid.sql",
# "table_study_period.sql",
# "table_dx.sql",
# "table_dx_sepsis.sql",
# "table_lab.sql",
# "table_rx.sql",
# "version.sql"
# ]
Comment on lines +10 to +26
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i've been doing this manually each time im working and then undoing it on commit - since we now remember that the opioid study is not working in library v2.3, im inclined to leave it commented until we migrate these tables


[counts_builder_config]
file_names = [
"counts.py"
]
# [counts_builder_config]
# file_names = [
# "counts.py"
# ]


[export_config]
export_list = [
"opioid__count_study_period_week",
"opioid__count_study_period_month",
"opioid__count_dx_sepsis_week",
"opioid__count_dx_sepsis_month",
"opioid__count_dx_month",
"opioid__count_dx_week",
"opioid__count_lab_month",
"opioid__count_lab_week",
"opioid__count_medicationrequest",
"opioid__count_rx",
"opioid__count_rx_opioid",
"opioid__count_rx_buprenorphine",
"opioid__count_rx_naloxone",
"opioid__meta_version",
]
# [export_config]
# export_list = [
# "opioid__count_study_period_week",
# "opioid__count_study_period_month",
# "opioid__count_dx_sepsis_week",
# "opioid__count_dx_sepsis_month",
# "opioid__count_dx_month",
# "opioid__count_dx_week",
# "opioid__count_lab_month",
# "opioid__count_lab_week",
# "opioid__count_medicationrequest",
# "opioid__count_rx",
# "opioid__count_rx_opioid",
# "opioid__count_rx_buprenorphine",
# "opioid__count_rx_naloxone",
# "opioid__meta_version",
# ]
1 change: 1 addition & 0 deletions cumulus_library_opioid/reference_sql/additional_rules_builder.sql
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Expand Up @@ -85,6 +85,7 @@ WHERE
r.REL NOT IN ('RB', 'PAR')
AND length(r.keyword) >= 4


-- ###########################################################

CREATE TABLE opioid__acep_combined_ruleset AS
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