Switched to RxNorm db for rxnconso

smart-on-fhir · Aug 1, 2024 · 1f4dd1b · 1f4dd1b
1 parent b2e5d49
commit 1f4dd1b
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Showing 15 changed files with 3,735 additions and 2,006,352 deletions.
diff --git a/cumulus_library_opioid/manifest.toml b/cumulus_library_opioid/manifest.toml
@@ -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"
+# ]
 
-[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",
+# ]
diff --git a/cumulus_library_opioid/reference_sql/additional_rules_builder.sql b/cumulus_library_opioid/reference_sql/additional_rules_builder.sql
@@ -85,6 +85,7 @@ WHERE
     r.REL NOT IN ('RB', 'PAR')
     AND length(r.keyword) >= 4
 
+
 -- ###########################################################
 
 CREATE TABLE opioid__acep_combined_ruleset AS