checking in incremental work. Figured out how to get dates.

RxMix/ASSOICATING NCTIDs to NDCs and Marketing dates.sql

@@ -0,0 +1,27 @@
+/*Get relationships between brands and branded drugs and packs*/
+select * from rxnorm_migrated.rxnorm_relations rr 
+where tty1 = 'BN' and tty2 in ('SBD', 'BPCK')
+limit 100;
+
+/*get all the ndc codes associated with an rxcui
+ * Same as query
+ * http://will-office:4000/REST/rxcui/1668240/allhistoricalndcs.json
+ * note the different formats of the dates.
+ * 
+ * Based on http://will-office:4000/RxNav/search?searchBy=RXCUI&searchTerm=1668240
+ * it appears that this rxcui is a sbd or bpck (branded drug or pack)
+ * 
+ * If I grab every brand, then every branded drug or pack associated with that drug and then every 
+ * */
+select * from ALLNDC_HISTORY ah 
+where RXCUI ='1668240'
+and SAB='RXNORM'
+;
+/** 
+ * If I grab every brand, then every branded drug or pack associated with that drug and then attach that to the nsde data I would get the marketing dates required.
+ * trial -> mesh_term -> IN/MIN (rxcui) -> BN (rxcui) -> SBD/BPCK (rxcui) -> ndc11 -> nsde (marketing dates)
+ * */
+
+/*
+ * I do need to figure out a way to change the date types when importing into postgres. In mariadb they ar mmYYYY wheras in the jsonapi they are YYYYmm but I want is YYYY-mm-01
+ */*/

RxMix/migrate_rxnav.py

@@ -85,7 +85,12 @@ if __name__ == "__main__":
     MARIADB_PORT = os.getenv("MARIADB_PORT")
 
     #get & convert datatypes for each table of interest
-    tables_of_interest = ["rxnorm_props","rxnorm_relations"]
+    tables_of_interest = [
+            "rxnorm_props"
+            ,"rxnorm_relations"
+            ,"ALLNDC_HISTORY"
+            ,"ALLRXCUI_HISTORY"
+            ]
     mschema="rxnorm_current"
     pschema="rxnorm_migrated"
 

justfile

@@ -16,6 +16,9 @@ docker_container := `docker container ls -a | grep aact_db | cut -f 1 -d " " | t
 #Various paths for docker stuff
 docker-compose_path := "./AACT_downloader/docker-compose.yaml"
 
+#rxnorm_mappings
+rxnorm_mappings_url := "https://dailymed-data.nlm.nih.gov/public-release-files/rxnorm_mappings.zip"
+
 #Number of historical trials to download.
 count := "100"
 
@@ -101,3 +104,9 @@ get-histories: download-trial-histories parse-trial-histories
 get-nsde:
     cd market_data && bash download_nsde.sh
     cd market_data && python extract_nsde.py
+
+get-rxnorm-mappings:
+    #this may not be needed, all it does is match spls to rxcuis and I think I already have that.
+    curl {{rxnorm_mappings_url}} > ./market_data/rxnorm_mappings.zip
+    cd ./market_data && unzip ./rxnorm_mappings.zip
+    rm ./market_data/rxnorm_mappings.zip

market_data/readme.md

@@ -0,0 +1 @@
+downloads and extracts nsde data.