added some data that had been left untracked

.gitattributes

@@ -1,2 +1,6 @@
 *.sql.gzip filter=lfs diff=lfs merge=lfs -text
 *.xlsx filter=lfs diff=lfs merge=lfs -text
+containers/AACT_Reloader/2023-09-06_aactdb_with_matches.sql.gz filter=lfs diff=lfs merge=lfs -text
+other_data/USP[[:space:]]DC/usp_dc_pub_2023_release_2.0_updated_final.csv filter=lfs diff=lfs merge=lfs -text
+other_data/USP[[:space:]]MMG/MMG_v8.0_Alignment_File.csv filter=lfs diff=lfs merge=lfs -text
+other_data/VA[[:space:]]Formulary/PharmacyProductSystem_NationalDrugCodeExtract.csv filter=lfs diff=lfs merge=lfs -text

containers/AACT_Reloader/StartRestoreContainer.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+RESTORE_DUMP_GZ=2023-09-06_aactdb_with_matches.sql.gz
+POSTGRES_USER=root
+POSTGRES_PASSWORD=root
+
+#start container
+podman run \
+    -e POSTGRES_PASSWORD="${POSTGRES_PASSWORD}" \
+    -e POSTGRES_USER="${POSTGRES_USER}" \
+    -e POSTGRES_DB=aact_db \
+    --name aact_db \
+    --detatch \
+    --shm-size=512mb \
+    --volume ${RESTORE_DUMP_GZ}:/backup/${RESTORE_DUMP_GZ} \
+    --ports 5432:5432\
+    postgres:14-alpine
+
+
+
+#execute within container
+podman exec aact_db \
+    "gzip --keep --stdout --decompress /backup/2023-09-06_aactdb_with_matches.sql.gz | psql -U ${POSTGRES_USER}"

justfile

@@ -5,23 +5,19 @@
 #   - move postgress login credentials (allow them to be printed from just while setting up)
 
 
-#paths for aact_db (postgres)
+data_link := "https://ctti-aact.nyc3.digitaloceanspaces.com/27grtsnhtccplxapj2o8ak9aotvv"
-aact_download_link := "https://ctti-aact.nyc3.digitaloceanspaces.com/27grtsnhtccplxapj2o8ak9aotvv"
+data_file := "2022-12-23_postgres_data.zip"
-aact_download_file := "2022-12-23_postgres_data.zip"
+data_path := "./containers/AACT_downloader/aact_downloads"
-aact_download_path := "./containers/AACT_downloader/aact_downloads"
+data_filepath := data_path / data_file
-aact_zipped_data_filepath := aact_download_path / aact_download_file
 
 #must match the 'container name: aact_db' in the docker-compose.yaml
-docker_container := `docker container ls -a | grep "aact_db|rxnav_db" | cut -f 1 -d " " | tr "\n" " "`
+docker_container := `docker container ls -a | grep aact_db | cut -f 1 -d " " | tr "\n" " "`
-
-#paths for rxnavinabox
-rxnav_path := "./containers/RxNav-In-a-box"
-rxnav_version := "rxnav-in-a-box-20230103"
-rxnav_data_path := rxnav_path / rxnav_version / "mysql" / "02_data.sql"
 
 #Various paths for docker stuff
-docker-compose_path := "./containers/docker-compose.yaml"
+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"
@@ -32,23 +28,18 @@ check-status:
     docker --version
     #check if python version > 3.10. 
     python --version
-    #python -c 'import sys; exit(sys.hexversion >= 50859504)'
+    python -c 'import sys; exit(sys.hexversion >= 50859504)'
     curl --version
     echo "current docker containers:{{docker_container}}"
 
-
+#Setup the AACT container
 setup-containers: 
-    echo "todo"
     @echo "Check for downloaded data"
-    #aact
+    [ -s {{data_path}}/postgres_data.dmp ]
-    [ -s {{aact_download_path}}/postgres_data.dmp ]
-    #rxnav
-    [ -s {{rxnav_data_path}} ]
 
     #run docker compose
-    @echo "Setting up AACT_db & RxNav_db container"
+    @echo "Setting up AACT container"
     docker-compose -f {{docker-compose_path}} up -d
-    
 
 #Stop the appropriate docker container
 stop-containers:
@@ -69,13 +60,10 @@ clean-docker: stop-containers
 
 #Download the AACT data
 download-aact-data:
-    #download
+    curl {{data_link}} > ./AACT_downloader/aact_downloads/{{data_file}}
-    curl {{aact_download_link}} > {{aact_zipped_data_filepath}}
+    unzip {{data_filepath}} -d {{data_path}}
-    unzip {{aact_zipped_data_filepath}} -d {{aact_download_path}}
+    rm {{data_filepath}}
-    rm {{aact_zipped_data_filepath}}
 
-download-rxnav-data:
-    echo "Currently manually downloaded."
 
 #build based on previously downloaded data
 build: check-status setup-containers
@@ -117,3 +105,8 @@ 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

scripts/drugtools/historical_nct_extractor.py

@@ -126,17 +126,18 @@ def extract_submission_dates(soup):
 
     version_date_dict = {}
 
-    for row in reversed(table_rows):
+    for row in table_rows:
         # if it is <td headers="VersionNumber">xx</td> then it contains what we need.
+        version_number = None
+        version_date = None
         for td in row.findChildren("td"):
             if ("headers" in td.attrs):
                 if (td.attrs["headers"][0]=="VersionNumber"):
                     version_number = int(td.text)
                 elif (td.attrs["headers"][0]=="VersionDate"):
-                    version_date = td.text
+                    version_date = datetime.strptime(td.text.strip() , "%B %d, %Y")
-            version_date_dict[version_number] = datetime.strptime(version_date , "%B %d, %Y")
 
-    print(version_date_dict)
+        version_date_dict[version_number] = version_date
     return version_date_dict
 
 def optional_strip(possible_string):
@@ -396,14 +397,12 @@ date_MMMM_DD_YYYY = "%B %d, %Y"
 
 def get_data_from_versions(nct_id,html, version_a_int, version_b_int):
     soup = BeautifulSoup(html,"lxml")
-    print(getting_data_from_versions)
 
     version_date_dict = extract_submission_dates(soup)
-    print(version_date_dict)
 
     #preallocate version data
-    version_a = VersionData(nct_id, version_a_int, version_date_dict[version_a_int])
+    version_a = VersionData(nct_id, version_a_int, version_date_dict.get(version_a_int))
-    version_b = VersionData(nct_id, version_b_int, version_date_dict[version_b_int])
+    version_b = VersionData(nct_id, version_b_int, version_date_dict.get(version_b_int))
 
     #extract data from html and put it in the preallocated objects
     get_forms(soup, version_a, version_b)
@@ -424,7 +423,6 @@ def run():
             curse.execute(sql)
             for response in tqdm(curse.fetchall()):
                 nct_id, version_a, version_b, html = response
-                print(nct_id)
 
                 print(nct_id, version_a, version_b) if VERBOSE else ""