justfile will download, create, and populate db with AACT data

AACT_downloader/readme.md

@@ -0,0 +1 @@
+This is what is needed to setup the database.

Orangebook/readme.md

@@ -0,0 +1 @@
+Most of these are related to potentially parsing orangebook data from the pdfs.

classifications/readme.md

@@ -0,0 +1 @@
+I believe this is for a ml classification or reasons for terminations.

justfile

@@ -13,6 +13,16 @@ data_filepath := data_path / data_file
 #must match the 'container name: aact_db' in the docker-compose.yaml
 docker_container := `docker container ls -a | grep aact_db | cut -f 1 -d " " | tr "\n" " "`
 
+#Various paths for docker stuff
+dockerdef_path := "./AACT_downloader/ClinicalTrialHistory"
+dockerdef_dockerfile := dockerdef_path / "Dockerfile"
+dockerdef_schema_path := dockerdef_path / "docker-entrypoint-initdb.d"
+dockerdef_schema_http := dockerdef_schema_path / "020_HttpSchema.sql"
+dockerdef_schema_hist:= dockerdef_schema_path / "030_HistoricalSchema.sql"
+dockerdef_schema_AViews := dockerdef_schema_path / "090_AnalysisViews.sql"
+docker-compose_path := "./AACT_downloader/docker-compose.yaml"
+
+
 #check for necessary dependencies
 check-status:
     docker --version
@@ -23,23 +33,29 @@ check-status:
 #Setup the AACT container
 setup-containers: 
     @echo "Check for downloaded data"
-    [ -f ./AACT_downloader/aact_downloads/{{data_file}} ]
+    [ -s {{data_path}}/postgres_data.dmp ]
-    @echo "Setting up AACT container"
+
+    @echo "Checking for key files"
     #check appropriate files and directories are setup
+    [ -s {{dockerdef_schema_http}} ]
+    [ -s {{dockerdef_schema_hist}} ]
+    [ -s {{dockerdef_schema_AViews}} ]
     
     #run docker compose
+    @echo "Setting up AACT container"
+    docker-compose -f {{docker-compose_path}} up -d
 
 #Stop the appropriate docker container
 stop-containers:
     #stop all docker containers if they are currently running.
     #The if statement is used because sometimes there are no running containers
-    if [ "{{docker_container}}" ]; then  docker stop {{docker_container}}; fi
+    if [ -n "{{docker_container}}" ]; then  docker stop {{docker_container}}; fi
     @echo "confirmed that docker containers {{docker_container}} are stopped"
 
 #Remove the appropriate docker container as well as associated volumes
 clean-docker: stop-containers
     # remove docker containers
-    if [ "{{docker_container}}" ]; then  docker rm {{docker_container}}; fi
+    if [ -n "{{docker_container}}" ]; then  docker rm {{docker_container}}; fi
     # cleanup docker network
     docker network prune
     # cleanup docker volumes