Added a justfile, adjusted docker networks, restructured how data is downloaded

.gitignore

@@ -180,8 +180,7 @@ Manifest.toml
 
 
 ###### Custom #####
-*_clinical_trials/
+aact_downloads/
-*_clinical_trials.zip
 NCT*.html
 /Orangebook/EOBZIP_*/
 /Orangebook/Orangebooks/

AACT_downloader/docker-compose.yaml

@@ -3,10 +3,15 @@ version: '3'
 volumes:
   aact_pg_database: #This is to hold the database.
 
-services:
+networks:
+  pharmaceutical_research:
+    external: true
 
+services:
   aact:
     build: ./ClinicalTrialHistory #build and use the clinical trial history db.
+    networks:
+      - pharmaceutical_research
     container_name: aact_db
     #restart: always #restart after crashes
     environment:
@@ -17,5 +22,5 @@ services:
       - "5432:5432" #host:container
     volumes: #host:container is the format.
       - aact_pg_database:/var/lib/postgresql/ # this is persistant storage for the database 
-      - ./20220201_clinical_trials/postgres_data.dmp:/mnt/host_data/postgres_data.dmp
+      - ./aact_downloads/postgres_data.dmp:/mnt/host_data/postgres_data.dmp
 

justfile

@@ -0,0 +1,65 @@
+#justfile, used for automating build/setup
+# TODO
+# - setup a .env file so things can be shared between just and docker
+#   - move network name to .env
+#   - move postgress login credentials (allow them to be printed from just while setting up)
+
+
+data_link := "https://ctti-aact.nyc3.digitaloceanspaces.com/27grtsnhtccplxapj2o8ak9aotvv"
+data_file := "postgres_data.dmp"
+
+#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" " "`
+
+#check for necessary dependencies
+check-status:
+    docker --version
+    python --version
+    curl --version
+    echo "current docker containers:{{docker_container}}"
+#Setup the AACT container
+setup-containers: 
+    @echo "Check for downloaded data"
+    [ -f ./AACT_downloader/aact_downloads/{{data_file}} ]
+    @echo "Setting up AACT container"
+    #check appropriate files and directories are setup
+    
+    #run docker compose
+
+#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
+    @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
+    # cleanup docker network
+    docker network prune
+    # cleanup docker volumes
+    docker volume prune
+
+#sets up the docker network
+setup-docker-network:
+    docker network create pharmaceutical_research
+
+#Download the AACT data
+download-aact-data:
+    curl {{data_link}} > ./AACT_downloader/aact_downloads/ {{data_file}}
+
+#Download and parse historical clinical trials data
+download-parse-historical-ct:
+    echo "not implemented"    
+
+#Build everything from scratch
+build-from-scratch: check-status download-aact-data setup-containers download-parse-historical-ct
+    echo "system will be built from scratch, including downloading data"
+
+#build based on previously downloaded data
+build-from-download: check-status setup-containers download-parse-historical-ct
+    echo "system will be built from downloading data"
+
+