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87 lines
3.1 KiB
Plaintext
87 lines
3.1 KiB
Plaintext
#justfile, used for automating build/setup
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# TODO
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# - setup a .env file so things can be shared between just and docker
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# - move network name to .env
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# - move postgress login credentials (allow them to be printed from just while setting up)
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data_link := "https://ctti-aact.nyc3.digitaloceanspaces.com/27grtsnhtccplxapj2o8ak9aotvv"
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data_file := "2022-12-23_postgres_data.zip"
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data_path := "./AACT_downloader/aact_downloads"
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data_filepath := data_path / data_file
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#must match the 'container name: aact_db' in the docker-compose.yaml
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docker_container := `docker container ls -a | grep aact_db | cut -f 1 -d " " | tr "\n" " "`
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#Various paths for docker stuff
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dockerdef_path := "./AACT_downloader/ClinicalTrialHistory"
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dockerdef_dockerfile := dockerdef_path / "Dockerfile"
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dockerdef_schema_path := dockerdef_path / "docker-entrypoint-initdb.d"
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dockerdef_schema_http := dockerdef_schema_path / "020_HttpSchema.sql"
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dockerdef_schema_hist:= dockerdef_schema_path / "030_HistoricalSchema.sql"
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dockerdef_schema_AViews := dockerdef_schema_path / "090_AnalysisViews.sql"
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docker-compose_path := "./AACT_downloader/docker-compose.yaml"
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#check for necessary dependencies
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check-status:
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docker --version
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python --version
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curl --version
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echo "current docker containers:{{docker_container}}"
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#Setup the AACT container
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setup-containers:
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@echo "Check for downloaded data"
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[ -s {{data_path}}/postgres_data.dmp ]
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@echo "Checking for key files"
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#check appropriate files and directories are setup
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[ -s {{dockerdef_schema_http}} ]
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[ -s {{dockerdef_schema_hist}} ]
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[ -s {{dockerdef_schema_AViews}} ]
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#run docker compose
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@echo "Setting up AACT container"
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docker-compose -f {{docker-compose_path}} up -d
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#Stop the appropriate docker container
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stop-containers:
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#stop all docker containers if they are currently running.
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#The if statement is used because sometimes there are no running containers
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if [ -n "{{docker_container}}" ]; then docker stop {{docker_container}}; fi
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@echo "confirmed that docker containers {{docker_container}} are stopped"
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#Remove the appropriate docker container as well as associated volumes
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clean-docker: stop-containers
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# remove docker containers
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if [ -n "{{docker_container}}" ]; then docker rm {{docker_container}}; fi
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# cleanup docker network
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docker network prune
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# cleanup docker volumes
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docker volume prune
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#sets up the docker network
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setup-docker-network:
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docker network create pharmaceutical_research
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#Download the AACT data
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download-aact-data:
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curl {{data_link}} > ./AACT_downloader/aact_downloads/{{data_file}}
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unzip {{data_filepath}} -d {{data_path}}
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rm {{data_filepath}}
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#Download and parse historical clinical trials data
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download-parse-historical-ct:
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echo "not implemented"
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#Build everything from scratch
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build-from-scratch: check-status download-aact-data setup-containers download-parse-historical-ct
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echo "system will be built from scratch, including downloading data"
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#build based on previously downloaded data
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build-from-download: check-status setup-containers download-parse-historical-ct
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echo "system will be built from downloading data"
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