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120 lines
3.9 KiB
Plaintext
120 lines
3.9 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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#paths for aact_db (postgres)
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aact_download_link := "https://ctti-aact.nyc3.digitaloceanspaces.com/27grtsnhtccplxapj2o8ak9aotvv"
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aact_download_file := "2022-12-23_postgres_data.zip"
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aact_download_path := "./containers/AACT_downloader/aact_downloads"
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aact_zipped_data_filepath := aact_download_path / aact_download_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|rxnav_db" | cut -f 1 -d " " | tr "\n" " "`
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#paths for rxnavinabox
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rxnav_path := "./containers/RxNav-In-a-box"
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rxnav_version := "rxnav-in-a-box-20230103"
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rxnav_data_path := rxnav_path / rxnav_version / "mysql" / "02_data.sql"
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#Various paths for docker stuff
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docker-compose_path := "./containers/docker-compose.yaml"
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#Number of historical trials to download.
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count := "100"
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#check for necessary dependencies
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check-status:
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docker --version
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#check if python version > 3.10.
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python --version
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#python -c 'import sys; exit(sys.hexversion >= 50859504)'
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curl --version
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echo "current docker containers:{{docker_container}}"
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setup-containers:
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echo "todo"
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@echo "Check for downloaded data"
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#aact
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[ -s {{aact_download_path}}/postgres_data.dmp ]
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#rxnav
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[ -s {{rxnav_data_path}} ]
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#run docker compose
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@echo "Setting up AACT_db & RxNav_db 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 [empty string] statement 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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#Download the AACT data
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download-aact-data:
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#download
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curl {{aact_download_link}} > {{aact_zipped_data_filepath}}
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unzip {{aact_zipped_data_filepath}} -d {{aact_download_path}}
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rm {{aact_zipped_data_filepath}}
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download-rxnav-data:
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echo "Currently manually downloaded."
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#build based on previously downloaded data
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build: check-status setup-containers
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#system built from downloaded data
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#remove containers and rebuild based on previously downloaded data
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rebuild: clean-docker build
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#system will be built from scratch, using previously downloaded data
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#download data and create the containers
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create: check-status download-aact-data build
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# downloaded data and built from scratch
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#remove containers, redownload data, then rebuild containers
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recreate: clean-docker create
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# removed containers, redownloaded data, then rebuilt containers
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#Register trials of interest in the database based on ./history_downloader/selected_trials.sql
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select-trials:
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cd history_downloader && python ./select_trials.py
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#Download trial histories based on registered trials of interest.
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download-trial-histories:
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cd history_downloader && python ./downloader.py --count {{count}}
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#Check if you can connect to the db
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test-db-connection:
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cd history_downloader && python db_connection.py
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#Parse previously downloaded histories into tables.
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parse-trial-histories:
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cd Parser && python extraction_lib.py
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#Download and install
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get-histories: download-trial-histories parse-trial-histories
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#download market data
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get-nsde:
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cd market_data && bash download_nsde.sh
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cd market_data && python extract_nsde.py
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