got downloads working

llm-extraction
youainti 3 years ago
parent e240fff07c
commit 91eeea100e

@ -6,7 +6,9 @@
data_link := "https://ctti-aact.nyc3.digitaloceanspaces.com/27grtsnhtccplxapj2o8ak9aotvv" data_link := "https://ctti-aact.nyc3.digitaloceanspaces.com/27grtsnhtccplxapj2o8ak9aotvv"
data_file := "postgres_data.dmp" data_file := "2022-12-23_postgres_data.zip"
data_path := "./AACT_downloader/aact_downloads"
data_filepath := data_path / data_file
#must match the 'container name: aact_db' in the docker-compose.yaml #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" " "` docker_container := `docker container ls -a | grep aact_db | cut -f 1 -d " " | tr "\n" " "`
@ -17,6 +19,7 @@ check-status:
python --version python --version
curl --version curl --version
echo "current docker containers:{{docker_container}}" echo "current docker containers:{{docker_container}}"
#Setup the AACT container #Setup the AACT container
setup-containers: setup-containers:
@echo "Check for downloaded data" @echo "Check for downloaded data"
@ -48,7 +51,9 @@ setup-docker-network:
#Download the AACT data #Download the AACT data
download-aact-data: download-aact-data:
curl {{data_link}} > ./AACT_downloader/aact_downloads/ {{data_file}} curl {{data_link}} > ./AACT_downloader/aact_downloads/{{data_file}}
unzip {{data_filepath}} -d {{data_path}}
rm {{data_filepath}}
#Download and parse historical clinical trials data #Download and parse historical clinical trials data
download-parse-historical-ct: download-parse-historical-ct:

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