From 1a106a553e8ee5e382eef222f123b5e68cacad16 Mon Sep 17 00:00:00 2001 From: youainti Date: Tue, 7 Feb 2023 11:57:49 -0800 Subject: [PATCH] moved containers to single location, ignored raw data --- .gitignore | 9 ++++++--- Parser/.vscode/launch.json | 16 ---------------- .../AACT_downloader}/db_store/readme.txt | 0 .../AACT_downloader}/docker-compose.yaml | 0 .../005_CreateAactUsers.sql | 0 .../010_load_db_dump.sh | 0 .../020_HttpSchema.sql | 0 .../030_HistoricalSchema.sql | 0 .../040_StructuredProductLabels_Schema.sql | 0 .../090_AnalysisViews.sql | 0 containers/RxNav-In-a-box/docker-compose.yml | 15 +++++++++++++++ .../download_extract_rxnavinabox.md | 7 +++++++ 12 files changed, 28 insertions(+), 19 deletions(-) delete mode 100644 Parser/.vscode/launch.json rename {AACT_downloader => containers/AACT_downloader}/db_store/readme.txt (100%) rename {AACT_downloader => containers/AACT_downloader}/docker-compose.yaml (100%) rename {AACT_downloader => containers/AACT_downloader}/docker-entrypoint-initdb.d/005_CreateAactUsers.sql (100%) rename {AACT_downloader => containers/AACT_downloader}/docker-entrypoint-initdb.d/010_load_db_dump.sh (100%) rename {AACT_downloader => containers/AACT_downloader}/docker-entrypoint-initdb.d/020_HttpSchema.sql (100%) rename {AACT_downloader => containers/AACT_downloader}/docker-entrypoint-initdb.d/030_HistoricalSchema.sql (100%) rename {AACT_downloader => containers/AACT_downloader}/docker-entrypoint-initdb.d/040_StructuredProductLabels_Schema.sql (100%) rename {AACT_downloader => containers/AACT_downloader}/docker-entrypoint-initdb.d/090_AnalysisViews.sql (100%) create mode 100644 containers/RxNav-In-a-box/docker-compose.yml create mode 100644 containers/RxNav-In-a-box/download_extract_rxnavinabox.md diff --git a/.gitignore b/.gitignore index dfc311e..cacea38 100644 --- a/.gitignore +++ b/.gitignore @@ -180,9 +180,12 @@ Manifest.toml ###### Custom ##### -aact_downloads/ NCT*.html -/Orangebook/EOBZIP_*/ -/Orangebook/Orangebooks/ *.json *.zip +#Ignore stuff from RxNavInABox +containers/RxNav-In-a-box/rxnav_data/* +containers/RxNav-In-a-box/rxnav-in-a-box-* +#Ignore stuff from AACT_downlaoder +containers/db_store/* + diff --git a/Parser/.vscode/launch.json b/Parser/.vscode/launch.json deleted file mode 100644 index 306f58e..0000000 --- a/Parser/.vscode/launch.json +++ /dev/null @@ -1,16 +0,0 @@ -{ - // Use IntelliSense to learn about possible attributes. - // Hover to view descriptions of existing attributes. - // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 - "version": "0.2.0", - "configurations": [ - { - "name": "Python: Current File", - "type": "python", - "request": "launch", - "program": "${file}", - "console": "integratedTerminal", - "justMyCode": true - } - ] -} \ No newline at end of file diff --git a/AACT_downloader/db_store/readme.txt b/containers/AACT_downloader/db_store/readme.txt similarity index 100% rename from AACT_downloader/db_store/readme.txt rename to containers/AACT_downloader/db_store/readme.txt diff --git a/AACT_downloader/docker-compose.yaml b/containers/AACT_downloader/docker-compose.yaml similarity index 100% rename from AACT_downloader/docker-compose.yaml rename to containers/AACT_downloader/docker-compose.yaml diff --git a/AACT_downloader/docker-entrypoint-initdb.d/005_CreateAactUsers.sql b/containers/AACT_downloader/docker-entrypoint-initdb.d/005_CreateAactUsers.sql similarity index 100% rename from AACT_downloader/docker-entrypoint-initdb.d/005_CreateAactUsers.sql rename to containers/AACT_downloader/docker-entrypoint-initdb.d/005_CreateAactUsers.sql diff --git a/AACT_downloader/docker-entrypoint-initdb.d/010_load_db_dump.sh b/containers/AACT_downloader/docker-entrypoint-initdb.d/010_load_db_dump.sh similarity index 100% rename from AACT_downloader/docker-entrypoint-initdb.d/010_load_db_dump.sh rename to containers/AACT_downloader/docker-entrypoint-initdb.d/010_load_db_dump.sh diff --git a/AACT_downloader/docker-entrypoint-initdb.d/020_HttpSchema.sql b/containers/AACT_downloader/docker-entrypoint-initdb.d/020_HttpSchema.sql similarity index 100% rename from AACT_downloader/docker-entrypoint-initdb.d/020_HttpSchema.sql rename to containers/AACT_downloader/docker-entrypoint-initdb.d/020_HttpSchema.sql diff --git a/AACT_downloader/docker-entrypoint-initdb.d/030_HistoricalSchema.sql b/containers/AACT_downloader/docker-entrypoint-initdb.d/030_HistoricalSchema.sql similarity index 100% rename from AACT_downloader/docker-entrypoint-initdb.d/030_HistoricalSchema.sql rename to containers/AACT_downloader/docker-entrypoint-initdb.d/030_HistoricalSchema.sql diff --git a/AACT_downloader/docker-entrypoint-initdb.d/040_StructuredProductLabels_Schema.sql b/containers/AACT_downloader/docker-entrypoint-initdb.d/040_StructuredProductLabels_Schema.sql similarity index 100% rename from AACT_downloader/docker-entrypoint-initdb.d/040_StructuredProductLabels_Schema.sql rename to containers/AACT_downloader/docker-entrypoint-initdb.d/040_StructuredProductLabels_Schema.sql diff --git a/AACT_downloader/docker-entrypoint-initdb.d/090_AnalysisViews.sql b/containers/AACT_downloader/docker-entrypoint-initdb.d/090_AnalysisViews.sql similarity index 100% rename from AACT_downloader/docker-entrypoint-initdb.d/090_AnalysisViews.sql rename to containers/AACT_downloader/docker-entrypoint-initdb.d/090_AnalysisViews.sql diff --git a/containers/RxNav-In-a-box/docker-compose.yml b/containers/RxNav-In-a-box/docker-compose.yml new file mode 100644 index 0000000..8ea4830 --- /dev/null +++ b/containers/RxNav-In-a-box/docker-compose.yml @@ -0,0 +1,15 @@ +version: '3.1' + +services: + rxnav-db: + image: mariadb:10.4 + restart: "no" + expose: + - "3306" + volumes: + - ./rxnav-in-a-box/mysql:/docker-entrypoint-initdb.d:ro + - ./rxnav_data:/ + environment: + MYSQL_RANDOM_ROOT_PASSWORD: "yes" + MYSQL_USER: webuser + MYSQL_PASSWORD: 9521354c77aa diff --git a/containers/RxNav-In-a-box/download_extract_rxnavinabox.md b/containers/RxNav-In-a-box/download_extract_rxnavinabox.md new file mode 100644 index 0000000..54105c9 --- /dev/null +++ b/containers/RxNav-In-a-box/download_extract_rxnavinabox.md @@ -0,0 +1,7 @@ +# Instructions: +Go go [RxNavInABox](https://lhncbc.nlm.nih.gov/RxNav/applications/RxNav-in-a-Box.html) and download the most recent version. + +I have included the version I use. + +Then unzip and run docker-compose.yaml +