Untested but reorganized docker setup
will king
4 years ago
parent
9a47199728
commit
0bd7965112
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FROM youainti/aact_from_dump
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LABEL AUTHOR 'Will King (youainti@protonmail.com)'
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LABEL DESCRIPTION 'add extra processing to the aact database in preparation for downloading history.'
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#copy additional init scripts
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COPY ./docker-entrypoint-initdb.d/ /docker-entrypoint-initdb.d/
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#these will be run after the database is initialized
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CREATE SCHEMA http;
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/*
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The purpose of this schema, tables, and associated roles to process HTTP responses.
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I may even include a table to keep track of the XML responses
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*/
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/*
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Add a role to manage permissions on the http schema
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*/
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CREATE ROLE http_requestor;
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GRANT CONNECT ON DATABASE aact_db to http_requestor;
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GRANT USAGE ON SCHEMA http TO http_requestor;
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GRANT INSERT,SELECT ON ALL TABLES IN SCHEMA http TO http_requestor;
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/* Create tables related to http requests
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As not every request will have an xml doc, split them.
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*/
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CREATE TABLE IF NOT EXISTS http.responses (
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id SERIAL PRIMARY KEY,
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nct VARCHAR(15),
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version SMALLINT
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url VARCHAR(255),
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response_code SMALLINT,
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response_date DATE
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);
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CREATE TABLE IF NOT EXISTS http.xml_documents (
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id SERIAL PRIMARY KEY,
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xml XML,
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CONSTRAINT http_response
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FOREIGN KEY (id)
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REFERENCES http.responses (id)
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ON DELETE CASCADE --remove xml if the request is deleted
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);
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-- Create a schema handling trial history.
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CREATE SCHEMA history;
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--Create role for anyone who needs to both select and insert on historical data
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CREATE ROLE history_writer;
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GRANT CONNECT ON DATABASE aact_db to history_writer;
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GRANT USAGE ON SCHEMA history TO history_writer;
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GRANT INSERT,SELECT ON ALL TABLES IN SCHEMA http TO history_writer;
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--Create role for anyone who only needs selection access to historical data, such as for analysis
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CREATE ROLE history_reader;
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GRANT CONNECT ON DATABASE aact_db to history_reader;
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GRANT USAGE ON SCHEMA history TO history_reader;
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GRANT SELECT ON ALL TABLES IN SCHEMA http TO history_reader;
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/* History Tables
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Below is where I would construct the parsed trial history tables that I need.
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*/
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@ -0,0 +1 @@
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--Eventually this should let me add necessary views during the construction of the DB.
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@ -0,0 +1,37 @@
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version: '3'
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volumes:
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aact_pg_database: #This is to hold the database.
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services:
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aact:
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build: ./ClinicalTrialHistory #build and use the clinical trial history db.
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container_name: aact_db
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#restart: always #restart after crashes
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environment:
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POSTGRES_USER: root
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POSTGRES_PASSWORD: root
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POSTGRES_DB: aact_db
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ports:
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- "5432:5432" #host:container
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volumes: #host:container is the format.
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- aact_pg_database:/var/lib/postgresql/ # this is persistant storage for the database
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- ./20220201_clinical_trials/postgres_data.dmp:/mnt/host_data/postgres_data.dmp
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pgadmin:
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container_name: pgadmin4_webservice
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image: dpage/pgadmin4
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#restart: always
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environment:
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PGADMIN_DEFAULT_EMAIL: admin@admin.com
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PGADMIN_DEFAULT_PASSWORD: root
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ports:
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- "5050:80"
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volumes: #host:container is the format.
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#The volume with server login information.
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- ./pgadmin4/servers.json:/pgadmin4/servers.json
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#Checklist for production
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# uncomment restart: always in both services.
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# add a python environment to run data collection etc
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@ -1,49 +0,0 @@
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version: '3'
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volumes:
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aact_pg_database: #This is to hold the database.
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aact_helpful_files: #This is to hold files that need accessed by both pgadmin and postgres. I honestly expect it to usually be empty.
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driver: local
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driver_opts:
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type: 'none'
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o: 'bind'
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device: /home/will/research/ClinicalTrialsDataProcessing/PostgressDocker/host_data/
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#change this path to match the path you are holding the dump file in
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services:
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aact:
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container_name: aact_db
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image: postgres
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#restart: always #restart to run things well.
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environment:
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POSTGRES_USER: admin
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POSTGRES_PASSWORD: root
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POSTGRES_DB: aact_db
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ports:
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- "5432:5432" #host:container
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volumes: #host:container is the format.
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#pull in a single file
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#- $HOME/research/ClinicalTrialsDataProcessing/PostgressDocker/infile:/infile
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#add a storage volumes
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- aact_pg_database:/var/lib/postgresql/ # this is the database that persits between uses
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- aact_helpful_files:/mnt/host_data #use :ro # to give read only permisions
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#entrypoint:
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#none yet
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#- echo "test" > /test.touched
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pgadmin:
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container_name: pgadmin4_webservice
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image: dpage/pgadmin4
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#restart: always
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environment:
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PGADMIN_DEFAULT_EMAIL: admin@admin.com
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PGADMIN_DEFAULT_PASSWORD: root
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ports:
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- "5050:80"
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volumes: #host:container is the format.
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#The volume with server login information.
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- ./pgadmin4/servers.json:/pgadmin4/servers.json
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#Checklist for production
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# uncomment restart: always in both services.
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# add a python environment to run data collection etc
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