Simplified the DB creation process by running a postgres container directly

AACT_downloader/ClinicalTrialHistory/Dockerfile

@@ -1,7 +0,0 @@
-FROM  youainti/aact_from_dump
-LABEL AUTHOR 'Will King (youainti@protonmail.com)'
-LABEL DESCRIPTION 'add extra processing to the aact database in preparation for downloading history.'
-
-#copy additional init scripts
-COPY ./docker-entrypoint-initdb.d/ /docker-entrypoint-initdb.d/
-#these will be run after the database is initialized

AACT_downloader/docker-compose.yaml

@@ -1,15 +1,14 @@
 version: '3'
 
 volumes:
-  aact_pg_database: #This is to hold the database.
+  aact_pg_database: #This is to hold the database, making it easy to purge if needed.
 
 networks:
-  pharmaceutical_research:
-    external: true
+  pharmaceutical_research: #because it helps to have a way to link specifically to this. 
 
 services:
-  aact:
-    build: ./ClinicalTrialHistory #build and use the clinical trial history db.
+  aact_db:
+    image: postgres:14-alpine
     networks:
       - pharmaceutical_research
     container_name: aact_db
@@ -21,6 +20,10 @@ services:
     ports:
       - "5432:5432" #host:container
     volumes: #host:container is the format.
-      - aact_pg_database:/var/lib/postgresql/ # this is persistant storage for the database 
+      # this is persistant storage for the database  
+      - aact_pg_database:/var/lib/postgresql/
+      # this is the database dump to restore from
       - ./aact_downloads/postgres_data.dmp:/mnt/host_data/postgres_data.dmp
+      # this is the folder containing entrypoint info.
+      - ./docker-entrypoint-initdb.d/:/docker-entrypoint-initdb.d/
 

AACT_downloader/docker-entrypoint-initdb.d/005_CreateAactUsers.sql

@@ -0,0 +1,21 @@
+--Create ctti user and grant permissions
+CREATE ROLE ctti;
+GRANT ALL PRIVILEGES ON DATABASE aact_db TO ctti;
+
+/*
+Add the root user if it doesn't exist. 
+With the default configuration this shouldn't be an issue, 
+but I can see myself forgetting and changing the default POSTGRES_USER
+*/
+DO LANGUAGE plpgsql
+$do$
+BEGIN
+   IF NOT EXISTS (
+      SELECT FROM pg_catalog.pg_roles  -- SELECT list can be empty for this
+      WHERE  rolname = 'root') 
+    THEN
+      CREATE ROLE root LOGIN PASSWORD 'root'; --SECURITY ISSUE 
+      GRANT ALL PRIVILEGES ON DATABASE aact_db TO root;
+   END IF;
+END
+$do$

AACT_downloader/docker-entrypoint-initdb.d/010_load_db_dump.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+set -e
+set -x
+
+
+# This file loads the database dump into the postgres database 
+
+dump_path="/mnt/host_data/postgres_data.dmp"
+
+#Double check the postgres user and database are set
+if [[ -z $POSTGRES_USER && -z $POSTGRES_DB ]]; #if either POSTGRES_USER or POSTGRES_DB are empty, throw an error.
+then
+    echo "Missing either the POSTGRESS_USER or the POSTGRES_DB environment variable"
+    exit 4
+else 
+    #restore the DB 
+    pg_restore -e -v -O -x --dbname="$POSTGRES_DB" --username="$POSTGRES_USER" --no-owner "$dump_path"
+fi

AACT_downloader/readme.md

@@ -1 +0,0 @@
-This is what is needed to setup the database.

history_downloader/db_connection.py

@@ -8,7 +8,7 @@ conn = psyco.connect(dbname="aact_db", user="root", host="will-office", password
 
 curse = conn.cursor()
 
-curse.execute("select * FROM http.responses LIMIT 100;")
+curse.execute("select nct_id FROM ctgov.studies LIMIT 10;")
 print(curse.fetchall())
 
 curse.close()