From 9a471997286601ea67242de58b5d027f6e8f677d Mon Sep 17 00:00:00 2001
From: youainti <youainti@protonmail.com>
Date: Tue, 15 Feb 2022 21:22:45 -0800
Subject: [PATCH] Moved the db_connection to another location, updated
 gitignore to avoid commiting data. DockerCompose is setting up properly.

---
 .gitignore                                    |  2 +-
 PostgressDocker/docker-compose.yaml           | 27 ++++++++++++-------
 .../db_connection.py                          |  2 +-
 3 files changed, 20 insertions(+), 11 deletions(-)
 rename {PostgressDocker => downloader}/db_connection.py (55%)

diff --git a/.gitignore b/.gitignore
index 2dfd14c..e934503 100644
--- a/.gitignore
+++ b/.gitignore
@@ -180,4 +180,4 @@ Manifest.toml
 
 
 ###### Custom #####
-/20220201_clinical_trials.zip
+**/host_data/*_clinical_trials/
diff --git a/PostgressDocker/docker-compose.yaml b/PostgressDocker/docker-compose.yaml
index 8c62f3a..1ebe243 100644
--- a/PostgressDocker/docker-compose.yaml
+++ b/PostgressDocker/docker-compose.yaml
@@ -1,5 +1,15 @@
 version: '3'
 
+volumes:
+  aact_pg_database: #This is to hold the database.
+  aact_helpful_files: #This is to hold files that need accessed by both pgadmin and postgres. I honestly expect it to usually be empty.
+    driver: local
+    driver_opts:
+      type: 'none'
+      o: 'bind'
+      device: /home/will/research/ClinicalTrialsDataProcessing/PostgressDocker/host_data/
+      #change this path to match the path you are holding the dump file in
+
 services:
   aact:
     container_name: aact_db
@@ -15,8 +25,11 @@ services:
       #pull in a single file
       #- $HOME/research/ClinicalTrialsDataProcessing/PostgressDocker/infile:/infile
       #add a storage volumes
-      - aact_pg_database:/var/lib/postgresql/
-      - aact_helpful_files:/mnt/host_data #the :ro give read only permisions
+      - aact_pg_database:/var/lib/postgresql/ # this is the database that persits between uses
+      - aact_helpful_files:/mnt/host_data #use :ro # to give read only permisions
+    #entrypoint:
+      #none yet
+      #- echo "test" > /test.touched
 
   pgadmin:
     container_name: pgadmin4_webservice
@@ -28,13 +41,9 @@ services:
     ports:
       - "5050:80"
     volumes: #host:container is the format.
-      #add a storage volumes
-      - aact_helpful_files:/mnt/host_data #addin :ro to the end would give read only permissions
-
-volumes:
-  aact_pg_database: #This is to hold the database.
-  aact_helpful_files: #This is to hold files that need accessed by both pgadmin and postgres. I honestly expect it to usually be empty.
+      #The volume with server login information.
+      - ./pgadmin4/servers.json:/pgadmin4/servers.json
 
 #Checklist for production
 # uncomment restart: always in both services.
-# add a python environment to run data collection
\ No newline at end of file
+# add a python environment to run data collection etc
\ No newline at end of file
diff --git a/PostgressDocker/db_connection.py b/downloader/db_connection.py
similarity index 55%
rename from PostgressDocker/db_connection.py
rename to downloader/db_connection.py
index 5f36471..e5df6fc 100644
--- a/PostgressDocker/db_connection.py
+++ b/downloader/db_connection.py
@@ -1,6 +1,6 @@
 import psycopg2 as psyco
 
-conn = psyco.connect(dbname="aact_db", user="access", host="localhost", password="access")
+conn = psyco.connect(dbname="aact_db", user="admin", host="localhost", password="root")
 
 curse = conn.cursor()