switch to PyMySQL to access DIRT DB (#301)

Computational-Plant-Science · May 31, 2022 · 8220e8c · 8220e8c
1 parent 2fb9442
commit 8220e8c
Show file tree

Hide file tree

Showing 4 changed files with 202 additions and 64 deletions.
diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml
@@ -68,7 +68,12 @@ services:
       - DIRT_MIGRATION_HOST=${DIRT_MIGRATION_HOST}
       - DIRT_MIGRATION_PORT=${DIRT_MIGRATION_PORT}
       - DIRT_MIGRATION_USERNAME=${DIRT_MIGRATION_USERNAME}
-      - DIRT_MIGRATION_DB_CONN_STR=${DIRT_MIGRATION_DB_CONN_STR}
+      # - DIRT_MIGRATION_DB_CONN_STR=${DIRT_MIGRATION_DB_CONN_STR}
+      - DIRT_MIGRATION_DB_HOST=${DIRT_MIGRATION_DB_HOST}
+      - DIRT_MIGRATION_DB_PORT=${DIRT_MIGRATION_DB_PORT}
+      - DIRT_MIGRATION_DB_USER=${DIRT_MIGRATION_DB_USER}
+      - DIRT_MIGRATION_DB_DATABASE=${DIRT_MIGRATION_DB_DATABASE}
+      - DIRT_MIGRATION_DB_PASSWORD=${DIRT_MIGRATION_DB_PASSWORD}
     command: ["/code/scripts/wait-for-postgres.sh", "postgres", "python", "manage.py", "runserver", "0.0.0.0:3000"]
     depends_on:
       - postgres
@@ -176,7 +181,12 @@ services:
       - DIRT_MIGRATION_HOST=${DIRT_MIGRATION_HOST}
       - DIRT_MIGRATION_PORT=${DIRT_MIGRATION_PORT}
       - DIRT_MIGRATION_USERNAME=${DIRT_MIGRATION_USERNAME}
-      - DIRT_MIGRATION_DB_CONN_STR=${DIRT_MIGRATION_DB_CONN_STR}
+      # - DIRT_MIGRATION_DB_CONN_STR=${DIRT_MIGRATION_DB_CONN_STR}
+      - DIRT_MIGRATION_DB_HOST=${DIRT_MIGRATION_DB_HOST}
+      - DIRT_MIGRATION_DB_PORT=${DIRT_MIGRATION_DB_PORT}
+      - DIRT_MIGRATION_DB_USER=${DIRT_MIGRATION_DB_USER}
+      - DIRT_MIGRATION_DB_DATABASE=${DIRT_MIGRATION_DB_DATABASE}
+      - DIRT_MIGRATION_DB_PASSWORD=${DIRT_MIGRATION_DB_PASSWORD}
     healthcheck:
       test: celery -A plantit status | grep "OK"
       interval: 60s
@@ -253,7 +263,12 @@ services:
       - DIRT_MIGRATION_HOST=${DIRT_MIGRATION_HOST}
       - DIRT_MIGRATION_PORT=${DIRT_MIGRATION_PORT}
       - DIRT_MIGRATION_USERNAME=${DIRT_MIGRATION_USERNAME}
-      - DIRT_MIGRATION_DB_CONN_STR=${DIRT_MIGRATION_DB_CONN_STR}
+      # - DIRT_MIGRATION_DB_CONN_STR=${DIRT_MIGRATION_DB_CONN_STR}
+      - DIRT_MIGRATION_DB_HOST=${DIRT_MIGRATION_DB_HOST}
+      - DIRT_MIGRATION_DB_PORT=${DIRT_MIGRATION_DB_PORT}
+      - DIRT_MIGRATION_DB_USER=${DIRT_MIGRATION_DB_USER}
+      - DIRT_MIGRATION_DB_DATABASE=${DIRT_MIGRATION_DB_DATABASE}
+      - DIRT_MIGRATION_DB_PASSWORD=${DIRT_MIGRATION_DB_PASSWORD}
     healthcheck:
       test: celery -A plantit status | grep "OK"
       interval: 60s

diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml
@@ -72,7 +72,12 @@ services:
       - DIRT_MIGRATION_HOST=${DIRT_MIGRATION_HOST}
       - DIRT_MIGRATION_PORT=${DIRT_MIGRATION_PORT}
       - DIRT_MIGRATION_USERNAME=${DIRT_MIGRATION_USERNAME}
-      - DIRT_MIGRATION_DB_CONN_STR=${DIRT_MIGRATION_DB_CONN_STR}
+      # - DIRT_MIGRATION_DB_CONN_STR=${DIRT_MIGRATION_DB_CONN_STR}
+      - DIRT_MIGRATION_DB_HOST=${DIRT_MIGRATION_DB_HOST}
+      - DIRT_MIGRATION_DB_PORT=${DIRT_MIGRATION_DB_PORT}
+      - DIRT_MIGRATION_DB_USER=${DIRT_MIGRATION_DB_USER}
+      - DIRT_MIGRATION_DB_DATABASE=${DIRT_MIGRATION_DB_DATABASE}
+      - DIRT_MIGRATION_DB_PASSWORD=${DIRT_MIGRATION_DB_PASSWORD}
     command: ["daphne", "-b", "0.0.0.0", "-p", "8000", "plantit.asgi:application"]
     networks:
       - ngnix_network
@@ -154,7 +159,12 @@ services:
       - DIRT_MIGRATION_HOST=${DIRT_MIGRATION_HOST}
       - DIRT_MIGRATION_PORT=${DIRT_MIGRATION_PORT}
       - DIRT_MIGRATION_USERNAME=${DIRT_MIGRATION_USERNAME}
-      - DIRT_MIGRATION_DB_CONN_STR=${DIRT_MIGRATION_DB_CONN_STR}
+      # - DIRT_MIGRATION_DB_CONN_STR=${DIRT_MIGRATION_DB_CONN_STR}
+      - DIRT_MIGRATION_DB_HOST=${DIRT_MIGRATION_DB_HOST}
+      - DIRT_MIGRATION_DB_PORT=${DIRT_MIGRATION_DB_PORT}
+      - DIRT_MIGRATION_DB_USER=${DIRT_MIGRATION_DB_USER}
+      - DIRT_MIGRATION_DB_DATABASE=${DIRT_MIGRATION_DB_DATABASE}
+      - DIRT_MIGRATION_DB_PASSWORD=${DIRT_MIGRATION_DB_PASSWORD}
     healthcheck:
       test: celery -A plantit status | grep "OK"
       interval: 60s
@@ -233,7 +243,12 @@ services:
       - DIRT_MIGRATION_HOST=${DIRT_MIGRATION_HOST}
       - DIRT_MIGRATION_PORT=${DIRT_MIGRATION_PORT}
       - DIRT_MIGRATION_USERNAME=${DIRT_MIGRATION_USERNAME}
-      - DIRT_MIGRATION_DB_CONN_STR=${DIRT_MIGRATION_DB_CONN_STR}
+      # - DIRT_MIGRATION_DB_CONN_STR=${DIRT_MIGRATION_DB_CONN_STR}
+      - DIRT_MIGRATION_DB_HOST=${DIRT_MIGRATION_DB_HOST}
+      - DIRT_MIGRATION_DB_PORT=${DIRT_MIGRATION_DB_PORT}
+      - DIRT_MIGRATION_DB_USER=${DIRT_MIGRATION_DB_USER}
+      - DIRT_MIGRATION_DB_DATABASE=${DIRT_MIGRATION_DB_DATABASE}
+      - DIRT_MIGRATION_DB_PASSWORD=${DIRT_MIGRATION_DB_PASSWORD}
     healthcheck:
       test: celery -A plantit status | grep "OK"
       interval: 60s

diff --git a/dockerfiles/plantit/requirements.txt b/dockerfiles/plantit/requirements.txt
@@ -50,4 +50,5 @@ statsmodels==0.13.1
 furo
 pycyapi
 aiomysql
-databases[aiomysql]
+databases[aiomysql]
+PyMySQL