diff --git a/.gitignore b/.gitignore
index 54df7491deccf4ca47f6741e0b672108ea7c70ee..86349bf9be9da3dc31a3d5e6adad5983979d5c9c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,5 @@ __pycache__/
.idea/
atlas_controller/venv/
atlas_controller/work_dir/
+atlas_server/mongodb/
+microdraw/mariadb/
\ No newline at end of file
diff --git a/atlas_server/README.md b/atlas_server/README.md
deleted file mode 100644
index 0b09d7e97c3973f21dd133eca5da0a64f9d857c6..0000000000000000000000000000000000000000
--- a/atlas_server/README.md
+++ /dev/null
@@ -1,12 +0,0 @@
-# atlas_server
-
-Flask server accepting data and requests from Microdraw, accessing and maintaining the MongoDB and contacting `atlas_controller`.
-Deployment is implemented using docker and docker-compose.
-Perform the following steps to start:
-
-```bash
-docker-compose build
-docker-compose up -d
-```
-
-This will start two docker containers: `uwsgi` hosting the flask application and `nginx` hosting the web server.
\ No newline at end of file
diff --git a/atlas_server/docker-compose.yml b/atlas_server/docker-compose.yml
deleted file mode 100644
index 8397161708a85803d4d5e7131fb0894e57e00047..0000000000000000000000000000000000000000
--- a/atlas_server/docker-compose.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-# docker-compose for atlas_server
-# atlas_server consists of two containers
-# - uwsgi: runs flask app using uwsgi
-# - nginx: runs nginx server
-version: '3'
-
-services:
- uwsgi:
- image: atlas-server-uwsgi
- build: "./uwsgi"
- volumes:
- - "./atlas_server:/src/atlas_server"
-
- nginx:
- image: atlas-server-nginx
- build: "./nginx"
- ports:
- - 5000:80
- depends_on:
- - uwsgi
\ No newline at end of file
diff --git a/atlas_server/nginx/Dockerfile b/atlas_server/nginx/Dockerfile
index 2c0a45369d3f13c300cd19c40817f86e6cf10b91..df323eca9969a60546bd79807fee0f500e0b7994 100644
--- a/atlas_server/nginx/Dockerfile
+++ b/atlas_server/nginx/Dockerfile
@@ -3,7 +3,7 @@ FROM nginx:latest
# Configuration
ENV NGINX_PORT 80
-ENV NGINX_CONFIG app.conf
+ENV NGINX_CONFIG atlas_server.conf
# Port for nginx
EXPOSE ${NGINX_PORT}
diff --git a/atlas_server/nginx/app.conf b/atlas_server/nginx/atlas_server.conf
similarity index 81%
rename from atlas_server/nginx/app.conf
rename to atlas_server/nginx/atlas_server.conf
index d3e4222329b63cd75a826fd04aa65d127368c6fe..38495788a406708f6e6234fca633cbeab2338f48 100644
--- a/atlas_server/nginx/app.conf
+++ b/atlas_server/nginx/atlas_server.conf
@@ -10,6 +10,6 @@ server {
location @app {
include uwsgi_params;
- uwsgi_pass uwsgi:5000;
+ uwsgi_pass atlas-server-uwsgi:5000;
}
}
\ No newline at end of file
diff --git a/atlas_server/atlas_server/__init__.py b/atlas_server/src/__init__.py
similarity index 100%
rename from atlas_server/atlas_server/__init__.py
rename to atlas_server/src/__init__.py
diff --git a/atlas_server/atlas_server/app.py b/atlas_server/src/app.py
similarity index 100%
rename from atlas_server/atlas_server/app.py
rename to atlas_server/src/app.py
diff --git a/atlas_server/atlas_server/config.py b/atlas_server/src/config.py
similarity index 58%
rename from atlas_server/atlas_server/config.py
rename to atlas_server/src/config.py
index 92456199cebe2df6d855f9d95f87f0adb06c5a55..9c212fe3c4e0bdacfacef7fd842049a04d67cc57 100644
--- a/atlas_server/atlas_server/config.py
+++ b/atlas_server/src/config.py
@@ -2,7 +2,7 @@
"""
Configuration for ATLaS server
"""
-DATABASE_HOST = "localhost"
+DATABASE_HOST = "mongodb"
DATABASE_PORT = 27017
DATABASE_NAME = "atlas_ui_db"
-ATLAS_CONTROLLER_URL = "http://localhost:8000/api"
+ATLAS_CONTROLLER_URL = "http://atlas-server-nginx:5000"
diff --git a/atlas_server/atlas_server/db.py b/atlas_server/src/db.py
similarity index 100%
rename from atlas_server/atlas_server/db.py
rename to atlas_server/src/db.py
diff --git a/atlas_server/atlas_server/models.py b/atlas_server/src/models.py
similarity index 100%
rename from atlas_server/atlas_server/models.py
rename to atlas_server/src/models.py
diff --git a/atlas_server/atlas_server/scheduler.py b/atlas_server/src/scheduler.py
similarity index 100%
rename from atlas_server/atlas_server/scheduler.py
rename to atlas_server/src/scheduler.py
diff --git a/atlas_server/atlas_server/static/__init__.py b/atlas_server/src/static/__init__.py
similarity index 100%
rename from atlas_server/atlas_server/static/__init__.py
rename to atlas_server/src/static/__init__.py
diff --git a/atlas_server/atlas_server/static/training/__init__.py b/atlas_server/src/static/training/__init__.py
similarity index 100%
rename from atlas_server/atlas_server/static/training/__init__.py
rename to atlas_server/src/static/training/__init__.py
diff --git a/atlas_server/atlas_server/static/training/config.py b/atlas_server/src/static/training/config.py
similarity index 100%
rename from atlas_server/atlas_server/static/training/config.py
rename to atlas_server/src/static/training/config.py
diff --git a/atlas_server/atlas_server/static/training/train.job.sh b/atlas_server/src/static/training/train.job.sh
similarity index 100%
rename from atlas_server/atlas_server/static/training/train.job.sh
rename to atlas_server/src/static/training/train.job.sh
diff --git a/docker-compose.yml b/docker-compose.yml
new file mode 100644
index 0000000000000000000000000000000000000000..dddbd716cb879da3e03983593e6080742d6db20c
--- /dev/null
+++ b/docker-compose.yml
@@ -0,0 +1,51 @@
+# docker-compose for atlas_server
+# atlas_server consists of two containers
+# - uwsgi: runs flask app using uwsgi
+# - nginx: runs nginx server
+version: '3'
+
+services:
+ atlas-server-uwsgi:
+ image: atlas-server-uwsgi
+ build: "./atlas_server/uwsgi"
+ volumes:
+ - "./atlas_server/src:/src/atlas_server"
+
+ atlas-server-nginx:
+ image: atlas-server-nginx
+ build: "./atlas_server/nginx"
+ ports:
+ - 5000:80
+ depends_on:
+ - atlas-server-uwsgi
+
+ microdraw:
+ image: microdraw
+ build: "./microdraw/"
+ ports:
+ - 5001:80
+ volumes:
+ - "./microdraw/src:/var/www/html/microdraw"
+
+ mongodb:
+ image: mongo
+ restart: always
+ ports:
+ - 27017:27017
+ environment:
+ MONGO_INITDB_ROOT_USERNAME: root
+ MONGO_INITDB_ROOT_PASSWORD: root
+ volumes:
+ - "./atlas_server/mongodb:/data/db"
+
+ mariadb:
+ image: mariadb
+ restart: always
+ ports:
+ - 3306:3306
+ environment:
+ MYSQL_ROOT_PASSWORD: root
+ MYSQL_USER: microdraw
+ MYSQL_PASSWORD: microdraw
+ volumes:
+ - "./microdraw/mariadb:/var/lib/mysql"
\ No newline at end of file
diff --git a/microdraw/Dockerfile b/microdraw/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..1267ea4cf604cbac95d3a019701ef44f795b0362
--- /dev/null
+++ b/microdraw/Dockerfile
@@ -0,0 +1,13 @@
+# Dockerfile for nginx
+FROM nginx:latest
+
+# Configuration
+ENV NGINX_PORT 80
+ENV NGINX_CONFIG microdraw.conf
+
+# Port for nginx
+EXPOSE ${NGINX_PORT}
+
+# Remove default configuration and add our custom configuration
+RUN rm /etc/nginx/conf.d/default.conf
+COPY ${NGINX_CONFIG} /etc/nginx/conf.d
\ No newline at end of file
diff --git a/microdraw/microdraw.conf b/microdraw/microdraw.conf
new file mode 100644
index 0000000000000000000000000000000000000000..4945eaf5c895b3c9e4bd449b1052325012c28628
--- /dev/null
+++ b/microdraw/microdraw.conf
@@ -0,0 +1,6 @@
+# Configuration for microdraw nginx
+
+server {
+ listen 80;
+ root /var/www/html/microdraw;
+}
\ No newline at end of file
diff --git a/microdraw/.gitignore b/microdraw/src/.gitignore
similarity index 100%
rename from microdraw/.gitignore
rename to microdraw/src/.gitignore
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diff --git a/microdraw/lib/openseadragonrgb/.jshintrc b/microdraw/src/lib/openseadragonrgb/.jshintrc
similarity index 100%
rename from microdraw/lib/openseadragonrgb/.jshintrc
rename to microdraw/src/lib/openseadragonrgb/.jshintrc
diff --git a/microdraw/lib/openseadragonrgb/Gulpfile.js b/microdraw/src/lib/openseadragonrgb/Gulpfile.js
similarity index 100%
rename from microdraw/lib/openseadragonrgb/Gulpfile.js
rename to microdraw/src/lib/openseadragonrgb/Gulpfile.js
diff --git a/microdraw/lib/openseadragonrgb/LICENSE b/microdraw/src/lib/openseadragonrgb/LICENSE
similarity index 100%
rename from microdraw/lib/openseadragonrgb/LICENSE
rename to microdraw/src/lib/openseadragonrgb/LICENSE
diff --git a/microdraw/lib/openseadragonrgb/README.md b/microdraw/src/lib/openseadragonrgb/README.md
similarity index 100%
rename from microdraw/lib/openseadragonrgb/README.md
rename to microdraw/src/lib/openseadragonrgb/README.md
diff --git a/microdraw/lib/openseadragonrgb/dist/openseadragonrgb.js b/microdraw/src/lib/openseadragonrgb/dist/openseadragonrgb.js
similarity index 100%
rename from microdraw/lib/openseadragonrgb/dist/openseadragonrgb.js
rename to microdraw/src/lib/openseadragonrgb/dist/openseadragonrgb.js
diff --git a/microdraw/lib/openseadragonrgb/package.json b/microdraw/src/lib/openseadragonrgb/package.json
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rename from microdraw/lib/openseadragonrgb/package.json
rename to microdraw/src/lib/openseadragonrgb/package.json
diff --git a/microdraw/lib/openseadragonrgb/src/rgb.js b/microdraw/src/lib/openseadragonrgb/src/rgb.js
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rename from microdraw/lib/openseadragonrgb/src/rgb.js
rename to microdraw/src/lib/openseadragonrgb/src/rgb.js
diff --git a/microdraw/lib/paper-full-0.10.2.min.js b/microdraw/src/lib/paper-full-0.10.2.min.js
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rename from microdraw/lib/paper-full-0.10.2.min.js
rename to microdraw/src/lib/paper-full-0.10.2.min.js
diff --git a/microdraw/lib/paper-full-0.9.11.min.js b/microdraw/src/lib/paper-full-0.9.11.min.js
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rename from microdraw/lib/paper-full-0.9.11.min.js
rename to microdraw/src/lib/paper-full-0.9.11.min.js
diff --git a/microdraw/lib/paper-full-0.9.25.min.js b/microdraw/src/lib/paper-full-0.9.25.min.js
similarity index 100%
rename from microdraw/lib/paper-full-0.9.25.min.js
rename to microdraw/src/lib/paper-full-0.9.25.min.js
diff --git a/microdraw/microdraw-ws.html b/microdraw/src/microdraw-ws.html
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rename from microdraw/microdraw-ws.html
rename to microdraw/src/microdraw-ws.html
diff --git a/microdraw/microdraw-ws.js b/microdraw/src/microdraw-ws.js
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rename from microdraw/microdraw-ws.js
rename to microdraw/src/microdraw-ws.js
diff --git a/microdraw/microdraw.html b/microdraw/src/microdraw.html
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rename from microdraw/microdraw.html
rename to microdraw/src/microdraw.html
diff --git a/microdraw/microdraw.js b/microdraw/src/microdraw.js
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rename from microdraw/microdraw.js
rename to microdraw/src/microdraw.js
diff --git a/microdraw/microdrawServer.js b/microdraw/src/microdrawServer.js
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rename from microdraw/microdrawServer.js
rename to microdraw/src/microdrawServer.js
diff --git a/microdraw/neurolex-ontology.js b/microdraw/src/neurolex-ontology.js
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rename from microdraw/neurolex-ontology.js
rename to microdraw/src/neurolex-ontology.js
diff --git a/microdraw/package-lock.json b/microdraw/src/package-lock.json
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rename from microdraw/package-lock.json
rename to microdraw/src/package-lock.json
diff --git a/microdraw/package.json b/microdraw/src/package.json
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rename from microdraw/package.json
rename to microdraw/src/package.json
diff --git a/microdraw/php/MyUsers.sql b/microdraw/src/php/MyUsers.sql
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rename from microdraw/php/MyUsers.sql
rename to microdraw/src/php/MyUsers.sql
diff --git a/microdraw/php/base.php.example b/microdraw/src/php/base.php.example
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rename from microdraw/php/base.php.example
rename to microdraw/src/php/base.php.example
diff --git a/microdraw/php/data.php b/microdraw/src/php/data.php
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rename from microdraw/php/data.php
rename to microdraw/src/php/data.php
diff --git a/microdraw/php/microdraw_db.php b/microdraw/src/php/microdraw_db.php
similarity index 100%
rename from microdraw/php/microdraw_db.php
rename to microdraw/src/php/microdraw_db.php
diff --git a/microdraw/php/microdraw_db.sql b/microdraw/src/php/microdraw_db.sql
similarity index 100%
rename from microdraw/php/microdraw_db.sql
rename to microdraw/src/php/microdraw_db.sql
diff --git a/scripts/create_database.sql b/scripts/create_database.sql
index 1e506c72185cf9a4b2d3bcf26202441687d609d2..1b930bbd59f545e15cce863277588e01bf171327 100644
--- a/scripts/create_database.sql
+++ b/scripts/create_database.sql
@@ -1,13 +1,13 @@
--- Create user microdraw, identified my microdraw
-CREATE USER "microdraw"@"localhost" identified by "microdraw";
+-- Create user microdraw, identified my microdraw (not needed if docker-compose is used, just for reference)
+-- CREATE USER "microdraw" identified by "microdraw";
-- Create user database
create database if not exists MyUsers;
use MyUsers;
create table if not exists Users( UserID int auto_increment primary key, Username varchar(65), Password varchar(32), EmailAddress varchar(255));
show tables;
-describe MyUsers;
+describe Users;
-- Create interact database
create database if not exists Interact;
@@ -17,4 +17,4 @@ show tables;
describe KeyValue;
-- Grant all priviliges to microdraw user
-grant all priviliges on *.* to "microdraw"@"localhost" with grant option;
\ No newline at end of file
+grant all on *.* to 'microdraw' with grant option;
\ No newline at end of file