Skip to content
Snippets Groups Projects
Commit 53c707f2 authored by Dalibor Stuchlík's avatar Dalibor Stuchlík
Browse files

Merge branch 'dev' into 'master'

Changes from sandbox1-dev (cBP3.x, new DataPortal)

See merge request !1
parents 7685f0a6 1f0a36b1
No related branches found
No related tags found
1 merge request!1Changes from sandbox1-dev (cBP3.x, new DataPortal)
...@@ -5,7 +5,7 @@ EMAIL_ADMIN_USER=dataportal-edirex@ics.muni.cz ...@@ -5,7 +5,7 @@ EMAIL_ADMIN_USER=dataportal-edirex@ics.muni.cz
ADMIN_PASSWORD=edirex ADMIN_PASSWORD=edirex
#PhpMyAdmin #PhpMyAdmin
PMA_HOST=db PMA_HOSTS=db, cbioportal-database
PMA_USER=root PMA_USER=root
PMA_PASSWORD=rootpwd PMA_PASSWORD=rootpwd
......
.idea .idea
__pycache__ __pycache__
venv venv
\ No newline at end of file log.txt
version: '3' version: '3.5'
services: services:
dataportal_app: dataportal_app:
...@@ -14,8 +14,11 @@ services: ...@@ -14,8 +14,11 @@ services:
- 8080 - 8080
volumes: volumes:
- ./import-data:/import-data - ./import-data:/import-data
networks:
- sandboxnet
neo4j: neo4j:
image: neo4j:3.2 image: neo4j:3.5.21
restart: always restart: always
container_name: neo4j container_name: neo4j
env_file: env_file:
...@@ -26,6 +29,8 @@ services: ...@@ -26,6 +29,8 @@ services:
volumes: volumes:
- neodata:/data/ - neodata:/data/
- ./neo4j-data:/neo4j-data - ./neo4j-data:/neo4j-data
networks:
- sandboxnet
# Datahub # Datahub
...@@ -34,12 +39,14 @@ services: ...@@ -34,12 +39,14 @@ services:
restart: always restart: always
env_file: env_file:
- .env - .env
image: registry.gitlab.ics.muni.cz:443/europdx/datahub/datahub-docker:master image: registry.gitlab.ics.muni.cz:443/europdx/datahub/datahub-docker:sandbox
# mem_limit: 10g # mem_limit: 10g
volumes: volumes:
- mdcache:/var/run/datahub-cache - mdcache:/var/run/datahub-cache
expose: expose:
- "5000" - "5000"
networks:
- sandboxnet
db: db:
container_name: db container_name: db
image: mysql:5.7 image: mysql:5.7
...@@ -50,6 +57,9 @@ services: ...@@ -50,6 +57,9 @@ services:
- dbdata:/var/lib/mysql - dbdata:/var/lib/mysql
ports: ports:
- "3306:3306" - "3306:3306"
networks:
- sandboxnet
phpmyadmin: phpmyadmin:
container_name: phpmyadmin container_name: phpmyadmin
...@@ -59,7 +69,8 @@ services: ...@@ -59,7 +69,8 @@ services:
restart: always restart: always
expose: expose:
- "80" - "80"
networks:
- sandboxnet
proxy: proxy:
container_name: proxy container_name: proxy
restart: always restart: always
...@@ -76,6 +87,8 @@ services: ...@@ -76,6 +87,8 @@ services:
- "5000:5000" - "5000:5000"
links: links:
- phpmyadmin:phpmyadmin - phpmyadmin:phpmyadmin
networks:
- sandboxnet
portainer: portainer:
container_name: portainer container_name: portainer
...@@ -85,6 +98,15 @@ services: ...@@ -85,6 +98,15 @@ services:
volumes: volumes:
- /var/run/docker.sock:/var/run/docker.sock - /var/run/docker.sock:/var/run/docker.sock
- portainer_data:/data - portainer_data:/data
networks:
- sandboxnet
networks:
sandboxnet:
name: sandbox_network
driver: bridge
driver_opts:
com.docker.network.driver.mtu: 1442
volumes: volumes:
......
*
*/
!.gitignore
\ No newline at end of file
File added
File added
# How to use a seed sb from this folder
To use a concrete seed db from this folder: copy the respective graph.tgz into ~/data4reset/neo4j-data/graph.tgz - it will be used in ~/sandbox-api/app/reset.sh and import.sh scripts
...@@ -5,9 +5,9 @@ LABEL maintainer="pesa@ics.muni.cz" ...@@ -5,9 +5,9 @@ LABEL maintainer="pesa@ics.muni.cz"
RUN apt-get update &&\ RUN apt-get update &&\
apt-get install -y apache2 &&\ apt-get install -y apache2 &&\
apt-get install -y libapache2-mod-auth-mellon &&\ apt-get install -y libapache2-mod-auth-mellon &&\
# apt-get install -y iputils-ping &&\ apt-get install -y iputils-ping &&\
# apt-get install -y curl &&\ apt-get install -y curl &&\
# apt-get install -y iproute2 &&\ apt-get install -y iproute2 &&\
apt-get clean apt-get clean
RUN ln -sf /proc/self/fd/1 /var/log/apache2/access.log && \ RUN ln -sf /proc/self/fd/1 /var/log/apache2/access.log && \
......
...@@ -104,7 +104,7 @@ ServerAdmin ${EMAILADMIN} ...@@ -104,7 +104,7 @@ ServerAdmin ${EMAILADMIN}
<Directory "/var/www/html"> <Directory "/var/www/html">
AuthType Basic AuthType Basic
AuthName "LAS Backend Access" AuthName "LAS Backend Access"
AuthUserFile /etc/apache2/conf/.htpasswd AuthUserFile /etc/apache2/.htpasswd
Require valid-user Require valid-user
</Directory> </Directory>
...@@ -114,7 +114,7 @@ ServerAdmin ${EMAILADMIN} ...@@ -114,7 +114,7 @@ ServerAdmin ${EMAILADMIN}
ProxyPassReverse http://phpmyadmin/ ProxyPassReverse http://phpmyadmin/
AuthType Basic AuthType Basic
AuthName "Sandbox Backend Access" AuthName "Sandbox Backend Access"
AuthUserFile /etc/apache2/conf/.htpasswd AuthUserFile /etc/apache2/.htpasswd
Require valid-user Require valid-user
</Location> </Location>
...@@ -124,7 +124,7 @@ ServerAdmin ${EMAILADMIN} ...@@ -124,7 +124,7 @@ ServerAdmin ${EMAILADMIN}
ProxyPassReverse http://portainer:9000/ ProxyPassReverse http://portainer:9000/
AuthType Basic AuthType Basic
AuthName "Sandbox Backend Access" AuthName "Sandbox Backend Access"
AuthUserFile /etc/apache2/conf/.htpasswd AuthUserFile /etc/apache2/.htpasswd
Require valid-user Require valid-user
</Location> </Location>
...@@ -138,7 +138,7 @@ ServerAdmin ${EMAILADMIN} ...@@ -138,7 +138,7 @@ ServerAdmin ${EMAILADMIN}
ProxyPassReverse http://neo4j:7474/browser/ ProxyPassReverse http://neo4j:7474/browser/
AuthType Basic AuthType Basic
AuthName "Sandbox Backend Access" AuthName "Sandbox Backend Access"
AuthUserFile /etc/apache2/conf/.htpasswd AuthUserFile /etc/apache2/.htpasswd
Require valid-user Require valid-user
</Location> </Location>
...@@ -148,7 +148,7 @@ ServerAdmin ${EMAILADMIN} ...@@ -148,7 +148,7 @@ ServerAdmin ${EMAILADMIN}
ProxyPassReverse http://neo4j:7474/db/data/ ProxyPassReverse http://neo4j:7474/db/data/
AuthType Basic AuthType Basic
AuthName "Sandbox Backend Access" AuthName "Sandbox Backend Access"
AuthUserFile /etc/apache2/conf/.htpasswd AuthUserFile /etc/apache2/.htpasswd
Require valid-user Require valid-user
</Location> </Location>
......
...@@ -5,7 +5,7 @@ echo "Define FQDN ${HOST}" >/etc/apache2/fqdn.conf ...@@ -5,7 +5,7 @@ echo "Define FQDN ${HOST}" >/etc/apache2/fqdn.conf
echo "Define EMAILADMIN ${ADMIN_USER}" >> /etc/apache2/fqdn.conf echo "Define EMAILADMIN ${ADMIN_USER}" >> /etc/apache2/fqdn.conf
# set password file # set password file
htpasswd -c -b /usr/local/apache2/conf/.htpasswd administrator ${ADMIN_PASSWORD} htpasswd -c -b /etc/apache2/.htpasswd administrator ${ADMIN_PASSWORD}
# run Apache # run Apache
/usr/sbin/apache2ctl -D FOREGROUND /usr/sbin/apache2ctl -D FOREGROUND
File added
# How to use the user data
(for testing purposes only)
- Unpack the data into /tmp/import folder (thus /tmp/import/europdx/... will be created) - this is the folder where the data from pipeline are normally uploaded
- run ~/sandbox-api/import.sh
- the data should appear in sandbox's dataportal
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment