diff --git a/.env b/.env
index 388e34bdf45cc2be1f82ce41d2ffddf086d469b6..f38a7aa5d3fc8b4474570b290006dff674d530fd 100644
--- a/.env
+++ b/.env
@@ -5,7 +5,7 @@ EMAIL_ADMIN_USER=dataportal-edirex@ics.muni.cz
ADMIN_PASSWORD=edirex
#PhpMyAdmin
-PMA_HOST=db
+PMA_HOSTS=db, cbioportal-database
PMA_USER=root
PMA_PASSWORD=rootpwd
diff --git a/.gitignore b/.gitignore
index 8c526efce44a9ad86b5d3613ba0d8ddec0574df5..163b0d597ecf3561c387002d6898c44e007ddaae 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
.idea
__pycache__
-venv
\ No newline at end of file
+venv
+log.txt
diff --git a/docker-compose.yml b/docker-compose.yml
index 548b737dfd7e883361a24da9cefa4b4eb190d7bf..ab176fba9ebf1569801aa3710b84710fd177d05a 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,4 +1,4 @@
-version: '3'
+version: '3.5'
services:
dataportal_app:
@@ -14,8 +14,11 @@ services:
- 8080
volumes:
- ./import-data:/import-data
+ networks:
+ - sandboxnet
+
neo4j:
- image: neo4j:3.2
+ image: neo4j:3.5.21
restart: always
container_name: neo4j
env_file:
@@ -26,6 +29,8 @@ services:
volumes:
- neodata:/data/
- ./neo4j-data:/neo4j-data
+ networks:
+ - sandboxnet
# Datahub
@@ -34,12 +39,14 @@ services:
restart: always
env_file:
- .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
volumes:
- mdcache:/var/run/datahub-cache
expose:
- "5000"
+ networks:
+ - sandboxnet
db:
container_name: db
image: mysql:5.7
@@ -50,6 +57,9 @@ services:
- dbdata:/var/lib/mysql
ports:
- "3306:3306"
+ networks:
+ - sandboxnet
+
phpmyadmin:
container_name: phpmyadmin
@@ -59,7 +69,8 @@ services:
restart: always
expose:
- "80"
-
+ networks:
+ - sandboxnet
proxy:
container_name: proxy
restart: always
@@ -76,6 +87,8 @@ services:
- "5000:5000"
links:
- phpmyadmin:phpmyadmin
+ networks:
+ - sandboxnet
portainer:
container_name: portainer
@@ -85,6 +98,15 @@ services:
volumes:
- /var/run/docker.sock:/var/run/docker.sock
- portainer_data:/data
+ networks:
+ - sandboxnet
+
+networks:
+ sandboxnet:
+ name: sandbox_network
+ driver: bridge
+ driver_opts:
+ com.docker.network.driver.mtu: 1442
volumes:
diff --git a/import-data/.gitignore b/import-data/.gitignore
deleted file mode 100644
index e7a210ec7dcb290f7c9247714741a9caee387a8f..0000000000000000000000000000000000000000
--- a/import-data/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-*
-*/
-!.gitignore
\ No newline at end of file
diff --git a/neo4j-seed-dbs/210701-seeddb-2.0.2-trace/graph.tgz b/neo4j-seed-dbs/210701-seeddb-2.0.2-trace/graph.tgz
new file mode 100644
index 0000000000000000000000000000000000000000..57213234e1ac73f8a28da13ffaf64c85d0ba8a89
Binary files /dev/null and b/neo4j-seed-dbs/210701-seeddb-2.0.2-trace/graph.tgz differ
diff --git a/neo4j-seed-dbs/210701-seeddb-2.0.2/graph.tgz b/neo4j-seed-dbs/210701-seeddb-2.0.2/graph.tgz
new file mode 100644
index 0000000000000000000000000000000000000000..108869978cfb47bef3903fc25b35aae3da8f8b9b
Binary files /dev/null and b/neo4j-seed-dbs/210701-seeddb-2.0.2/graph.tgz differ
diff --git a/neo4j-seed-dbs/README.md b/neo4j-seed-dbs/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..37b2997b967eaf929488ac0638768c3963edb27f
--- /dev/null
+++ b/neo4j-seed-dbs/README.md
@@ -0,0 +1,3 @@
+# 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
diff --git a/proxy/Dockerfile b/proxy/Dockerfile
index e56d5eb53973fad644d9c64b4b3fe2ec8485a99e..43279956ce1925ead4c5d486c959c334ea38910b 100644
--- a/proxy/Dockerfile
+++ b/proxy/Dockerfile
@@ -5,9 +5,9 @@ LABEL maintainer="pesa@ics.muni.cz"
RUN apt-get update &&\
apt-get install -y apache2 &&\
apt-get install -y libapache2-mod-auth-mellon &&\
-# apt-get install -y iputils-ping &&\
-# apt-get install -y curl &&\
-# apt-get install -y iproute2 &&\
+ apt-get install -y iputils-ping &&\
+ apt-get install -y curl &&\
+ apt-get install -y iproute2 &&\
apt-get clean
RUN ln -sf /proc/self/fd/1 /var/log/apache2/access.log && \
diff --git a/proxy/conf/proxy.conf b/proxy/conf/proxy.conf
index 76569e4a44d44954934656ed9a2086ace062ed67..404adab598d108dce8285dfaff6f6aa6565b41d0 100644
--- a/proxy/conf/proxy.conf
+++ b/proxy/conf/proxy.conf
@@ -104,7 +104,7 @@ ServerAdmin ${EMAILADMIN}
<Directory "/var/www/html">
AuthType Basic
AuthName "LAS Backend Access"
- AuthUserFile /etc/apache2/conf/.htpasswd
+ AuthUserFile /etc/apache2/.htpasswd
Require valid-user
</Directory>
@@ -114,7 +114,7 @@ ServerAdmin ${EMAILADMIN}
ProxyPassReverse http://phpmyadmin/
AuthType Basic
AuthName "Sandbox Backend Access"
- AuthUserFile /etc/apache2/conf/.htpasswd
+ AuthUserFile /etc/apache2/.htpasswd
Require valid-user
</Location>
@@ -124,7 +124,7 @@ ServerAdmin ${EMAILADMIN}
ProxyPassReverse http://portainer:9000/
AuthType Basic
AuthName "Sandbox Backend Access"
- AuthUserFile /etc/apache2/conf/.htpasswd
+ AuthUserFile /etc/apache2/.htpasswd
Require valid-user
</Location>
@@ -138,7 +138,7 @@ ServerAdmin ${EMAILADMIN}
ProxyPassReverse http://neo4j:7474/browser/
AuthType Basic
AuthName "Sandbox Backend Access"
- AuthUserFile /etc/apache2/conf/.htpasswd
+ AuthUserFile /etc/apache2/.htpasswd
Require valid-user
</Location>
@@ -148,7 +148,7 @@ ServerAdmin ${EMAILADMIN}
ProxyPassReverse http://neo4j:7474/db/data/
AuthType Basic
AuthName "Sandbox Backend Access"
- AuthUserFile /etc/apache2/conf/.htpasswd
+ AuthUserFile /etc/apache2/.htpasswd
Require valid-user
</Location>
diff --git a/proxy/start.sh b/proxy/start.sh
index d59c2a4820addc47a94cad1a7a7cd83adaac6c28..6ec755c8b92e034f17d8940c4d958b42d6711408 100644
--- a/proxy/start.sh
+++ b/proxy/start.sh
@@ -5,7 +5,7 @@ echo "Define FQDN ${HOST}" >/etc/apache2/fqdn.conf
echo "Define EMAILADMIN ${ADMIN_USER}" >> /etc/apache2/fqdn.conf
# 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
/usr/sbin/apache2ctl -D FOREGROUND
diff --git a/user-data-examples/210701-NKIX-data/europdx.zip b/user-data-examples/210701-NKIX-data/europdx.zip
new file mode 100644
index 0000000000000000000000000000000000000000..ed219629ed8c54da8587e732fdb80e5425ddb24f
Binary files /dev/null and b/user-data-examples/210701-NKIX-data/europdx.zip differ
diff --git a/user-data-examples/README.md b/user-data-examples/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..3a2768ebd158397f0d0aeff90c64eb5ff487e69e
--- /dev/null
+++ b/user-data-examples/README.md
@@ -0,0 +1,7 @@
+# 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