Galaxy IE - 502 (Bad Gateway)

Question: Galaxy IE - 502 (Bad Gateway)

2.3 years ago by

Hi all,

I am trying to integrate IE (jupyter and rstudio) into my galaxy server. I am following instructions from here and galaxy wiki page.

My galaxy.ini is:

dynamic_proxy_manage=True
dynamic_proxy_session_map=database/session_map.sqlite
dynamic_proxy_bind_port=8800
dynamic_proxy_bind_ip=0.0.0.0
dynamic_proxy_debug=True
dynamic_proxy_external_proxy=True
dynamic_proxy_prefix=gie_proxy

And Nginx configuration file:

# Global GIE configuration
location /gie_proxy {
    proxy_pass http://localhost:8800/gie_proxy;
    proxy_redirect off;
}

# IPython specific. Other IEs may require their own routes.
location /gie_proxy/ipython/api/kernels {
    proxy_pass http://localhost:8800/gie_proxy/ipython/api/kernels;
    proxy_redirect off;
    proxy_http_version 1.1;
    proxy_set_header Upgrade $http_upgrade;
    proxy_set_header Connection "upgrade";
}

Galaxy log file:

galaxy.web.base.interactive_environments INFO 2016-07-27 14:01:45,141 Starting docker container for IE jupyter with command [docker run --sig-proxy=true -e DEBUG=true -e DEFAULT_CONTAINER_RUNTIME=120 -e "GALAXY_URL=https://galaxy.medunigraz.at" -e "CORS_ORIGIN=https://galaxy.medunigraz.at" -e "GALAXY_WEB_PORT=None" -e "HISTORY_ID=218251f991cbe2f9" -e "NOTEBOOK_PASSWORD=none" -e "DATASET_HID=None" -e "PROXY_PREFIX=/gie_proxy/jupyter" -e "API_KEY=b27201ca5ac4cc7e469c77f13ad05b91" -e "REMOTE_HOST=10.200.168.222" -e "USER_EMAIL=marija.durdevic@medunigraz.at" -d -P   bgruening/docker-jupyter-notebook:16.01]
galaxy.web.base.interactive_environments DEBUG 2016-07-27 14:01:46,982 Container id: 441fbecd4348167ed31536565ddb2a71ece1e9f0e6fc11438f834b07c5aa0523
galaxy.web.base.interactive_environments INFO 2016-07-27 14:01:46,983 Inspecting docker container 441fbecd4348167ed31536565ddb2a71ece1e9f0e6fc11438f834b07c5aa0523 with command [docker inspect 441fbecd4348167ed31536565ddb2a71ece1e9f0e6fc11438f834b07c5aa0523]
galaxy.web.proxy INFO 2016-07-27 14:01:47,052 Attempting to start dynamic proxy process
galaxy.web.proxy DEBUG 2016-07-27 14:01:47,053 Cmd: lib/galaxy/web/proxy/js/lib/main.js --sessions /home/data/galaxy_database/session_map.sqlite --ip 0.0.0.0 --port 8800 --verbose
10.200.168.222 - - [27/Jul/2016:14:01:45 +0200] "GET /plugins/interactive_environments/jupyter/show?dataset_id=d4870b8b64a5b380 HTTP/1.1" 200 - "https://galaxy.medunigraz.at/" "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36"
[pid: 5599|app: 0|req: 30/47] 10.200.168.222 () {46 vars in 1016 bytes} [Wed Jul 27 14:01:45 2016] GET /plugins/interactive_environments/jupyter/show?dataset_id=d4870b8b64a5b380 => generated 1641 bytes in 2058 msecs (HTTP/1.1 200) 2 headers in 73 bytes (1 switches on core 1)

IE is not working and error message is 502 (Bad Gateway).

Can anybody help me with this please?

Regards, Marija

galaxy • 1.8k views

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modified 2.3 years ago by nitesh.turaga ♦ 100 • written 2.3 years ago by marija.durdevic • 10

2.3 years ago by

nitesh.turaga ♦ 100

United States

nitesh.turaga ♦ 100 wrote:

Can you try docker inspect <container> on the image? And post the json?

ADD COMMENT • link modified 2.3 years ago • written 2.3 years ago by nitesh.turaga ♦ 100

Here is the json file when I did docker inspect.

ADD REPLY • link written 2.3 years ago by marija.durdevic • 10

Can you try to npm install again? and maybe see if that process is working properly.

ADD REPLY • link written 2.3 years ago by nitesh.turaga ♦ 100

I fixed my error adding additional code in nginx config:

proxy_http_version 1.1;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection "upgrade";
proxy_redirect off;
proxy_set_header        Host            $host;
proxy_set_header        X-Real-IP       $remote_addr;
proxy_set_header        X-Forwarded-For $proxy_add_x_forwarded_for;

Now I am having issue that dynamic_proxy_manage=True is not working properly. I have to run it manually and then jupyter works:

node galaxy/lib/galaxy/web/proxy/js/lib/main.js --sessions /home/data/galaxy_database/session_map.sqlite --ip 0.0.0.0 --port 8800 --verbose

ADD REPLY • link written 2.3 years ago by marija.durdevic • 10

2.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

iPython for GIEs has been deprecated as of 16.04. Jupyter replaces it and will be fully incorporated into the upcoming 16.07 release.

The change is captured in this prior Q&A C: Ipython on local galaxy - and we will be updating the wiki to reflect the changes/include the link below.

How to set up a GIE: http://galaxy.readthedocs.io/en/master/admin/interactive_environments.html

Hopefully this helps! The development is new, please let us know if you have any issues.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k

Ps: I updated the http://galaxyproject.org wiki to note the changes and to link to the documentation, for others looking for the same help. Please see: https://wiki.galaxyproject.org/Admin/GIEs

ADD REPLY • link written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k

2.3 years ago by

marija.durdevic • 10

marija.durdevic • 10 wrote:

Hi,

Thank you for the answer. I sow changing from iPython to Jupyter and I adapt my nginx. config file:

#Global GIE configuration
location /gie_proxy {
proxy_pass http://localhost:8800/gie_proxy;
proxy_redirect off;
}

# IPython specific. Other IEs may require their own routes.
 location /gie_proxy/jupyter/api/kernels {
proxy_pass http://localhost:8800/gie_proxy/gie_proxy/jupyter/api/kernels;
proxy_redirect off;
proxy_http_version 1.1;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection "upgrade";
}

Everything is the same! I cannot realize where the problem is?

ADD COMMENT • link written 2.3 years ago by marija.durdevic • 10

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