Set up docker for genenetwork #29

npklein · 2019-07-29T14:00:28Z

No description provided.

…ckerfiles

Neleor

Some stuff needs to be changed before it can be merged (see comments). Others I have to check myself before I can approve a merge.

config/domain.js

config/local.js

views/homepage.ejs

data_scripts/parseTermsToElastic.js

data_scripts/parseGenesToElastic.js

Neleor · 2019-07-29T15:08:06Z

data_scripts/parseGenesToElastic.js

@@ -3,11 +3,11 @@ var level = require('level')
 var elasticsearch = require('elasticsearch')

 var client = new elasticsearch.Client({
-    host: 'localhost:9200',


this *might break current GN

Should I change it back? Without this change docker won't work

I will test this locally and get back to you

Neleor · 2019-07-29T15:08:22Z

data_scripts/createElasticIndex.js

@@ -2,7 +2,7 @@ var elasticsearch = require('elasticsearch')
 var async = require('async')

 var CLIENT = new elasticsearch.Client({
-    host: 'localhost:9200',


this *might break current GN

Should I change it back? Without this change docker won't work

I will test this locally and get back to you

Neleor · 2019-07-29T15:11:17Z

api/controllers/requestHandlers/handlePathwayAnalysis.js

@@ -3,7 +3,12 @@ var dbutil = require('../utils/dbutil')
 var genedesc = require('../utils/genedesc')
 var quicksortobj = require('../utils/quicksortobj')

-var Queue = kue.createQueue() // this does not create a new queue, it's just redis access


need to test if this would break anything

Should I change it back? Without this change docker won't work

This breaks running locally, will investigate how to make it work in both instances

royoelen

will need to do some testing and get back to you

sidohaakma · 2019-10-01T18:47:31Z

Dockerfile

+COPY . .
+
+# Make port 80 available to the world outside this container
+EXPOSE 80


do not use expose in the dockerfile only specify it in the docker-compose file

sidohaakma · 2019-10-01T18:48:04Z

docker-compose.yml

+  web:
+    # replace username/repo:tag with your name and image details
+    image: metabrainnetwork
+    build: ./


remove this, use only the image tag

sidohaakma · 2019-10-01T18:48:12Z

docker-compose.yml

+    build: ./
+    ports:
+      - "1337:1337"
+      - "4000:85"


remove - "4000:85", only expose 1337

sidohaakma · 2019-10-01T18:50:07Z

docker-compose.yml

+      - ELASTICSEARCH_HOST=elasticsearch
+  redis:
+    image: redis
+    ports:


Use expose instead of the port binding. The expose variant will only make the port available within the docker-compose stack itself.

sidohaakma · 2019-10-01T18:50:34Z

docker-compose.yml

+      - "6379:6379"
+  elasticsearch:
+    image: elasticsearch:2.4
+    ports:


Use expose instead of the port binding. The expose variant will only make the port available within the docker-compose stack itself.

sidohaakma · 2019-10-01T18:50:47Z

docker-compose.yml

+      - "/data:/data"
+  pwasserver:
+    image: pwasserver
+    build: ./docker/pwasServer/


Use image tags

sidohaakma · 2019-10-01T18:51:19Z

docker/predictionServer/Dockerfile

+COPY . .
+
+# Make port 80 available to the world outside this container
+EXPOSE 80


Remove EXPOSE 80 from dockerfile, only specify ports in docker-compose with expose

sidohaakma · 2019-10-01T18:51:40Z

docker-compose.yml

+      - 9300:9300
+  predictionserver:
+    image: predictionserver
+    build: ./docker/predictionServer


Use image tags

sidohaakma

Maybe create another repository for the metabrain app? Check comments on code lines as well.

npklein added 24 commits June 11, 2019 13:15

update package.json to get it to install

f64227a

Merge branch 'master' of https://github.com/molgenis/molgenis-app-gen…

5a67a7a

…enetwork

add docker files

a97b231

fixes to make page open, api not working yet

3d6dc5d

need host: redis otherwise will try to connect to localhost

c21fde7

add elasticsearch

a4b3adf

domain should point to nothing

c0fc4f7

update lcoal for metabrain

4cb5a38

add scripts for keeping

500b544

remove min to work locally

14d8eaf

session also hast o use redis as host

7f7f934

elasticsearch is on the network elasticsearch, not localhost

01bf6d4

change network to elasticsearch

0c3faab

update docker-compose for connecting elasticsearch to webapp container

26a3484

fix typo

f905fb6

networks was not necesarry

112f739

separate Dockerfile for prediction server and pwas server

3d2472e

fill elasticsearch with entrypoint script

b3a1a47

remove extra CMD lines and add entrypoint script

72bc6a5

add fake gene pred. scores

59d5fe5

remove networks, add predictionserver and pwasserver

62ec3fd

connect to redis container and use local node path

cd169d7

upgrade package (not sure if necesasrry)

ee9f746

configs have to be in same directory as pwas and prediction server Do…

e450091

…ckerfiles

npklein changed the title ~~Docker~~ Set up docker for genenetwork Jul 29, 2019

Neleor suggested changes Jul 29, 2019

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npklein added 4 commits July 30, 2019 09:52

update

720b580

add min back

551f94a

add domain back

8013ee7

change back to genenetwork locations

44460b2

npklein added 2 commits July 30, 2019 11:00

change back to genenetwork

acec6fa

chagne to genenetwork

a281665

royoelen reviewed Jul 30, 2019

View reviewed changes

sidohaakma reviewed Oct 1, 2019

View reviewed changes

docker-compose.yml

build: ./

ports:

- "1337:1337"

- "4000:85"

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remove - "4000:85", only expose 1337

sidohaakma reviewed Oct 1, 2019

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docker-compose.yml

- "/data:/data"

pwasserver:

image: pwasserver

build: ./docker/pwasServer/

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sidohaakma Oct 1, 2019

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Use image tags

sidohaakma reviewed Oct 1, 2019

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docker-compose.yml

- 9300:9300

predictionserver:

image: predictionserver

build: ./docker/predictionServer

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sidohaakma Oct 1, 2019

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Use image tags

sidohaakma requested changes Oct 1, 2019

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Set up docker for genenetwork #29

Set up docker for genenetwork #29

npklein commented Jul 29, 2019

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