Open Genes CMS for biologists

This is a headless content management system for managing data in Open Genes database. It's based on Yii 2 framework and also includes DB and migrations.

Dev environment

Build or rebuild backend

sh open-genes-cms.sh build

Build & run backend

sh open-genes-cms.sh up --build

Build & run backend, detached mode (runs in background)

sh open-genes-cms.sh up -d --build

Run backend, detached mode (runs in background)

sh open-genes-cms.sh up

Stop backend, detached mode

sh open-genes-cms.sh down

Run backend, foreground mode

sh open-genes-cms.sh up --no-detach

Build composer dependencies

docker run --rm -v $PWD/app:/app composer install

Add to your /etc/hosts:

127.0.0.1 open-genes.develop cms.open-genes.develop

if you haven't local .env file yet, copy it from .env.sample

cp app/.env.sample app/.env

Open http://cms.open-genes.develop:8081/

The default credentials are admin 123

DB will be available at http://localhost:3307/
user root pass secret

Enter php container:

docker ps

copy hash of opengenes_php container

docker exec -it (container_hash) bash

Inside the php container you can:

• run data parsers: (see more in "parsers" section)

  cd console
  php yii.php  get-data/get-diseases-from-biocomp       [onlyNew default=true] true [geneNcbiIds default null] 1,2,3
  php yii.php get-data/get-gene-expression              [onlyNew default=true] true [geneNcbiIds default null] 1,2,3
  php yii.php get-data/get-gene-info                    [onlyNew default=true] true [geneNcbiIds default null] 1,2,3
  php yii.php get-data/get-go-terms                     [onlyNew default=true] true [geneNcbiIds default null] 1,2,3 [countRows default 2000] 2000
  php yii.php get-data/get-protein-atlas                [onlyNew default=true] true [geneNcbiIds default null] 1,2,3 [geneSearchName default null] BLM
  php yii.php get-data/get-protein-classes              [onlyNew default=true] true [geneNcbiIds default null] 1,2,3 [geneSearchName default null] BLM
  php yii.php get-data/get-orthologs                    [geneIdsAfter default=0]
  ...

• apply db migrations:

  cd console
  php yii.php migrate
  

• create new user for cms:

  cd console
  php yii.php user/create user_name password email role
  

• re-assign roles for user:

  cd console
  php yii.php user/assign user_name role [revokeOtherRoles=]true
  

  The available roles are: admin, editor, contributor, manager

Use xdebug

Build & run with xdebug enabled:

./open-genes-cms.sh up --build xdebug

or ./open-genes-cms.sh up --build xdebug <your ip address> in case your ip address is not automatically detected by open-genes-cms.sh

setup PHP Storm: https://blog.denisbondar.com/post/phpstorm_docker_xdebug

open-genes-cms.sh detects xdebug ip address as follows:

    ip -4 -br addr show | grep "$CLIENT_HOST"

Port 9003 is default one for xdebug v3 and it cannot be changed

Run data parsers:

On a droplet (test/demo/prod) or inside the docker container (dev):

cd console
# parse diseases from http://edgar.biocomp.unibo.it/gene_disease_db/csv_files/
php yii.php  get-data/get-diseases-from-biocomp       [onlyNew default=true] true [geneNcbiIds default null] 1,2,3

# parse gene expression from ncbi
php yii.php get-data/get-gene-expression              [onlyNew default=true] true [geneNcbiIds default null] 1,2,3

# parse gene summary from mygene.com
php yii.php get-data/get-gene-info                    [onlyNew default=true] true [geneNcbiIds default null] 1,2,3

# parse GO-terms from http://api.geneontology.org
php yii.php get-data/get-go-terms                     [onlyNew default=true] true [geneNcbiIds default null] 1,2,3 [countRows default 2000] 2000

# parse full protein info from https://www.proteinatlas.org/search/
php yii.php get-data/get-protein-atlas                [onlyNew default=true] true [geneNcbiIds default null] 1,2,3 [geneSearchName default null] BLM

# parse protein classes from https://www.proteinatlas.org/search/
php yii.php get-data/get-protein-classes              [onlyNew default=true] true [geneNcbiIds default null] 1,2,3 [geneSearchName default null] BLM

# parse orthologs from https://api.ncbi.nlm.nih.gov/
php yii.php get-data/get-orthologs                    [geneIdsAfter default=0]

# examples:
# php yii.php  get-data/get-diseases-from-biocomp - get diseases only for the new genes
# php yii.php  get-data/get-diseases-from-biocomp false - get diseases for ALL genes
# php yii.php  get-data/get-diseases-from-biocomp false 114548,3600 - get diseases only for 114548 and 3600 genes

# php yii.php get-data/get-go-terms - get GO terms only for the new genes
# php yii.php get-data/get-go-terms false 114548,3600 - get GO terms only for 114548 and 3600 genes
...

Run tests

  sh open-genes-cms-test.sh db up
  sh open-genes-cms-test.sh
  sh open-genes-cms-test.sh db down