HEG-Arc/MiCorr - Githubissues

TO START MICORR IN LOCAL MODE

FIRST STEP TO ENSURE GOOD EOL CHARACTERS FOR GIT

On windows 10:

Modify the global gitconfig file

Go to your gitconfig file: C:\Users\<username>\.gitconfig
Open it with notepad++ and add the following options:
```
[core]
eol = lf
autocrlf = false
```
Save file and exit.

Modify the system gitconfig file

Go to your gitconfig file:
\mingw64\etc\gitconfig
Open it with notepad++ as administrator and add the following options:
```
[core]
eol = lf
autocrlf = false
```
Save file and exit

PULL THE MICORR PROJECT FROM THE GIT REPOSITORY

Actual adress of MiCorr git repository https://github.com/HEG-Arc/MiCorr.git

SET THE DOCKER COMPOSE FILE FOR DEV VERSION

Those steps shall always be done when you enter in your project

Set the var for the docker compose file:
```
source local.sh
```
Verify that the compose file is properly set up:
```
echo $COMPOSE_FILE
```
That command should output the following in the terminal:

dev.yml

TO BUILD YOUR MICORR PROJECT

Create new .env file from env.example into project root:
```
cp env.example .env
```
Cleanup of everything (containers, volumes and networks) to start a clean project:

DO NOT USE THIS COMMAND IF YOU WANT TO KEEP THE DATAS IN YOUR DATABASES

docker-compose down --rmi all -v --remove-orphans

Add the postgres password into the dev.yml file:

Open .env file and search for POSTGRES_PASSWORD variable

Add to dev.yml into services under the postgres container the environment variable - POSTGRES_PASSWORD=mysecretpass as follow:

services:
postgres:
build: ./compose/postgres
volumes:
- postgres_data:/var/lib/postgresql/data
- ./data/psql-backup:/backups
environment:
- POSTGRES_USER=micorr
- POSTGRES_PASSWORD=mysecretpass    # <= THIS IS WHERE YOU MUST ADD THE VALUE
ports:
- "5432:5432"

Build and start your containers with the following shell command:
```
docker-compose up -d
```

ALTERNATIVE (to use only if the code of the containers has been changed):

Force the build of your containers before starting them with the following shell command:

docker-compose up -d --build

Verify that all your containers are up and running:

docker ps

This command shall output a similar list (the names and ports of the containers should be the same):

CONTAINER ID   IMAGE                        ...   STATUS          PORTS                                                                                            NAMES
eaf1a1d62287   81bc6fbcaf09                 ...   Up 55 minutes   0.0.0.0:8080->8080/tcp, :::8080->8080/tcp                                                        micorr_node_1
8852aac1d306   efeea1848592                 ...   Up 55 minutes   0.0.0.0:7474->7474/tcp, :::7474->7474/tcp, 7473/tcp, 0.0.0.0:7687->7687/tcp, :::7687->7687/tcp   micorr_neo4j_1
4a4cc9b23f0e   d8dc93872711                 ...   Up 55 minutes   0.0.0.0:5432->5432/tcp, :::5432->5432/tcp                                                        micorr_postgres_1
7129958fc202   9ebd8a2d29ba                 ...   Up 2 seconds    0.0.0.0:8000->8000/tcp, :::8000->8000/tcp                                                        micorr_django_1
153bc1d7e39d   blacktop/elasticsearch:2.4   ...   Up 55 minutes   0.0.0.0:9200->9200/tcp, :::9200->9200/tcp, 9300/tcp                                              micorr_elast

If one container is not running, you can start it with the following command:

docker compose start <container name>

If the container is not starting after this command, restart from step 4: Cleanup of everything.

Copy the all the backups into your root:

backup_2021_07_15T13_58_16.sql
micorr-media-2021-07-15.tar.gz
graphdb_20210715_152917.dump

Stop django container:
```
docker compose stop django
```
Copy the postgres backup into the volume of postgres ./data/psql-backup/:
```
cp backup_2021_07_15T13_58_16.sql ./data/psql-backup/backup_2021_07_15T13_58_16.sql
```
Check that the backup is present in the postgres container with:

docker compose exec postgres list-backups

The command shall return a list as the following one with the name of the backup backup_2021_07_15T13_58_16.sql present:

listing available backups
-------------------------
backup_2021_07_15T13_58_16.sql  backup_2021_07_15T15_19_44.sql

De-tar the media archive:

tar -xzvf micorr-media-2021-07-15.tar.gz

A media directory at ./micorr/media was created with all the resources inside the .tar file.

Restore the postgres db with the backup:

docker compose exec postgres restore backup_2021_07_15T13_58_16.sql

Stop the neo4j container
```
docker compose stop neo4j
```
Copy the no4j initial data dump into the neo4j compose files:
```
cp graphdb_20210715_152917.dump compose/neo4j/initial_neo4j-admin.dump
```
The neo4j db dockerfile will copy the file named initial_neo4j-admin.dump into the neo4j container and the script bootstrap_data.sh will initialize the neo4j db with the content of initial_neo4j-admin.dump.

Rebuild the neo4j container

docker compose build neo4j

The terminal shall indicate the copy of initial_neo4j-admin.dump into the neo4j container:

[+] Building 5.8s (10/10) FINISHED
...
=> [1/4] FROM docker.io/library/neo4j:4.0.11@sha256:2b8d71eb2e6e6e162a723c733c1c6a27a62c54774108523a5a4c15cf9aa55c19   0.0s
=> [internal] load build context                                                                                       1.0s
=> => transferring context: 26.08MB                                                                                    1.0s
=> CACHED [2/4] COPY backup.sh bootstrap_data.sh initial_neo4j-admin*.dump /                                           0.0s
=> CACHED [3/4] COPY apoc-4.0.0.18-all.jar /var/lib/neo4j/plugins                                                      0.0s
=> CACHED [4/4] RUN chmod +x /backup.sh                                                                                0.0s
...

Rename the initial_neo4j-admin.dump from the compose/neo4j/ directory into no_initial_neo4j-admin.dump to prevent the rewrite of neo4j db contents at container startup
```
mv compose/neo4j/initial_neo4j-admin.dump compose/neo4j/no_initial_neo4j-admin.dump
```
Restart all containers with
```
docker compose up -d
```

HEG-Arc / MiCorr

readme

TO START MICORR IN LOCAL MODE