docker-dev: A Shell repository from PaulVanSchayck

Config

Add irods.secrets.cfg file

INGEST_PASSWORD=
INGEST_USER=
INGEST_MOUNT=
LDAP_PASSWORD=
USE_SAMBA=false
DATAVERSE_TOKEN=

Specify the default values and versions for environment vars in the .env file

# iRODS and iRES
ENV_IRODS_VERSION=4.2.4
ENV_IRODS_EXT_CLANG_VERSION=3.8-0
ENV_IRODS_EXT_CLANG_RUNTIME_VERSION=3.8-0

<...>

# Other (used in various containers)
ENV_DOCKERIZE_VERSION=v0.2.0
ENV_FILEBEAT_VERSION=5.2.0

Get external repositories

./rit.sh externals clone

Run

./rit.sh build
./rit.sh down
./rit.sh up

# Special
./rit.sh build --no-cache
./rit.sh build --pull --no-cache     # Attempts to pull a newer version of the upstream base image

NOTE: Please be aware that these containers depend on a running proxy container from docker-common in order to be accessible on their VIRTUAL_HOST address.

Usage of the i command

First build the icommands image:

./i build

To execute a command:

./i [user] ils

Where [user] is a valid iRODS user as defined in irods/bootstrap_irods.sh. You can omit the domain, this is added automatically.

You can also execute commands from the irods-ruleset repository like this:

./i [user] irule -F rules/projects/listContributingProjects.r 
./i [user] irule -F rules/projects/detailsProject.r "*project='P000000001'" "*inherited='false'"
./i [user] imeta add -C /nlmumc/ingest/zones/[collectionName] [attribute] [value] [unit]
etc..

Advanced usage

How to add a new version variable 'FOO' to the project?

Add this entry to .env : ENV_FOO=bar

Add to docker-compose.yml :

# if required at build time
servicename:
  build:
    args:
      ENV_FOO: ${ENV_FOO}

# if required at run time
servicename:
  environment:
    ENV_FOO: ${ENV_FOO}

(applies only to build time) Add to servicename/Dockerfile :
```
ARG ENV_FOO
```
Build the project as usual with ./rit.sh build

iRODS setup responses

Unattended installation of iRODS requires a 'setup_responses' file. This file is different for the iCAT-enabled-server and the iRODS-resource-server. The order of the elements is important!

iCAT-enabled-server (or iCAT provider)

1. IRODS_SERVICE_ACCOUNT_NAME
2. IRODS_SERVICE_ACCOUNT_GROUP
3. IRODS_SERVER_ROLE               # 1. provider, 2. consumer
4. ODBC_DRIVER_FOR_POSTGRES        # 1. PostgreSQL ANSI, 2. PostgreSQL Unicode
5. IRODS_DATABASE_SERVER_HOSTNAME
6. IRODS_DATABASE_SERVER_PORT
7. IRODS_DATABASE_NAME
8. IRODS_DATABASE_USER_NAME
9. CONFIRMATION_ANSWER (yes)
10. IRODS_DATABASE_PASSWORD
11. IRODS_DATABASE_USER_PASSWORD_SALT
12. IRODS_ZONE_NAME
13. IRODS_PORT
14. IRODS_PORT_RANGE_BEGIN
15. IRODS_PORT_RANGE_END
16. IRODS_CONTROL_PLANE_PORT
17. IRODS_SCHEMA_VALIDATION
18. IRODS_SERVER_ADMINISTRATOR_USER_NAME
19. CONFIRMATION_ANSWER (yes)
20. IRODS_SERVER_ZONE_KEY
21. IRODS_SERVER_NEGOTIATION_KEY
22. IRODS_CONTROL_PLANE_KEY
23. IRODS_SERVER_ADMINISTRATOR_PASSWORD
24. IRODS_VAULT_DIRECTORY

iRODS-resource-server (or iCAT consumer)

1. IRODS_SERVICE_ACCOUNT_NAME
2. IRODS_SERVICE_ACCOUNT_GROUP
3. IRODS_SERVER_ROLE               # 1. provider, 2. consumer
4. IRODS_ZONE_NAME
5. ICAT_PROVIDER_HOSTNAME
6. IRODS_PORT
7. IRODS_PORT_RANGE_BEGIN
8. IRODS_PORT_RANGE_END
9. IRODS_CONTROL_PLANE_PORT
10. IRODS_SCHEMA_VALIDATION
11. IRODS_SERVER_ADMINISTRATOR_USER_NAME
12. CONFIRMATION_ANSWER (yes)
13. IRODS_SERVER_ZONE_KEY
14. IRODS_SERVER_NEGOTIATION_KEY
15. IRODS_CONTROL_PLANE_KEY
16. IRODS_SERVER_ADMINISTRATOR_PASSWORD
17. IRODS_VAULT_DIRECTORY

Faker

Create fake ingest zones and project collections

./rit.sh create-ingest-zones
./rit.sh create-project-collections

PaulVanSchayck/docker-dev