irods-capability-automated-ingest 0.1.0

Implement filesystem scanners and landing zones

iRODS Automated Ingest Framework

The automated ingest framework gives iRODS an enterprise solution that solves two major use cases: getting existing data under management and ingesting incoming data hitting a landing zone.

Based on the Python iRODS Client and RedisQueue, this framework can scale up to match the demands of data coming off instruments, satellites, or parallel filesystems.

The example diagrams below show a filesystem scanner and a landing zone.

Usage options

available --event_handler methods

method	effect	default
pre_data_obj_create	user-defined python	none
post_data_obj_create	user-defined python	none
pre_data_obj_modify	user-defined python	none
post_data_obj_modify	user-defined python	none
pre_coll_create	user-defined python	none
post_coll_create	user-defined python	none
as_user	takes action as this iRODS user	authenticated user
target_path	set mount path on the irods server which can be different from client mount path	client mount path
to_resource	defines target resource request of operation	as provided by client environment
operation	defines the mode of operation	Operation.REGISTER_SYNC

operation mode

operation	new files	updated files
Operation.REGISTER_SYNC (default)	registers in catalog	updates size in catalog
Operation.REGISTER_AS_REPLICA_SYNC	registers first or additional replica	updates size in catalog
Operation.PUT	copies file to target vault, and registers in catalog	no action
Operation.PUT_SYNC	copies file to target vault, and registers in catalog	copies entire file again, and updates catalog
Operation.PUT_APPEND	copies file to target vault, and registers in catalog	copies only appended part of file, and updates catalog

--event_handler usage examples can be found in the examples directory.

Deployment

Basic: manual redis, rq-scheduler, pip

setting up irods environment file

redis

https://redis.io/topics/quickstart

start redis

redis-server

virtualenv

pip3 install virtualenv

You may need to upgrade pip

pip3 install --upgrade pip

virtualenv rodssync

source rodssync/bin/activate

clone repo

rq

• rq
• rq-scheduler
• python-redis-lock

pip install rq python-redis-lock rq-scheduler

make sure you are in the repo for the following commands

cd <repo dir>

start rqscheduler

rqscheduler -i 1

start rq worker(s)

rq worker restart path file

or

for i in {1..<n>}; do rq worker restart path file & done

job monitoring

pip install rq-dashboard

rq-dashboard

or alternately, just use rq to monitor progress

rq info

irods prc

pip install python-irodsclient==0.8.0

tested with python 3.4+

run test

The tests should be run without running rq workers.

python -m irods_capability_automated_ingest.test.test_irods_sync

start

python -m irods_capability_automated_ingest.irods_sync start <local_dir> <collection> [-i <restart interval>] [ --event_handler <module name> ] [ --job_name <job name> ]

If -i is not present, then only sync once

list restarting jobs

python -m irods_capability_automated_ingest.irods_sync list

stop

python -m irods_capability_automated_ingest.irods_sync stop <job name>

Intermediate: dockerize, manually config

/tmp/event_handler.py

from irods_capability_automated_ingest.core import Core
from irods_capability_automated_ingest.utils import Operation

class event_handler(Core):

    @staticmethod
    def target_path(session, target, path, **options):
        return "/tmp/host" + path

icommands.env

IRODS_PORT=1247
IRODS_HOST=172.17.0.1
IRODS_USER_NAME=rods
IRODS_ZONE_NAME=tempZone
IRODS_PASSWORD=rods

docker run --rm --name some-redis -d redis:4.0.8

docker run --rm --link some-redis:redis irods_rq-scheduler:0.1.0 worker -u redis://redis:6379/0 restart path file

docker run --rm --link some-redis:redis -v /tmp/host/event_handler.py:/event_handler.py irods_capability_automated_ingest:0.1.0 start /data /tempZone/home/rods/data --redis_host=redis --event_handler=event_handler

docker run --rm --link some-redis:redis --env-file icommands.env -v /tmp/host/data:/data -v /tmp/host/event_handler.py:/event_handler.py irods_rq:0.1.0 worker -u redis://redis:6379/0 restart path file

Advanced: kubernetes

This does not assume that your iRODS installation is in kubernetes.

install minikube and helm

set memory to at least 8g and cpu to at least 4

minikube start --memory 8192 --cpus 4

enable ingress on minikube

minikube addons enable ingress

mount host dirs

This is where you data and event handler. In this setup, we assume that your event handler is under /tmp/host/event_handler and you data is under /tmp/host/data. We will mount /tmp/host/data into /host/data in minikube which will mount /host/data into /data in containers,

/tmp/host/data -> minikube /host/data -> container /data.

and similarly,

/tmp/host/event_handler -> minikube /host/event_handler -> container /event_handler. Your setup may differ.

mkdir /tmp/host/event_handler
mkdir /tmp/host/data

/tmp/host/event_handler/event_handler.py

from irods_capability_automated_ingest.core import Core
from irods_capability_automated_ingest.utils import Operation

class event_handler(Core):

    @staticmethod
    def target_path(session, target, path, **options):
        return "/tmp/host" + path

minikube mount /tmp/host:/host

enable incubator

helm repo add incubator https://kubernetes-charts-incubator.storage.googleapis.com/

build local docker images (optional)

If you want to use local docker images, you can build the docker images into minikube as follows:

fish

eval (minikube docker-env)

bash

eval $(minikube docker-env)

cd <repo>/docker
docker build . -t irods_capability_automated_ingest:0.1.0

cd <repo>/docker/rq
docker build . -t irods_rq:0.1.0

cd <repo>/docker/rq-scheduler
docker build . -t irods_rq-scheduler:0.1.0

update irods configurations

Set configurations in <repo>/kubernetes/chart/values.yaml or --set command line argument.

install chart

cd <repo>/kubernetes/chart
helm dependency update

We call our release icai.

cd <repo>/kubernetes
helm install ./chart --name icai

scale rq workers

kubectl scale deployment.apps/icai-rq-deployment --replicas=<n>

access by REST API (recommended)

submit job

fish

curl -XPUT "http://"(minikube ip)"/job/<job name>?source=/data&target=/tempZone/home/rods/data&interval=<interval>&event_handler=event_handler"

bash

curl -XPUT "http://$(minikube ip)/job/<job name>?source=/data&target=/tempZone/home/rods/data&interval=<interval>&event_handler=event_handler"

fish

curl -XPUT "http://"(minikube ip)"/job?source=/data&target=/tempZone/home/rods/data&interval=<interval>&event_handler=event_handler"

bash

curl -XPUT "http://$(minikube ip)/job?source=/data&target=/tempZone/home/rods/data&interval=<interval>&event_handler=event_handler"

list job

fish

curl -XGET "http://"(minikube ip)"/job"

bash

curl -XGET "http://$(minikube ip)/job"

delete job

fish

curl -XDELETE "http://"(minikube ip)"/job/<job name>"

bash

curl -XDELETE "http://$(minikube ip)/job/<job name>"

access by command line (not recommended)

submit job

kubectl run --rm -i icai --image=irods_capability_automated_ingest:0.1.0 --restart=Never -- start /data /tempZone/home/rods/data -i <interval> --event_handler=event_handler --job_name=<job name> --redis_host icai-redis-master

list job

kubectl run --rm -i icai --image=irods_capability_automated_ingest:0.1.0 --restart=Never -- list --redis_host icai-redis-master

delete job

kubectl run --rm -i icai --image=irods_capability_automated_ingest:0.1.0 --restart=Never -- stop <job name> --redis_host icai-redis-master

install logging tool

Install chart with set log_level to INFO.

helm del --purge icai

cd <repo>/kubernetes
helm install ./chart --set log_level=INFO --name icai

set parameters for elasticsearch

minikube ssh 'echo "sysctl -w vm.max_map_count=262144" | sudo tee -a /var/lib/boot2docker/bootlocal.sh'
minikube stop
minikube start

cd <repo>/kubernetes
helm install ./elk --name icai-elk

Grafana

look for service port

kubectl get svc icai-elk-grafana

forward port

kubectl port-forward svc/icai-elk-grafana 8000:80

If --set grafana.adminPassword="" system generates a random password, lookup admin password

kubectl get secret --namespace default icai-elk-grafana -o jsonpath="{.data.admin-password}" | base64 --decode ; echo

open browser url localhost:8000

login with username admin and password admin click on icai dashboard

Kibana

Uncomment kibana sections in the yaml files under the <repo>/kubernetes/elk directory

look for service port

kubectl get svc icai-elk-kibana

forward port

kubectl port-forward svc/icai-elk-kibana 8000:443

open browser url localhost:8000