Implement filesystem scanners and landing zones
Project description
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
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