Administration

Automated Ingest

June 25-28, 2019

iRODS User Group Meeting 2019

Utrecht, Netherlands

Administration

Automated Ingest

Terrell Russell, Ph.D.

@terrellrussell

Chief Technologist, iRODS Consortium

iRODS Capabilities

  • Packaged and supported solutions
  • Require configuration not code
  • Derived from the majority of use cases observed in the user community

Automated Ingest

Provide a flexible and highly scalable mechanism for data ingest

  • Directly ingest files to vault
  • Capture streaming data
  • Register data in place
  • Synchronize a file system with the catalog
  • Extract and apply metadata

Architecture Overview

  • Implemented with Python iRODS Client
  • Based on Redis and Celery
  • Any number of Celery workers distributed across servers
  • File system metadata cached in Redis to detect changes
  • iRODS API is invoked only to update the catalog
  • Policy defined through event callbacks to user-provided python functions

File System Scanning

File System Scanning

This implementation periodically scans a source directory, registers the data in place, or updates system metadata for changed files.

 

In this use case, the file system is considered the single point of truth for ingest.  Changes are detected during the scan, and the system metadata is updated within the catalog.

Getting Started

sudo apt-get install -y redis-server python-pip
sudo service redis-server start

As the ubuntu user - start Redis server

pip install virtualenv --user
python -m virtualenv -p python3 rodssync
source rodssync/bin/activate
pip install irods_capability_automated_ingest

As the irods user - install automated ingest via pip

Getting Started

export CELERY_BROKER_URL=redis://127.0.0.1:6379/0
export PYTHONPATH=`pwd`
celery -A irods_capability_automated_ingest.sync_task worker -l error -Q restart,path,file

Open a new terminal, activate rodssync, and set environment variables for the scanner

As the irods user - start Celery workers

source rodssync/bin/activate
export CELERY_BROKER_URL=redis://127.0.0.1:6379/0
export PYTHONPATH=`pwd`

Getting Started

mkdir /tmp/test_dir
for i in $(seq 1 200); do touch /tmp/test_dir/file$i; done

 

mkdir ./src_dir
cp -r /tmp/test_dir ./src_dir/dir0

Generate some source data and "stage" it

Having never scanned this before, we refer to this as the "initial ingest"

Default Ingest Behavior

By default the framework will register the data in place against the default resource into the given collection

imkdir reg_coll
python -m irods_capability_automated_ingest.irods_sync start ./src_dir /tempZone/home/rods/reg_coll --synchronous --progress

--synchronous and --progress are not required but give visual indication of progress - scans are asynchronous by default.

Check that our results are registered in place

$ ils -L reg_coll/dir0/file199
  rods              0 demoResc            0 2018-11-08.15:00 & file199
        generic    /var/lib/irods/src_dir/dir0/file199

Default Ingest Behavior

Stage a different set of data and re-run the ingest

cp -r /tmp/test_dir ./src_dir/dir1

python -m irods_capability_automated_ingest.irods_sync start ./src_dir /tempZone/home/rods/reg_coll --synchronous --progress
$ ils -L reg_coll/dir1/file199
  rods              0 demoResc            0 2018-11-08.15:03 & file199
        generic    /var/lib/irods/src_dir/dir1/file199

Check our results

Now we will demonstrate that the filesystem cache allows the scanner to only ingest changes - a "delta sync"

Customizing the Ingest Behavior

The ingest tool is a callback based system in which the system invokes methods within the custom event handler module provided by the administrator.

 

These events may then take action such as setting ACLs, providing additional context such as selection of storage resources, or extracting and applying metadata.

Customizing the Ingest Behavior

Method Effect Default
pre/post_data_obj_create user-defined python none
pre/post_coll_create ​user-defined python none
pre/post_data_obj_modify ​user-defined python none
pre/post_coll_modify ​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
max_retries defines max number of retries on failure 0
timeout defines seconds until job times out 3600
delay defines seconds between retries 0

Available --event_handler methods

Customizing the Ingest Behavior

The operation mode is returned during the 'operation' method which informs the ingest tool as to which behavior is desired for a given ingest job.

 

To override the default behavior, one of these operations must be selected and returned.  These operations are hard coded into the tool, and cover the typical use cases of data ingest.

Customizing the Ingest Behavior

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

Operation.NO_OP no action no action

Available Operations

Custom Metadata Annotation

We will implement the operation, to_resource, and post_data_obj_create methods in our event handler

 

Using the python iRODS client we will apply filesystem metadata from 'stat'

 

Create a new target resource and ingest collection, and stage data again

iadmin mkresc targetResc unixfilesystem `hostname`:/tmp/irods/target_vault

imkdir put_coll
cp -r /tmp/test_dir ./src_dir/dir2

Custom Metadata Annotation

# /var/lib/irods/stat_eventhandler.py
from irods_capability_automated_ingest.core import Core
from irods_capability_automated_ingest.utils import Operation
from irods.meta import iRODSMeta
import subprocess

class event_handler(Core):
    @staticmethod
    def to_resource(session, meta, **options):
        return "targetResc"
    @staticmethod
    def operation(session, meta, **options):
        return Operation.PUT
    @staticmethod
    def post_data_obj_create(hdlr_mod, logger, session, meta, **options):
        args = ['stat', '--printf', '%04a,%U,%G,%x,%y', meta['path']]
        out, err = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
        s = str(out.decode('UTF-8')).split(',')
        print(s)
        obj = session.data_objects.get(meta['target'])
        obj.metadata.add("filesystem::perms", s[0], '')
        obj.metadata.add("filesystem::owner", s[1], '')
        obj.metadata.add("filesystem::group", s[2], '')
        obj.metadata.add("filesystem::atime", s[3], '')
        obj.metadata.add("filesystem::mtime", s[4], '')
        session.cleanup()

Create custom event handler locally

Custom Metadata Annotation

Should we want this module to register in place, we can simply change the operation returned to REGISTER_SYNC or REGISTER_AS_REPLICA_SYNC

python -m irods_capability_automated_ingest.irods_sync start ./src_dir /tempZone/home/rods/put_coll --event_handler stat_eventhandler --synchronous --progress

Launch the ingest job

$ ils -L put_coll/dir2/file199
  rods              0 targetResc            0 2018-11-08.16:51 & file199
        generic    /tmp/irods/target_vault/home/rods/put_coll/dir2/file199

Check our results

Custom Metadata Annotation

$ imeta ls -d put_coll/dir2/file199

AVUs defined for dataObj put_coll/dir2/file199:
attribute: filesystem::group
value: irods
units:
----
attribute: filesystem::perms
value: 0644
units:
----
attribute: filesystem::atime
value: 2018-11-08 16:51:29.378976820 +0000
units:
----
attribute: filesystem::mtime
value: 2018-11-08 16:46:18.937475894 +0000
units:
----
attribute: filesystem::owner
value: irods
units:

Inspect our newly annotated metadata

The Landing Zone

The Landing Zone

In this use case, data is written to disk by an instrument or another source we can run an ingest job on that directory.​  Once data is ingested it is moved out of the way in order to improve ingest performance.  These ingested files can be removed later as a matter of local administrative policy.

 

 

The critical difference between a pure file system scan and a landing zone is that the LZ is not considered the single point of truth, it is a staging area for ingest (moving files out of the way).

 

In a file system scan, the file system is the canonical replica and the catalog and other replicas are kept in sync.

The Landing Zone

Create a new ingest collection

imkdir lz_coll

Create the landing zone and ingested directories

mkdir /tmp/landing_zone
mkdir /tmp/ingested

Stage data for ingest

cp -r /tmp/test_dir /tmp/landing_zone/dir0

Preparing a Landing Zone

The Landing Zone

# /var/lib/irods/lz_eventhandler.py
import os
from irods_capability_automated_ingest.core import Core
from irods_capability_automated_ingest.utils import Operation

class event_handler(Core):
    @staticmethod
    def operation(session, meta, **options):
        return Operation.PUT
    @staticmethod
    def post_data_obj_create(hdlr_mod, logger, session, meta, **options):
        path = meta['path']
        new_path = path.replace('/tmp/landing_zone', '/tmp/ingested')
        try:
            dir_name = os.path.dirname(new_path)
            os.makedirs(dir_name, exist_ok=True)
            os.rename(path, new_path)
        except:
            logger.info('FAILED to move ['+path+'] to ['+new_path+']')

Using default resource (demoResc)

The Landing Zone

python -m irods_capability_automated_ingest.irods_sync start /tmp/landing_zone /tempZone/home/rods/lz_coll --event_handler lz_eventhandler --synchronous --progress

Launch the ingest job

ls -l /tmp/ingested/dir0

Check the ingested directory for the files

ls -l /tmp/landing_zone/dir0

Ensure landing zone directory is clean

ils -L lz_coll/dir0/file199

Check the landing zone collection

Streaming Ingest

For this use case some instruments periodically append output to a file or set of files.

 

We will configure an ingest job for a file to which a process will periodically append some data.

#!/bin/bash
file=$1
touch $file
for i in {1..1000}; do
    echo "do more science!!!!" >> $file
    sleep 2
done

Edit append_data.sh (make sure it's executable)

Streaming Ingest

Modify:

./rodssync/lib/python3.5/site-packages/irods_capability_automated_ingest/examples/append_with_resc_name.py

from irods_capability_automated_ingest.core import Core
from irods_capability_automated_ingest.utils import Operation
class event_handler(Core):    
    @staticmethod
    def to_resource(session, meta, **options):
        return "demoResc"

    @staticmethod
    def operation(session, meta, **options):
        return Operation.PUT_APPEND

"regiResc2a" should become "demoResc"

Streaming Ingest

Let's cleanup the src_dir before we start.  First remove the data objects that were registered from src_dir and and then remove this directory.

$ irm -rf reg_coll
$ rm -r ./src_dir/*

In another terminal start the data creation process

$ ./append_data.sh ./src_dir/science.txt

Create a new ingest collection

$ imkdir stream_coll

Streaming Ingest

Check the results --- science.txt is growing in size

$ ils -l stream_coll/science.txt
  rods              0 demoResc          374 2018-05-23.10:13 & science.txt
$ ils -l stream_coll/science.txt
  rods              0 demoResc          418 2018-05-23.10:13 & science.txt
$ ils -l stream_coll/science.txt
  rods              0 demoResc          440 2018-05-23.10:13 & science.txt
<SNIP>

Start the ingest process with a restart interval of 1s

$ python -m irods_capability_automated_ingest.irods_sync start ./src_dir /tempZone/home/rods/stream_coll --event_handler irods_capability_automated_ingest.examples.append_with_resc_name -i 1

Streaming Ingest

Managing a periodic ingest job

$ python -m irods_capability_automated_ingest.irods_sync list
{"singlepass": [], "periodic": ["493676ba-8ee4-11e9-b745-125ca36ad160"]}

Halting a periodic ingest job

$ python -m irods_capability_automated_ingest.irods_sync stop 
493676ba-8ee4-11e9-b745-125ca36ad160

Stop the celery workers by doing a control-c in the window where they were started.

Scanning S3 buckets

$ python -m irods_capability_automated_ingest.irods_sync start \ 
    /bucket_name/path/to/s3/folder \
    /tempZone/home/rods/dest_coll \
    --s3_keypair /path/to/keypair_file \
    --s3_endpoint_domain s3.amazonaws.com \
    --s3_region_name us-east-1 \
    --s3_proxy_url myproxy.example.org

Just point the scanner at the bucket

S3 object semantics notwithstanding, this is exactly the same as a filesystem scan

Questions?

UGM 2019 - Administration Automated Ingest

By iRODS Consortium

UGM 2019 - Administration Automated Ingest

iRODS User Group Meeting 2019 - Administration Training Module

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