iRODS Tutorial

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iRODS Tutorial
I. Getting Started
iRODS Tutorial Preview
I. 
iRODS Getting Started
–  unix client
–  usage
II.  iRODS Data (Grid) Administration
–  installing server and iCAT
–  setting up users
–  adding new resources to a data grid/zone
–  federating with other grids/zones, remote users
–  microservices and rules for policy implementation and
enforcement
2!
I.  iRODS Getting Started
3!
iRODS Info
•  Main page: http://www.irods.org
•  Chat list: [email protected]
•  iRODS Documentation:
https://www.irods.org/index.php/Documentation
•  On-line tutorial:
https://www.irods.org/index.php/Tutorial
4!
iRODS Books
Available from Amazon
•  iRODS Primer: integrated Rule-Oriented Data System (Synthesis
Lectures on Information Concepts, Retrieval, and Services)
http://www.amazon.com/dp/1608453332
•  The integrated Rule-Oriented Data System (iRODS) Micro-service
Workbook
http://www.amazon.com/dp/1466469129
5!
iRODS Download
•  Download link from the iRODS main page:
https://www.irods.org/download.html
•  BSD license
•  registration/agreement
6!
iRODS Download
Untar irods3.1.tgz
•  cd into a directory where you want to install iRODS, eg
$HOME/tutorial
•  Move the tarball there: mv ~/irods3.1.tgz .
•  Untar the tarball: tar –zxvf irods3.1.tgz
•  cd into iRODS/
7!
iRODS Installation – unix client only
•  Run the install script: ./irodssetup
•  Can install three main components using irodssetup:
1.  an iRODS server (iCAT-enabled or not)
2.  the iCAT catalog metadata database
3.  ’icommands' – the unix client
• 
Install only the icommands for now…
8!
iRODS Installation - icommands
•  ./irodssetup
•  “No” to all prompts except last two:
–  Save configuration (irods.config) [yes]? yes
–  Start iRODS build [yes]? yes
•  Set PATH to include the path to the icommands
tcsh:
setenv PATH $PATH:$HOME/tutorial/iRODS/clients/icommands/bin
bash:
export PATH=$PATH:$HOME/tutorial/iRODS/clients/icommands/bin
9!
Working with a Demo Data Grid
•  If you have an account on an iRODS data grid, find your account
name and password.
•  Get your iRODS environment info from the .irodsEnv file that goes with
this data grid.
•  Make directory .irods/ in your home directory: mkdir ~/.irods
•  Copy the .irodsEnv file into ~/.irods; edit if necessary to insert your user
name.
•  This will direct your client to the intended data grid, as the intended
user.
10!
Sample .irodsEnv file
RENCI Demo Data Grid: compZone
# iRODS server host name:
irodsHost 'ischia2.renci.org'
# iRODS server port number:
irodsPort 1250
# Default storage resource name:
irodsDefResource 'comp523Resc'
The .irodsEnv file
determines which
data grid (zone)
the icommands
client connects to.
# Home directory in iRODS:
irodsHome '/compZone/home/leesa'
# Current directory in iRODS:
irodsCwd '/compZone/home/leesa'
# Account name:
irodsUserName ’leesa'
In this example, user name is “leesa” # Zone:
irodsZone 'compZone’
# Xmsg port:
xmsgPort 1237
If you’ll be using the Xmsg service 11!
Some iRODS Clients
•  iDrop web – iDrop, iDrop-lite
http://iren-web.renci.org:8080/idrop-web/login/login
•  PHP web browser
http://iren-web.renci.org/rodsweb
•  icommands – unix client
https://www.irods.org/index.php/icommands
•  FUSE (Filesystem in Userspace) client
https://www.irods.org/index.php/iRODS_FUSE
•  Many others supplied by user communities
12!
Unix client: icommands
See
https://www.irods.org/index.php/icommands
Unix-like
ils
ipwd
icd
ichmod
irm
imkdir
ipasswd
irsync
ichksum
imv
icp
ienv
FTP-like
iinit
iexit
iput
iget
(Not an exhaustive list.)
13!
icommands (continued)
Metadata
imeta
iquest
idbo
Informational
ienv
ilsresc
iuserinfo
ihelp
Functional
ireg
ibun
irepl
Rule-oriented
irule
iqstat
iqdel
iqmod
idbug
14!
icommands
> iinit
Enter your current iRODS password:
> ipwd
/compZone/home/leesa
Directory naming convention:
/zone/home/user_name/collection_name
> ils
/compZone/home/leesa:
fuse-notes
test_write.txt
C- /compZone/home/leesa/slides
> ils -L
/compZone/home/leesa:
leesa
0 comp523Resc
799 2012-01-08.13:59 & fuse-notes
447a6462e578cb69ee8b0d82ade1f397 /vault2/comp523Vault/home/leesa/
fuse-notes
leesa
0 comp523Resc
13 2012-01-08.13:59 & test_write.txt
59ca0efa9f5633cb0371bbc0355478d8 /vault2/comp523Vault/home/leesa/
test_write.txt
C- /compZone/home/leesa/slides
15!
icommands - ACLs
> ils -A
/compZone/home/leesa:
ACL - leesa#compZone:own
Inheritance - Disabled
fuse-notes
ACL - leesa#compZone:own
test_write.txt
ACL - leesa#compZone:own
C- /compZone/home/leesa/slides
> ichmod read baretto fuse-notes
> ils -A
/compZone/home/leesa:
ACL - leesa#compZone:own
Inheritance - Disabled
fuse-notes
ACL - leesa#compZone:own
baretto#compZone:read object
test_write.txt
ACL - leesa#compZone:own
C- /compZone/home/leesa/slides16!
ienv
> ienv
NOTICE: Release Version = rods3.1beta, API Version = d
NOTICE: irodsHost=ischia2.renci.org
NOTICE: irodsPort=1250
NOTICE: irodsDefResource=comp523Resc
NOTICE: irodsHome=/compZone/home/rods
NOTICE: irodsCwd=/compZone/home/rods
NOTICE: irodsUserName=rods
NOTICE: irodsZone=compZone
NOTICE: xmsgHost=ischia2.renci.org
NOTICE: xmsgPort=1237
17!
Group “public”
> ichmod -r read public slides
Every user in the data grid is a member of user group “public” > ils -A slides
/compZone/home/leesa/slides:
ACL - public#compZone:read object
baretto#compZone:read object leesa#compZone:own
rods#compZone:read object mikec#compZone:read object
comp523#compZone:read object guerline#compZone:read object
holston#compZone:read object Username#compZone:read object
leesa#compZone:read object
Inheritance - Disabled
1-overview.ppt
ACL - public#compZone:read object leesa#compZone:own
slide-list.html
ACL - public#compZone:read object leesa#compZone:own
18!
icommands – putting & getting data
> iput -K derby.log (calculate and store checksums)
> iput notes (no checksums)
> ils -L
/compZone/home/leesa:
leesa
0 comp523Resc
419 2012-01-10.11:59 & derby.log
11adc3cf922e31db8dfd4a2806581f99
/vault2/comp523Vault/home/leesa/derby.log
leesa
0 comp523Resc
799 2012-01-08.13:59 & fuse-notes
447a6462e578cb69ee8b0d82ade1f397
/vault2/comp523Vault/home/leesa/fuse-notes
leesa
0 comp523Resc
3645 2012-01-10.12:00 & notes
/vault2/comp523Vault/home/leesa/notes
leesa
0 comp523Resc
13 2012-01-08.13:59 & test_write.txt
59ca0efa9f5633cb0371bbc0355478d8
/vault2/comp523Vault/home/leesa/test_write.txt
C- /compZone/home/leesa/slides
> iget –k notes (verify checksum without storing)
-­‐k and –K options for checksum calculation 19!
icommands – replicating data objects
•  > ils
/compZone/home/leesa/rods:
hello
C- /compZone/home/leesa/rods/rules
Replication is not the same as copying: a replica is the same logical object as the original; a copy is a new logical object. •  > irepl -R demoResc hello
•  > ils
Replicated object (“hello”) appears as a single logical object /compZone/home/leesa/rods:
hello
C- /compZone/home/leesa/rods/rules
•  > ils -L
Do the long listing (ils –L) to see all replicas of an object (“hello”) and physical locations /compZone/home/leesa/rods:
rods
0 comp523Resc
11 2011-09-19.15:42 & hello
/vault2/comp523Vault/home/leesa/rods/hello
rods
1 demoResc
11 2012-02-02.11:51 & hello
/vault2/demoVault/home/leesa/rods/hello
C- /compZone/home/leesa/rods/rules
20!
ireg – register data into iRODS
Get data into iRODS without making an additional copy or moving it
Example: directory /vault2/state-data contains state LiDAR data that
we now want in an iRODS repository… without copying it
1.  /vault2/state-data is mounted on the iRODS server host
2.  Data admin sets up existing directory as an iRODS resource
3.  User registers existing data into iRODS iCAT:
ireg -C /vault2/state-data /compZone/home/leesa/state-data
(-­‐f option for picking up unregistered files) Register incoming files rigorously OR modify a directory only through iRODS
once it has been registered to keep the iCAT consistent with the directory.
21!
ibun – for bundling files
•  Tar up and expand files for efficient iput/iget
•  iput a tarball and expand it within iRODS:
–  tar -chlf tutorials.tar -C tutorials .
–  iput -Dtar tutorials.tar .
–  ibun -x tutorials.tar tutorials
•  Tar up files in iRODS for iget:
–  ibun -cDtar slides.tar slides
–  iget slides.tar
–  tar –xvf slides.tar –C slides
22!
ilsresc
See resources available on your data grid
•  compZone:
> ilsresc
msoResc2
demoResc
msoResc1
bundleResc
comp523Resc
stateResc
cpsresc
msoRescGroup (resource group)
23!
iquest – querying the iCAT
•  Pre-defined queries:
> iquest "SELECT DATA_NAME, DATA_CHECKSUM WHERE
DATA_RESC_NAME like 'demo%'"
DATA_NAME = cps.test1.txt
DATA_CHECKSUM =
(Checksums displayed only for -----------------------------------------------------------those that have already been DATA_NAME = hello
calculated and stored) DATA_CHECKSUM =
-----------------------------------------------------------DATA_NAME = homewood_info.doc
DATA_CHECKSUM = 67614aedf5b41cae0487eb5fe9b0d3ae
------------------------------------------------------------
•  > iquest attrs to see attributes that can be queried
•  See https://www.irods.org/index.php/iquest for examples
24!
iquest – querying the iCAT
•  Useful when you want to remove a resource and you discover it isn’t
empty:
> iquest "SELECT DATA_NAME, USER_NAME, COLL_NAME WHERE
DATA_RESC_NAME like ‘msoResc1'"
DATA_NAME = slide-list-html
USER_NAME = rods
COLL_NAME = /compZone/trash/home/rods/DataNet
------------------------------------------------------------------------------
•  Admin can add SQL strings to be invoked by users of the
data grid
•  Data grid-specific queries ( added by admin)
> iquest --sql 'pre-defined SQL string' [format] [arguments]
25!
imeta – add, view, modify metadata
•  imeta add –d hello “Date” “2 february 2012”
•  imeta ls –d hello
AVUs defined for dataObj hello:
attribute: Meta1
value: hello
units:
---attribute: Date
value: 2 february 2012
units:
•  imeta rm –d hello “Meta1” “hello”
26!
Realizable Objects
•  Typical iRODS objects contain data
•  Realizable objects:
–  symbolic links to iRODS objects
–  symbolic links to external data sources
–  workflow procedures to regenerate data
•  Symbolic links implemented so far
–  instantiated through a compound resource
•  mso resource (mso: microservice object)
•  cache resource
–  symbolic links implemented for http and Z39.50
27!
Symbolic Links to an http Source
1.  Admin user must set up the mso resource and resource
group, for example:
– 
– 
mso resource: httpResc
mso group: httpGroup
2.  User registers external data
> ireg -D mso -R httpResc -G httpGroup
"//http://www.renci.org/~leesa/irodsEnv-files/irodsEnv-compZone"
/compZone/home/leesa/tutorial/env-files/irodsEnv-compZone
28!
Symbolic Links to an http Source
• 
User puts symbolic link in his collection (registers external
data)
•  Data is then accessible to anyone with read authorization
to the user’s collection
•  iget causes a replica to be made in the disk cache of the
mso resource group (compound resource)
–  do an iget of a file in this directory and see
29!
Cloud Resources
1.  Admin user must set up the cloud resource and
resource group, for example:
– 
– 
S3 Resource: s3Resc
S3 Group: s3Group
2.  This is just another iRODS resource for the users, who can
manage their cloud data just as all other data:
> iput –K –R s3Resc my_file (put data into the cloud resource)
> irepl –R s3Resc another_file (replicate into the cloud resource)
> ichmod read public my_file (give public access to cloud data)
30!
Database Resources
•  Database Resource (DBR): a database, queried and updated via
SQL (or other, for non-SQL)
•  Database object (DBO): an interface to a DBR, typically a (SQL)
query that returns results
•  iRODS agent will open and close DB as needed; results of the
query are directly returned to user
•  Query results are stored to an iRODS data object, a DBO Results
file (DBOR).
•  iRODS access controls are applied on the DBR and DBO.
31!
Database Resources
•  https://www.irods.org/index.php/Database_Resources and
https://www.irods.org/index.php/Database_Resource_Administration
•  idbo command – to access the external DB resource
idbo Command
•  Accepts commands on the command line
•  If no command is given, goes into interactive mode
•  Commands:
– 
– 
– 
– 
– 
– 
– 
– 
– 
open DBR
(open a database resource)
close DBR
(close a database resource)
exec DBR DBO [arguments] (execute a DBO on a DBR)
output [-f] DBOR (store 'exec' results in another data-object)
commit DBR (commit updates to a DBR (done via a DBO))
rollback DBR (rollback updates instead)
ls
(list defined Database-Objects in the Zone)
help (or h) [command] (this help, or help on a command)
quit (or 'q', exit idbo)
Where DBR and DBO are the names of a Database Resource and
Database Object.
Access Controls for DBRs
•  iRODS administrators can create DBOs, since they can give
anyone (including themselves) 'write' access to the DBR.
•  iRODS users with 'write' access to the DBR will also be allowed
to create DBOs.
•  iRODS users with 'read' access to the DBR will be allowed to
execute DBOs that were created by users with 'write' access
to the same DBR.
The 'read' users, for some DBO SQL, will provide parameters to
include in the SQL, which will be executed as SQL bind
variables (to restrict capabilities).
This access mode will allow more privileged users to create
controlled access for additional users.
Rules
•  New rule engine with 3.0
•  See
https://www.irods.org/index.php/
Changes_and_Improvements_to_the_Rule_Language_and_
the_Rule_Engine
•  Implement computer actionable policies
– 
– 
– 
– 
– 
– 
– 
– 
– 
Reten%on, distribu%on, arrangement Authen%city, provenance, descrip%on Integrity, replica%on, synchroniza%on Dele%on, trash cans, versioning Archiving, staging, caching Authen%ca%on, authoriza%on, redac%on Access, approval, IRB, audit trails, report genera%on Assessment criteria, valida%on Derived data product genera%on, format parsing 35!
Microservices
•  C code
•  the unit of work within iRODS
•  called by rules
•  composed into workflows by rules
36!
Running Rules
•  triggered by events/policy points
•  contained in the (distributed) rule base:
–  iRODS_dir/server/config/reConfigs/core.re
–  first rule with satisfied condition is executed; others are skipped
•  can be run with irule: manual execution
•  delayed execution
–  iqstat
–  iqdel
37!
irule – to run a rule manually
•  Example rules to tweak and run in the software distribution
iRODS/clients/icommands/test/rules3.0
• 
irule -F listMS.r
• 
irule -F rulemsiAdmShowCoreRE.r can only be run by admin users
38!
iDrop Client
•  YouTube video overviews:
http://www.youtube.com/user/diceresearch?feature=guide
–  iDrop – iDrop Suite Overview
–  iDrop-web: iDrop Suite Overview part 2
•  Test iDrop server:
iren-web.renci.org:8080/idrop-web
39!
iDrop Client
•  iRODS Tree View
–  Right click on a file
–  Expand: New folder: Delete: Rename
•  Tag a file
–  iRODS info -> Click on a file
–  Add tag (no spaces in tag) -> Update Info
•  Comment a file
–  iRODS info -> Click on a file
–  Add comment
•  Search
–  By name (file)
–  By tag
–  By name and tag
40!
iDrop Client
•  Supports
– 
– 
– 
– 
Drag and drop
Replication
Browsing
Searching
•  Manages a queue of transfer requests
– 
– 
– 
– 
– 
Checkmark -> Show Current and Past Activity
Transfer Summary -> select a transfer
Transfer Details
Purge: Delete: Resubmit: Restart: Refresh
View: list subset of transfers
•  Should be able to disconnect, and iDrop will continue
transmissions when reconnected
41!
iDrop Client
•  Metadata
•  Replication
•  Synchronizing a directory
– 
– 
– 
– 
Tools -> Preferences -> Synchronization
Pick local directory
Pick iRODS directory
Select synchronization period (1 day)
•  Caveats
–  To synchronize, a list of files in the local directory is generated, which
can take a long time for large directories
–  Keep the local directory small

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