We are working on using [https://www.irods.org], as a way to increase storage for users of the HUB. Possible uses include simple staging of data for simulation, and housing searchable collections of documents.

We are using two servers to test iRods at CCR. The first is both a data and metadata server. The second is just a data server.

== Common Problems ==
 
* Client cannot connect to server.

Server may go down unexpectedly. Admin should log onto irods1.ccr.buffalo.edu, change to the iRods directory and type
 
irodsctl istart

Check the server log to see whether the restart succeded. The log is in /data/iRODS/iRODS/server/log
and it is named by the date, e.g. rodsLog.2010.7.11


== Idea for submitted apps to get irods files ==

Use file browser to get path to file.

* Parse path to get file name.

* when submit arrives, it makes a symbolic link to the file name and 
name the link with the file name.

* remove the symbolic link  after the app runs.

ln -s irods/username/pathToFile/filename filename

submit execs app, file "resides" in cwd.

rm filename


== To use a remote command-line client: ==


Get a copy of the file .irodsEnv from us ('''Note''': the irodsHost needs to be an '''''IP address''''' 
rather than a domain name) and
have us set up your '''login name''' and '''password''' on the
iRods server.

From your home directory on the hub:
mkdir ~/.irods
move the .irodsEnv we gave you into  ~/.irods

Download iRods from [https://www.irods.org/index.php/Downloads] 

Follow the instructions at [https://www.irods.org/index.php/Installation]
for '''installing additional clients'''.

At this point you will need to set the path:

PATH=home/vhub/username/iRODS/clients/icommands/bin:$PATH

It's easiest if you put this command in your .bashrc or .profile
file so the commands are available every time you open a terminal. 

== Some basic concepts ==
* collection: a directory

* resource: represents a physical data server location that can hold many collections

* zone: multiple resources can be members of the same zone

== Some useful commands ==
* iinit : enter your password and it will get cahed so you don't have to give your password for every command.

* ils: list files

* imkdir: create a directory (also called a collection)

* iput: put a file into iRods

* ireg: copy a directory revursively into iRods
note that if you add files to the actual physical directory, this is not reflected in iRods.

ireg -C /data/iRODS/testIreg/ /tempZone/home/rods/newCol
ils newCol
/tempZone/home/rods/newCol:
   foo1
   foo2
cd testIreg/
touch bar
ils newCol
/tempZone/home/rods/newCol:
   foo1
   foo2


== iRods FUSE notes ==

Install: Need to install libfuse-dev to get the header files in the same path as
the library

edit iRODS/config/config.mk:

uncomment IRODS_FS = 1

set fuseHomeDir=path/to/fuse where the path is just above include/fuse.h and lib/libfuse.a

on your vhub account this is simply  fuseHomeDir=/usr


in iRODS/client/fuse do '''make'''

Add another path so that you can mount with the command ''irodsFs''

'''NOTE: You cannot unmount on  your vhub account, once you've mounted irods.
Only a vhub dministrator can run fusermount.'''

PATH=/home/alisanee/iRods/iRODS/clients/icommands/bin:/home/alisanee/iRods/iRODS/clients/fuse/bin:$PATH

== Administrators' To Do List For Installing on HUB ==

put the icommands in the path for every user

install .irods directory for every user and provide an irodsEnv file with their Hub ID as the user name

do iinit once with their user name and password. This will create a file, .irods/.irodsA which holds the user's encrypted password, so that they won't have to enter their password to do an icoomand.

in irods, create a home directory for the user and set the group to the user name.

irodsFs mount in an empty folder named irods

'''irodsFs irods'''

===For New User===
As the 'rods' administrator, for a new hub user: 

'''iadmin mkuser username#vhub rodsuser''' ''create new user (use rodsadmin if they are an admin)''

'''iadmin moduser username password somepassword ''' ''set user's password''

'''imkdir username''' ''make home directory for new user''

'''ichmod -V own username username''' ''let user rwx her home directory''

'''ichmod read vhub username'''       ''let vhub rwx user's home directory''

'''ichmod write vhub username'''

'''ichmod inherit username'''       ''let vhub rwx the subdirectories and files the user creates''

users can then do 

iput <file> <directory>

iput foo username

Note that the irods1.ccr.buffalo.edu name is not available to a DNS server, so until that
changes, the irodsEnv has to be edited to have the IP address instead.

Edit .bashrc in iRods server(done):
PATH=/data/iRODS/iRODS/clients/icommands/bin:$PATH

Install iRods on vhub@u2-grid (done)

edit .bashrc: PATH=/san/user/vhub/u2/iRODS/clients/icommands/bin:$PATH

iadmin mkuser username rodsuser 
 
iadmin mkuser vhub rodsadmin

==Uninstalling iRODS server==

remove the collections (i.e. directories and files), e.g.

'''irm  -r aneeman'''

turn irods off 

'''irodsctl stop'''

remove directories for irods and its postgres installation.

== Move a collection or file to a specific server ==

'''iphymv -r resource2Collection -R demoResc2'''

-r recursive
-R resource name

The "mount" always looks the same, regardless of the physical location.
You can move a file to any data server.