python-irodsclient 0.7.0

A python API for iRODS

iRODS is an open source distributed data management system. This is a client API implemented in python.

Currently supported:

• Establish a connection to iRODS, authenticate

• Implement basic Gen Queries (select columns and filtering)

• Support more advanced Gen Queries with limits, offsets, and aggregations

• Query the collections and data objects within a collection

• Execute direct SQL queries

• Execute iRODS rules

• Support read, write, and seek operations for files

• PUT/GET data objects

• Create data objects

• Delete data objects

• Create collections

• Delete collections

• Rename data objects

• Rename collections

• Register files and directories

• Query metadata for collections and data objects

• Add, edit, remove metadata

• Replicate data objects to different resource servers

• Connection pool management

• Implement gen query result sets as lazy queries

• Return empty result sets when CAT_NO_ROWS_FOUND is raised

• Manage permissions

• Manage users and groups

• Manage resources

• GSI authentication

• Unicode strings

• Ticket based access

• iRODS connection over SSL

• Python 2.7, 3.4 or newer

Installing

PRC requires Python 2.7 or 3.4+. To install with pip:

pip install python-irodsclient

or:

pip install git+https://github.com/irods/python-irodsclient.git[@branch|@commit|@tag]

Uninstalling

pip uninstall python-irodsclient

Establishing a connection

Using environment files in ~/.irods/:

>>> import os
>>> from irods.session import iRODSSession
>>> try:
...     env_file = os.environ['IRODS_ENVIRONMENT_FILE']
... except KeyError:
...     env_file = os.path.expanduser('~/.irods/irods_environment.json')
...
>>> with iRODSSession(irods_env_file=env_file) as session:
...     pass
...
>>>

Passing iRODS credentials as keyword arguments:

>>> from irods.session import iRODSSession
>>> with iRODSSession(host='localhost', port=1247, user='bob', password='1234', zone='tempZone') as session:
...     pass
...
>>>

If you’re an administrator acting on behalf of another user:

>>> from irods.session import iRODSSession
>>> with iRODSSession(host='localhost', port=1247, user='rods', password='1234', zone='tempZone',
           client_user='bob', client_zone='possibly_another_zone') as session:
...     pass
...
>>>

If no client_zone is provided, the zone parameter is used in its place.

Working with collections

>>> coll = session.collections.get("/tempZone/home/rods")

>>> coll.id
45798

>>> coll.path
/tempZone/home/rods

>>> for col in coll.subcollections:
>>>   print col
<iRODSCollection /tempZone/home/rods/subcol1>
<iRODSCollection /tempZone/home/rods/subcol2>

>>> for obj in coll.data_objects:
>>>   print obj
<iRODSDataObject /tempZone/home/rods/file.txt>
<iRODSDataObject /tempZone/home/rods/file2.txt>

Create a new collection:

>>> coll = session.collections.create("/tempZone/home/rods/testdir")
>>> coll.id
45799

Working with data objects (files)

Create a new data object:

>>> obj = session.data_objects.create("/tempZone/home/rods/test1")
<iRODSDataObject /tempZone/home/rods/test1>

Get an existing data object:

>>> obj = session.data_objects.get("/tempZone/home/rods/test1")
>>> obj.id
12345

>>> obj.name
test1
>>> obj.collection
<iRODSCollection /tempZone/home/rods>

>>> for replica in obj.replicas:
...     print replica.resource_name
...     print replica.number
...     print replica.path
...     print replica.status
...
demoResc
0
/var/lib/irods/Vault/home/rods/test1
1

Reading and writing files

PRC provides file-like objects

>>> obj = session.data_objects.get("/tempZone/home/rods/test1")
>>> with obj.open('r+') as f:
...   f.write('foo\nbar\n')
...   f.seek(0,0)
...   for line in f:
...      print line
...
foo
bar

Working with metadata

>>> obj = session.data_objects.get("/tempZone/home/rods/test1")
>>> print obj.metadata.items()
[]

>>> obj.metadata.add('key1', 'value1', 'units1')
>>> obj.metadata.add('key1', 'value2')
>>> obj.metadata.add('key2', 'value3')
>>> print obj.metadata.items()
[<iRODSMeta (key1, value1, units1, 10014)>, <iRODSMeta (key2, value3, None, 10017)>,
<iRODSMeta (key1, value2, None, 10020)>]

>>> print obj.metadata.get_all('key1')
[<iRODSMeta (key1, value1, units1, 10014)>, <iRODSMeta (key1, value2, None, 10020)>]

>>> print obj.metadata.get_one('key2')
<iRODSMeta (key2, value3, None, 10017)>

>>> obj.metadata.remove('key1', 'value1', 'units1')
>>> print obj.metadata.items()
[<iRODSMeta (key2, value3, None, 10017)>, <iRODSMeta (key1, value2, None, 10020)>]

General queries

>>> import os
>>> from irods.session import iRODSSession
>>> from irods.models import Collection, DataObject
>>>
>>> env_file = os.path.expanduser('~/.irods/irods_environment.json')
>>> with iRODSSession(irods_env_file=env_file) as session:
...     query = session.query(Collection.name, DataObject.id, DataObject.name, DataObject.size)
...
...     for result in query.get_results():
...             print '{}/{} id={} size={}'.format(result[Collection.name], result[DataObject.name], result[DataObject.id], result[DataObject.size])
...
/tempZone/home/rods/manager/access_manager.py id=212665 size=2164
/tempZone/home/rods/manager/access_manager.pyc id=212668 size=2554
/tempZone/home/rods/manager/collection_manager.py id=212663 size=4472
/tempZone/home/rods/manager/collection_manager.pyc id=212664 size=4464
/tempZone/home/rods/manager/data_object_manager.py id=212662 size=10291
/tempZone/home/rods/manager/data_object_manager.pyc id=212667 size=8772
/tempZone/home/rods/manager/__init__.py id=212670 size=79
/tempZone/home/rods/manager/__init__.pyc id=212671 size=443
/tempZone/home/rods/manager/metadata_manager.py id=212660 size=4263
/tempZone/home/rods/manager/metadata_manager.pyc id=212659 size=4119
/tempZone/home/rods/manager/resource_manager.py id=212666 size=5329
/tempZone/home/rods/manager/resource_manager.pyc id=212661 size=4570
/tempZone/home/rods/manager/user_manager.py id=212669 size=5509
/tempZone/home/rods/manager/user_manager.pyc id=212658 size=5233

Query with aggregation(min, max, sum, avg, count):

>>> with iRODSSession(irods_env_file=env_file) as session:
...     query = session.query(DataObject.owner_name).count(DataObject.id).sum(DataObject.size)
...     print next(query.get_results())
{<irods.column.Column 411 D_OWNER_NAME>: 'rods', <irods.column.Column 407 DATA_SIZE>: 62262, <irods.column.Column 401 D_DATA_ID>: 14}

In this case since we are expecting only one row we can directly call query.execute():

>>> with iRODSSession(irods_env_file=env_file) as session:
...     query = session.query(DataObject.owner_name).count(DataObject.id).sum(DataObject.size)
...     print query.execute()
+--------------+-----------+-----------+
| D_OWNER_NAME | D_DATA_ID | DATA_SIZE |
+--------------+-----------+-----------+
| rods         | 14        | 62262     |
+--------------+-----------+-----------+

Specific Queries

>>> import os
>>> from irods.session import iRODSSession
>>> from irods.models import Collection, DataObject
>>> from irods.query import SpecificQuery
>>>
>>> env_file = os.path.expanduser('~/.irods/irods_environment.json')
>>> with iRODSSession(irods_env_file=env_file) as session:
...     # define our query
...     sql = "select data_name, data_id from r_data_main join r_coll_main using (coll_id) where coll_name = '/tempZone/home/rods/manager'"
...     alias = 'list_data_name_id'
...     columns = [DataObject.name, DataObject.id] # optional, if we want to get results by key
...     query = SpecificQuery(session, sql, alias, columns)
...
...     # register specific query in iCAT
...     _ = query.register()
...
...     for result in query.get_results():
...             print '{} {}'.format(result[DataObject.name], result[DataObject.id])
...
...     # delete specific query
...     _ = query.remove()
...
user_manager.pyc 212658
metadata_manager.pyc 212659
metadata_manager.py 212660
resource_manager.pyc 212661
data_object_manager.py 212662
collection_manager.py 212663
collection_manager.pyc 212664
access_manager.py 212665
resource_manager.py 212666
data_object_manager.pyc 212667
access_manager.pyc 212668
user_manager.py 212669
__init__.py 212670
__init__.pyc 212671

And more…

Additional code samples are available in the test directory