Now maintained by iRODS at irods/python-irodsclient

For version 0.5.0, see https://github.com/irods/python-irodsclient/

Or, install via GitHub:

pip install git+git://github.com/irods/python-irodsclient.git

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python-irodsclient - version 0.4.0

iRODS is an open-source distributed filesystem manager. This a client API implemented in python.

This project should be considered pre-alpha. Here's what works:

• Establish a connection to iRODS, authenticaate
• 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
• Support read, write, and seek operations for files
• Delete data objects
• Create collections
• Delete collections
• Rename data objects
• Rename collections
• 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 zones
• Manage resources

Installation

pycommands requires Python 2.7. Installation with pip is easy!

pip install git+git://github.com/iPlantCollaborativeOpenSource/pycommands.git

Establishing a connection

>>>fromirods.sessionimportiRODSSession>>>sess=iRODSSession(host='localhost', port=1247, user='rods', password='rods', zone='tempZone')

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

>>>fromirods.sessionimportiRODSSession>>>sess=iRODSSession(host='localhost', port=1247, user='rods', password='rods', zone='tempZone', client_user='another_user', client_zone='another_zone')

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

Working with collections

>>>coll=sess.collections.get("/tempZone/home/rods")
>>>coll.id45798>>>coll.path/tempZone/home/rods>>>forcolincoll.subcollections:
>>>printcol<iRODSCollection/tempZone/home/rods/subcol1><iRODSCollection/tempZone/home/rods/subcol2>>>>forobjincoll.data_objects:
>>>printobj<iRODSDataObject/tempZone/home/rods/file.txt><iRODSDataObject/tempZone/home/rods/file2.txt>

Create a new collection:

>>>coll=sess.collections.create("/tempZone/home/rods/testdir")
>>>coll.id45799

Working with data objects (files)

Create a new data object:

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

Get an existing data object:

>>>obj=sess.data_objects.get("/tempZone/home/rods/test1")
>>>obj.id12345>>>obj.nametest1>>>obj.collection<iRODSCollection/tempZone/home/rods>

Reading and writing files

pycommands provides file-like objects for reading and writing files

>>>obj=sess.data_objects.get("/tempZone/home/rods/test1")
>>>withobj.open('r+') asf:
... f.write('foo\nbar\n')
... f.seek(0,0)
... forlineinf:
... printline
...
foobar

Working with metadata

>>>obj=sess.data_objects.get("/tempZone/home/rods/test1")
>>>printobj.metadata.items()
[]
>>>obj.metadata.add('key1', 'value1', 'units1')
>>>obj.metadata.add('key1', 'value2')
>>>obj.metadata.add('key2', 'value3')
>>>printobj.metadata.items()
[<iRODSMeta (key1, value1, units1, 10014)>, <iRODSMeta (key2, value3, None, 10017)>, <iRODSMeta (key1, value2, None, 10020)>]
>>>printobj.metadata.get_all('key1')
[<iRODSMeta (key1, value1, units1, 10014)>, <iRODSMeta (key1, value2, None, 10020)>]
>>>printobj.metadata.get_one('key2')
<iRODSMeta (key2, value3, None, 10017)>>>>obj.metadata.remove('key1', 'value1', 'units1')
>>>printobj.metadata.items()
[<iRODSMeta (key2, value3, None, 10017)>, <iRODSMeta (key1, value2, None, 10020)>]

Performing general queries

>>>fromirods.sessionimportiRODSSession>>>fromirods.modelsimportCollection, User, DataObject>>>sess=iRODSSession(host='localhost', port=1247, user='rods', password='rods', zone='tempZone')
>>>results=sess.query(DataObject.id, DataObject.name, DataObject.size, \
User.id, User.name, Collection.name).all()
>>>printresults+---------+-----------+-----------+---------------+--------------------------------+-----------+|USER_ID|USER_NAME|D_DATA_ID|DATA_NAME|COLL_NAME|DATA_SIZE|+---------+-----------+-----------+---------------+--------------------------------+-----------+|10007|rods|10012|runDoxygen.rb|/tempZone/home/rods|5890||10007|rods|10146|test1|/tempZone/home/rods|0||10007|rods|10147|test2|/tempZone/home/rods|0||10007|rods|10148|test3|/tempZone/home/rods|8||10007|rods|10153|test5|/tempZone/home/rods|0||10007|rods|10154|test6|/tempZone/home/rods|8||10007|rods|10049| .gitignore|/tempZone/home/rods/pycommands|12||10007|rods|10054|README.md|/tempZone/home/rods/pycommands|3795||10007|rods|10052|coll_test.py|/tempZone/home/rods/pycommands|658||10007|rods|10014|file_test.py|/tempZone/home/rods/pycommands|465|+---------+-----------+-----------+---------------+--------------------------------+-----------+