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
- 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 resources
- GSI authentication
- Unicode strings
- Python 2.7, 3.4 or newer
PRC requires Python 2.7 or 3.4+. To install with pip:
pip install python-irodsclientor:
pip install git+https://github.com/irods/python-irodsclient.git[@branch|@commit|@tag]pip uninstall python-irodsclient>>> from irods.session import iRODSSession >>> sess = iRODSSession(host='localhost', port=1247, user='rods', password='rods', zone='tempZone')If you're an administrator acting on behalf of another user:
>>> from irods.session import iRODSSession >>> 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.
>>> coll = sess.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 = sess.collections.create("/tempZone/home/rods/testdir") >>> coll.id 45799Create 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.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 1PRC provides file-like objects for reading and writing files
>>> obj = sess.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>>> obj = sess.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)>]>>> from irods.session import iRODSSession >>> from irods.models import Collection, 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() >>> print results +---------+-----------+-----------+---------------+--------------------------------+-----------+ | 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 | +---------+-----------+-----------+---------------+--------------------------------+-----------+Query with aggregation(min, max, sum, avg, count):
>>> results = sess.query(DataObject.owner_name).count(DataObject.id).sum(DataObject.size).all() >>> print results +--------------+-----------+-----------+ | D_OWNER_NAME | D_DATA_ID | DATA_SIZE | +--------------+-----------+-----------+ | rods | 10 | 10836 | +--------------+-----------+-----------+Run a Specifc Query (similar to iquest --sql ), using the 0.6.0 additional functionality of reading the iRODS environment files:
>>> import os >>> import json >>> >>> from irods.session import iRODSSession >>> from irods.models import Collection, DataObject, Resource >>> from irods.query import SpecificQuery >>> >>> >>> def get_session(): ... """ ... establish a session to the iCAT server, using the iRODS environment env_file ... (MUST use library version >= 0.6.0) ... evaluate where to get the session information from, ... return an iRODS session *and* array with irods_environment.json info encoded for later use ... example decoded irods_environment.json; ... >>> pprint(ienv) ... {u'irods_authentication_scheme': u'KRB', ... u'irods_cwd': u'/DevZone/home/john', ... u'irods_def_resource': u'wtsiusers', ... u'irods_home': u'/DevZone/home/john', ... u'irods_host': u'icat.genomeresearch.ac.uk', ... u'irods_port': 1247, ... u'irods_user_name': u'john', ... u'irods_zone_name': u'DevZone'} ... """ ... try: ... env_file = os.environ['IRODS_ENVIRONMENT_FILE'] ... except KeyError: ... env_file = os.path.expanduser('~/.irods/irods_environment.json') ... with open(env_file) as data_file: ... ienv = json.load(data_file) ... return (iRODSSession(irods_env_file=env_file), ienv) ... >>> >>> >>> (SESS, ienv_info) = get_session() >>> >>> #test session working OK ... col_to_check = "/{}/home/irods".format(ienv_info['irods_zone_name']) >>> coll = SESS.collections.get(col_to_check) >>> print coll.id 10286 >>> >>> CompoundResourceTree = "root" >>> # make specific query ... sql = "select count(*) from r_data_main where resc_name = '{}' and data_is_dirty = '0'".format(CompoundResourceTree) >>> sql_alias = 'DirtyReplicas{}'.format(CompoundResourceTree) >>> query = SpecificQuery(SESS, sql, sql_alias) >>> >>> # register query in iCAT ... query.register() <irods.message.iRODSMessage object at 0x1face50> >>> >>> #run the Specific Query ... res_q = SpecificQuery(SESS, alias=sql_alias) >>> res_q.get_results() <generator object get_results at 0x1d2e730> >>> for r in res_q.get_results(): ... print(r[0]) ... 0