def test_clear1(self):
bd1 = SetBDMap()
for k, v in self.mdat2:
bd1[k] = v
bd1.clear()
self.assertItemsEqual({}, bd1.fwd_map)
self.assertItemsEqual({}, bd1.bwd_map)
def __init__(self, **kwargs):
r"""
Parameters
----------
kwargs : dict
any keyworded arguments that may be used by the user for finer control (e.g.
in sublass); currently, no arguments are used
"""
self._jgmap = SetBDMap()
def configure(self, domains=None, recognized_relations=None):
r"""
Configure this manager.
Parameters
----------
domains : iterable of string/None
iterable of GO domains that this manager will recognize; if None, all domains
are recognized; None by default
recognized_relations : iterable of string/None
iterable of inter--term relations that this manager will recognize; if None,
default relations will be recognized (:data:`GO_DEF_RECOGNIZED_RELATIONS`); None by default
"""
# resolve recognized relations
if recognized_relations is None:
self.recognizedRelations = list(GO_DEF_RECOGNIZED_RELATIONS)
else:
self.recognizedRelations = recognized_relations
# constant iterable of PK recognized domains
if domains is None:
self.domains = tuple(GO_DS)
else:
self.domains = tuple(domains)
# direct dictionary of term data
self.terms = dict()
# additional map of synonym GO terms
self.synonyms = SetBDMap()
# additional map of terms grouped according to recognized relations
self.termsRelationsHierarchy = dict([
(r, SetBDMap()) for r in self.recognizedRelations
])
# additional map of term hierarchy (parent->child independently of relations)
self.termsPlainHierarchy = SetBDMap()
# configuration is finished
self.configured = True
def test_del1(self):
bd1 = SetBDMap()
bd1['a'] = 1
bd1['a'] = 1
bd1['a'] = 2
bd1['a'] = 2
bd1['b'] = 1
bd1['b'] = 1
bd1['b'] = 2
bd1['b'] = 2
ref1_fwd = {'a': set([1, 2]), 'b': set([1, 2])}
ref1_bwd = {1: set(['a', 'b']), 2: set(['a', 'b'])}
self.assertEqual(ref1_fwd, bd1.dumpFwdMap())
self.assertEqual(ref1_bwd, bd1.dumpBwdMap())
del bd1['b']
ref2_fwd = {'a': set([1, 2])}
ref2_bwd = {1: set(['a']), 2: set(['a'])}
self.assertEqual(ref2_fwd, bd1.dumpFwdMap())
self.assertEqual(ref2_bwd, bd1.dumpBwdMap())
def __init__(self):
super(PKCIDMapGOGPL, self).__init__()
self.domains_map = dict([(d, SetBDMap()) for d in GO_DS])
self.dbt = None
self.built = False
class JobGroupManager(object):
r"""
Simple manager of groups of jobs. Can be used for finer execution control and
to facilitate reporting.
"""
def __init__(self, **kwargs):
r"""
Parameters
----------
kwargs : dict
any keyworded arguments that may be used by the user for finer control (e.g.
in sublass); currently, no arguments are used
"""
self._jgmap = SetBDMap()
def addJobIDToGroup(self, group_name, jobID):
r"""
Add requested job to specified job group. If group was not defined before, it will
be created.
Parameters
----------
group_name : string
name of the group
jobID : string
job ID
"""
self._jgmap[group_name] = jobID
def addGroup(self, group_name, group_job_ids):
r"""
Add series of jobs to specified job group (shortcut). If group was not defined before, it will
be created.
Parameters
----------
group_name : string
name of the group
group_job_ids : iterable of string
job IDs
"""
for jid in group_job_ids:
self.addJobIDToGroup(group_name, jid)
def remGroup(self, group_name):
r"""
Remove specified job group from this manager. All associated job IDs are removed as
well. NOTE: physical jobs are left intact.
Parameters
----------
group_name : string
name of the group
"""
del self._jgmap[group_name]
def clear(self):
r"""
Removes all job groups from this manager.
"""
self._jgmap.clear()
def getGroupJobsIDs(self, group_name):
r"""
Get list of job IDs associated with specified job group name.
Parameters
----------
group_name : string
name of the group
Returns
-------
jobIDs : iterable of string
all job IDs from requested group, if exists
"""
return list(self._jgmap.getFwdMap()[group_name])
def findGroupByJobID(self, jobID):
r"""
Identify job group of the requested job ID.
Parameters
----------
jobID : string
job ID
Returns
-------
group_name : string
name of the group with requested job, if exists
Raises
------
Error
if jobID is found in more than one group
"""
gr = self._jgmap.getBwdMap()[jobID]
if len(gr) > 1:
# should not happen with SetBDMap but to be safe...
raise Error(
'Job shall be internally assigned to single group! (got %s)' %
gr)
# return single element from the set
return next(iter(gr))
def getGroups(self):
r"""
Get list of all job group names managed by this manager.
"""
return self._jgmap.getFwdMap().keys()
def __init__(self):
# all considered prior knowledge domains (separated groups of concepts, e.g. thematic)
self.domains = tuple()
# concept IDs grouped according to domains
self.domain2concepts = SetBDMap()
self.configured = False
def test_get1(self):
bd1 = SetBDMap()
bd1['a'] = 1
self.assertEqual(set([1]), bd1['a'])
self.assertEqual(bd1.keyIsMissing(), bd1['XXX'])
def test_set3(self):
bd1 = SetBDMap()
for k, v in self.mdat3:
bd1[k] = v
self.assertEqual(self.fwdmap3, bd1.dumpFwdMap())
self.assertEqual(self.bwdmap3, bd1.dumpBwdMap())
def test_set1(self):
bd1 = SetBDMap()
bd1['a'] = 1
bd1[1] = 'a'
self.assertEqual(self.circular, bd1.dumpFwdMap())
self.assertEqual(self.circular, bd1.dumpBwdMap())
def test_init2(self):
bd1 = SetBDMap(initial_map=self.mdict1)
self.assertEqual(self.fwdmap1, bd1.dumpFwdMap())
self.assertEqual(self.bwdmap1, bd1.dumpBwdMap())
def test_init1(self):
bd1 = SetBDMap()
self.assertEqual(self.emptyFwdMap, bd1.getFwdMap())
self.assertEqual(self.emptyBwdMap, bd1.getBwdMap())