def test_ForwardDbFpSupplier(self):
# Additional tests to complete code coverage
conn = DbConnect(RDConfig.RDTestDatabase, 'simple_combined')
self.assertRaises(ValueError, DbFpSupplier.ForwardDbFpSupplier, conn.GetData(),
fpColName='typo')
suppl = DbFpSupplier.ForwardDbFpSupplier(conn.GetData(), fpColName='AutoFragmentFp')
self.assertIn('ID', suppl.GetColumnNames())
def test6Update(self):
p = subprocess.Popen(('python', 'CreateDb.py','--dbDir=testData/bzr','--molFormat=smiles',
'testData/bzr.smi'))
res=p.wait()
self.assertFalse(res)
p=None
self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt'))
self.assertTrue(os.path.exists('testData/bzr/AtomPairs.sqlt'))
self.assertTrue(os.path.exists('testData/bzr/Descriptors.sqlt'))
self.assertTrue(os.path.exists('testData/bzr/Fingerprints.sqlt'))
conn = DbConnect('testData/bzr/Compounds.sqlt')
d = conn.GetData('molecules',fields='count(*)')
self.assertEqual(d[0][0],10)
conn = DbConnect('testData/bzr/AtomPairs.sqlt')
d = conn.GetData('atompairs',fields='count(*)')
self.assertEqual(d[0][0],10)
conn = DbConnect('testData/bzr/Descriptors.sqlt')
d = conn.GetData('descriptors_v1',fields='count(*)')
self.assertEqual(d[0][0],10)
conn = DbConnect('testData/bzr/Fingerprints.sqlt')
d = conn.GetData('rdkitfps',fields='count(*)')
self.assertEqual(d[0][0],10)
p = subprocess.Popen(('python', 'CreateDb.py','--dbDir=testData/bzr','--molFormat=smiles',
'--updateDb',
'testData/bzr.2.smi'))
res=p.wait()
self.assertFalse(res)
p=None
self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt'))
self.assertTrue(os.path.exists('testData/bzr/AtomPairs.sqlt'))
self.assertTrue(os.path.exists('testData/bzr/Descriptors.sqlt'))
self.assertTrue(os.path.exists('testData/bzr/Fingerprints.sqlt'))
conn = DbConnect('testData/bzr/Compounds.sqlt')
d = conn.GetData('molecules',fields='count(*)')
self.assertEqual(d[0][0],20)
conn = DbConnect('testData/bzr/AtomPairs.sqlt')
d = conn.GetData('atompairs',fields='count(*)')
self.assertEqual(d[0][0],20)
conn = DbConnect('testData/bzr/Descriptors.sqlt')
d = conn.GetData('descriptors_v1',fields='count(*)')
self.assertEqual(d[0][0],20)
conn = DbConnect('testData/bzr/Fingerprints.sqlt')
d = conn.GetData('rdkitfps',fields='count(*)')
self.assertEqual(d[0][0],20)
def SupplierFromDetails(details):
from rdkit.VLib.NodeLib.DbMolSupply import DbMolSupplyNode
from rdkit.VLib.NodeLib.SmilesSupply import SmilesSupplyNode
if details.dbName:
conn = DbConnect(details.dbName, details.tableName)
suppl = DbMolSupplyNode(conn.GetData())
else:
suppl = SmilesSupplyNode(details.inFileName, delim=details.delim, nameColumn=details.nameCol,
smilesColumn=details.smiCol, titleLine=details.hasTitle)
if isinstance(details.actCol, int):
suppl.reset()
m = next(suppl)
actName = m.GetPropNames()[details.actCol]
details.actCol = actName
if isinstance(details.nameCol, int):
suppl.reset()
m = next(suppl)
nameName = m.GetPropNames()[details.nameCol]
details.nameCol = nameName
suppl.reset()
if isinstance(details.actCol, int):
suppl.reset()
m = next(suppl)
actName = m.GetPropNames()[details.actCol]
details.actCol = actName
if isinstance(details.nameCol, int):
suppl.reset()
m = next(suppl)
nameName = m.GetPropNames()[details.nameCol]
details.nameCol = nameName
suppl.reset()
return suppl
def test_InsertData(self):
newTblName = 'NEW_TABLE'
conn = DbConnect(self.tempDbName)
try:
conn.GetCursor().execute('drop table %s' % (newTblName))
except Exception:
pass
conn.Commit()
conn.AddTable(newTblName, 'id int,val1 int, val2 int')
for i in range(10):
conn.InsertData(newTblName, (i, i + 1, 2 * i))
conn.Commit()
d = conn.GetData(table=newTblName)
assert len(d) == 10
self.assertEqual(len(conn.GetColumnNames(table=newTblName)), 3)
conn.AddColumn(newTblName, 'val3', 'int')
conn.Commit()
self.assertEqual(len(conn.GetColumnNames(table=newTblName)), 4)
d = conn.GetColumns('id,val3', table=newTblName)
self.assertEqual(len(d), 10)
self.assertTrue(all(r[1] is None for r in d))
for r in d:
conn.InsertColumnData(newTblName, 'val3', r[0],
'id={0}'.format(r[0]))
conn.Commit()
d = conn.GetColumns('id,val3', table=newTblName)
self.assertTrue(all(r[0] == r[1] for r in d))
d = None
try:
conn.GetCursor().execute('drop table %s' % (newTblName))
except Exception:
assert 0, 'drop table failed'
def test1Create(self):
p = subprocess.Popen(
(sys.executable, 'CreateDb.py', '--dbDir=testData/bzr',
'--molFormat=smiles', 'testData/bzr.smi'))
res = p.wait()
self.assertFalse(res)
p = None
self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt'))
self.assertTrue(os.path.exists('testData/bzr/AtomPairs.sqlt'))
self.assertTrue(os.path.exists('testData/bzr/Descriptors.sqlt'))
self.assertTrue(os.path.exists('testData/bzr/Fingerprints.sqlt'))
conn = DbConnect('testData/bzr/Compounds.sqlt')
d = conn.GetData('molecules', fields='count(*)')
self.assertTrue(d[0][0] == 10)
conn = DbConnect('testData/bzr/AtomPairs.sqlt')
d = conn.GetData('atompairs', fields='count(*)')
self.assertTrue(d[0][0] == 10)
conn = DbConnect('testData/bzr/Descriptors.sqlt')
d = conn.GetData('descriptors_v1', fields='count(*)')
self.assertTrue(d[0][0] == 10)
conn = DbConnect('testData/bzr/Fingerprints.sqlt')
d = conn.GetData('rdkitfps', fields='count(*)')
self.assertTrue(d[0][0] == 10)
p = subprocess.Popen(
(sys.executable, 'CreateDb.py', '--dbDir=testData/bzr',
'--molFormat=sdf', '--doGobbi2D', 'testData/bzr.sdf'))
res = p.wait()
self.assertFalse(res)
p = None
self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt'))
self.assertTrue(os.path.exists('testData/bzr/AtomPairs.sqlt'))
self.assertTrue(os.path.exists('testData/bzr/Descriptors.sqlt'))
self.assertTrue(os.path.exists('testData/bzr/Fingerprints.sqlt'))
conn = DbConnect('testData/bzr/Compounds.sqlt')
d = conn.GetData('molecules', fields='count(*)')
self.assertTrue(d[0][0] == 163)
conn = DbConnect('testData/bzr/AtomPairs.sqlt')
d = conn.GetData('atompairs', fields='count(*)')
self.assertTrue(d[0][0] == 163)
conn = DbConnect('testData/bzr/Descriptors.sqlt')
d = conn.GetData('descriptors_v1', fields='count(*)')
self.assertTrue(d[0][0] == 163)
conn = DbConnect('testData/bzr/Fingerprints.sqlt')
d = conn.GetData('rdkitfps', fields='count(*)')
self.assertTrue(d[0][0] == 163)
def testGetData1(self):
""" basic functionality
"""
conn = DbConnect(self.dbName, 'ten_elements')
d = conn.GetData(randomAccess=1)
assert len(d) == 10
assert tuple(d[0]) == (0, 11)
assert tuple(d[2]) == (4, 31)
self.assertRaises(IndexError, lambda: d[11])
def testGetData2(self):
""" using removeDups
"""
conn = DbConnect(self.dbName, 'ten_elements_dups')
d = conn.GetData(randomAccess=1, removeDups=1)
assert tuple(d[0]) == (0, 11)
assert tuple(d[2]) == (4, 31)
assert len(d) == 10
self.assertRaises(IndexError, lambda: d[11])
def testGetData3(self):
""" without removeDups
"""
conn = DbConnect(self.dbName, 'ten_elements_dups')
d = conn.GetData(randomAccess=1, removeDups=-1)
assert tuple(d[0]) == (0, 11)
assert tuple(d[2]) == (2, 21)
assert len(d) == 20
self.assertRaises(IndexError, lambda: d[21])
# repeat that test to make sure the table argument works
conn = DbConnect(self.dbName, 'ten_elements')
d = conn.GetData(table='ten_elements_dups',
randomAccess=1,
removeDups=-1)
assert tuple(d[0]) == (0, 11)
assert tuple(d[2]) == (2, 21)
assert len(d) == 20
self.assertRaises(IndexError, lambda: d[21])
def testGetData5(self):
""" using a RandomAccessDbResultSet with a Transform
"""
fn = lambda x: (x[0], x[1] * 2)
conn = DbConnect(self.dbName, 'ten_elements')
d = conn.GetData(randomAccess=1, transform=fn)
assert tuple(d[0]) == (0, 22), str(d[0])
assert tuple(d[2]) == (4, 62)
assert len(d) == 10
self.assertRaises(IndexError, lambda: d[11])
def GetComposites(details):
res = []
if details.persistTblName and details.inNote:
conn = DbConnect(details.dbName,details.persistTblName)
mdls = conn.GetData(fields='MODEL',where="where note='%s'"%(details.inNote))
for row in mdls:
rawD = row[0]
res.append(cPickle.loads(str(rawD)))
elif details.composFileName:
res.append(cPickle.load(open(details.composFileName,'rb')))
return res
def DBToData(dbName, tableName, user='******', password='******', dupCol=-1, what='*', where='',
join='', pickleCol=-1, pickleClass=None, ensembleIds=None):
""" constructs an _MLData.MLDataSet_ from a database
**Arguments**
- dbName: the name of the database to be opened
- tableName: the table name containing the data in the database
- user: the user name to be used to connect to the database
- password: the password to be used to connect to the database
- dupCol: if nonzero specifies which column should be used to recognize
duplicates.
**Returns**
an _MLData.MLDataSet_
**Notes**
- this uses Dbase.DataUtils functionality
"""
conn = DbConnect(dbName, tableName, user, password)
res = conn.GetData(fields=what, where=where, join=join, removeDups=dupCol, forceList=1)
nPts = len(res)
vals = [None] * nPts
ptNames = [None] * nPts
classWorks = True
for i in range(nPts):
tmp = list(res[i])
ptNames[i] = tmp.pop(0)
if pickleCol >= 0:
if not pickleClass or not classWorks:
tmp[pickleCol] = cPickle.loads(str(tmp[pickleCol]))
else:
try:
tmp[pickleCol] = pickleClass(str(tmp[pickleCol]))
except Exception:
tmp[pickleCol] = cPickle.loads(str(tmp[pickleCol]))
classWorks = False
if ensembleIds:
tmp[pickleCol] = BitUtils.ConstructEnsembleBV(tmp[pickleCol], ensembleIds)
else:
if ensembleIds:
tmp = TakeEnsemble(tmp, ensembleIds, isDataVect=True)
vals[i] = tmp
varNames = conn.GetColumnNames(join=join, what=what)
data = MLData.MLDataSet(vals, varNames=varNames, ptNames=ptNames)
return data
def testGetData4(self):
""" non random access
"""
conn = DbConnect(self.dbName, 'ten_elements')
d = conn.GetData(randomAccess=0)
self.assertRaises(TypeError, lambda: len(d))
rs = []
for thing in d:
rs.append(thing)
assert len(rs) == 10
assert tuple(rs[0]) == (0, 11)
assert tuple(rs[2]) == (4, 31)
def testGetData6(self):
""" using a DbResultSet with a Transform
"""
fn = lambda x: (x[0], x[1] * 2)
conn = DbConnect(self.dbName, 'ten_elements')
d = conn.GetData(randomAccess=0, transform=fn)
self.assertRaises(TypeError, lambda: len(d))
rs = []
for thing in d:
rs.append(thing)
assert len(rs) == 10
assert tuple(rs[0]) == (0, 22)
assert tuple(rs[2]) == (4, 62)
def getTestData(self):
dbName = RDConfig.RDTestDatabase
conn = DbConnect(dbName, 'simple_mols1')
mols = []
for smi, ID in conn.GetData():
mol = Chem.MolFromSmiles(str(smi))
mol.SetProp('_Name', str(ID))
mols.append(mol)
# Calculate fingerprints
probefps = []
for mol in mols:
fp = Chem.RDKFingerprint(mol)
fp._id = mol.GetProp('_Name')
probefps.append(fp)
return probefps
def testGetData1(self):
""" basic functionality
"""
conn = DbConnect(self.dbName, 'ten_elements')
d = conn.GetData(randomAccess=1)
assert len(d) == 10
assert tuple(d[0]) == (0, 11)
assert tuple(d[2]) == (4, 31)
self.assertRaises(IndexError, lambda: d[11])
d = conn.GetColumns(fields='id,val')
self.assertEqual(len(d), 10)
assert tuple(d[0]) == (0, 11)
assert tuple(d[2]) == (4, 31)
self.assertEqual(conn.GetDataCount(), 10)
def testInsertData(self):
""" tests InsertData and InsertColumnData functionalities """
newTblName = 'NEW_TABLE'
conn = DbConnect(self.tempDbName)
try:
conn.GetCursor().execute('drop table %s' % (newTblName))
except Exception:
pass
conn.Commit()
conn.AddTable(newTblName, 'id int,val1 int, val2 int')
for i in range(10):
conn.InsertData(newTblName, (i, i + 1, 2 * i))
conn.Commit()
d = conn.GetData(table=newTblName)
assert len(d) == 10
d = None
try:
conn.GetCursor().execute('drop table %s' % (newTblName))
except Exception:
assert 0, 'drop table failed'
elif arg == '--enrich':
enrich = int(val)
composites = []
if db is None:
for arg in extras:
composite = cPickle.load(open(arg, 'rb'))
composites.append(composite)
else:
tbl = extras[0]
conn = DbConnect(db, tbl)
if note:
where = "where note='%s'" % (note)
else:
where = ''
if not skip:
pkls = conn.GetData(fields='model', where=where)
composites = []
for pkl in pkls:
pkl = str(pkl[0])
comp = cPickle.loads(pkl)
composites.append(comp)
if len(composites):
ProcessIt(composites, count, verbose=verbose)
elif not skip:
print('ERROR: no composite models found')
sys.exit(-1)
if db:
res = ErrorStats(conn, where, enrich=enrich)
if res:
def GetNode(dbName, tableName):
from rdkit.Dbase.DbConnection import DbConnect
conn = DbConnect(dbName, tableName)
return DbMolSupplyNode(conn.GetData())
from rdkit import Chem
from rdkit import RDConfig
from rdkit.Dbase import DbModule
from rdkit.Dbase.DbConnection import DbConnect
import pickle
if RDConfig.usePgSQL:
dbName = "::RDTests"
else:
dbName = "data.sqlt"
molTblName = 'simple_mols1'
fpTblName = 'simple_mols1_fp'
conn = DbConnect(dbName, molTblName)
conn.AddTable(fpTblName,
'id varchar(10),autofragmentfp %s' % DbModule.binaryTypeName)
d = conn.GetData()
for smi, ID in d:
print(repr(ID), repr(smi))
mol = Chem.MolFromSmiles(smi)
fp = Chem.RDKFingerprint(mol)
pkl = pickle.dumps(fp)
conn.InsertData(fpTblName, (ID, DbModule.binaryHolder(pkl)))
conn.Commit()
def test4CreateOptions(self):
if os.path.exists('testData/bzr/Compounds.sqlt'):
os.unlink('testData/bzr/Compounds.sqlt')
if os.path.exists('testData/bzr/AtomPairs.sqlt'):
os.unlink('testData/bzr/AtomPairs.sqlt')
if os.path.exists('testData/bzr/Descriptors.sqlt'):
os.unlink('testData/bzr/Descriptors.sqlt')
if os.path.exists('testData/bzr/Fingerprints.sqlt'):
os.unlink('testData/bzr/Fingerprints.sqlt')
p = subprocess.Popen(('python', 'CreateDb.py', '--dbDir=testData/bzr',
'--molFormat=smiles', '--noExtras', '--noSmiles',
'testData/bzr.smi'))
res = p.wait()
self.failIf(res)
p = None
self.failUnless(os.path.exists('testData/bzr/Compounds.sqlt'))
self.failIf(os.path.exists('testData/bzr/AtomPairs.sqlt'))
self.failIf(os.path.exists('testData/bzr/Descriptors.sqlt'))
self.failIf(os.path.exists('testData/bzr/Fingerprints.sqlt'))
conn = DbConnect('testData/bzr/Compounds.sqlt')
d = conn.GetData('molecules', fields='count(*)')
self.failUnlessEqual(d[0][0], 10)
d = conn.GetData('molecules', fields='*')
self.failUnlessEqual(len(d), 10)
cns = [x.lower() for x in d.GetColumnNames()]
self.failIf('smiles' in cns)
conn = None
d = None
if os.path.exists('testData/bzr/Compounds.sqlt'):
os.unlink('testData/bzr/Compounds.sqlt')
if os.path.exists('testData/bzr/AtomPairs.sqlt'):
os.unlink('testData/bzr/AtomPairs.sqlt')
if os.path.exists('testData/bzr/Descriptors.sqlt'):
os.unlink('testData/bzr/Descriptors.sqlt')
if os.path.exists('testData/bzr/Fingerprints.sqlt'):
os.unlink('testData/bzr/Fingerprints.sqlt')
p = subprocess.Popen(
('python', 'CreateDb.py', '--dbDir=testData/bzr',
'--molFormat=smiles', '--noSmiles', '--noFingerprints',
'--noLayeredFps', '--noMorganFps', '--noPairs', '--noDescriptors',
'testData/bzr.smi'))
res = p.wait()
self.failIf(res)
p = None
self.failUnless(os.path.exists('testData/bzr/Compounds.sqlt'))
self.failIf(os.path.exists('testData/bzr/AtomPairs.sqlt'))
self.failIf(os.path.exists('testData/bzr/Descriptors.sqlt'))
self.failIf(os.path.exists('testData/bzr/Fingerprints.sqlt'))
conn = DbConnect('testData/bzr/Compounds.sqlt')
d = conn.GetData('molecules', fields='count(*)')
self.failUnless(d[0][0] == 10)
d = conn.GetData('molecules', fields='*')
self.failUnless(len(d) == 10)
cns = [x.lower() for x in d.GetColumnNames()]
self.failIf('smiles' in cns)
p = subprocess.Popen(
('python', 'CreateDb.py', '--dbDir=testData/bzr',
'--molFormat=smiles', '--noProps', '--noFingerprints',
'--noLayeredFps', '--noMorganFps', '--noPairs', '--noDescriptors',
'testData/bzr.smi'))
res = p.wait()
self.failIf(res)
p = None
self.failUnless(os.path.exists('testData/bzr/Compounds.sqlt'))
self.failIf(os.path.exists('testData/bzr/AtomPairs.sqlt'))
self.failIf(os.path.exists('testData/bzr/Descriptors.sqlt'))
self.failIf(os.path.exists('testData/bzr/Fingerprints.sqlt'))
conn = DbConnect('testData/bzr/Compounds.sqlt')
d = conn.GetData('molecules', fields='count(*)')
self.failUnlessEqual(d[0][0], 10)
d = conn.GetData('molecules', fields='*')
self.failUnlessEqual(len(d), 10)
cns = [x.lower() for x in d.GetColumnNames()]
self.failUnless('smiles' in cns)
p = subprocess.Popen(
('python', 'CreateDb.py', '--dbDir=testData/bzr',
'--molFormat=smiles', '--noFingerprints', '--noLayeredFps',
'--noMorganFps', '--noPairs', '--noDescriptors',
'--maxRowsCached=4', 'testData/bzr.smi'))
res = p.wait()
self.failIf(res)
p = None
self.failUnless(os.path.exists('testData/bzr/Compounds.sqlt'))
self.failIf(os.path.exists('testData/bzr/AtomPairs.sqlt'))
self.failIf(os.path.exists('testData/bzr/Descriptors.sqlt'))
self.failIf(os.path.exists('testData/bzr/Fingerprints.sqlt'))
conn = DbConnect('testData/bzr/Compounds.sqlt')
d = conn.GetData('molecules', fields='count(*)')
self.failUnlessEqual(d[0][0], 10)
d = conn.GetData('molecules', fields='*')
self.failUnlessEqual(len(d), 10)
cns = [x.lower() for x in d.GetColumnNames()]
self.failUnless('smiles' in cns)
p = subprocess.Popen(
('python', 'CreateDb.py', '--dbDir=testData/bzr',
'--molFormat=smiles', '--noFingerprints', '--noPairs',
'--noDescriptors', '--maxRowsCached=4', 'testData/bzr.smi'))
res = p.wait()
self.failIf(res)
p = None
self.failUnless(os.path.exists('testData/bzr/Compounds.sqlt'))
self.failIf(os.path.exists('testData/bzr/AtomPairs.sqlt'))
self.failIf(os.path.exists('testData/bzr/Descriptors.sqlt'))
self.failUnless(os.path.exists('testData/bzr/Fingerprints.sqlt'))
