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robustify w.r.t. sqlalchemy

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This commit is contained in:
Greg Landrum
2009-06-27 15:40:10 +00:00
parent fd81448571
commit f9c716684b
2 changed files with 25 additions and 100 deletions
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13
Projects/DbCLI/SearchDb.py
View File

@@ -452,19 +452,26 @@ if __name__=='__main__':
if molsOut and ids:
molDbName = os.path.join(options.dbDir,options.molDbName)
conn = DbConnect(molDbName)
cns = conn.GetColumnNames('molecules')
cns = list(conn.GetColumnNames('molecules'))
if cns[0]=='guid':
# from sqlalchemy, ditch it:
del cns[0]
if cns[-1]!='molpkl':
cns.remove('molpkl')
cns.append('molpkl')
curs = conn.GetCursor()
ids = [(x,) for x in ids]
curs.execute('create temporary table _tmpTbl (%(idName)s varchar)'%locals())
curs.executemany('insert into _tmpTbl values (?)',ids)
curs.execute('select * from molecules join _tmpTbl using (%(idName)s)'%locals())
cnText=','.join(cns)
curs.execute('select %(cnText)s from molecules join _tmpTbl using (%(idName)s)'%locals())
row=curs.fetchone()
while row:
m = Chem.Mol(str(row[-1]))
if sdfOut:
m.SetProp('_Name',str(row[0]))
print >>sdfOut,Chem.MolToMolBlock(m)
for i in range(1,len(cns)-2):
for i in range(1,len(cns)-1):
pn = cns[i]
pv = str(row[i])
print >>sdfOut,'> <%s>\n%s\n'%(pn,pv)

112
Projects/DbCLI/TestDbCLI.py
View File

@@ -279,92 +279,6 @@ class TestCase(unittest.TestCase):
self.failUnless(len(lines)==25)
os.unlink('testData/bzr/search.out')
def test3_1SDSearch(self):
self.failUnless(os.path.exists('testData/bzr/Compounds.sqlt'))
p = subprocess.Popen(('python', 'SDSearch.py','--dbName=testData/bzr/Compounds.sqlt',
'--nameOut=testData/bzr/search.out'))
res=p.wait()
self.failIf(res)
p=None
self.failUnless(os.path.exists('testData/bzr/search.out'))
inF = file('testData/bzr/search.out','r')
lines=inF.readlines()
inF=None
self.failUnless(len(lines)==163)
os.unlink('testData/bzr/search.out')
def test3_2SDSearch(self):
self.failUnless(os.path.exists('testData/bzr/Compounds.sqlt'))
p = subprocess.Popen(('python', 'SDSearch.py','--dbName=testData/bzr/Compounds.sqlt',
'--nameOut=testData/bzr/search.out', '-q activity<6.0'))
res=p.wait()
self.failIf(res)
p=None
self.failUnless(os.path.exists('testData/bzr/search.out'))
inF = file('testData/bzr/search.out','r')
lines=inF.readlines()
inF=None
self.failUnless(len(lines)==17)
os.unlink('testData/bzr/search.out')
def test3_3SDSearch(self):
from rdkit import Chem
self.failUnless(os.path.exists('testData/bzr/Compounds.sqlt'))
p = subprocess.Popen(('python', 'SDSearch.py','--dbName=testData/bzr/Compounds.sqlt',
'--nameOut=testData/bzr/search.out', '--smarts=cncncc',
'--sdOut=testData/bzr/search.out.sdf'))
res=p.wait()
self.failIf(res)
p=None
self.failUnless(os.path.exists('testData/bzr/search.out'))
inF = file('testData/bzr/search.out','r')
lines=inF.readlines()
inF=None
self.failUnless(len(lines)==49)
suppl=Chem.SDMolSupplier('testData/bzr/search.out.sdf')
ms = [x for x in suppl]
suppl=None
self.failUnless(len(ms)==49)
for i,m in enumerate(ms):
self.failUnless(m.GetProp('_Name')==lines[i].strip())
os.unlink('testData/bzr/search.out')
os.unlink('testData/bzr/search.out.sdf')
def test3_4SDSearch(self):
from rdkit import Chem
self.failUnless(os.path.exists('testData/bzr/Compounds.sqlt'))
p = subprocess.Popen(('python', 'SDSearch.py','--dbName=testData/bzr/Compounds.sqlt',
'--nameOut=testData/bzr/search.out', '--smarts=cncncc',
'-q activity<6.0',
'--sdOut=testData/bzr/search.out.sdf'))
res=p.wait()
self.failIf(res)
p=None
self.failUnless(os.path.exists('testData/bzr/search.out'))
inF = file('testData/bzr/search.out','r')
lines=inF.readlines()
inF=None
self.failUnless(len(lines)==5)
suppl=Chem.SDMolSupplier('testData/bzr/search.out.sdf')
ms = [x for x in suppl]
suppl=None
self.failUnless(len(ms)==5)
for i,m in enumerate(ms):
self.failUnless(m.GetProp('_Name')==lines[i].strip())
os.unlink('testData/bzr/search.out')
os.unlink('testData/bzr/search.out.sdf')
def test4CreateOptions(self):
if os.path.exists('testData/bzr/Compounds.sqlt'):
@@ -390,10 +304,12 @@ class TestCase(unittest.TestCase):
conn = DbConnect('testData/bzr/Compounds.sqlt')
d = conn.GetData('molecules',fields='count(*)')
self.failUnless(d[0][0]==10)
self.failUnlessEqual(d[0][0],10)
d = conn.GetData('molecules',fields='*')
self.failUnless(len(d)==10)
self.failUnless(len(d[0])==2)
self.failUnlessEqual(len(d),10)
cns = [x.lower() for x in d.GetColumnNames()]
self.failIf('smiles' in cns)
conn=None
d=None
@@ -423,9 +339,9 @@ class TestCase(unittest.TestCase):
self.failUnless(d[0][0]==10)
d = conn.GetData('molecules',fields='*')
self.failUnless(len(d)==10)
self.failUnless(len(d[0])==2)
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','--noPairs','--noDescriptors',
'testData/bzr.smi'))
@@ -440,10 +356,11 @@ class TestCase(unittest.TestCase):
conn = DbConnect('testData/bzr/Compounds.sqlt')
d = conn.GetData('molecules',fields='count(*)')
self.failUnless(d[0][0]==10)
self.failUnlessEqual(d[0][0],10)
d = conn.GetData('molecules',fields='*')
self.failUnless(len(d)==10)
self.failUnless(len(d[0])==3)
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',
@@ -460,10 +377,11 @@ class TestCase(unittest.TestCase):
conn = DbConnect('testData/bzr/Compounds.sqlt')
d = conn.GetData('molecules',fields='count(*)')
self.failUnless(d[0][0]==10)
self.failUnlessEqual(d[0][0],10)
d = conn.GetData('molecules',fields='*')
self.failUnless(len(d)==10)
self.failUnless(len(d[0])==3)
self.failUnlessEqual(len(d),10)
cns = [x.lower() for x in d.GetColumnNames()]
self.failUnless('smiles' in cns)