def createdb(local=None,
server=None,
project=None,
username=None,
norecs=1000):
"""Create and add some test data"""
if local != None:
if os.path.exists(local):
for i in ['.lock', '.index', '']:
try:
os.remove(local + i)
except:
pass
DB = PDatabase(local=local)
elif server != None:
DB = PDatabase(server=server,
username=username,
password='******',
project=project)
import string
import DNAtool.mutation as mutation
choices = ['a', 'b', 'c', 'd']
DB.addField('choice', 'text')
DB.addField('stab', 'text')
DB.addField('activity', 'text')
#DB.addField('ekin', 'General')
E = EkinProject()
data = E.readDataset('Ekin/test.Ekindat')
E.insertDataset(data['data'], 'test', fit=data['fit'])
print 'creating dummy data..'
j = 0
count = 0
for i in range(norecs):
if j > 3: j = 0
c = ''
for k in range(10):
c += random.choice(string.letters)
DB.add(c)
DB.data[c].choice = choices[j]
DB.data[c].DNASeq = simulate_sequence(300)
AAseqs3, AAseqs1 = mutation.translate(DB.data[c].DNASeq)
DB.addProtseq(c, AAseqs3[1][5:80], 1)
DB.data[c].stab = str(round(random.normalvariate(1, 2), 3))
DB.data[c].activity = str(round(random.normalvariate(30, 4), 3))
#DB.data[c].ekin = E
j += 1
count += 1
if count > 3000:
print 'saving..'
DB.commit()
DB.db.cacheMinimize()
count = 0
DB.commit()
return DB
def speedTest1():
"""benchmark read and write"""
DB = PDatabase(server='localhost',port=8090)
#DB = PDatabase(local='./Data.fs')
for i in range(100,300):
DB.add(i)
for i in range(100,290):
DB.delete(i)
DB.commit()
print DB
DB.close()
return
def speedTest1():
"""benchmark read and write"""
DB = PDatabase(server='localhost', port=8090)
#DB = PDatabase(local='./Data.fs')
for i in range(100, 300):
DB.add(i)
for i in range(100, 290):
DB.delete(i)
DB.commit()
print DB
DB.close()
return
def createdb(local=None, server=None, project=None, username=None, norecs=1000):
"""Create and add some test data"""
if local != None:
if os.path.exists(local):
for i in ['.lock','.index','']:
try:
os.remove(local+i)
except:
pass
DB = PDatabase(local=local)
elif server!=None:
DB = PDatabase(server=server, username=username,
password='******', project=project)
import string
import DNAtool.mutation as mutation
choices = ['a','b','c','d']
DB.addField('choice', 'text')
DB.addField('stab', 'text')
DB.addField('activity', 'text')
#DB.addField('ekin', 'General')
E = EkinProject()
data=E.readDataset('Ekin/test.Ekindat')
E.insertDataset(data['data'], 'test', fit=data['fit'])
print 'creating dummy data..'
j=0
count=0
for i in range(norecs):
if j>3: j=0
c=''
for k in range(10):
c += random.choice(string.letters)
DB.add(c)
DB.data[c].choice = choices[j]
DB.data[c].DNASeq = simulate_sequence(300)
AAseqs3,AAseqs1 = mutation.translate(DB.data[c].DNASeq)
DB.addProtseq(c, AAseqs3[1][5:80], 1)
DB.data[c].stab = str(round(random.normalvariate(1,2),3))
DB.data[c].activity = str(round(random.normalvariate(30,4),3))
#DB.data[c].ekin = E
j+=1
count+=1
if count>3000:
print 'saving..'
DB.commit()
DB.db.cacheMinimize()
count=0
DB.commit()
return DB
def testBlob():
"""write a file as binary data to blob and read back"""
from ZODB.PersistentMapping import PersistentMapping
import mimetypes
from PILView import PILViewer
DB = PDatabase(server='localhost',port=8090,
username='******',
password='******')
def addfile(fname):
myblob = Blob()
b=myblob.open('w')
o=open(fname)
data = o.read()
b.write(data)
print b.name
b.close()
return myblob
dirlist=os.listdir(os.getcwd())
for f in dirlist:
m = mimetypes.guess_type(f)[0]
if m != None and 'image' in m:
print f
b=addfile(f)
DB.add(f)
DB.data[f]['testfile']=FileRecord(name=f,blob=b)
DB.commit()
for k in DB.data:
if not DB.data[k].has_key('testfile'):
continue
rec = DB.data[k]['testfile']
myblob = rec.blob
f = myblob.open("r")
print f.name
#app = PILViewer(imgfile=f.name)
#app.mainloop()
DB.close()
return
def testBlob():
"""write a file as binary data to blob and read back"""
from ZODB.PersistentMapping import PersistentMapping
import mimetypes
from PILView import PILViewer
DB = PDatabase(server='localhost',
port=8090,
username='******',
password='******')
def addfile(fname):
myblob = Blob()
b = myblob.open('w')
o = open(fname)
data = o.read()
b.write(data)
print b.name
b.close()
return myblob
dirlist = os.listdir(os.getcwd())
for f in dirlist:
m = mimetypes.guess_type(f)[0]
if m != None and 'image' in m:
print f
b = addfile(f)
DB.add(f)
DB.data[f]['testfile'] = FileRecord(name=f, blob=b)
DB.commit()
for k in DB.data:
if not DB.data[k].has_key('testfile'):
continue
rec = DB.data[k]['testfile']
myblob = rec.blob
f = myblob.open("r")
print f.name
#app = PILViewer(imgfile=f.name)
#app.mainloop()
DB.close()
return