def createProjects(files):
"""Create multiple projects at once from csv files"""
for filename in files:
print filename
name = os.path.splitext(filename)[0]
#create/open db
DB = PDatabase(local=os.path.join(savepath,name))
DB.add('wt')
#add wt pdb
stream = DBActions.fetchPDB(name)
DBActions.addPDBFile(DB, 'wt', pdbdata=stream, pdbname=name, gui=False)
DB.meta.refprotein = 'wt'
DB.meta.info['protein'] = name
#import data from csv
DB.importCSV(os.path.join(cpath,filename), namefield='Mutations')
print 'imported ok'
DB.deleteField('PDB')
DB.commit()
DB.close()
print 'done'
return
def importOldProj(datadir,local=None, server=None,
project=None, username=None):
"""Import old peat projects"""
import PEAT_DB.Database as peatDB
from PEAT_DB.PEAT_dict import PEAT_dict, sub_dict
import copy
if local != None:
newDB = PDatabase(local=local)
elif server != None:
newDB = PDatabase(server=server, username=username, port=8080,
password='******', project=project)
print newDB
PT = peatDB.Database(datadir, Tk=False)
oldDB = PT.DB
print 'got old peat_db with %s proteins' %len(PT.proteins)
print PT.DB.keys()
#import meta stuff like userfields, table
for p in newDB.meta.special:
if not p in PT.DB.keys():
continue
print 'adding',p
for k in PT.DB[p]:
newDB.meta[p][k] = copy.deepcopy(PT.DB[p][k])
newDB.meta._p_changed = 1
for p in PT.proteins:
if p in newDB.meta.special:
continue
name = oldDB[p]['Name']
rec = PEATRecord(name=name)
for col in oldDB[p].keys():
cdata = oldDB[p][col]
recdata = {}
if col == 'name':
cdata = oldDB[p]['Name']
if oldDB['userfields'].has_key(col) and oldDB['userfields'][col]['field_type'] in ekintypes:
E=EkinProject(data=cdata)
E.length = len(E.datasets)
if len(E.datasets)==0:
continue
cdata = E
if type(cdata) == sub_dict:
for k in cdata.keys():
recdata[k] = copy.deepcopy(cdata[k])
else:
recdata = cdata
if cdata != '' and cdata != None:
rec.addField(col, data=recdata)
newDB.add(p,rec)
print newDB.meta.userfields
#remove any file cols, too hard to import
for m in newDB.meta.userfields.keys()[:]:
if newDB.meta.userfields[m]['field_type'] == 'File':
newDB.deleteField(m)
newDB.commit(user='******', note='import')
newDB.close()
print 'import done'
return
def importOldProj(datadir,
local=None,
server=None,
project=None,
username=None):
"""Import old peat projects"""
import PEAT_DB.Database as peatDB
from PEAT_DB.PEAT_dict import PEAT_dict, sub_dict
import copy
if local != None:
newDB = PDatabase(local=local)
elif server != None:
newDB = PDatabase(server=server,
username=username,
port=8080,
password='******',
project=project)
print newDB
PT = peatDB.Database(datadir, Tk=False)
oldDB = PT.DB
print 'got old peat_db with %s proteins' % len(PT.proteins)
print PT.DB.keys()
#import meta stuff like userfields, table
for p in newDB.meta.special:
if not p in PT.DB.keys():
continue
print 'adding', p
for k in PT.DB[p]:
newDB.meta[p][k] = copy.deepcopy(PT.DB[p][k])
newDB.meta._p_changed = 1
for p in PT.proteins:
if p in newDB.meta.special:
continue
name = oldDB[p]['Name']
rec = PEATRecord(name=name)
for col in oldDB[p].keys():
cdata = oldDB[p][col]
recdata = {}
if col == 'name':
cdata = oldDB[p]['Name']
if oldDB['userfields'].has_key(col) and oldDB['userfields'][col][
'field_type'] in ekintypes:
E = EkinProject(data=cdata)
E.length = len(E.datasets)
if len(E.datasets) == 0:
continue
cdata = E
if type(cdata) == sub_dict:
for k in cdata.keys():
recdata[k] = copy.deepcopy(cdata[k])
else:
recdata = cdata
if cdata != '' and cdata != None:
rec.addField(col, data=recdata)
newDB.add(p, rec)
print newDB.meta.userfields
#remove any file cols, too hard to import
for m in newDB.meta.userfields.keys()[:]:
if newDB.meta.userfields[m]['field_type'] == 'File':
newDB.deleteField(m)
newDB.commit(user='******', note='import')
newDB.close()
print 'import done'
return
