def editlist(self, *args, **kw):
"""Let the user know that's visiting a protected controller."""
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter(User.user_name == userid).first()
users = DBSession.query(User).order_by(User.display_name).all()
id = args[0]
mylist = DBSession.query(UserLists).get(id)
assert mylist.tg_user_id == user.user_id, u"Brak uprawnien edycji"
if kw:
if not (kw.has_key('name') and kw['name'] != u''):
flash(l_(u'Name is required'), 'error')
else:
if kw.has_key('name') and kw['name'] != mylist.name:
mylist.name=kw['name']
# if kw.has_key('table') and kw['table'] != mylist.table:
# mylist.table=kw['table']
if kw.has_key('notes') and kw['notes'] != mylist.notes:
mylist.notes = kw['notes']
if kw.has_key('permitusers') and kw['permitusers'] != u'':
if isinstance(kw['permitusers'], (list, tuple)):
permitusers = [usr for usr in users if usr.user_name in kw['permitusers']]
else:
permitusers = [usr for usr in users if usr.user_name == kw['permitusers']]
if permitusers != mylist.permitusers:
mylist.permitusers = permitusers
DBSession.flush()
flash(l_(u'Task completed successfully'))
redirect(request.headers['Referer'])
return dict(mylist=mylist, user=user, users=users, page='index', pname=None)
def addlist(self, *args, **kw):
"""Let the user know that's visiting a protected controller."""
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter(User.user_name == userid).first()
users = DBSession.query(User).order_by(User.display_name).all()
allproj = DBSession.query(Projects).order_by('id').all()
if args and len(args) >= 2:
ntable = args[0]
get_args = args[1:]
else:
ntable, get_args = [None, ()]
if kw:
if not (kw.has_key('name') and kw['name'] != u''):
flash(l_(u'Name is required'), 'error')
redirect(request.headers['Referer'])
elif not (kw.has_key('table') and kw['table'] != u''):
flash(l_(u'Table is required'), 'error')
redirect(request.headers['Referer'])
elif not (kw.has_key('project') and kw['project'] != u''):
flash(l_(u'Project is required'), 'error')
redirect(request.headers['Referer'])
else:
lista = UserLists()
lista.name = kw['name']
lista.table = kw['table']
lista.pname = kw['project']
if kw.has_key('notes') and kw['notes'] != u'':
lista.notes = kw['notes']
if kw.has_key('permitusers') and kw['permitusers'] != u'':
if isinstance(kw['permitusers'], (list, tuple)):
permitusers = [
usr for usr in users
if usr.user_name in kw['permitusers']
]
else:
permitusers = [
usr for usr in users
if usr.user_name == kw['permitusers']
]
lista.permitusers = permitusers
if kw.has_key('argv') and kw['argv'] != u'':
elements = []
for arg in kw['argv']:
elements.append(arg)
import pickle
lista.elements = pickle.dumps(elements)
user.lists.append(lista)
DBSession.add(lista)
DBSession.flush()
flash(l_(u'Task completed successfully'))
redirect(request.headers['Referer'])
return dict(user=user,
allproj=allproj,
users=users,
page='index',
ntable=ntable,
get_args=get_args,
pname=None)
def tags(self, **kw):
pname = request.environ['PATH_INFO'].split('/')[1]
userid = request.identity['repoze.who.userid']
alltags = [tag for tag in DBSession.query(Tags).order_by('name').all()]
if kw:
try:
usun = kw['button1']
except Exception:
usun = None
if usun:
try:
if isinstance(kw['deltags'], basestring):
tagi = [DBSession.query(Tags).get(int(kw['deltags']))]
else:
tagi = [
DBSession.query(Tags).get(int(id))
for id in kw['deltags']
]
except Exception:
tagi = None
if tagi:
for tag in tagi:
for compound in DBSession.query(Compound).all():
if tag in compound.tags:
compound.tags.remove(tag)
history = History()
history.user = userid
history.status = u'Usuwanie tagu'
history.changes = u'Usunieto tag %s ' % tag.name
compound.history += [history]
DBSession.add(history)
DBSession.delete(tag)
DBSession.flush()
flash(l_(u'Task completed successfully'))
alltags = [
tag for tag in DBSession.query(Tags).order_by(
'name').all()
]
else:
try:
if kw['addtag'] != '':
tagname = kw['addtag']
else:
tagname = None
except Exception:
tagname = None
if tagname:
tag = Tags()
tag.name = tagname
flash(l_(u'Task completed successfully'))
DBSession.add(tag)
DBSession.flush()
alltags = [
tg
for tg in DBSession.query(Tags).order_by('name').all()
]
else:
flash(l_(u'Name required'), 'warning')
return dict(alltags=alltags, page='kierownik', pname=pname)
def setUp(self):
"""Setup test fixture for each model test method."""
try:
new_attrs = {}
new_attrs.update(self.attrs)
new_attrs.update(self.do_get_dependencies())
self.obj = self.klass(**new_attrs)
DBSession.add(self.obj)
DBSession.flush()
return self.obj
except:
DBSession.rollback()
raise
def setUp(self):
"""Setup test fixture for each model test method."""
try:
new_attrs = {}
new_attrs.update(self.attrs)
new_attrs.update(self.do_get_dependencies())
self.obj = self.klass(**new_attrs)
DBSession.add(self.obj)
DBSession.flush()
return self.obj
except:
DBSession.rollback()
raise
def tags(self, **kw):
pname = request.environ['PATH_INFO'].split('/')[1]
userid = request.identity['repoze.who.userid']
alltags =[tag for tag in DBSession.query(Tags).order_by('name').all() ]
if kw:
try:
usun = kw['button1']
except Exception:
usun = None
if usun:
try:
if isinstance(kw['deltags'], basestring):
tagi = [DBSession.query( Tags ).get(int(kw['deltags']))]
else:
tagi = [DBSession.query( Tags ).get(int(id)) for id in kw['deltags']]
except Exception:
tagi = None
if tagi:
for tag in tagi:
for compound in DBSession.query(Compound).all():
if tag in compound.tags:
compound.tags.remove(tag)
history = History()
history.user = userid
history.status = u'Usuwanie tagu'
history.changes = u'Usunieto tag %s ' % tag.name
compound.history += [history]
DBSession.add(history)
DBSession.delete(tag)
DBSession.flush()
flash(l_(u'Task completed successfully'))
alltags =[tag for tag in DBSession.query(Tags).order_by('name').all() ]
else:
try:
if kw['addtag'] != '':
tagname = kw['addtag']
else:
tagname = None
except Exception:
tagname = None
if tagname:
tag = Tags()
tag.name = tagname
flash(l_(u'Task completed successfully'))
DBSession.add(tag)
DBSession.flush()
alltags =[tg for tg in DBSession.query(Tags).order_by('name').all() ]
else:
flash(l_(u'Name required'), 'warning')
return dict(alltags=alltags, page='kierownik', pname=pname)
def addlist(self, *args, **kw):
"""Let the user know that's visiting a protected controller."""
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter(User.user_name == userid).first()
users = DBSession.query(User).order_by(User.display_name).all()
allproj = DBSession.query(Projects).order_by('id').all()
if args and len(args) >= 2:
ntable = args[0]
get_args = args[1:]
else:
ntable, get_args = [None, ()]
if kw:
if not (kw.has_key('name') and kw['name'] != u''):
flash(l_(u'Name is required'), 'error')
redirect(request.headers['Referer'])
elif not (kw.has_key('table') and kw['table'] != u''):
flash(l_(u'Table is required'), 'error')
redirect(request.headers['Referer'])
elif not (kw.has_key('project') and kw['project'] != u''):
flash(l_(u'Project is required'), 'error')
redirect(request.headers['Referer'])
else:
lista = UserLists()
lista.name = kw['name']
lista.table = kw['table']
lista.pname = kw['project']
if kw.has_key('notes') and kw['notes'] != u'':
lista.notes = kw['notes']
if kw.has_key('permitusers') and kw['permitusers'] != u'':
if isinstance(kw['permitusers'], (list, tuple)):
permitusers = [usr for usr in users if usr.user_name in kw['permitusers']]
else:
permitusers = [usr for usr in users if usr.user_name == kw['permitusers']]
lista.permitusers = permitusers
if kw.has_key('argv') and kw['argv'] != u'':
elements = []
for arg in kw['argv']:
elements.append(arg)
import pickle
lista.elements = pickle.dumps(elements)
user.lists.append(lista)
DBSession.add(lista)
DBSession.flush()
flash(l_(u'Task completed successfully'))
redirect(request.headers['Referer'])
return dict(user=user, allproj=allproj, users=users, page='index', ntable=ntable, get_args=get_args, pname=None)
def removelist(self, *args, **kw):
"""Let the user know that's visiting a protected controller."""
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter(User.user_name == userid).first()
id = args[0]
mylist = DBSession.query(UserLists).get(id)
if mylist.tg_user_id != user.user_id:
flash(l_(u'Permission denied'), 'error')
redirect(request.headers['Referer'])
assert mylist.tg_user_id == user.user_id, u"Brak uprawnien usuwania"
if mylist:
DBSession.delete(mylist)
DBSession.flush()
flash(l_(u'Task completed successfully'))
redirect(request.headers['Referer'])
else:
flash(l_(u'List is required'), 'warning')
redirect(request.headers['Referer'])
def removelist(self, *args, **kw):
"""Let the user know that's visiting a protected controller."""
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter(User.user_name == userid).first()
id = args[0]
mylist = DBSession.query(UserLists).get(id)
if mylist.tg_user_id != user.user_id:
flash(l_(u'Permission denied'), 'error')
redirect(request.headers['Referer'])
assert mylist.tg_user_id == user.user_id, u"Brak uprawnien usuwania"
if mylist:
DBSession.delete(mylist)
DBSession.flush()
flash(l_(u'Task completed successfully'))
redirect(request.headers['Referer'])
else:
flash(l_(u'List is required'), 'warning')
redirect(request.headers['Referer'])
def editlist(self, *args, **kw):
"""Let the user know that's visiting a protected controller."""
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter(User.user_name == userid).first()
users = DBSession.query(User).order_by(User.display_name).all()
id = args[0]
mylist = DBSession.query(UserLists).get(id)
assert mylist.tg_user_id == user.user_id, u"Brak uprawnien edycji"
if kw:
if not (kw.has_key('name') and kw['name'] != u''):
flash(l_(u'Name is required'), 'error')
else:
if kw.has_key('name') and kw['name'] != mylist.name:
mylist.name = kw['name']
# if kw.has_key('table') and kw['table'] != mylist.table:
# mylist.table=kw['table']
if kw.has_key('notes') and kw['notes'] != mylist.notes:
mylist.notes = kw['notes']
if kw.has_key('permitusers') and kw['permitusers'] != u'':
if isinstance(kw['permitusers'], (list, tuple)):
permitusers = [
usr for usr in users
if usr.user_name in kw['permitusers']
]
else:
permitusers = [
usr for usr in users
if usr.user_name == kw['permitusers']
]
if permitusers != mylist.permitusers:
mylist.permitusers = permitusers
DBSession.flush()
flash(l_(u'Task completed successfully'))
redirect(request.headers['Referer'])
return dict(mylist=mylist,
user=user,
users=users,
page='index',
pname=None)
def put(self, *args, **kw):
pname = request.environ['PATH_INFO'].split('/')[1]
sid = int(args[0])
userid = request.identity['repoze.who.userid']
scompound = DBSession.query(SCompound).get(sid)
shistory = SHistory()
shistory.gid = scompound.mol.gid
shistory.user = userid
shistory.status = u'Edycja'
schanges = u''
try:
reason = kw['reason']
except Exception:
reason = None
pass
if reason and reason != u'':
schanges += u'UWAGA! niestandardowa zmiana z powodu:' + reason
etap = int(kw['etap'])
etap_max = int(kw['etap_max'])
if etap < etap_max:
scompound.effort[-1].etap = etap
scompound.effort[-1].etap_max = etap_max
scompound.status = DBSession.query( SStatus ).get(2)
schanges += u'; Bieżący etap: ' + str(etap)
schanges += u'; Liczba etapow: ' + str(etap_max)
else:
flash(l_(u'Completed step must be smaller by 2 than the number of stages'), 'error')
redirect(request.headers['Referer'])
# scompound.status_date = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
if kw.has_key('lso') and kw['lso'] != scompound.lso:
scompound.lso = kw['lso']
schanges += u'; LSO: ' + kw['lso']
if kw.has_key('notes') and kw['notes'] != scompound.notes:
scompound.notes = kw['notes']
schanges += u';Notes: ' + kw['notes']
try:
filename = kw['loadfile'].filename
import os
filename = os.path.basename(filename)
except Exception as msg:
filename = None
pass
try:
reaction_file = kw['reaction'].filename
import os
reaction_file = os.path.basename(reaction_file)
except Exception as msg:
reaction_file = None
pass
if kw['owner'] != scompound.owner:
scompound.owner = kw['owner']
schanges += u'; Wlasciciel:' + kw['owner']
if kw['principal'] != scompound.principal:
scompound.principal = kw['principal']
schanges += u'; Odbiorca:' + kw['principal']
if kw.has_key('priority') and kw['priority'] != u'':
scompound.priority = int(kw['priority'])
schanges += u'; Priorytet:' + kw['priority']
pcompound = DBSession.query(PCompound).get(scompound.pid)
if pcompound:
pcompound.priority = int(kw['priority'])
phistory = PHistory()
phistory.project = pname
phistory.date = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
phistory.user = userid
phistory.status = 'Priorytet'
phistory.changes = u'Priority: ' + kw['priority']
pcompound.history += [phistory]
DBSession.add(phistory)
if filename or reaction_file:
if filename:
number = DBSession.query(SFiles).count() + 1
newfilename = str(number) + '_' + userid + '_' + str(sid) + '_' + filename
newfilename.replace(' ', '_')
f_path = os.path.join(files_dir, newfilename)
try:
f = file(f_path, "w")
f.write(kw['loadfile'].value)
f.close()
except Exception as msg:
flash(l_(msg), 'error')
redirect(request.headers['Referer'])
sfile = SFiles()
sfile.name = filename
sfile.filename = newfilename
if kw['opis']:
sfile.description = kw['opis']
schanges += u'; Plik: ' + filename + u' ( ' + newfilename + u' )'
DBSession.add(sfile)
if reaction_file:
number2 = DBSession.query(SFiles).count() + 1
newfilename2 = str(number2) + '_' + userid + '_' + str(sid) + '_' + reaction_file
newfilename2.replace(' ', '_')
f_path2 = os.path.join(files_dir, newfilename2)
try:
f2 = file(f_path2, "w")
f2.write(kw['reaction'].value)
f2.close()
except Exception as msg:
flash(l_(msg), 'error')
redirect(request.headers['Referer'])
reaction_sfile = SFiles()
reaction_sfile.name = reaction_file
reaction_sfile.filename = newfilename2
schanges += u'; Sciezka reakcji: ' + reaction_file + u' ( ' + newfilename2 + u' )'
DBSession.add(reaction_sfile)
shistory.changes = schanges
scompound.history += [shistory]
DBSession.add(shistory)
DBSession.flush()
#transaction.commit()
scompound2 = DBSession.query(SCompound).get(sid)
if filename:
sfile2 = [sfile]
sfile2 += scompound2.filename
scompound2.filename = sfile2
if reaction_file:
reaction_sfile = [reaction_sfile]
# reaction_sfile += scompound2.reaction
scompound2.reaction = reaction_sfile
else:
shistory.changes = schanges
scompound.history += [shistory]
DBSession.add(shistory)
DBSession.flush()
flash(l_(u'Task completed successfully'))
if kw and kw.has_key('come_from'):
come_from = kw['come_from']
else:
come_from = request.headers['Referer']
redirect(come_from)
def multiedit(self, *args, **kw):
pname = request.environ['PATH_INFO'].split('/')[1]
alltags =[tag for tag in DBSession.query(Tags).order_by('name').all() ]
principals = DBSession.query (Group).get(3)
owners = DBSession.query (Group).get(2)
come_from = request.headers['Referer']
if kw:
try:
if isinstance(kw['argv'], basestring):
argv = [kw['argv']]
else:
argv = [id for id in kw['argv']]
except Exception:
argv = None
try:
if kw.has_key('notes') != u'':
notes = kw['notes']
else:
notes = None
except Exception:
notes = None
try:
priority = int(kw['priority'])
except Exception:
priority = None
if argv:
userid = request.identity['repoze.who.userid']
for arg in argv:
try:
if isinstance(kw['text_tags'], basestring):
tagi = [DBSession.query( Tags ).get(int(kw['text_tags']))]
else:
tagi = [DBSession.query( Tags ).get(int(id)) for id in kw['text_tags']]
except Exception:
tagi = None
scompound = DBSession.query(SCompound).get(int(arg))
shistory = SHistory()
shistory.gid = scompound.mol.gid
shistory.user = userid
shistory.status = u'Multi - edit'
shistory.changes = u''
if kw.has_key('owner') and kw['owner'] != u'None' and kw['owner'] != scompound.owner:
scompound.owner = kw['owner']
shistory.changes += u' Właściciel: ' + kw['owner'] + ';'
if kw.has_key('principal') and kw['principal'] != u'None' and kw['principal'] != scompound.principal:
scompound.principal = kw['principal']
shistory.changes += u' Odbiorca: ' + kw['principal'] + ';'
if priority and priority != scompound.priority:
scompound.priority = int(kw['priority'])
shistory.changes += u'; Priorytet: ' + kw['priority'] + ';'
pcompound = DBSession.query(PCompound).get(scompound.pid)
if pcompound:
pcompound.priority = int(kw['priority'])
phistory = PHistory()
phistory.project = pname
phistory.date = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
phistory.user = userid
phistory.status = 'Priorytet'
phistory.changes = u'Priority: ' + kw['priority']
pcompound.history += [phistory]
DBSession.add(phistory)
if tagi and scompound.mol.tags != tagi:
scompound.mol.tags = tagi
shistory.changes += u' Tags: '
for tag in tagi:
shistory.changes += str(tag.name) + ';'
if notes and notes != scompound.notes:
scompound.notes = notes
shistory.changes += u' Notes: ' + notes
scompound.history += [shistory]
DBSession.add(shistory)
DBSession.flush()
#transaction.commit()
if kw.has_key('come_from'):
come_from = kw['come_from']
else:
come_from = request.headers['Referer']
flash(l_(u'Task completed successfully'))
redirect(come_from)
return dict(alltags=alltags, args=args, users=principals.users, owners=owners.users, come_from=come_from, page='kierownik', pname=pname)
def new_user(self, *args, **kw):
"""
Add new User.
"""
try:
come_from = request.headers['Referer']
except Exception:
come_from = request.path_url
groups = DBSession.query(Group).all()
if kw:
if 'come_from' in kw and kw['come_from'] != u'':
come_from = kw['come_from']
if 'password' in kw and kw['password'] != u'':
new = kw['password']
if 'verification' in kw and kw[
'verification'] != u'' and new != kw['verification']:
flash(l_(u'Password not match'), 'error')
redirect(come_from)
else:
flash(l_('Verification error'), 'error')
else:
flash(l_(u'Password is required'), 'error')
redirect(come_from)
if 'email' in kw and kw['email'] != u'':
email = kw['email']
else:
flash(l_('Email is required'), 'error')
redirect(come_from)
if 'items_per_page' in kw and kw['items_per_page'] != u'':
try:
items_per_page = int(kw['items_per_page'])
except Exception:
flash(l_('Compounds per page should be a number'), 'error')
else:
flash(l_('Compounds per page required'), 'error')
redirect(come_from)
if 'user_name' in kw and kw['user_name'] != u'':
user = User()
user.user_name = kw['user_name'].strip().replace(' ', '.')
else:
flash(l_('User name is required'), 'error')
redirect(come_from)
if 'display_name' in kw and kw['display_name'] != u'':
user.display_name = kw['display_name']
if 'groups' in kw and kw['groups'] != u'':
if isinstance(kw['groups'], basestring):
groups = [DBSession.query(Group).get(kw['groups'])]
else:
groups = [
DBSession.query(Group).get(group_id)
for group_id in kw['groups']
]
else:
flash(l_('Group is required'), 'error')
redirect(come_from)
if items_per_page:
if items_per_page > 10 and items_per_page < 150:
user.items_per_page = items_per_page
else:
flash(
l_(u'Number of Compound per page should be between 10 and 150'
), 'error')
redirect(come_from)
if email:
import re
if len(email) >= 6:
if re.match(
"^.+\\@(\\[?)[a-zA-Z0-9\\-\\.]+\\.([a-zA-Z]{2,3}|[0-9]{1,3})(\\]?)$",
email) != None:
user.email_address = email
else:
flash(l_(u'Email error'), 'warning')
redirect(come_from)
else:
flash(l_(u'Email error'), 'warning')
redirect(come_from)
else:
flash(l_(u'Email not changed'), 'warning')
if new:
if len(new) >= 6:
user._set_password(new)
else:
flash(l_(u'Password error'), 'error')
redirect(come_from)
else:
flash(l_('Password is required'), 'error')
redirect(come_from)
if groups:
for group in groups:
group.users.append(user)
else:
flash(l_('Gropus error'), 'error')
redirect(come_from)
DBSession.add(user)
DBSession.flush()
flash(l_(u'Task completed successfully'))
redirect(come_from)
return dict(page='index',
come_from=come_from,
groups=groups,
pname=None)
def edit_project(self, *args, **kw):
"""
Edit Project.
If you wish to allow users acces to the project- add them to group named as a project.
"""
try:
project_id = args[0]
except:
redirect("error")
userid = request.identity['repoze.who.userid']
# user = DBSession.query(User).filter_by(user_name=userid).first()
try:
come_from = request.headers['Referer']
except Exception:
come_from = request.path_url
try:
project = DBSession.query(Projects).get(project_id)
except:
flash("Project not exist", "error")
redirect(come_from)
if kw:
if 'come_from' in kw and kw['come_from'] != u'':
come_from = kw['come_from']
if 'name' in kw and kw['name'] != u'':
fp_lines = []
ct_lines = []
htrf_lines = []
for k, v in kw.iteritems():
if 'FP_Line_' in str(k) and v != u'':
fp_lines.append(v)
if 'CT_Line_' in str(k) and v != u'':
ct_lines.append(v)
if 'HTRF_Line_' in str(k) and v != u'':
htrf_lines.append(v)
if 'CT_Old_Line' in kw and kw['CT_Old_Line'] != u'':
if isinstance(kw['CT_Old_Line'], basestring):
if kw['CT_Old_Line'] != u'':
ct_lines.append(kw['CT_Old_Line'])
else:
ct_lines += [
cell for cell in kw['CT_Old_Line'] if cell != u''
]
if 'FP_Old_Line' in kw and kw['FP_Old_Line'] != u'':
if isinstance(kw['FP_Old_Line'], basestring):
if kw['FP_Old_Line'] != u'':
fp_lines.append(kw['FP_Old_Line'])
else:
fp_lines += [
cell for cell in kw['FP_Old_Line'] if cell != u''
]
if 'HTRF_Old_Line' in kw and kw['HTRF_Old_Line'] != u'':
if isinstance(kw['HTRF_Old_Line'], basestring):
if kw['HTRF_Old_Line'] != u'':
htrf_lines.append(kw['HTRF_Old_Line'])
else:
htrf_lines += [
cell for cell in kw['HTRF_Old_Line'] if cell != u''
]
if not ct_lines:
flash(l_(u'At least 1 CT_Line is required'), 'error')
redirect(come_from)
if not fp_lines:
flash(l_(u'At least 1 FP_Line is required'), 'error')
redirect(come_from)
if not htrf_lines:
flash(l_(u'At least 1 HTRF_Line is required'), 'error')
redirect(come_from)
#edit project name:
if project.name != kw['name']:
#change group name:
gr = DBSession.query(Group).filter_by(
group_name=project.name).first()
gr.group_name = kw['name']
gr.display_name = kw['name']
#change permission name:
perm = DBSession.query(Permission).filter(
Permission.permission_name == project.name).first()
perm.permission_name = kw['name']
project.name = kw['name']
#add description:
if 'description' in kw and kw['description'] != u'' and kw[
'description'] != project.description:
project.description = kw['description']
#add cell lines
import pickle
if ct_lines:
pickle_dump1 = pickle.dumps(ct_lines)
ct_test = [
test for test in project.tests if test.name == 'CT'
][0]
ct_test.cell_line = pickle_dump1
if fp_lines:
pickle_dump2 = pickle.dumps(fp_lines)
fp_test = [
test for test in project.tests if test.name == 'FP'
][0]
fp_test.cell_line = pickle_dump2
if htrf_lines:
pickle_dump3 = pickle.dumps(htrf_lines)
htrf_test = [
test for test in project.tests if test.name == 'HTRF'
][0]
htrf_test.cell_line = pickle_dump3
DBSession.flush()
flash(l_(u'Task completed successfully'))
redirect(come_from)
else:
flash(l_(u'Name is required'), 'error')
redirect(come_from)
return dict(page='index',
userid=userid,
project=project,
come_from=come_from)
def new_project(self, *args, **kw):
"""
Create new project & group with correct permissions asigned.
If you wish to allow users acces to the project- add them to group named as a project.
"""
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter_by(user_name=userid).first()
try:
come_from = request.headers['Referer']
except Exception:
come_from = request.path_url
if kw:
if 'come_from' in kw and kw['come_from'] != u'':
come_from = kw['come_from']
if 'name' in kw and kw['name'] != u'':
cell_lines = []
fp_lines = []
htrf_lines = []
for k, v in kw.iteritems():
if 'Cell_Line_' in str(k) and v != u'':
cell_lines.append(v.strip().replace(' ', '_'))
if 'FP_Line_' in str(k) and v != u'':
fp_lines.append(v.strip().replace(' ', '_'))
if 'HTRF_Line_' in str(k) and v != u'':
htrf_lines.append(v.strip().replace(' ', '_'))
if not cell_lines:
flash(l_(u'At least 1 Cell_Line is required'), 'error')
redirect(come_from)
if not fp_lines:
flash(l_(u'At least 1 FP_Line is required'), 'error')
redirect(come_from)
if not htrf_lines:
flash(l_(u'At least 1 HTRF_Line is required'), 'error')
redirect(come_from)
#create new project:
project = Projects()
project.name = kw['name'].strip().replace(' ', '_')
#add group named as a project:
gr = Group()
gr.group_name = kw['name'].strip().replace(' ', '_')
gr.display_name = kw['name']
gr.users.append(user)
#add permission named as a project and assign it to group:
from molgears.model import Permission
perm = Permission()
perm.permission_name = kw['name'].strip().replace(' ', '_')
perm.groups += [gr]
#add description:
if 'description' in kw and kw['description'] != u'':
project.description = kw['description']
#add test and cell lines
ptest = ProjectTests()
ptest.name = 'CT'
fp_ptest = ProjectTests()
fp_ptest.name = 'FP'
htrf_ptest = ProjectTests()
htrf_ptest.name = 'HTRF'
project.tests = [fp_ptest, ptest, htrf_ptest]
import pickle
if cell_lines:
pickle_dump1 = pickle.dumps(cell_lines)
ptest.cell_line = pickle_dump1
if fp_lines:
pickle_dump2 = pickle.dumps(fp_lines)
fp_ptest.cell_line = pickle_dump2
if htrf_lines:
pickle_dump3 = pickle.dumps(htrf_lines)
htrf_ptest.cell_line = pickle_dump3
DBSession.add(perm)
DBSession.add(gr)
DBSession.add(ptest)
DBSession.add(fp_ptest)
DBSession.add(project)
DBSession.flush()
flash(l_(u'Task completed successfully'))
redirect(come_from)
else:
flash(l_(u'Name is required'), 'error')
redirect(come_from)
return dict(page='index', userid=userid, come_from=come_from)
def multiedit(self, *args, **kw):
pname = request.environ['PATH_INFO'].split('/')[1]
alltags = [tag for tag in DBSession.query(Tags).order_by('name').all()]
principals = DBSession.query(Group).get(3)
owners = DBSession.query(Group).get(2)
come_from = request.headers['Referer']
if kw:
try:
if isinstance(kw['argv'], basestring):
argv = [kw['argv']]
else:
argv = [id for id in kw['argv']]
except Exception:
argv = None
try:
if kw.has_key('notes') != u'':
notes = kw['notes']
else:
notes = None
except Exception:
notes = None
try:
priority = int(kw['priority'])
except Exception:
priority = None
if argv:
userid = request.identity['repoze.who.userid']
for arg in argv:
try:
if isinstance(kw['text_tags'], basestring):
tagi = [
DBSession.query(Tags).get(int(kw['text_tags']))
]
else:
tagi = [
DBSession.query(Tags).get(int(id))
for id in kw['text_tags']
]
except Exception:
tagi = None
scompound = DBSession.query(SCompound).get(int(arg))
shistory = SHistory()
shistory.gid = scompound.mol.gid
shistory.user = userid
shistory.status = u'Multi - edit'
shistory.changes = u''
if kw.has_key('owner') and kw['owner'] != u'None' and kw[
'owner'] != scompound.owner:
scompound.owner = kw['owner']
shistory.changes += u' Właściciel: ' + kw['owner'] + ';'
if kw.has_key(
'principal') and kw['principal'] != u'None' and kw[
'principal'] != scompound.principal:
scompound.principal = kw['principal']
shistory.changes += u' Odbiorca: ' + kw[
'principal'] + ';'
if priority and priority != scompound.priority:
scompound.priority = int(kw['priority'])
shistory.changes += u'; Priorytet: ' + kw[
'priority'] + ';'
pcompound = DBSession.query(PCompound).get(
scompound.pid)
if pcompound:
pcompound.priority = int(kw['priority'])
phistory = PHistory()
phistory.project = pname
phistory.date = datetime.now().strftime(
"%Y-%m-%d %H:%M:%S")
phistory.user = userid
phistory.status = 'Priorytet'
phistory.changes = u'Priority: ' + kw['priority']
pcompound.history += [phistory]
DBSession.add(phistory)
if tagi and scompound.mol.tags != tagi:
scompound.mol.tags = tagi
shistory.changes += u' Tags: '
for tag in tagi:
shistory.changes += str(tag.name) + ';'
if notes and notes != scompound.notes:
scompound.notes = notes
shistory.changes += u' Notes: ' + notes
scompound.history += [shistory]
DBSession.add(shistory)
DBSession.flush()
#transaction.commit()
if kw.has_key('come_from'):
come_from = kw['come_from']
else:
come_from = request.headers['Referer']
flash(l_(u'Task completed successfully'))
redirect(come_from)
return dict(alltags=alltags,
args=args,
users=principals.users,
owners=owners.users,
come_from=come_from,
page='kierownik',
pname=pname)
def put(self, *args, **kw):
pname = request.environ['PATH_INFO'].split('/')[1]
sid = int(args[0])
userid = request.identity['repoze.who.userid']
scompound = DBSession.query(SCompound).get(sid)
shistory = SHistory()
shistory.gid = scompound.mol.gid
shistory.user = userid
shistory.status = u'Edycja'
schanges = u''
try:
reason = kw['reason']
except Exception:
reason = None
pass
if reason and reason != u'':
schanges += u'UWAGA! niestandardowa zmiana z powodu:' + reason
etap = int(kw['etap'])
etap_max = int(kw['etap_max'])
if etap < etap_max:
scompound.effort[-1].etap = etap
scompound.effort[-1].etap_max = etap_max
scompound.status = DBSession.query(SStatus).get(2)
schanges += u'; Bieżący etap: ' + str(etap)
schanges += u'; Liczba etapow: ' + str(etap_max)
else:
flash(
l_(u'Completed step must be smaller by 2 than the number of stages'
), 'error')
redirect(request.headers['Referer'])
# scompound.status_date = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
if kw.has_key('lso') and kw['lso'] != scompound.lso:
scompound.lso = kw['lso']
schanges += u'; LSO: ' + kw['lso']
if kw.has_key('notes') and kw['notes'] != scompound.notes:
scompound.notes = kw['notes']
schanges += u';Notes: ' + kw['notes']
try:
filename = kw['loadfile'].filename
import os
filename = os.path.basename(filename)
except Exception as msg:
filename = None
pass
try:
reaction_file = kw['reaction'].filename
import os
reaction_file = os.path.basename(reaction_file)
except Exception as msg:
reaction_file = None
pass
if kw['owner'] != scompound.owner:
scompound.owner = kw['owner']
schanges += u'; Wlasciciel:' + kw['owner']
if kw['principal'] != scompound.principal:
scompound.principal = kw['principal']
schanges += u'; Odbiorca:' + kw['principal']
if kw.has_key('priority') and kw['priority'] != u'':
scompound.priority = int(kw['priority'])
schanges += u'; Priorytet:' + kw['priority']
pcompound = DBSession.query(PCompound).get(scompound.pid)
if pcompound:
pcompound.priority = int(kw['priority'])
phistory = PHistory()
phistory.project = pname
phistory.date = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
phistory.user = userid
phistory.status = 'Priorytet'
phistory.changes = u'Priority: ' + kw['priority']
pcompound.history += [phistory]
DBSession.add(phistory)
if filename or reaction_file:
if filename:
number = DBSession.query(SFiles).count() + 1
newfilename = str(number) + '_' + userid + '_' + str(
sid) + '_' + filename
newfilename.replace(' ', '_')
f_path = os.path.join(files_dir, newfilename)
try:
f = file(f_path, "w")
f.write(kw['loadfile'].value)
f.close()
except Exception as msg:
flash(l_(msg), 'error')
redirect(request.headers['Referer'])
sfile = SFiles()
sfile.name = filename
sfile.filename = newfilename
if kw['opis']:
sfile.description = kw['opis']
schanges += u'; Plik: ' + filename + u' ( ' + newfilename + u' )'
DBSession.add(sfile)
if reaction_file:
number2 = DBSession.query(SFiles).count() + 1
newfilename2 = str(number2) + '_' + userid + '_' + str(
sid) + '_' + reaction_file
newfilename2.replace(' ', '_')
f_path2 = os.path.join(files_dir, newfilename2)
try:
f2 = file(f_path2, "w")
f2.write(kw['reaction'].value)
f2.close()
except Exception as msg:
flash(l_(msg), 'error')
redirect(request.headers['Referer'])
reaction_sfile = SFiles()
reaction_sfile.name = reaction_file
reaction_sfile.filename = newfilename2
schanges += u'; Sciezka reakcji: ' + reaction_file + u' ( ' + newfilename2 + u' )'
DBSession.add(reaction_sfile)
shistory.changes = schanges
scompound.history += [shistory]
DBSession.add(shistory)
DBSession.flush()
#transaction.commit()
scompound2 = DBSession.query(SCompound).get(sid)
if filename:
sfile2 = [sfile]
sfile2 += scompound2.filename
scompound2.filename = sfile2
if reaction_file:
reaction_sfile = [reaction_sfile]
# reaction_sfile += scompound2.reaction
scompound2.reaction = reaction_sfile
else:
shistory.changes = schanges
scompound.history += [shistory]
DBSession.add(shistory)
DBSession.flush()
flash(l_(u'Task completed successfully'))
if kw and kw.has_key('come_from'):
come_from = kw['come_from']
else:
come_from = request.headers['Referer']
redirect(come_from)
