def check(self):
compounds = DBSession.query(Compound).all()
pains1 = DBSession.query(PAINS1).all()
pains2 = DBSession.query(PAINS2).all()
pains3 = DBSession.query(PAINS3).all()
ID = ''
for compound in compounds:
m = Chem.MolFromSmiles(str(compound.structure))
mol = Chem.AddHs(m)
for p1 in pains1:
patt = Chem.MolFromSmarts(str(p1.structure))
if patt:
if mol.HasSubstructMatch(patt):
compound.pains1 = p1
else:
flash(l_(u'Pattern error'), 'error')
redirect(request.headers['Referer'])
for p2 in pains2:
patt = Chem.MolFromSmarts(str(p2.structure))
if patt:
if mol.HasSubstructMatch(patt):
compound.pains2 = p2
else:
flash(l_(u'Pattern error'), 'error')
redirect(request.headers['Referer'])
for p3 in pains3:
patt = Chem.MolFromSmarts(str(p3.structure))
if patt:
if mol.HasSubstructMatch(patt):
compound.pains3 = p3
else:
flash(l_(u'Pattern error'), 'error')
redirect(request.headers['Referer'])
flash(l_(u'Task completed successfully'))
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)
class child(FormLayout):
image_small_id = HiddenField()
image_big_id = HiddenField()
name = TextField(label=l_('Name'),
css_class='form-control',
validator=Required)
description = TextArea(label=l_('Description'),
rows=10,
css_class='form-control',
validator=Required)
image_small = FileField(label=pluggable_config.get(
'image1_label', l_('Small Image')),
css_class='form-control',
attrs=dict(accept='image/*'))
image_big = FileField(label=pluggable_config.get(
'image2_label', l_('Big Image')),
css_class='form-control',
attrs=dict(accept='image/*'))
parent_id = SingleSelectField(
css_class='form-control',
options=Deferred(lambda: [(c._id, c.name) for c in model.provider.
query(model.Category, filters={})[1]]))
class child(twf.TableLayout):
inline_engine_name = 'kajiki'
template = '''
<div style="padding-top:20px">
<py:for each="c in w.children_hidden">
${c.display()}
</py:for>
<div class="col-md-12 ks-section-name">
Recover password
<hr/>
</div>
<div class="row">
<div class="form-group col-md-4">
${w.children.password.display()}
<span class="help-block" py:content="w.children.password.error_msg"/>
</div>
</div>
<div class="row">
<div class="form-group col-md-4">
${w.children.password_confirm.display()}
<span class="help-block" py:content="w.children.password_confirm.error_msg"/>
</div>
</div>
</div>
'''
data = HiddenField()
password = PasswordField(label=l_('New password'), validator=Validator(required=True), css_class='form-control', placeholder=l_('New password'))
password_confirm = PasswordField(label=l_('Confirm new password'), validator=Validator(required=True), css_class='form-control', placeholder=l_('Confirm password'))
validator = FieldsMatch('password', 'password_confirm')
class BuyProductForm(Form):
child = CustomListLayout
css_class = "form-horizontal"
product = HiddenField(validator=Validator(required=True))
quantity = SingleSelectField(label=l_("Quantity"), options=[],
validator=IntValidator(min=1, required=True),
container_attrs={'class': 'form-group'},
label_attrs={'class': 'col-sm-12'},
wrapper_attrs={'class': 'col-sm-4'},
css_class="form-control -quantity")
submit = None
submit1 = SubmitButton(value=l_('Add to cart'), key='add_to_cart', name='action',
css_class='btn btn-block btn-success stroller2-buy-product-submit-button')
submit2 = SubmitButton(value=l_('Buy now'), key='buy_now', name='action',
css_class='btn btn-block btn-success stroller2-buy-product-submit-button')
def prepare(self):
super(BuyProductForm, self).prepare()
product_field = self.child.children.product
quantity_field = self.child.children.quantity
product = app_globals.shop.product.get(_id=product_field.value)
opts = [({'value': c}, c) for c in range(1, product.configurations[0].qty + 1)]
quantity_field.grouped_options = [(None, opts)]
class ActionDescription(object):
"""
Allowed status are:
- open
- closed-validated
- closed-invalidated
- closed-deprecated
"""
ARCHIVING = 'archiving'
COMMENT = 'content-comment'
CREATION = 'creation'
DELETION = 'deletion'
EDITION = 'edition' # Default action if unknow
REVISION = 'revision'
STATUS_UPDATE = 'status-update'
UNARCHIVING = 'unarchiving'
UNDELETION = 'undeletion'
MOVE = 'move'
_ICONS = {
'archiving': 'fa fa-archive',
'content-comment': 'fa-comment-o',
'creation': 'fa-magic',
'deletion': 'fa-trash',
'edition': 'fa-edit',
'revision': 'fa-history',
'status-update': 'fa-random',
'unarchiving': 'fa-file-archive-o',
'undeletion': 'fa-trash-o',
'move': 'fa-arrows'
}
_LABELS = {
'archiving': l_('archive'),
'content-comment': l_('Item commented'),
'creation': l_('Item created'),
'deletion': l_('Item deleted'),
'edition': l_('item modified'),
'revision': l_('New revision'),
'status-update': l_('New status'),
'unarchiving': l_('Item unarchived'),
'undeletion': l_('Item undeleted'),
'move': l_('Item moved')
}
def __init__(self, id):
assert id in ActionDescription.allowed_values()
self.id = id
self.label = ActionDescription._LABELS[id]
self.icon = ActionDescription._ICONS[id]
self.css = ''
@classmethod
def allowed_values(cls):
return [
cls.ARCHIVING, cls.COMMENT, cls.CREATION, cls.DELETION,
cls.EDITION, cls.REVISION, cls.STATUS_UPDATE, cls.UNARCHIVING,
cls.UNDELETION, cls.MOVE
]
def _admin_init_attrs(self):
if 'child' not in self.__base_widget_args__:
self.__base_widget_args__['child'] = _BootstrapFormLayout
if 'submit' not in self.__base_widget_args__:
if isinstance(self, AddRecordForm):
submit_text = l_('Create')
else:
submit_text = l_('Save')
self.__base_widget_args__['submit'] = SubmitButton(css_class='btn btn-primary',
value=submit_text)
for f in self.__fields__:
try:
field = self.__metadata__[f]
except KeyError:
continue
field_options = self.FIELD_OPTIONS.copy()
field_widget_type = self._do_get_field_widget_type(f, field)
if field_widget_type in (SubDocument, SubDocumentsList):
field_options.pop('css_class')
field_options['children_attrs'] = self.FIELD_OPTIONS
if field_widget_type == SubDocument:
field_options['template'] = 'tgext.admin.templates.bootstrap_form_layout'
if field_widget_type == SubDocumentsList:
field_options['child'] = SubDocument(template='tgext.admin.templates.bootstrap_form_layout')
self.__field_widget_args__[f] = _merge_dicts(field_options,
self.__field_widget_args__.get(f, {}))
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 mylists(self, page=1, *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()
mylists = user.lists
import pickle as pcl
dsc = True
tmpl = ''
selection = None
order = "id"
try:
if kw['search'] != u'':
search_clicked = kw['search']
else:
search_clicked = None
except Exception:
search_clicked = None
if kw:
delkw = []
for k, v in kw.iteritems():
if str(k) == 'desc' and str(v) != '1':
dsc = None
elif str(k) == 'order_by':
order = v
if str(k) != 'select' and str(k) != 'remove' and str(v) != u'':
tmpl += str(k) + '=' + str(v) + '&'
elif str(k) == 'select':
try:
if isinstance(kw['select'], basestring):
selection = [kw['select']]
else:
selection = [id for id in kw['select']]
except Exception:
selection = None
elif str(v) == u'':
delkw.append(k)
for k in delkw:
del kw[k]
mylists = sorted(mylists, key=lambda list: list.__getattribute__(order))
if dsc:
mylists.reverse()
if selection and not search_clicked:
argv =''
for arg in selection:
argv += '/' + arg
if kw['akcja'] == u'edit':
if len(selection) == 1:
redirect('/myaccount/editlist%s' %argv)
else:
flash(l_(u'Editing only one by one'), 'warning')
redirect(request.headers['Referer'])
elif kw['akcja'] == u'delete':
redirect('/myaccount/removelist%s' % argv)
else:
flash(l_(u'Action error'), 'error')
redirect(request.headers['Referer'])
return dict(mylists=mylists, pcl=pcl, page='index', tmpl=tmpl, pname=None)
class NewPasswordForm(TableForm):
data = HiddenField()
password = PasswordField(label=l_('New password'),
validator=Validator(required=True))
password_confirm = PasswordField(label=l_('Confirm new password'),
validator=Validator(required=True))
validator = FieldsMatch('password', 'password_confirm')
submit = SubmitButton(value=l_('Save new password'))
class NewCategoryForm(ListForm):
name = TextField(label=l_('Name'), validator=Validator(required=True), css_class='form-control',
container_attrs={'class': 'form-group'})
parent_id = SingleSelectField(label=l_('Parent'),
css_class="form-control", container_attrs={'class': 'form-group'},
options=Deferred(lambda: [(c._id, c.name[tg.config.lang])
for c in app_globals.shop.category.get_all()]))
submit = SubmitButton(value=l_('Create'), css_class='btn btn-default')
class fields(WidgetsList):
name = TextField(
label_text=l_("Calendar Name"),
validator=validators.UnicodeString(not_empty=True))
events_type = SingleSelectField(
label_text=l_('Events Type'),
options=lambda:
[e.name for e in config['_calendarevents']['event_types']],
validator=validators.UnicodeString(not_empty=False))
class NewCalendarForm(TableForm):
name = TextField(label=l_("Calendar Name"), validator=Required)
events_type = SingleSelectField(
label=l_('Events Type'),
prompt_text=None,
validator=Required,
options=Deferred(
lambda:
[e.name for e in config['_calendarevents']['event_types']]))
def _validate_python(self, value, state=None):
document_accepted_type = ['output']
for cond in value:
if cond['type'] == 'output':
output = model.Output.query.get(_id=ObjectId(cond['content']))
if not output:
raise ValidationError(l_(u'Output not found.'), self)
else:
raise ValidationError(l_(u'Invalid Filter.'), self)
class Details(twf.ListFieldSet):
label = None
key = 'details'
email = twf.TextField(validator=twc.Validator(required=True),
css_class="form-control",
label=l_("Email"))
phone = twf.TextField(validator=twc.Validator(),
css_class="form-control",
label=l_("Telefono"))
def index(self, workspace, **kw):
return dict(
page='precondition-index',
fields={
'columns_name': [l_('Label'), l_('Type'), l_('Owner')],
'fields_name': ['title', 'type', 'owner']
},
entities=model.Precondition.precondition_available_for_user(request.identity['user']._id, workspace=workspace),
actions_content=[l_('New Output'),l_('New Q/A')],
workspace=workspace
)
def _validate_python(self, value, state=None):
for cond in value:
if cond['type'] == 'qa_response':
qa = model.Qa.query.get(_id=ObjectId(cond['content']))
if not qa:
raise ValidationError(l_(u'Question not found.'), self)
elif cond['type'] == 'output':
out = model.Output.query.get(_id=ObjectId(cond['content']))
if not out:
raise ValidationError(l_(u'Output not found'), self)
else:
raise ValidationError(l_(u'Invalid Filter.'), self)
class fields(WidgetsList):
user_name = TextField(
label_text=l_('User Name'),
validator=UniqueUserValidator(not_empty=True))
email_address = TextField(
label_text=l_('Email'),
validator=UniqueEmailValidator(not_empty=True))
password = PasswordField(
label_text=l_('Password'),
validator=validators.UnicodeString(not_empty=True))
password_confirm = PasswordField(
label_text=l_('Confirm Password'),
validator=validators.UnicodeString(not_empty=True))
class child(KajikiBootstrapFormLayout):
permission_name = TextField(label=l_('Name'),
css_class='form-control',
validator=UnicodeString(not_empty=True))
description = TextArea(label=l_('Description'),
rows=10,
css_class='form-control',
validator=UnicodeString(not_empty=True))
groups = MultipleSelectField(label=l_('Groups'),
css_class="form-control",
options=Deferred(h.query_groups))
class RegistrationForm(TableForm):
# set additional extra info here to bring them across the registration process
# you might want to serialize the extra info in json or something similar
extra = HiddenField()
user_name = TextField(label=l_('User Name'),
validator=UniqueUserValidator(not_empty=True))
email_address = TextField(
label=l_('Email'), validator=UniqueEmailValidator(not_empty=True))
password = PasswordField(label=l_('Password'), validator=Required)
password_confirm = PasswordField(label=l_('Confirm Password'),
validator=Required)
validator = validators.FieldsMatch('password', 'password_confirm')
class fields(WidgetsList):
event = HiddenField()
cal = HiddenField(validator=SQLAEntityConverter(model.Calendar))
name = TextField(
label_text=l_('Event Name'),
validator=validators.UnicodeString(not_empty=True))
summary = TextArea(
label_text=l_('Event short summary'),
validator=validators.UnicodeString(not_empty=False))
datetime = CalendarDateTimePicker(label_text=l_('Event date'))
location = TextField(
label_text=l_('Event Location (es: turin,it)'),
validator=validators.UnicodeString(not_empty=True))
linked_entity = SingleSelectField(label_text=l_('Linked Entity'))
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)
class ManagementController(BaseController):
# Uncomment this line if your controller requires an authenticated user
allow_only = predicates.has_permission('administration',
msg=l_('Only for administrators'))
history = HistoryController()
def _before(self, *args, **kw):
tmpl_context.page_name = "Fortressd"
@expose('fortress.templates.management.index')
def index(self):
"""Handle the front-page."""
return dict(page='index')
@expose('fortress.templates.management.data_centers')
def data_centers(self):
"""Handle the front-page."""
return dict(page='index')
@expose('fortress.templates.management.data_servers')
def data_servers(self):
"""Handle the front-page."""
return dict(page='index')
@expose('fortress.templates.management.users')
def users(self):
"""Handle the front-page."""
return dict(page='index')
@expose('fortress.templates.management.authorizations')
def authorizations(self):
"""Handle the front-page."""
return dict(page='index')
def login(self, came_from=lurl('/start')):
"""Start the user login."""
login_counter = request.environ.get('repoze.who.logins', 0)
if login_counter > 0:
flash(l_('Wrong credentials'), 'warning')
return dict(page='login', login_counter=str(login_counter),
came_from=came_from)
def _admin_init_attrs(self):
if 'child' not in self.__base_widget_args__:
self.__base_widget_args__['child'] = _BootstrapFormLayout
if 'submit' not in self.__base_widget_args__:
if isinstance(self, AddRecordForm):
submit_text = l_('Create')
else:
submit_text = l_('Save')
self.__base_widget_args__['submit'] = SubmitButton(css_class='btn btn-primary',
value=submit_text)
for f in self.__fields__:
self.__field_widget_args__[f] = _merge_dicts(self.FIELD_OPTIONS,
self.__field_widget_args__.get(f, {}))
class SecureController(BaseController):
"""Sample controller-wide authorization"""
# The predicate that must be met for all the actions in this controller:
allow_only = has_permission(
'manage', msg=l_('Only for people with the "manage" permission'))
@expose('addrbook.templates.index')
def index(self):
"""Let the user know that's visiting a protected controller."""
flash(_("Secure Controller here"))
try:
username = self.username()
except:
username = ""
return dict(page='index',
contacts=[],
user="******",
total=0,
partial=0)
@expose('addrbook.templates.index')
def some_where(self):
"""Let the user know that this action is protected too."""
return dict(page='some_where')
class UsersController(BaseController):
"""Subcontrollers for lookup.
MAIN SITE FOR PROJECT INSTANCE.
Parmission allowed only for logged user with added permision named as a project.
"""
# The predicate that must be met for all the actions in this controller:
allow_only = has_permission(
project_name,
msg=l_('Permission is not sufficient for this user.'))
molecules = MoleculesController()
select = SelectController()
synthesis = SynthesisController()
library = LibraryController()
results = ResultsController()
@expose('molgears.templates.users.index')
def index(self):
"""Main site for project."""
userid = request.identity['repoze.who.userid']
projects = DBSession.query(Projects).all()
user = DBSession.query(User).filter_by(
user_name=userid).first()
perms = [p.permission_name for p in list(user.permissions)]
return dict(page='index',
userid=userid,
projects=projects,
perms=perms,
pname=project_name)
class RootController(TGController):
allow_only = in_any_group(
'voter',
'managers',
msg=l_('Only for people with the "manage" permission'))
invitation = InvitationController(model,
model.DBSession,
config_type=TGAdminConfig)
voter = VoterController(model, model.DBSession, config_type=TGAdminConfig)
publication = PublicationController(model,
model.DBSession,
config_type=TGAdminConfig)
project = ProjectController(model,
model.DBSession,
config_type=TGAdminConfig)
account = AccountController(model,
model.DBSession,
config_type=TGAdminConfig)
script = LoadDataControllers(model,
model.DBSession,
config_type=TGAdminConfig)
def __init__(self):
self.utility = Utility()
@expose('managepoll.templates.index')
def index(self):
flash(_("Hello World!"))
return dict(page='index', idproject=None)
class EditDescriptionForm(Form):
action = 'update_description'
class child(BaseLayout):
inline_engine_name = 'kajiki'
template = '''
<div py:strip="">
<py:for each="c in w.children_hidden">
${c.display()}
</py:for>
<div class="form form-horizontal">
<div class="form-group">
<div class="mail-templates-title">Edit model description</div>
<div class="col-md-12">
<div py:with="c=w.children.description"
class="form-group ${c.error_msg and 'has-error' or ''}">
<label for="${c.compound_id}" class="col-md-2 control-label">${c.label}</label>
<div class="col-md-10">
${c.display()}
<span class="help-block" py:content="c.error_msg"/>
</div>
</div>
</div>
</div>
</div>
</div>
'''
model_id = HiddenField()
description = TextArea(label='Description', css_class='form-control')
submit = SubmitButton(css_class='btn btn-primary pull-right', value=l_('Save'))
def _admin_init_attrs(self):
if 'child' not in self.__base_widget_args__:
self.__base_widget_args__['child'] = _BootstrapFormLayout
if 'submit' not in self.__base_widget_args__:
if isinstance(self, AddRecordForm):
submit_text = l_('Create')
else:
submit_text = l_('Save')
self.__base_widget_args__['submit'] = SubmitButton(
css_class='btn btn-primary', value=submit_text)
for f in self.__fields__:
self.__field_widget_args__[f] = _merge_dicts(
self.FIELD_OPTIONS, self.__field_widget_args__.get(f, {}))
def _convert_to_python(self, value, state=None):
if value['field'] == 'status_changes.changed_at':
try:
value['filt'] = datetime.strptime(value['filt'], self.date_format)
except:
raise twc.ValidationError(l_('Date format must be dd/mm/yyyy'))
return value
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)
class CategoryController(RestController):
allow_only = predicates.has_any_permission('manage',
'lawyer', msg=l_('Only for admin or lawyer'))
@expose('json')
@validate({
'id': CategoryExistValidator(required=True),
}, error_handler=validation_errors_response)
def get_one(self, id, **kw):
qa = Category.query.get(_id=ObjectId(id))
return dict(qa=qa)
@expose('json')
def get_all(self):
query = {'_owner': {'$in': [request.identity['user']._id, None]}, 'visible': True}
categories = Category.query.find(query).sort('_id').all()
return dict(categories=categories)
@decode_params('json')
@expose('json')
@validate({
'workspace_name': StringLengthValidator(min=2),
}, error_handler=validation_errors_response)
def create(self, workspace_name=None, **kw):
user = request.identity['user']
ws = Category.query.find({'name': str(workspace_name), '_owner': user._id}).first()
if ws:
response.status_code = 412
return dict(errors={'workspace_name': 'This category already exists'})
workspace = Category(
visible=True,
name=str(workspace_name),
_owner=user._id
)
flash(_("Workspace %s successfully created!" % workspace.name))
return dict(workspaces=self.get_all())
@decode_params('json')
@expose('json')
@validate({
'workspace_id': CategoryExistValidator(required=True),
}, error_handler=validation_errors_response)
def delete(self, workspace_id=None, **kw):
workspace = Category.query.get(_id=ObjectId(workspace_id))
if not workspace.owner:
flash(_('This workspace can not be deleted'), 'warning')
return dict(workspaces=self.get_all())
Qa.query.remove({'_category': ObjectId(workspace_id)})
Output.query.remove({'_category': ObjectId(workspace_id)})
Precondition.query.remove({'_category': ObjectId(workspace_id)})
documents = Document.query.find({'_category': ObjectId(workspace_id)}).all()
doc = [document._id for document in documents]
Questionary.query.remove({'_document': {'$in': doc}})
Document.query.remove({'_id': {'$in': doc}})
Category.query.remove({'_id': ObjectId(workspace_id)})
flash(_("Category and all entities associated deleted"))
return dict(workspaces=self.get_all())
def post_logout(self, came_from=lurl('/')):
"""
Redirect the user to the initially requested page on logout and say
goodbye as well.
"""
flash(l_('We hope to see you soon!'))
return HTTPFound(location=came_from)
def post_logout(self, came_from=lurl('/')):
"""
Redirect the user to the initially requested page on logout and say
goodbye as well.
"""
flash(l_('We hope to see you soon!'))
return HTTPFound(location=came_from)
def get_user_data(user):
user_data = get_profile_data(
user, {
'display_name': (l_('Display Name'), user.display_name),
'email_address': (l_('Email Address'), user.email_address),
})
user_avatar = user_data.pop('avatar', [None, None])[1]
if user_avatar is None:
fbauth_info = getattr(user, 'fbauth', None)
if fbauth_info is not None:
user_avatar = fbauth_info.profile_picture + '?type=large'
else:
user_avatar = _get_user_gravatar(user_data['email_address'][1])
return user_data, user_avatar
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'])
class UploadFileForm(twf.Form):
class child(twf.TableLayout):
inline_engine_name = 'kajiki'
template = '''
'''
upload = FileField(label='')
submit = SubmitButton(css_class="btn btn-primary", value=l_("Import"))
action = lurl('/')
def save(self, **kw):
order = Order.query.get(_id=ObjectId(kw['_id']))
if kw.get('bill'):
for k, v in kw.get('bill_info').iteritems():
setattr(order.bill_info, k, v)
for k, v in kw.get('shipment_info').iteritems():
setattr(order.shipment_info, k, v)
for k, v in kw.get('details').iteritems():
setattr(order.details, k, v)
flash(l_('Order successfully edited'))
return redirect(self.mount_point + '/orders')
def deletefromlist(self, ulist_id, *args):
"""
Delete compound from User List.
"""
ulist = DBSession.query(UserLists).get(ulist_id)
# pname = request.environ['PATH_INFO'].split('/')[1]
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter_by(user_name=userid).first()
# ulists = [l for l in user.lists if l.table == 'Results']
if (ulist in user.lists) or (user in ulist.permitusers):
if ulist.elements:
import pickle
elements = [int(el) for el in pickle.loads(ulist.elements)]
for arg in args:
if int(arg) in elements:
elements.remove(int(arg))
ulist.elements = pickle.dumps(elements)
flash(l_(u'Task completed successfully'))
else:
flash(l_(u'Permission denied'), 'error')
redirect(request.headers['Referer'])
def add_to_list(self, *args, **kw):
if args:
listid = args[0]
# table = args[1]
ulist = DBSession.query(UserLists).get(listid)
values = []
if args[2:]:
for arg in args[2:]:
values.append(arg)
import pickle
if ulist and ulist.elements and ulist.elements != u"":
elements = pickle.loads(ulist.elements)
else:
elements = []
new_elements = set(elements + values)
ulist.elements = pickle.dumps(list(new_elements))
flash(l_(u'Task completed successfully'))
redirect(request.headers['Referer'])
else:
flash(l_(u'Args error'), 'error')
redirect("/")
def post_login(self, came_from=lurl('/start')):
"""
Redirect the user to the initially requested page on successful
authentication or redirect her back to the login page if login failed.
"""
if not request.identity:
login_counter = request.environ.get('repoze.who.logins', 0) + 1
redirect('/login',
params=dict(came_from=came_from, __logins=login_counter))
userid = request.identity['repoze.who.userid']
flash(l_('Welcome back, %s!') % userid)
redirect(came_from)
def remove_from_list(self, *args, **kw):
ulistid = args[0]
ulist = DBSession.query(UserLists).get(ulistid)
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter(User.user_name == userid).first()
if (ulist in user.lists):
if ulist.elements:
import pickle
elements = pickle.loads(ulist.elements)
if args[1:]:
for arg in args[1:]:
elements.remove(arg)
ulist.elements = pickle.dumps(elements)
flash(l_(u'Task completed successfully'))
redirect(request.headers['Referer'])
else:
flash(l_(u'Args error'), 'error')
redirect(request.headers['Referer'])
else:
flash(l_(u'List error'), 'error')
redirect(request.headers['Referer'])
else:
flash(l_(u'Permission denied'), 'error')
redirect(request.headers['Referer'])
def start(self):
"""
Home page for authorized users.
"""
from tg.predicates import not_anonymous
if not not_anonymous():
flash(l_(u'Permission is not sufficient for this user'), 'error')
redirect('/')
userid = request.identity['repoze.who.userid']
projects = DBSession.query(Projects).order_by('id').all()
user = DBSession.query(User).filter_by(user_name=userid).first()
perms = list(user.permissions)
perms_names = [p.permission_name for p in perms]
user_projects = [project for project in projects if project.name in perms_names]
# flash(l_(u'Alpha version. Please send error reporting to: [email protected]. \t\t :)'), 'warning')
return dict(page='start', projects=user_projects, pname=None)
def __actions__(self, obj):
primary_fields = self.__provider__.get_primary_fields(self.__entity__)
pklist = '/'.join(map(lambda x: str(getattr(obj, x)), primary_fields))
return Markup('''
<a href="%(pklist)s/edit" class="btn btn-primary">
<span class="glyphicon glyphicon-pencil"></span>
</a>
<div class="hidden-lg hidden-md"> </div>
<form method="POST" action="%(pklist)s" style="display: inline">
<input type="hidden" name="_method" value="DELETE" />
<button type="submit" class="btn btn-danger" onclick="return confirm('%(msg)s')">
<span class="glyphicon glyphicon-trash"></span>
</button>
</form>
''' % dict(msg=l_('Are you sure?'),
pklist=pklist))
def prefs(self, **kwargs):
user = request.identity['user']
if kwargs:
DBSession.add(user)
for key, value in kwargs.iteritems():
setattr(user, key, value)
flash(l_('Your settings have been updated.'))
if not user.firstname or not user.lastname or not user.email:
ldap_firstname, ldap_lastname, ldap_email = nimsutil.ldap_query(user.uid)
firstname = user.firstname or ldap_firstname
lastname = user.lastname or ldap_lastname
email = user.email or ldap_email
prefs = OrderedDict()
prefs['firstname'] = ('First Name', firstname)
prefs['lastname'] = ('Last Name', lastname)
prefs['email'] = ('Email Address', email)
return dict(page='prefs', prefs=prefs)
def _lookup(self, project_name, *remainder):
"""
Project instance lookup.
"""
from tg.predicates import not_anonymous
try:
came_from = request.headers['Referer']
except Exception:
came_from = request.path_url
if not not_anonymous():
flash(l_('Permission is not sufficient for this user.'), 'error')
redirect('/login?came_from=%s' % came_from)
if DBSession.query(Projects).filter(Projects.name==project_name).first():
class UsersController(BaseController):
"""Subcontrollers for lookup.
MAIN SITE FOR PROJECT INSTANCE.
Parmission allowed only for logged user with added permision named as a project.
"""
# The predicate that must be met for all the actions in this controller:
allow_only = has_permission(project_name,
msg=l_('Permission is not sufficient for this user.'))
molecules = MoleculesController()
select = SelectController()
synthesis = SynthesisController()
library = LibraryController()
results = ResultsController()
@expose('molgears.templates.users.index')
def index(self):
"""Main site for project."""
userid = request.identity['repoze.who.userid']
projects = DBSession.query(Projects).all()
user = DBSession.query(User).filter_by(user_name=userid).first()
perms = [p.permission_name for p in list(user.permissions)]
return dict(page='index', userid=userid, projects=projects, perms=perms, pname=project_name)
users = UsersController()
else:
users = ErrorController()
return users, remainder
def index(self, page=1, *args, **kw):
"""
Index controller for molecules
"""
pname = request.environ['PATH_INFO'].split('/')[1]
project = DBSession.query(Projects).filter(Projects.name==pname).first()
alltags =[tag for tag in DBSession.query(Tags).order_by('name').all() ]
from sqlalchemy import or_
compound = DBSession.query(Compound).filter(Compound.project.any(Projects.name==pname)).filter(or_(Compound.pcompounds != None, Compound.lcompounds != None))
dsc = True
tmpl = ''
selection = None
similarity = None
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter_by(user_name=userid).first()
threshold = float(user.threshold)/100.0
items = user.items_per_page
order = "gid"
try:
if kw['search'] != u'':
search_clicked = kw['search']
else:
search_clicked = None
except Exception:
search_clicked = None
if kw:
delkw = []
for k, v in kw.iteritems():
if str(k) == 'desc' and str(v) != '1':
dsc = None
elif str(k) == 'order_by':
order = v
if str(k) != 'select' and str(k) != 'remove' and str(v) != u'':
tmpl += str(k) + '=' + str(v) + '&'
elif str(k) == 'select':
try:
if isinstance(kw['select'], basestring):
selection = [kw['select']]
else:
selection = [id for id in kw['select']]
except Exception:
selection = None
elif str(v) == u'':
delkw.append(k)
for k in delkw:
del kw[k]
if search_clicked:
try:
smiles = str(kw['smiles'])
except Exception:
smiles = None
pass
try:
method = str(kw['method'])
except Exception:
method = None
pass
if smiles:
if checksmi(smiles):
from razi.functions import functions
from razi.expression import TxtMoleculeElement
if method == 'similarity':
from razi.postgresql_rdkit import tanimoto_threshold
DBSession.execute(tanimoto_threshold.set(threshold))
query_bfp = functions.morgan_b(TxtMoleculeElement(smiles), 2)
constraint = Compound.morgan.tanimoto_similar(query_bfp)
tanimoto_sml = Compound.morgan.tanimoto_similarity(query_bfp).label('tanimoto')
limit = user.limit_sim
search = DBSession.query(Compound, tanimoto_sml).filter(constraint).filter(Compound.project.any(Projects.name==pname)).order_by(desc(tanimoto_sml)).limit(limit).all()
compound = ()
similarity = ()
for row in search:
compound += (row[0], )
similarity += (row[1], )
page_url = paginate.PageURL_WebOb(request)
currentPage = paginate.Page(compound, page, url=page_url, items_per_page=items)
return dict(length=len(compound), compound=currentPage.items, currentPage=currentPage, tmpl=tmpl, page='samples', pname=pname, alltags=alltags, similarity=similarity)
elif method == 'substructure':
constraint = Compound.structure.contains(smiles)
compound = DBSession.query(Compound).filter(constraint).filter(Compound.project.any(Projects.name==pname))
elif method == 'identity':
compound = DBSession.query(Compound).filter(Compound.structure.equals(smiles)).filter(Compound.project.any(Projects.name==pname))
else:
flash(l_(u'Smiles error'), 'warning')
redirect(request.headers['Referer'])
if kw.has_key('text_GID') and kw['text_GID'] !=u'':
try:
gid = int(kw['text_GID'])
compound = compound.filter_by(gid = gid )
except Exception as msg:
flash(l_(u'GID should be a number: %s' % msg), 'error')
redirect(request.headers['Referer'])
if kw.has_key('text_name') and kw['text_name'] !=u'':
compound = compound.filter(Compound.names.any(Names.name.like(kw['text_name'].strip().replace('*', '%'))))
if kw.has_key('text_creator') and kw['text_creator'] !=u'':
compound = compound.filter(Compound.creator.like(kw['text_creator'].replace('*', '%')))
if kw.has_key('text_notes') and kw['text_notes'] !=u'':
compound = compound.filter(Compound.notes.like(kw['text_notes'].replace('*', '%')))
if kw.has_key('date_from') and kw['date_from'] !=u'':
date_from = datetime.strptime(str(kw['date_from']), '%Y-%m-%d')
compound = compound.filter(Compound.create_date > date_from)
else:
date_from = None
if kw.has_key('date_to') and kw['date_to'] !=u'':
date_to = datetime.strptime(str(kw['date_to']), '%Y-%m-%d')
if date_from:
if date_to>date_from:
compound = compound.filter(Compound.create_date < date_to)
else:
flash(l_(u'The End date must be later than the initial'), 'error')
redirect(request.headers['Referer'])
else:
compound = compound.filter(Compound.create_date < date_to)
try:
tags = kw['text_tags']
except Exception:
tags = None
pass
if tags:
if isinstance(tags, basestring):
tagi = eval(tags)
if type(tagi) != type([]):
tagi = [int(tags)]
else:
tagi = [int(id) for id in tags]
# import sqlalchemy
compound = compound.filter(Compound.tags.any(Tags.id.in_(tagi)))
if selection and not search_clicked:
argv =''
for arg in selection:
argv += '/' + arg
if kw['akcja'] == u'edit':
if len(selection) == 1:
redirect('/%s/samples/edit%s' % (pname, argv))
else:
redirect('/%s/samples/multiedit/index%s' % (pname, argv))
elif kw['akcja'] == u'accept':
if len(selection) == 1:
redirect('/%s/samples/accept%s' % (pname, argv))
else:
redirect('/%s/samples/multiaccept/index%s' % (pname, argv))
elif kw['akcja'] == u'library':
if len(selection) == 1:
redirect('/%s/samples/library%s' % (pname, argv))
else:
redirect('/%s/samples/multilibrary/index%s' % (pname, argv))
elif kw['akcja'] == u'pdf':
redirect('/%s/samples/index/download%s/pdf/samples_selected.pdf' % (pname, argv))
elif kw['akcja'] == u'xls':
redirect('/%s/samples/download%s/xls/samples_selected.xls' % (pname, argv))
elif kw['akcja'] == u'txt':
redirect('/%s/samples/download%s/txt/samples_selected.txt' % (pname, argv))
elif kw['akcja'] == u'delete':
redirect('/%s/samples/remove%s' % (pname, argv))
else:
flash(l_(u'Action error'), 'error')
redirect(request.headers['Referer'])
else:
try:
akcja = kw['akcja']
except Exception:
akcja = None
if akcja:
if akcja == u'pdf':
redirect('/%s/samples/index/download/pdf/samples_all.pdf' % pname)
elif akcja == u'xls':
redirect('/%s/samples/download/xls/samples_all.xls' % pname)
elif akcja == u'txt':
redirect('/%s/samples/download/txt/samples_all.txt' % pname)
if dsc:
compound = compound.order_by(desc(order).nullslast())
else:
compound = compound.order_by((order))
page_url = paginate.PageURL_WebOb(request)
currentPage = paginate.Page(compound, page, url=page_url, items_per_page=items)
return dict(compound=currentPage.items, currentPage=currentPage, tmpl=tmpl, page='samples', pname=pname, alltags=alltags, similarity=similarity)
def index(self, page=1, *args, **kw):
pname = request.environ['PATH_INFO'].split('/')[1]
project = DBSession.query(Projects).filter_by(name=pname).first()
page_url = paginate.PageURL_WebOb(request)
import pickle
try:
cells = pickle.loads([test.cell_line for test in project.tests if test.name == 'CT'][0])
except:
cells = None
lcompound = DBSession.query(LCompound).join(LCompound.mol).filter(Compound.project.any(Projects.name==pname)).filter(LCompound.showme==True)
dsc = True
order = LCompound.id
tmpl = ''
alltags =[tag for tag in DBSession.query(Tags).order_by('name').all() ]
selection = None
similarity = None
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter_by(user_name=userid).first()
ulist = None
ulists = set([l for l in user.lists if l.table == 'Results'] + [l for l in user.tg_user_lists if l.table == 'Results'])
items = user.items_per_page
try:
if kw['search'] != u'':
search_clicked = kw['search']
else:
search_clicked = None
except Exception:
search_clicked = None
if kw:
if kw.has_key('mylist'):
try:
ulist_id = int(kw['mylist'])
ulist = DBSession.query(UserLists).get(ulist_id)
except Exception:
flash(l_(u'List error'), 'error')
redirect(request.headers['Referer'])
if (ulist in user.lists) or (user in ulist.permitusers):
if ulist.elements:
import pickle
elements = [int(el) for el in pickle.loads(ulist.elements)]
if ulist.table == 'Results':
lcompound = DBSession.query(LCompound).join(LCompound.mol).filter(Compound.project.any(Projects.name==pname)).filter(LCompound.id.in_(elements))
else:
flash(l_(u'Table error'), 'error')
redirect(request.headers['Referer'])
else:
flash(l_(u'Permission denied'), 'error')
redirect(request.headers['Referer'])
for k, v in kw.iteritems():
if str(k) == 'desc' and str(v) != '1':
dsc = None
elif str(k) == 'order_by':
if v in ('gid', 'create_date', 'box', 'form', 'state', 'entry', 'source', 'MDM2', 'MDM4', 'lcode'):
if v=='lcode':
order = LCompound.lcode
else:
order = LCompound.__getattribute__(LCompound, v)
else:
if v=='last_point':
lcompound=lcompound.join(LCompound.solubility)
order = v
elif hasattr(LCompound, v):
order = LCompound.__getattribute__(LCompound, v)
elif 'CTOX_' in v:
v = v.replace('CTOX_', '')
all_lcompounds = DBSession.query(LCompound).join(LCompound.mol).filter(Compound.project.any(Projects.name==pname)).all()
for l in all_lcompounds:
l.avg_ct = v.replace('pp', '+')
order = '_avg_ct'
else:
order = v
if str(k) != 'select' and str(k) != 'remove' and str(v) != u'':
tmpl += str(k) + '=' + str(v) + '&'
elif str(k) == 'select':
try:
if isinstance(kw['select'], basestring):
selection = [kw['select']]
else:
selection = [id for id in kw['select']]
except Exception:
selection = None
if search_clicked:
try:
smiles = str(kw['smiles'])
if 'pp' in smiles:
smiles = smiles.replace('pp', '+')
method = str(kw['method'])
except Exception:
smiles = None
method = None
if smiles:
if checksmi(smiles):
from razi.functions import functions
from razi.expression import TxtMoleculeElement
if method == 'similarity':
# from razi.postgresql_rdkit import tanimoto_threshold
query_bfp = functions.morgan_b(TxtMoleculeElement(smiles), 2)
constraint = Compound.morgan.tanimoto_similar(query_bfp)
tanimoto_sml = Compound.morgan.tanimoto_similarity(query_bfp).label('tanimoto')
search = DBSession.query(LCompound, tanimoto_sml).join(LCompound.mol).join(LCompound.purity).filter(Compound.project.any(Projects.name==pname)).filter(constraint)
if order != LCompound.id:
if order == 'purity':
order = LPurity.value
if dsc:
search = search.order_by(desc(order).nullslast())
else:
search = search.order_by(order)
else:
search = search.order_by(desc(tanimoto_sml)).all()
lcompound = ()
similarity = ()
for row in search:
lcompound += (row[0], )
similarity += (row[1], )
currentPage = paginate.Page(lcompound, page, url=page_url, items_per_page=items)
return dict(currentPage=currentPage,tmpl=tmpl, page='results', pname=pname, alltags=alltags, similarity=similarity,htmlRgb=htmlRgb, htmlRgb100=htmlRgb100, Num2Rgb=Num2Rgb, cells=cells, ulists=ulists, ulist=ulist)
elif method == 'substructure':
constraint = Compound.structure.contains(smiles)
lcompound = DBSession.query(LCompound).join(LCompound.mol).filter(Compound.project.any(Projects.name==pname)).filter(constraint)
elif method == 'identity':
lcompound = DBSession.query(LCompound).filter(Compound.project.any(Projects.name==pname)).join(LCompound.mol).filter(Compound.structure.equals(smiles))
else:
if method == 'smarts':
if dsc:
lcompound = lcompound.order_by(desc(order).nullslast())
else:
lcompound = lcompound.order_by(order)
search = lcompound.all()
sub_lcompounds = ()
patt = Chem.MolFromSmarts(smiles)
if not patt:
flash(l_(u'SMARTS error'), 'warning')
redirect(request.headers['Referer'])
for row in search:
m = Chem.MolFromSmiles(str(row.mol.structure))
mol = Chem.AddHs(m)
if mol.HasSubstructMatch(patt):
sub_lcompounds += (row, )
currentPage = paginate.Page(sub_lcompounds, page, url=page_url, items_per_page=items)
return dict(currentPage=currentPage,tmpl=tmpl, page='results', pname=pname, alltags=alltags, similarity=similarity,htmlRgb=htmlRgb, htmlRgb100=htmlRgb100, Num2Rgb=Num2Rgb, cells=cells, ulists=ulists, ulist=ulist)
else:
flash(l_(u'SMILES error'), 'warning')
redirect(request.headers['Referer'])
if kw.has_key('text_GID') and kw['text_GID'] !=u'':
try:
gid = int(kw['text_GID'])
lcompound = lcompound.filter(LCompound.gid == gid)
except Exception as msg:
flash(l_(u'GID should be a number: %s' % msg), 'error')
redirect(request.headers['Referer'])
if kw.has_key('text_ID') and kw['text_ID'] !=u'':
try:
id = int(kw['text_ID'])
lcompound = lcompound.filter(LCompound.id == id)
except Exception as msg:
flash(l_(u'ID should be a number: %s' % msg), 'error')
redirect(request.headers['Referer'])
if kw.has_key('text_name') and kw['text_name'] !=u'':
lcompound = lcompound.filter(Compound.names.any(Names.name.like(kw['text_name'].strip().replace('*', '%'))))
if kw.has_key('text_notes') and kw['text_notes'] !=u'':
lcompound = lcompound.filter(LCompound.notes.like(kw['text_notes'].replace('*', '%')))
if kw.has_key('text_lso') and kw['text_lso'] !=u'':
lcompound = lcompound.filter(LCompound.lso.like(kw['text_lso'].replace('*', '%')))
if kw.has_key('text_entry') and kw['text_entry'] !=u'':
lcompound = lcompound.filter(LCompound.entry.like(kw['text_entry'].replace('*', '%')))
if kw.has_key('text_box') and kw['text_box'] !=u'':
lcompound = lcompound.filter(LCompound.box.like(kw['text_box'].replace('*', '%')))
if kw.has_key('date_from') and kw['date_from'] !=u'':
date_from = datetime.strptime(str(kw['date_from']), '%Y-%m-%d')
lcompound = lcompound.filter(LCompound.create_date > date_from)
else:
date_from = None
if kw.has_key('date_to') and kw['date_to'] !=u'':
date_to = datetime.strptime(str(kw['date_to']), '%Y-%m-%d')
if date_from:
if date_to>date_from:
lcompound = lcompound.filter(LCompound.create_date < date_to)
else:
flash(l_(u'The End date must be later than the initial'), 'error')
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.create_date < date_to)
if kw.has_key('text_mdm2_hill_from') and kw['text_mdm2_hill_from'] !=u'':
text_mdm2_hill_from = float(kw['text_mdm2_hill_from'])
lcompound = lcompound.filter(LCompound.avg_hillslope_mdm2 >= text_mdm2_hill_from)
else:
text_mdm2_hill_from = None
if kw.has_key('text_mdm2_hill_to') and kw['text_mdm2_hill_to'] !=u'':
text_mdm2_hill_to = float(kw['text_mdm2_hill_to'])
if text_mdm2_hill_from:
if text_mdm2_hill_to>=text_mdm2_hill_from:
lcompound = lcompound.filter(LCompound.avg_hillslope_mdm2 <= text_mdm2_hill_to)
else:
flash(l_(u'The final value must be greater than the initial'))
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.avg_hillslope_mdm2 <= text_mdm2_hill_to)
if kw.has_key('text_mdm2_fluor_from') and kw['text_mdm2_fluor_from'] !=u'':
text_mdm2_fluor_from = float(kw['text_mdm2_fluor_from'])
lcompound = lcompound.filter(LCompound.avg_fluorescence_mdm2 >= text_mdm2_fluor_from)
else:
text_mdm2_fluor_from = None
if kw.has_key('text_mdm2_fluor_to') and kw['text_mdm2_fluor_to'] !=u'':
text_mdm2_fluor_to = float(kw['text_mdm2_fluor_to'])
if text_mdm2_fluor_from:
if text_mdm2_fluor_to>=text_mdm2_fluor_from:
lcompound = lcompound.filter(LCompound.avg_fluorescence_mdm2 <= text_mdm2_fluor_to)
else:
flash(l_(u'The final value must be greater than the initial'))
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.avg_fluorescence_mdm2 <= text_mdm2_fluor_to)
if kw.has_key('text_mdm2_ki_from') and kw['text_mdm2_ki_from'] !=u'':
text_mdm2_ki_from = float(kw['text_mdm2_ki_from'])
lcompound = lcompound.filter(LCompound.avg_ki_mdm2 >= text_mdm2_ki_from)
else:
text_mdm2_ki_from = None
if kw.has_key('text_mdm2_ki_to') and kw['text_mdm2_ki_to'] !=u'':
text_mdm2_ki_to = float(kw['text_mdm2_ki_to'])
if text_mdm2_ki_from:
if text_mdm2_ki_to>=text_mdm2_ki_from:
lcompound = lcompound.filter(LCompound.avg_ki_mdm2 <= text_mdm2_ki_to)
else:
flash(l_(u'The final value must be greater than the initial'))
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.avg_ki_mdm2 <= text_mdm2_ki_to)
if kw.has_key('text_mdm4_hill_from') and kw['text_mdm4_hill_from'] !=u'':
text_mdm4_hill_from = float(kw['text_mdm4_hill_from'])
lcompound = lcompound.filter(LCompound.avg_hillslope_mdm4 >= text_mdm4_hill_from)
else:
text_mdm4_hill_from = None
if kw.has_key('text_mdm4_hill_to') and kw['text_mdm4_hill_to'] !=u'':
text_mdm4_hill_to = float(kw['text_mdm4_hill_to'])
if text_mdm4_hill_from:
if text_mdm4_hill_to>=text_mdm4_hill_from:
lcompound = lcompound.filter(LCompound.avg_hillslope_mdm4 <= text_mdm4_hill_to)
else:
flash(l_(u'The final value must be greater than the initial'))
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.avg_hillslope_mdm4 <= text_mdm4_hill_to)
if kw.has_key('text_mdm4_fluor_from') and kw['text_mdm4_fluor_from'] !=u'':
text_mdm4_fluor_from = float(kw['text_mdm4_fluor_from'])
lcompound = lcompound.filter(LCompound.avg_fluorescence_mdm4 >= text_mdm4_fluor_from)
else:
text_mdm4_fluor_from = None
if kw.has_key('text_mdm4_fluor_to') and kw['text_mdm4_fluor_to'] !=u'':
text_mdm4_fluor_to = float(kw['text_mdm4_fluor_to'])
if text_mdm4_fluor_from:
if text_mdm4_fluor_to>=text_mdm4_fluor_from:
lcompound = lcompound.filter(LCompound.avg_fluorescence_mdm4 <= text_mdm4_fluor_to)
else:
flash(l_(u'The final value must be greater than the initial'))
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.avg_fluorescence_mdm4 <= text_mdm4_fluor_to)
if kw.has_key('text_mdm4_ki_from') and kw['text_mdm4_ki_from'] !=u'':
text_mdm4_ki_from = float(kw['text_mdm4_ki_from'])
lcompound = lcompound.filter(LCompound.avg_ki_mdm4 >= text_mdm4_ki_from)
else:
text_mdm4_ki_from = None
if kw.has_key('text_mdm4_ki_to') and kw['text_mdm4_ki_to'] !=u'':
text_mdm4_ki_to = float(kw['text_mdm4_ki_to'])
if text_mdm4_ki_from:
if text_mdm4_ki_to>=text_mdm4_ki_from:
lcompound = lcompound.filter(LCompound.avg_ki_mdm4 <= text_mdm4_ki_to)
else:
flash(l_(u'The final value must be greater than the initial'))
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.avg_ki_mdm4 <= text_mdm4_ki_to)
try:
tags = kw['text_tags']
except Exception:
tags = None
pass
if tags:
if isinstance(tags, basestring):
tagi = eval(tags)
if type(tagi) != type([]):
tagi = [int(tags)]
else:
tagi = [int(tid) for tid in tags]
lcompound = lcompound.filter(Compound.tags.any(Tags.id.in_(tagi)))
if dsc:
lcompound = lcompound.order_by(desc(order).nullslast())
else:
lcompound = lcompound.order_by(order)
if search_clicked and kw['search'] == "Download":
if kw['file_type'] and kw['file_type'] != u'' and kw['sell_type'] and kw['sell_type'] != u'':
if kw['sell_type'] == u'all':
lcompounds = lcompound.all()
elif kw['sell_type'] == u'selected':
if selection:
lcompounds = ()
for el in selection:
lcompounds += (DBSession.query(LCompound).get(el), )
else:
flash(l_(u'Lack of selected structures for download'), 'error')
redirect(request.headers['Referer'])
elif kw['sell_type'] == u'range':
lcompounds = lcompound.all()
if kw.has_key('select_from') and kw['select_from'] != u'':
try:
select_from = int(kw['select_from']) -1
if select_from<1 or select_from>len(lcompounds):
select_from = 0
except Exception:
select_from = 0
else:
select_from = 0
if kw.has_key('select_to') and kw['select_to'] != u'':
try:
select_to = int(kw['select_to'])
if select_to<2 or select_to>len(lcompounds):
select_to = len(lcompounds)
except Exception:
select_to = len(lcompounds)
else:
select_to = len(lcompounds)
lcompounds_new = ()
for el in range(select_from, select_to):
lcompounds_new += (lcompounds[el], )
lcompounds = lcompounds_new
else:
flash(l_(u'Lack of items to download'), 'error')
redirect(request.headers['Referer'])
try:
if isinstance(kw['options'], basestring):
options = [kw['options']]
else:
options = kw['options']
except Exception:
flash(l_('Choose download options'), 'error')
redirect(request.headers['Referer'])
if 'getsize' in kw:
size = int(kw['getsize']), int(kw['getsize'])
else:
size = 100, 100
if kw['file_type'] == 'pdf':
filename = userid + '_selected.pdf'
from xhtml2pdf.pisa import CreatePDF
from tg.render import render as render_template
import cStringIO
html = render_template({"length":len(lcompounds), "lcompound":lcompounds, "cells":cells, "options":options, "size":size}, "genshi", "molgears.templates.users.results.print2", doctype=None)
dest = './molgears/files/pdf/' + filename
result = file(dest, "wb")
CreatePDF(cStringIO.StringIO(html.encode("UTF-8")), result, encoding="utf-8")
result.close()
import paste.fileapp
f = paste.fileapp.FileApp('./molgears/files/pdf/'+ filename)
from tg import use_wsgi_app
return use_wsgi_app(f)
elif kw['file_type'] == 'xls':
filename = userid + '_selected.xls'
filepath = os.path.join('./molgears/files/download/', filename)
from PIL import Image
import xlwt
wbk = xlwt.Workbook()
sheet = wbk.add_sheet('sheet1')
j=0
if 'nr' in options:
sheet.write(0,j,u'Nr.')
j+=1
if 'gid' in options:
sheet.write(0,j,u'GID')
j+=1
if 'id' in options:
sheet.write(0,j,u'ID')
j+=1
if 'name' in options:
sheet.write(0,j,u'Name')
j+=1
if 'names' in options:
sheet.write(0,j,u'Names')
j+=1
if 'image' in options:
sheet.write(0,j,u'Image')
j+=1
if 'smiles' in options:
sheet.write(0,j,u'SMILES')
j+=1
if 'inchi' in options:
sheet.write(0,j,u'InChi')
j+=1
if 'lso' in options:
sheet.write(0,j,u'LSO')
j+=1
if 'num_atoms' in options:
sheet.write(0,j,u'Atoms')
j+=1
if 'mw' in options:
sheet.write(0,j,u'MW')
j+=1
if 'hba' in options:
sheet.write(0,j,u'hba')
j+=1
if 'hbd' in options:
sheet.write(0,j,u'hbd')
j+=1
if 'tpsa' in options:
sheet.write(0,j,u'tpsa')
j+=1
if 'logp' in options:
sheet.write(0,j,u'logP')
j+=1
if 'purity' in options:
sheet.write(0,j, u'Purity')
j+=1
if 'create_date' in options:
sheet.write(0,j,u'Date')
j+=1
if 'box' in options:
sheet.write(0,j,u'Box')
j+=1
if 'entry' in options:
sheet.write(0,j,u'Entry')
j+=1
if 'source' in options:
sheet.write(0,j,u'Source')
j+=1
if 'content' in options:
sheet.write(0,j,u'Content')
j+=1
if 'tags' in options:
sheet.write(0,j,u'Tags')
j+=1
if 'notes' in options:
sheet.write(0,j,u'Notes')
j+=1
for cell_line in cells:
if '_CT_%s' % cell_line in options:
sheet.write(0,j,u'CT %s' % cell_line)
j+=1
i = 1
for row in lcompounds:
j=0
if 'nr' in options:
sheet.write(i,j, str(i))
j+=1
if 'gid' in options:
sheet.write(i,j, row.gid)
j+=1
if 'id' in options:
sheet.write(i,j, row.id)
j+=1
if 'name' in options:
sheet.write(i,j, row.mol.name)
j+=1
if 'names' in options:
names = u''
for n in row.mol.names:
names += n.name + u', '
sheet.write(i,j, names)
j+=1
if 'image' in options:
file_in = './molgears/public/img/%s.png' % row.gid
img = Image.open(file_in)
file_out = './molgears/public/img/bitmap/thumb%s.bmp' %row.gid
img.thumbnail(size, Image.ANTIALIAS)
img.save(file_out)
sheet.insert_bitmap(file_out , i,j, 5, 5)
j+=1
if 'smiles' in options:
sheet.write(i,j, str(row.mol.structure))
j+=1
if 'inchi' in options:
sheet.write(i,j, str(row.mol.inchi))
j+=1
if 'lso' in options:
sheet.write(i,j, row.lso)
j+=1
if 'num_atoms' in options:
sheet.write(i,j,str(row.mol.num_hvy_atoms)+'/'+str(row.mol.num_atoms))
j+=1
if 'mw' in options:
sheet.write(i,j, str(row.mol.mw))
j+=1
if 'hba' in options:
sheet.write(i,j, str(row.mol.hba))
j+=1
if 'hbd' in options:
sheet.write(i,j, str(row.mol.hbd))
j+=1
if 'tpsa' in options:
sheet.write(i,j, str(row.mol.tpsa))
j+=1
if 'logp' in options:
sheet.write(i,j, str(row.mol.logp))
j+=1
if 'state' in options:
sheet.write(i,j, str(row.state))
j+=1
if 'purity' in options:
pur = u''
for p in sorted(row.purity, key=lambda p: p.value, reverse=True):
pur += u'%s : %s\n' % (p.value, p.type)
sheet.write(i,j, pur)
j+=1
if 'create_date' in options:
sheet.write(i,j, str(row.create_date))
j+=1
if 'owner' in options:
sheet.write(i,j, row.owner)
j+=1
if 'box' in options:
sheet.write(i,j, row.box)
j+=1
if 'entry' in options:
sheet.write(i,j, row.entry)
j+=1
if 'source' in options:
sheet.write(i,j, row.source)
j+=1
if 'content' in options:
if row.content:
sheet.write(i,j, str(row.content.value))
else:
sheet.write(i,j, 'None')
j+=1
if 'tags' in options:
tagsy=u''
for tag in row.mol.tags:
tagsy += tag.name + u', '
sheet.write(i,j,tagsy)
j+=1
if 'notes' in options:
sheet.write(i,j, row.notes)
j+=1
for cell_line in cells:
if '_CT_%s' % cell_line in options:
res = []
if row.ctoxicity:
for ct in sorted(row.ctoxicity, key=lambda ct: ct.id):
if ct.cell_line==cell_line:
res.append(ct.ic50)
if len(res)>0:
sheet.write(i,j, str(round(sum(res)/len(res), 3)))
else:
sheet.write(i,j, '')
j+=1
i += 1
wbk.save(filepath)
import paste.fileapp
f = paste.fileapp.FileApp(filepath)
from tg import use_wsgi_app
return use_wsgi_app(f)
elif kw['file_type'] == 'sdf':
filepath = './molgears/files/download/out.sdf'
ww = Chem.SDWriter(filepath)
from rdkit.Chem import AllChem
for row in lcompounds:
m2 = Chem.MolFromSmiles(str(row.mol.structure))
AllChem.Compute2DCoords(m2)
AllChem.EmbedMolecule(m2)
AllChem.UFFOptimizeMolecule(m2)
if 'smiles' in options:
m2.SetProp("smiles", str(row.mol.structure))
if 'name' in options:
m2.SetProp("_Name", str(row.mol.name.encode('ascii', 'ignore')))
if 'nr' in options:
m2.SetProp("Nr", str(lcompounds.index(row)+1))
if 'gid' in options:
m2.SetProp("GID", str(row.gid))
if 'names' in options:
names = u''
for n in row.mol.names:
names += n.name + ', '
m2.SetProp("names", str(names.encode('ascii', 'ignore')))
if 'inchi' in options:
m2.SetProp("InChi", str(row.mol.inchi))
if 'lso' in options:
m2.SetProp("LSO", str(row.lso))
if 'num_atoms' in options:
m2.SetProp("atoms", str(row.mol.num_hvy_atoms)+'/'+str(row.mol.num_atoms))
if 'mw' in options:
m2.SetProp("mw", str(row.mol.mw))
if 'hba' in options:
m2.SetProp("hba", str(row.mol.hba))
if 'hbd' in options:
m2.SetProp("hbd", str(row.mol.hbd))
if 'tpsa' in options:
m2.SetProp("TPSA", str(row.mol.tpsa))
if 'logp' in options:
m2.SetProp("logP", str(row.mol.tpsa))
if 'create_date' in options:
m2.SetProp("create_date", str(row.create_date))
if 'owner' in options:
m2.SetProp("owner", str(row.owner))
if 'tags' in options:
tagsy=u''
for tag in row.mol.tags:
tagsy += tag.name + u', '
m2.SetProp("tagi", str(tagsy.encode('ascii', 'ignore')))
if 'purity' in options:
pur = u''
for p in sorted(row.purity, key=lambda p: p.value, reverse=True):
pur += u'%s : %s \n' % (p.value, p.type)
m2.SetProp("purity", str(pur.encode('ascii', 'ignore')))
if 'content' in options:
if row.content:
m2.SetProp("content", str(row.content.value))
else:
m2.SetProp("content", "None")
j+=1
if 'box' in options:
m2.SetProp("box", str(row.box))
if 'entry' in options:
m2.SetProp("entry", str(row.entry))
if 'notes' in options:
if row.notes:
m2.SetProp("notes", str(row.notes.encode('ascii', 'ignore')))
else:
m2.SetProp("notes", " ")
for cell_line in cells:
if '_CT_%s' % cell_line in options:
res = []
if row.ctoxicity:
for ct in sorted(row.ctoxicity, key=lambda ct: ct.id):
if ct.cell_line==cell_line:
res.append(ct.ic50)
if len(res)>0:
m2.SetProp('CT_%s' % cell_line, str(round(sum(res)/len(res), 3)))
else:
m2.SetProp('CT_%s' % cell_line, ' ')
ww.write(m2)
ww.close()
import paste.fileapp
f = paste.fileapp.FileApp(filepath)
from tg import use_wsgi_app
return use_wsgi_app(f)
elif kw['file_type'] == 'csv' or 'txt':
filename = userid + '_selected.' + kw['file_type']
filepath = os.path.join('./molgears/files/download/', filename)
from molgears.widgets.unicodeCSV import UnicodeWriter
import csv
if kw['file_type'] == u'csv':
delimiter = ';'
else:
delimiter = ' '
with open(filepath, 'wb') as csvfile:
spamwriter = UnicodeWriter(csvfile, delimiter=delimiter,
quotechar='|', quoting=csv.QUOTE_MINIMAL)
for row in lcompounds:
line =[]
if 'smiles' in options:
line.append(str(row.mol.structure))
if 'name' in options:
line.append(row.mol.name)
if 'nr' in options:
line.append(unicode(lcompounds.index(row)+1))
if 'gid' in options:
line.append(unicode(row.gid))
if 'names' in options:
names = u''
for n in row.mol.names:
names += n.name + u', '
line.append(names)
if 'inchi' in options:
line.append(row.mol.inchi)
if 'lso' in options:
line.append(row.lso)
if 'num_atoms' in options:
line.append(unicode(row.mol.num_hvy_atoms)+'/'+unicode(row.mol.num_atoms))
if 'mw' in options:
line.append(unicode(row.mol.mw))
if 'hba' in options:
line.append(unicode(row.mol.hba))
if 'hbd' in options:
line.append(unicode(row.mol.hbd))
if 'tpsa' in options:
line.append(unicode(row.mol.tpsa))
if 'logp' in options:
line.append(unicode(row.mol.logp))
if 'purity' in options:
pur = u''
for p in sorted(row.purity, key=lambda p: p.value, reverse=True):
pur += u'%s : %s\n' % (p.value, p.type)
line.append(pur)
if 'create_date' in options:
line.append(unicode(row.create_date))
if 'owner' in options:
line.append(row.owner)
if 'box' in options:
line.append(row.box)
if 'entry' in options:
line.append(row.entry)
if 'source' in options:
line.append(row.source)
if 'content' in options:
if row.content:
line.append(unicode(row.content.value))
else:
line.append(u'None')
if 'tags' in options:
tagsy= ''
for tag in row.mol.tags:
tagsy += tag.name + ', '
line.append(tagsy)
if 'notes' in options:
line.append(row.notes)
spamwriter.writerow(line)
import paste.fileapp
f = paste.fileapp.FileApp(filepath)
from tg import use_wsgi_app
return use_wsgi_app(f)
if selection and not search_clicked:
argv =''
gids = ''
for arg in selection:
argv += '/' + arg
tmp_result = DBSession.query(LCompound).get(arg)
gids += '/' + str(tmp_result.gid)
if kw['akcja'] == u'edit':
redirect('/%s/molecules/multiedit/index%s' % (pname, gids))
elif kw['akcja'] == u'results':
if len(selection) == 1:
redirect('/%s/results/new_result%s' % (pname, argv))
else:
redirect('/%s/results/multiresults/index%s' % (pname, argv))
elif kw['akcja'] == u'htrf':
if len(selection) == 1:
redirect('/%s/results/htrf/add_result2%s' % (pname, argv))
currentPage = paginate.Page(lcompound, page, url=page_url, items_per_page=items)
return dict(currentPage=currentPage,tmpl=tmpl, page='results', htmlRgb=htmlRgb, htmlRgb100=htmlRgb100, Num2Rgb=Num2Rgb, pname=pname, alltags=alltags, similarity=similarity, cells=cells, ulists=ulists, ulist=ulist)
from tg.i18n import lazy_ugettext as l_
from tw.forms.validators import FieldStorageUploadConverter
from skylines.forms import BootstrapForm, MultiFileField, pilot
file_field_validator = FieldStorageUploadConverter(
not_empty=True,
messages=dict(empty=l_("Please add one or more IGC or ZIP files")),
accept_iterator=True
)
file_field = MultiFileField(
'file', label_text=l_("IGC or ZIP file(s)"), validator=file_field_validator)
form = BootstrapForm('upload_form', submit_text="Upload", action='do', children=[
file_field,
pilot.SelectField('pilot', label_text=l_("Pilot"))
])
# on login:
base_config.sa_auth.post_login_url = '/post_login'
# You may optionally define a page where you want users to be redirected to
# on logout:
base_config.sa_auth.post_logout_url = '/post_logout'
# INFO - This is the way to specialize the resetpassword email properties
# plug(base_config, 'resetpassword', None, mail_subject=reset_password_email_subject)
plug(base_config, 'resetpassword', 'reset_password')
replace_template(base_config, 'resetpassword.templates.index', 'tracim.templates.reset_password_index')
replace_template(base_config, 'resetpassword.templates.change_password', 'mako:tracim.templates.reset_password_change_password')
# Note: here are fake translatable strings that allow to translate messages for reset password email content
duplicated_email_subject = l_('Password reset request')
duplicated_email_body = l_('''
We've received a request to reset the password for this account.
Please click this link to reset your password:
%(password_reset_link)s
If you no longer wish to make the above change, or if you did not initiate this request, please disregard and/or delete this e-mail.
''')
#######
#
# INFO - D.A. - 2014-10-31
# The following code is a dirty way to integrate translation for resetpassword tgapp in tracim
# TODO - Integrate these translations into tgapp-resetpassword
#
def edit(self, **kw):
order = Order.query.get(_id=ObjectId(kw.get('order_id', kw.get('_id'))))
if order.status == 'shipped':
flash(l_('Is not possible to edit a shipped Order'), 'error')
return redirect(self.mount_point + '/orders')
return dict(form=get_edit_order_form(), value=order)
"""This method showcases how you can use the same controller for a data page and a display page"""
seishub_stations = "http://10.110.0.134/seismology/station/getList?format=json&network_id=BL"
req = urllib2.Request(seishub_stations)
opener = urllib2.build_opener()
f = opener.open(req)
json = loads(f.read())
#return dict(params=kw)
return dict(params=dict(args=kw, json=json))
@expose('portal.templates.authentication')
def auth(self):
"""Display some information about auth* on this application."""
return dict(page='auth')
@expose('portal.templates.index')
@require(predicates.has_permission('manage', msg=l_('Permitido apenas para funcionários')))
def manage_permission_only(self, **kw):
"""Illustrate how a page for managers only works."""
return dict(page='managers stuff')
@expose('portal.templates.index')
@require(predicates.is_user('editor', msg=l_('Permitido apenas para editor')))
def editor_user_only(self, **kw):
"""Illustrate how a page exclusive for the editor works."""
return dict(page='editor stuff')
@expose('portal.templates.login')
def login(self, came_from=url('/')):
"""Start the user login."""
login_counter = request.environ['repoze.who.logins']
if login_counter > 0:
(u'mph', lambda value: format_decimal(value * 2.23693629, format=u'0.0 mph')),
)
lift_units = (
(u'm/s', lambda value: format_decimal(value, format=u'0.0 m/s')),
(u'kt', lambda value: format_decimal(value * 1.94384449, format=u'0.0 kt')),
(u'ft/min', lambda value: format_decimal(value * 196.850394,
format=u'0 ft/min')),
)
altitude_units = (
(u'm', lambda value: "%d m" % value),
(u'ft', lambda value: "%d ft" % (value * 3.2808399))
)
unit_presets = (
(l_("Custom"), {}),
(l_("European (metric)"),
{'distance_unit': u'km',
'speed_unit': u'km/h',
'lift_unit': u'm/s',
'altitude_unit': u'm'
}),
(l_("British (imperial, distance in km)"),
{'distance_unit': u'km',
'speed_unit': u'kt',
'lift_unit': u'kt',
'altitude_unit': u'ft'
}),
continue
fixes = map(lambda x: (x.longitude, x.latitude), contest_trace.locations)
times = []
for time in contest_trace.times:
times.append(flight.takeoff_time.hour * 3600 + flight.takeoff_time.minute * 60 + flight.takeoff_time.second + \
(time - flight.takeoff_time).days * 86400 + (time - flight.takeoff_time).seconds)
contest_traces.append(dict(name=contest['contest_type'] + " " + contest['trace_type'],
turnpoints=encoder.encode(fixes, [0] * len(fixes))['points'],
times=encoder.encodeList(times)))
return contest_traces
CIRCDIR_NAMES = {None: "",
FlightPhase.CD_LEFT: l_("Left"),
FlightPhase.CD_MIXED: l_("Mixed"),
FlightPhase.CD_RIGHT: l_("Right"),
FlightPhase.CD_TOTAL: l_("Total")}
PHASETYPE_NAMES = {None: "",
FlightPhase.PT_POWERED: l_("Powered"),
FlightPhase.PT_CIRCLING: l_("Circling"),
FlightPhase.PT_CRUISE: l_("Cruise")}
def format_phase(phase):
"""Format phase properties to human readable format
"""
is_circling = phase.phase_type == FlightPhase.PT_CIRCLING
r = dict(start="%s" % format_time(phase.start_time),
class NewClubForm(AddRecordForm):
__base_widget_type__ = BootstrapForm
__model__ = Club
__limit_fields__ = ['name']
__field_widget_args__ = { 'name': dict(label_text=l_('Name')) }
name = TextField
new_club_form = NewClubForm(DBSession)
user_validator = Schema(chained_validators=(FieldsMatch('password',
'verify_password',
messages={'invalidNoMatch':
l_('Passwords do not match')}),))
class NewUserForm(AddRecordForm):
__base_widget_type__ = BootstrapForm
__model__ = User
__required_fields__ = ['password']
__limit_fields__ = ['email_address', 'display_name', 'password', 'verify_password', 'club']
__base_validator__ = user_validator
__field_widget_args__ = {
'email_address': dict(label_text=l_('eMail Address')),
'display_name': dict(label_text=l_('Name')),
'club': dict(label_text=l_('Club')),
'password': dict(label_text=l_('Password')),
'verify_password': dict(label_text=l_('Verify Password')),
}
# coding=utf-8
from __future__ import unicode_literals
from datetime import date, datetime
from itertools import groupby
from bson import ObjectId
from tg import TGController, expose, validate, lurl, redirect, request, tmpl_context, config, flash, predicates
from tg.i18n import lazy_ugettext as l_
import tw2.core as twc
import tw2.forms as twf
from tw2.forms.widgets import BaseLayout
from tgext.ecommerce.lib import get_edit_order_form
from tgext.ecommerce.model import Order
FILTER_FIELDS = [('status_changes.changed_at', l_('date')), ('status', l_('status')), ('user', l_('user'))]
class MaybeDateValidator(twc.Validator):
date_format = '%d/%m/%Y'
def _convert_to_python(self, value, state=None):
if value['field'] == 'status_changes.changed_at':
try:
value['filt'] = datetime.strptime(value['filt'], self.date_format)
except:
raise twc.ValidationError(l_('Date format must be dd/mm/yyyy'))
return value
def _convert_from_python(self, value, state=None):
if value['field'] == 'status_changes.changed_at':
value['filt'] = value['filt'].strftime(self.date_format)
