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| author | Muriithi Frederick Muriuki | 2018-03-31 14:45:17 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2018-03-31 14:45:17 +0300 |
| commit | 31747256e466456cc88aac60780836a6534f18cd (patch) | |
| tree | a7b371e4ec217ffb37594e15f5e603ae28511dc2 /wqflask | |
| parent | cfce6d80be4fb38573c37d1943db2687d54cf2fc (diff) | |
| parent | 5424741a4a126bfd5f04df7cbcdc30b4e1376b86 (diff) | |
| download | genenetwork2-31747256e466456cc88aac60780836a6534f18cd.tar.gz | |
Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into testing
* Fix conflicts
Diffstat (limited to 'wqflask')
69 files changed, 708 insertions, 3198 deletions
diff --git a/wqflask/flask_security/__init__.py b/wqflask/flask_security/__init__.py deleted file mode 100644 index 81e6c89e..00000000 --- a/wqflask/flask_security/__init__.py +++ /dev/null @@ -1,25 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security - ~~~~~~~~~~~~~~~~~~ - - Flask-Security is a Flask extension that aims to add quick and simple - security via Flask-Login, Flask-Principal, Flask-WTF, and passlib. - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" - -__version__ = '1.6.0' - -from .core import Security, RoleMixin, UserMixin, AnonymousUser, current_user -from .datastore import SQLAlchemyUserDatastore, MongoEngineUserDatastore, PeeweeUserDatastore -from .decorators import auth_token_required, http_auth_required, \ - login_required, roles_accepted, roles_required -from .forms import ForgotPasswordForm, LoginForm, RegisterForm, \ - ResetPasswordForm, PasswordlessLoginForm, ConfirmRegisterForm -from .signals import confirm_instructions_sent, password_reset, \ - reset_password_instructions_sent, user_confirmed, user_registered -from .utils import login_user, logout_user, url_for_security - -print "Using our own flask.ext.security"
\ No newline at end of file diff --git a/wqflask/flask_security/changeable.py b/wqflask/flask_security/changeable.py deleted file mode 100644 index 4447b655..00000000 --- a/wqflask/flask_security/changeable.py +++ /dev/null @@ -1,45 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.changeable - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - Flask-Security recoverable module - - :copyright: (c) 2012 by Matt Wright. - :author: Eskil Heyn Olsen - :license: MIT, see LICENSE for more details. -""" - -from flask import current_app as app, request -from werkzeug.local import LocalProxy - -from .signals import password_changed -from .utils import send_mail, encrypt_password, url_for_security, \ - config_value - - -# Convenient references -_security = LocalProxy(lambda: app.extensions['security']) - -_datastore = LocalProxy(lambda: _security.datastore) - - -def send_password_changed_notice(user): - """Sends the password changed notice email for the specified user. - - :param user: The user to send the notice to - """ - send_mail(config_value('EMAIL_SUBJECT_PASSWORD_CHANGE_NOTICE'), user.email, - 'change_notice', user=user) - - -def change_user_password(user, password): - """Change the specified user's password - - :param user: The user to change_password - :param password: The unencrypted new password - """ - user.password = encrypt_password(password) - _datastore.put(user) - send_password_changed_notice(user) - password_changed.send(user, app=app._get_current_object()) diff --git a/wqflask/flask_security/confirmable.py b/wqflask/flask_security/confirmable.py deleted file mode 100644 index a7caf6cd..00000000 --- a/wqflask/flask_security/confirmable.py +++ /dev/null @@ -1,83 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.confirmable - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - Flask-Security confirmable module - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" - -from datetime import datetime - -from flask import current_app as app, request -from werkzeug.local import LocalProxy - -from .utils import send_mail, md5, url_for_security, get_token_status,\ - config_value -from .signals import user_confirmed, confirm_instructions_sent - - -# Convenient references -_security = LocalProxy(lambda: app.extensions['security']) - -_datastore = LocalProxy(lambda: _security.datastore) - - -def generate_confirmation_link(user): - token = generate_confirmation_token(user) - url = url_for_security('confirm_email', token=token) - return request.url_root[:-1] + url, token - - -def send_confirmation_instructions(user): - """Sends the confirmation instructions email for the specified user. - - :param user: The user to send the instructions to - :param token: The confirmation token - """ - - confirmation_link, token = generate_confirmation_link(user) - - send_mail(config_value('EMAIL_SUBJECT_CONFIRM'), user.email, - 'confirmation_instructions', user=user, - confirmation_link=confirmation_link) - - confirm_instructions_sent.send(user, app=app._get_current_object()) - return token - - -def generate_confirmation_token(user): - """Generates a unique confirmation token for the specified user. - - :param user: The user to work with - """ - data = [str(user.id), md5(user.email)] - return _security.confirm_serializer.dumps(data) - - -def requires_confirmation(user): - """Returns `True` if the user requires confirmation.""" - return _security.confirmable and user.confirmed_at == None - - -def confirm_email_token_status(token): - """Returns the expired status, invalid status, and user of a confirmation - token. For example:: - - expired, invalid, user = confirm_email_token_status('...') - - :param token: The confirmation token - """ - return get_token_status(token, 'confirm', 'CONFIRM_EMAIL') - - -def confirm_user(user): - """Confirms the specified user - - :param user: The user to confirm - """ - user.confirmed_at = datetime.utcnow() - _datastore.put(user) - user_confirmed.send(user, app=app._get_current_object()) diff --git a/wqflask/flask_security/core.py b/wqflask/flask_security/core.py deleted file mode 100644 index 0f3a231f..00000000 --- a/wqflask/flask_security/core.py +++ /dev/null @@ -1,382 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.core - ~~~~~~~~~~~~~~~~~~~~~~~ - - Flask-Security core module - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" - -from flask import current_app -from flask.ext.login import AnonymousUser as AnonymousUserBase, \ - UserMixin as BaseUserMixin, LoginManager, current_user -from flask.ext.principal import Principal, RoleNeed, UserNeed, Identity, \ - identity_loaded -from itsdangerous import URLSafeTimedSerializer -from passlib.context import CryptContext -from werkzeug.datastructures import ImmutableList -from werkzeug.local import LocalProxy - -from .utils import config_value as cv, get_config, md5, url_for_security -from .views import create_blueprint -from .forms import LoginForm, ConfirmRegisterForm, RegisterForm, \ - ForgotPasswordForm, ChangePasswordForm, ResetPasswordForm, \ - SendConfirmationForm, PasswordlessLoginForm - -# Convenient references -_security = LocalProxy(lambda: current_app.extensions['security']) - - -#: Default Flask-Security configuration -_default_config = { - 'BLUEPRINT_NAME': 'security', - 'URL_PREFIX': None, - 'SUBDOMAIN': None, - 'FLASH_MESSAGES': True, - 'PASSWORD_HASH': 'plaintext', - 'PASSWORD_SALT': None, - 'LOGIN_URL': '/login', - 'LOGOUT_URL': '/logout', - 'REGISTER_URL': '/register', - 'RESET_URL': '/reset', - 'CHANGE_URL': '/change', - 'CONFIRM_URL': '/confirm', - 'POST_LOGIN_VIEW': '/', - 'POST_LOGOUT_VIEW': '/', - 'CONFIRM_ERROR_VIEW': None, - 'POST_REGISTER_VIEW': None, - 'POST_CONFIRM_VIEW': None, - 'POST_RESET_VIEW': None, - 'POST_CHANGE_VIEW': None, - 'UNAUTHORIZED_VIEW': None, - 'FORGOT_PASSWORD_TEMPLATE': 'security/forgot_password.html', - 'LOGIN_USER_TEMPLATE': 'security/login_user.html', - 'REGISTER_USER_TEMPLATE': 'security/register_user.html', - 'RESET_PASSWORD_TEMPLATE': 'security/reset_password.html', - 'SEND_CONFIRMATION_TEMPLATE': 'security/send_confirmation.html', - 'SEND_LOGIN_TEMPLATE': 'security/send_login.html', - 'CONFIRMABLE': False, - 'REGISTERABLE': False, - 'RECOVERABLE': False, - 'TRACKABLE': False, - 'PASSWORDLESS': False, - 'CHANGEABLE': False, - 'SEND_REGISTER_EMAIL': True, - 'LOGIN_WITHIN': '1 days', - 'CONFIRM_EMAIL_WITHIN': '5 days', - 'RESET_PASSWORD_WITHIN': '5 days', - 'LOGIN_WITHOUT_CONFIRMATION': False, - 'EMAIL_SENDER': 'no-reply@localhost', - 'TOKEN_AUTHENTICATION_KEY': 'auth_token', - 'TOKEN_AUTHENTICATION_HEADER': 'Authentication-Token', - 'CONFIRM_SALT': 'confirm-salt', - 'RESET_SALT': 'reset-salt', - 'LOGIN_SALT': 'login-salt', - 'CHANGE_SALT': 'change-salt', - 'REMEMBER_SALT': 'remember-salt', - 'DEFAULT_HTTP_AUTH_REALM': 'Login Required', - 'EMAIL_SUBJECT_REGISTER': 'Welcome', - 'EMAIL_SUBJECT_CONFIRM': 'Please confirm your email', - 'EMAIL_SUBJECT_PASSWORDLESS': 'Login instructions', - 'EMAIL_SUBJECT_PASSWORD_NOTICE': 'Your password has been reset', - 'EMAIL_SUBJECT_PASSWORD_CHANGE_NOTICE': 'Your password has been changed', - 'EMAIL_SUBJECT_PASSWORD_RESET': 'Password reset instructions' -} - -#: Default Flask-Security messages -_default_messages = { - 'UNAUTHORIZED': ('You do not have permission to view this resource.', 'error'), - 'CONFIRM_REGISTRATION': ('Thank you. Confirmation instructions have been sent to %(email)s.', 'success'), - 'EMAIL_CONFIRMED': ('Thank you. Your email has been confirmed.', 'success'), - 'ALREADY_CONFIRMED': ('Your email has already been confirmed.', 'info'), - 'INVALID_CONFIRMATION_TOKEN': ('Invalid confirmation token.', 'error'), - 'EMAIL_ALREADY_ASSOCIATED': ('%(email)s is already associated with an account.', 'error'), - 'PASSWORD_MISMATCH': ('Password does not match', 'error'), - 'RETYPE_PASSWORD_MISMATCH': ('Passwords do not match', 'error'), - 'INVALID_REDIRECT': ('Redirections outside the domain are forbidden', 'error'), - 'PASSWORD_RESET_REQUEST': ('Instructions to reset your password have been sent to %(email)s.', 'info'), - 'PASSWORD_RESET_EXPIRED': ('You did not reset your password within %(within)s. New instructions have been sent to %(email)s.', 'error'), - 'INVALID_RESET_PASSWORD_TOKEN': ('Invalid reset password token.', 'error'), - 'CONFIRMATION_REQUIRED': ('Email requires confirmation.', 'error'), - 'CONFIRMATION_REQUEST': ('Confirmation instructions have been sent to %(email)s.', 'info'), - 'CONFIRMATION_EXPIRED': ('You did not confirm your email within %(within)s. New instructions to confirm your email have been sent to %(email)s.', 'error'), - 'LOGIN_EXPIRED': ('You did not login within %(within)s. New instructions to login have been sent to %(email)s.', 'error'), - 'LOGIN_EMAIL_SENT': ('Instructions to login have been sent to %(email)s.', 'success'), - 'INVALID_LOGIN_TOKEN': ('Invalid login token.', 'error'), - 'DISABLED_ACCOUNT': ('Account is disabled.', 'error'), - 'EMAIL_NOT_PROVIDED': ('Email not provided', 'error'), - 'INVALID_EMAIL_ADDRESS': ('Invalid email address', 'error'), - 'PASSWORD_NOT_PROVIDED': ('Password not provided', 'error'), - 'USER_DOES_NOT_EXIST': ('Specified user does not exist', 'error'), - 'INVALID_PASSWORD': ('Invalid password', 'error'), - 'PASSWORDLESS_LOGIN_SUCCESSFUL': ('You have successfuly logged in.', 'success'), - 'PASSWORD_RESET': ('You successfully reset your password and you have been logged in automatically.', 'success'), - 'PASSWORD_CHANGE': ('You successfully changed your password.', 'success'), - 'LOGIN': ('Please log in to access this page.', 'info'), - 'REFRESH': ('Please reauthenticate to access this page.', 'info'), -} - -_allowed_password_hash_schemes = [ - 'bcrypt', - 'des_crypt', - 'pbkdf2_sha256', - 'pbkdf2_sha512', - 'sha256_crypt', - 'sha512_crypt', - # And always last one... - 'plaintext' -] - -_default_forms = { - 'login_form': LoginForm, - 'confirm_register_form': ConfirmRegisterForm, - 'register_form': RegisterForm, - 'forgot_password_form': ForgotPasswordForm, - 'reset_password_form': ResetPasswordForm, - 'change_password_form': ChangePasswordForm, - 'send_confirmation_form': SendConfirmationForm, - 'passwordless_login_form': PasswordlessLoginForm, -} - - -def _user_loader(user_id): - return _security.datastore.find_user(id=user_id) - - -def _token_loader(token): - try: - data = _security.remember_token_serializer.loads(token) - user = _security.datastore.find_user(id=data[0]) - if user and md5(user.password) == data[1]: - return user - except: - pass - - return None - - -def _identity_loader(): - if not isinstance(current_user._get_current_object(), AnonymousUser): - identity = Identity(current_user.id) - return identity - - -def _on_identity_loaded(sender, identity): - if hasattr(current_user, 'id'): - identity.provides.add(UserNeed(current_user.id)) - - for role in current_user.roles: - identity.provides.add(RoleNeed(role.name)) - - identity.user = current_user - - -def _get_login_manager(app): - lm = LoginManager() - lm.anonymous_user = AnonymousUser - lm.login_view = '%s.login' % cv('BLUEPRINT_NAME', app=app) - lm.user_loader(_user_loader) - lm.token_loader(_token_loader) - lm.login_message, lm.login_message_category = cv('MSG_LOGIN', app=app) - lm.needs_refresh_message, lm.needs_refresh_message_category = cv('MSG_REFRESH', app=app) - lm.init_app(app) - return lm - - -def _get_principal(app): - p = Principal(app, use_sessions=False) - p.identity_loader(_identity_loader) - return p - - -def _get_pwd_context(app): - pw_hash = cv('PASSWORD_HASH', app=app) - if pw_hash not in _allowed_password_hash_schemes: - allowed = ', '.join(_allowed_password_hash_schemes[:-1]) + ' and ' + _allowed_password_hash_schemes[-1] - raise ValueError("Invalid hash scheme %r. Allowed values are %s" % (pw_hash, allowed)) - return CryptContext(schemes=_allowed_password_hash_schemes, default=pw_hash) - - -def _get_serializer(app, name): - secret_key = app.config.get('SECRET_KEY') - salt = app.config.get('SECURITY_%s_SALT' % name.upper()) - return URLSafeTimedSerializer(secret_key=secret_key, salt=salt) - - -def _get_state(app, datastore, **kwargs): - for key, value in get_config(app).items(): - print "in _get_state [{}]: {}".format(key, value) - kwargs[key.lower()] = value - - kwargs.update(dict( - app=app, - datastore=datastore, - login_manager=_get_login_manager(app), - principal=_get_principal(app), - pwd_context=_get_pwd_context(app), - remember_token_serializer=_get_serializer(app, 'remember'), - login_serializer=_get_serializer(app, 'login'), - reset_serializer=_get_serializer(app, 'reset'), - confirm_serializer=_get_serializer(app, 'confirm'), - _context_processors={}, - _send_mail_task=None - )) - - for key, value in _default_forms.items(): - if key not in kwargs or not kwargs[key]: - kwargs[key] = value - - return _SecurityState(**kwargs) - - -def _context_processor(): - return dict(url_for_security=url_for_security, security=_security) - - -class RoleMixin(object): - """Mixin for `Role` model definitions""" - def __eq__(self, other): - return (self.name == other or \ - self.name == getattr(other, 'name', None)) - - def __ne__(self, other): - return (self.name != other and - self.name != getattr(other, 'name', None)) - - -class UserMixin(BaseUserMixin): - """Mixin for `User` model definitions""" - - def is_active(self): - """Returns `True` if the user is active.""" - return self.active - - def get_auth_token(self): - """Returns the user's authentication token.""" - data = [str(self.id), md5(self.password)] - return _security.remember_token_serializer.dumps(data) - - def has_role(self, role): - """Returns `True` if the user identifies with the specified role. - - :param role: A role name or `Role` instance""" - return role in self.roles - - -class AnonymousUser(AnonymousUserBase): - """AnonymousUser definition""" - - def __init__(self): - super(AnonymousUser, self).__init__() - self.roles = ImmutableList() - - def has_role(self, *args): - """Returns `False`""" - return False - - -class _SecurityState(object): - - def __init__(self, **kwargs): - for key, value in kwargs.items(): - setattr(self, key.lower(), value) - - def _add_ctx_processor(self, endpoint, fn): - group = self._context_processors.setdefault(endpoint, []) - fn not in group and group.append(fn) - - def _run_ctx_processor(self, endpoint): - rv, fns = {}, [] - for g in [None, endpoint]: - for fn in self._context_processors.setdefault(g, []): - rv.update(fn()) - return rv - - def context_processor(self, fn): - self._add_ctx_processor(None, fn) - - def forgot_password_context_processor(self, fn): - self._add_ctx_processor('forgot_password', fn) - - def login_context_processor(self, fn): - self._add_ctx_processor('login', fn) - - def register_context_processor(self, fn): - self._add_ctx_processor('register', fn) - - def reset_password_context_processor(self, fn): - self._add_ctx_processor('reset_password', fn) - - def change_password_context_processor(self, fn): - self._add_ctx_processor('change_password', fn) - - def send_confirmation_context_processor(self, fn): - self._add_ctx_processor('send_confirmation', fn) - - def send_login_context_processor(self, fn): - self._add_ctx_processor('send_login', fn) - - def mail_context_processor(self, fn): - self._add_ctx_processor('mail', fn) - - def send_mail_task(self, fn): - self._send_mail_task = fn - - -class Security(object): - """The :class:`Security` class initializes the Flask-Security extension. - - :param app: The application. - :param datastore: An instance of a user datastore. - """ - def __init__(self, app=None, datastore=None, **kwargs): - self.app = app - self.datastore = datastore - - if app is not None and datastore is not None: - self._state = self.init_app(app, datastore, **kwargs) - - def init_app(self, app, datastore=None, register_blueprint=True, - login_form=None, confirm_register_form=None, - register_form=None, forgot_password_form=None, - reset_password_form=None, change_password_form=None, - send_confirmation_form=None, passwordless_login_form=None): - """Initializes the Flask-Security extension for the specified - application and datastore implentation. - - :param app: The application. - :param datastore: An instance of a user datastore. - :param register_blueprint: to register the Security blueprint or not. - """ - datastore = datastore or self.datastore - - for key, value in _default_config.items(): - app.config.setdefault('SECURITY_' + key, value) - - for key, value in _default_messages.items(): - app.config.setdefault('SECURITY_MSG_' + key, value) - - identity_loaded.connect_via(app)(_on_identity_loaded) - - state = _get_state(app, datastore, - login_form=login_form, - confirm_register_form=confirm_register_form, - register_form=register_form, - forgot_password_form=forgot_password_form, - reset_password_form=reset_password_form, - change_password_form=change_password_form, - send_confirmation_form=send_confirmation_form, - passwordless_login_form=passwordless_login_form) - - if register_blueprint: - app.register_blueprint(create_blueprint(state, __name__)) - app.context_processor(_context_processor) - - app.extensions['security'] = state - - return state - - def __getattr__(self, name): - return getattr(self._state, name, None) diff --git a/wqflask/flask_security/datastore.py b/wqflask/flask_security/datastore.py deleted file mode 100644 index 634399d9..00000000 --- a/wqflask/flask_security/datastore.py +++ /dev/null @@ -1,261 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.datastore - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - This module contains an user datastore classes. - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" - -class Datastore(object): - def __init__(self, db): - self.db = db - - def commit(self): - pass - - def put(self, model): - raise NotImplementedError - - def delete(self, model): - raise NotImplementedError - - -class SQLAlchemyDatastore(Datastore): - def commit(self): - self.db.session.commit() - - def put(self, model): - self.db.session.add(model) - return model - - def delete(self, model): - self.db.session.delete(model) - - -class MongoEngineDatastore(Datastore): - def put(self, model): - model.save() - return model - - def delete(self, model): - model.delete() - - -class PeeweeDatastore(Datastore): - def put(self, model): - model.save() - return model - - def delete(self, model): - model.delete_instance() - - -class UserDatastore(object): - """Abstracted user datastore. - - :param user_model: A user model class definition - :param role_model: A role model class definition - """ - - def __init__(self, user_model, role_model): - self.user_model = user_model - self.role_model = role_model - - def _prepare_role_modify_args(self, user, role): - if isinstance(user, basestring): - user = self.find_user(email=user) - if isinstance(role, basestring): - role = self.find_role(role) - return user, role - - def _prepare_create_user_args(self, **kwargs): - kwargs.setdefault('active', True) - roles = kwargs.get('roles', []) - for i, role in enumerate(roles): - rn = role.name if isinstance(role, self.role_model) else role - # see if the role exists - roles[i] = self.find_role(rn) - kwargs['roles'] = roles - return kwargs - - def find_user(self, *args, **kwargs): - """Returns a user matching the provided parameters.""" - raise NotImplementedError - - def find_role(self, *args, **kwargs): - """Returns a role matching the provided name.""" - raise NotImplementedError - - def add_role_to_user(self, user, role): - """Adds a role tp a user - - :param user: The user to manipulate - :param role: The role to add to the user - """ - rv = False - user, role = self._prepare_role_modify_args(user, role) - if role not in user.roles: - rv = True - user.roles.append(role) - return rv - - def remove_role_from_user(self, user, role): - """Removes a role from a user - - :param user: The user to manipulate - :param role: The role to remove from the user - """ - rv = False - user, role = self._prepare_role_modify_args(user, role) - if role in user.roles: - rv = True - user.roles.remove(role) - return rv - - def toggle_active(self, user): - """Toggles a user's active status. Always returns True.""" - user.active = not user.active - return True - - def deactivate_user(self, user): - """Deactivates a specified user. Returns `True` if a change was made. - - :param user: The user to deactivate - """ - if user.active: - user.active = False - return True - return False - - def activate_user(self, user): - """Activates a specified user. Returns `True` if a change was made. - - :param user: The user to activate - """ - if not user.active: - user.active = True - return True - return False - - def create_role(self, **kwargs): - """Creates and returns a new role from the given parameters.""" - - role = self.role_model(**kwargs) - return self.put(role) - - def find_or_create_role(self, name, **kwargs): - """Returns a role matching the given name or creates it with any - additionally provided parameters - """ - kwargs["name"] = name - return self.find_role(name) or self.create_role(**kwargs) - - def create_user(self, **kwargs): - """Creates and returns a new user from the given parameters.""" - - user = self.user_model(**self._prepare_create_user_args(**kwargs)) - print "in abstraced create_user, user is:", user - return self.put(user) - - def delete_user(self, user): - """Delete the specified user - - :param user: The user to delete - """ - self.delete(user) - - -class SQLAlchemyUserDatastore(SQLAlchemyDatastore, UserDatastore): - """A SQLAlchemy datastore implementation for Flask-Security that assumes the - use of the Flask-SQLAlchemy extension. - """ - def __init__(self, db, user_model, role_model): - SQLAlchemyDatastore.__init__(self, db) - UserDatastore.__init__(self, user_model, role_model) - - def find_user(self, **kwargs): - return self.user_model.query.filter_by(**kwargs).first() - - def find_role(self, role): - return self.role_model.query.filter_by(name=role).first() - - -class MongoEngineUserDatastore(MongoEngineDatastore, UserDatastore): - """A MongoEngine datastore implementation for Flask-Security that assumes - the use of the Flask-MongoEngine extension. - """ - def __init__(self, db, user_model, role_model): - MongoEngineDatastore.__init__(self, db) - UserDatastore.__init__(self, user_model, role_model) - - def find_user(self, **kwargs): - return self.user_model.objects(**kwargs).first() - - def find_role(self, role): - return self.role_model.objects(name=role).first() - - -class PeeweeUserDatastore(PeeweeDatastore, UserDatastore): - """A PeeweeD datastore implementation for Flask-Security that assumes - the use of the Flask-Peewee extension. - - :param user_model: A user model class definition - :param role_model: A role model class definition - :param role_link: A model implementing the many-to-many user-role relation - """ - def __init__(self, db, user_model, role_model, role_link): - PeeweeDatastore.__init__(self, db) - UserDatastore.__init__(self, user_model, role_model) - self.UserRole = role_link - - def find_user(self, **kwargs): - try: - return self.user_model.filter(**kwargs).get() - except self.user_model.DoesNotExist: - return None - - def find_role(self, role): - try: - return self.role_model.filter(name=role).get() - except self.role_model.DoesNotExist: - return None - - def create_user(self, **kwargs): - """Creates and returns a new user from the given parameters.""" - roles = kwargs.pop('roles', []) - user = self.user_model(**self._prepare_create_user_args(**kwargs)) - user = self.put(user) - for role in roles: - self.add_role_to_user(user, role) - return user - - - def add_role_to_user(self, user, role): - """Adds a role tp a user - - :param user: The user to manipulate - :param role: The role to add to the user - """ - user, role = self._prepare_role_modify_args(user, role) - if self.UserRole.select().where(self.UserRole.user==user, self.UserRole.role==role).count(): - return False - else: - self.UserRole.create(user=user, role=role) - return True - - def remove_role_from_user(self, user, role): - """Removes a role from a user - - :param user: The user to manipulate - :param role: The role to remove from the user - """ - user, role = self._prepare_role_modify_args(user, role) - if self.UserRole.select().where(self.UserRole.user==user, self.UserRole.role==role).count(): - self.UserRole.delete().where(self.UserRole.user==user, self.UserRole.role==role) - return True - else: - return False - diff --git a/wqflask/flask_security/decorators.py b/wqflask/flask_security/decorators.py deleted file mode 100644 index 0ea1105c..00000000 --- a/wqflask/flask_security/decorators.py +++ /dev/null @@ -1,207 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.decorators - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - Flask-Security decorators module - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" - -from functools import wraps - -from flask import current_app, Response, request, redirect, _request_ctx_stack -from flask.ext.login import current_user, login_required -from flask.ext.principal import RoleNeed, Permission, Identity, identity_changed -from werkzeug.local import LocalProxy - -from . import utils - - -# Convenient references -_security = LocalProxy(lambda: current_app.extensions['security']) - - -_default_unauthorized_html = """ - <h1>Unauthorized</h1> - <p>The server could not verify that you are authorized to access the URL - requested. You either supplied the wrong credentials (e.g. a bad password), - or your browser doesn't understand how to supply the credentials required.</p> - """ - - -def _get_unauthorized_response(text=None, headers=None): - text = text or _default_unauthorized_html - headers = headers or {} - return Response(text, 401, headers) - - -def _get_unauthorized_view(): - cv = utils.get_url(utils.config_value('UNAUTHORIZED_VIEW')) - utils.do_flash(*utils.get_message('UNAUTHORIZED')) - return redirect(cv or request.referrer or '/') - - -def _check_token(): - header_key = _security.token_authentication_header - args_key = _security.token_authentication_key - header_token = request.headers.get(header_key, None) - token = request.args.get(args_key, header_token) - if request.json: - token = request.json.get(args_key, token) - serializer = _security.remember_token_serializer - - try: - data = serializer.loads(token) - except: - return False - - user = _security.datastore.find_user(id=data[0]) - - if utils.md5(user.password) == data[1]: - app = current_app._get_current_object() - _request_ctx_stack.top.user = user - identity_changed.send(app, identity=Identity(user.id)) - return True - - -def _check_http_auth(): - auth = request.authorization or dict(username=None, password=None) - user = _security.datastore.find_user(email=auth.username) - - if user and utils.verify_and_update_password(auth.password, user): - _security.datastore.commit() - app = current_app._get_current_object() - _request_ctx_stack.top.user = user - identity_changed.send(app, identity=Identity(user.id)) - return True - - return False - - -def http_auth_required(realm): - """Decorator that protects endpoints using Basic HTTP authentication. - The username should be set to the user's email address. - - :param realm: optional realm name""" - - def decorator(fn): - @wraps(fn) - def wrapper(*args, **kwargs): - if _check_http_auth(): - return fn(*args, **kwargs) - r = _security.default_http_auth_realm if callable(realm) else realm - h = {'WWW-Authenticate': 'Basic realm="%s"' % r} - return _get_unauthorized_response(headers=h) - return wrapper - - if callable(realm): - return decorator(realm) - return decorator - - -def auth_token_required(fn): - """Decorator that protects endpoints using token authentication. The token - should be added to the request by the client by using a query string - variable with a name equal to the configuration value of - `SECURITY_TOKEN_AUTHENTICATION_KEY` or in a request header named that of - the configuration value of `SECURITY_TOKEN_AUTHENTICATION_HEADER` - """ - - @wraps(fn) - def decorated(*args, **kwargs): - if _check_token(): - return fn(*args, **kwargs) - return _get_unauthorized_response() - return decorated - - -def auth_required(*auth_methods): - """ - Decorator that protects enpoints through multiple mechanisms - Example:: - - @app.route('/dashboard') - @auth_required('token', 'session') - def dashboard(): - return 'Dashboard' - - :param auth_methods: Specified mechanisms. - """ - login_mechanisms = { - 'token': lambda: _check_token(), - 'basic': lambda: _check_http_auth(), - 'session': lambda: current_user.is_authenticated() - } - - def wrapper(fn): - @wraps(fn) - def decorated_view(*args, **kwargs): - mechanisms = [login_mechanisms.get(method) for method in auth_methods] - for mechanism in mechanisms: - if mechanism and mechanism(): - return fn(*args, **kwargs) - return _get_unauthorized_response() - return decorated_view - return wrapper - - -def roles_required(*roles): - """Decorator which specifies that a user must have all the specified roles. - Example:: - - @app.route('/dashboard') - @roles_required('admin', 'editor') - def dashboard(): - return 'Dashboard' - - The current user must have both the `admin` role and `editor` role in order - to view the page. - - :param args: The required roles. - """ - def wrapper(fn): - @wraps(fn) - def decorated_view(*args, **kwargs): - perms = [Permission(RoleNeed(role)) for role in roles] - for perm in perms: - if not perm.can(): - return _get_unauthorized_view() - return fn(*args, **kwargs) - return decorated_view - return wrapper - - -def roles_accepted(*roles): - """Decorator which specifies that a user must have at least one of the - specified roles. Example:: - - @app.route('/create_post') - @roles_accepted('editor', 'author') - def create_post(): - return 'Create Post' - - The current user must have either the `editor` role or `author` role in - order to view the page. - - :param args: The possible roles. - """ - def wrapper(fn): - @wraps(fn) - def decorated_view(*args, **kwargs): - perm = Permission(*[RoleNeed(role) for role in roles]) - if perm.can(): - return fn(*args, **kwargs) - return _get_unauthorized_view() - return decorated_view - return wrapper - - -def anonymous_user_required(f): - @wraps(f) - def wrapper(*args, **kwargs): - if current_user.is_authenticated(): - return redirect(utils.get_url(_security.post_login_view)) - return f(*args, **kwargs) - return wrapper diff --git a/wqflask/flask_security/forms.py b/wqflask/flask_security/forms.py deleted file mode 100644 index 54677e77..00000000 --- a/wqflask/flask_security/forms.py +++ /dev/null @@ -1,286 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.forms - ~~~~~~~~~~~~~~~~~~~~~~~~ - - Flask-Security forms module - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" - -import inspect -import urlparse - -import flask_wtf as wtf - -from flask import request, current_app -from flask_wtf import Form as BaseForm, TextField, PasswordField, \ - SubmitField, HiddenField, BooleanField, ValidationError, Field -from flask_login import current_user -from werkzeug.local import LocalProxy - -from .confirmable import requires_confirmation -from .utils import verify_and_update_password, get_message - -# Convenient reference -_datastore = LocalProxy(lambda: current_app.extensions['security'].datastore) - -_default_field_labels = { - 'email': 'Email Address', - 'password': 'Password', - 'remember_me': 'Remember Me', - 'login': 'Login', - 'retype_password': 'Retype Password', - 'register': 'Register', - 'send_confirmation': 'Resend Confirmation Instructions', - 'recover_password': 'Recover Password', - 'reset_password': 'Reset Password', - 'retype_password': 'Retype Password', - 'new_password': 'New Password', - 'change_password': 'Change Password', - 'send_login_link': 'Send Login Link' -} - - -class ValidatorMixin(object): - def __call__(self, form, field): - if self.message and self.message.isupper(): - self.message = get_message(self.message)[0] - return super(ValidatorMixin, self).__call__(form, field) - - -class EqualTo(ValidatorMixin, wtf.EqualTo): - pass - - -class Required(ValidatorMixin, wtf.Required): - pass - - -class Email(ValidatorMixin, wtf.Email): - pass - - -class Length(ValidatorMixin, wtf.Length): - pass - - -email_required = Required(message='EMAIL_NOT_PROVIDED') -email_validator = Email(message='INVALID_EMAIL_ADDRESS') -password_required = Required(message='PASSWORD_NOT_PROVIDED') - - -def get_form_field_label(key): - return _default_field_labels.get(key, '') - - -def unique_user_email(form, field): - if _datastore.find_user(email=field.data) is not None: - msg = get_message('EMAIL_ALREADY_ASSOCIATED', email=field.data)[0] - raise ValidationError(msg) - - -def valid_user_email(form, field): - form.user = _datastore.find_user(email=field.data) - if form.user is None: - raise ValidationError(get_message('USER_DOES_NOT_EXIST')[0]) - - -class Form(BaseForm): - def __init__(self, *args, **kwargs): - #print "importing tracer" - #from wqflask import tracer - #tracer.turn_on() - #print "imported tracer" - print "in Form, args:", args - print "in Form, kwargs:", kwargs - if current_app.testing: - self.TIME_LIMIT = None - super(Form, self).__init__(*args, **kwargs) - - -class EmailFormMixin(): - email = TextField(get_form_field_label('email'), - validators=[email_required, - email_validator]) - - -class UserEmailFormMixin(): - user = None - email = TextField(get_form_field_label('email'), - validators=[email_required, - email_validator, - valid_user_email]) - - -class UniqueEmailFormMixin(): - email = TextField(get_form_field_label('email'), - validators=[email_required, - email_validator, - unique_user_email]) - - -class PasswordFormMixin(): - password = PasswordField(get_form_field_label('password'), - validators=[password_required]) - - -class NewPasswordFormMixin(): - password = PasswordField(get_form_field_label('password'), - validators=[password_required, - Length(min=6, max=128)]) - - -class PasswordConfirmFormMixin(): - password_confirm = PasswordField( - get_form_field_label('retype_password'), - validators=[EqualTo('password', message='RETYPE_PASSWORD_MISMATCH')]) - - -class NextFormMixin(): - next = HiddenField() - - def validate_next(self, field): - url_next = urlparse.urlsplit(field.data) - url_base = urlparse.urlsplit(request.host_url) - if url_next.netloc and url_next.netloc != url_base.netloc: - field.data = '' - raise ValidationError(get_message('INVALID_REDIRECT')[0]) - - -class RegisterFormMixin(): - submit = SubmitField(get_form_field_label('register')) - - def to_dict(form): - def is_field_and_user_attr(member): - print "in ifaua:", member - return isinstance(member, Field) and \ - hasattr(_datastore.user_model, member.name) - - print("green:", vars(form)) - fields = inspect.getmembers(form, is_field_and_user_attr) - print("fields:" ,vars(form)) - return dict((key, value.data) for key, value in fields) - - -class SendConfirmationForm(Form, UserEmailFormMixin): - """The default forgot password form""" - - submit = SubmitField(get_form_field_label('send_confirmation')) - - def __init__(self, *args, **kwargs): - super(SendConfirmationForm, self).__init__(*args, **kwargs) - if request.method == 'GET': - self.email.data = request.args.get('email', None) - - def validate(self): - if not super(SendConfirmationForm, self).validate(): - return False - if self.user.confirmed_at is not None: - self.email.errors.append(get_message('ALREADY_CONFIRMED')[0]) - return False - return True - - -class ForgotPasswordForm(Form, UserEmailFormMixin): - """The default forgot password form""" - - submit = SubmitField(get_form_field_label('recover_password')) - - -class PasswordlessLoginForm(Form, UserEmailFormMixin): - """The passwordless login form""" - - submit = SubmitField(get_form_field_label('send_login_link')) - - def __init__(self, *args, **kwargs): - super(PasswordlessLoginForm, self).__init__(*args, **kwargs) - - def validate(self): - if not super(PasswordlessLoginForm, self).validate(): - return False - if not self.user.is_active(): - self.email.errors.append(get_message('DISABLED_ACCOUNT')[0]) - return False - return True - - -class LoginForm(Form, NextFormMixin): - """The default login form""" - - email = TextField(get_form_field_label('email')) - password = PasswordField(get_form_field_label('password')) - remember = BooleanField(get_form_field_label('remember_me')) - submit = SubmitField(get_form_field_label('login')) - - def __init__(self, *args, **kwargs): - super(LoginForm, self).__init__(*args, **kwargs) - - def validate(self): - if not super(LoginForm, self).validate(): - return False - - if self.email.data.strip() == '': - self.email.errors.append(get_message('EMAIL_NOT_PROVIDED')[0]) - return False - - if self.password.data.strip() == '': - self.password.errors.append(get_message('PASSWORD_NOT_PROVIDED')[0]) - return False - - self.user = _datastore.find_user(email=self.email.data) - - if self.user is None: - self.email.errors.append(get_message('USER_DOES_NOT_EXIST')[0]) - return False - if not verify_and_update_password(self.password.data, self.user): - self.password.errors.append(get_message('INVALID_PASSWORD')[0]) - return False - if requires_confirmation(self.user): - self.email.errors.append(get_message('CONFIRMATION_REQUIRED')[0]) - return False - if not self.user.is_active(): - self.email.errors.append(get_message('DISABLED_ACCOUNT')[0]) - return False - return True - - -class ConfirmRegisterForm(Form, RegisterFormMixin, - UniqueEmailFormMixin, NewPasswordFormMixin): - pass - - -class RegisterForm(ConfirmRegisterForm, PasswordConfirmFormMixin): - pass - - -class ResetPasswordForm(Form, NewPasswordFormMixin, PasswordConfirmFormMixin): - """The default reset password form""" - - submit = SubmitField(get_form_field_label('reset_password')) - - -class ChangePasswordForm(Form, PasswordFormMixin): - """The default change password form""" - - new_password = PasswordField(get_form_field_label('new_password'), - validators=[password_required, - Length(min=6, max=128)]) - - new_password_confirm = PasswordField(get_form_field_label('retype_password'), - validators=[EqualTo('new_password', message='RETYPE_PASSWORD_MISMATCH')]) - - submit = SubmitField(get_form_field_label('change_password')) - - def validate(self): - if not super(ChangePasswordForm, self).validate(): - return False - - if self.password.data.strip() == '': - self.password.errors.append(get_message('PASSWORD_NOT_PROVIDED')[0]) - return False - if not verify_and_update_password(self.password.data, current_user): - self.password.errors.append(get_message('INVALID_PASSWORD')[0]) - return False - return True diff --git a/wqflask/flask_security/passwordless.py b/wqflask/flask_security/passwordless.py deleted file mode 100644 index b0accb2c..00000000 --- a/wqflask/flask_security/passwordless.py +++ /dev/null @@ -1,59 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.passwordless - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - Flask-Security passwordless module - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" - -from flask import request, current_app as app -from werkzeug.local import LocalProxy - -from .signals import login_instructions_sent -from .utils import send_mail, url_for_security, get_token_status, \ - config_value - - -# Convenient references -_security = LocalProxy(lambda: app.extensions['security']) - -_datastore = LocalProxy(lambda: _security.datastore) - - -def send_login_instructions(user): - """Sends the login instructions email for the specified user. - - :param user: The user to send the instructions to - :param token: The login token - """ - token = generate_login_token(user) - url = url_for_security('token_login', token=token) - login_link = request.url_root[:-1] + url - - send_mail(config_value('EMAIL_SUBJECT_PASSWORDLESS'), user.email, - 'login_instructions', user=user, login_link=login_link) - - login_instructions_sent.send(dict(user=user, login_token=token), - app=app._get_current_object()) - - -def generate_login_token(user): - """Generates a unique login token for the specified user. - - :param user: The user the token belongs to - """ - return _security.login_serializer.dumps([str(user.id)]) - - -def login_token_status(token): - """Returns the expired status, invalid status, and user of a login token. - For example:: - - expired, invalid, user = login_token_status('...') - - :param token: The login token - """ - return get_token_status(token, 'login', 'LOGIN') diff --git a/wqflask/flask_security/recoverable.py b/wqflask/flask_security/recoverable.py deleted file mode 100644 index 6aafc111..00000000 --- a/wqflask/flask_security/recoverable.py +++ /dev/null @@ -1,80 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.recoverable - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - Flask-Security recoverable module - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" - -from flask import current_app as app, request -from werkzeug.local import LocalProxy - -from .signals import password_reset, reset_password_instructions_sent -from .utils import send_mail, md5, encrypt_password, url_for_security, \ - get_token_status, config_value - - -# Convenient references -_security = LocalProxy(lambda: app.extensions['security']) - -_datastore = LocalProxy(lambda: _security.datastore) - - -def send_reset_password_instructions(user): - """Sends the reset password instructions email for the specified user. - - :param user: The user to send the instructions to - """ - token = generate_reset_password_token(user) - url = url_for_security('reset_password', token=token) - reset_link = request.url_root[:-1] + url - - send_mail(config_value('EMAIL_SUBJECT_PASSWORD_RESET'), user.email, - 'reset_instructions', - user=user, reset_link=reset_link) - - reset_password_instructions_sent.send(dict(user=user, token=token), - app=app._get_current_object()) - - -def send_password_reset_notice(user): - """Sends the password reset notice email for the specified user. - - :param user: The user to send the notice to - """ - send_mail(config_value('EMAIL_SUBJECT_PASSWORD_NOTICE'), user.email, - 'reset_notice', user=user) - - -def generate_reset_password_token(user): - """Generates a unique reset password token for the specified user. - - :param user: The user to work with - """ - data = [str(user.id), md5(user.password)] - return _security.reset_serializer.dumps(data) - - -def reset_password_token_status(token): - """Returns the expired status, invalid status, and user of a password reset - token. For example:: - - expired, invalid, user = reset_password_token_status('...') - - :param token: The password reset token - """ - return get_token_status(token, 'reset', 'RESET_PASSWORD') - -def update_password(user, password): - """Update the specified user's password - - :param user: The user to update_password - :param password: The unencrypted new password - """ - user.password = encrypt_password(password) - _datastore.put(user) - send_password_reset_notice(user) - password_reset.send(user, app=app._get_current_object()) diff --git a/wqflask/flask_security/registerable.py b/wqflask/flask_security/registerable.py deleted file mode 100644 index 4606c7c6..00000000 --- a/wqflask/flask_security/registerable.py +++ /dev/null @@ -1,44 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.registerable - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - Flask-Security registerable module - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" - -from flask import current_app as app -from werkzeug.local import LocalProxy - -from .confirmable import generate_confirmation_link -from .signals import user_registered -from .utils import do_flash, get_message, send_mail, encrypt_password, \ - config_value - -# Convenient references -_security = LocalProxy(lambda: app.extensions['security']) - -_datastore = LocalProxy(lambda: _security.datastore) - - -def register_user(**kwargs): - print "in register_user kwargs:", kwargs - confirmation_link, token = None, None - kwargs['password'] = encrypt_password(kwargs['password']) - user = _datastore.create_user(**kwargs) - _datastore.commit() - - if _security.confirmable: - confirmation_link, token = generate_confirmation_link(user) - do_flash(*get_message('CONFIRM_REGISTRATION', email=user.email)) - - user_registered.send(dict(user=user, confirm_token=token), - app=app._get_current_object()) - - if config_value('SEND_REGISTER_EMAIL'): - send_mail(config_value('EMAIL_SUBJECT_REGISTER'), user.email, 'welcome', - user=user, confirmation_link=confirmation_link) - - return user diff --git a/wqflask/flask_security/script.py b/wqflask/flask_security/script.py deleted file mode 100644 index 9c9a2469..00000000 --- a/wqflask/flask_security/script.py +++ /dev/null @@ -1,130 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.script - ~~~~~~~~~~~~~~~~~~~~~~~~~ - - Flask-Security script module - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" -try: - import simplejson as json -except ImportError: - import json - -import re - -from flask import current_app -from flask.ext.script import Command, Option -from werkzeug.local import LocalProxy - -from .utils import encrypt_password - - -_datastore = LocalProxy(lambda: current_app.extensions['security'].datastore) - - -def pprint(obj): - print json.dumps(obj, sort_keys=True, indent=4) - - -def commit(fn): - def wrapper(*args, **kwargs): - fn(*args, **kwargs) - _datastore.commit() - return wrapper - - -class CreateUserCommand(Command): - """Create a user""" - - option_list = ( - Option('-e', '--email', dest='email', default=None), - Option('-p', '--password', dest='password', default=None), - Option('-a', '--active', dest='active', default=''), - ) - - @commit - def run(self, **kwargs): - # sanitize active input - ai = re.sub(r'\s', '', str(kwargs['active'])) - kwargs['active'] = ai.lower() in ['', 'y', 'yes', '1', 'active'] - - from flask_security.forms import ConfirmRegisterForm - from werkzeug.datastructures import MultiDict - - form = ConfirmRegisterForm(MultiDict(kwargs), csrf_enabled=False) - - if form.validate(): - kwargs['password'] = encrypt_password(kwargs['password']) - _datastore.create_user(**kwargs) - print 'User created successfully.' - kwargs['password'] = '****' - pprint(kwargs) - else: - print 'Error creating user' - pprint(form.errors) - - -class CreateRoleCommand(Command): - """Create a role""" - - option_list = ( - Option('-n', '--name', dest='name', default=None), - Option('-d', '--desc', dest='description', default=None), - ) - - @commit - def run(self, **kwargs): - _datastore.create_role(**kwargs) - print 'Role "%(name)s" created successfully.' % kwargs - - -class _RoleCommand(Command): - option_list = ( - Option('-u', '--user', dest='user_identifier'), - Option('-r', '--role', dest='role_name'), - ) - - -class AddRoleCommand(_RoleCommand): - """Add a role to a user""" - - @commit - def run(self, user_identifier, role_name): - _datastore.add_role_to_user(user_identifier, role_name) - print "Role '%s' added to user '%s' successfully" % (role_name, user_identifier) - - -class RemoveRoleCommand(_RoleCommand): - """Add a role to a user""" - - @commit - def run(self, user_identifier, role_name): - _datastore.remove_role_from_user(user_identifier, role_name) - print "Role '%s' removed from user '%s' successfully" % (role_name, user_identifier) - - -class _ToggleActiveCommand(Command): - option_list = ( - Option('-u', '--user', dest='user_identifier'), - ) - - -class DeactivateUserCommand(_ToggleActiveCommand): - """Deactive a user""" - - @commit - def run(self, user_identifier): - _datastore.deactivate_user(user_identifier) - print "User '%s' has been deactivated" % user_identifier - - -class ActivateUserCommand(_ToggleActiveCommand): - """Deactive a user""" - - @commit - def run(self, user_identifier): - _datastore.activate_user(user_identifier) - print "User '%s' has been activated" % user_identifier diff --git a/wqflask/flask_security/signals.py b/wqflask/flask_security/signals.py deleted file mode 100644 index e1c29548..00000000 --- a/wqflask/flask_security/signals.py +++ /dev/null @@ -1,29 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.signals - ~~~~~~~~~~~~~~~~~~~~~~~~~~ - - Flask-Security signals module - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" - -import blinker - - -signals = blinker.Namespace() - -user_registered = signals.signal("user-registered") - -user_confirmed = signals.signal("user-confirmed") - -confirm_instructions_sent = signals.signal("confirm-instructions-sent") - -login_instructions_sent = signals.signal("login-instructions-sent") - -password_reset = signals.signal("password-reset") - -password_changed = signals.signal("password-changed") - -reset_password_instructions_sent = signals.signal("password-reset-instructions-sent") diff --git a/wqflask/flask_security/templates/.DS_Store b/wqflask/flask_security/templates/.DS_Store Binary files differdeleted file mode 100644 index b72f1d98..00000000 --- a/wqflask/flask_security/templates/.DS_Store +++ /dev/null diff --git a/wqflask/flask_security/templates/security/.DS_Store b/wqflask/flask_security/templates/security/.DS_Store Binary files differdeleted file mode 100644 index 5008ddfc..00000000 --- a/wqflask/flask_security/templates/security/.DS_Store +++ /dev/null diff --git a/wqflask/flask_security/templates/security/_macros.html b/wqflask/flask_security/templates/security/_macros.html deleted file mode 100644 index 8575f3db..00000000 --- a/wqflask/flask_security/templates/security/_macros.html +++ /dev/null @@ -1,16 +0,0 @@ -{% macro render_field_with_errors(field) %} - <p> - {{ field.label }} {{ field(**kwargs)|safe }} - {% if field.errors %} - <ul> - {% for error in field.errors %} - <li>{{ error }}</li> - {% endfor %} - </ul> - {% endif %} - </p> -{% endmacro %} - -{% macro render_field(field) %} - <p>{{ field(**kwargs)|safe }}</p> -{% endmacro %}
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/_menu.html b/wqflask/flask_security/templates/security/_menu.html deleted file mode 100644 index 5291f809..00000000 --- a/wqflask/flask_security/templates/security/_menu.html +++ /dev/null @@ -1,15 +0,0 @@ -{% if security.registerable or security.recoverable or security.confirmabled %} -<h2>Menu</h2> -<ul> - <li><a href="{{ url_for_security('login') }}">Login</a></li> - {% if security.registerable %} - <li><a href="{{ url_for_security('register') }}">Register</a><br/></li> - {% endif %} - {% if security.recoverable %} - <li><a href="{{ url_for_security('forgot_password') }}">Forgot password</a><br/></li> - {% endif %} - {% if security.confirmable %} - <li><a href="{{ url_for_security('send_confirmation') }}">Confirm account</a></li> - {% endif %} -</ul> -{% endif %} diff --git a/wqflask/flask_security/templates/security/_messages.html b/wqflask/flask_security/templates/security/_messages.html deleted file mode 100644 index 179d0636..00000000 --- a/wqflask/flask_security/templates/security/_messages.html +++ /dev/null @@ -1,9 +0,0 @@ -{%- with messages = get_flashed_messages(with_categories=true) -%} - {% if messages %} - <ul class="flashes"> - {% for category, message in messages %} - <li class="{{ category }}">{{ message }}</li> - {% endfor %} - </ul> - {% endif %} -{%- endwith %}
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/change_password.html b/wqflask/flask_security/templates/security/change_password.html deleted file mode 100644 index 8ee3eb73..00000000 --- a/wqflask/flask_security/templates/security/change_password.html +++ /dev/null @@ -1,11 +0,0 @@ -{% from "security/_macros.html" import render_field_with_errors, render_field %} -{% include "security/_messages.html" %} -<h1>Change password</h1> -<form action="{{ url_for_security('change_password') }}" method="POST" name="change_password_form"> - {{ change_password_form.hidden_tag() }} - {{ render_field_with_errors(change_password_form.password) }} - {{ render_field_with_errors(change_password_form.new_password) }} - {{ render_field_with_errors(change_password_form.new_password_confirm) }} - {{ render_field(change_password_form.submit) }} -</form> - diff --git a/wqflask/flask_security/templates/security/email/change_notice.html b/wqflask/flask_security/templates/security/email/change_notice.html deleted file mode 100644 index d1224cf5..00000000 --- a/wqflask/flask_security/templates/security/email/change_notice.html +++ /dev/null @@ -1,4 +0,0 @@ -<p>Your password has been changed.</p> -{% if security.recoverable %} -<p>If you did not change your password, <a href="{{ url_for_security('forgot_password', _external=True) }}">click here to reset it</a>.</p> -{% endif %} diff --git a/wqflask/flask_security/templates/security/email/change_notice.txt b/wqflask/flask_security/templates/security/email/change_notice.txt deleted file mode 100644 index e74bd80d..00000000 --- a/wqflask/flask_security/templates/security/email/change_notice.txt +++ /dev/null @@ -1,5 +0,0 @@ -Your password has been changed -{% if security.recoverable %} -If you did not change your password, click the link below to reset it. -{{ url_for_security('forgot_password', _external=True) }} -{% endif %} diff --git a/wqflask/flask_security/templates/security/email/confirmation_instructions.html b/wqflask/flask_security/templates/security/email/confirmation_instructions.html deleted file mode 100644 index 5082a9a8..00000000 --- a/wqflask/flask_security/templates/security/email/confirmation_instructions.html +++ /dev/null @@ -1,3 +0,0 @@ -<p>Please confirm your email through the link below:</p> - -<p><a href="{{ confirmation_link }}">Confirm my account</a></p>
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/email/confirmation_instructions.txt b/wqflask/flask_security/templates/security/email/confirmation_instructions.txt deleted file mode 100644 index fb435b55..00000000 --- a/wqflask/flask_security/templates/security/email/confirmation_instructions.txt +++ /dev/null @@ -1,3 +0,0 @@ -Please confirm your email through the link below: - -{{ confirmation_link }}
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/email/login_instructions.html b/wqflask/flask_security/templates/security/email/login_instructions.html deleted file mode 100644 index 45a7cb57..00000000 --- a/wqflask/flask_security/templates/security/email/login_instructions.html +++ /dev/null @@ -1,5 +0,0 @@ -<p>Welcome {{ user.email }}!</p> - -<p>You can log into your through the link below:</p> - -<p><a href="{{ login_link }}">Login now</a></p>
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/email/login_instructions.txt b/wqflask/flask_security/templates/security/email/login_instructions.txt deleted file mode 100644 index 1364ed65..00000000 --- a/wqflask/flask_security/templates/security/email/login_instructions.txt +++ /dev/null @@ -1,5 +0,0 @@ -Welcome {{ user.email }}! - -You can log into your through the link below: - -{{ login_link }}
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/email/reset_instructions.html b/wqflask/flask_security/templates/security/email/reset_instructions.html deleted file mode 100644 index fd0b48d8..00000000 --- a/wqflask/flask_security/templates/security/email/reset_instructions.html +++ /dev/null @@ -1 +0,0 @@ -<p><a href="{{ reset_link }}">Click here to reset your password</a></p>
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/email/reset_instructions.txt b/wqflask/flask_security/templates/security/email/reset_instructions.txt deleted file mode 100644 index 91ac288e..00000000 --- a/wqflask/flask_security/templates/security/email/reset_instructions.txt +++ /dev/null @@ -1,3 +0,0 @@ -Click the link below to reset your password: - -{{ reset_link }}
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/email/reset_notice.html b/wqflask/flask_security/templates/security/email/reset_notice.html deleted file mode 100644 index 536e2961..00000000 --- a/wqflask/flask_security/templates/security/email/reset_notice.html +++ /dev/null @@ -1 +0,0 @@ -<p>Your password has been reset</p>
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/email/reset_notice.txt b/wqflask/flask_security/templates/security/email/reset_notice.txt deleted file mode 100644 index a3fa0b4b..00000000 --- a/wqflask/flask_security/templates/security/email/reset_notice.txt +++ /dev/null @@ -1 +0,0 @@ -Your password has been reset
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/email/welcome.html b/wqflask/flask_security/templates/security/email/welcome.html deleted file mode 100644 index 55eaed61..00000000 --- a/wqflask/flask_security/templates/security/email/welcome.html +++ /dev/null @@ -1,7 +0,0 @@ -<p>Welcome {{ user.email }}!</p> - -{% if security.confirmable %} -<p>You can confirm your email through the link below:</p> - -<p><a href="{{ confirmation_link }}">Confirm my account</a></p> -{% endif %}
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/email/welcome.txt b/wqflask/flask_security/templates/security/email/welcome.txt deleted file mode 100644 index fb6ee5b5..00000000 --- a/wqflask/flask_security/templates/security/email/welcome.txt +++ /dev/null @@ -1,7 +0,0 @@ -Welcome {{ user.email }}! - -{% if security.confirmable %} -You can confirm your email through the link below: - -{{ confirmation_link }} -{% endif %}
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/forgot_password.html b/wqflask/flask_security/templates/security/forgot_password.html deleted file mode 100644 index 90fcaf66..00000000 --- a/wqflask/flask_security/templates/security/forgot_password.html +++ /dev/null @@ -1,9 +0,0 @@ -{% from "security/_macros.html" import render_field_with_errors, render_field %} -{% include "security/_messages.html" %} -<h1>Send password reset instructions</h1> -<form action="{{ url_for_security('forgot_password') }}" method="POST" name="forgot_password_form"> - {{ forgot_password_form.hidden_tag() }} - {{ render_field_with_errors(forgot_password_form.email) }} - {{ render_field(forgot_password_form.submit) }} -</form> -{% include "security/_menu.html" %}
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/login_user.html b/wqflask/flask_security/templates/security/login_user.html deleted file mode 100644 index d781ce08..00000000 --- a/wqflask/flask_security/templates/security/login_user.html +++ /dev/null @@ -1,12 +0,0 @@ -{% from "security/_macros.html" import render_field_with_errors, render_field %} -{% include "security/_messages.html" %} -<h1>Login</h1> -<form action="{{ url_for_security('login') }}" method="POST" name="login_user_form"> - {{ login_user_form.hidden_tag() }} - {{ render_field_with_errors(login_user_form.email) }} - {{ render_field_with_errors(login_user_form.password) }} - {{ render_field_with_errors(login_user_form.remember) }} - {{ render_field(login_user_form.next) }} - {{ render_field(login_user_form.submit) }} -</form> -{% include "security/_menu.html" %}
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/register_user.html b/wqflask/flask_security/templates/security/register_user.html deleted file mode 100644 index 87cf9b1d..00000000 --- a/wqflask/flask_security/templates/security/register_user.html +++ /dev/null @@ -1,13 +0,0 @@ -{% from "security/_macros.html" import render_field_with_errors, render_field %} -{% include "security/_messages.html" %} -<h1>Register</h1> -<form action="{{ url_for_security('register') }}" method="POST" name="register_user_form"> - {{ register_user_form.hidden_tag() }} - {{ render_field_with_errors(register_user_form.email) }} - {{ render_field_with_errors(register_user_form.password) }} - {% if register_user_form.password_confirm %} - {{ render_field_with_errors(register_user_form.password_confirm) }} - {% endif %} - {{ render_field(register_user_form.submit) }} -</form> -{% include "security/_menu.html" %}
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/reset_password.html b/wqflask/flask_security/templates/security/reset_password.html deleted file mode 100644 index e6fc3f58..00000000 --- a/wqflask/flask_security/templates/security/reset_password.html +++ /dev/null @@ -1,10 +0,0 @@ -{% from "security/_macros.html" import render_field_with_errors, render_field %} -{% include "security/_messages.html" %} -<h1>Reset password</h1> -<form action="{{ url_for_security('reset_password', token=reset_password_token) }}" method="POST" name="reset_password_form"> - {{ reset_password_form.hidden_tag() }} - {{ render_field_with_errors(reset_password_form.password) }} - {{ render_field_with_errors(reset_password_form.password_confirm) }} - {{ render_field(reset_password_form.submit) }} -</form> -{% include "security/_menu.html" %}
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/send_confirmation.html b/wqflask/flask_security/templates/security/send_confirmation.html deleted file mode 100644 index 3e828407..00000000 --- a/wqflask/flask_security/templates/security/send_confirmation.html +++ /dev/null @@ -1,9 +0,0 @@ -{% from "security/_macros.html" import render_field_with_errors, render_field %} -{% include "security/_messages.html" %} -<h1>Resend confirmation instructions</h1> -<form action="{{ url_for_security('send_confirmation') }}" method="POST" name="send_confirmation_form"> - {{ send_confirmation_form.hidden_tag() }} - {{ render_field_with_errors(send_confirmation_form.email) }} - {{ render_field(send_confirmation_form.submit) }} -</form> -{% include "security/_menu.html" %}
\ No newline at end of file diff --git a/wqflask/flask_security/templates/security/send_login.html b/wqflask/flask_security/templates/security/send_login.html deleted file mode 100644 index 15611c57..00000000 --- a/wqflask/flask_security/templates/security/send_login.html +++ /dev/null @@ -1,9 +0,0 @@ -{% from "security/_macros.html" import render_field_with_errors, render_field %} -{% include "security/_messages.html" %} -<h1>Login</h1> -<form action="{{ url_for_security('login') }}" method="POST" name="send_login_form"> - {{ send_login_form.hidden_tag() }} - {{ render_field_with_errors(send_login_form.email) }} - {{ render_field(send_login_form.submit) }} -</form> -{% include "security/_menu.html" %}
\ No newline at end of file diff --git a/wqflask/flask_security/utils.py b/wqflask/flask_security/utils.py deleted file mode 100644 index 7397ab4f..00000000 --- a/wqflask/flask_security/utils.py +++ /dev/null @@ -1,379 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.utils - ~~~~~~~~~~~~~~~~~~~~~~~~ - - Flask-Security utils module - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" - -import base64 -import blinker -import functools -import hashlib -import hmac -from contextlib import contextmanager -from datetime import datetime, timedelta - -from flask import url_for, flash, current_app, request, session, render_template -from flask.ext.login import login_user as _login_user, \ - logout_user as _logout_user -from flask.ext.mail import Message -from flask.ext.principal import Identity, AnonymousIdentity, identity_changed -from itsdangerous import BadSignature, SignatureExpired -from werkzeug.local import LocalProxy - -from .signals import user_registered, user_confirmed, \ - confirm_instructions_sent, login_instructions_sent, \ - password_reset, password_changed, reset_password_instructions_sent - -# Convenient references -_security = LocalProxy(lambda: current_app.extensions['security']) - -_datastore = LocalProxy(lambda: _security.datastore) - -_pwd_context = LocalProxy(lambda: _security.pwd_context) - - -def login_user(user, remember=True): - """Performs the login and sends the appropriate signal.""" - - if not _login_user(user, remember): - return False - - if _security.trackable: - old_current_login, new_current_login = user.current_login_at, datetime.utcnow() - remote_addr = request.remote_addr or 'untrackable' - old_current_ip, new_current_ip = user.current_login_ip, remote_addr - - user.last_login_at = old_current_login or new_current_login - user.current_login_at = new_current_login - user.last_login_ip = old_current_ip or new_current_ip - user.current_login_ip = new_current_ip - user.login_count = user.login_count + 1 if user.login_count else 1 - - _datastore.put(user) - - identity_changed.send(current_app._get_current_object(), - identity=Identity(user.id)) - return True - - -def logout_user(): - for key in ('identity.name', 'identity.auth_type'): - session.pop(key, None) - identity_changed.send(current_app._get_current_object(), - identity=AnonymousIdentity()) - _logout_user() - - -def get_hmac(password): - if _security.password_hash == 'plaintext': - return password - - if _security.password_salt is None: - raise RuntimeError('The configuration value `SECURITY_PASSWORD_SALT` ' - 'must not be None when the value of `SECURITY_PASSWORD_HASH` is ' - 'set to "%s"' % _security.password_hash) - - h = hmac.new(_security.password_salt, password.encode('utf-8'), hashlib.sha512) - return base64.b64encode(h.digest()) - - -def verify_password(password, password_hash): - return _pwd_context.verify(get_hmac(password), password_hash) - - -def verify_and_update_password(password, user): - verified, new_password = _pwd_context.verify_and_update(get_hmac(password), user.password) - if verified and new_password: - user.password = new_password - _datastore.put(user) - return verified - - -def encrypt_password(password): - return _pwd_context.encrypt(get_hmac(password)) - - -def md5(data): - return hashlib.md5(data).hexdigest() - - -def do_flash(message, category=None): - """Flash a message depending on if the `FLASH_MESSAGES` configuration - value is set. - - :param message: The flash message - :param category: The flash message category - """ - if config_value('FLASH_MESSAGES'): - flash(message, category) - - -def get_url(endpoint_or_url): - """Returns a URL if a valid endpoint is found. Otherwise, returns the - provided value. - - :param endpoint_or_url: The endpoint name or URL to default to - """ - try: - return url_for(endpoint_or_url) - except: - return endpoint_or_url - - -def get_security_endpoint_name(endpoint): - return '%s.%s' % (_security.blueprint_name, endpoint) - - -def url_for_security(endpoint, **values): - """Return a URL for the security blueprint - - :param endpoint: the endpoint of the URL (name of the function) - :param values: the variable arguments of the URL rule - :param _external: if set to `True`, an absolute URL is generated. Server - address can be changed via `SERVER_NAME` configuration variable which - defaults to `localhost`. - :param _anchor: if provided this is added as anchor to the URL. - :param _method: if provided this explicitly specifies an HTTP method. - """ - endpoint = get_security_endpoint_name(endpoint) - return url_for(endpoint, **values) - - -def get_post_login_redirect(): - """Returns the URL to redirect to after a user logs in successfully.""" - return (get_url(request.args.get('next')) or - get_url(request.form.get('next')) or - find_redirect('SECURITY_POST_LOGIN_VIEW')) - - -def find_redirect(key): - """Returns the URL to redirect to after a user logs in successfully. - - :param key: The session or application configuration key to search for - """ - rv = (get_url(session.pop(key.lower(), None)) or - get_url(current_app.config[key.upper()] or None) or '/') - return rv - - -def get_config(app): - """Conveniently get the security configuration for the specified - application without the annoying 'SECURITY_' prefix. - - :param app: The application to inspect - """ - items = app.config.items() - prefix = 'SECURITY_' - - def strip_prefix(tup): - return (tup[0].replace('SECURITY_', ''), tup[1]) - - return dict([strip_prefix(i) for i in items if i[0].startswith(prefix)]) - - -def get_message(key, **kwargs): - rv = config_value('MSG_' + key) - return rv[0] % kwargs, rv[1] - - -def config_value(key, app=None, default=None): - """Get a Flask-Security configuration value. - - :param key: The configuration key without the prefix `SECURITY_` - :param app: An optional specific application to inspect. Defaults to Flask's - `current_app` - :param default: An optional default value if the value is not set - """ - app = app or current_app - return get_config(app).get(key.upper(), default) - - -def get_max_age(key, app=None): - now = datetime.utcnow() - expires = now + get_within_delta(key + '_WITHIN', app) - td = (expires - now) - return (td.microseconds + (td.seconds + td.days * 24 * 3600) * 1e6) / 1e6 - - -def get_within_delta(key, app=None): - """Get a timedelta object from the application configuration following - the internal convention of:: - - <Amount of Units> <Type of Units> - - Examples of valid config values:: - - 5 days - 10 minutes - - :param key: The config value key without the 'SECURITY_' prefix - :param app: Optional application to inspect. Defaults to Flask's - `current_app` - """ - txt = config_value(key, app=app) - values = txt.split() - return timedelta(**{values[1]: int(values[0])}) - - -def send_mail(subject, recipient, template, **context): - """Send an email via the Flask-Mail extension. - - :param subject: Email subject - :param recipient: Email recipient - :param template: The name of the email template - :param context: The context to render the template with - """ - - context.setdefault('security', _security) - context.update(_security._run_ctx_processor('mail')) - - msg = Message(subject, - sender=_security.email_sender, - recipients=[recipient]) - - ctx = ('security/email', template) - msg.body = render_template('%s/%s.txt' % ctx, **context) - msg.html = render_template('%s/%s.html' % ctx, **context) - - if _security._send_mail_task: - _security._send_mail_task(msg) - return - - mail = current_app.extensions.get('mail') - mail.send(msg) - - -def get_token_status(token, serializer, max_age=None): - serializer = getattr(_security, serializer + '_serializer') - max_age = get_max_age(max_age) - user, data = None, None - expired, invalid = False, False - - try: - data = serializer.loads(token, max_age=max_age) - except SignatureExpired: - d, data = serializer.loads_unsafe(token) - expired = True - except BadSignature: - invalid = True - - if data: - user = _datastore.find_user(id=data[0]) - - expired = expired and (user is not None) - return expired, invalid, user - - -@contextmanager -def capture_passwordless_login_requests(): - login_requests = [] - - def _on(data, app): - login_requests.append(data) - - login_instructions_sent.connect(_on) - - try: - yield login_requests - finally: - login_instructions_sent.disconnect(_on) - - -@contextmanager -def capture_registrations(): - """Testing utility for capturing registrations. - - :param confirmation_sent_at: An optional datetime object to set the - user's `confirmation_sent_at` to - """ - registrations = [] - - def _on(data, app): - registrations.append(data) - - user_registered.connect(_on) - - try: - yield registrations - finally: - user_registered.disconnect(_on) - - -@contextmanager -def capture_reset_password_requests(reset_password_sent_at=None): - """Testing utility for capturing password reset requests. - - :param reset_password_sent_at: An optional datetime object to set the - user's `reset_password_sent_at` to - """ - reset_requests = [] - - def _on(request, app): - reset_requests.append(request) - - reset_password_instructions_sent.connect(_on) - - try: - yield reset_requests - finally: - reset_password_instructions_sent.disconnect(_on) - - -class CaptureSignals(object): - """Testing utility for capturing blinker signals. - - Context manager which mocks out selected signals and registers which are `sent` on and what - arguments were sent. Instantiate with a list of blinker `NamedSignals` to patch. Each signal - has it's `send` mocked out. - """ - def __init__(self, signals): - """Patch all given signals and make them available as attributes. - - :param signals: list of signals - """ - self._records = {} - self._receivers = {} - for signal in signals: - self._records[signal] = [] - self._receivers[signal] = functools.partial(self._record, signal) - - def __getitem__(self, signal): - """All captured signals are available via `ctxt[signal]`. - """ - if isinstance(signal, blinker.base.NamedSignal): - return self._records[signal] - else: - super(CaptureSignals, self).__setitem__(signal) - - def _record(self, signal, *args, **kwargs): - self._records[signal].append((args, kwargs)) - - def __enter__(self): - for signal, receiver in self._receivers.iteritems(): - signal.connect(receiver) - return self - - def __exit__(self, type, value, traceback): - for signal, receiver in self._receivers.iteritems(): - signal.disconnect(receiver) - - def signals_sent(self): - """Return a set of the signals sent. - :rtype: list of blinker `NamedSignals`. - """ - return set([signal for signal, _ in self._records.iteritems() if self._records[signal]]) - - -def capture_signals(): - """Factory method that creates a `CaptureSignals` with all the flask_security signals.""" - return CaptureSignals([user_registered, user_confirmed, - confirm_instructions_sent, login_instructions_sent, - password_reset, password_changed, - reset_password_instructions_sent]) - - diff --git a/wqflask/flask_security/views.py b/wqflask/flask_security/views.py deleted file mode 100644 index 1b8488d8..00000000 --- a/wqflask/flask_security/views.py +++ /dev/null @@ -1,359 +0,0 @@ -# -*- coding: utf-8 -*- -""" - flask.ext.security.views - ~~~~~~~~~~~~~~~~~~~~~~~~ - - Flask-Security views module - - :copyright: (c) 2012 by Matt Wright. - :license: MIT, see LICENSE for more details. -""" - -from flask import current_app, redirect, request, render_template, jsonify, \ - after_this_request, Blueprint -from flask_login import current_user -from werkzeug.datastructures import MultiDict -from werkzeug.local import LocalProxy - -from .confirmable import send_confirmation_instructions, \ - confirm_user, confirm_email_token_status -from .decorators import login_required, anonymous_user_required -from .passwordless import send_login_instructions, \ - login_token_status -from .recoverable import reset_password_token_status, \ - send_reset_password_instructions, update_password -from .changeable import change_user_password -from .registerable import register_user -from .utils import get_url, get_post_login_redirect, do_flash, \ - get_message, login_user, logout_user, url_for_security as url_for, \ - config_value - - -# Convenient references -_security = LocalProxy(lambda: current_app.extensions['security']) - -_datastore = LocalProxy(lambda: _security.datastore) - - -def _render_json(form, include_auth_token=False): - has_errors = len(form.errors) > 0 - - if has_errors: - code = 400 - response = dict(errors=form.errors) - else: - code = 200 - response = dict(user=dict(id=str(form.user.id))) - if include_auth_token: - token = form.user.get_auth_token() - response['user']['authentication_token'] = token - - return jsonify(dict(meta=dict(code=code), response=response)) - - -def _commit(response=None): - _datastore.commit() - return response - - -def _ctx(endpoint): - return _security._run_ctx_processor(endpoint) - - -@anonymous_user_required -def login(): - """View function for login view""" - - form_class = _security.login_form - - if request.json: - form = form_class(MultiDict(request.json)) - else: - form = form_class() - - if form.validate_on_submit(): - login_user(form.user, remember=form.remember.data) - after_this_request(_commit) - - if not request.json: - return redirect(get_post_login_redirect()) - - form.next.data = get_url(request.args.get('next')) \ - or get_url(request.form.get('next')) or '' - - if request.json: - return _render_json(form, True) - - return render_template(config_value('LOGIN_USER_TEMPLATE'), - login_user_form=form, - **_ctx('login')) - - -@login_required -def logout(): - """View function which handles a logout request.""" - - logout_user() - - return redirect(request.args.get('next', None) or - get_url(_security.post_logout_view)) - - -def register(): - """View function which handles a registration request.""" - - if _security.confirmable or request.json: - form_class = _security.confirm_register_form - else: - form_class = _security.register_form - - if request.json: - form_data = MultiDict(request.json) - else: - form_data = request.form - - form = form_class(form_data) - - if form.validate_on_submit(): - user = register_user(**form.to_dict()) - form.user = user - - if not _security.confirmable or _security.login_without_confirmation: - after_this_request(_commit) - login_user(user) - - if not request.json: - post_register_url = get_url(_security.post_register_view) - post_login_url = get_url(_security.post_login_view) - return redirect(post_register_url or post_login_url) - - if request.json: - return _render_json(form) - - return render_template(config_value('REGISTER_USER_TEMPLATE'), - register_user_form=form, - **_ctx('register')) - - -def send_login(): - """View function that sends login instructions for passwordless login""" - - form_class = _security.passwordless_login_form - - if request.json: - form = form_class(MultiDict(request.json)) - else: - form = form_class() - - if form.validate_on_submit(): - send_login_instructions(form.user) - if request.json is None: - do_flash(*get_message('LOGIN_EMAIL_SENT', email=form.user.email)) - - if request.json: - return _render_json(form) - - return render_template(config_value('SEND_LOGIN_TEMPLATE'), - send_login_form=form, - **_ctx('send_login')) - - -@anonymous_user_required -def token_login(token): - """View function that handles passwordless login via a token""" - - expired, invalid, user = login_token_status(token) - - if invalid: - do_flash(*get_message('INVALID_LOGIN_TOKEN')) - if expired: - send_login_instructions(user) - do_flash(*get_message('LOGIN_EXPIRED', email=user.email, - within=_security.login_within)) - if invalid or expired: - return redirect(url_for('login')) - - login_user(user, True) - after_this_request(_commit) - do_flash(*get_message('PASSWORDLESS_LOGIN_SUCCESSFUL')) - - return redirect(get_post_login_redirect()) - - -def send_confirmation(): - """View function which sends confirmation instructions.""" - - form_class = _security.send_confirmation_form - - if request.json: - form = form_class(MultiDict(request.json)) - else: - form = form_class() - - if form.validate_on_submit(): - send_confirmation_instructions(form.user) - if request.json is None: - do_flash(*get_message('CONFIRMATION_REQUEST', email=form.user.email)) - - if request.json: - return _render_json(form) - - return render_template(config_value('SEND_CONFIRMATION_TEMPLATE'), - send_confirmation_form=form, - **_ctx('send_confirmation')) - - -@anonymous_user_required -def confirm_email(token): - """View function which handles a email confirmation request.""" - - expired, invalid, user = confirm_email_token_status(token) - - if not user or invalid: - invalid = True - do_flash(*get_message('INVALID_CONFIRMATION_TOKEN')) - if expired: - send_confirmation_instructions(user) - do_flash(*get_message('CONFIRMATION_EXPIRED', email=user.email, - within=_security.confirm_email_within)) - if invalid or expired: - return redirect(get_url(_security.confirm_error_view) or - url_for('send_confirmation')) - - confirm_user(user) - login_user(user, True) - after_this_request(_commit) - do_flash(*get_message('EMAIL_CONFIRMED')) - - return redirect(get_url(_security.post_confirm_view) or - get_url(_security.post_login_view)) - - -def forgot_password(): - """View function that handles a forgotten password request.""" - - form_class = _security.forgot_password_form - - if request.json: - form = form_class(MultiDict(request.json)) - else: - form = form_class() - - if form.validate_on_submit(): - send_reset_password_instructions(form.user) - if request.json is None: - do_flash(*get_message('PASSWORD_RESET_REQUEST', email=form.user.email)) - - if request.json: - return _render_json(form) - - return render_template(config_value('FORGOT_PASSWORD_TEMPLATE'), - forgot_password_form=form, - **_ctx('forgot_password')) - - -@anonymous_user_required -def reset_password(token): - """View function that handles a reset password request.""" - - expired, invalid, user = reset_password_token_status(token) - - if invalid: - do_flash(*get_message('INVALID_RESET_PASSWORD_TOKEN')) - if expired: - do_flash(*get_message('PASSWORD_RESET_EXPIRED', email=user.email, - within=_security.reset_password_within)) - if invalid or expired: - return redirect(url_for('forgot_password')) - - form = _security.reset_password_form() - - if form.validate_on_submit(): - after_this_request(_commit) - update_password(user, form.password.data) - do_flash(*get_message('PASSWORD_RESET')) - login_user(user, True) - return redirect(get_url(_security.post_reset_view) or - get_url(_security.post_login_view)) - - return render_template(config_value('RESET_PASSWORD_TEMPLATE'), - reset_password_form=form, - reset_password_token=token, - **_ctx('reset_password')) - - -@login_required -def change_password(): - """View function which handles a change password request.""" - - form_class = _security.change_password_form - - if request.json: - form = form_class(MultiDict(request.json)) - else: - form = form_class() - - if form.validate_on_submit(): - after_this_request(_commit) - change_user_password(current_user, form.new_password.data) - if request.json is None: - do_flash(*get_message('PASSWORD_CHANGE')) - return redirect(get_url(_security.post_change_view) or - get_url(_security.post_login_view)) - - if request.json: - return _render_json(form) - - return render_template('security/change_password.html', - change_password_form=form, - **_ctx('change_password')) - - -def create_blueprint(state, import_name): - """Creates the security extension blueprint""" - - bp = Blueprint(state.blueprint_name, import_name, - url_prefix=state.url_prefix, - subdomain=state.subdomain, - template_folder='templates') - - bp.route(state.logout_url, endpoint='logout')(logout) - - if state.passwordless: - bp.route(state.login_url, - methods=['GET', 'POST'], - endpoint='login')(send_login) - bp.route(state.login_url + '/<token>', - endpoint='token_login')(token_login) - else: - bp.route(state.login_url, - methods=['GET', 'POST'], - endpoint='login')(login) - - if state.registerable: - bp.route(state.register_url, - methods=['GET', 'POST'], - endpoint='register')(register) - - if state.recoverable: - bp.route(state.reset_url, - methods=['GET', 'POST'], - endpoint='forgot_password')(forgot_password) - bp.route(state.reset_url + '/<token>', - methods=['GET', 'POST'], - endpoint='reset_password')(reset_password) - - if state.changeable: - bp.route(state.change_url, - methods=['GET', 'POST'], - endpoint='change_password')(change_password) - - if state.confirmable: - bp.route(state.confirm_url, - methods=['GET', 'POST'], - endpoint='send_confirmation')(send_confirmation) - bp.route(state.confirm_url + '/<token>', - methods=['GET', 'POST'], - endpoint='confirm_email')(confirm_email) - - return bp diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py index ebe3add5..adffdca3 100644 --- a/wqflask/run_gunicorn.py +++ b/wqflask/run_gunicorn.py @@ -7,12 +7,12 @@ # from flask import Flask # application = Flask(__name__) -print "Starting up Gunicorn process" +print "===> Starting up Gunicorn process" from wqflask import app +from utility.startup_config import app_config -app.config['SESSION_TYPE'] = 'filesystem' -app.config['SECRET_KEY'] = 'super secret key' +app_config() @app.route("/gunicorn") def hello(): diff --git a/wqflask/runserver.py b/wqflask/runserver.py index a0c76e51..5f41d04d 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -21,22 +21,9 @@ GREEN = '\033[92m' BOLD = '\033[1m' ENDC = '\033[0m' -import os -app.config['SECRET_KEY'] = os.urandom(24) +from utility.startup_config import app_config -from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting,get_setting_bool - -port = get_setting_int("SERVER_PORT") - -print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]") - -if get_setting_bool("USE_GN_SERVER"): - import requests - page = requests.get(get_setting("GN_SERVER_URL")) - if page.status_code != 200: - raise Exception("API server not found!") - -print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL"))) +app_config() werkzeug_logger = logging.getLogger('werkzeug') diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index 2d3d5add..075a8f65 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -6,6 +6,11 @@ logger = getLogger(__name__) from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT +def test_elasticsearch_connection(): + es = Elasticsearch(['http://'+ELASTICSEARCH_HOST+":"+str(ELASTICSEARCH_PORT)+'/'], verify_certs=True) + if not es.ping(): + logger.warning("Elasticsearch is DOWN") + def get_elasticsearch_connection(): logger.info("get_elasticsearch_connection") es = None diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py new file mode 100644 index 00000000..5a62cc50 --- /dev/null +++ b/wqflask/utility/startup_config.py @@ -0,0 +1,39 @@ + +from wqflask import app +from utility.tools import WEBSERVER_MODE, show_settings, get_setting_int, get_setting, get_setting_bool + +import utility.logger +logger = utility.logger.getLogger(__name__ ) + +BLUE = '\033[94m' +GREEN = '\033[92m' +BOLD = '\033[1m' +ENDC = '\033[0m' + +def app_config(): + app.config['SESSION_TYPE'] = 'filesystem' + if not app.config.get('SECRET_KEY'): + import os + app.config['SECRET_KEY'] = str(os.urandom(24)) + + mode = WEBSERVER_MODE + if mode == "DEV" or mode == "DEBUG": + app.config['TEMPLATES_AUTO_RELOAD'] = True + # if mode == "DEBUG": + # app.config['EXPLAIN_TEMPLATE_LOADING'] = True <--- use overriding app param instead + print("==========================================") + show_settings() + + port = get_setting_int("SERVER_PORT") + + if get_setting_bool("USE_GN_SERVER"): + print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]") + import requests + page = requests.get(get_setting("GN_SERVER_URL")) + if page.status_code != 200: + raise Exception("API server not found!") + + import utility.elasticsearch_tools as es + es.test_elasticsearch_connection() + + print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL"))) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 8c9fed96..59bb49d8 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -54,7 +54,7 @@ def get_setting(command_id,guess=None): # print("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) if command is None or command == "": - command = OVERRIDES.get(command_id) + command = OVERRIDES.get(command_id) # currently not in use if command is None: # ---- Check whether setting exists in app command = value(app.config.get(command_id)) @@ -220,7 +220,7 @@ def show_settings(): logger.info(OVERRIDES) logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC) - print "runserver.py: ****** Webserver configuration ******" + print "runserver.py: ****** Webserver configuration - k,v pairs from app.config ******" keylist = app.config.keys() keylist.sort() for k in keylist: @@ -254,18 +254,23 @@ JS_GN_PATH = get_setting('JS_GN_PATH') GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID') GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET') GITHUB_AUTH_URL = None -if GITHUB_CLIENT_ID and GITHUB_CLIENT_SECRET: - GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id="+GITHUB_CLIENT_ID+"&client_secret="+GITHUB_CLIENT_SECRET -GITHUB_API_URL = get_setting('GITHUB_API_URL') +if GITHUB_CLIENT_ID != 'UNKNOWN' and GITHUB_CLIENT_SECRET: + GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id=" + \ + GITHUB_CLIENT_ID+"&client_secret="+GITHUB_CLIENT_SECRET + GITHUB_API_URL = get_setting('GITHUB_API_URL') + ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID') ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET') ORCID_AUTH_URL = None -if ORCID_CLIENT_ID and ORCID_CLIENT_SECRET: - ORCID_AUTH_URL = "https://sandbox.orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id="+ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET -ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL') +if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET: + ORCID_AUTH_URL = "https://sandbox.orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \ + ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET + ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL') ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST') ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT') +import utility.elasticsearch_tools as es +es.test_elasticsearch_connection() SMTP_CONNECT = get_setting('SMTP_CONNECT') SMTP_USERNAME = get_setting('SMTP_USERNAME') @@ -285,18 +290,5 @@ assert_dir(JS_TWITTER_POST_FETCHER_PATH) from six import string_types -if os.environ.get('WQFLASK_OVERRIDES'): - jsonfn = get_setting('WQFLASK_OVERRIDES') - logger.info("WQFLASK_OVERRIDES: %s" % jsonfn) - with open(jsonfn) as data_file: - overrides = json.load(data_file) - for k in overrides: - cmd = overrides[k] - if isinstance(cmd, string_types): - OVERRIDES[k] = eval(cmd) - else: - OVERRIDES[k] = cmd - logger.debug(OVERRIDES) - # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py new file mode 100644 index 00000000..220e5f62 --- /dev/null +++ b/wqflask/utility/type_checking.py @@ -0,0 +1,42 @@ +# Type checking functions + +def is_float(value): + try: + float(value) + return True + except: + return False + +def is_int(value): + try: + int(value) + return True + except: + return False + +def is_str(value): + if value is None: + return False + try: + str(value) + return True + except: + return False + +def get_float(vars,name,default=None): + if name in vars: + if is_float(vars[name]): + return float(vars[name]) + return None + +def get_int(vars,name,default=None): + if name in vars: + if is_int(vars[name]): + return float(vars[name]) + return default + +def get_string(vars,name,default=None): + if name in vars: + if not vars[name] is None: + return str(vars[name]) + return default diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index 2188ce17..bc8e9900 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -13,8 +13,8 @@ logging.basicConfig(level=logging.INFO) app = Flask(__name__) app.config.from_object('cfg.default_settings') # Get the defaults from cfg.default_settings -app.config.from_envvar('WQFLASK_SETTINGS') # See http://flask.pocoo.org/docs/config/#configuring-from-files -# Note we also use WQFLASK_OVERRIDES +app.config.from_envvar('GN2_SETTINGS') # See http://flask.pocoo.org/docs/config/#configuring-from-files +# Note no longer use the badly named WQFLASK_OVERRIDES (nyi) app.jinja_env.globals.update( undefined = jinja2.StrictUndefined, diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 2f6c3a96..629977ac 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -36,6 +36,10 @@ from utility.formatting import numify from base import trait from base.data_set import create_dataset +import logging +from utility.logger import getLogger +logger = getLogger(__name__) + def get_collection(): if g.user_session.logged_in: return UserCollection() @@ -93,7 +97,7 @@ class AnonCollection(object): self.traits = list(process_traits(params['traits'])) #len_before = len(Redis.smembers(self.key)) existing_collections = Redis.get(self.key) - print("existing_collections:", existing_collections) + logger.debug("existing_collections:", existing_collections) if existing_collections != None and existing_collections != "None": collections_list = json.loads(existing_collections) collection_position = 0 #ZS: Position of collection in collection_list, if it exists @@ -158,8 +162,8 @@ class UserCollection(object): """User is logged in""" def add_traits(self, params, collection_name): - print("---> params are:", params.keys()) - print(" type(params):", type(params)) + logger.debug("---> params are:", params.keys()) + logger.debug(" type(params):", type(params)) if collection_name=="Default": uc = g.user_session.user_ob.get_collection_by_name("Default") # Doesn't exist so we'll create it @@ -187,7 +191,7 @@ class UserCollection(object): db_session.commit() - print("added to existing, now set is:" + str(uc.members)) + logger.debug("added to existing, now set is:" + str(uc.members)) report_change(len_before, len_now) # Probably have to change that @@ -210,12 +214,12 @@ def process_traits(unprocessed_traits): def report_change(len_before, len_now): new_length = len_now - len_before if new_length: - print("We've added {} to your collection.".format( + logger.debug("We've added {} to your collection.".format( numify(new_length, 'new trait', 'new traits'))) flash("We've added {} to your collection.".format( numify(new_length, 'new trait', 'new traits'))) else: - print("No new traits were added.") + logger.debug("No new traits were added.") @app.route("/collections/add") @@ -224,7 +228,7 @@ def collections_add(): if g.user_session.logged_in: user_collections = g.user_session.user_ob.user_collections - print("user_collections are:", user_collections) + logger.debug("user_collections are:", user_collections) return render_template("collections/add.html", traits = traits, collections = user_collections, @@ -246,11 +250,11 @@ def collections_new(): if "sign_in" in params: return redirect(url_for('login')) if "create_new" in params: - print("in create_new") + logger.debug("in create_new") collection_name = params['new_collection'] return create_new(collection_name) elif "add_to_existing" in params: - print("in add to existing") + logger.debug("in add to existing") collection_name = params['existing_collection'].split(":")[1] if g.user_session.logged_in: return UserCollection().add_traits(params, collection_name) @@ -270,7 +274,7 @@ def create_new(collection_name): if g.user_session.logged_in: uc = model.UserCollection() uc.name = collection_name - print("user_session:", g.user_session.__dict__) + logger.debug("user_session:", g.user_session.__dict__) uc.user = g.user_session.user_id uc.members = json.dumps(list(traits)) db_session.add(uc) @@ -286,17 +290,17 @@ def create_new(collection_name): @app.route("/collections/list") def list_collections(): params = request.args - print("PARAMS:", params) + logger.debug("PARAMS:", params) if g.user_session.logged_in: user_collections = list(g.user_session.user_ob.user_collections) - print("user_collections are:", user_collections) + logger.debug("user_collections are:", user_collections) return render_template("collections/list.html", params = params, collections = user_collections, ) else: anon_collections = user_manager.AnonUser().get_collections() - print("anon_collections are:", anon_collections) + logger.debug("anon_collections are:", anon_collections) return render_template("collections/list.html", params = params, collections = anon_collections) @@ -305,17 +309,17 @@ def list_collections(): @app.route("/collections/remove", methods=('POST',)) def remove_traits(): params = request.form - print("params are:", params) + logger.debug("params are:", params) if "uc_id" in params: uc_id = params['uc_id'] uc = model.UserCollection.query.get(uc_id) traits_to_remove = params.getlist('traits[]') traits_to_remove = process_traits(traits_to_remove) - print("\n\n after processing, traits_to_remove:", traits_to_remove) + logger.debug("\n\n after processing, traits_to_remove:", traits_to_remove) all_traits = uc.members_as_set() members_now = all_traits - traits_to_remove - print(" members_now:", members_now) + logger.debug(" members_now:", members_now) uc.members = json.dumps(list(members_now)) uc.changed_timestamp = datetime.datetime.utcnow() db_session.commit() @@ -332,7 +336,7 @@ def remove_traits(): @app.route("/collections/delete", methods=('POST',)) def delete_collection(): params = request.form - print("params:", params) + logger.debug("params:", params) if g.user_session.logged_in: uc_id = params['uc_id'] if len(uc_id.split(":")) > 1: @@ -349,8 +353,11 @@ def delete_collection(): db_session.delete(uc) db_session.commit() else: - collection_name = params['collection_name'] - user_manager.AnonUser().delete_collection(collection_name) + if "collection_name" in params: + collection_name = params['collection_name'] + else: + for this_collection in params['uc_id'].split(":"): + user_manager.AnonUser().delete_collection(this_collection) flash("We've deleted the collection: {}.".format(collection_name), "alert-info") @@ -360,7 +367,7 @@ def delete_collection(): @app.route("/collections/view") def view_collection(): params = request.args - print("PARAMS in view collection:", params) + logger.debug("PARAMS in view collection:", params) if "uc_id" in params: uc_id = params['uc_id'] @@ -376,7 +383,7 @@ def view_collection(): #this_collection = user_collections[params['collection_id']] traits = this_collection['members'] - print("in view_collection traits are:", traits) + logger.debug("in view_collection traits are:", traits) trait_obs = [] json_version = [] @@ -402,7 +409,7 @@ def view_collection(): collection_info = dict(trait_obs=trait_obs, collection_name=this_collection['name']) if "json" in params: - print("json_version:", json_version) + logger.debug("json_version:", json_version) return json.dumps(json_version) else: return render_template("collections/view.html", diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 3d1c0d17..2c6c3a14 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -32,6 +32,7 @@ import pp import math import collections import resource +import json import scipy @@ -51,6 +52,8 @@ import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions from utility.benchmark import Bench import utility.webqtlUtil +from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string +from wqflask import user_manager from MySQLdb import escape_string as escape @@ -75,47 +78,6 @@ def print_mem(stage=""): mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss #print("{}: {}".format(stage, mem/1024)) -def is_float(value): - try: - float(value) - return True - except: - return False - -def is_int(value): - try: - int(value) - return True - except: - return False - -def is_str(value): - if value is None: - return False - try: - str(value) - return True - except: - return False - -def get_float(vars,name,default=None): - if name in vars: - if is_float(vars[name]): - return float(vars[name]) - return None - -def get_int(vars,name,default=None): - if name in vars: - if is_int(vars[name]): - return float(vars[name]) - return default - -def get_string(vars,name,default=None): - if name in vars: - if not vars[name] is None: - return str(vars[name]) - return default - class AuthException(Exception): pass @@ -248,7 +210,7 @@ class CorrelationResults(object): else: self.this_trait_vals.append("None") num_overlap = len(self.this_trait_vals) - + logger.debug("DOING PARALLEL") self.do_parallel_correlation(db_filename, num_overlap) else: for trait, values in self.target_dataset.trait_data.iteritems(): @@ -335,6 +297,7 @@ class CorrelationResults(object): #print("self.correlation_results: ", pf(self.correlation_results)) + self.json_results = generate_corr_json(self.correlation_results, self.this_trait, self.dataset, self.target_dataset) #XZ, 09/18/2008: get all information about the user selected database. #target_db_name = fd.corr_dataset @@ -1195,6 +1158,17 @@ class CorrelationResults(object): import math import reaper + def cmpOrder2(A,B): + try: + if A[-1] < B[-1]: + return -1 + elif A[-1] == B[-1]: + return 0 + else: + return 1 + except: + return 0 + def calCorrelation(dbdata,userdata,N): X = [] Y = [] @@ -1420,3 +1394,61 @@ class CorrelationResults(object): # for one_result in results: # for one_traitinfo in one_result: # allcorrelations.append( one_traitinfo ) + +def generate_corr_json(corr_results, this_trait, dataset, target_dataset): + results_list = [] + for i, trait in enumerate(corr_results): + results_dict = {} + results_dict['checkbox'] = "<INPUT TYPE='checkbox' NAME='searchResult' class='checkbox trait_checkbox' style='padding-right: 0px;' VALUE='" + user_manager.data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) + "'>" + results_dict['index'] = i + 1 + results_dict['trait_id'] = "<a href='/show_trait?trait_id="+str(trait.name)+"&dataset="+str(dataset.name)+"'>"+str(trait.name)+"</a>" + if target_dataset.type == "ProbeSet": + results_dict['symbol'] = trait.symbol + results_dict['description'] = trait.description_display + results_dict['location'] = trait.location_repr + results_dict['mean'] = float(trait.mean) + if trait.LRS_score_repr != "N/A": + results_dict['lrs_score'] = "%.1f" % float(trait.LRS_score_repr) + else: + results_dict['lrs_score'] = "N/A" + results_dict['lrs_location'] = trait.LRS_location_repr + if trait.additive != "": + results_dict['additive'] = "%0.3f" % float(trait.additive) + else: + results_dict['additive'] = "N/A" + results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % float(trait.sample_r) + "</a>" + results_dict['num_overlap'] = trait.num_overlap + results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) + if trait.lit_corr == "" or trait.lit_corr == 0: + results_dict['lit_corr'] = "--" + else: + results_dict['lit_corr'] = "%0.3f" % float(trait.lit_corr) + if trait.tissue_corr == "" or trait.tissue_corr == 0: + results_dict['tissue_corr'] = "--" + else: + results_dict['tissue_corr'] = "%0.3f" % float(trait.tissue_corr) + elif target_dataset.type == "Publish": + results_dict['description'] = trait.description_display + results_dict['authors'] = trait.authors + if trait.pubmed_id: + results_dict['pubmed'] = "<a href='" + trait.pubmed_link + "'> " + trait.pubmed_text + "</a>" + else: + results_dict['pubmed'] = "N/A" + results_dict['lrs_score'] = trait.LRS_score_repr + results_dict['lrs_location'] = trait.LRS_location_repr + if trait.additive != "": + results_dict['additive'] = "%0.3f" % float(trait.additive) + else: + results_dict['additive'] = "N/A" + results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % trait.sample_r + "</a>" + results_dict['num_overlap'] = trait.num_overlap + results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) + else: + results_dict['lrs_location'] = trait.LRS_location_repr + results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % float(trait.sample_r) + "</a>" + results_dict['num_overlap'] = trait.num_overlap + results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) + + results_list.append(results_dict) + + return json.dumps(results_list) diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index b34beb7b..077386a3 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -173,9 +173,12 @@ class CorrelationMatrix(object): for sample in self.all_sample_list: groups.append(1) - pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors) - - self.loadings_array = self.process_loadings() + try: + self.pca_works = "True" + pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors) + self.loadings_array = self.process_loadings() + except: + self.pca_works = "False" self.js_data = dict(traits = [trait.name for trait in self.traits], groups = groups, diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index e33e04e1..fe1e17d2 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -5,6 +5,7 @@ from base.data_set import create_dataset from base.trait import GeneralTrait from db import webqtlDatabaseFunction +from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string from utility.benchmark import Bench from utility.logger import getLogger @@ -13,8 +14,13 @@ logger = getLogger(__name__) class GSearch(object): def __init__(self, kw): + assert('type' in kw) + assert('terms' in kw) + self.type = kw['type'] self.terms = kw['terms'] + assert(is_str(self.type)) + if self.type == "gene": sql = """ SELECT diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 68920130..7563eb2c 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -3,7 +3,7 @@ import os, math, string, random, json from base import webqtlConfig from base.trait import GeneralTrait from base.data_set import create_dataset -from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file +from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -11,7 +11,6 @@ logger = utility.logger.getLogger(__name__ ) def run_gemma(this_dataset, samples, vals, covariates, method, use_loco): """Generates p-values for each marker using GEMMA""" - assert_bin(GEMMA_COMMAND); if this_dataset.group.genofile != None: genofile_name = this_dataset.group.genofile[:-5] else: @@ -193,7 +192,7 @@ def parse_gemma_output(genofile_name): # if marker['chr'] != previous_chr: # previous_chr = marker['chr'] marker['Mb'] = float(line.split("\t")[2]) / 1000000 - marker['p_value'] = float(line.split("\t")[10]) + marker['p_value'] = float(line.split("\t")[11]) if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 #marker['lrs_value'] = 0 @@ -203,20 +202,15 @@ def parse_gemma_output(genofile_name): marker_obs.append(marker) included_markers.append(line.split("\t")[1]) - p_values.append(float(line.split("\t")[10])) + p_values.append(float(line.split("\t")[11])) return marker_obs def parse_loco_output(this_dataset, gwa_output_filename): output_filelist = [] - jsonfn = "{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json" - assert_file(jsonfn) - try: - with open(jsonfn) as data_file: - data = json.load(data_file) - except: - logger.error("Can not parse "+jsonfn) + with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file: + data = json.load(data_file) files = data['files'] for file in files: @@ -241,7 +235,7 @@ def parse_loco_output(this_dataset, gwa_output_filename): else: marker['chr'] = line.split("\t")[0] marker['Mb'] = float(line.split("\t")[2]) / 1000000 - marker['p_value'] = float(line.split("\t")[10]) + marker['p_value'] = float(line.split("\t")[11]) if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 #marker['lrs_value'] = 0 @@ -251,6 +245,6 @@ def parse_loco_output(this_dataset, gwa_output_filename): marker_obs.append(marker) included_markers.append(line.split("\t")[1]) - p_values.append(float(line.split("\t")[10])) + p_values.append(float(line.split("\t")[11])) - return marker_obs + return marker_obs
\ No newline at end of file diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index c189fb96..3ec61e55 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -228,6 +228,7 @@ class MarkerRegression(object): results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait, self.dataset, self.samples, + self.vals, self.json_data, self.num_perm, self.bootCheck, diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 211cf187..66884b0c 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -1204,6 +1204,8 @@ class MarkerRegression(object): else: if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam": string2 = 'Using GEMMA mapping method with no control for other QTLs.' + if self.covariates != "": + string3 = 'Using following traits as covariates: ' + self.covariates elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno": string2 = 'Using R/qtl mapping method with no control for other QTLs.' elif self.mapping_method == "plink": diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 50228b5e..6b58190f 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -1,17 +1,20 @@ -def gen_reaper_results(this_trait, dataset, samples_before, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): +import utility.logger +logger = utility.logger.getLogger(__name__ ) + +def gen_reaper_results(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): genotype = dataset.group.read_genotype_file() if manhattan_plot != True: genotype = genotype.addinterval() - samples, values, variances, sample_aliases = this_trait.export_informative() - trimmed_samples = [] trimmed_values = [] - for i in range(0, len(samples)): - if this_trait.data[samples[i]].name in samples_before: - trimmed_samples.append(samples[i]) - trimmed_values.append(values[i]) + for i in range(0, len(samples_before)): + try: + trimmed_values.append(float(trait_vals[i])) + trimmed_samples.append(samples_before[i]) + except: + pass perm_output = [] bootstrap_results = [] diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 59e100d8..53c96591 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -10,6 +10,7 @@ import time import math import datetime import collections +import re from pprint import pformat as pf @@ -25,6 +26,7 @@ from db import webqtlDatabaseFunction from flask import render_template from utility import formatting +from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string from utility.logger import getLogger logger = getLogger(__name__ ) @@ -64,14 +66,26 @@ views.py). else: self.and_or = "and" self.search_terms = kw['search_terms_and'] - self.search_term_exists = True + search = self.search_terms + # check for dodgy search terms + rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*',re.IGNORECASE) + if rx.match(search): + logger.info("Regex failed search") + self.search_term_exists = False + return + else: + self.search_term_exists = True + self.results = [] - if kw['type'] == "Phenotypes": # split datatype on type field + type = kw.get('type') + if type == "Phenotypes": # split datatype on type field dataset_type = "Publish" - elif kw['type'] == "Genotypes": + elif type == "Genotypes": dataset_type = "Geno" else: dataset_type = "ProbeSet" # ProbeSet is default + + assert(is_str(kw.get('dataset'))) self.dataset = create_dataset(kw['dataset'], dataset_type) logger.debug("search_terms:", self.search_terms) self.search() @@ -145,6 +159,7 @@ statement and executes else: combined_where_clause += "OR" else: + logger.debug("Search failed 1") self.search_term_exists = False if self.search_term_exists: combined_where_clause = "(" + combined_where_clause + ")" @@ -155,6 +170,7 @@ statement and executes else: logger.debug("len(search_terms)<=1") if self.search_terms == []: + logger.debug("Search failed 2") self.search_term_exists = False else: for a_search in self.search_terms: @@ -162,6 +178,7 @@ statement and executes if the_search != None: self.results.extend(the_search.run()) else: + logger.debug("Search failed 3") self.search_term_exists = False if self.search_term_exists: diff --git a/wqflask/wqflask/static/dbdoc/TODO.md b/wqflask/wqflask/static/dbdoc/TODO.md new file mode 100644 index 00000000..c0a8bab7 --- /dev/null +++ b/wqflask/wqflask/static/dbdoc/TODO.md @@ -0,0 +1 @@ +TODO: Add all database documentation into this folder diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js index 43ac6086..bf0a14e6 100644 --- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js +++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js @@ -1,6 +1,7 @@ var chart; +var srchart; -function drawg () { +function drawg() { // chart = nv.models.scatterChart(); // @@ -27,11 +28,45 @@ function drawg () { chart.yAxis.tickFormat(d3.format(checkformat(yrange))); // chart.tooltip.contentGenerator(function (obj) { - // return '<b style="font-size: 18px">(' + obj.point.x + ', ' + obj.point.y + ')</b>'; - return '<b style="font-size: 18px">' + obj.point.name + '</b>'; + return tiptext(obj); }); } +function srdrawg() { + // + srchart = nv.models.scatterChart(); + // + srchart.showLegend(false); + srchart.duration(300); + srchart.color(d3.scale.category10().range()); + srchart.pointRange([0, 400]); + srchart.pointDomain([0, 10]); + // + srchart.xAxis.axisLabel(js_data.trait_1); + srchart.xAxis.axisLabelDistance(11); + srchart.yAxis.axisLabel(js_data.trait_2); + srchart.yAxis.axisLabelDistance(11); + // + xmin = d3.min(js_data.rdata[0]); + xmax = d3.max(js_data.rdata[0]); + xrange = xmax - xmin; + ymin = d3.min(js_data.rdata[1]); + ymax = d3.max(js_data.rdata[1]); + yrange = ymax - ymin; + srchart.xDomain([0, xmax + xrange/10]); + srchart.yDomain([0, ymax + yrange/10]); + srchart.xAxis.tickFormat(d3.format(checkformat(xrange))); + srchart.yAxis.tickFormat(d3.format(checkformat(yrange))); + // + srchart.tooltip.contentGenerator(function (obj) { + return tiptext(obj); + }); +} + +function tiptext(obj) { + return '<b style="font-size: 18px">' + obj.point.name + " (" + obj.point.x + ', ' + obj.point.y + ')</b>'; +} + function getdata(size, shape) { var data = []; data.push({ @@ -50,6 +85,25 @@ function getdata(size, shape) { } return data; } + +function srgetdata(size, shape) { + var data = []; + data.push({ + values: [], + slope: js_data.srslope, + intercept: js_data.srintercept + }); + for (j = 0; j < js_data.rdata[0].length; j++) { + data[0].values.push({ + x: js_data.rdata[0][j], + y: js_data.rdata[1][j], + name: js_data.indIDs[j], + size: size, + shape: shape + }); + } + return data; +} function checkformat(range) { cell = range / 10.0; @@ -64,50 +118,47 @@ function checkformat(range) { function chartupdate() { // - var axisxcolor = $("#axisxcolor").val(); - $(".nvd3 .nv-axis.nv-x text").css("fill", axisxcolor); + var labelcolor = $("#labelcolor").val(); + $(".nvd3 .nv-axis.nv-x text").css("fill", labelcolor); + $(".nvd3 .nv-axis.nv-y text").css("fill", labelcolor); // - var axisycolor = $("#axisycolor").val(); - $(".nvd3 .nv-axis.nv-y text").css("fill", axisycolor); + var labelfont = $("#labelfont").val(); + $(".nvd3 .nv-axis.nv-x text").css("font-size", labelfont); + $(".nvd3 .nv-axis.nv-y text").css("font-size", labelfont); // - var axisxfont = $("#axisxfont").val(); - $(".nvd3 .nv-axis.nv-x text").css("font-size", axisxfont); + var numbercolor = $("#numbercolor").val(); + $("g.tick text").css("fill", numbercolor); // - var axisyfont = $("#axisyfont").val(); - $(".nvd3 .nv-axis.nv-y text").css("font-size", axisyfont); + var numberfont = $("#numberfont").val(); + $("g.tick text").css("font-size", numberfont); // - var domainxcolor = $("#domainxcolor").val(); - $(".nv-x .nv-axis g path.domain").css("stroke", domainxcolor); - // - var domainycolor = $("#domainycolor").val(); - $(".nv-y .nv-axis g path.domain").css("stroke", domainycolor); - // - var domainxwidth = $("#domainxwidth").val(); - $(".nv-x .nv-axis g path.domain").css("stroke-width", domainxwidth); + var axiscolor = $("#axiscolor").val(); + $(".nv-x .nv-axis g path.domain").css("stroke", axiscolor); + $(".nv-y .nv-axis g path.domain").css("stroke", axiscolor); // - var domainywidth = $("#domainywidth").val(); - $(".nv-y .nv-axis g path.domain").css("stroke-width", domainywidth); + var axiswidth = $("#axiswidth").val(); + $(".nv-x .nv-axis g path.domain").css("stroke-width", axiswidth); + $(".nv-y .nv-axis g path.domain").css("stroke-width", axiswidth); // - var clinecolor = $("#clinecolor").val(); - $("line.nv-regLine").css("stroke", clinecolor); + var linecolor = $("#linecolor").val(); + $("line.nv-regLine").css("stroke", linecolor); // - var clinewidth = $("#clinewidth").val(); - $("line.nv-regLine").css("stroke-width", clinewidth); + var linewidth = $("#linewidth").val(); + $("line.nv-regLine").css("stroke-width", linewidth); // - var axiscolor = $("#axiscolor").val(); - $(".tick").css("stroke", axiscolor); - // - var axiswidth = $("#axiswidth").val(); - $("line.nv-regLine").css("stroke-width", axiswidth); + var markcolor = $("#markcolor").val(); + $(".nvd3 g path").css("fill", markcolor); } function chartupdatewh() { // var width = $("#width").val(); $("#scatterplot2 svg").css("width", width); + $("#srscatterplot2 svg").css("width", width); // var height = $("#height").val(); $("#scatterplot2 svg").css("height", height); + $("#srscatterplot2 svg").css("height", height); // window.dispatchEvent(new Event('resize')); } @@ -118,7 +169,9 @@ function chartupdatedata() { var shape = $("#markshape").val(); // d3.select('#scatterplot2 svg').datum(nv.log(getdata(size, shape))).call(chart); + d3.select('#srscatterplot2 svg').datum(nv.log(srgetdata(size, shape))).call(srchart); nv.utils.windowResize(chart.update); + nv.utils.windowResize(srchart.update); } function savesvg(svgEl, name) { @@ -140,10 +193,14 @@ function saveassvg_pcs() { savesvg($("#svg_pcs")[0], "Pearson Correlation Scatterplot.svg"); } +function saveassvg_srcs() { + savesvg($("#svg_srcs")[0], "Spearman Rank Correlation Scatterplot.svg"); +} + drawg(); -chartupdate(); -chartupdatewh(); -chartupdatedata(); +srdrawg(); + + $(".chartupdate").change(function () { chartupdate(); @@ -156,3 +213,10 @@ $(".chartupdatewh").change(function () { $(".chartupdatedata").change(function () { chartupdatedata(); }); + +$(document).ready(function(){ + //chartupdate(); +//chartupdatewh(); +chartupdatedata(); +//chartupdate(); +});
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2_sr.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2_sr.js deleted file mode 100644 index d0392dd7..00000000 --- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2_sr.js +++ /dev/null @@ -1,137 +0,0 @@ -var srchart; - -function srdrawg () { - // - srchart = nv.models.scatterChart(); - // - srchart.showLegend(false); - srchart.duration(300); - srchart.color(d3.scale.category10().range()); - srchart.pointRange([0, 400]); - srchart.pointDomain([0, 10]); - // - srchart.xAxis.axisLabel(js_data.trait_1); - srchart.xAxis.axisLabelDistance(11); - srchart.yAxis.axisLabel(js_data.trait_2); - srchart.yAxis.axisLabelDistance(11); - // - xmin = d3.min(js_data.rdata[0]); - xmax = d3.max(js_data.rdata[0]); - xrange = xmax - xmin; - ymin = d3.min(js_data.rdata[1]); - ymax = d3.max(js_data.rdata[1]); - yrange = ymax - ymin; - srchart.xDomain([0, xmax + xrange/10]); - srchart.yDomain([0, ymax + yrange/10]); - srchart.xAxis.tickFormat(d3.format(srcheckformat(xrange))); - srchart.yAxis.tickFormat(d3.format(srcheckformat(yrange))); - // - srchart.tooltip.contentGenerator(function (obj) { - // return '<b style="font-size: 18px">(' + obj.point.x + ', ' + obj.point.y + ')</b>'; - return '<b style="font-size: 18px">' + obj.point.name + '</b>'; - }); -} - -function srgetdata(size, shape) { - var data = []; - data.push({ - values: [], - slope: js_data.srslope, - intercept: js_data.srintercept - }); - for (j = 0; j < js_data.rdata[0].length; j++) { - data[0].values.push({ - x: js_data.rdata[0][j], - y: js_data.rdata[1][j], - name: js_data.indIDs[j], - size: size, - shape: shape - }); - } - return data; -} - -function srcheckformat(range) { - cell = range / 10.0; - if (cell >= 1) { - return ",r"; - } else { - cell = -Math.log(cell); - n = cell.toString().split(".")[0].length; - return ",.0" + n + "f"; - } -} - -function srchartupdate() { - // - var axisxcolor = $("#axisxcolor").val(); - $(".nvd3 .nv-axis.nv-x text").css("fill", axisxcolor); - // - var axisycolor = $("#axisycolor").val(); - $(".nvd3 .nv-axis.nv-y text").css("fill", axisycolor); - // - var axisxfont = $("#axisxfont").val(); - $(".nvd3 .nv-axis.nv-x text").css("font-size", axisxfont); - // - var axisyfont = $("#axisyfont").val(); - $(".nvd3 .nv-axis.nv-y text").css("font-size", axisyfont); - // - var domainxcolor = $("#domainxcolor").val(); - $(".nv-x .nv-axis g path.domain").css("stroke", domainxcolor); - // - var domainycolor = $("#domainycolor").val(); - $(".nv-y .nv-axis g path.domain").css("stroke", domainycolor); - // - var domainxwidth = $("#domainxwidth").val(); - $(".nv-x .nv-axis g path.domain").css("stroke-width", domainxwidth); - // - var domainywidth = $("#domainywidth").val(); - $(".nv-y .nv-axis g path.domain").css("stroke-width", domainywidth); - // - var clinecolor = $("#clinecolor").val(); - $("line.nv-regLine").css("stroke", clinecolor); - // - var clinewidth = $("#clinewidth").val(); - $("line.nv-regLine").css("stroke-width", clinewidth); -} - -function srchartupdatewh() { - // - var width = $("#srwidth").val(); - $("#srscatterplot2 svg").css("width", width); - // - var height = $("#srheight").val(); - $("#srscatterplot2 svg").css("height", height); - // - window.dispatchEvent(new Event('resize')); -} - -function srchartupdatedata() { - // - var size = $("#srmarksize").val(); - var shape = $("#srmarkshape").val(); - // - d3.select('#srscatterplot2 svg').datum(nv.log(srgetdata(size, shape))).call(srchart); - nv.utils.windowResize(srchart.update); -} - -function saveassvg_srcs() { - savesvg($("#svg_srcs")[0], "Spearman Rank Correlation Scatterplot.svg"); -} - -srdrawg(); -srchartupdate(); -srchartupdatewh(); -srchartupdatedata(); - -$(".srchartupdate").change(function () { - srchartupdate(); -}); - -$(".srchartupdatewh").change(function () { - srchartupdatewh(); -}); - -$(".srchartupdatedata").change(function () { - srchartupdatedata(); -}); diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js index 92e2b13b..f2e694d8 100644 --- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js +++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js @@ -24,6 +24,7 @@ collection_click = function() { submit_click = function() { var covariates_string = ""; + var covariates_display_string = ""; $('#collections_holder').find('input[type=checkbox]:checked').each(function() { var this_dataset, this_trait; this_trait = $(this).parents('tr').find('.trait').text(); @@ -31,12 +32,15 @@ submit_click = function() { this_dataset = $(this).parents('tr').find('.dataset').text(); console.log("this_dataset is:", this_dataset); covariates_string += this_trait + ":" + this_dataset + "," + covariates_display_string += this_trait + "\n" }); // Trim the last comma covariates_string = covariates_string.substring(0, covariates_string.length - 1) + //covariates_display_string = covariates_display_string.substring(0, covariates_display_string.length - 2) console.log("COVARIATES:", covariates_string) $("input[name=covariates]").val(covariates_string) + $(".selected_covariates").val(covariates_display_string) return $.colorbox.close(); }; @@ -46,6 +50,7 @@ trait_click = function() { trait = $(this).parent().find('.trait').text(); dataset = $(this).parent().find('.dataset').text(); $("input[name=covariates]").val(trait + ":" + dataset) + $(".selected_covariates").text(trait) return $.colorbox.close(); }; diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 099d8010..df10c060 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -88,7 +88,8 @@ }; })(this)); $("#remove_covariates").click(function () { - $("input[name=covariates]").val("") + $("input[name=covariates]").val("") + $(".selected_covariates").val("") }); d3.select("#clear_compare_trait").on("click", (function(_this) { return function() { diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html index ad72052e..e7f3229b 100644 --- a/wqflask/wqflask/templates/collections/list.html +++ b/wqflask/wqflask/templates/collections/list.html @@ -26,13 +26,13 @@ {% endif %} </div> <div> - <form id="collections_form" action="/delete" method="post"> - <input type="hidden" name="uc_id" id="uc_id" value="" /> - </form> + <form id="collections_form" action="/delete" method="post"> + <input type="hidden" name="uc_id" id="uc_id" value="" /> + </form> <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button> <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button> <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button> - <button class="btn btn-danger" id="remove_collections" data-url="/collections/delete">Remove Collections</button> + <button class="btn btn-danger" id="remove_collections" data-url="/collections/delete">Remove Collections</button> </div> <br> <div id="collections_list" style="width:50%;"> @@ -51,7 +51,11 @@ <tbody> {% for uc in collections %} <tr class="collection_line"> + {% if g.user_session.user_ob %} <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td> + {% else %} + <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.name }}"></td> + {% endif %} <td align="right">{{ loop.index }} {% if g.user_session.user_ob %} <td><a class="collection_name" href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td> diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html index fb2bd55c..bb509270 100644 --- a/wqflask/wqflask/templates/corr_scatterplot.html +++ b/wqflask/wqflask/templates/corr_scatterplot.html @@ -75,72 +75,16 @@ <table class="table">
<tr>
-
- <td>Axis X Color</td>
- <td><input class="chartupdate" id="axisxcolor" type="color" value="#000000"></td>
-
- <td>Axis X Font</td>
- <td><input class="chartupdate" id="axisxfont" type="text" value="16" style="width: 44px;"> px</td>
-
- <td>Domain X Color</td>
- <td><input class="chartupdate" id="domainxcolor" type="color" value="#000000"></td>
-
- <td>Domain X Width</td>
- <td><input class="chartupdate" id="domainxwidth" type="text" value="2" style="width: 44px;"> px</td>
-
- <td>Correlation Line Color</td>
- <td><input class="chartupdate" id="clinecolor" type="color" value="#000000"></td>
-
- <td>Axis Line Color</td>
- <td><input class="chartupdate" id="axiscolor" type="color" value="#000000"></td>
-
- </tr>
- <tr>
-
- <td>Axis Y Color</td>
- <td><input class="chartupdate" id="axisycolor" type="color" value="#000000"></td>
-
- <td>Axis Y Font</td>
- <td><input class="chartupdate" id="axisyfont" type="text" value="16" style="width: 44px;"> px</td>
-
- <td>Domain Y Color</td>
- <td><input class="chartupdate" id="domainycolor" type="color" value="#000000"></td>
-
- <td>Domain Y Width</td>
- <td><input class="chartupdate" id="domainywidth" type="text" value="2" style="width: 44px;"> px</td>
-
- <td>Correlation Line Width</td>
- <td><input class="chartupdate" id="clinewidth" type="text" value="1" style="width: 44px;"> px</td>
-
- <td>Axis Line Width</td>
- <td><input class="chartupdate" id="axiswidth" type="text" value="1" style="width: 44px;"> px</td>
-
- </tr>
+ <td style="vertical-align: middle;">Width <input class="chartupdatewh" id="width" type="text" value="1000" style="width: 44px; height: 22px;"> px</td>
+ <td style="vertical-align: middle;">Height <input class="chartupdatewh" id="height" type="text" value="800" style="width: 44px; height: 22px;"> px</td>
+ </tr>
</table>
-<br>
-
-<ul class="nav nav-tabs">
- <li class="active"><a href="#tp1" data-toggle="tab">Pearson</a></li>
- <li> <a href="#tp2" data-toggle="tab">Spearman Rank</a></li>
-</ul>
-
-<div class="tab-content">
- <div class="tab-pane active" id="tp1">
-
-<br>
<table class="table">
- <tr>
-
- <td>Width</td>
- <td><input class="chartupdatewh" id="width" type="text" value="1000" style="width: 44px;"> px</td>
-
- <td>Height</td>
- <td><input class="chartupdatewh" id="height" type="text" value="800" style="width: 44px;"> px</td>
-
- <td>Size</td>
- <td>
- <select class="chartupdatedata" id="marksize" style="width: 100px;">
+ <tr>
+ <td style="vertical-align: middle;">Mark
+ <input class="chartupdate" id="markcolor" type="color" value="#8fbbda">
+ <select class="chartupdatedata" id="marksize" style="width: 44px; height: 22px;">
<option value="0">0</option>
<option value="1">1</option>
<option value="2">2</option>
@@ -152,12 +96,12 @@ <option value="8">8</option>
<option value="9">9</option>
<option value="10">10</option>
+ <option value="15">15</option>
+ <option value="20">20</option>
+ <option value="25">25</option>
+ <option value="30">30</option>
</select>
- </td>
-
- <td>Shape</td>
- <td>
- <select class="chartupdatedata" id="markshape" style="width: 100px;">
+ <select class="chartupdatedata" id="markshape" style="width: 100px; height: 22px;">
<option value="circle" selected>Circle</option>
<option value="cross">Cross</option>
<option value="triangle-up">Triangle-up</option>
@@ -166,23 +110,47 @@ <option value="square">Square</option>
</select>
</td>
-
- </tr>
+ </tr>
</table>
-<div><a id="a_svg_pcs" href="#" onclick="javascript:saveassvg_pcs();" class="btn btn-primary">Save as SVG</a></div>
+<table class="table">
+ <tr>
+ <td style="vertical-align: middle;">Label
+ <input class="chartupdate" id="labelcolor" type="color" value="#000000">
+ <input class="chartupdate" id="labelfont" type="text" value="16" style="width: 44px; height: 22px;"> px
+ </td>
+ <td style="vertical-align: middle;">Number
+ <input class="chartupdate" id="numbercolor" type="color" value="#000000">
+ <input class="chartupdate" id="numberfont" type="text" value="16" style="width: 44px; height: 22px;"> px
+ </td>
+ <td style="vertical-align: middle;">Axis
+ <input class="chartupdate" id="axiscolor" type="color" value="#000000">
+ <input class="chartupdate" id="axiswidth" type="text" value="2" style="width: 44px; height: 22px;"> px
+ </td>
+ <td style="vertical-align: middle;">Line
+ <input class="chartupdate" id="linecolor" type="color" value="#8fbbda">
+ <input class="chartupdate" id="linewidth" type="text" value="1" style="width: 44px; height: 22px;"> px
+ </td>
+ </tr>
+</table>
-<div style="width: 1000px; text-align: center;"><h2>Pearson Correlation Scatterplot</h2></div>
+<br>
-<div id="scatterplot2">
- <svg id="svg_pcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
-</div>
+<ul class="nav nav-tabs">
+ <li class="active"><a href="#tp1" data-toggle="tab">Pearson</a></li>
+ <li> <a href="#tp2" data-toggle="tab">Spearman Rank</a></li>
+</ul>
+
+<div class="tab-content">
+ <div class="tab-pane active" id="tp1">
<br>
-<div class="alert alert-info" style="width: 200px; margin-left: 80px;">
- y = {{'%0.3f' % jsdata.slope}} * x + {{'%0.3f' % jsdata.intercept}}
-</div>
+<div><a id="a_svg_pcs" href="#" onclick="javascript:saveassvg_pcs();" class="btn btn-primary">Save as SVG</a></div>
+
+<div style="width: 1000px; text-align: center;"><h2>Pearson Correlation Scatterplot</h2></div>
+
+<div id="scatterplot2"><svg id="svg_pcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg></div>
<br>
@@ -196,6 +164,13 @@ <tr><td>Intercept</td> <td>{{'%0.3f' % jsdata.intercept}}</td></tr>
<tr><td>r value</td> <td>{{'%0.3f' % jsdata.r_value}}</td></tr>
<tr><td>P value</td> <td>{% if jsdata.p_value < 0.001 %}{{'%0.3e' % jsdata.p_value}}{% else %}{{'%0.3f' % jsdata.p_value}}{% endif %}</td></tr>
+ <tr>
+ <td style="text-align: left;" colspan="2">
+ Regression Line
+ <br>
+ y = {{'%0.3f' % jsdata.slope}} * x + {{'%0.3f' % jsdata.intercept}}
+ </td>
+ </tr>
</tbody>
</table>
@@ -204,54 +179,12 @@ <div class="tab-pane" id="tp2">
<br>
-<table class="table">
- <tr>
-
- <td>Width</td>
- <td><input class="srchartupdatewh" id="srwidth" type="text" value="1000" style="width: 44px;"> px</td>
-
- <td>Height</td>
- <td><input class="srchartupdatewh" id="srheight" type="text" value="800" style="width: 44px;"> px</td>
-
- <td>Size</td>
- <td>
- <select class="srchartupdatedata" id="srmarksize" style="width: 100px;">
- <option value="0">0</option>
- <option value="1">1</option>
- <option value="2">2</option>
- <option value="3">3</option>
- <option value="4">4</option>
- <option value="5" selected>5</option>
- <option value="6">6</option>
- <option value="7">7</option>
- <option value="8">8</option>
- <option value="9">9</option>
- <option value="10">10</option>
- </select>
- </td>
-
- <td>Shape</td>
- <td>
- <select class="srchartupdatedata" id="srmarkshape" style="width: 100px;">
- <option value="circle" selected>Circle</option>
- <option value="cross">Cross</option>
- <option value="triangle-up">Triangle-up</option>
- <option value="triangle-down">Triangle-down</option>
- <option value="diamond">Diamond</option>
- <option value="square">Square</option>
- </select>
- </td>
-
- </tr>
-</table>
<div><a id="a_svg_srcs" href="#" onclick="javascript:saveassvg_srcs();" class="btn btn-primary">Save as SVG</a></div>
<div style="width: 1000px; text-align: center;"><h2>Spearman Rank Correlation Scatterplot</h2></div>
-<div id="srscatterplot2">
- <svg id="svg_srcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
-</div>
+<div id="srscatterplot2"><svg id="svg_srcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg></div>
<br>
@@ -287,5 +220,4 @@ <script language="javascript" type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot-2.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot-2_sr.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index ab793d58..d27788a8 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -61,6 +61,7 @@ <br> <button class="btn btn-default" id="short_labels">Short Labels</button> <button class="btn btn-default" id="long_labels">Long Labels</button> +{% if pca_works == "True" %} <br> <br> <h2>Factor Loadings Plot</h2> @@ -93,7 +94,7 @@ </tbody> </table> </div> - +{% endif %} {% endblock %} {% block js %} diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index fa9e3585..fb4e19a1 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -1,8 +1,7 @@ {% extends "base.html" %} {% block css %} + <link rel="stylesheet" type="text/css" href="/static/new/packages/tabulator/css/tabulator.css" /> <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> - <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" /> - <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" /> <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" /> {% endblock %} {% block content %} @@ -63,15 +62,15 @@ </div> <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1400px{% else %}800px{% endif %};"> - <table id="trait_table" class="display dataTable nowrap" style="float: left;"> + <table id="trait_table" class="display dataTable nowrap" style="font-size: 12px; float: left;"> <thead> <tr> - <th style="width: 30px;"></th> + <th></th> {% for header in target_dataset.header_fields %} {% if header == 'Year' %} <th>{{header}}</th> {% elif header == 'Max LRS' %} - <th>Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th>Max LRS</th> {% elif header == 'Max LRS Location' %} <th>{{header}}</th> {% elif header == 'Location' %} @@ -79,7 +78,7 @@ {% elif header == 'Mean' %} <th>{{header}}</th> {% elif header == 'Additive Effect' %} - <th>Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th>Additive Effect</th> {% elif header == 'Index' %} <th>{{header}}</th> {% elif header == 'N' %} @@ -91,7 +90,7 @@ {% if target_dataset.type == "ProbeSet" %} {% if corr_method == 'pearson' %} <th>Sample r</th> - <th> N</th> + <th>N</th> <th>Sample p(r)</th> <th>Lit r</th> <th>Tissue r</th> @@ -129,8 +128,8 @@ <tbody> {% for trait in correlation_results %} <tr> - <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td> - <td align="right">{{ loop.index }}</td> + <td><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td> + <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;">{{ loop.index }}</td> <td> <a href="{{ url_for('show_trait_page', trait_id = trait.name, @@ -191,13 +190,15 @@ {% block js %} <script type="text/javascript" src="/static/new/javascript/search_results.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> + <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> + <script type="text/javascript" charset="utf-8"> function getValue(x) { if (x.indexOf('input') >= 0) { @@ -213,7 +214,8 @@ } return parseFloat(x); } - + + jQuery.fn.dataTableExt.oSort['numeric-html-asc'] = function(a,b) { a = Math.abs(parseFloat($(a).text())); b = Math.abs(parseFloat($(b).text())); @@ -263,6 +265,8 @@ $(document).ready( function () { + var table_json = {{ json_results | safe }} + $('#trait_table tr').click(function(event) { if (event.target.type !== 'checkbox') { $(':checkbox', this).trigger('click'); diff --git a/wqflask/wqflask/templates/empty_collection.html b/wqflask/wqflask/templates/empty_collection.html new file mode 100644 index 00000000..d1b779ef --- /dev/null +++ b/wqflask/wqflask/templates/empty_collection.html @@ -0,0 +1,15 @@ +{% extends "base.html" %} +{% block title %}{{ tool }}{% endblock %} +{% block content %} +<!-- Start of body --> + {{ header("Error") }} + + <div class="container"> + <input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}"> + <p>You must select at least two traits to use the {{ tool }}.</p> + </div> + + +<!-- End of body --> + +{% endblock %} diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html index 0dae3503..949760b6 100644 --- a/wqflask/wqflask/templates/new_security/login_user.html +++ b/wqflask/wqflask/templates/new_security/login_user.html @@ -15,7 +15,6 @@ <h4>Don't have an account?</h4> - {% if es_server: %} <a href="/n/register" class="btn btn-primary modalize">Create a new account</a> {% else: %} @@ -88,10 +87,17 @@ </form> {% else: %} <div class="alert alert-warning"> - <p>You cannot login at this moment using your GeneNetwork account.<br /> + <p>You cannot login at this moment using your GeneNetwork account (the authentication service is down).<br /> Please try again later.</p> </div> {% endif %} + {% if not es_server and not external_login: %} + <hr> + <div class="alert alert-warning"> + Note: it is safe to use GeneNetwork without a login. Login is only required for keeping track of + collections and getting access to some types of restricted data. + </div> + {% endif %} </div> </div> diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index c5f815ce..ef233333 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -1,9 +1,10 @@ <div> + <div class="col-xs-7"> <div style="padding: 20px" class="form-horizontal"> <div class="form-group"> - <label for="corr_type" class="col-xs-1 control-label">Method</label> - <div class="col-xs-2 controls"> + <label for="corr_type" class="col-xs-2 control-label">Method</label> + <div class="col-xs-3 controls"> <select name="corr_type" class="form-control"> <option value="sample">Sample r</option> <option value="lit">Literature r</option> @@ -13,8 +14,8 @@ </div> <div class="form-group"> - <label for="corr_dataset" class="col-xs-1 control-label">Database</label> - <div class="col-xs-6 controls"> + <label for="corr_dataset" class="col-xs-2 control-label">Database</label> + <div class="col-xs-10 controls"> <select name="corr_dataset" class="form-control"> {% for tissue in corr_tools.dataset_menu %} {% if tissue.tissue %} @@ -37,8 +38,8 @@ </div> <div class="form-group"> - <label for="corr_return_results" class="col-xs-1 control-label">Return</label> - <div class="col-xs-2 controls"> + <label for="corr_return_results" class="col-xs-2 control-label">Return</label> + <div class="col-xs-3 controls"> <select name="corr_return_results" class="form-control"> {% for return_result in corr_tools.return_results_menu %} <option value="{{ return_result }}" @@ -53,8 +54,8 @@ </div> <div class="form-group"> - <label for="corr_samples_group" class="col-xs-1 control-label">Samples</label> - <div class="col-xs-2 controls"> + <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label> + <div class="col-xs-3 controls"> <select name="corr_samples_group" class="form-control"> {% for group, pretty_group in sample_group_types.items() %} <option value="{{ group }}">{{ pretty_group }}</option> @@ -64,8 +65,8 @@ </div> <div id="corr_sample_method" class="form-group"> - <label for="corr_sample_method" class="col-xs-1 control-label">Type</label> - <div class="col-xs-2 controls"> + <label for="corr_sample_method" class="col-xs-2 control-label">Type</label> + <div class="col-xs-3 controls"> <select name="corr_sample_method" class="form-control"> <option value="pearson">Pearson</option> <option value="spearman">Spearman Rank</option> @@ -73,14 +74,14 @@ </div> </div> <div class="form-group"> - <label class="col-xs-1 control-label">Min Expr</label> - <div class="col-xs-2 controls"> + <label class="col-xs-2 control-label">Min Expr</label> + <div class="col-xs-3 controls"> <input name="min_expr" value="" type="text" class="form-control" style="width: 50px;"> </div> </div> <div class="form-group"> - <label class="col-xs-1 control-label">Location</label> - <div class="col-xs-4 controls"> + <label class="col-xs-2 control-label">Location</label> + <div class="col-xs-5 controls"> <span> Chr: <input name="loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;"> Mb: <input name="min_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> to <input name="max_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> @@ -89,8 +90,8 @@ </div> </div> <div class="form-group"> - <label class="col-xs-1 control-label">Range</label> - <div class="col-xs-4 controls"> + <label class="col-xs-2 control-label">Range</label> + <div class="col-xs-5 controls"> <input name="p_range_lower" value="" type="hidden"> <input name="p_range_upper" value="" type="hidden"> <span style="display: inline;"> @@ -103,48 +104,45 @@ </div> <div class="form-group"> - <label for="corr_sample_method" class="col-xs-1 control-label"></label> - <div class="col-xs-4 controls"> + <label for="corr_sample_method" class="col-xs-2 control-label"></label> + <div class="col-xs-3 controls"> <button class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation"> <i class="icon-ok-circle icon-white"></i> Compute </button> </div> </div> - - <div class="form-group"> - <label for="descriptions" class="col-xs-1 control-label"></label> - <div class="col-xs-6 controls"> - <span id="sample_r_desc" class="correlation_desc fs12"> - The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a> - is computed - between trait data and any - other traits in the sample database selected above. Use - <a href="http://www.genenetwork.org/glossary.html#Correlations">Spearman - Rank</a> - when the sample size is small (<20) or when there are influential outliers. - </span> - <span id="lit_r_desc" style="display: none;" class="correlation_desc fs12"> - The <a href="http://genenetwork.org/correlationAnnotation.html#literatureCorr">Literature Correlation</a> - (Lit r) between - this gene and all other genes is computed<br> - using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html"> - Semantic Gene Organizer</a> - and human, rat, and mouse data from PubMed. - Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br> - <a href="http://genenetwork.org/glossary.html#Literature">More on using Lit r</a> - </span> - <span id="tissue_r_desc" style="display: none;" class="correlation_desc fs12"> - The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a> - (Tissue r) - estimates the similarity of expression of two genes - or transcripts across different cells, tissues, or organs - (<a href="http://genenetwork.org/correlationAnnotation.html#tissueCorr">glossary</a>). - Tissue correlations - are generated by analyzing expression in multiple samples usually taken from single cases.<br> - <strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been - computed for all pairs of genes using data from mouse samples.<br> - </span> - </div> - </div> </div> + </div> + <div class="col-xs-5"> + <span id="sample_r_desc" class="correlation_desc fs12"> + The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a> + is computed + between trait data and any + other traits in the sample database selected above. Use + <a href="http://www.genenetwork.org/glossary.html#Correlations">Spearman + Rank</a> + when the sample size is small (<20) or when there are influential outliers. + </span> + <span id="lit_r_desc" style="display: none;" class="correlation_desc fs12"> + The <a href="http://genenetwork.org/correlationAnnotation.html#literatureCorr">Literature Correlation</a> + (Lit r) between + this gene and all other genes is computed<br> + using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html"> + Semantic Gene Organizer</a> + and human, rat, and mouse data from PubMed. + Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br> + <a href="http://genenetwork.org/glossary.html#Literature">More on using Lit r</a> + </span> + <span id="tissue_r_desc" style="display: none;" class="correlation_desc fs12"> + The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a> + (Tissue r) + estimates the similarity of expression of two genes + or transcripts across different cells, tissues, or organs + (<a href="http://genenetwork.org/correlationAnnotation.html#tissueCorr">glossary</a>). + Tissue correlations + are generated by analyzing expression in multiple samples usually taken from single cases.<br> + <strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been + computed for all pairs of genes using data from mouse samples.<br> + </span> + </div> </div>
\ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index dcec2b9e..03590c2c 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -1,6 +1,6 @@ <div> - {% if (use_pylmm_rqtl and dataset.group.species != "human") or use_plink_gemma %} - <div class="col-xs-4"> + {% if dataset.group.mapping_names|length > 0 %} + <div class="col-xs-5"> <div class="tabbable"> <!-- Only required for left/right tabs --> <ul class="nav nav-pills"> @@ -38,11 +38,11 @@ {# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #} {% if dataset.group.mapping_id == "1" %} <div class="tab-pane active" id="gemma"> - <div style="padding-top: 10px;" class="form-horizontal"> + <div style="padding-top: 20px;" class="form-horizontal"> {% if genofiles and genofiles|length>0 %} <div class="mapping_method_fields form-group"> - <label for="genofiles" class="col-xs-3 control-label">Genotypes</label> - <div style="margin-left: 20px;" class="col-xs-8 controls"> + <label for="genofiles" style="text-align: right;" class="col-xs-3 control-label">Genotypes</label> + <div style="margin-left:20px;" class="col-xs-4 controls"> <select id="genofile_gemma" class="form-control"> {% for item in genofiles %} <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> @@ -52,50 +52,72 @@ </div> {% endif %} <div class="mapping_method_fields form-group"> - <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label> - <div style="margin-left: 20px;" class="col-xs-3 controls"> + <label for="maf_gemma" style="text-align: right;" class="col-xs-3 control-label">MAF</label> + <div style="margin-left:20px;" class="col-xs-4 controls"> <input name="maf_gemma" value="0.01" type="text" class="form-control"> </div> </div> <div class="mapping_method_fields form-group"> - <label class="col-xs-4 control-label">Use LOCO</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> + <label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label> + <div style="margin-left:20px;" class="col-xs-6 controls"> <label class="radio-inline"> - <input type="radio" name="use_loco" value="True"> + <input type="radio" name="use_loco" value="True" checked=""> Yes </label> <label class="radio-inline"> - <input type="radio" name="use_loco" value="False" checked=""> + <input type="radio" name="use_loco" value="False"> No </label> </div> </div> + <!-- </div> <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal"> + --> <div class="mapping_method_fields form-group"> - <button type="button" id="select_covariates" class="btn btn-default"> - Select Covariates - </button> - <button type="button" id="remove_covariates" class="btn btn-default"> - Remove Covariates + <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label> + <div style="margin-left:20px;" class="col-xs-7"> + {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %} + No collections available. Please add traits to a collection to use them as covariates. + {% elif g.cookie_session.display_num_collections() == "" %} + No collections available. Please add traits to a collection to use them as covariates. + {% else %} + <div style="margin-bottom: 10px;" class="btn-group" role="group"> + <button type="button" id="select_covariates" class="btn btn-default">Select</button> + <button type="button" id="remove_covariates" class="btn btn-default">Remove</button> + </div> + <textarea rows="3" cols="20" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none;" class="selected_covariates"></textarea> + {% endif %} + </div> + </div> + <div class="mapping_method_fields form-group"> + <label class="col-xs-3 control-label"></label> + <div style="margin-left:20px;" class="col-xs-6"> + <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression"> + Compute </button> + </div> </div> </div> - +<!-- <div class="form-group"> <div class="col-xs-4 controls"> + <label class="col-xs-2 control-label"></label> + <div class="col-xs-4"> <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression"> Compute </button> + </div> </div> </div> +--> </div> <div class="tab-pane" id="interval_mapping"> <div style="margin-top: 20px" class="form-horizontal"> {% if genofiles and genofiles|length>0 %} <div class="mapping_method_fields form-group"> - <label for="genofiles" class="col-xs-3 control-label">Genotypes</label> - <div style="margin-left: 20px;" class="col-xs-8 controls"> + <label style="text-align: right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label> + <div style="margin-left:20px;" class="col-xs-4 controls"> <select id="genofile_reaper" class="form-control"> {% for item in genofiles %} <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> @@ -105,20 +127,20 @@ </div> {% endif %} <div class="mapping_method_fields form-group"> - <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> + <label style="text-align: right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label> + <div style="margin-left:20px;" class="col-xs-4 controls"> <input name="num_perm_reaper" value="2000" type="text" class="form-control"> </div> </div> <div class="mapping_method_fields form-group"> - <label for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> + <label style="text-align: right;" for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label> + <div style="margin-left:20px;" class="col-xs-4 controls"> <input name="num_bootstrap" value="2000" type="text" class="form-control"> </div> </div> <div class="mapping_method_fields form-group"> - <label for="control_for" class="col-xs-3 control-label">Control for</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> + <label style="text-align: right;" for="control_for" class="col-xs-3 control-label">Control for</label> + <div style="margin-left:20px;" class="col-xs-6 controls"> {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} <input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" /> {% else %} @@ -162,8 +184,8 @@ <div class="mapping_method_fields form-group"> - <label style="text-align:left;" class="col-xs-3 control-label">Marker<br>Regression</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> + <label style="text-align: right;" class="col-xs-3 control-label">Marker<br>Regression</label> + <div style="margin-left:20px;" class="col-xs-6 controls"> <label class="radio-inline"> <input type="radio" name="manhattan_plot_reaper" value="True"> Yes @@ -174,11 +196,12 @@ </label> </div> </div> - <div class="form-group"> - <div style="padding-left:15px;" class="controls"> - <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping"> - <i class="icon-ok-circle icon-white"></i> Compute - </button> + <div class="mapping_method_fields form-group"> + <label class="col-xs-3 control-label"></label> + <div style="margin-left:20px;" class="col-xs-6"> + <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping"> + Compute + </button> </div> </div> <!--<div id="alert_placeholder"></div>--> @@ -189,8 +212,8 @@ <div style="margin-top: 20px" class="form-horizontal"> {% if genofiles and genofiles|length>0 %} <div class="mapping_method_fields form-group"> - <label for="genofiles" class="col-xs-3 control-label">Genotypes</label> - <div style="margin-left: 20px;" class="col-xs-8 controls"> + <label style="text-align:right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label> + <div style="margin-left:20px;" class="col-xs-4 controls"> <select id="genofile_rqtl_geno" class="form-control"> {% for item in genofiles %} <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> @@ -200,17 +223,14 @@ </div> {% endif %} <div class="mapping_method_fields form-group"> - <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> - <input name="num_perm_rqtl_geno" value="" type="text" class="form-control"> + <label style="text-align:right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label> + <div style="margin-left:20px;" class="col-xs-4 controls"> + <input name="num_perm_rqtl_geno" value="2000" type="text" class="form-control"> </div> </div> - <div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;"> - Please be aware that permutations can take a very long time (~20 minutes for 500 permutations) - </div> <div class="mapping_method_fields form-group"> - <label for="control_for" class="col-xs-3 control-label">Control for</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> + <label style="text-align:right;" for="control_for" class="col-xs-3 control-label">Control for</label> + <div style="margin-left:20px;" class="col-xs-6 controls"> {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} <input name="control_rqtl_geno" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" /> {% else %} @@ -228,8 +248,8 @@ </div> <div class="mapping_method_fields form-group"> - <label for="mapmethod_rqtl_geno" style="text-align:left;" class="col-xs-3 control-label">Method</label> - <div class="col-xs-4 controls"> + <label style="text-align:right;" for="mapmethod_rqtl_geno" class="col-xs-3 control-label">Method</label> + <div style="margin-left:20px;" class="col-xs-4 controls"> <select name="mapmethod_rqtl_geno" class="form-control"> <option value="em">em</option> <option value="imp">imp</option> @@ -243,8 +263,8 @@ </div> <div class="mapping_method_fields form-group"> - <label for="mapmodel_rqtl_geno" style="text-align:left;" class="col-xs-3 control-label">Model</label> - <div class="col-xs-4 controls"> + <label style="text-align:right;" for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label> + <div style="margin-left:20px;" class="col-xs-4 controls"> <select name="mapmodel_rqtl_geno" class="form-control"> <option value="normal">normal</option> <!--<option value="binary">binary</option> @@ -269,8 +289,8 @@ </div> --> <div class="mapping_method_fields form-group"> - <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label> - <div class="col-xs-12 controls"> + <label style="text-align:right;" class="col-xs-3 control-label">Marker<br>Regression</label> + <div style="margin-left:20px;" class="col-xs-6 controls"> <label class="radio-inline"> <input type="radio" name="manhattan_plot_rqtl" value="True"> Yes @@ -282,11 +302,12 @@ </div> </div> - <div class="form-group"> - <div style="padding-left:15px;" class="controls"> - <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression"> - <i class="icon-ok-circle icon-white"></i> Compute - </button> + <div class="mapping_method_fields form-group"> + <label class="col-xs-3 control-label"></label> + <div style="margin-left:20px;" class="col-xs-6"> + <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping"> + Compute + </button> </div> </div> </div> @@ -295,8 +316,8 @@ <div style="margin-top: 20px" class="form-horizontal"> {% if genofiles and genofiles|length>0 %} <div class="mapping_method_fields form-group"> - <label for="genofiles" class="col-xs-3 control-label">Genotypes</label> - <div style="margin-left: 20px;" class="col-xs-8 controls"> + <label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label> + <div style="margin-left: 20px;" class="col-xs-4 controls"> <select id="genofile_pylmm" class="form-control"> {% for item in genofiles %} <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> @@ -305,44 +326,12 @@ </div> </div> {% endif %} -<!-- <div class="mapping_method_fields form-group"> - <label for="control_for" class="col-xs-3 control-label">Control for</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> - {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} - <input name="control_pylmm" value="{{ nearest_marker }}" type="text" /> - {% else %} - <input name="control_pylmm" value="" type="text" /> - {% endif %} - <label class="radio-inline"> - <input type="radio" name="do_control_pylmm" value="true"> - Yes - </label> - <label class="radio-inline"> - <input type="radio" name="do_control_pylmm" value="false" checked=""> - No - </label> - </div> - </div> - <div class="mapping_method_fields form-group"> - <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label> - <div class="col-xs-12 controls"> - <label class="radio-inline"> - <input type="radio" name="manhattan_plot_pylmm" value="True"> - Yes - </label> - <label class="radio-inline"> - <input type="radio" name="manhattan_plot_pylmm" value="False" checked=""> - No - </label> - </div> - </div> ---> - <div class="form-group"> - <div style="padding-left:15px;" class="controls"> - <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression"> - <i class="icon-ok-circle icon-white"></i> Compute - </button> + <label class="col-xs-3 control-label"></label> + <div style="margin-left:20px;" class="col-xs-6"> + <button id="pylmm_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping"> + Compute + </button> </div> </div> </div> @@ -354,8 +343,8 @@ <div style="padding-top: 10px;" class="form-horizontal"> {% if genofiles and genofiles|length>0 %} <div class="mapping_method_fields form-group"> - <label for="genofiles" class="col-xs-3 control-label">Genotypes</label> - <div style="margin-left: 20px;" class="col-xs-8 controls"> + <label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label> + <div style="margin-left: 20px;" class="col-xs-4 controls"> <select id="genofile_gemma" class="form-control"> {% for item in genofiles %} <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> @@ -365,29 +354,34 @@ </div> {% endif %} <div class="mapping_method_fields form-group"> - <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label> - <div style="margin-left: 20px;" class="col-xs-3 controls"> + <label style="text-align:right;" class="col-xs-3 control-label">MAF</label> + <div style="margin-left: 20px;" class="col-xs-4 controls"> <input name="maf_gemma" value="0.01" type="text" class="form-control"> </div> </div> - </div> - - <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal"> <div class="mapping_method_fields form-group"> - <button type="button" id="select_covariates" class="btn btn-default"> - Select Covariates - </button> - <button type="button" id="remove_covariates" class="btn btn-default"> - Remove Covariates - </button> + <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label> + <div style="margin-left:20px;" class="col-xs-7"> + {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %} + No collections available. Please add traits to a collection to use them as covariates. + {% elif g.cookie_session.display_num_collections() == "" %} + No collections available. Please add traits to a collection to use them as covariates. + {% else %} + <div style="margin-bottom: 10px;" class="btn-group" role="group"> + <button type="button" id="select_covariates" class="btn btn-default">Select</button> + <button type="button" id="remove_covariates" class="btn btn-default">Remove</button> + </div> + <textarea rows="3" cols="20" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none;" class="selected_covariates"></textarea> + {% endif %} + </div> </div> - </div> - - <div class="form-group"> - <div class="col-xs-4 controls"> + <div class="mapping_method_fields form-group"> + <label class="col-xs-3 control-label"></label> + <div style="margin-left:20px;" class="col-xs-6"> <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression"> Compute </button> + </div> </div> </div> </div> @@ -395,16 +389,16 @@ <div class="tab-pane" id="plink"> <div style="padding: 20px" class="form-horizontal"> <div class="mapping_method_fields form-group"> - <label for="maf_plink" class="col-xs-3 control-label">Minor allele threshold</label> - <div style="margin-left: 20px;" class="col-xs-3 controls"> + <label style="text-align: right;" class="col-xs-3 control-label">MAF</label> + <div style="margin-left: 20px;" class="col-xs-4 controls"> <input name="maf_plink" value="0.01" type="text" class="form-control"> </div> </div> </div> <div class="form-group"> - <label for="plink_compute" class="col-xs-1 control-label"></label> - <div style="margin-left:20px;" class="col-xs-4 controls"> + <label style="text-align: right;" class="col-xs-3 control-label"></label> + <div style="margin-left:20px;" class="col-xs-6 controls"> <button id="plink_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression"> Compute </button> @@ -416,25 +410,29 @@ </div> </div> </div> - <div class="col-xs-6"> + <div class="col-xs-5"> {% if dataset.group.mapping_id == "1" %} <dl> + <dt>GEMMA</dt> + <dd>GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).</dd> <dt>Interval Mapping</dt> <dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.</dd> - <dt>pyLMM</dt> - <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd> <dt>R/qtl</dt> <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd> + <dt>pyLMM</dt> + <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd> </dl> {% else %} <dl> + {% if mapping_method == "GEMMA" %} <dt>GEMMA</dt> <dd> GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).<br> - Note: There currently exists an issue where GEMMA can't be run on traits from the same group simultaneously. If you receive an error, please wait a few minutes and try again. </dd> + {% elif mapping_method == "PLINK" %} <dt>PLINK</dt> <dd>PLINK is a free, open-source whole genome association analysis toolset.</dd> + {% endif %} </dl> {% endif %} </div> diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index c344ea27..ebca4807 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -55,7 +55,10 @@ logger = getLogger(__name__) from base.data_set import create_datasets_list import requests -from utility.elasticsearch_tools import get_elasticsearch_connection, get_user_by_unique_column, save_user +from utility.elasticsearch_tools import get_elasticsearch_connection, get_user_by_unique_column, get_item_by_unique_column, save_user, es_save_data + +from smtplib import SMTP +from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD THREE_DAYS = 60 * 60 * 24 * 3 #THREE_DAYS = 45 @@ -386,6 +389,7 @@ class ForgotPasswordEmail(VerificationEmail): "email_address": toaddr, "timestamp": timestamp() } + es = get_elasticsearch_connection() es_save_data(es, self.key_prefix, "local", data, verification_code) subject = self.subject @@ -437,12 +441,12 @@ def verify_email(): @app.route("/n/password_reset", methods=['GET']) def password_reset(): logger.debug("in password_reset request.url is:", request.url) - # We do this mainly just to assert that it's in proper form for displaying next page # Really not necessary but doesn't hurt # user_encode = DecodeUser(ForgotPasswordEmail.key_prefix).reencode_standalone() verification_code = request.args.get('code') hmac = request.args.get('hm') + es = get_elasticsearch_connection() if verification_code: code_details = get_item_by_unique_column( es @@ -466,7 +470,6 @@ def password_reset(): @app.route("/n/password_reset_step2", methods=('POST',)) def password_reset_step2(): - from utility.elasticsearch_tools import es logger.debug("in password_reset request.url is:", request.url) errors = [] @@ -626,13 +629,12 @@ class LoginUser(object): logger.debug("in login params are:", params) es = get_elasticsearch_connection() if not params: - from utility.tools import GITHUB_AUTH_URL, ORCID_AUTH_URL - external_login = None - if GITHUB_AUTH_URL or ORCID_AUTH_URL: - external_login={ - "github": GITHUB_AUTH_URL, - "orcid": ORCID_AUTH_URL - } + from utility.tools import GITHUB_AUTH_URL, GITHUB_CLIENT_ID, ORCID_AUTH_URL, ORCID_CLIENT_ID + external_login = {} + if GITHUB_AUTH_URL and GITHUB_CLIENT_ID != 'UNKNOWN': + external_login["github"] = GITHUB_AUTH_URL + if ORCID_AUTH_URL and ORCID_CLIENT_ID != 'UNKNOWN': + external_login["orcid"] = ORCID_AUTH_URL assert(es is not None) return render_template( "new_security/login_user.html" @@ -749,6 +751,7 @@ def forgot_password(): def forgot_password_submit(): params = request.form email_address = params['email_address'] + es = get_elasticsearch_connection() user_details = get_user_by_unique_column(es, "email_address", email_address) if user_details: ForgotPasswordEmail(user_details["email_address"]) @@ -915,15 +918,26 @@ app.jinja_env.globals.update(url_for_hmac=url_for_hmac, # Redis.rpush("mail_queue", msg) def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"): - from smtplib import SMTP - from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD - server = SMTP(SMTP_CONNECT) - server.starttls() - server.login(SMTP_USERNAME, SMTP_PASSWORD) - server.sendmail(fromaddr, toaddr, msg) - server.quit() - - + """Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not + 'UNKNOWN' TLS is used + + """ + if SMTP_USERNAME == 'UNKNOWN': + logger.debug("SMTP: connecting with host "+SMTP_CONNECT) + server = SMTP(SMTP_CONNECT) + server.sendmail(fromaddr, toaddr, msg) + else: + logger.debug("SMTP: connecting TLS with host "+SMTP_CONNECT) + server = SMTP(SMTP_CONNECT) + server.starttls() + logger.debug("SMTP: login with user "+SMTP_USERNAME) + server.login(SMTP_USERNAME, SMTP_PASSWORD) + logger.debug("SMTP: "+fromaddr) + logger.debug("SMTP: "+toaddr) + logger.debug("SMTP: "+msg) + server.sendmail(fromaddr, toaddr, msg) + server.quit() + logger.info("Successfully sent email to "+toaddr) class GroupsManager(object): def __init__(self, kw): diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 4e81c29c..a65924d8 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -123,7 +123,7 @@ def handle_bad_request(e): @app.route("/") def index_page(): logger.info("Sending index_page") - logger.error(request.url) + logger.info(request.url) params = request.args if 'import_collections' in params: import_collections = params['import_collections'] @@ -141,7 +141,7 @@ def index_page(): def tmp_page(img_path): logger.info("In tmp_page") logger.info("img_path:", img_path) - logger.error(request.url) + logger.info(request.url) initial_start_vars = request.form logger.info("initial_start_vars:", initial_start_vars) imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb') @@ -174,7 +174,7 @@ def twitter(filename): @app.route("/search", methods=('GET',)) def search_page(): logger.info("in search_page") - logger.error(request.url) + logger.info(request.url) if 'info_database' in request.args: logger.info("Going to sharing_info_page") template_vars = sharing_info_page() @@ -199,21 +199,22 @@ def search_page(): logger.info("request.args is", request.args) the_search = search_results.SearchResultPage(request.args) result = the_search.__dict__ + valid_search = result['search_term_exists'] logger.debugf("result", result) - if USE_REDIS: + if USE_REDIS and valid_search: Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) Redis.expire(key, 60*60) - if result['search_term_exists']: + if valid_search: return render_template("search_result_page.html", **result) else: return render_template("search_error.html") @app.route("/gsearch", methods=('GET',)) def gsearchact(): - logger.error(request.url) + logger.info(request.url) result = gsearch.GSearch(request.args).__dict__ type = request.args['type'] if type == "gene": @@ -224,7 +225,7 @@ def gsearchact(): @app.route("/gsearch_updating", methods=('POST',)) def gsearch_updating(): logger.info("REQUEST ARGS:", request.values) - logger.error(request.url) + logger.info(request.url) result = update_search_results.GSearch(request.args).__dict__ return result['results'] # type = request.args['type'] @@ -235,31 +236,31 @@ def gsearch_updating(): @app.route("/docedit") def docedit(): - logger.error(request.url) + logger.info(request.url) doc = docs.Docs(request.args['entry']) return render_template("docedit.html", **doc.__dict__) @app.route('/generated/<filename>') def generated_file(filename): - logger.error(request.url) + logger.info(request.url) return send_from_directory(GENERATED_IMAGE_DIR,filename) @app.route("/help") def help(): - logger.error(request.url) + logger.info(request.url) doc = docs.Docs("help") return render_template("docs.html", **doc.__dict__) @app.route("/wgcna_setup", methods=('POST',)) def wcgna_setup(): logger.info("In wgcna, request.form is:", request.form) # We are going to get additional user input for the analysis - logger.error(request.url) + logger.info(request.url) return render_template("wgcna_setup.html", **request.form) # Display them using the template @app.route("/wgcna_results", methods=('POST',)) def wcgna_results(): logger.info("In wgcna, request.form is:", request.form) - logger.error(request.url) + logger.info(request.url) wgcna = wgcna_analysis.WGCNA() # Start R, load the package and pointers and create the analysis wgcnaA = wgcna.run_analysis(request.form) # Start the analysis, a wgcnaA object should be a separate long running thread result = wgcna.process_results(wgcnaA) # After the analysis is finished store the result @@ -268,13 +269,13 @@ def wcgna_results(): @app.route("/ctl_setup", methods=('POST',)) def ctl_setup(): logger.info("In ctl, request.form is:", request.form) # We are going to get additional user input for the analysis - logger.error(request.url) + logger.info(request.url) return render_template("ctl_setup.html", **request.form) # Display them using the template @app.route("/ctl_results", methods=('POST',)) def ctl_results(): logger.info("In ctl, request.form is:", request.form) - logger.error(request.url) + logger.info(request.url) ctl = ctl_analysis.CTL() # Start R, load the package and pointers and create the analysis ctlA = ctl.run_analysis(request.form) # Start the analysis, a ctlA object should be a separate long running thread result = ctl.process_results(ctlA) # After the analysis is finished store the result @@ -313,13 +314,13 @@ def environments(): @app.route("/submit_trait") def submit_trait_form(): - logger.error(request.url) + logger.info(request.url) species_and_groups = get_species_groups() return render_template("submit_trait.html", **{'species_and_groups' : species_and_groups, 'gn_server_url' : GN_SERVER_URL, 'version' : GN_VERSION}) @app.route("/create_temp_trait", methods=('POST',)) def create_temp_trait(): - logger.error(request.url) + logger.info(request.url) print("REQUEST.FORM:", request.form) #template_vars = submit_trait.SubmitTrait(request.form) @@ -332,7 +333,7 @@ def export_trait_excel(): """Excel file consisting of the sample data from the trait data and analysis page""" logger.info("In export_trait_excel") logger.info("request.form:", request.form) - logger.error(request.url) + logger.info(request.url) sample_data = export_trait_data.export_sample_table(request.form) logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) @@ -358,7 +359,7 @@ def export_trait_csv(): """CSV file consisting of the sample data from the trait data and analysis page""" logger.info("In export_trait_csv") logger.info("request.form:", request.form) - logger.error(request.url) + logger.info(request.url) sample_data = export_trait_data.export_sample_table(request.form) logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) @@ -379,7 +380,7 @@ def export_traits_csv(): """CSV file consisting of the traits from the search result page""" logger.info("In export_traits_csv") logger.info("request.form:", request.form) - logger.error(request.url) + logger.info(request.url) csv_data = export_traits.export_search_results_csv(request.form) return Response(csv_data, @@ -389,7 +390,7 @@ def export_traits_csv(): @app.route('/export_perm_data', methods=('POST',)) def export_perm_data(): """CSV file consisting of the permutation data for the mapping results""" - logger.error(request.url) + logger.info(request.url) num_perm = float(request.form['num_perm']) perm_data = json.loads(request.form['perm_results']) @@ -412,7 +413,7 @@ def export_perm_data(): @app.route("/show_temp_trait", methods=('POST',)) def show_temp_trait_page(): - logger.error(request.url) + logger.info(request.url) template_vars = show_trait.ShowTrait(request.form) #logger.info("js_data before dump:", template_vars.js_data) template_vars.js_data = json.dumps(template_vars.js_data, @@ -427,7 +428,7 @@ def show_temp_trait_page(): @app.route("/show_trait") def show_trait_page(): - logger.error(request.url) + logger.info(request.url) template_vars = show_trait.ShowTrait(request.args) #logger.info("js_data before dump:", template_vars.js_data) template_vars.js_data = json.dumps(template_vars.js_data, @@ -443,7 +444,7 @@ def show_trait_page(): @app.route("/heatmap", methods=('POST',)) def heatmap_page(): logger.info("In heatmap, request.form is:", pf(request.form)) - logger.error(request.url) + logger.info(request.url) start_vars = request.form temp_uuid = uuid.uuid4() @@ -493,7 +494,7 @@ def mapping_results_container_page(): @app.route("/loading", methods=('POST',)) def loading_page(): - logger.error(request.url) + logger.info(request.url) initial_start_vars = request.form logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items()) #temp_uuid = initial_start_vars['temp_uuid'] @@ -552,7 +553,7 @@ def loading_page(): def marker_regression_page(): initial_start_vars = request.form logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items()) - logger.error(request.url) + logger.info(request.url) temp_uuid = initial_start_vars['temp_uuid'] wanted = ( 'trait_id', @@ -582,7 +583,7 @@ def marker_regression_page(): 'control_marker', 'control_marker_db', 'do_control', - 'genofile', + 'genofile_string', 'pair_scan', 'startMb', 'endMb', @@ -678,7 +679,7 @@ def marker_regression_page(): @app.route("/export_mapping_results", methods = ('POST',)) def export_mapping_results(): logger.info("request.form:", request.form) - logger.error(request.url) + logger.info(request.url) file_path = request.form.get("results_path") results_csv = open(file_path, "r").read() response = Response(results_csv, @@ -691,7 +692,7 @@ def export_mapping_results(): @app.route("/export", methods = ('POST',)) def export(): logger.info("request.form:", request.form) - logger.error(request.url) + logger.info(request.url) svg_xml = request.form.get("data", "Invalid data") filename = request.form.get("filename", "manhattan_plot_snp") response = Response(svg_xml, mimetype="image/svg+xml") @@ -702,7 +703,7 @@ def export(): def export_pdf(): import cairosvg logger.info("request.form:", request.form) - logger.error(request.url) + logger.info(request.url) svg_xml = request.form.get("data", "Invalid data") logger.info("svg_xml:", svg_xml) filename = request.form.get("filename", "interval_map_pdf") @@ -715,7 +716,7 @@ def export_pdf(): @app.route("/network_graph", methods=('POST',)) def network_graph_page(): logger.info("In network_graph, request.form is:", pf(request.form)) - logger.error(request.url) + logger.info(request.url) start_vars = request.form traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] if traits[0] != "": @@ -731,7 +732,7 @@ def network_graph_page(): @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): logger.info("In corr_compute, request.form is:", pf(request.form)) - logger.error(request.url) + logger.info(request.url) #fd = webqtlFormData.webqtlFormData(request.form) template_vars = show_corr_results.CorrelationResults(request.form) return render_template("correlation_page.html", **template_vars.__dict__) @@ -739,11 +740,11 @@ def corr_compute_page(): @app.route("/corr_matrix", methods=('POST',)) def corr_matrix_page(): logger.info("In corr_matrix, request.form is:", pf(request.form)) - logger.error(request.url) + logger.info(request.url) start_vars = request.form traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] - if traits[0] != "": + if len(traits) > 1: template_vars = show_corr_matrix.CorrelationMatrix(start_vars) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, @@ -755,7 +756,7 @@ def corr_matrix_page(): @app.route("/corr_scatter_plot") def corr_scatter_plot_page(): - logger.error(request.url) + logger.info(request.url) template_vars = corr_scatter_plot.CorrScatterPlot(request.args) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, @@ -764,7 +765,7 @@ def corr_scatter_plot_page(): @app.route("/submit_bnw", methods=('POST',)) def submit_bnw(): - logger.error(request.url) + logger.info(request.url) template_vars = get_bnw_input(request.form) return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) @@ -772,7 +773,7 @@ def submit_bnw(): def sharing_info_page(): """Info page displayed when the user clicks the "Info" button next to the dataset selection""" logger.info("In sharing_info_page") - logger.error(request.url) + logger.info(request.url) fd = webqtlFormData.webqtlFormData(request.args) template_vars = SharingInfoPage.SharingInfoPage(fd) return template_vars @@ -780,7 +781,7 @@ def sharing_info_page(): # Take this out or secure it before putting into production @app.route("/get_temp_data") def get_temp_data(): - logger.error(request.url) + logger.info(request.url) temp_uuid = request.args['key'] return flask.jsonify(temp_data.TempData(temp_uuid).get_all()) |