def create_role(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
name = util.restore_text(params.get('name', ''))
description = util.restore_text(params.get('description', ''))
in_users = util.listify(params.get('in_users', []))
out_users = util.listify(params.get('out_users', []))
in_groups = util.listify(params.get('in_groups', []))
out_groups = util.listify(params.get('out_groups', []))
create_group_for_role = params.get('create_group_for_role', '')
create_group_for_role_checked = CheckboxField.is_checked(create_group_for_role)
ok = True
if params.get('create_role_button', False):
if not name or not description:
message = "Enter a valid name and a description."
status = 'error'
ok = False
elif trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.name == name).first():
message = "Role names must be unique and a role with that name already exists, so choose another name."
status = 'error'
ok = False
else:
# Create the role
role, num_in_groups = trans.app.security_agent.create_role(
name, description, in_users, in_groups, create_group_for_role=create_group_for_role_checked)
message = "Role '%s' has been created with %d associated users and %d associated groups. " \
% (role.name, len(in_users), num_in_groups)
if create_group_for_role_checked:
message += 'One of the groups associated with this role is the newly created group with the same name.'
trans.response.send_redirect(web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='done'))
if ok:
for user in trans.sa_session.query(trans.app.model.User) \
.filter(trans.app.model.User.table.c.deleted == false()) \
.order_by(trans.app.model.User.table.c.email):
out_users.append((user.id, user.email))
for group in trans.sa_session.query(trans.app.model.Group) \
.filter(trans.app.model.Group.table.c.deleted == false()) \
.order_by(trans.app.model.Group.table.c.name):
out_groups.append((group.id, group.name))
return trans.fill_template('/webapps/tool_shed/admin/dataset_security/role/role_create.mako',
name=name,
description=description,
in_users=in_users,
out_users=out_users,
in_groups=in_groups,
out_groups=out_groups,
create_group_for_role_checked=create_group_for_role_checked,
message=message,
status=status)
def edit_review( self, trans, **kwd ):
# The value of the received id is the encoded review id.
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
review_id = kwd.get( 'id', None )
review = review_util.get_review( trans.app, review_id )
components_dict = odict()
for component in review_util.get_components( trans.app ):
components_dict[ component.name ] = dict( component=component, component_review=None )
repository = review.repository
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
for component_review in review.component_reviews:
if component_review and component_review.component:
component_name = component_review.component.name
if component_name in components_dict:
component_review_dict = components_dict[ component_name ]
component_review_dict[ 'component_review' ] = component_review
components_dict[ component_name ] = component_review_dict
# Handle a Save button click.
save_button_clicked = False
save_buttons = [ '%s%sreview_button' % ( comp_name, STRSEP ) for comp_name in components_dict.keys() ]
save_buttons.append( 'revision_approved_button' )
for save_button in save_buttons:
if save_button in kwd:
save_button_clicked = True
break
if save_button_clicked:
# Handle the revision_approved_select_field value.
revision_approved = kwd.get( 'revision_approved', None )
revision_approved_setting_changed = False
if revision_approved:
revision_approved = str( revision_approved )
if review.approved != revision_approved:
revision_approved_setting_changed = True
review.approved = revision_approved
trans.sa_session.add( review )
trans.sa_session.flush()
saved_component_names = []
for component_name in components_dict.keys():
flushed = False
# Retrieve the review information from the form.
# The star rating form field is a radio button list, so it will not be received if it was not clicked in the form.
# Due to this behavior, default the value to 0.
rating = 0
for k, v in kwd.items():
if k.startswith( '%s%s' % ( component_name, STRSEP ) ):
component_review_attr = k.replace( '%s%s' % ( component_name, STRSEP ), '' )
if component_review_attr == 'component_id':
component_id = str( v )
elif component_review_attr == 'comment':
comment = str( v )
elif component_review_attr == 'private':
private = CheckboxField.is_checked( v )
elif component_review_attr == 'approved':
approved = str( v )
elif component_review_attr == 'rating':
rating = int( str( v ) )
component = review_util.get_component( trans.app, component_id )
component_review = \
review_util.get_component_review_by_repository_review_id_component_id( trans.app,
review_id,
component_id )
if component_review:
# See if the existing component review should be updated.
if component_review.comment != comment or \
component_review.private != private or \
component_review.approved != approved or \
component_review.rating != rating:
component_review.comment = comment
component_review.private = private
component_review.approved = approved
component_review.rating = rating
trans.sa_session.add( component_review )
trans.sa_session.flush()
flushed = True
saved_component_names.append( component_name )
else:
# See if a new component_review should be created.
if comment or private or approved != trans.model.ComponentReview.approved_states.NO or rating:
component_review = trans.model.ComponentReview( repository_review_id=review.id,
component_id=component.id,
comment=comment,
approved=approved,
rating=rating )
trans.sa_session.add( component_review )
trans.sa_session.flush()
flushed = True
saved_component_names.append( component_name )
if flushed:
# Update the repository rating value to be the average of all component review ratings.
average_rating = trans.sa_session.query( func.avg( trans.model.ComponentReview.table.c.rating ) ) \
.filter( and_( trans.model.ComponentReview.table.c.repository_review_id == review.id,
trans.model.ComponentReview.table.c.deleted == false(),
trans.model.ComponentReview.table.c.approved != trans.model.ComponentReview.approved_states.NA ) ) \
.scalar()
if average_rating is not None:
review.rating = int( average_rating )
trans.sa_session.add( review )
trans.sa_session.flush()
# Update the information in components_dict.
if component_name in components_dict:
component_review_dict = components_dict[ component_name ]
component_review_dict[ 'component_review' ] = component_review
components_dict[ component_name ] = component_review_dict
if revision_approved_setting_changed:
message += 'Approved value <b>%s</b> saved for this revision.<br/>' % review.approved
if saved_component_names:
message += 'Reviews were saved for components: %s' % ', '.join( saved_component_names )
if not revision_approved_setting_changed and not saved_component_names:
message += 'No changes were made to this review, so nothing was saved.'
if review and review.approved:
selected_value = review.approved
else:
selected_value = trans.model.ComponentReview.approved_states.NO
revision_approved_select_field = grids_util.build_approved_select_field( trans,
name='revision_approved',
selected_value=selected_value,
for_component=False )
rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, review.changeset_revision )
return trans.fill_template( '/webapps/tool_shed/repository_review/edit_review.mako',
repository=repository,
review=review,
changeset_revision_label=changeset_revision_label,
revision_approved_select_field=revision_approved_select_field,
components_dict=components_dict,
message=message,
status=status )
def create(self, trans, cntrller='user', redirect_url='', refresh_frames=None, **kwd):
refresh_frames = refresh_frames or []
params = util.Params(kwd)
# If the honeypot field is not empty we are dealing with a bot.
honeypot_field = params.get('bear_field', '')
if honeypot_field != '':
return trans.show_error_message("You've been flagged as a possible bot. If you are not, please try registering again and fill the form out carefully. <a target=\"_top\" href=\"%s\">Go to the home page</a>.") % url_for('/')
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
use_panels = util.string_as_bool(kwd.get('use_panels', True))
email = util.restore_text(params.get('email', ''))
# Do not sanitize passwords, so take from kwd
# instead of params ( which were sanitized )
password = kwd.get('password', '')
confirm = kwd.get('confirm', '')
username = util.restore_text(params.get('username', ''))
subscribe = params.get('subscribe', '')
subscribe_checked = CheckboxField.is_checked(subscribe)
referer = trans.request.referer or ''
redirect = kwd.get('redirect', referer).strip()
is_admin = trans.user_is_admin
success = False
show_user_prepopulate_form = False
if not trans.app.config.allow_user_creation and not trans.user_is_admin:
message = 'User registration is disabled. Please contact your local Galaxy administrator for an account.'
if trans.app.config.error_email_to is not None:
message += f' Contact: {trans.app.config.error_email_to}'
status = 'error'
else:
# check user is allowed to register
message, status = trans.app.auth_manager.check_registration_allowed(email, username, password)
if not message:
# Create the user, save all the user info and login to Galaxy
if params.get('create_user_button', False):
# Check email and password validity
message = self.__validate(trans, email, password, confirm, username)
if not message:
# All the values are valid
message, status, user, success = self.__register(trans, subscribe_checked=subscribe_checked, **kwd)
if success and not is_admin:
# The handle_user_login() method has a call to the history_set_default_permissions() method
# (needed when logging in with a history), user needs to have default permissions set before logging in
trans.handle_user_login(user)
trans.log_event("User created a new account")
trans.log_event("User logged in")
else:
status = 'error'
registration_warning_message = trans.app.config.registration_warning_message
if success:
if is_admin:
redirect_url = web.url_for('/admin/users?status=success&message=Created new user account.')
else:
redirect_url = web.url_for('/')
return trans.fill_template('/webapps/tool_shed/user/register.mako',
cntrller=cntrller,
email=email,
username=username,
subscribe_checked=subscribe_checked,
show_user_prepopulate_form=show_user_prepopulate_form,
use_panels=use_panels,
redirect=redirect,
redirect_url=redirect_url,
refresh_frames=refresh_frames,
registration_warning_message=registration_warning_message,
message=message,
status=status)
def create_role(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
name = util.restore_text(params.get('name', ''))
description = util.restore_text(params.get('description', ''))
in_users = util.listify(params.get('in_users', []))
out_users = util.listify(params.get('out_users', []))
in_groups = util.listify(params.get('in_groups', []))
out_groups = util.listify(params.get('out_groups', []))
create_group_for_role = params.get('create_group_for_role', '')
create_group_for_role_checked = CheckboxField.is_checked(
create_group_for_role)
ok = True
if params.get('create_role_button', False):
if not name or not description:
message = "Enter a valid name and a description."
status = 'error'
ok = False
elif trans.sa_session.query(trans.app.model.Role).filter(
trans.app.model.Role.table.c.name == name).first():
message = "Role names must be unique and a role with that name already exists, so choose another name."
status = 'error'
ok = False
else:
# Create the role
role, num_in_groups = trans.app.security_agent.create_role(
name,
description,
in_users,
in_groups,
create_group_for_role=create_group_for_role_checked)
message = "Role '%s' has been created with %d associated users and %d associated groups. " \
% (role.name, len(in_users), num_in_groups)
if create_group_for_role_checked:
message += 'One of the groups associated with this role is the newly created group with the same name.'
trans.response.send_redirect(
web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='done'))
if ok:
for user in trans.sa_session.query(trans.app.model.User) \
.filter(trans.app.model.User.table.c.deleted == false()) \
.order_by(trans.app.model.User.table.c.email):
out_users.append((user.id, user.email))
for group in trans.sa_session.query(trans.app.model.Group) \
.filter(trans.app.model.Group.table.c.deleted == false()) \
.order_by(trans.app.model.Group.table.c.name):
out_groups.append((group.id, group.name))
return trans.fill_template(
'/webapps/tool_shed/admin/dataset_security/role/role_create.mako',
name=name,
description=description,
in_users=in_users,
out_users=out_users,
in_groups=in_groups,
out_groups=out_groups,
create_group_for_role_checked=create_group_for_role_checked,
message=message,
status=status)
def create_group(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
name = util.restore_text(params.get('name', ''))
in_users = util.listify(params.get('in_users', []))
out_users = util.listify(params.get('out_users', []))
in_roles = util.listify(params.get('in_roles', []))
out_roles = util.listify(params.get('out_roles', []))
create_role_for_group = params.get('create_role_for_group', '')
create_role_for_group_checked = CheckboxField.is_checked(
create_role_for_group)
ok = True
if params.get('create_group_button', False):
if not name:
message = "Enter a valid name."
status = 'error'
ok = False
elif trans.sa_session.query(trans.app.model.Group).filter(
trans.app.model.Group.table.c.name == name).first():
message = "Group names must be unique and a group with that name already exists, so choose another name."
status = 'error'
ok = False
else:
# Create the group
group = trans.app.model.Group(name=name)
trans.sa_session.add(group)
trans.sa_session.flush()
# Create the UserRoleAssociations
for user in [
trans.sa_session.query(trans.app.model.User).get(x)
for x in in_users
]:
uga = trans.app.model.UserGroupAssociation(user, group)
trans.sa_session.add(uga)
# Create the GroupRoleAssociations
for role in [
trans.sa_session.query(trans.app.model.Role).get(x)
for x in in_roles
]:
gra = trans.app.model.GroupRoleAssociation(group, role)
trans.sa_session.add(gra)
if create_role_for_group_checked:
# Create the role
role = trans.app.model.Role(
name=name, description='Role for group %s' % name)
trans.sa_session.add(role)
# Associate the role with the group
gra = trans.model.GroupRoleAssociation(group, role)
trans.sa_session.add(gra)
num_in_roles = len(in_roles) + 1
else:
num_in_roles = len(in_roles)
trans.sa_session.flush()
message = "Group '%s' has been created with %d associated users and %d associated roles. " \
% (group.name, len(in_users), num_in_roles)
if create_role_for_group_checked:
message += 'One of the roles associated with this group is the newly created role with the same name.'
trans.response.send_redirect(
web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status='done'))
if ok:
for user in trans.sa_session.query(trans.app.model.User) \
.filter(trans.app.model.User.table.c.deleted == false()) \
.order_by(trans.app.model.User.table.c.email):
out_users.append((user.id, user.email))
for role in trans.sa_session.query(trans.app.model.Role) \
.filter(trans.app.model.Role.table.c.deleted == false()) \
.order_by(trans.app.model.Role.table.c.name):
out_roles.append((role.id, role.name))
return trans.fill_template(
'/webapps/tool_shed/admin/dataset_security/group/group_create.mako',
name=name,
in_users=in_users,
out_users=out_users,
in_roles=in_roles,
out_roles=out_roles,
create_role_for_group_checked=create_role_for_group_checked,
message=message,
status=status)
def create_group(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
name = util.restore_text(params.get('name', ''))
in_users = util.listify(params.get('in_users', []))
out_users = util.listify(params.get('out_users', []))
in_roles = util.listify(params.get('in_roles', []))
out_roles = util.listify(params.get('out_roles', []))
create_role_for_group = params.get('create_role_for_group', '')
create_role_for_group_checked = CheckboxField.is_checked(create_role_for_group)
ok = True
if params.get('create_group_button', False):
if not name:
message = "Enter a valid name."
status = 'error'
ok = False
elif trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == name).first():
message = "Group names must be unique and a group with that name already exists, so choose another name."
status = 'error'
ok = False
else:
# Create the group
group = trans.app.model.Group(name=name)
trans.sa_session.add(group)
trans.sa_session.flush()
# Create the UserRoleAssociations
for user in [trans.sa_session.query(trans.app.model.User).get(x) for x in in_users]:
uga = trans.app.model.UserGroupAssociation(user, group)
trans.sa_session.add(uga)
# Create the GroupRoleAssociations
for role in [trans.sa_session.query(trans.app.model.Role).get(x) for x in in_roles]:
gra = trans.app.model.GroupRoleAssociation(group, role)
trans.sa_session.add(gra)
if create_role_for_group_checked:
# Create the role
role = trans.app.model.Role(name=name, description='Role for group %s' % name)
trans.sa_session.add(role)
# Associate the role with the group
gra = trans.model.GroupRoleAssociation(group, role)
trans.sa_session.add(gra)
num_in_roles = len(in_roles) + 1
else:
num_in_roles = len(in_roles)
trans.sa_session.flush()
message = "Group '%s' has been created with %d associated users and %d associated roles. " \
% (group.name, len(in_users), num_in_roles)
if create_role_for_group_checked:
message += 'One of the roles associated with this group is the newly created role with the same name.'
trans.response.send_redirect(web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status='done'))
if ok:
for user in trans.sa_session.query(trans.app.model.User) \
.filter(trans.app.model.User.table.c.deleted == false()) \
.order_by(trans.app.model.User.table.c.email):
out_users.append((user.id, user.email))
for role in trans.sa_session.query(trans.app.model.Role) \
.filter(trans.app.model.Role.table.c.deleted == false()) \
.order_by(trans.app.model.Role.table.c.name):
out_roles.append((role.id, role.name))
return trans.fill_template('/webapps/tool_shed/admin/dataset_security/group/group_create.mako',
name=name,
in_users=in_users,
out_users=out_users,
in_roles=in_roles,
out_roles=out_roles,
create_role_for_group_checked=create_role_for_group_checked,
message=message,
status=status)
