def __save_external_service( self, trans, **kwd ):
# Here we save a newly created external_service or save changed
# attributes of an existing external_service.
params = util.Params( kwd )
external_service_id = params.get( 'id', None )
name = util.restore_text( params.get( 'external_service_name', '' ) )
description = util.restore_text( params.get( 'external_service_description', '' ) )
version = util.restore_text( params.get( 'external_service_version', '' ) )
external_service_type_id = params.get( 'external_service_type_id', '' )
if external_service_id:
# We're saving changed attributes of an existing external_service.
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
external_service.name = name
external_service.description = description
external_service.version = version
external_service.form_values.content = self.get_form_values( trans, trans.user, external_service.form_definition, **kwd )
trans.sa_session.add( external_service )
trans.sa_session.add( external_service.form_values )
trans.sa_session.flush()
else:
# We're saving a newly created external_service
external_service_type = self.get_external_service_type( trans, external_service_type_id )
external_service = trans.model.ExternalService( name, description, external_service_type_id, version )
external_service.form_definition = external_service_type.form_definition
# Get the form values from kwd, some of which may be different than the defaults in the external service
# type config because the user could have overwritten them.
values = self.get_form_values( trans, trans.user, external_service.form_definition, **kwd )
external_service.form_values = trans.model.FormValues( external_service.form_definition, values )
trans.sa_session.add( external_service )
trans.sa_session.add( external_service.form_definition )
trans.sa_session.add( external_service.form_values )
trans.sa_session.flush()
return external_service
def __build_external_service_widgets( self, trans, external_service=None, **kwd ):
params = util.Params( kwd )
if external_service:
name = external_service.name
description = external_service.description
version = external_service.version
seq_type = external_service.external_service_type_id
else:
name = util.restore_text( params.get( 'external_service_name', '' ) )
description = util.restore_text( params.get( 'external_service_description', '' ) )
version = util.restore_text( params.get( 'external_service_version', '' ) )
selected_seq_type = params.get( 'external_service_type_id', '' )
if trans.app.external_service_types.all_external_service_types.has_key( selected_seq_type ):
seq_type = trans.app.external_service_types.all_external_service_types[ selected_seq_type ].id
else:
seq_type = 'none'
widgets = [ dict( label='Name',
widget=TextField( 'external_service_name', 40, name ),
helptext='' ),
dict( label='Description',
widget=TextField( 'external_service_description', 40, description ),
helptext='' ),
dict( label='Version',
widget=TextField( 'external_service_version', 40, version ),
helptext='' ) ]
# Do not show the external_service_type selectfield when editing a external_service
if not external_service:
widgets.append( dict( label='External service type',
widget=self.__build_external_service_type_select_field( trans, seq_type, visible_external_service_types_only=True ),
helptext='') )
return widgets
def create_category( 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', '' ) ).strip()
description = util.restore_text( params.get( 'description', '' ) ).strip()
if params.get( 'create_category_button', False ):
if not name or not description:
message = 'Enter a valid name and a description'
status = 'error'
elif suc.get_category_by_name( trans, name ):
message = 'A category with that name already exists'
status = 'error'
else:
# Create the category
category = trans.app.model.Category( name=name, description=description )
trans.sa_session.add( category )
trans.sa_session.flush()
message = "Category '%s' has been created" % category.name
status = 'done'
trans.response.send_redirect( web.url_for( controller='admin',
action='manage_categories',
message=message,
status=status ) )
return trans.fill_template( '/webapps/community/category/create_category.mako',
name=name,
description=description,
message=message,
status=status )
def parse_request_tup(self, request_tup, **kwd):
redirect_action = util.restore_text(kwd.get('redirect_action', ''))
titles = util.restore_text(kwd.get('titles', ''))
JobId = util.restore_text(kwd.get('JobId', ''))
sample_id = util.restore_text(kwd.get('sample_id', ''))
message = util.restore_text(kwd.get('message', ''))
status = kwd.get('status', 'done')
url, http_method, request_params, response_type = request_tup
url = unquote_plus(url)
# Handle URLs in which we replace param values, which will look something like:
# http://127.0.0.1/getinfo/{id}.
replace_with_param = url.find('{') > 0
if replace_with_param:
# Handle the special-case {JobId} param.
if url.find('{JobId}') > 0:
if JobId:
url = url.replace('{JobId}', str(JobId))
for key, value in kwd.items():
# Don't attempt to replace if there is nothing with which to do it
# or if the value itself should be replaced with something.
if value and not value.startswith('{'):
replace_str = '{%s}' % key
if url.find(replace_str) > 0:
url = url.replace(replace_str, value)
# Handle request parameters in which we replace param values.
for key, val in request_params.items():
if val and val.startswith('{'):
replace_key = val.lstrip('{').rstrip('}')
if replace_key in kwd:
request_params[key] = kwd[replace_key]
return url, http_method, request_params, response_type
def edit_component(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
id = params.get('id', None)
if not id:
message = "No component ids received for editing"
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=message,
status='error'))
component = suc.get_component(trans, id)
if params.get('edit_component_button', False):
new_description = util.restore_text(params.get('description',
'')).strip()
if component.description != new_description:
component.description = new_description
trans.sa_session.add(component)
trans.sa_session.flush()
message = "The information has been saved for the component named <b>%s</b>" % (
component.name)
status = 'done'
return trans.response.send_redirect(
web.url_for(controller='repository_review',
action='manage_components',
message=message,
status=status))
return trans.fill_template(
'/webapps/community/repository_review/edit_component.mako',
component=component,
message=message,
status=status)
def create_component(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', ''))
if params.get('create_component_button', False):
if not name or not description:
message = 'Enter a valid name and a description'
status = 'error'
elif suc.get_component_by_name(trans, name):
message = 'A component with that name already exists'
status = 'error'
else:
component = trans.app.model.Component(name=name,
description=description)
trans.sa_session.add(component)
trans.sa_session.flush()
message = "Component '%s' has been created" % component.name
status = 'done'
trans.response.send_redirect(
web.url_for(controller='repository_review',
action='manage_components',
message=message,
status=status))
return trans.fill_template(
'/webapps/community/repository_review/create_component.mako',
name=name,
description=description,
message=message,
status=status)
def register(self, trans, email=None, username=None, password=None, confirm=None, subscribe=False):
"""
Register a new user.
"""
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 += " Contact: %s" % trans.app.config.error_email_to
return None, message
if not email or not username or not password or not confirm:
return None, "Please provide email, username and password."
message = "\n".join([validate_email(trans, email),
validate_password(trans, password, confirm),
validate_publicname(trans, username)]).rstrip()
if message:
return None, message
email = util.restore_text(email)
username = util.restore_text(username)
message, status = trans.app.auth_manager.check_registration_allowed(email, username, password)
if message:
return None, message
if subscribe:
message = self.send_subscription_email(email)
if message:
return None, message
user = self.create(email=email, username=username, password=password)
if self.app.config.user_activation_on:
self.send_activation_email(trans, email, username)
return user, None
def __get_field( self, index, **kwd ):
'''
This method retrieves all the user-entered details of a field and
returns a dict.
'''
params = util.Params( kwd )
label = util.restore_text( params.get( 'field_label_%i' % index, '' ) )
name = util.restore_text( params.get( 'field_name_%i' % index, '' ) )
helptext = util.restore_text( params.get( 'field_helptext_%i' % index, '' ) )
required = params.get( 'field_required_%i' % index, False )
field_type = util.restore_text( params.get( 'field_type_%i' % index, '' ) )
layout = params.get( 'field_layout_%i' % index, '0' )
default = util.restore_text( params.get( 'field_default_%i' % index, '' ) )
if not name.strip():
name = '%i_field_name' % index
if field_type == 'SelectField':
options = self.__get_select_field_options(index, **kwd)
return { 'name': name,
'label': label,
'helptext': helptext,
'visible': True,
'required': required,
'type': field_type,
'selectlist': options,
'layout': layout,
'default': default }
return { 'name': name,
'label': label,
'helptext': helptext,
'visible': True,
'required': required,
'type': field_type,
'layout': layout,
'default': default }
def create_form_definition( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
self.__imported_from_file = False
if params.get( 'create_form_button', False ):
form_definition, message = self.save_form_definition( trans, form_definition_current_id=None, **kwd )
if not form_definition:
return trans.response.send_redirect( web.url_for( controller='forms',
action='create_form_definition',
message=message,
status='error',
name=util.restore_text( params.get( 'name', '' ) ),
description=util.restore_text( params.get( 'description', '' ) ) ))
if self.__imported_from_file:
return trans.response.send_redirect( web.url_for( controller='forms',
action='edit_form_definition',
id=trans.security.encode_id( form_definition.current.id )) )
else:
return trans.response.send_redirect( web.url_for( controller='forms',
action='edit_form_definition',
id=trans.security.encode_id( form_definition.current.id ),
add_field_button='Add field',
name=form_definition.name,
description=form_definition.desc,
form_type_select_field=form_definition.type ) )
inputs = [ ( 'Name', TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ) ),
( 'Description', TextField( 'description', 40, util.restore_text( params.get( 'description', '' ) ) ) ),
( 'Type', self.__build_form_types_widget( trans, selected=params.get( 'form_type', 'none' ) ) ),
( 'Import from csv file (Optional)', FileField( 'file_data', 40, '' ) ) ]
return trans.fill_template( '/admin/forms/create_form.mako',
inputs=inputs,
message=message,
status=status )
def create(self, trans, payload, **kwd):
"""
POST /api/libraries
Creates a new library.
"""
if not trans.user_is_admin():
raise HTTPForbidden(
detail='You are not authorized to create a new library.')
params = util.Params(payload)
name = util.restore_text(params.get('name', None))
if not name:
raise HTTPBadRequest(detail="Missing required parameter 'name'.")
description = util.restore_text(params.get('description', ''))
synopsis = util.restore_text(params.get('synopsis', ''))
if synopsis in ['None', None]:
synopsis = ''
library = trans.app.model.Library(name=name,
description=description,
synopsis=synopsis)
root_folder = trans.app.model.LibraryFolder(name=name, description='')
library.root_folder = root_folder
trans.sa_session.add_all((library, root_folder))
trans.sa_session.flush()
encoded_id = trans.security.encode_id(library.id)
rval = {}
rval['url'] = url_for('library', id=encoded_id)
rval['name'] = name
rval['id'] = encoded_id
return [rval]
def create_category(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', '')).strip()
description = util.restore_text(params.get('description', '')).strip()
if params.get('create_category_button', False):
if not name or not description:
message = 'Enter a valid name and a description'
status = 'error'
elif suc.get_category_by_name(trans, name):
message = 'A category with that name already exists'
status = 'error'
else:
# Create the category
category = trans.app.model.Category(name=name,
description=description)
trans.sa_session.add(category)
trans.sa_session.flush()
message = "Category '%s' has been created" % category.name
status = 'done'
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=message,
status=status))
return trans.fill_template(
'/webapps/community/category/create_category.mako',
name=name,
description=description,
message=message,
status=status)
def create_component( 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', '' ) )
if params.get( 'create_component_button', False ):
if not name or not description:
message = 'Enter a valid name and a description'
status = 'error'
elif suc.get_component_by_name( trans, name ):
message = 'A component with that name already exists'
status = 'error'
else:
component = trans.app.model.Component( name=name, description=description )
trans.sa_session.add( component )
trans.sa_session.flush()
message = "Component '%s' has been created" % component.name
status = 'done'
trans.response.send_redirect( web.url_for( controller='repository_review',
action='manage_components',
message=message,
status=status ) )
return trans.fill_template( '/webapps/community/repository_review/create_component.mako',
name=name,
description=description,
message=message,
status=status )
def edit_component( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
id = params.get( 'id', None )
if not id:
message = "No component ids received for editing"
trans.response.send_redirect( web.url_for( controller='admin',
action='manage_categories',
message=message,
status='error' ) )
component = suc.get_component( trans, id )
if params.get( 'edit_component_button', False ):
new_description = util.restore_text( params.get( 'description', '' ) ).strip()
if component.description != new_description:
component.description = new_description
trans.sa_session.add( component )
trans.sa_session.flush()
message = "The information has been saved for the component named <b>%s</b>" % ( component.name )
status = 'done'
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='manage_components',
message=message,
status=status ) )
return trans.fill_template( '/webapps/community/repository_review/edit_component.mako',
component=component,
message=message,
status=status )
def create( self, trans, payload, **kwd ):
"""
create( self, trans, payload, **kwd )
* POST /api/libraries:
Creates a new library. Only ``name`` parameter is required.
.. note:: Currently, only admin users can create libraries.
:param payload: dictionary structure containing::
'name': the new library's name (required)
'description': the new library's description (optional)
'synopsis': the new library's synopsis (optional)
:type payload: dict
:returns: detailed library information
:rtype: dict
:raises: ItemAccessibilityException, RequestParameterMissingException
"""
params = util.Params( payload )
name = util.restore_text( params.get( 'name', None ) )
if not name:
raise exceptions.RequestParameterMissingException( "Missing required parameter 'name'." )
description = util.restore_text( params.get( 'description', '' ) )
synopsis = util.restore_text( params.get( 'synopsis', '' ) )
if synopsis in [ 'None', None ]:
synopsis = ''
library = self.library_manager.create( trans, name, description, synopsis )
library_dict = self.library_manager.get_library_dict( trans, library )
return library_dict
def manage_user_info(self, trans, cntrller, **kwd):
'''Manage a user's login, password, public username, type, addresses, etc.'''
params = util.Params(kwd)
user_id = params.get('id', None)
if user_id:
user = trans.sa_session.query(trans.app.model.User).get(
trans.security.decode_id(user_id))
else:
user = trans.user
if not user:
raise AssertionError("The user id (%s) is not valid" %
str(user_id))
email = util.restore_text(params.get('email', user.email))
username = util.restore_text(params.get('username', ''))
if not username:
username = user.username
message = escape(util.restore_text(params.get('message', '')))
status = params.get('status', 'done')
return trans.fill_template('/webapps/tool_shed/user/manage_info.mako',
cntrller=cntrller,
user=user,
email=email,
username=username,
message=message,
status=status)
def parse_request_tup( self, request_tup, **kwd ):
redirect_action = util.restore_text( kwd.get( 'redirect_action', '' ) )
titles = util.restore_text( kwd.get( 'titles', '' ) )
JobId = util.restore_text( kwd.get( 'JobId', '' ) )
sample_id = util.restore_text( kwd.get( 'sample_id', '' ) )
message = util.restore_text( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
url, http_method, request_params, response_type = request_tup
url = unquote_plus( url )
# Handle URLs in which we replace param values, which will look something like:
# http://127.0.0.1/getinfo/{id}.
replace_with_param = url.find( '{' ) > 0
if replace_with_param:
# Handle the special-case {JobId} param.
if url.find( '{JobId}' ) > 0:
if JobId:
url = url.replace( '{JobId}', str( JobId ) )
for key, value in kwd.items():
# Don't attempt to replace if there is nothing with which to do it
# or if the value itself should be replaced with something.
if value and not value.startswith( '{' ):
replace_str = '{%s}' % key
if url.find( replace_str ) > 0:
url = url.replace( replace_str, value )
# Handle request parameters in which we replace param values.
for key, val in request_params.items():
if val and val.startswith( '{' ):
replace_key = val.lstrip( '{' ).rstrip( '}' )
if replace_key in kwd:
request_params[ key ] = kwd[ replace_key ]
return url, http_method, request_params, response_type
def create( self, trans, payload, **kwd ):
"""
POST /api/libraries
Creates a new library.
"""
if not trans.user_is_admin():
raise HTTPForbidden( detail='You are not authorized to create a new library.' )
params = util.Params( payload )
name = util.restore_text( params.get( 'name', None ) )
if not name:
raise HTTPBadRequest( detail="Missing required parameter 'name'." )
description = util.restore_text( params.get( 'description', '' ) )
synopsis = util.restore_text( params.get( 'synopsis', '' ) )
if synopsis in [ 'None', None ]:
synopsis = ''
library = trans.app.model.Library( name=name, description=description, synopsis=synopsis )
root_folder = trans.app.model.LibraryFolder( name=name, description='' )
library.root_folder = root_folder
trans.sa_session.add_all( ( library, root_folder ) )
trans.sa_session.flush()
encoded_id = trans.security.encode_id( library.id )
rval = {}
rval['url'] = url_for( 'library', id=encoded_id )
rval['name'] = name
rval['id'] = encoded_id
return rval
def __save_external_service( self, trans, **kwd ):
# Here we save a newly created external_service or save changed
# attributes of an existing external_service.
params = util.Params( kwd )
external_service_id = params.get( 'id', None )
name = util.restore_text( params.get( 'external_service_name', '' ) )
description = util.restore_text( params.get( 'external_service_description', '' ) )
version = util.restore_text( params.get( 'external_service_version', '' ) )
external_service_type_id = params.get( 'external_service_type_id', '' )
if external_service_id:
# We're saving changed attributes of an existing external_service.
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
external_service.name = name
external_service.description = description
external_service.version = version
external_service.form_values.content = self.get_form_values( trans, trans.user, external_service.form_definition, **kwd )
trans.sa_session.add( external_service )
trans.sa_session.add( external_service.form_values )
trans.sa_session.flush()
else:
# We're saving a newly created external_service
external_service_type = self.get_external_service_type( trans, external_service_type_id )
external_service = trans.model.ExternalService( name, description, external_service_type_id, version )
external_service.form_definition = external_service_type.form_definition
# Get the form values from kwd, some of which may be different than the defaults in the external service
# type config because the user could have overwritten them.
values = self.get_form_values( trans, trans.user, external_service.form_definition, **kwd )
external_service.form_values = trans.model.FormValues( external_service.form_definition, values )
trans.sa_session.add( external_service )
trans.sa_session.add( external_service.form_definition )
trans.sa_session.add( external_service.form_values )
trans.sa_session.flush()
return external_service
def __build_external_service_widgets( self, trans, external_service=None, **kwd ):
params = util.Params( kwd )
if external_service:
name = external_service.name
description = external_service.description
version = external_service.version
seq_type = external_service.external_service_type_id
else:
name = util.restore_text( params.get( 'external_service_name', '' ) )
description = util.restore_text( params.get( 'external_service_description', '' ) )
version = util.restore_text( params.get( 'external_service_version', '' ) )
selected_seq_type = params.get( 'external_service_type_id', '' )
if selected_seq_type in trans.app.external_service_types.all_external_service_types:
seq_type = trans.app.external_service_types.all_external_service_types[ selected_seq_type ].id
else:
seq_type = 'none'
widgets = [ dict( label='Name',
widget=TextField( 'external_service_name', 40, name ),
helptext='' ),
dict( label='Description',
widget=TextField( 'external_service_description', 40, description ),
helptext='' ),
dict( label='Version',
widget=TextField( 'external_service_version', 40, version ),
helptext='' ) ]
# Do not show the external_service_type selectfield when editing a external_service
if not external_service:
widgets.append( dict( label='External service type',
widget=self.__build_external_service_type_select_field( trans, seq_type, visible_external_service_types_only=True ),
helptext='') )
return widgets
def create(self, trans, payload, **kwd):
"""
create( self, trans, payload, **kwd )
* POST /api/libraries:
Creates a new library. Only ``name`` parameter is required.
.. note:: Currently, only admin users can create libraries.
:param payload: dictionary structure containing::
'name': the new library's name (required)
'description': the new library's description (optional)
'synopsis': the new library's synopsis (optional)
:type payload: dict
:returns: detailed library information
:rtype: dict
:raises: ItemAccessibilityException, RequestParameterMissingException
"""
params = util.Params(payload)
name = util.restore_text(params.get('name', None))
if not name:
raise exceptions.RequestParameterMissingException(
"Missing required parameter 'name'.")
description = util.restore_text(params.get('description', ''))
synopsis = util.restore_text(params.get('synopsis', ''))
if synopsis in ['None', None]:
synopsis = ''
library = self.library_manager.create(trans, name, description,
synopsis)
library_dict = self.library_manager.get_library_dict(trans, library)
return library_dict
def get_params(self, kwargs):
params = util.Params(kwargs)
# set defaults if unset
updates = dict(webapp=params.get('webapp', 'galaxy'),
message=util.restore_text(params.get('message', '')),
status=util.restore_text(params.get('status', 'done')))
params.update(updates)
return params
def get_params(self, kwargs):
params = util.Params(kwargs)
# set defaults if unset
updates = dict(webapp=params.get('webapp', 'galaxy'),
message=util.restore_text(params.get('message', '')),
status=util.restore_text(params.get('status', 'done')))
params.update(updates)
return params
def create( self, trans, payload, **kwd ):
"""
create( self, trans, payload, **kwd )
* POST /api/repositories:
Creates a new repository.
Only ``name`` and ``synopsis`` parameters are required.
:param payload: dictionary structure containing::
'name': new repo's name (required)
'synopsis': new repo's synopsis (required)
'description': new repo's description (optional)
'remote_repository_url': new repo's remote repo (optional)
'homepage_url': new repo's homepage url (optional)
'category_ids[]': list of existing encoded TS category ids
the new repo should be associated with (optional)
'type': new repo's type, defaults to ``unrestricted`` (optional)
:type payload: dict
:returns: detailed repository information
:rtype: dict
:raises: RequestParameterMissingException
"""
params = util.Params( payload )
name = util.restore_text( params.get( 'name', None ) )
if not name:
raise exceptions.RequestParameterMissingException( "Missing required parameter 'name'." )
synopsis = util.restore_text( params.get( 'synopsis', None ) )
if not synopsis:
raise exceptions.RequestParameterMissingException( "Missing required parameter 'synopsis'." )
description = util.restore_text( params.get( 'description', '' ) )
remote_repository_url = util.restore_text( params.get( 'remote_repository_url', '' ) )
homepage_url = util.restore_text( params.get( 'homepage_url', '' ) )
category_ids = util.listify( params.get( 'category_ids[]', '' ) )
selected_categories = [ trans.security.decode_id( id ) for id in category_ids ]
repo_type = kwd.get( 'type', rt_util.UNRESTRICTED )
if repo_type not in rt_util.types:
raise exceptions.RequestParameterInvalidException( 'This repository type is not valid' )
invalid_message = repository_util.validate_repository_name( trans.app, name, trans.user )
if invalid_message:
raise exceptions.RequestParameterInvalidException( invalid_message )
repo, message = repository_util.create_repository( app=trans.app,
name=name,
type=repo_type,
description=synopsis,
long_description=description,
user_id = trans.user.id,
category_ids=category_ids,
remote_repository_url=remote_repository_url,
homepage_url=homepage_url )
return repo.to_dict( view='element', value_mapper=self.__get_value_mapper( trans ) )
def __register(self,
trans,
email=None,
username=None,
password=None,
subscribe_checked=False,
**kwd):
"""Registers a new user."""
email = util.restore_text(email)
username = util.restore_text(username)
status = None
message = None
is_admin = trans.user_is_admin
user = self.user_manager.create(email=email,
username=username,
password=password)
if subscribe_checked:
# subscribe user to email list
if trans.app.config.smtp_server is None:
status = "error"
message = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed because mail is not configured for this Galaxy instance. <br>Please contact your local Galaxy administrator."
else:
body = 'Join Mailing list.\n'
to = trans.app.config.mailing_join_addr
frm = email
subject = 'Join Mailing List'
try:
util.send_mail(frm, to, subject, body, trans.app.config)
except Exception:
log.exception(
'Subscribing to the mailing list has failed.')
status = "warning"
message = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed."
if status != "error":
if 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")
if trans.app.config.user_activation_on:
is_activation_sent = self.user_manager.send_activation_email(
trans, email, username)
if is_activation_sent:
message = 'Now logged in as %s.<br>Verification email has been sent to your email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.<br><a target="_top" href="%s">Return to the home page.</a>' % (
escape(user.email), url_for('/'))
else:
status = "error"
message = 'Unable to send activation email, please contact your local Galaxy administrator.'
if trans.app.config.error_email_to is not None:
message += ' Contact: %s' % trans.app.config.error_email_to
else:
# User activation is OFF, proceed without sending the activation email.
message = 'Now logged in as %s.<br><a target="_top" href="%s">Return to the home page.</a>' % (
escape(user.email), url_for('/'))
return message, status, user, status is None
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 rename_datasets( self, trans, **kwd ):
# This method is called from the DataTransferGrid when a user is renaming 1 or more
# SampleDatasets.
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
sample_id = kwd.get( 'sample_id', None )
try:
sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) )
except:
return invalid_id_redirect( trans, 'requests_admin', sample_id, 'sample' )
# id_list is list of SampleDataset ids, which is a subset of all
# of the SampleDatasets associated with the Sample. The user may
# or may not have selected all of the SampleDatasets for renaming.
id_list = util.listify( kwd.get( 'id_list', [] ) )
# Get all of the SampleDatasets
sample_datasets = []
for sample_dataset_id in id_list:
sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) )
sample_datasets.append( sample_dataset )
if params.get( 'rename_datasets_button', False ):
incorrect_dataset_names = []
for sample_dataset in sample_datasets:
encoded_id = trans.security.encode_id( sample_dataset.id )
selected_option = util.restore_text( params.get( 'rename_datasets_for_sample_%s' % encoded_id, '' ) )
new_name = util.restore_text( params.get( 'new_name_%s' % encoded_id, '' ) )
if not new_name:
incorrect_dataset_names.append( sample_dataset.name )
continue
new_name = util.sanitize_for_filename( new_name )
if selected_option == 'none':
sample_dataset.name = new_name
else:
sample_dataset.name = '%s_%s' % ( selected_option, new_name )
trans.sa_session.add( sample_dataset )
trans.sa_session.flush()
if len( sample_datasets ) == len( incorrect_dataset_names ):
status = 'error'
message = 'All datasets renamed incorrectly.'
elif len( incorrect_dataset_names ):
status = 'done'
message = 'Changes saved successfully. The following datasets were renamed incorrectly: %s.' % str( incorrect_dataset_names )
else:
message = 'Changes saved successfully.'
return trans.fill_template( '/admin/requests/rename_datasets.mako',
sample=sample,
id_list=id_list,
message=message,
status=status )
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='manage_datasets',
sample_id=sample_id ) )
def rename_datasets( self, trans, **kwd ):
# This method is called from the DataTransferGrid when a user is renaming 1 or more
# SampleDatasets.
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
sample_id = kwd.get( 'sample_id', None )
try:
sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) )
except:
return invalid_id_redirect( trans, 'requests_admin', sample_id, 'sample' )
# id_list is list of SampleDataset ids, which is a subset of all
# of the SampleDatasets associated with the Sample. The user may
# or may not have selected all of the SampleDatasets for renaming.
id_list = util.listify( kwd.get( 'id_list', [] ) )
# Get all of the SampleDatasets
sample_datasets = []
for sample_dataset_id in id_list:
sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) )
sample_datasets.append( sample_dataset )
if params.get( 'rename_datasets_button', False ):
incorrect_dataset_names = []
for sample_dataset in sample_datasets:
encoded_id = trans.security.encode_id( sample_dataset.id )
selected_option = util.restore_text( params.get( 'rename_datasets_for_sample_%s' % encoded_id, '' ) )
new_name = util.restore_text( params.get( 'new_name_%s' % encoded_id, '' ) )
if not new_name:
incorrect_dataset_names.append( sample_dataset.name )
continue
new_name = util.sanitize_for_filename( new_name )
if selected_option == 'none':
sample_dataset.name = new_name
else:
sample_dataset.name = '%s_%s' % ( selected_option, new_name )
trans.sa_session.add( sample_dataset )
trans.sa_session.flush()
if len( sample_datasets ) == len( incorrect_dataset_names ):
status = 'error'
message = 'All datasets renamed incorrectly.'
elif len( incorrect_dataset_names ):
status = 'done'
message = 'Changes saved successfully. The following datasets were renamed incorrectly: %s.' % str( incorrect_dataset_names )
else:
message = 'Changes saved successfully.'
return trans.fill_template( '/admin/requests/rename_datasets.mako',
sample=sample,
id_list=id_list,
message=message,
status=status )
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='manage_datasets',
sample_id=sample_id ) )
def get_quota_params(self, kwargs):
params = self.get_params(kwargs)
updates = dict(name=util.restore_text(params.get('name', '')),
description=util.restore_text(params.get('description', '')),
amount=util.restore_text(params.get('amount', '').strip()),
operation=params.get('operation', ''),
default=params.get('default', ''),
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', [])))
params.update(updates)
return params
def __validate_form( self, **kwd ):
'''
This method checks the following text inputs are filled out by the user
- the name of form
- form type
'''
params = util.Params( kwd )
# form name
if not util.restore_text( params.name ):
return None, 'Form name must be filled.'
# form type
if util.restore_text( params.form_type_select_field ) == 'none':
return None, 'Form type must be selected.'
return True, ''
def __get_populated_request_type_widgets(self, trans, **kwd):
request_form_definitions = self.get_all_forms(
trans,
filter=dict(deleted=False),
form_type=trans.model.FormDefinition.types.REQUEST)
sample_form_definitions = self.get_all_forms(
trans,
filter=dict(deleted=False),
form_type=trans.model.FormDefinition.types.SAMPLE)
if not request_form_definitions or not sample_form_definitions:
return [], []
params = util.Params(kwd)
request_form_id = params.get('request_form_id', 'none')
sample_form_id = params.get('sample_form_id', 'none')
request_form_id_select_field = build_select_field(
trans,
objs=request_form_definitions,
label_attr='name',
select_field_name='request_form_id',
selected_value=request_form_id,
refresh_on_change=False)
sample_form_id_select_field = build_select_field(
trans,
objs=sample_form_definitions,
label_attr='name',
select_field_name='sample_form_id',
selected_value=sample_form_id,
refresh_on_change=False)
rt_info_widgets = [
dict(label='Name',
widget=TextField('name', 40,
util.restore_text(params.get('name', '')))),
dict(label='Description',
widget=TextField('desc', 40,
util.restore_text(params.get('desc', '')))),
dict(label='Request form', widget=request_form_id_select_field),
dict(label='Sample form', widget=sample_form_id_select_field)
]
# Unsaved sample states being defined for this request type
rt_states = []
i = 0
while True:
if 'state_name_%i' % i in kwd:
rt_states.append(
(util.restore_text(params.get('state_name_%i' % i, '')),
util.restore_text(params.get('state_desc_%i' % i, ''))))
i += 1
else:
break
return rt_info_widgets, rt_states
def create(self, trans, payload, **kwd):
"""
create( self, trans, payload, **kwd )
* POST /api/libraries:
Creates a new library. Only ``name`` parameter is required.
.. note:: Currently, only admin users can create libraries.
:param payload: dictionary structure containing::
'name': the new library's name (required)
'description': the new library's description (optional)
'synopsis': the new library's synopsis (optional)
:type payload: dict
:returns: detailed library information
:rtype: dict
:raises: ItemAccessibilityException, RequestParameterMissingException
"""
if not trans.user_is_admin():
raise exceptions.ItemAccessibilityException(
'Only administrators can create libraries.')
params = util.Params(payload)
name = util.restore_text(params.get('name', None))
if not name:
raise exceptions.RequestParameterMissingException(
"Missing required parameter 'name'.")
description = util.restore_text(params.get('description', ''))
synopsis = util.restore_text(params.get('synopsis', ''))
if synopsis in ['None', None]:
synopsis = ''
library = trans.app.model.Library(name=name,
description=description,
synopsis=synopsis)
root_folder = trans.app.model.LibraryFolder(name=name, description='')
library.root_folder = root_folder
trans.sa_session.add_all((library, root_folder))
trans.sa_session.flush()
item = library.to_dict(view='element',
value_mapper={
'id': trans.security.encode_id,
'root_folder_id': trans.security.encode_id
})
item['can_user_add'] = True
item['can_user_modify'] = True
item['can_user_manage'] = True
if trans.app.security_agent.library_is_public(library, contents=False):
item['public'] = True
return item
def get_quota_params(self, kwargs):
params = self.get_params(kwargs)
updates = dict(
name=util.restore_text(params.get('name', '')),
description=util.restore_text(params.get('description', '')),
amount=util.restore_text(params.get('amount', '').strip()),
operation=params.get('operation', ''),
default=params.get('default', ''),
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', [])))
params.update(updates)
return params
def edit_username(self, trans, cntrller, **kwd):
params = util.Params(kwd)
is_admin = cntrller == 'admin' and trans.user_is_admin()
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
user_id = params.get('user_id', None)
if user_id and is_admin:
user = trans.sa_session.query(trans.app.model.User).get(
trans.security.decode_id(user_id))
else:
user = trans.user
if user and params.get('change_username_button', False):
username = kwd.get('username', '')
if username:
message = validate_publicname(trans, username, user)
if message:
status = 'error'
else:
user.username = username
trans.sa_session.add(user)
trans.sa_session.flush()
message = 'The username has been updated with the changes.'
return trans.fill_template('/webapps/tool_shed/user/username.mako',
cntrller=cntrller,
user=user,
username=user.username,
message=message,
status=status)
def view_editable_request_type(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
request_type_id = params.get('id', None)
try:
request_type = trans.sa_session.query(trans.model.RequestType).get(
trans.security.decode_id(request_type_id))
except:
return invalid_id_redirect(trans,
'request_type',
request_type_id,
'request type',
action='browse_request_types')
# See if we have any associated templates
widgets = request_type.get_template_widgets(trans)
widget_fields_have_contents = self.widget_fields_have_contents(widgets)
# get all the external services selected till now
external_service_select_fields_list = []
for index, external_service in enumerate(
request_type.external_services):
external_service_select_field = self.__build_external_service_select_field(
trans, 'external_service_id_%i' % index, external_service)
external_service_select_fields_list.append(
external_service_select_field)
return trans.fill_template(
'/admin/request_type/edit_request_type.mako',
request_type=request_type,
widgets=widgets,
widget_fields_have_contents=widget_fields_have_contents,
external_service_select_fields_list=
external_service_select_fields_list,
message=message,
status=status)
def user_disk_usage(self, trans, **kwd):
message = escape(util.restore_text(kwd.get("message", "")))
specs = sorter("disk_usage", kwd)
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
if order == "desc":
_order = True
else:
_order = False
user_cutoff = int(kwd.get("user_cutoff", 60))
# disk_usage isn't indexed
users = sorted(
trans.sa_session.query(galaxy.model.User).all(), key=operator.attrgetter(str(sort_id)), reverse=_order
)
if user_cutoff:
users = users[:user_cutoff]
return trans.fill_template(
"/webapps/reports/users_user_disk_usage.mako",
order=order,
arrow=arrow,
sort_id=sort_id,
users=users,
user_cutoff=user_cutoff,
message=message,
)
def handle_library_params(trans, params, folder_id, replace_dataset=None):
# FIXME: the received params has already been parsed by util.Params() by the time it reaches here,
# so no complex objects remain. This is not good because it does not allow for those objects to be
# manipulated here. The received params should be the original kwd from the initial request.
library_bunch = util.bunch.Bunch()
library_bunch.replace_dataset = replace_dataset
library_bunch.message = params.get('ldda_message', '')
# See if we have any template field contents
library_bunch.template_field_contents = {}
template_id = params.get('template_id', None)
library_bunch.folder = trans.sa_session.query(
trans.app.model.LibraryFolder).get(trans.security.decode_id(folder_id))
# We are inheriting the folder's info_association, so we may have received inherited contents or we may have redirected
# here after the user entered template contents ( due to errors ).
if template_id not in [None, 'None']:
library_bunch.template = trans.sa_session.query(
trans.app.model.FormDefinition).get(template_id)
for field in library_bunch.template.fields:
field_name = field['name']
if params.get(field_name, False):
field_value = util.restore_text(params.get(field_name, ''))
library_bunch.template_field_contents[field_name] = field_value
else:
library_bunch.template = None
library_bunch.roles = []
for role_id in util.listify(params.get('roles', [])):
role = trans.sa_session.query(trans.app.model.Role).get(role_id)
library_bunch.roles.append(role)
return library_bunch
def specified_date(self, trans, **kwd):
message = util.restore_text(kwd.get('message', ''))
# If specified_date is not received, we'll default to the current month
specified_date = kwd.get('specified_date',
datetime.utcnow().strftime("%Y-%m-%d"))
year, month, day = map(int, specified_date.split("-"))
start_date = date(year, month, day)
end_date = start_date + timedelta(days=1)
day_of_month = start_date.strftime("%d")
day_label = start_date.strftime("%A")
month_label = start_date.strftime("%B")
year_label = start_date.strftime("%Y")
q = sa.select((sa.func.date_trunc(
'day', sa.func.date(
galaxy.model.User.table.c.create_time)).label('date'),
galaxy.model.User.table.c.email),
whereclause=sa.and_(
galaxy.model.User.table.c.create_time >= start_date,
galaxy.model.User.table.c.create_time < end_date),
from_obj=[galaxy.model.User.table],
order_by=[galaxy.model.User.table.c.email])
users = []
for row in q.execute():
users.append((row.email))
return trans.fill_template(
'/webapps/reports/registered_users_specified_date.mako',
specified_date=start_date,
day_label=day_label,
month_label=month_label,
year_label=year_label,
day_of_month=day_of_month,
users=users,
message=message)
def request_type_permissions(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
request_type_id = kwd.get('id', '')
try:
request_type = trans.sa_session.query(trans.model.RequestType).get(trans.security.decode_id(request_type_id))
except:
return invalid_id_redirect(trans, 'request_type', request_type_id, 'request type', action='browse_request_types')
roles = trans.sa_session.query(trans.model.Role) \
.filter(trans.model.Role.table.c.deleted == false()) \
.order_by(trans.model.Role.table.c.name)
if params.get('update_roles_button', False):
permissions = {}
for k, v in trans.model.RequestType.permitted_actions.items():
in_roles = [trans.sa_session.query(trans.model.Role).get(x) for x in util.listify(params.get(k + '_in', []))]
permissions[trans.app.security_agent.get_action(v.action)] = in_roles
trans.app.security_agent.set_request_type_permissions(request_type, permissions)
trans.sa_session.refresh(request_type)
message = "Permissions updated for request type '%s'" % request_type.name
return trans.fill_template('/admin/request_type/request_type_permissions.mako',
request_type=request_type,
roles=roles,
status=status,
message=message)
def user_disk_usage(self, trans, **kwd):
message = escape(util.restore_text(kwd.get('message', '')))
specs = sorter('disk_usage', kwd)
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
if order == "desc":
_order = True
else:
_order = False
user_cutoff = int(kwd.get('user_cutoff', 60))
# disk_usage isn't indexed
users = sorted(trans.sa_session.query(galaxy.model.User).all(),
key=operator.attrgetter(str(sort_id)),
reverse=_order)
if user_cutoff:
users = users[:user_cutoff]
return trans.fill_template(
'/webapps/reports/users_user_disk_usage.mako',
order=order,
arrow=arrow,
sort_id=sort_id,
users=users,
user_cutoff=user_cutoff,
message=message)
def user_per_month(self, trans, **kwd):
params = util.Params(kwd)
message = ''
specs = sorter('date', kwd)
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
email = util.restore_text(params.get('email', ''))
user_id = trans.security.decode_id(params.get('id', ''))
q = sa.select(
(self.select_month(
model.StoredWorkflow.table.c.create_time).label('date'),
sa.func.count(
model.StoredWorkflow.table.c.id).label('total_workflows')),
whereclause=model.StoredWorkflow.table.c.user_id == user_id,
from_obj=[model.StoredWorkflow.table],
group_by=self.group_by_month(
model.StoredWorkflow.table.c.create_time),
order_by=[_order])
all_workflows_user_month = sa.select(
(self.select_day(
model.StoredWorkflow.table.c.create_time).label('date'),
model.StoredWorkflow.table.c.id),
whereclause=model.StoredWorkflow.table.c.user_id == user_id,
from_obj=[model.StoredWorkflow.table])
trends = dict()
for workflow in all_workflows_user_month.execute():
workflow_day = int(workflow.date.strftime("%-d")) - 1
workflow_month = int(workflow.date.strftime("%-m"))
workflow_month_name = workflow.date.strftime("%B")
workflow_year = workflow.date.strftime("%Y")
key = str(workflow_month_name + workflow_year)
try:
trends[key][workflow_day] += 1
except KeyError:
workflow_year = int(workflow_year)
wday, day_range = calendar.monthrange(workflow_year,
workflow_month)
trends[key] = [0] * day_range
trends[key][workflow_day] += 1
workflows = []
for row in q.execute():
workflows.append(
(row.date.strftime("%Y-%m"), row.total_workflows,
row.date.strftime("%B"), row.date.strftime("%Y")))
return trans.fill_template(
'/webapps/reports/workflows_user_per_month.mako',
email=util.sanitize_text(email),
order=order,
arrow=arrow,
sort_id=sort_id,
trends=trends,
workflows=workflows,
message=message)
def user_per_month(self, trans, **kwd):
params = util.Params(kwd)
message = ''
email = util.restore_text(params.get('email', ''))
q = sa.select(
(sa.func.date_trunc(
'month', sa.func.date(
model.Job.table.c.create_time)).label('date'),
sa.func.count(model.Job.table.c.id).label('total_jobs')),
whereclause=sa.and_(
model.Job.table.c.session_id == model.GalaxySession.table.c.id,
model.GalaxySession.table.c.user_id == model.User.table.c.id,
model.User.table.c.email == email),
from_obj=[sa.join(model.Job.table, model.User.table)],
group_by=[
sa.func.date_trunc('month',
sa.func.date(model.Job.table.c.create_time))
],
order_by=[sa.desc('date')])
jobs = []
for row in q.execute():
jobs.append((row.date.strftime("%Y-%m"), row.total_jobs,
row.date.strftime("%B"), row.date.strftime("%Y")))
return trans.fill_template('/webapps/reports/jobs_user_per_month.mako',
email=util.sanitize_text(email),
jobs=jobs,
message=message)
def specified_date( self, trans, **kwd ):
message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
# If specified_date is not received, we'll default to the current month
specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) )
year, month, day = map( int, specified_date.split( "-" ) )
start_date = date( year, month, day )
end_date = start_date + timedelta( days=1 )
day_of_month = start_date.strftime( "%d" )
day_label = start_date.strftime( "%A" )
month_label = start_date.strftime( "%B" )
year_label = start_date.strftime( "%Y" )
q = sa.select( ( self.select_day( galaxy.model.User.table.c.create_time ).label( 'date' ),
galaxy.model.User.table.c.email ),
whereclause=sa.and_( galaxy.model.User.table.c.create_time >= start_date,
galaxy.model.User.table.c.create_time < end_date ),
from_obj=[ galaxy.model.User.table ],
order_by=[ galaxy.model.User.table.c.email ] )
users = []
for row in q.execute():
users.append( ( row.email ) )
return trans.fill_template( '/webapps/reports/registered_users_specified_date.mako',
specified_date=start_date,
day_label=day_label,
month_label=month_label,
year_label=year_label,
day_of_month=day_of_month,
users=users,
message=message )
def specified_month( self, trans, **kwd ):
message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
# If specified_date is not received, we'll default to the current month
specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) )
specified_month = specified_date[ :7 ]
year, month = map( int, specified_month.split( "-" ) )
start_date = date( year, month, 1 )
end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] )
month_label = start_date.strftime( "%B" )
year_label = start_date.strftime( "%Y" )
q = sa.select( ( self.select_day( galaxy.model.User.table.c.create_time ).label( 'date' ),
sa.func.count( galaxy.model.User.table.c.id ).label( 'num_users' ) ),
whereclause=sa.and_( galaxy.model.User.table.c.create_time >= start_date,
galaxy.model.User.table.c.create_time < end_date ),
from_obj=[ galaxy.model.User.table ],
group_by=self.group_by_day( galaxy.model.User.table.c.create_time ),
order_by=[ sa.desc( 'date' ) ] )
users = []
for row in q.execute():
users.append( ( row.date.strftime( "%Y-%m-%d" ),
row.date.strftime( "%d" ),
row.num_users,
row.date.strftime( "%A" ) ) )
return trans.fill_template( '/webapps/reports/registered_users_specified_month.mako',
month_label=month_label,
year_label=year_label,
month=month,
users=users,
message=message )
def create( self, trans, payload, **kwd ):
"""
create( trans, payload )
* POST /api/histories:
create a new history
:type payload: dict
:param payload: (optional) dictionary structure containing:
* name: the new history's name
* current: if passed, set the new history to be the user's 'current'
history
:rtype: dict
:returns: element view of new history
"""
hist_name = None
if payload.get( 'name', None ):
hist_name = restore_text( payload['name'] )
new_history = trans.app.model.History( user=trans.user, name=hist_name )
trans.sa_session.add( new_history )
trans.sa_session.flush()
#item = new_history.to_dict(view='element', value_mapper={'id':trans.security.encode_id})
item = self.get_history_dict( trans, new_history )
item['url'] = url_for( 'history', id=item['id'] )
#TODO: possibly default to True here - but favor explicit for now (and backwards compat)
current = string_as_bool( payload[ 'current' ] ) if 'current' in payload else False
if current:
trans.history = new_history
#TODO: copy own history
#TODO: import an importable history
#TODO: import from archive
return item
def view_editable_request_type(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
request_type_id = params.get('id', None)
try:
request_type = trans.sa_session.query(trans.model.RequestType).get(trans.security.decode_id(request_type_id))
except:
return invalid_id_redirect(trans, 'request_type', request_type_id, 'request type', action='browse_request_types')
# See if we have any associated templates
widgets = request_type.get_template_widgets(trans)
widget_fields_have_contents = self.widget_fields_have_contents(widgets)
# get all the external services selected till now
external_service_select_fields_list = []
for index, external_service in enumerate(request_type.external_services):
external_service_select_field = self.__build_external_service_select_field(trans,
'external_service_id_%i' % index,
external_service)
external_service_select_fields_list.append(external_service_select_field)
return trans.fill_template('/admin/request_type/edit_request_type.mako',
request_type=request_type,
widgets=widgets,
widget_fields_have_contents=widget_fields_have_contents,
external_service_select_fields_list=external_service_select_fields_list,
message=message,
status=status)
def edit_request_type(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
request_type_id = params.get('id', None)
try:
request_type = trans.sa_session.query(trans.model.RequestType).get(trans.security.decode_id(request_type_id))
except:
return invalid_id_redirect(trans, 'request_type', request_type_id, 'request type', action='browse_request_types')
# See if we have any associated templates
widgets = request_type.get_template_widgets(trans)
widget_fields_have_contents = self.widget_fields_have_contents(widgets)
# get all the external services selected till now
external_service_select_fields_list = []
external_services_list = self.__get_external_services(trans, request_type, **kwd)
if params.get('edit_request_type_button', False):
request_type = self.__save_request_type(trans, action='edit_request_type', **kwd)
message = 'Changes made to request type (%s) have been saved' % request_type.name
elif params.get('add_external_service_button', False):
external_services_list.append(None)
elif params.get('remove_external_service_button', False):
index = int(kwd['remove_external_service_button'].split(' ')[3]) - 1
del external_services_list[index]
for index, external_service in enumerate(external_services_list):
external_service_select_field = self.__build_external_service_select_field(trans,
'external_service_id_%i' % index,
external_service)
external_service_select_fields_list.append(external_service_select_field)
return trans.fill_template('/admin/request_type/edit_request_type.mako',
request_type=request_type,
widgets=widgets,
widget_fields_have_contents=widget_fields_have_contents,
external_service_select_fields_list=external_service_select_fields_list,
message=message,
status=status)
def registered_users_per_month(self, trans, **kwd):
message = escape(util.restore_text(kwd.get('message', '')))
specs = sorter('date', kwd)
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
q = sa.select(
(self.select_month(
galaxy.model.User.table.c.create_time).label('date'),
sa.func.count(galaxy.model.User.table.c.id).label('num_users')),
from_obj=[galaxy.model.User.table],
group_by=self.group_by_month(
galaxy.model.User.table.c.create_time),
order_by=[_order])
users = []
for row in q.execute():
users.append((row.date.strftime("%Y-%m"), row.num_users,
row.date.strftime("%B"), row.date.strftime("%Y")))
return trans.fill_template(
'/webapps/reports/registered_users_per_month.mako',
order=order,
arrow=arrow,
sort_id=sort_id,
users=users,
message=message)
def last_access_date(self, trans, **kwd):
message = util.restore_text(kwd.get('message', ''))
not_logged_in_for_days = kwd.get('not_logged_in_for_days', 90)
if not not_logged_in_for_days:
not_logged_in_for_days = 0
cutoff_time = datetime.utcnow() - timedelta(
days=int(not_logged_in_for_days))
now = strftime("%Y-%m-%d %H:%M:%S")
users = []
for user in trans.sa_session.query( galaxy.model.User ) \
.filter( galaxy.model.User.table.c.deleted==False ) \
.order_by( galaxy.model.User.table.c.email ):
if user.galaxy_sessions:
last_galaxy_session = user.galaxy_sessions[0]
if last_galaxy_session.update_time < cutoff_time:
users.append(
(user.email,
last_galaxy_session.update_time.strftime("%Y-%m-%d")))
else:
# The user has never logged in
users.append((user.email, "never logged in"))
users = sorted(users, key=operator.itemgetter(1), reverse=True)
return trans.fill_template(
'/webapps/reports/users_last_access_date.mako',
users=users,
not_logged_in_for_days=not_logged_in_for_days,
message=message)
def specified_month(self, trans, **kwd):
message = escape(util.restore_text(kwd.get('message', '')))
# If specified_date is not received, we'll default to the current month
specified_date = kwd.get('specified_date',
datetime.utcnow().strftime("%Y-%m-%d"))
specified_month = specified_date[:7]
year, month = map(int, specified_month.split("-"))
start_date = date(year, month, 1)
end_date = start_date + timedelta(
days=calendar.monthrange(year, month)[1])
month_label = start_date.strftime("%B")
year_label = start_date.strftime("%Y")
q = sa.select(
(self.select_day(
galaxy.model.User.table.c.create_time).label('date'),
sa.func.count(galaxy.model.User.table.c.id).label('num_users')),
whereclause=sa.and_(
galaxy.model.User.table.c.create_time >= start_date,
galaxy.model.User.table.c.create_time < end_date),
from_obj=[galaxy.model.User.table],
group_by=self.group_by_day(galaxy.model.User.table.c.create_time),
order_by=[sa.desc('date')])
users = []
for row in q.execute():
users.append(
(row.date.strftime("%Y-%m-%d"), row.date.strftime("%d"),
row.num_users, row.date.strftime("%A")))
return trans.fill_template(
'/webapps/reports/registered_users_specified_month.mako',
month_label=month_label,
year_label=year_label,
month=month,
users=users,
message=message)
def edit_username( self, trans, cntrller, **kwd ):
params = util.Params( kwd )
is_admin = cntrller == 'admin' and trans.user_is_admin()
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
user_id = params.get( 'user_id', None )
if user_id and is_admin:
user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) )
else:
user = trans.user
if user and params.get( 'change_username_button', False ):
username = kwd.get( 'username', '' )
if username:
message = validate_publicname( trans, username, user )
if message:
status = 'error'
else:
user.username = username
trans.sa_session.add( user )
trans.sa_session.flush()
message = 'The username has been updated with the changes.'
return trans.fill_template( '/webapps/tool_shed/user/username.mako',
cntrller=cntrller,
user=user,
username=user.username,
message=message,
status=status )
def history_per_user(self, trans, **kwd):
message = escape(util.restore_text(kwd.get('message', '')))
user_cutoff = int(kwd.get('user_cutoff', 60))
sorting = 0 if kwd.get('sorting', 'User') == 'User' else 1
descending = 1 if kwd.get('descending', 'desc') == 'desc' else -1
sorting_functions = [
lambda first, second: descending if first[0].lower() > second[0].lower() else -descending,
lambda first, second: descending if first[1] < second[1] else -descending]
req = sa.select(
(sa.func.count(galaxy.model.History.table.c.id).label('history'),
galaxy.model.User.table.c.username.label('username')),
from_obj=[sa.outerjoin(galaxy.model.History.table, galaxy.model.User.table)],
whereclause=galaxy.model.History.table.c.user_id == galaxy.model.User.table.c.id,
group_by=['username'],
order_by=[sa.desc('username'), 'history'])
histories = [(_.username if _.username is not None else "Unknown", _.history) for _ in req.execute()]
histories.sort(sorting_functions[sorting])
if user_cutoff != 0:
histories = histories[:user_cutoff]
return trans.fill_template('/webapps/reports/history_per_user.mako',
histories=histories,
user_cutoff=user_cutoff,
sorting=sorting,
descending=descending,
message=message)
def user_per_month( self, trans, **kwd ):
params = util.Params( kwd )
message = ''
specs = sorter( 'date', kwd )
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
email = util.restore_text( params.get( 'email', '' ) )
user_id = trans.security.decode_id( params.get( 'id', '' ) )
q = sa.select( ( self.select_month( model.StoredWorkflow.table.c.create_time ).label( 'date' ),
sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ),
whereclause=model.StoredWorkflow.table.c.user_id == user_id,
from_obj=[ model.StoredWorkflow.table ],
group_by=self.group_by_month( model.StoredWorkflow.table.c.create_time ),
order_by=[ _order ] )
workflows = []
for row in q.execute():
workflows.append( ( row.date.strftime( "%Y-%m" ),
row.total_workflows,
row.date.strftime( "%B" ),
row.date.strftime( "%Y" ) ) )
return trans.fill_template( '/webapps/reports/workflows_user_per_month.mako',
email=util.sanitize_text( email ),
order=order,
arrow=arrow,
sort_id=sort_id,
workflows=workflows,
message=message )
def registered_users_per_month(self, trans, **kwd):
message = escape(util.restore_text(kwd.get('message', '')))
specs = sorter('date', kwd)
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
q = sa.select((self.select_month(galaxy.model.User.table.c.create_time).label('date'),
sa.func.count(galaxy.model.User.table.c.id).label('num_users')),
from_obj=[galaxy.model.User.table],
group_by=self.group_by_month(galaxy.model.User.table.c.create_time),
order_by=[_order])
users = []
for row in q.execute():
users.append((row.date.strftime("%Y-%m"),
row.num_users,
row.date.strftime("%B"),
row.date.strftime("%Y")))
return trans.fill_template('/webapps/reports/registered_users_per_month.mako',
order=order,
arrow=arrow,
sort_id=sort_id,
users=users,
message=message)
def create(self, trans, payload, **kwd):
"""
create( trans, payload )
* POST /api/histories:
create a new history
:type payload: dict
:param payload: (optional) dictionary structure containing:
* name: the new history's name
* current: if passed, set the new history to be the user's
'current' history
* history_id: the id of the history to copy
* archive_source: the url that will generate the archive to import
* archive_type: 'url' (default)
:rtype: dict
:returns: element view of new history
"""
hist_name = None
if payload.get('name', None):
hist_name = restore_text(payload['name'])
#TODO: possibly default to True here - but favor explicit for now (and backwards compat)
set_as_current = string_as_bool(
payload['current']) if 'current' in payload else False
copy_this_history_id = payload.get('history_id', None)
if "archive_source" in payload:
archive_source = payload["archive_source"]
archive_type = payload.get("archive_type", "url")
self.queue_history_import(trans,
archive_type=archive_type,
archive_source=archive_source)
return {}
new_history = None
# if a history id was passed, copy that history
if copy_this_history_id:
original_history = self.mgrs.histories.get(
trans,
self._decode_id(trans, copy_this_history_id),
check_ownership=False,
check_accessible=True)
hist_name = hist_name or ("Copy of '%s'" % original_history.name)
new_history = original_history.copy(name=hist_name,
target_user=trans.user)
# otherwise, create a new empty history
else:
new_history = trans.app.model.History(user=trans.user,
name=hist_name)
trans.sa_session.add(new_history)
trans.sa_session.flush()
if set_as_current:
trans.history = new_history
item = {}
item = self.get_history_dict(trans, new_history)
item['url'] = url_for('history', id=item['id'])
return item
def handle_library_params(trans, params, folder_id, replace_dataset=None):
# FIXME: the received params has already been parsed by util.Params() by the time it reaches here,
# so no complex objects remain. This is not good because it does not allow for those objects to be
# manipulated here. The received params should be the original kwd from the initial request.
library_bunch = util.bunch.Bunch()
library_bunch.replace_dataset = replace_dataset
library_bunch.message = params.get('ldda_message', '')
# See if we have any template field contents
library_bunch.template_field_contents = {}
template_id = params.get('template_id', None)
library_bunch.folder = trans.sa_session.query(trans.app.model.LibraryFolder).get(trans.security.decode_id(folder_id))
# We are inheriting the folder's info_association, so we may have received inherited contents or we may have redirected
# here after the user entered template contents ( due to errors ).
if template_id not in [None, 'None']:
library_bunch.template = trans.sa_session.query(trans.app.model.FormDefinition).get(template_id)
for field in library_bunch.template.fields:
field_name = field['name']
if params.get(field_name, False):
field_value = util.restore_text(params.get(field_name, ''))
library_bunch.template_field_contents[field_name] = field_value
else:
library_bunch.template = None
library_bunch.roles = []
for role_id in util.listify(params.get('roles', [])):
role = trans.sa_session.query(trans.app.model.Role).get(role_id)
library_bunch.roles.append(role)
return library_bunch
def user_per_month( self, trans, **kwd ):
params = util.Params( kwd )
message = ''
email = util.restore_text( params.get( 'email', '' ) )
specs = sorter( 'date', kwd )
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
q = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ),
sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ),
whereclause=sa.and_( model.Job.table.c.session_id == model.GalaxySession.table.c.id,
model.GalaxySession.table.c.user_id == model.User.table.c.id,
model.User.table.c.email == email ),
from_obj=[ sa.join( model.Job.table, model.User.table ) ],
group_by=self.group_by_month( model.Job.table.c.create_time ),
order_by=[ _order ] )
jobs = []
for row in q.execute():
jobs.append( ( row.date.strftime( "%Y-%m" ),
row.total_jobs,
row.date.strftime( "%B" ),
row.date.strftime( "%Y" ) ) )
return trans.fill_template( '/webapps/reports/jobs_user_per_month.mako',
order=order,
arrow=arrow,
sort_id=sort_id,
id=kwd.get('id'),
email=util.sanitize_text( email ),
jobs=jobs, message=message )
def reject_request( self, trans, **kwd ):
params = util.Params( kwd )
request_id = params.get( 'id', '' )
status = params.get( 'status', 'done' )
message = params.get( 'message', 'done' )
if params.get( 'cancel_reject_button', False ):
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='view_request',
cntrller='requests_admin',
id=request_id ) )
try:
request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) )
except:
return invalid_id_redirect( trans, 'requests_admin', request_id )
# Validate
comment = util.restore_text( params.get( 'comment', '' ) )
if not comment:
status='error'
message='A reason for rejecting the request is required.'
return trans.fill_template( '/admin/requests/reject.mako',
cntrller='requests_admin',
request=request,
status=status,
message=message )
# Create an event with state 'Rejected' for this request
event_comment = "Sequencing request marked rejected by %s. Reason: %s " % ( trans.user.email, comment )
event = trans.model.RequestEvent( request, request.states.REJECTED, event_comment )
trans.sa_session.add( event )
trans.sa_session.flush()
message='Sequencing request (%s) has been rejected.' % request.name
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='browse_requests',
status=status,
message=message,
**kwd ) )