def manage_data_manager(self, trans, **kwd):
not_is_admin = not trans.user_is_admin()
if not_is_admin and not trans.app.config.enable_data_manager_user_view:
raise paste.httpexceptions.HTTPUnauthorized(
"This Galaxy instance is not configured to allow non-admins to view the data manager."
)
message = escape(kwd.get('message', ''))
status = escape(kwd.get('status', 'info'))
data_manager_id = kwd.get('id', None)
data_manager = trans.app.data_managers.get_manager(data_manager_id)
if data_manager is None:
return trans.response.send_redirect(
web.url_for(controller="data_manager",
action="index",
message="Invalid Data Manager (%s) was requested" %
data_manager_id,
status="error"))
jobs = list(
reversed([
assoc.job for assoc in trans.sa_session.query(
trans.app.model.DataManagerJobAssociation).filter_by(
data_manager_id=data_manager_id)
]))
return trans.fill_template("data_manager/manage_data_manager.mako",
data_manager=data_manager,
jobs=jobs,
view_only=not_is_admin,
message=message,
status=status)
def index( self, trans, **kwd ):
not_is_admin = not trans.user_is_admin()
if not_is_admin and not trans.app.config.enable_data_manager_user_view:
raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." )
message = escape( kwd.get( 'message', '' ) )
status = escape( kwd.get( 'status', 'info' ) )
return trans.fill_template( "data_manager/index.mako", data_managers=trans.app.data_managers, tool_data_tables=trans.app.tool_data_tables, view_only=not_is_admin, message=message, status=status )
def manage_data_table(self, trans, **kwd):
not_is_admin = not trans.user_is_admin()
if not_is_admin and not trans.app.config.enable_data_manager_user_view:
raise paste.httpexceptions.HTTPUnauthorized(
"This Galaxy instance is not configured to allow non-admins to view the data manager."
)
message = escape(kwd.get('message', ''))
status = escape(kwd.get('status', 'info'))
data_table_name = kwd.get('table_name', None)
if not data_table_name:
return trans.response.send_redirect(
web.url_for(controller="data_manager", action="index"))
data_table = trans.app.tool_data_tables.get(data_table_name, None)
if data_table is None:
return trans.response.send_redirect(
web.url_for(controller="data_manager",
action="index",
message="Invalid Data table (%s) was requested" %
data_table_name,
status="error"))
return trans.fill_template("data_manager/manage_data_table.mako",
data_table=data_table,
view_only=not_is_admin,
message=message,
status=status)
def index( self, trans, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = escape( kwd.get( 'status', 'done' ) )
default_action = kwd.get( 'default_action', None )
return trans.fill_template( "/library/index.mako",
default_action=default_action,
message=message,
status=status )
def index(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = escape(kwd.get('status', 'done'))
default_action = kwd.get('default_action', None)
return trans.fill_template("/library/index.mako",
default_action=default_action,
message=message,
status=status)
def manage_data_manager( self, trans, **kwd ):
not_is_admin = not trans.user_is_admin()
if not_is_admin and not trans.app.config.enable_data_manager_user_view:
raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." )
message = escape( kwd.get( 'message', '' ) )
status = escape( kwd.get( 'status', 'info' ) )
data_manager_id = kwd.get( 'id', None )
data_manager = trans.app.data_managers.get_manager( data_manager_id )
if data_manager is None:
return trans.response.send_redirect( web.url_for( controller="data_manager", action="index", message="Invalid Data Manager (%s) was requested" % data_manager_id, status="error" ) )
jobs = list( reversed( [ assoc.job for assoc in trans.sa_session.query( trans.app.model.DataManagerJobAssociation ).filter_by( data_manager_id=data_manager_id ) ] ) )
return trans.fill_template( "data_manager/manage_data_manager.mako", data_manager=data_manager, jobs=jobs, view_only=not_is_admin, message=message, status=status )
def manage_data_table( self, trans, **kwd ):
not_is_admin = not trans.user_is_admin()
if not_is_admin and not trans.app.config.enable_data_manager_user_view:
raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." )
message = escape( kwd.get( 'message', '' ) )
status = escape( kwd.get( 'status', 'info' ) )
data_table_name = kwd.get( 'table_name', None )
if not data_table_name:
return trans.response.send_redirect( web.url_for( controller="data_manager", action="index" ) )
data_table = trans.app.tool_data_tables.get( data_table_name, None )
if data_table is None:
return trans.response.send_redirect( web.url_for( controller="data_manager", action="index", message="Invalid Data table (%s) was requested" % data_table_name, status="error" ) )
return trans.fill_template( "data_manager/manage_data_table.mako", data_table=data_table, view_only=not_is_admin, message=message, status=status )
def view_job( self, trans, **kwd ):
not_is_admin = not trans.user_is_admin()
if not_is_admin and not trans.app.config.enable_data_manager_user_view:
raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." )
message = escape( kwd.get( 'message', '' ) )
status = escape( kwd.get( 'status', 'info' ) )
job_id = kwd.get( 'id', None )
try:
job_id = trans.security.decode_id( job_id )
job = trans.sa_session.query( trans.app.model.Job ).get( job_id )
except Exception, e:
job = None
log.error( "Bad job id (%s) passed to view_job: %s" % ( job_id, e ) )
def index(self, trans, **kwd):
not_is_admin = not trans.user_is_admin()
if not_is_admin and not trans.app.config.enable_data_manager_user_view:
raise paste.httpexceptions.HTTPUnauthorized(
"This Galaxy instance is not configured to allow non-admins to view the data manager."
)
message = escape(kwd.get('message', ''))
status = escape(kwd.get('status', 'info'))
return trans.fill_template("data_manager/index.mako",
data_managers=trans.app.data_managers,
tool_data_tables=trans.app.tool_data_tables,
view_only=not_is_admin,
message=message,
status=status)
def view_job(self, trans, **kwd):
not_is_admin = not trans.user_is_admin()
if not_is_admin and not trans.app.config.enable_data_manager_user_view:
raise paste.httpexceptions.HTTPUnauthorized(
"This Galaxy instance is not configured to allow non-admins to view the data manager."
)
message = escape(kwd.get('message', ''))
status = escape(kwd.get('status', 'info'))
job_id = kwd.get('id', None)
try:
job_id = trans.security.decode_id(job_id)
job = trans.sa_session.query(trans.app.model.Job).get(job_id)
except Exception, e:
job = None
log.error("Bad job id (%s) passed to view_job: %s" % (job_id, e))
def imp( self, trans, id ):
""" Import a visualization into user's workspace. """
# Set referer message.
referer = trans.request.referer
if referer is not "":
referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer)
else:
referer_message = "<a href='%s'>go to Galaxy's start page</a>" % web.url_for( '/' )
# Do import.
session = trans.sa_session
visualization = self.get_visualization( trans, id, check_ownership=False )
if visualization.importable == False:
return trans.show_error_message( "The owner of this visualization has disabled imports via this link.<br>You can %s" % referer_message, use_panels=True )
elif visualization.deleted:
return trans.show_error_message( "You can't import this visualization because it has been deleted.<br>You can %s" % referer_message, use_panels=True )
else:
# Create imported visualization via copy.
# TODO: need to handle custom db keys.
imported_visualization = visualization.copy( user=trans.user, title="imported: " + visualization.title )
# Persist
session = trans.sa_session
session.add( imported_visualization )
session.flush()
# Redirect to load galaxy frames.
return trans.show_ok_message(
message="""Visualization "%s" has been imported. <br>You can <a href="%s">start using this visualization</a> or %s."""
% ( visualization.title, web.url_for( controller='visualization' ), referer_message ), use_panels=True )
def data_source_redirect( self, trans, tool_id=None ):
"""
Redirects a user accessing a Data Source tool to its target action link.
This method will subvert mix-mode content blocking in several browsers when
accessing non-https data_source tools from an https galaxy server.
Tested as working on Safari 7.0 and FireFox 26
Subverting did not work on Chrome 31
"""
if tool_id is None:
return trans.response.send_redirect( url_for( controller="root", action="welcome" ) )
tool_version_select_field, tools, tool = self.__get_tool_components( tool_id,
tool_version=None,
get_loaded_tools_by_lineage=False,
set_selected=False )
# No tool matching the tool id, display an error (shouldn't happen)
if not tool:
log.error( "data_source_redirect called with tool id '%s' but no such tool exists", tool_id )
trans.log_event( "Tool id '%s' does not exist" % tool_id )
trans.response.status = 404
return trans.show_error_message("Tool '%s' does not exist." % ( escape(tool_id) ))
if isinstance( tool, DataSourceTool ):
link = url_for( tool.action, **tool.get_static_param_values( trans ) )
else:
link = url_for( controller='tool_runner', tool_id=tool.id )
return trans.response.send_redirect( link )
def imp( self, trans, id ):
""" Import a visualization into user's workspace. """
# Set referer message.
referer = trans.request.referer
if referer is not "":
referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer)
else:
referer_message = "<a href='%s'>go to Galaxy's start page</a>" % web.url_for( '/' )
# Do import.
session = trans.sa_session
visualization = self.get_visualization( trans, id, check_ownership=False )
if visualization.importable == False:
return trans.show_error_message( "The owner of this visualization has disabled imports via this link.<br>You can %s" % referer_message, use_panels=True )
elif visualization.deleted:
return trans.show_error_message( "You can't import this visualization because it has been deleted.<br>You can %s" % referer_message, use_panels=True )
else:
# Create imported visualization via copy.
# TODO: need to handle custom db keys.
imported_visualization = visualization.copy( user=trans.user, title="imported: " + visualization.title )
# Persist
session = trans.sa_session
session.add( imported_visualization )
session.flush()
# Redirect to load galaxy frames.
return trans.show_ok_message(
message="""Visualization "%s" has been imported. <br>You can <a href="%s">start using this visualization</a> or %s."""
% ( visualization.title, web.url_for( controller='visualization' ), referer_message ), use_panels=True )
def data_source_redirect( self, trans, tool_id=None ):
"""
Redirects a user accessing a Data Source tool to its target action link.
This method will subvert mix-mode content blocking in several browsers when
accessing non-https data_source tools from an https galaxy server.
Tested as working on Safari 7.0 and FireFox 26
Subverting did not work on Chrome 31
"""
if tool_id is None:
return trans.response.send_redirect( url_for( controller="root", action="welcome" ) )
tool_version_select_field, tools, tool = self.__get_tool_components( tool_id,
tool_version=None,
get_loaded_tools_by_lineage=False,
set_selected=False )
# No tool matching the tool id, display an error (shouldn't happen)
if not tool:
log.error( "data_source_redirect called with tool id '%s' but no such tool exists", tool_id )
trans.log_event( "Tool id '%s' does not exist" % tool_id )
trans.response.status = 404
return trans.show_error_message("Tool '%s' does not exist." % ( escape(tool_id) ))
if isinstance( tool, DataSourceTool ):
link = url_for( tool.action, **tool.get_static_param_values( trans ) )
else:
link = url_for( controller='tool_runner', tool_id=tool.id )
return trans.response.send_redirect( link )
def admin_api_keys( self, trans, cntrller, uid, **kwd ):
params = util.Params( kwd )
message = escape( util.restore_text( params.get( 'message', '' ) ) )
status = params.get( 'status', 'done' )
uid = params.get('uid', uid)
if params.get( 'new_api_key_button', False ):
new_key = trans.app.model.APIKeys()
new_key.user_id = uid
new_key.key = trans.app.security.get_new_guid()
trans.sa_session.add( new_key )
trans.sa_session.flush()
message = "A new web API key has been generated for (%s)" % escape( new_key.user.email )
status = "done"
return trans.response.send_redirect( web.url_for( controller='userskeys',
action='all_users',
cntrller=cntrller,
message=message,
status=status ) )
def index( self, trans, tool_id=None, from_noframe=None, **kwd ):
# No tool id passed, redirect to main page
if tool_id is None:
return trans.response.send_redirect( url_for( controller="root", action="welcome" ) )
# When the tool form is initially loaded, the received kwd will not include a 'refresh'
# entry (which only is included when another option is selected in the tool_version_select_field),
# so the default selected option should be the most recent version of the tool. The following
# check will mae sure this occurs.
refreshed_on_change = kwd.get( 'refresh', False )
tool_version_select_field, tools, tool = self.__get_tool_components( tool_id,
tool_version=None,
get_loaded_tools_by_lineage=False,
set_selected=refreshed_on_change )
# No tool matching the tool id, display an error (shouldn't happen)
if not tool:
log.error( "index called with tool id '%s' but no such tool exists", tool_id )
trans.log_event( "Tool id '%s' does not exist" % tool_id )
trans.response.status = 404
return trans.show_error_message("Tool '%s' does not exist." % ( escape(tool_id) ))
if tool.require_login and not trans.user:
message = "You must be logged in to use this tool."
status = "info"
redirect = url_for( controller='tool_runner', action='index', tool_id=tool_id, **kwd )
return trans.response.send_redirect( url_for( controller='user',
action='login',
cntrller='user',
message=message,
status=status,
redirect=redirect ) )
params = galaxy.util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers
#do param translation here, used by datasource tools
if tool.input_translator:
tool.input_translator.translate( params )
# We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ),
# so make sure to create a new history if we've never had one before.
history = tool.get_default_history_by_trans( trans, create=True )
template, vars = tool.handle_input( trans, params.__dict__ )
if len( params ) > 0:
trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id )
add_frame = AddFrameData()
add_frame.debug = trans.debug
if from_noframe is not None:
add_frame.wiki_url = trans.app.config.wiki_url
add_frame.from_noframe = True
return trans.fill_template( template,
history=history,
toolbox=self.get_toolbox(),
tool_version_select_field=tool_version_select_field,
tool=tool,
util=galaxy.util,
add_frame=add_frame,
form_input_auto_focus=True,
**vars )
def share( self, trans, id=None, email="", use_panels=False ):
""" Handle sharing a visualization with a particular user. """
msg = mtype = None
visualization = self.get_visualization( trans, id, check_ownership=True )
if email:
other = trans.sa_session.query( model.User ) \
.filter( and_( model.User.table.c.email==email,
model.User.table.c.deleted==False ) ) \
.first()
if not other:
mtype = "error"
msg = ( "User '%s' does not exist" % escape( email ) )
elif other == trans.get_user():
mtype = "error"
msg = ( "You cannot share a visualization with yourself" )
elif trans.sa_session.query( model.VisualizationUserShareAssociation ) \
.filter_by( user=other, visualization=visualization ).count() > 0:
mtype = "error"
msg = ( "Visualization already shared with '%s'" % escape( email ) )
else:
share = model.VisualizationUserShareAssociation()
share.visualization = visualization
share.user = other
session = trans.sa_session
session.add( share )
self.create_item_slug( session, visualization )
session.flush()
viz_title = escape( visualization.title )
other_email = escape( other.email )
trans.set_message( "Visualization '%s' shared with user '%s'" % ( viz_title, other_email ) )
return trans.response.send_redirect( web.url_for(controller='visualization', action='sharing', id=id ) )
return trans.fill_template( "/ind_share_base.mako",
message = msg,
messagetype = mtype,
item=visualization,
email=email,
use_panels=use_panels )
def share( self, trans, id=None, email="", use_panels=False ):
""" Handle sharing a visualization with a particular user. """
msg = mtype = None
visualization = self.get_visualization( trans, id, check_ownership=True )
if email:
other = trans.sa_session.query( model.User ) \
.filter( and_( model.User.table.c.email==email,
model.User.table.c.deleted==False ) ) \
.first()
if not other:
mtype = "error"
msg = ( "User '%s' does not exist" % escape( email ) )
elif other == trans.get_user():
mtype = "error"
msg = ( "You cannot share a visualization with yourself" )
elif trans.sa_session.query( model.VisualizationUserShareAssociation ) \
.filter_by( user=other, visualization=visualization ).count() > 0:
mtype = "error"
msg = ( "Visualization already shared with '%s'" % escape( email ) )
else:
share = model.VisualizationUserShareAssociation()
share.visualization = visualization
share.user = other
session = trans.sa_session
session.add( share )
self.create_item_slug( session, visualization )
session.flush()
viz_title = escape( visualization.title )
other_email = escape( other.email )
trans.set_message( "Visualization '%s' shared with user '%s'" % ( viz_title, other_email ) )
return trans.response.send_redirect( web.url_for(controller='visualization', action='sharing', id=id ) )
return trans.fill_template( "/ind_share_base.mako",
message = msg,
messagetype = mtype,
item=visualization,
email=email,
use_panels=use_panels )
def all_users( self, trans, cntrller="userskeys", **kwd ):
params = util.Params( kwd )
message = escape( util.restore_text( params.get( 'message', '' ) ) )
status = params.get( 'status', 'done' )
users = []
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 ):
uid = int(user.id)
userkey = ""
for api_user in trans.sa_session.query(trans.app.model.APIKeys) \
.filter( trans.app.model.APIKeys.user_id == uid):
userkey = api_user.key
users.append({'uid':uid, 'email':user.email, 'key':userkey})
return trans.fill_template( 'webapps/galaxy/user/list_users.mako',
cntrller=cntrller,
users=users,
message=message,
status=status )
class DataManager(BaseUIController):
@web.expose
def index(self, trans, **kwd):
not_is_admin = not trans.user_is_admin()
if not_is_admin and not trans.app.config.enable_data_manager_user_view:
raise paste.httpexceptions.HTTPUnauthorized(
"This Galaxy instance is not configured to allow non-admins to view the data manager."
)
message = escape(kwd.get('message', ''))
status = escape(kwd.get('status', 'info'))
return trans.fill_template("data_manager/index.mako",
data_managers=trans.app.data_managers,
tool_data_tables=trans.app.tool_data_tables,
view_only=not_is_admin,
message=message,
status=status)
@web.expose
def manage_data_manager(self, trans, **kwd):
not_is_admin = not trans.user_is_admin()
if not_is_admin and not trans.app.config.enable_data_manager_user_view:
raise paste.httpexceptions.HTTPUnauthorized(
"This Galaxy instance is not configured to allow non-admins to view the data manager."
)
message = escape(kwd.get('message', ''))
status = escape(kwd.get('status', 'info'))
data_manager_id = kwd.get('id', None)
data_manager = trans.app.data_managers.get_manager(data_manager_id)
if data_manager is None:
return trans.response.send_redirect(
web.url_for(controller="data_manager",
action="index",
message="Invalid Data Manager (%s) was requested" %
data_manager_id,
status="error"))
jobs = list(
reversed([
assoc.job for assoc in trans.sa_session.query(
trans.app.model.DataManagerJobAssociation).filter_by(
data_manager_id=data_manager_id)
]))
return trans.fill_template("data_manager/manage_data_manager.mako",
data_manager=data_manager,
jobs=jobs,
view_only=not_is_admin,
message=message,
status=status)
@web.expose
def view_job(self, trans, **kwd):
not_is_admin = not trans.user_is_admin()
if not_is_admin and not trans.app.config.enable_data_manager_user_view:
raise paste.httpexceptions.HTTPUnauthorized(
"This Galaxy instance is not configured to allow non-admins to view the data manager."
)
message = escape(kwd.get('message', ''))
status = escape(kwd.get('status', 'info'))
job_id = kwd.get('id', None)
try:
job_id = trans.security.decode_id(job_id)
job = trans.sa_session.query(trans.app.model.Job).get(job_id)
except Exception, e:
job = None
log.error("Bad job id (%s) passed to view_job: %s" % (job_id, e))
if not job:
return trans.response.send_redirect(
web.url_for(controller="data_manager",
action="index",
message="Invalid job (%s) was requested" % job_id,
status="error"))
data_manager_id = job.data_manager_association.data_manager_id
data_manager = trans.app.data_managers.get_manager(data_manager_id)
hdas = [assoc.dataset for assoc in job.get_output_datasets()]
data_manager_output = []
error_messages = []
for hda in hdas:
try:
data_manager_json = loads(open(hda.get_file_name()).read())
except Exception, e:
data_manager_json = {}
error_messages.append(
escape(
"Unable to obtain data_table info for hda (%s): %s" %
(hda.id, e)))
values = []
for key, value in data_manager_json.get('data_tables',
{}).iteritems():
values.append((key, value))
data_manager_output.append(values)
def index( self, trans, tool_id=None, from_noframe=None, **kwd ):
# No tool id passed, redirect to main page
if tool_id is None:
return trans.response.send_redirect( url_for( controller="root", action="welcome" ) )
# When the tool form is initially loaded, the received kwd will not include a 'refresh'
# entry (which only is included when another option is selected in the tool_version_select_field),
# so the default selected option should be the most recent version of the tool. The following
# check will mae sure this occurs.
refreshed_on_change = kwd.get( 'refresh', False )
tool_version_select_field, tools, tool = self.__get_tool_components( tool_id,
tool_version=None,
get_loaded_tools_by_lineage=False,
set_selected=refreshed_on_change )
# No tool matching the tool id, display an error (shouldn't happen)
if not tool or not tool.allow_user_access( trans.user ):
log.error( "index called with tool id '%s' but no such tool exists", tool_id )
trans.log_event( "Tool id '%s' does not exist" % tool_id )
trans.response.status = 404
return trans.show_error_message("Tool '%s' does not exist." % ( escape(tool_id) ))
if tool.require_login and not trans.user:
message = "You must be logged in to use this tool."
status = "info"
redirect = url_for( controller='tool_runner', action='index', tool_id=tool_id, **kwd )
return trans.response.send_redirect( url_for( controller='user',
action='login',
cntrller='user',
message=message,
status=status,
redirect=redirect ) )
def _validated_params_for( kwd ):
params = galaxy.util.Params( kwd, sanitize=False ) # Sanitize parameters when substituting into command line via input wrappers
#do param translation here, used by datasource tools
if tool.input_translator:
tool.input_translator.translate( params )
return params
params = _validated_params_for( kwd )
# We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ),
# so make sure to create a new history if we've never had one before.
history = tool.get_default_history_by_trans( trans, create=True )
try:
template, vars = tool.handle_input( trans, params.__dict__ )
except KeyError:
# This error indicates (or at least can indicate) there was a
# problem with the stored tool_state - it is incompatible with
# this variant of the tool - possibly because the tool changed
# or because the tool version changed.
del kwd[ "tool_state" ]
params = _validated_params_for( kwd )
template, vars = tool.handle_input( trans, params.__dict__ )
if len( params ) > 0:
trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id )
add_frame = AddFrameData()
add_frame.debug = trans.debug
if from_noframe is not None:
add_frame.wiki_url = trans.app.config.wiki_url
add_frame.from_noframe = True
return trans.fill_template( template,
history=history,
toolbox=self.get_toolbox(),
tool_version_select_field=tool_version_select_field,
tool=tool,
util=galaxy.util,
add_frame=add_frame,
form_input_auto_focus=True,
**vars )
