commit/galaxy-central: greg: Add the ability to upload exported Galaxy workflow files. Makew a first pass at fixing bugs when importing a workflow into a Galaxy instance that does not have all of the required tools. This code is still full of bugs.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/5cfec3f4f17c/ changeset: 5cfec3f4f17c user: greg date: 2011-10-14 18:14:54 summary: Add the ability to upload exported Galaxy workflow files. Makew a first pass at fixing bugs when importing a workflow into a Galaxy instance that does not have all of the required tools. This code is still full of bugs. affected #: 8 files (-1 bytes)
--- a/lib/galaxy/web/base/controller.py Fri Oct 14 09:58:59 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Fri Oct 14 12:14:54 2011 -0400 @@ -1299,9 +1299,8 @@ @web.require_admin def index( self, trans, **kwd ): webapp = kwd.get( 'webapp', 'galaxy' ) - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if webapp == 'galaxy': cloned_repositories = trans.sa_session.query( trans.model.ToolShedRepository ) \ .filter( trans.model.ToolShedRepository.deleted == False ) \ @@ -1320,10 +1319,16 @@ @web.require_admin def center( self, trans, **kwd ): webapp = kwd.get( 'webapp', 'galaxy' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if webapp == 'galaxy': - return trans.fill_template( '/webapps/galaxy/admin/center.mako' ) + return trans.fill_template( '/webapps/galaxy/admin/center.mako', + message=message, + status=status ) else: - return trans.fill_template( '/webapps/community/admin/center.mako' ) + return trans.fill_template( '/webapps/community/admin/center.mako', + message=message, + status=status ) @web.expose @web.require_admin def reload_tool( self, trans, **kwd ):
--- a/lib/galaxy/web/controllers/workflow.py Fri Oct 14 09:58:59 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Fri Oct 14 12:14:54 2011 -0400 @@ -792,10 +792,10 @@ 'data_outputs': [], 'form_html': invalid_tool_form_html, 'annotation' : annotation_str, + 'input_connections' : {}, 'post_job_actions' : {}, 'workflow_outputs' : [] } - step_dict['input_connections'] = input_conn_dict # Position step_dict['position'] = step.position # Add to return value @@ -958,19 +958,13 @@ """ stored = self.get_stored_workflow( trans, id, check_ownership=False, check_accessible=True ) return trans.fill_template( "/workflow/export.mako", item=stored, use_panels=True ) - - @web.expose @web.require_login( "use workflows" ) def import_from_myexp( self, trans, myexp_id, myexp_username=None, myexp_password=None ): """ Imports a workflow from the myExperiment website. """ - - # # Get workflow XML. - # - # Get workflow content. conn = httplib.HTTPConnection( self.__myexp_url ) # NOTE: blocks web thread. @@ -985,17 +979,16 @@ parser = SingleTagContentsParser( "content" ) parser.feed( workflow_xml ) workflow_content = base64.b64decode( parser.tag_content ) - - # # Process workflow XML and create workflow. - # parser = SingleTagContentsParser( "galaxy_json" ) parser.feed( workflow_content ) workflow_dict = from_json_string( parser.tag_content ) - # Create workflow. - workflow = self._workflow_from_dict( trans, workflow_dict, source="myExperiment" ).latest_workflow - + workflow, missing_tool_tups = self._workflow_from_dict( trans, workflow_dict, source="myExperiment" ).latest_workflow + if missing_tool_tups: + # TODO: handle the case where the imported workflow requires tools that are not available in + # the local Galaxy instance. + pass # Provide user feedback. if workflow.has_errors: return trans.show_warn_message( "Imported, but some steps in this workflow have validation errors" ) @@ -1003,7 +996,6 @@ return trans.show_warn_message( "Imported, but this workflow contains cycles" ) else: return trans.show_message( "Workflow '%s' imported" % workflow.name ) - @web.expose @web.require_login( "use workflows" ) def export_to_myexp( self, trans, id, myexp_username, myexp_password ): @@ -1102,40 +1094,91 @@ return stored_dict
@web.expose - def import_workflow( self, trans, workflow_text=None, url=None ): - if workflow_text is None and url is None: - return form( url_for(), "Import Workflow", submit_text="Import", use_panels=True ) \ - .add_text( "url", "Workflow URL", "" ) \ - .add_input( "textarea", "Encoded workflow (as generated by export workflow)", "workflow_text", "" ) - if url: - # Load workflow from external URL - # NOTE: blocks the web thread. - try: - workflow_data = urllib2.urlopen( url ).read() - except Exception, e: - return trans.show_error_message( "Failed to open URL %s<br><br>Message: %s" % ( url, str( e ) ) ) - else: - workflow_data = workflow_text - # Convert incoming workflow data from json - try: - data = simplejson.loads( workflow_data ) - except Exception, e: - return trans.show_error_message( "Data at '%s' does not appear to be a Galaxy workflow<br><br>Message: %s" % ( url, str( e ) ) ) - - # Create workflow. - workflow = self._workflow_from_dict( trans, data, source="uploaded file" ).latest_workflow - - # Provide user feedback and show workflow list. - if workflow.has_errors: - trans.set_message( "Imported, but some steps in this workflow have validation errors", - type="warning" ) - if workflow.has_cycles: - trans.set_message( "Imported, but this workflow contains cycles", - type="warning" ) - else: - trans.set_message( "Workflow '%s' imported" % workflow.name ) - return self.list( trans ) - + def import_workflow( self, trans, **kwd ): + url = kwd.get( 'url', '' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + if kwd.get( 'import_button', False ): + workflow_data = None + if url: + # Load workflow from external URL + # NOTE: blocks the web thread. + try: + workflow_data = urllib2.urlopen( url ).read() + except Exception, e: + message = "Failed to open URL: <b>%s</b><br>Exception: %s" % ( url, str( e ) ) + status = 'error' + else: + # Load workflow from browsed file. + file_data = kwd.get( 'file_data', '' ) + if file_data in ( '', None ): + message = 'No exported Galaxy workflow files were selected.' + status = 'error' + else: + uploaded_file = file_data.file + uploaded_file_name = uploaded_file.name + uploaded_file_filename = file_data.filename + if os.path.getsize( os.path.abspath( uploaded_file_name ) ) > 0: + # We're reading the file as text so we can re-use the existing code below. + # This may not be ideal... + workflow_data = uploaded_file.read() + else: + message= 'You attempted to upload an empty file.' + status = 'error' + if workflow_data: + # Convert incoming workflow data from json + try: + data = simplejson.loads( workflow_data ) + except Exception, e: + data = None + message = "The data content does not appear to be a Galaxy workflow.<br/>Exception: %s" % str( e ) + status = 'error' + if data: + # Create workflow if possible. If a required tool is not available in the local + # Galaxy instance, the tool information will be available in the step_dict. + workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="uploaded file" ) + workflow = workflow.latest_workflow + # Provide user feedback and show workflow list. + if workflow.has_errors: + message += "Imported, but some steps in this workflow have validation errors. " + status = "error" + if workflow.has_cycles: + message += "Imported, but this workflow contains cycles. " + status = "error" + else: + message += "Workflow '%s' imported successfully. " % workflow.name + if missing_tool_tups: + if trans.user_is_admin(): + # A required tool is not available in the local Galaxy instance. + # TODO: It would sure be nice to be able to redirec to a mako tempalte here that displays a nice + # page including the links to the configured tool shed instead of this stupd message, but trying + # to get the panels back is a nightmare since workflow eliminates the Galaxy panels. Someone + #involved in workflow development needs to figure out what it will take to get the Galaxy panels back... + galaxy_url = trans.request.host + message += "The workflow requires the following tools that are not available in this Galaxy instance." + message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>" + for missing_tool_tup in missing_tool_tups: + missing_tool_id = missing_tool_tup[0] + for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items(): + if tool_shed_url.endswith( '/' ): + tool_shed_url = tool_shed_url.rstrip( '/' ) + url = '%s/repository/find_tools?tool_id=%s&galaxy_url=%s&webapp=community' % ( tool_shed_url, missing_tool_id, galaxy_url ) + message += '<a href="%s">%s</a><br/>' % ( url, tool_shed_name ) + status = 'error' + return trans.response.send_redirect( web.url_for( controller='admin', + action='index', + webapp='galaxy', + message=message, + status=status ) ) + else: + # TODO: Figure out what to do here... + pass + return self.list( trans ) + return trans.fill_template( "workflow/import.mako", + url=url, + message=message, + status=status, + use_panels=True ) @web.json def get_datatypes( self, trans ): ext_to_class_name = dict() @@ -1605,8 +1648,7 @@ step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) annotation_str = "" if step_annotation: - annotation_str = step_annotation.annotation - + annotation_str = step_annotation.annotation # Step info step_dict = { 'id': step.order_index, @@ -1620,7 +1662,6 @@ ## 'data_outputs': module.get_data_outputs(), 'annotation' : annotation_str } - # Add post-job actions to step dict. if module.type == 'tool': pja_dict = {} @@ -1629,7 +1670,6 @@ output_name = pja.output_name, action_arguments = pja.action_arguments ) step_dict[ 'post_job_actions' ] = pja_dict - # Data inputs step_dict['inputs'] = [] if module.type == "data_input": @@ -1647,7 +1687,6 @@ for partname, partval in val.items(): if type( partval ) == RuntimeValue: step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) - # User outputs step_dict['user_outputs'] = [] """ @@ -1668,7 +1707,6 @@ if type( module ) is ToolModule: for output in module.get_data_outputs(): step_dict['outputs'].append( { 'name' : output['name'], 'type' : output['extensions'][0] } ) - # Connections input_connections = step.input_connections if step.type is None or step.type == 'tool': @@ -1692,7 +1730,6 @@ # Add to return value data['steps'][step.order_index] = step_dict return data - def _workflow_from_dict( self, trans, data, source=None ): """ Creates a workflow from a dict. Created workflow is stored in the database and returned. @@ -1714,8 +1751,12 @@ # The editor will provide ids for each step that we don't need to save, # but do need to use to make connections steps_by_external_id = {} + # Keep track of tools required by the workflow that are not available in + # the local Galaxy instance. Each tuple in the list of missing_tool_tups + # will be ( tool_id, tool_name, tool_version ). + missing_tool_tups = [] # First pass to build step objects and populate basic values - for key, step_dict in data['steps'].iteritems(): + for key, step_dict in data[ 'steps' ].iteritems(): # Create the model class for the step step = model.WorkflowStep() steps.append( step ) @@ -1723,6 +1764,11 @@ # FIXME: Position should be handled inside module step.position = step_dict['position'] module = module_factory.from_dict( trans, step_dict, secure=False ) + if module.tool is None: + # A required tool is not available in the local Galaxy instance. + missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) + if missing_tool_tup not in missing_tool_tups: + missing_tool_tups.append( missing_tool_tup ) module.save_to_step( step ) if step.tool_errors: workflow.has_errors = True @@ -1761,7 +1807,7 @@ # Persist trans.sa_session.add( stored ) trans.sa_session.flush() - return stored + return stored, missing_tool_tups
## ---- Utility methods -------------------------------------------------------
--- a/lib/galaxy/webapps/community/controllers/repository.py Fri Oct 14 09:58:59 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Fri Oct 14 12:14:54 2011 -0400 @@ -251,8 +251,7 @@ RevisionColumn( "Revision" ), UserColumn( "Owner", model_class=model.User, - attach_popup=False, - key="User.username" ) + attach_popup=False ) ] operations = [] standard_filters = []
--- a/lib/galaxy/workflow/modules.py Fri Oct 14 09:58:59 2011 -0400 +++ b/lib/galaxy/workflow/modules.py Fri Oct 14 12:14:54 2011 -0400 @@ -8,6 +8,9 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.jobs.actions.post import ActionBox from galaxy.model import PostJobAction +import logging + +log = logging.getLogger( __name__ )
class WorkflowModule( object ):
@@ -163,29 +166,46 @@ def __init__( self, trans, tool_id ): self.trans = trans self.tool_id = tool_id - self.tool = trans.app.toolbox.tools_by_id[ tool_id ] + try: + self.tool = trans.app.toolbox.tools_by_id[ tool_id ] + except KeyError, e: + # Handle the case where the workflow requires a tool not available in the local Galaxy instance. + self.tool = None + # TODO: Instead of parsing the guid, get the tool_id and version from the shed_tool_conf.xml, + # which requires enhancements to the tool loading process. + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if available_tool_id.find( tool_id ) >=0: + # We're attempting to match tool id against a tool guid. + # TODO: match by tool_id (and version if we attempt that, but + # workflows will break) is not good enough because + # 2 tools installed from a tool shed could both match this. We + # need to present a select list here. + self.tool = available_tool + break self.post_job_actions = {} self.workflow_outputs = [] self.state = None - self.errors = None - + if self.tool: + self.errors = None + else: + self.errors = {} + self.errors[ tool_id ] = 'Tool unavailable' @classmethod def new( Class, trans, tool_id=None ): module = Class( trans, tool_id ) module.state = module.tool.new_state( trans, all_pages=True ) return module - @classmethod def from_dict( Class, trans, d, secure=True ): - tool_id = d['tool_id'] + tool_id = d[ 'tool_id' ] module = Class( trans, tool_id ) module.state = DefaultToolState() - module.state.decode( d["tool_state"], module.tool, module.trans.app, secure=secure ) + if module.tool is not None: + module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure ) module.errors = d.get( "tool_errors", None ) - module.post_job_actions = d.get("post_job_actions", {}) - module.workflow_outputs = d.get("workflow_outputs", []) + module.post_job_actions = d.get( "post_job_actions", {} ) + module.workflow_outputs = d.get( "workflow_outputs", [] ) return module - @classmethod def from_workflow_step( Class, trans, step ): tool_id = step.tool_id @@ -203,12 +223,15 @@ pjadict[pja.action_type] = pja module.post_job_actions = pjadict return module - def save_to_step( self, step ): step.type = self.type step.tool_id = self.tool_id - step.tool_version = self.get_tool_version() - step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app ) + if self.tool: + step.tool_version = self.get_tool_version() + step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app ) + else: + step.tool_version = None + step.tool_inputs = None step.tool_errors = self.errors for k, v in self.post_job_actions.iteritems(): # Must have action_type, step. output and a_args are optional. @@ -221,7 +244,6 @@ else: action_arguments = None n_p = PostJobAction(v['action_type'], step, output_name, action_arguments) - def get_name( self ): return self.tool.name def get_tool_id( self ): @@ -234,7 +256,6 @@ return self.errors def get_tooltip( self ): return self.tool.help - def get_data_inputs( self ): data_inputs = [] def callback( input, value, prefixed_name, prefixed_label ): @@ -268,15 +289,12 @@ formats.append( format ) data_outputs.append( dict( name=name, extensions=formats ) ) return data_outputs - def get_post_job_actions( self ): return self.post_job_actions - def get_config_form( self ): self.add_dummy_datasets() return self.trans.fill_template( "workflow/editor_tool_form.mako", tool=self.tool, values=self.state.inputs, errors=( self.errors or {} ) ) - def update_state( self, incoming ): # Build a callback that handles setting an input to be required at # runtime. We still process all other parameters the user might have @@ -306,10 +324,8 @@ # Update state using incoming values errors = self.tool.update_state( self.trans, self.tool.inputs, self.state.inputs, incoming, item_callback=item_callback ) self.errors = errors or None - def check_and_update_state( self ): return self.tool.check_and_update_param_values( self.state.inputs, self.trans ) - def add_dummy_datasets( self, connections=None): if connections: # Store onnections by input name @@ -324,8 +340,7 @@ if connections is None or prefixed_name in input_connections_by_name: return DummyDataset() visit_input_values( self.tool.inputs, self.state.inputs, callback ) - - + class WorkflowModuleFactory( object ): def __init__( self, module_types ): self.module_types = module_types
--- a/templates/webapps/galaxy/admin/center.mako Fri Oct 14 09:58:59 2011 -0400 +++ b/templates/webapps/galaxy/admin/center.mako Fri Oct 14 12:14:54 2011 -0400 @@ -1,187 +1,192 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /><%def name="title()">Galaxy Administration</%def><h2>Administration</h2>
-<p>The menu on the left provides the following features</p> -<ul> - <li><strong>Security</strong> - see the <strong>Data Security and Data Libraries</strong> section below for details +%if message: + ${render_msg( message, status )} +%else: + <p>The menu on the left provides the following features</p> + <ul> + <li><strong>Security</strong> - see the <strong>Data Security and Data Libraries</strong> section below for details + <p/> + <ul> + <li> + <strong>Manage users</strong> - provides a view of the registered users and all groups and non-private roles associated + with each user. + </li> + <p/> + <li> + <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with + each group (both private and non-private roles). The group names include a link to a page that allows you to manage the users and + roles that are associated with the group. + </li> + <p/> + <li> + <strong>Manage roles</strong> - provides a view of all non-private roles along with the role type, and the users and groups that + are associated with the role. The role names include a link to a page that allows you to manage the users and groups that are associated + with the role. The page also includes a view of the data library datasets that are associated with the role and the permissions applied + to each dataset. + </li> + </ul> + </li><p/> - <ul> - <li> - <strong>Manage users</strong> - provides a view of the registered users and all groups and non-private roles associated - with each user. - </li> + <li><strong>Data</strong><p/> - <li> - <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with - each group (both private and non-private roles). The group names include a link to a page that allows you to manage the users and - roles that are associated with the group. - </li> + <ul> + <li> + <strong>Manage data libraries</strong> - Data libraries enable a Galaxy administrator to upload datasets into a data library. Currently, + only administrators can create data libraries. + <p/> + When a data library is first created, it is considered "public" since it will be displayed in the "Data Libraries" view for any user, even + those that are not logged in. The Galaxy administrator can restrict access to a data library by associating roles with the data library's + "access library" permission. This permission will conservatively override the [dataset] "access" permission for the data library's contained + datasets. + <p/> + For example, if a data library's "access library" permission is associated with Role1 and the data library contains "public" datasets, the + data library will still only be displayed to those users that have Role1. However, if the data library's "access library" permission is + associated with both Role1 and Role2 and the data library contains datasets whose [dataset] "access" permission is associated with only Role1, + then users that have Role2 will be able to access the library, but will not see those contained datasets whose [dataset] "access" permission + is associated with only Role1. + <p/> + In addition to the "access library" permission, permission to perform the following functions on the data library (and it's contents) can + be granted to users (a library item is one of: a data library, a library folder, a library dataset). + <p/> + <ul> + <li><strong>add library item</strong> - Users that have the role can add library items to this data library or folder</li> + <li><strong>modify library item</strong> - Users that have the role can modify this library item</li> + <li><strong>manage library permissions</strong> - Users that have the role can manage permissions applied to this library item</li> + </ul> + <p/> + The default behavior is for no permissions to be applied to a data library item, but applied permissions are inherited downward (with the exception + of the "access library" permission, which is only available on the data library itself). Because of this, it is important to set desired permissions + on a new data library when it is created. When this is done, new folders and datasets added to the data library will automatically inherit those + permissions. In the same way, permissions can be applied to a folder, which will be automatically inherited by all contained datasets and sub-folders. + <p/> + The "Data Libraries" menu item allows users to access the datasets in a data library as long as they are not restricted from accessing them. + Importing a library dataset into a history will not make a copy of the dataset, but will be a "pointer" to the dataset on disk. This + approach allows for multiple users to use a single (possibly very large) dataset file. + </li> + </ul> + </li> + <p/> + <li><strong>Server</strong><p/> - <li> - <strong>Manage roles</strong> - provides a view of all non-private roles along with the role type, and the users and groups that - are associated with the role. The role names include a link to a page that allows you to manage the users and groups that are associated - with the role. The page also includes a view of the data library datasets that are associated with the role and the permissions applied - to each dataset. - </li> - </ul> - </li> + <ul> + <li> + <strong>Reload a tool's configuration</strong> - allows a new version of a tool to be loaded while the server is running + </li> + <p/> + <li> + <strong>Profile memory usage</strong> - measures system memory used for certain Galaxy functions + </li> + <p/> + <li> + <strong>Manage jobs</strong> - displays all jobs that are currently not finished (i.e., their state is new, waiting, queued, or + running). Administrators are able to cleanly stop long-running jobs. + </li> + </ul> + </li> + <p/> + <li><strong>Forms</strong> + <p/>To be completed + </li> + <p/> + <li><strong>Sequencing Requests</strong> + <p/>To be completed + </li> + <p/> + <li><strong>Cloud</strong> + <p/>To be completed + </li> + </ul><p/> - <li><strong>Data</strong> + <p><strong>Data Security and Data Libraries</strong></p> + <p/> + <strong>Security</strong> - Data security in Galaxy is a new feature, so familiarize yourself with the details which can be found + here or in our <a href="http://g2.trac.bx.psu.edu/wiki/SecurityFeatures" target="_blank">data security page</a>. The data security + process incorporates users, groups and roles, and enables the application of certain permissions on datasets, specifically "access" + and "manage permissions". By default, the "manage permissions" permission is associated with the dataset owner's private role, and + the "access" permission is not set, making the dataset public. With these default permissions, users should not see any difference + in the way Galaxy has behaved in the past. + <ul> + <li> + <strong>Users</strong> - registered Galaxy users that have created a Galaxy account. Users can belong to groups and can + be associated with 1 or more roles. If a user is not authenticated during a Galaxy session, they will not have access to any + of the security features, and datasets they create during that session will have no permissions applied to them (i.e., they + will be considered "public", and no one will be allowed to change permissions on them). + </li><p/> - <ul> - <li> - <strong>Manage data libraries</strong> - Data libraries enable a Galaxy administrator to upload datasets into a data library. Currently, - only administrators can create data libraries. - <p/> - When a data library is first created, it is considered "public" since it will be displayed in the "Data Libraries" view for any user, even - those that are not logged in. The Galaxy administrator can restrict access to a data library by associating roles with the data library's - "access library" permission. This permission will conservatively override the [dataset] "access" permission for the data library's contained - datasets. - <p/> - For example, if a data library's "access library" permission is associated with Role1 and the data library contains "public" datasets, the - data library will still only be displayed to those users that have Role1. However, if the data library's "access library" permission is - associated with both Role1 and Role2 and the data library contains datasets whose [dataset] "access" permission is associated with only Role1, - then users that have Role2 will be able to access the library, but will not see those contained datasets whose [dataset] "access" permission - is associated with only Role1. - <p/> - In addition to the "access library" permission, permission to perform the following functions on the data library (and it's contents) can - be granted to users (a library item is one of: a data library, a library folder, a library dataset). - <p/> - <ul> - <li><strong>add library item</strong> - Users that have the role can add library items to this data library or folder</li> - <li><strong>modify library item</strong> - Users that have the role can modify this library item</li> - <li><strong>manage library permissions</strong> - Users that have the role can manage permissions applied to this library item</li> - </ul> - <p/> - The default behavior is for no permissions to be applied to a data library item, but applied permissions are inherited downward (with the exception - of the "access library" permission, which is only available on the data library itself). Because of this, it is important to set desired permissions - on a new data library when it is created. When this is done, new folders and datasets added to the data library will automatically inherit those - permissions. In the same way, permissions can be applied to a folder, which will be automatically inherited by all contained datasets and sub-folders. - <p/> - The "Data Libraries" menu item allows users to access the datasets in a data library as long as they are not restricted from accessing them. - Importing a library dataset into a history will not make a copy of the dataset, but will be a "pointer" to the dataset on disk. This - approach allows for multiple users to use a single (possibly very large) dataset file. - </li> - </ul> - </li> - <p/> - <li><strong>Server</strong> + <li> + <strong>Groups</strong> - a set of 0 or more users which are considered members of the group. Groups can be associated with 0 + or more roles, simplifying the process of applying permissions to the data between a select group of users. + </li><p/> - <ul> - <li> - <strong>Reload a tool's configuration</strong> - allows a new version of a tool to be loaded while the server is running - </li> - <p/> - <li> - <strong>Profile memory usage</strong> - measures system memory used for certain Galaxy functions - </li> - <p/> - <li> - <strong>Manage jobs</strong> - displays all jobs that are currently not finished (i.e., their state is new, waiting, queued, or - running). Administrators are able to cleanly stop long-running jobs. - </li> - </ul> - </li> - <p/> - <li><strong>Forms</strong> - <p/>To be completed - </li> - <p/> - <li><strong>Sequencing Requests</strong> - <p/>To be completed - </li> - <p/> - <li><strong>Cloud</strong> - <p/>To be completed - </li> -</ul> -<p/> -<p><strong>Data Security and Data Libraries</strong></p> -<p/> -<strong>Security</strong> - Data security in Galaxy is a new feature, so familiarize yourself with the details which can be found -here or in our <a href="http://g2.trac.bx.psu.edu/wiki/SecurityFeatures" target="_blank">data security page</a>. The data security -process incorporates users, groups and roles, and enables the application of certain permissions on datasets, specifically "access" -and "manage permissions". By default, the "manage permissions" permission is associated with the dataset owner's private role, and -the "access" permission is not set, making the dataset public. With these default permissions, users should not see any difference -in the way Galaxy has behaved in the past. -<ul> - <li> - <strong>Users</strong> - registered Galaxy users that have created a Galaxy account. Users can belong to groups and can - be associated with 1 or more roles. If a user is not authenticated during a Galaxy session, they will not have access to any - of the security features, and datasets they create during that session will have no permissions applied to them (i.e., they - will be considered "public", and no one will be allowed to change permissions on them). - </li> - <p/> - <li> - <strong>Groups</strong> - a set of 0 or more users which are considered members of the group. Groups can be associated with 0 - or more roles, simplifying the process of applying permissions to the data between a select group of users. - </li> - <p/> - <li> - <strong>Roles</strong> - associate users and groups with specific permissions on datasets. For example, users in groups A and B - can be associated with role C which gives them the "access" permission on datasets D, E and F. Roles have a type which is currently - one of the following: - <ul> - <li> - <strong>private</strong> - every user is associated automatically with their own private role. Administrators cannot - manage private roles. - </li> - <li> - <strong>user</strong> - this is currently not used, but eventually any registered user will be able to create a new role - and this will be it's type. - </li> - <li> - <strong>sharing</strong> - a role created automatically during a Galaxy session that enables a user to share data with - another user. This can generally be considered a temporary role. - </li> - <li><strong>admin</strong> - a role created by a Galaxy administrator.</li> - </ul> - </li> - <p/> - <li> - <strong>Dataset Permissions</strong> - applying the following permissions will to a dataset will result in the behavior described. - <ul> - <li> - <strong>access</strong> - users associated with the role can import this dataset into their history for analysis. - <p> - If no roles with the "access" permission are associated with a dataset, the dataset is "public" and may be accessed by anyone - that can access the data library in which it is contained. See the <strong>Manage data libraries</strong> section above for - details. Public datasets contained in public data libraries will be accessible to all users (as well as anyone not logged in - during a Galaxy session) from the list of data libraries displayed when the "Data Libraries" menu item is selected. - </p> - <p> - Associating a dataset with a role that includes the "access" permission restricts the set of users that can access it. - For example, if 'Role A' includes the "access" permission and 'Role A' is associated with the dataset, only those users - and groups who are associated with 'Role A' may access the dataset. - </p> - <p> - If multiple roles that include the "access" permission are associated with a dataset, access to the dataset is derived - from the intersection of the users associated with the roles. For example, if 'Role A' and 'Role B' are associated with - a dataset, only those users and groups who are associated with both 'Role A' AND 'Role B' may access the dataset. When - the "access" permission is applied to a dataset, Galaxy checks to make sure that at least 1 user belongs to all groups and - roles associated with the "access" permission (otherwise the dataset would be restricted from everyone). - </p> - <p> - In order for a user to make a dataset private (i.e., only they can access it), they should associate the dataset with - their private role (the role identical to their Galaxy user name / email address). Associating additional roles that - include the "access" permission is not possible, since it would render the dataset inaccessible to everyone. - <p> - To make a dataset private to themselves and one or more other users, the user can create a new role and associate the dataset - with that role, not their "private role". Galaxy makes this easy by telling the user they are about to share a private dataset - and giving them the option of doing so. If they respond positively, the sharing role is automatically created for them. - </p> - <p> - Private data (data associated with roles that include the "access" permission) must be made public in order to be used - with external applications like the "view at UCSC" link, or the "Perform genome analysis and prediction with EpiGRAPH" - tool. Being made publically accessible means removing the association of all roles that include the "access" permission - from the dataset. - <p> - </li> - <li><strong>manage permissions</strong> - Role members can manage the permissions applied to this dataset</li> - </ul> - </li> -</ul> -<br/> + <li> + <strong>Roles</strong> - associate users and groups with specific permissions on datasets. For example, users in groups A and B + can be associated with role C which gives them the "access" permission on datasets D, E and F. Roles have a type which is currently + one of the following: + <ul> + <li> + <strong>private</strong> - every user is associated automatically with their own private role. Administrators cannot + manage private roles. + </li> + <li> + <strong>user</strong> - this is currently not used, but eventually any registered user will be able to create a new role + and this will be it's type. + </li> + <li> + <strong>sharing</strong> - a role created automatically during a Galaxy session that enables a user to share data with + another user. This can generally be considered a temporary role. + </li> + <li><strong>admin</strong> - a role created by a Galaxy administrator.</li> + </ul> + </li> + <p/> + <li> + <strong>Dataset Permissions</strong> - applying the following permissions will to a dataset will result in the behavior described. + <ul> + <li> + <strong>access</strong> - users associated with the role can import this dataset into their history for analysis. + <p> + If no roles with the "access" permission are associated with a dataset, the dataset is "public" and may be accessed by anyone + that can access the data library in which it is contained. See the <strong>Manage data libraries</strong> section above for + details. Public datasets contained in public data libraries will be accessible to all users (as well as anyone not logged in + during a Galaxy session) from the list of data libraries displayed when the "Data Libraries" menu item is selected. + </p> + <p> + Associating a dataset with a role that includes the "access" permission restricts the set of users that can access it. + For example, if 'Role A' includes the "access" permission and 'Role A' is associated with the dataset, only those users + and groups who are associated with 'Role A' may access the dataset. + </p> + <p> + If multiple roles that include the "access" permission are associated with a dataset, access to the dataset is derived + from the intersection of the users associated with the roles. For example, if 'Role A' and 'Role B' are associated with + a dataset, only those users and groups who are associated with both 'Role A' AND 'Role B' may access the dataset. When + the "access" permission is applied to a dataset, Galaxy checks to make sure that at least 1 user belongs to all groups and + roles associated with the "access" permission (otherwise the dataset would be restricted from everyone). + </p> + <p> + In order for a user to make a dataset private (i.e., only they can access it), they should associate the dataset with + their private role (the role identical to their Galaxy user name / email address). Associating additional roles that + include the "access" permission is not possible, since it would render the dataset inaccessible to everyone. + <p> + To make a dataset private to themselves and one or more other users, the user can create a new role and associate the dataset + with that role, not their "private role". Galaxy makes this easy by telling the user they are about to share a private dataset + and giving them the option of doing so. If they respond positively, the sharing role is automatically created for them. + </p> + <p> + Private data (data associated with roles that include the "access" permission) must be made public in order to be used + with external applications like the "view at UCSC" link, or the "Perform genome analysis and prediction with EpiGRAPH" + tool. Being made publically accessible means removing the association of all roles that include the "access" permission + from the dataset. + <p> + </li> + <li><strong>manage permissions</strong> - Role members can manage the permissions applied to this dataset</li> + </ul> + </li> + </ul> + <br/> +%endif
--- a/templates/webapps/galaxy/admin/index.mako Fri Oct 14 09:58:59 2011 -0400 +++ b/templates/webapps/galaxy/admin/index.mako Fri Oct 14 12:14:54 2011 -0400 @@ -1,4 +1,5 @@ <%inherit file="/webapps/galaxy/base_panels.mako"/> +<%namespace file="/message.mako" import="render_msg" />
## Default title <%def name="title()">Galaxy Administration</%def> @@ -102,6 +103,6 @@ </%def><%def name="center_panel()"> - <% center_url = h.url_for( action='center', webapp='galaxy' ) %> + <% center_url = h.url_for( controller='admin', action='center', webapp='galaxy', message=message, status=status ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def>
--- a/templates/workflow/list.mako Fri Oct 14 09:58:59 2011 -0400 +++ b/templates/workflow/list.mako Fri Oct 14 12:14:54 2011 -0400 @@ -37,7 +37,7 @@ </a></li><li> - <a class="action-button" href="${h.url_for( action='import_workflow' )}"> + <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow' )}"><img src="${h.url_for('/static/images/fugue/arrow-090.png')}" /><span>Upload or import workflow</span></a> @@ -63,22 +63,20 @@ ## <td>${str(workflow.update_time)[:19]}</td><td><div popupmenu="wf-${i}-popup"> - <a class="action-button" href="${h.url_for( action='editor', id=trans.security.encode_id(workflow.id) )}" target="_parent">Edit</a> - <a class="action-button" href="${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id(workflow.id) )}" target="_parent">Run</a> - <a class="action-button" href="${h.url_for( action='sharing', id=trans.security.encode_id(workflow.id) )}">Share or Publish</a> - <a class="action-button" href="${h.url_for( action='export', id=trans.security.encode_id(workflow.id) )}">Download or Export</a> - <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(workflow.id) )}">Clone</a> - <a class="action-button" href="${h.url_for( action='rename', id=trans.security.encode_id(workflow.id) )}">Rename</a> - <a class="action-button" confirm="Are you sure you want to delete workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( action='delete', id=trans.security.encode_id(workflow.id) )}">Delete</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='editor', id=trans.security.encode_id( workflow.id ) )}" target="_parent">Edit</a> + <a class="action-button" href="${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id( workflow.id ) )}" target="_parent">Run</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='sharing', id=trans.security.encode_id( workflow.id ) )}">Share or Publish</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='export', id=trans.security.encode_id( workflow.id ) )}">Download or Export</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='clone', id=trans.security.encode_id( workflow.id ) )}">Clone</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='rename', id=trans.security.encode_id( workflow.id ) )}">Rename</a> + <a class="action-button" confirm="Are you sure you want to delete workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( controller='workflow', action='delete', id=trans.security.encode_id( workflow.id ) )}">Delete</a></div></td></tr> %endfor </table> %else: - You have no workflows. - %endif
<h2>Workflows shared with you by others</h2> @@ -101,18 +99,16 @@ <td>${len(workflow.latest_workflow.steps)}</td><td><div popupmenu="shared-${i}-popup"> - <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug)}" target="_top">View</a> - <a class="action-button" href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">Run</a> - <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(workflow.id) )}">Clone</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug )}" target="_top">View</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">Run</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='clone', id=trans.security.encode_id( workflow.id ) )}">Clone</a></div></td></tr> %endfor </table> %else: - No workflows have been shared with you. - %endif
<h2>Other options</h2>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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