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history panel: better bootstrapped history and hda data; UsesHistoryDatasetAssociationMixin: don't try to provide full data for deleted, purged, or non-accessible hda
This commit is contained in:
Carl Eberhard
@@ -334,31 +334,40 @@ class UsesHistoryDatasetAssociationMixin:
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def get_hda_dict( self, trans, hda ):
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hda_dict = hda.get_api_value( view='element' )
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history = hda.history
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hda_dict[ 'api_type' ] = "file"
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# Add additional attributes that depend on trans can hence must be added here rather than at the model level.
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can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset )
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can_access_hda = ( trans.user_is_admin() or can_access_hda )
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hda_dict[ 'accessible' ] = can_access_hda
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# return here if deleted and purged or can't access
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purged = ( hda.purged or hda.dataset.purged )
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if ( hda.deleted and purged ) or not can_access_hda:
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return trans.security.encode_dict_ids( hda_dict )
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if trans.user_is_admin() or trans.app.config.expose_dataset_path:
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hda_dict[ 'file_name' ] = hda.file_name
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if not hda_dict[ 'deleted' ]:
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hda_dict[ 'download_url' ] = url_for( 'history_contents_display', history_id = trans.security.encode_id( history.id ),
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history_content_id = trans.security.encode_id( hda.id ) )
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hda_dict[ 'download_url' ] = url_for( 'history_contents_display',
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history_id = trans.security.encode_id( history.id ),
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history_content_id = trans.security.encode_id( hda.id ) )
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can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset )
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hda_dict[ 'accessible' ] = ( trans.user_is_admin() or can_access_hda )
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hda_dict[ 'api_type' ] = "file"
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if not( hda.purged or hda.deleted or hda.dataset.purged ):
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meta_files = []
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for meta_type in hda.metadata.spec.keys():
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if isinstance( hda.metadata.spec[ meta_type ].param, FileParameter ):
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meta_files.append( dict( file_type=meta_type ) )
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if meta_files:
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hda_dict[ 'meta_files' ] = meta_files
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meta_files = []
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for meta_type in hda.metadata.spec.keys():
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if isinstance( hda.metadata.spec[ meta_type ].param, FileParameter ):
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meta_files.append( dict( file_type=meta_type ) )
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if meta_files:
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hda_dict[ 'meta_files' ] = meta_files
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hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda )
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hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda )
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hda_dict[ 'visualizations' ] = hda.get_visualizations()
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# return here if deleted
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if hda.deleted and not purged:
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return trans.security.encode_dict_ids( hda_dict )
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if hda.creating_job and hda.creating_job.tool_id:
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tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id )
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if tool_used and tool_used.force_history_refresh:
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@@ -813,7 +822,6 @@ class UsesHistoryMixin( SharableItemSecurityMixin ):
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history = self.get_object( trans, id, 'History', check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted )
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return self.security_check( trans, history, check_ownership, check_accessible )
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def get_history_datasets( self, trans, history, show_deleted=False, show_hidden=False, show_purged=False ):
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""" Returns history's datasets. """
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query = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \
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@@ -11,7 +11,7 @@ from galaxy.model.item_attrs import UsesAnnotations
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log = logging.getLogger( __name__ )
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class RootController( BaseUIController, UsesHistoryMixin, UsesAnnotations ):
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class RootController( BaseUIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesAnnotations ):
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@web.expose
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def default(self, trans, target1=None, target2=None, **kwd):
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@@ -130,8 +130,39 @@ class RootController( BaseUIController, UsesHistoryMixin, UsesAnnotations ):
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else:
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# get all datasets server-side, client-side will get flags and render appropriately
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datasets = self.get_history_datasets( trans, history,
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show_deleted=True, show_hidden=True, show_purged=True )
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hdas = self.get_history_datasets( trans, history,
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show_deleted=True, show_hidden=True, show_purged=True )
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#TODO: would be good to re-use the hdas above to get the history data...
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history_dictionary = self.get_history_dict( trans, history )
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#TODO: blech - all here for now - duplication of hist. contents, index
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hda_dictionaries = []
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for hda in hdas:
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try:
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hda_dictionaries.append( self.get_hda_dict( trans, hda ) )
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except Exception, exc:
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# don't fail entire list if hda err's, record and move on
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# (making sure http recvr knows it's err'd)
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encoded_hda_id = trans.security.encode_id( hda.id )
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log.error( "Error in history API at listing contents with history %s, hda %s: (%s) %s",
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history_dictionary[ 'id' ], encoded_hda_id, type( exc ), str( exc ) )
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return_val = {
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'id' : encoded_hda_id,
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'name' : hda.name,
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'hid' : hda.hid,
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'history_id': history_dictionary[ 'id' ],
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'state' : trans.model.Dataset.states.ERROR,
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'visible' : True,
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'misc_info' : str( exception ),
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'misc_blurb': 'Failed to retrieve dataset information.',
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'error' : str( exception )
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}
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hda_dictionaries.append( return_val )
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history = history_dictionary
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datasets = hda_dictionaries
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return trans.stream_template_mako( history_panel_template,
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history = history,
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@@ -90,7 +90,7 @@ ${ h.to_json_string( dict([ ( string, _(string) ) for string in strings_to_local
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<%
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from urllib import unquote_plus
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history_class_name = history.__class__.__name__
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history_class_name = 'History'
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encoded_id_template = '<%= id %>'
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url_dict = {
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@@ -189,12 +189,9 @@ ${ unquote_plus( h.to_json_string( url_dict ) ) }
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## I'd rather do without these (esp. the get_hdas which hits the db twice)
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## but we'd need a common map producer (something like get_api_value but more complete)
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##TODO: api/web controllers should use common code, and this section should call that code
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<%def name="get_history( id )">
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<%def name="get_history( history )">
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<%
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history_json = trans.webapp.api_controllers[ 'histories' ].show( trans, trans.security.encode_id( id ) )
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#assert isinstance( history, dict ), (
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# 'Bootstrapped history was expecting a dictionary: %s' %( str( history ) ) )
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return history_json
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return h.to_json_string( history )
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%>
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</%def>
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@@ -207,16 +204,9 @@ ${ unquote_plus( h.to_json_string( url_dict ) ) }
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%>
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</%def>
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<%def name="get_hdas( history_id, hdas )">
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<%def name="get_hdas( hdas )">
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<%
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#BUG: one inaccessible dataset will error entire list
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if not hdas:
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return '[]'
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# rather just use the history.id (wo the datasets), but...
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hda_json = trans.webapp.api_controllers[ 'history_contents' ].index(
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trans, trans.security.encode_id( history_id ),
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ids=( ','.join([ trans.security.encode_id( hda.id ) for hda in hdas ]) ) )
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return hda_json
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return h.to_json_string( hdas )
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%>
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</%def>
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@@ -324,8 +314,8 @@ $(function(){
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page_show_hidden = ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) },
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user = ${ get_current_user() },
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history = ${ get_history( history.id ) },
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hdas = ${ get_hdas( history.id, datasets ) };
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history = ${ get_history( history ) },
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hdas = ${ get_hdas( datasets ) };
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// add user data to history
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// i don't like this history+user relationship, but user authentication changes views/behaviour
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