galaxy-commits October 2012

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commit/galaxy-central: 2 new changesets
by Bitbucket 17 Oct '12

17 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/605f4d69d5db/ changeset: 605f4d69d5db user: jgoecks date: 2012-10-16 19:43:57 summary: Circster cleanup: remove track indexes and make renderers into views. affected #: 1 file diff -r 0391351559dd124f305245a9d27f071f28debc54 -r 605f4d69d5db3f9bbfc949ac22ba5ee744649a5f static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -1,8 +1,5 @@ define(["libs/underscore", "libs/d3", "viz/visualization"], function(_, d3, visualization) { -// General backbone style inheritence -var Base = function() { this.initialize && this.initialize.apply(this, arguments); }; Base.extend = Backbone.Model.extend; - var SVGUtils = Backbone.Model.extend({ /** @@ -51,11 +48,10 @@ this.track_gap = 5; this.label_arc_height = 20; this.scale = 1; - this.track_renderers = null; + this.track_views = null; // When track added to the model, add to view as well. this.model.get('tracks').on('add', this.add_track, this); - }, /** @@ -103,7 +99,7 @@ "translate(" + d3.event.translate + ")" + " scale(" + scale + ")"); - // Propagate scale changes to renderers. + // Propagate scale changes to views. if (self.scale !== scale) { // Use timeout to wait for zooming/dragging to stop before rendering more detail. if (self.zoom_drag_timeout) { @@ -111,8 +107,8 @@ } self.zoom_drag_timeout = setTimeout(function() { // Render more detail in tracks' visible elements. - _.each(self.track_renderers, function(renderer) { - renderer.update_scale(scale); + _.each(self.track_views, function(view) { + view.update_scale(scale); }); }, 400); } @@ -123,23 +119,23 @@ // -- Render each dataset in the visualization. -- - // Create a renderer for each track in the visualiation and render. - this.track_renderers = tracks.map(function(track, index) { - track_renderer_class = (track.get('track_type') === 'LineTrack' ? - CircsterBigWigTrackRenderer : - CircsterSummaryTreeTrackRenderer ); + // Create a view for each track in the visualiation and render. + this.track_views = tracks.map(function(track, index) { + track_view_class = (track.get('track_type') === 'LineTrack' ? + CircsterBigWigTrackView : + CircsterSummaryTreeTrackView ); - return new track_renderer_class({ + return new track_view_class({ + el: svg.append('g')[0], track: track, - track_index: index, radius_bounds: tracks_bounds[index], genome: self.genome, total_gap: self.total_gap }); }); - _.each(this.track_renderers, function(renderer) { - renderer.render(svg); + _.each(this.track_views, function(view) { + view.render(); }); // -- Render chromosome labels. -- @@ -147,56 +143,57 @@ // Set radius start = end for track bounds. var track_bounds = tracks_bounds[tracks.length]; track_bounds[1] = track_bounds[0]; - this.label_track_renderer = new CircsterLabelTrackRenderer({ + this.label_track_view = new CircsterLabelTrackView({ + el: svg.append('g')[0], track: new CircsterLabelTrack(), - track_index: tracks.length, radius_bounds: track_bounds, genome: self.genome, total_gap: self.total_gap }); - this.label_track_renderer.render(svg); + this.label_track_view.render(); }, /** * Render a single track on the outside of the current visualization. */ add_track: function(new_track) { - // Reset scale and zoom. + // TODO: Reset scale and zoom. // Recompute and update track bounds. var new_track_bounds = this.get_tracks_bounds(); - _.each(this.track_renderers, function(track_renderer, i) { + _.each(this.track_views, function(track_view, i) { //console.log(self.get_tracks_bounds(), i); - track_renderer.update_radius_bounds(new_track_bounds[i]); + track_view.update_radius_bounds(new_track_bounds[i]); }); // Render new track. - var track_index = this.track_renderers.length - track_renderer_class = (new_track.get('track_type') === 'LineTrack' ? - CircsterBigWigTrackRenderer : - CircsterSummaryTreeTrackRenderer ), - track_renderer = new track_renderer_class({ + var track_index = this.track_views.length + track_view_class = (new_track.get('track_type') === 'LineTrack' ? + CircsterBigWigTrackView : + CircsterSummaryTreeTrackView ), + track_view = new track_view_class({ + el: d3.select('g.tracks').append('g')[0], track: new_track, - track_index: track_index, radius_bounds: new_track_bounds[track_index], genome: this.genome, total_gap: this.total_gap }); - track_renderer.render(d3.select('g.tracks')); - this.track_renderers.push(track_renderer); + track_view.render(); + this.track_views.push(track_view); // Update label track. var track_bounds = new_track_bounds[ new_track_bounds.length-1 ]; track_bounds[1] = track_bounds[0]; - this.label_track_renderer.update_radius_bounds(track_bounds); + this.label_track_view.update_radius_bounds(track_bounds); } }); /** * Renders a track in a Circster visualization. */ -var CircsterTrackRenderer = Base.extend({ +var CircsterTrackView = Backbone.View.extend({ + tagName: 'g', /* ----------------------- Public Methods ------------------------- */ @@ -210,17 +207,20 @@ this.options.chroms_layout = this._chroms_layout(); this.options.data_bounds = []; this.options.scale = 1; - this.options.parent_elt = null; + this.options.parent_elt = d3.select(this.$el[0]); }, /** * Render track's data by adding SVG elements to parent. */ - render: function(parent) { + render: function() { // -- Create track group element. -- - this.options.parent_elt = parent.append("g").attr("id", "parent-" + this.options.track_index); var track_parent_elt = this.options.parent_elt; + if (!track_parent_elt) { + console.log('no parent elt'); + } + // -- Render background arcs. -- var genome_arcs = this.options.chroms_layout, arc_gen = d3.svg.arc() @@ -306,7 +306,7 @@ }, /** - * Update renderer scale. This fetches more data if scale is increased. + * Update view scale. This fetches more data if scale is increased. */ update_scale: function(new_scale) { // -- Update scale and return if new scale is less than old scale. -- @@ -432,13 +432,12 @@ /** * Render chromosome labels. */ -var CircsterLabelTrackRenderer = CircsterTrackRenderer.extend({ +var CircsterLabelTrackView = CircsterTrackView.extend({ initialize: function(options) { - this.options = options; + CircsterTrackView.prototype.initialize.call(this, options); this.options.bg_stroke = 'fff'; this.options.bg_fill = 'fff'; - this.options.chroms_layout = this._chroms_layout(); }, /** @@ -467,9 +466,9 @@ }); /** - * Rendered for quantitative data. + * View for quantitative track in Circster. */ -var CircsterQuantitativeTrackRenderer = CircsterTrackRenderer.extend({ +var CircsterQuantitativeTrackView = CircsterTrackView.extend({ /** * Renders quantitative data with the form [x, value] and assumes data is equally spaced across @@ -533,7 +532,7 @@ /** * Layout for summary tree data in a circster visualization. */ -var CircsterSummaryTreeTrackRenderer = CircsterQuantitativeTrackRenderer.extend({ +var CircsterSummaryTreeTrackView = CircsterQuantitativeTrackView.extend({ get_data_bounds: function(data) { // Get max across data. @@ -546,9 +545,9 @@ }); /** - * Layout for BigWig data in a circster visualization. + * Bigwig track view in Circster */ -var CircsterBigWigTrackRenderer = CircsterQuantitativeTrackRenderer.extend({ +var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({ get_data_bounds: function(data) { // Set max across dataset by extracting all values, flattening them into a https://bitbucket.org/galaxy/galaxy-central/changeset/e1ea65232d19/ changeset: e1ea65232d19 user: jgoecks date: 2012-10-16 19:45:08 summary: Merge affected #: 1 file diff -r 605f4d69d5db3f9bbfc949ac22ba5ee744649a5f -r e1ea65232d19a053be0725a91b47a1d81e309ee6 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -259,7 +259,7 @@ can_generate_dependency_metadata = False tool_dependency_name = elem.get( 'name', None ) if tool_dependency_name and tool_dependency_version: - for tool_dict in metadata_dict[ 'tools' ]: + for tool_dict in metadata_dict.get( 'tools', [] ): requirements = tool_dict.get( 'requirements', [] ) for requirement_dict in requirements: req_name = requirement_dict.get( 'name', None ) @@ -281,7 +281,7 @@ # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> env_var_name = env_var_elem.get( 'name', None ) if env_var_name: - for tool_dict in metadata_dict[ 'tools' ]: + for tool_dict in metadata_dict.get( 'tools', [] ): requirements = tool_dict.get( 'requirements', [] ) for requirement_dict in requirements: # {"name": "R_SCRIPT_PATH", "type": "set_environment", "version": null} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Better handle missing 'tool' entry in tool repository metadata.
by Bitbucket 17 Oct '12

17 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fd80283b2436/ changeset: fd80283b2436 user: dan date: 2012-10-16 19:43:06 summary: Better handle missing 'tool' entry in tool repository metadata. affected #: 1 file diff -r 0391351559dd124f305245a9d27f071f28debc54 -r fd80283b2436db14f08e050711f619d393941cca lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -259,7 +259,7 @@ can_generate_dependency_metadata = False tool_dependency_name = elem.get( 'name', None ) if tool_dependency_name and tool_dependency_version: - for tool_dict in metadata_dict[ 'tools' ]: + for tool_dict in metadata_dict.get( 'tools', [] ): requirements = tool_dict.get( 'requirements', [] ) for requirement_dict in requirements: req_name = requirement_dict.get( 'name', None ) @@ -281,7 +281,7 @@ # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> env_var_name = env_var_elem.get( 'name', None ) if env_var_name: - for tool_dict in metadata_dict[ 'tools' ]: + for tool_dict in metadata_dict.get( 'tools', [] ): requirements = tool_dict.get( 'requirements', [] ) for requirement_dict in requirements: # {"name": "R_SCRIPT_PATH", "type": "set_environment", "version": null} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: smcmanus: Adding folders controller.
by Bitbucket 17 Oct '12

17 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0391351559dd/ changeset: 0391351559dd user: smcmanus date: 2012-10-16 19:04:28 summary: Adding folders controller. affected #: 2 files diff -r ea21a868746118d30ddb5668a506b0187ecbfc27 -r 0391351559dd124f305245a9d27f071f28debc54 lib/galaxy/webapps/galaxy/api/folders.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/folders.py @@ -0,0 +1,117 @@ +""" +API operations on folders +""" +import logging, os, string, shutil, urllib, re, socket, traceback +from cgi import escape, FieldStorage +from galaxy import util, datatypes, jobs, web, util +from galaxy.web.base.controller import * +from galaxy.util.sanitize_html import sanitize_html +from galaxy.model.orm import * + +log = logging.getLogger( __name__ ) + +class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): + + @web.expose_api + def index( self, trans, **kwd ): + """ + GET /api/folders/ + This would normally display a list of folders. However, that would + be across multiple libraries, so it's not implemented yet. + """ + pass + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + GET /api/folders/{encoded_folder_id} + Displays information about a folder + """ + # Eliminate any 'F' in front of the folder id. Just take the + # last 16 characters: + if ( len( id ) >= 17 ): + id = id[-16:] + # Retrieve the folder and return its contents encoded. Note that the + # check_ownership=false since we are only displaying it. + content = self.get_library_folder( trans, id, check_ownership=False, + check_accessible=True ) + return self.encode_all_ids( trans, content.get_api_value( view='element' ) ) + + @web.expose_api + def create( self, trans, payload, **kwd ): + """ + POST /api/folders/{encoded_folder_id} + Create a new object underneath the one specified in the parameters. + This will use the same parameters and semantics as + /api/libraries/{LibID}/contents/{ContentId} for consistency. + This means that datasets and folders can be generated. Note that + /api/libraries/{LibID}/contents/{ContentId} did not need the library + id to function properly, which is why this functionality has been + moved here. + + o payload's relevant params: + - create_type: "file" or "folder" (required) + - folder_id: This is the parent folder's id (required) + """ + log.debug( "FoldersController.create: enter" ) + # TODO: Create a single point of exit if possible. For now we only + # exit at the end and on exceptions. + if 'folder_id' not in payload: + trans.response.status = 400 + return "Missing requred 'folder_id' parameter." + else: + folder_id = payload.pop( 'folder_id' ) + class_name, folder_id = self.__decode_library_content_id( trans, folder_id ) + + try: + # security is checked in the downstream controller + parent_folder = self.get_library_folder( trans, folder_id, check_ownership=False, check_accessible=False ) + except Exception, e: + return str( e ) + + real_parent_folder_id = trans.security.encode_id( parent_folder.id ) + + # Note that this will only create a folder; the library_contents will + # also allow files to be generated, though that encompasses generic + # contents: + # TODO: reference or change create_folder, which points to the + # library browsing; we just want to point to the /api/folders URI. + status, output = trans.webapp.controllers['library_common'].create_folder( trans, 'api', real_parent_folder_id, '', **payload ) + rval = [] + + # SM: When a folder is sucessfully created: + # - get all of the created folders. We know that they're + # folders, so prepend an "F" to them. + if 200 == status: + for k, v in output.items(): + if type( v ) == trans.app.model.LibraryDatasetDatasetAssociation: + v = v.library_dataset + encoded_id = 'F' + trans.security.encode_id( v.id ) + rval.append( dict( id = encoded_id, + name = v.name, + url = url_for( 'folder', id=encoded_id ) ) ) + else: + log.debug( "Error creating folder; setting output and status" ) + trans.response.status = status + rval = output + return rval + + @web.expose_api + def update( self, trans, id, library_id, payload, **kwd ): + """ + PUT /api/folders/{encoded_folder_id} + For now this does nothing. There are no semantics for folders that + indicates that an update operation is needed; the existing + library_contents folder does not allow for update, either. + """ + pass + + # TODO: Move this to library_common. This doesn't really belong in any + # of the other base controllers. + def __decode_library_content_id( self, trans, content_id ): + if ( len( content_id ) % 16 == 0 ): + return 'LibraryDataset', content_id + elif ( content_id.startswith( 'F' ) ): + return 'LibraryFolder', content_id[1:] + else: + raise HTTPBadRequest( 'Malformed library content id ( %s ) specified, unable to decode.' % str( content_id ) ) diff -r ea21a868746118d30ddb5668a506b0187ecbfc27 -r 0391351559dd124f305245a9d27f071f28debc54 templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -48,6 +48,7 @@ <%def name="javascripts()"> ${parent.javascripts()} + ${h.js("libs/json2")} ${h.js("libs/jquery/jstorage")} ${common_javascripts()} ${self.grid_javascripts()} @@ -206,7 +207,7 @@ </script></%def> -<%def name="render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )"> +<%def name="render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )"><% ## The received ldda must always be a LibraryDatasetDatasetAssociation object. The object id passed to methods ## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying @@ -214,22 +215,14 @@ ## library_dataset, so we display the attributes from the ldda. from galaxy.webapps.galaxy.controllers.library_common import branch_deleted - + is_admin = trans.user_is_admin() and cntrller == 'library_admin' - - if ldda == library_dataset.library_dataset_dataset_association: - current_version = True - if is_admin: - can_modify = can_manage = True - elif cntrller in [ 'library', 'requests' ]: - can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library_dataset ) - can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library_dataset ) - else: - can_modify = can_manage = False - else: - current_version = False + current_version = ( ldda == library_dataset.library_dataset_dataset_association ) if current_version and ldda.state not in ( 'ok', 'error', 'empty', 'deleted', 'discarded' ): tracked_datasets[ldda.id] = ldda.state + # SM: This causes a query to be emitted, but it quickly goes down a + # rabbit hole of many possible inheritable cases. It may not be + # possible to easily eliminate the extra query from this call. info_association, inherited = ldda.get_info_association( restrict=True ) form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE %> @@ -310,9 +303,21 @@ %endif </%def> +<%def name="format_delta( tdelta )"> + <% + from datetime import datetime + return "%d.%.6d" % ( tdelta.seconds, tdelta.microseconds ) + %> +</%def> + <%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False, simple=False )"><% - from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, branch_deleted + from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, map_library_datasets_to_lddas, branch_deleted, datasets_for_lddas + + # SM: DELETEME + from datetime import datetime, timedelta + import logging + log = logging.getLogger( __name__ ) is_admin = trans.user_is_admin() and cntrller == 'library_admin' has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) @@ -325,6 +330,9 @@ pad = folder_pad + 20 expander = h.url_for("/static/images/silk/resultset_next.png") folder_img = h.url_for("/static/images/silk/folder.png") + # SM: If this is a comma-delimited list of LDDAs, then split them up + # into a list. For anything else, turn created_ldda_ids into a single + # item list. if created_ldda_ids: created_ldda_ids = util.listify( created_ldda_ids ) if str( folder.id ) in hidden_folder_ids: @@ -426,47 +434,39 @@ %> %endif <% + # TODO: If show_deleted is set to True, then nothing is displayed. Why? This wasn't the case + # in the past. if show_deleted: sub_folders, library_datasets = activatable_folders_and_library_datasets( trans, folder ) else: sub_folders, library_datasets = active_folders_and_library_datasets( trans, folder ) + # Render all the subfolders: + # TODO: Check permissions first. + for sub_folder in sub_folders: + render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False ) + + # Map LibraryDatasets to LDDAs, then map LDDAs to Datasets. + # Then determine which Datasets are accessible and which are not. + # For every LibraryDataset, if there's an LDDA for it and it's + # accessible then display it. + if ( len( library_datasets ) > 0 ): + lib_dataset_ldda_map = map_library_datasets_to_lddas( trans, library_datasets ) + dataset_list = datasets_for_lddas( trans, lib_dataset_ldda_map.values() ) + #can_access_datasets = trans.app.security_agent.dataset_access_mapping( trans, current_user_roles, dataset_list ) + can_access_datasets = trans.app.security_agent.dataset_permission_map_for_access( trans, current_user_roles, dataset_list ) + can_modify_datasets = trans.app.security_agent.item_permission_map_for_modify( trans, current_user_roles, dataset_list ) + can_manage_datasets = trans.app.security_agent.item_permission_map_for_manage( trans, current_user_roles, dataset_list ) + for library_dataset in library_datasets: + ldda = lib_dataset_ldda_map[ library_dataset.id ] + if ldda: + # SMTODO: Fix awkard modify/manage permission checks. + can_access = is_admin or can_access_datasets[ ldda.dataset_id ] + can_modify = is_admin or ( cntrller in ['library', 'requests'] and can_modify_datasets[ ldda.dataset_id ]) + can_manage = is_admin or ( cntrller in ['library', 'requests'] and can_manage_datasets[ ldda.dataset_id ]) + selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids + if can_access: + render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted ) %> - %if is_admin: - %for sub_folder in sub_folders: - ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} - %endfor - %for library_dataset in library_datasets: - <% - ldda = library_dataset.library_dataset_dataset_association - if ldda: - # There should always be an ldda, but some users running their own instances have reported that - # some of their LibraryDatasets have no associated lddas - selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids - %> - %if ldda: - ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )} - %endif - %endfor - %else: - %for sub_folder in sub_folders: - ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False, simple=simple )} - %endfor - %for library_dataset in library_datasets: - <% - ldda = library_dataset.library_dataset_dataset_association - if ldda: - # There should always be an ldda, but some users running their own instances have reported that - # some of their LibraryDatasets have no associated lddas - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ldda.dataset ) - selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids - else: - can_access = False - %> - %if can_access: - ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted, simple=simple )} - %endif - %endfor - %endif </%def><%def name="render_content(simple=False)"> @@ -474,6 +474,8 @@ from galaxy import util from galaxy.webapps.galaxy.controllers.library_common import branch_deleted from time import strftime + import logging + log = logging.getLogger( __name__ ) is_admin = trans.user_is_admin() and cntrller == 'library_admin' @@ -489,6 +491,8 @@ info_association, inherited = library.get_info_association() form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE + # SM: These are mostly display-specific; ignore them for now. + # The has_accessible_folders determines if anything can be shown - use it. self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles ) root_folder_has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False ) has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles ) @@ -581,13 +585,16 @@ </tr></thead><% row_counter = RowCounter() %> + ## SM: Here is where we render the libraries based on admin/non-admin privileges: %if cntrller in [ 'library', 'requests' ]: ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True, simple=simple )} + ## SM: TODO: WTF? %if not library.deleted and self.has_accessible_datasets and not simple: ${render_actions_on_multiple_items()} %endif %elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ): ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} + ## SM: TODO: WTF? %if not library.deleted and not show_deleted and self.has_accessible_datasets: ${render_actions_on_multiple_items()} %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add debug logging when tool dependency information is incorrect in tool shed repositories.
by Bitbucket 17 Oct '12

17 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ea21a8687461/ changeset: ea21a8687461 user: dan date: 2012-10-16 18:52:21 summary: Add debug logging when tool dependency information is incorrect in tool shed repositories. affected #: 1 file diff -r 6fa63ee539a7d6fb32693509808e035bd7a05dff -r ea21a868746118d30ddb5668a506b0187ecbfc27 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -695,7 +695,7 @@ element_tree_root = element_tree.getroot() is_tool = element_tree_root.tag == 'tool' except Exception, e: - print "Error parsing %s", full_path, ", exception: ", str( e ) + log.debug( "Error parsing %s, exception: %s" % ( full_path, str( e ) ) ) is_tool = False if is_tool: tool, valid, error_message = load_tool_from_config( app, full_path ) @@ -793,6 +793,8 @@ # Handle tool dependency installation via other means here (future). if tool_dependencies_dict: metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict + else: + log.debug( "Name, version and type from the <requirement> tag does not match the information in the tool_dependencies.xml file. Tool dependencies will be ignored." ) if tool_dependencies_dict: if original_tool_dependencies_dict: # We're generating metadata on an update pulled to a tool shed repository installed into a Galaxy instance, so handle changes to Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for tool shed get_category_by_name when category does not exist.
by Bitbucket 17 Oct '12

17 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6fa63ee539a7/ changeset: 6fa63ee539a7 user: dan date: 2012-10-16 18:20:05 summary: Fix for tool shed get_category_by_name when category does not exist. affected #: 1 file diff -r 3b292aa60eae153e4c162df30221b9d28bc26017 -r 6fa63ee539a7d6fb32693509808e035bd7a05dff lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -378,7 +378,10 @@ return trans.sa_session.query( trans.model.Category ).get( trans.security.decode_id( id ) ) def get_category_by_name( trans, name ): """Get a category from the database via name""" - return trans.sa_session.query( trans.model.Category ).filter_by( name=name ).one() + try: + return trans.sa_session.query( trans.model.Category ).filter_by( name=name ).one() + except sqlalchemy.orm.exc.NoResultFound: + return None def get_categories( trans ): """Get all categories from the database""" return trans.sa_session.query( trans.model.Category ) \ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 17 Oct '12

17 Oct '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3dafc5ce805f/ changeset: 3dafc5ce805f user: jgoecks date: 2012-10-16 17:26:42 summary: Circster: enable tracks to be added dynamically. affected #: 4 files diff -r 1425614da4ea5eb4011f8176eb8afbb4a4dea6a1 -r 3dafc5ce805ffb12086e0697fc607450025bd681 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -51,6 +51,33 @@ this.track_gap = 5; this.label_arc_height = 20; this.scale = 1; + this.track_renderers = null; + + // When track added to the model, add to view as well. + this.model.get('tracks').on('add', this.add_track, this); + + }, + + /** + * Returns a list of tracks' radius bounds. + */ + get_tracks_bounds: function() { + var dataset_arc_height = this.dataset_arc_height, + min_dimension = Math.min(this.$el.width(), this.$el.height()), + // Compute radius start based on model, will be centered + // and fit entirely inside element by default. + radius_start = min_dimension / 2 - + this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) - + (this.label_arc_height + this.track_gap), + + // Compute range of track starting radii. + tracks_start_radii = d3.range(radius_start, min_dimension / 2, this.dataset_arc_height + this.track_gap); + + // Map from track start to bounds; for label track + var self = this; + return _.map(tracks_start_radii, function(radius) { + return [radius, radius + self.dataset_arc_height]; + }); }, render: function() { @@ -58,31 +85,11 @@ dataset_arc_height = this.dataset_arc_height, width = self.$el.width(), height = self.$el.height(), - // Compute radius start based on model, will be centered - // and fit entirely inside element by default. - init_radius_start = Math.min(width, height) / 2 - - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) - - (this.label_arc_height + this.track_gap), tracks = this.model.get('tracks'), + tracks_bounds = this.get_tracks_bounds(), - // Create a renderer for each track in the visualiation. - track_renderers = tracks.map(function(track, index) { - var radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap), - track_renderer_class = (track.get('track_type') === 'LineTrack' ? - CircsterBigWigTrackRenderer : - CircsterSummaryTreeTrackRenderer ); - - return new track_renderer_class({ - track: track, - track_index: index, - radius_bounds: [radius_start, radius_start + dataset_arc_height], - genome: self.genome, - total_gap: self.total_gap - }); - }); - - // Set up SVG element. - var svg = d3.select(self.$el[0]) + // Set up SVG element. + svg = d3.select(self.$el[0]) .append("svg") .attr("width", width) .attr("height", height) @@ -104,32 +111,85 @@ } self.zoom_drag_timeout = setTimeout(function() { // Render more detail in tracks' visible elements. - _.each(track_renderers, function(renderer) { + _.each(self.track_renderers, function(renderer) { renderer.update_scale(scale); }); }, 400); } })) .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") - .append('svg:g'); + .append('svg:g').attr('class', 'tracks'); // -- Render each dataset in the visualization. -- - _.each(track_renderers, function(renderer) { + + // Create a renderer for each track in the visualiation and render. + this.track_renderers = tracks.map(function(track, index) { + track_renderer_class = (track.get('track_type') === 'LineTrack' ? + CircsterBigWigTrackRenderer : + CircsterSummaryTreeTrackRenderer ); + + return new track_renderer_class({ + track: track, + track_index: index, + radius_bounds: tracks_bounds[index], + genome: self.genome, + total_gap: self.total_gap + }); + }); + + _.each(this.track_renderers, function(renderer) { renderer.render(svg); }); // -- Render chromosome labels. -- - var radius_start = init_radius_start + tracks.length * (dataset_arc_height + self.track_gap) + self.track_gap; - var chrom_labels_track = new CircsterLabelTrackRenderer({ + + // Set radius start = end for track bounds. + var track_bounds = tracks_bounds[tracks.length]; + track_bounds[1] = track_bounds[0]; + this.label_track_renderer = new CircsterLabelTrackRenderer({ track: new CircsterLabelTrack(), track_index: tracks.length, - radius_bounds: [radius_start, radius_start], + radius_bounds: track_bounds, genome: self.genome, total_gap: self.total_gap }); + + this.label_track_renderer.render(svg); + }, - chrom_labels_track.render(svg); + /** + * Render a single track on the outside of the current visualization. + */ + add_track: function(new_track) { + // Reset scale and zoom. + + // Recompute and update track bounds. + var new_track_bounds = this.get_tracks_bounds(); + _.each(this.track_renderers, function(track_renderer, i) { + //console.log(self.get_tracks_bounds(), i); + track_renderer.update_radius_bounds(new_track_bounds[i]); + }); + + // Render new track. + var track_index = this.track_renderers.length + track_renderer_class = (new_track.get('track_type') === 'LineTrack' ? + CircsterBigWigTrackRenderer : + CircsterSummaryTreeTrackRenderer ), + track_renderer = new track_renderer_class({ + track: new_track, + track_index: track_index, + radius_bounds: new_track_bounds[track_index], + genome: this.genome, + total_gap: this.total_gap + }); + track_renderer.render(d3.select('g.tracks')); + this.track_renderers.push(track_renderer); + + // Update label track. + var track_bounds = new_track_bounds[ new_track_bounds.length-1 ]; + track_bounds[1] = track_bounds[0]; + this.label_track_renderer.update_radius_bounds(track_bounds); } }); @@ -172,8 +232,9 @@ .data(genome_arcs).enter().append('svg:g'), // Draw chrom arcs/paths. - chroms_paths = chroms_elts.append("path") + chroms_paths = chroms_elts.append('path') .attr("d", arc_gen) + .attr('class', 'chrom-background') .style("stroke", this.options.bg_stroke) .style("fill", this.options.loading_bg_fill); @@ -203,6 +264,48 @@ }, /** + * Update radius bounds. + */ + update_radius_bounds: function(radius_bounds) { + // Update bounds. + this.options.radius_bounds = radius_bounds; + + // -- Update background arcs. -- + var new_d = d3.svg.arc() + .innerRadius(this.options.radius_bounds[0]) + .outerRadius(this.options.radius_bounds[1]); + + this.options.parent_elt.selectAll('g>path.chrom-background').transition().duration(1000).attr('d', new_d); + + // -- Update chrom data. -- + var track = this.options.track, + chrom_arcs = this.options.chroms_layout, + chrom_data_paths = this.options.parent_elt.selectAll('g>path.chrom-data'), + num_paths = chrom_data_paths[0].length; + + if (num_paths > 0) { + var self = this; + $.when(track.get('data_manager').get_genome_wide_data(this.options.genome)).then(function(genome_wide_data) { + // Map chrom data to path data, filtering out null values. + var path_data = _.reject( _.map(genome_wide_data, function(chrom_data, i) { + var rval = null, + path_fn = self._compute_path_data(chrom_arcs[i], chrom_data); + if (path_fn) { + rval = path_fn(chrom_data.data); + } + return rval; + }), function(p_data) { return p_data === null; } ); + + // Transition each path. + chrom_data_paths.each(function(path, index) { + d3.select(this).transition().duration(1000).attr('d', path_data[index]); + }); + + }); + } + }, + + /** * Update renderer scale. This fetches more data if scale is increased. */ update_scale: function(new_scale) { @@ -304,7 +407,7 @@ /** * Returns data for creating a path for the given data using chrom_arc and data bounds. */ - _compute_path_data: function(chrom_arc, data) {}, + _compute_path_data: function(chrom_arc, chrom_data) {}, /** * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle @@ -373,14 +476,11 @@ * chromosome. Attachs a dict with track and chrom name information to DOM element. */ _render_chrom_data: function(svg, chrom_arc, chrom_data) { - // If no chrom data, return null. - if (typeof chrom_data === "string" || !chrom_data.data || chrom_data.data.length === 0) { - return null; - } + var path_data = this._compute_path_data(chrom_arc, chrom_data); - var path_data = this._compute_path_data(chrom_arc, chrom_data.data); + if (!path_data) { return null; } - // Render data. + // There is path data, so render as path. var parent = svg.datum(chrom_data.data), path = parent.append('path') .attr('class', 'chrom-data') @@ -393,7 +493,12 @@ /** * Returns data for creating a path for the given data using chrom_arc, radius bounds, and data bounds. */ - _compute_path_data: function(chrom_arc, data) { + _compute_path_data: function(chrom_arc, chrom_data) { + // If no chrom data, return null. + if (typeof chrom_data === "string" || !chrom_data.data || chrom_data.data.length === 0) { + return null; + } + // Radius scaler. var radius = d3.scale.linear() .domain(this.options.data_bounds) @@ -401,7 +506,7 @@ // Scaler for placing data points across arc. var angle = d3.scale.linear() - .domain([0, data.length]) + .domain([0, chrom_data.data.length]) .range([chrom_arc.startAngle, chrom_arc.endAngle]); // Use line generator to create area. diff -r 1425614da4ea5eb4011f8176eb8afbb4a4dea6a1 -r 3dafc5ce805ffb12086e0697fc607450025bd681 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -907,7 +907,7 @@ // Introduction div shown when there are no tracks. this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container).hide(); var add_tracks_button = $("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () { - visualization.select_datasets(select_datasets_url, add_track_async_url, function(tracks) { + visualization.select_datasets(select_datasets_url, add_track_async_url, { "f-dbkey": view.dbkey }, function(tracks) { _.each(tracks, function(track) { view.add_drawable( object_from_template(track, view, view) ); }); diff -r 1425614da4ea5eb4011f8176eb8afbb4a4dea6a1 -r 3dafc5ce805ffb12086e0697fc607450025bd681 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -48,7 +48,7 @@ // them sequentially. $.when.apply($, requests).then(function() { // jQuery always returns an Array for arguments, so need to look at first element - // to determine whether multiple requests were made and consequently how to + // to determine whether multiple requests were made and consequently how to // map arguments to track definitions. var track_defs = (arguments[0] instanceof Array ? $.map(arguments, function(arg) { return arg[0]; }) : @@ -795,8 +795,11 @@ } ], - add_track: function(track) { - this.get('tracks').push(track); + /** + * Add a track or array of tracks to the visualization. + */ + add_tracks: function(tracks) { + this.get('tracks').add(tracks); } }); diff -r 1425614da4ea5eb4011f8176eb8afbb4a4dea6a1 -r 3dafc5ce805ffb12086e0697fc607450025bd681 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -37,16 +37,32 @@ } }); - require( [ "viz/visualization", "viz/circster" ], function(visualization, circster ) { + require( [ "viz/visualization", "viz/circster" ], function(visualization_mod, circster ) { $(function() { + // -- Viz set up. -- + var genome = new visualization_mod.Genome(JSON.parse('${ h.to_json_string( genome ) }')) + vis = new visualization_mod.GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')), + viz_view = new circster.CircsterView({ + el: $('#vis'), + // Gap is difficult to set because it very dependent on chromosome size and organization. + total_gap: 2 * Math.PI * 0.1, + genome: genome, + model: vis, + dataset_arc_height: 25 + }); + + // -- Render viz. -- + + viz_view.render(); + // -- Visualization menu and set up. var menu = create_icon_buttons_menu([ { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { - visualization.select_datasets(select_datasets_url, add_track_async_url, {}, function(tracks) { - console.log(tracks); - }); + visualization_mod.select_datasets(select_datasets_url, add_track_async_url, {}, function(tracks) { + vis.add_tracks(tracks); + }); } }, { icon_class: 'disk--arrow', title: 'Save', on_click: function() { // Show saving dialog box @@ -88,24 +104,6 @@ $("#center .unified-panel-header-inner").append(menu.$el); // Manual tooltip config because default gravity is S and cannot be changed. $(".menu-button").tooltip( { placement: 'bottom' } ); - - // -- Viz set up. -- - - var genome = new visualization.Genome(JSON.parse('${ h.to_json_string( genome ) }')) - vis = new visualization.GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')), - viz_view = new circster.CircsterView({ - el: $('#vis'), - // Gap is difficult to set because it very dependent on chromosome size and organization. - total_gap: 2 * Math.PI * 0.1, - genome: genome, - model: vis, - dataset_arc_height: 25 - }); - - // -- Render viz. -- - - viz_view.render(); - }); }); </script> https://bitbucket.org/galaxy/galaxy-central/changeset/8fd7bc979e07/ changeset: 8fd7bc979e07 user: jgoecks date: 2012-10-16 17:32:55 summary: When adding datasets to visualization, pass dbky directly rather than in dict. affected #: 4 files diff -r 3dafc5ce805ffb12086e0697fc607450025bd681 -r 8fd7bc979e07c089b0476d11157df5ce5a4bba95 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -907,7 +907,7 @@ // Introduction div shown when there are no tracks. this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container).hide(); var add_tracks_button = $("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () { - visualization.select_datasets(select_datasets_url, add_track_async_url, { "f-dbkey": view.dbkey }, function(tracks) { + visualization.select_datasets(select_datasets_url, add_track_async_url, view.dbkey, function(tracks) { _.each(tracks, function(track) { view.add_drawable( object_from_template(track, view, view) ); }); diff -r 3dafc5ce805ffb12086e0697fc607450025bd681 -r 8fd7bc979e07c089b0476d11157df5ce5a4bba95 static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -20,7 +20,7 @@ var self = this, menu = create_icon_buttons_menu([ { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { - visualization.select_datasets(select_datasets_url, add_track_async_url, { "f-dbkey": view.dbkey }, function(tracks) { + visualization.select_datasets(select_datasets_url, add_track_async_url, view.dbkey, function(tracks) { _.each(tracks, function(track) { view.add_drawable( object_from_template(track, view, view) ); }); diff -r 3dafc5ce805ffb12086e0697fc607450025bd681 -r 8fd7bc979e07c089b0476d11157df5ce5a4bba95 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -15,10 +15,11 @@ * track definitions are obtained from the server and the success_fn is called with the list of * definitions for selected datasets. */ -var select_datasets = function(dataset_url, add_track_async_url, filter_params, success_fn) { +var select_datasets = function(dataset_url, add_track_async_url, dbkey, success_fn) { $.ajax({ url: dataset_url, - data: filter_params, + // Filter by dbkey if available. + data: ( dbkey ? { 'f-dbkey': dbkey } : {} ), error: function() { alert( "Grid failed" ); }, success: function(table_html) { show_modal( diff -r 3dafc5ce805ffb12086e0697fc607450025bd681 -r 8fd7bc979e07c089b0476d11157df5ce5a4bba95 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -60,9 +60,10 @@ // -- Visualization menu and set up. var menu = create_icon_buttons_menu([ { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { - visualization_mod.select_datasets(select_datasets_url, add_track_async_url, {}, function(tracks) { - vis.add_tracks(tracks); - }); + visualization_mod.select_datasets(select_datasets_url, add_track_async_url, vis.get('dbkey'), function(tracks) { + vis.add_tracks(tracks); + } + ); } }, { icon_class: 'disk--arrow', title: 'Save', on_click: function() { // Show saving dialog box https://bitbucket.org/galaxy/galaxy-central/changeset/3b292aa60eae/ changeset: 3b292aa60eae user: jgoecks date: 2012-10-16 18:12:52 summary: Merge affected #: 1 file diff -r 8fd7bc979e07c089b0476d11157df5ce5a4bba95 -r 3b292aa60eae153e4c162df30221b9d28bc26017 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -314,11 +314,15 @@ repository_clone_url = self.__generate_clone_url( trans, repository ) repository.deleted = False repository.status = trans.model.ToolShedRepository.installation_status.INSTALLED - trans.sa_session.add( repository ) - trans.sa_session.flush() if repository.includes_tools: metadata = repository.metadata - repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) + try: + repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) + except Exception, e: + error = "Error activating repository %s: %s" % ( repository.name, str( e ) ) + log.debug( error ) + return trans.show_error_message( '%s.<br/>You may be able to resolve this by uninstalling and then reinstalling the repository. Click <a href="%s">here</a> to uninstall the repository.' + % ( error, web.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) ) ) ) # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] add_to_tool_panel( trans.app, @@ -330,6 +334,8 @@ shed_tool_conf, tool_panel_dict, new_install=False ) + trans.sa_session.add( repository ) + trans.sa_session.flush() if repository.includes_datatypes: repository_install_dir = os.path.abspath ( relative_install_dir ) # Deactivate proprietary datatypes. @@ -476,7 +482,11 @@ removed = True except Exception, e: log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) ) - removed = False + if isinstance( e, OSError ) and not os.path.exists( repository_install_dir ): + removed = True + log.debug( "Repository directory does not exist on disk, marking as uninstalled." ) + else: + removed = False if removed: tool_shed_repository.uninstalled = True # Remove all installed tool dependencies. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: More graceful handling of uninstalling or deactivating toolshed repositories that have already been removed from disk.
by Bitbucket 16 Oct '12

16 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/81110680ad98/ changeset: 81110680ad98 user: dan date: 2012-10-16 17:44:20 summary: More graceful handling of uninstalling or deactivating toolshed repositories that have already been removed from disk. affected #: 1 file diff -r 1425614da4ea5eb4011f8176eb8afbb4a4dea6a1 -r 81110680ad9886085dca4d052f52e196e8ed782e lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -314,11 +314,15 @@ repository_clone_url = self.__generate_clone_url( trans, repository ) repository.deleted = False repository.status = trans.model.ToolShedRepository.installation_status.INSTALLED - trans.sa_session.add( repository ) - trans.sa_session.flush() if repository.includes_tools: metadata = repository.metadata - repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) + try: + repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) + except Exception, e: + error = "Error activating repository %s: %s" % ( repository.name, str( e ) ) + log.debug( error ) + return trans.show_error_message( '%s.<br/>You may be able to resolve this by uninstalling and then reinstalling the repository. Click <a href="%s">here</a> to uninstall the repository.' + % ( error, web.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) ) ) ) # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] add_to_tool_panel( trans.app, @@ -330,6 +334,8 @@ shed_tool_conf, tool_panel_dict, new_install=False ) + trans.sa_session.add( repository ) + trans.sa_session.flush() if repository.includes_datatypes: repository_install_dir = os.path.abspath ( relative_install_dir ) # Deactivate proprietary datatypes. @@ -476,7 +482,11 @@ removed = True except Exception, e: log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) ) - removed = False + if isinstance( e, OSError ) and not os.path.exists( repository_install_dir ): + removed = True + log.debug( "Repository directory does not exist on disk, marking as uninstalled." ) + else: + removed = False if removed: tool_shed_repository.uninstalled = True # Remove all installed tool dependencies. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for dataset display.
by Bitbucket 16 Oct '12

16 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1425614da4ea/ changeset: 1425614da4ea user: dan date: 2012-10-16 15:47:20 summary: Fix for dataset display. affected #: 1 file diff -r cfaa85995d3682d2441db70e6d110f98a12e8d35 -r 1425614da4ea5eb4011f8176eb8afbb4a4dea6a1 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -323,6 +323,8 @@ @web.expose def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, chunk=None, **kwd): data = self._check_dataset(trans, dataset_id) + if not isinstance( data, trans.app.model.DatasetInstance ): + return data return data.datatype.display_data(trans, data, preview, filename, to_ext, chunk, **kwd) @web.expose Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for 7945:4bab7894219e.
by Bitbucket 16 Oct '12

16 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cfaa85995d36/ changeset: cfaa85995d36 user: dan date: 2012-10-16 15:26:37 summary: Fix for 7945:4bab7894219e. affected #: 1 file diff -r 7bd38888e04befd09bde273bc4fc11921483b941 -r cfaa85995d3682d2441db70e6d110f98a12e8d35 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -163,8 +163,8 @@ assert hda and self._can_access_dataset( trans, hda ) return hda.creating_job - def _can_access_dataset( self, trans, dataset, allow_admin=True ): - return ( allow_admin and trans.user_is_admin() ) or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), dataset ) + def _can_access_dataset( self, trans, dataset_association, allow_admin=True ): + return ( allow_admin and trans.user_is_admin() ) or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), dataset_association.dataset ) @web.expose def errors( self, trans, id ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: smcmanus: WIP: /api/folders/{folder_id}. The url_for call needs to be fixed.
by Bitbucket 16 Oct '12

16 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7bd38888e04b/ changeset: 7bd38888e04b user: smcmanus date: 2012-10-16 05:48:30 summary: WIP: /api/folders/{folder_id}. The url_for call needs to be fixed. affected #: 2 files diff -r fc394a686d61920b17db1226b7c702612e747015 -r 7bd38888e04befd09bde273bc4fc11921483b941 lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -36,6 +36,9 @@ if not admin: can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) if (admin or can_access) and not ld.deleted: + log.debug( "type(folder): %s" % type( folder ) ) + log.debug( "type(api_path): %s; folder.api_path: %s" % ( type(folder.api_path), folder.api_path ) ) + #log.debug( "attributes of folder: %s" % str(dir(folder)) ) ld.api_path = folder.api_path + '/' + ld.name ld.api_type = 'file' rval.append( ld ) @@ -52,11 +55,13 @@ if not library or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( current_user_roles, library ) ): trans.response.status = 400 return "Invalid library id ( %s ) specified." % str( library_id ) + log.debug( "Root folder type: %s" % type( library.root_folder ) ) encoded_id = 'F' + trans.security.encode_id( library.root_folder.id ) rval.append( dict( id = encoded_id, type = 'folder', name = '/', url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) + log.debug( "Root folder attributes: %s" % str(dir(library.root_folder)) ) library.root_folder.api_path = '' for content in traverse( library.root_folder ): encoded_id = trans.security.encode_id( content.id ) diff -r fc394a686d61920b17db1226b7c702612e747015 -r 7bd38888e04befd09bde273bc4fc11921483b941 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -63,7 +63,12 @@ # The /folders section is experimental at this point: log.debug( "app.config.api_folders: %s" % app.config.api_folders ) if app.config.api_folders: - webapp.api_mapper.resource( 'folder', 'folders', path_prefix='/api' ) + #webapp.api_mapper.resource( 'folder', 'folders', path_prefix='/api' ) + webapp.api_mapper.resource( 'content', 'contents', + controller='folder_contents', + name_prefix='folder_', + path_prefix='/api/folders/:folder_id', + parent_resources=dict( member_name='folder', collection_name='folders' ) ) webapp.api_mapper.resource( 'content', 'contents', controller='library_contents', @@ -79,7 +84,7 @@ webapp.api_mapper.resource( 'permission', 'permissions', path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) + parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.api_mapper.resource( 'user', 'users', controller='group_users', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits October 2012