July 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Trackster: make sliders more responsive by waiting before drawing.
by Bitbucket 14 Jul '12

14 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0da18c7ba18d/ changeset: 0da18c7ba18d user: jgoecks date: 2012-07-14 01:44:21 summary: Trackster: make sliders more responsive by waiting before drawing. affected #: 1 file diff -r 02ce2ca3fa2dac4c4155b7f07f0699d519b4d853 -r 0da18c7ba18dcc0eaf9e14596b5ff0dc348457bc static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -2083,7 +2083,6 @@ // Set up slider for filter. var slider_div = $("<div/>").addClass("slider").appendTo(filter.parent_div); filter.control_element = $("<div/>").attr("id", filter.name + "-filter-control").appendTo(slider_div); - var prev_values = [0,0]; filter.control_element.slider({ range: true, min: this.min, @@ -2193,17 +2192,23 @@ * Handle slide events. */ slide: function(event, ui) { - var values = ui.values; + var values = ui.values; + + // Set new values in UI. + this.values_span.text(values[0] + "-" + values[1]); + + // Set new values in filter. + this.low = values[0]; + this.high = values[1]; - // Set new values in UI. - this.values_span.text(values[0] + "-" + values[1]); + // Set timeout to update if filter low, high are stable. + var self = this; + setTimeout(function() { + if (values[0] === self.low && values[1] === self.high) { + self.manager.track.request_draw(true, true); + } + }, 25); - // Set new values in filter. - this.low = values[0]; - this.high = values[1]; - - // Redraw track. - this.manager.track.request_draw(true, true); }, /** * Returns true if filter can be applied to element. 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: greg: Make sure a shed related tool config is defined in universe_wsgi.ini before allowing automatic tool installs from a tool shed.
by Bitbucket 14 Jul '12

14 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/02ce2ca3fa2d/ changeset: 02ce2ca3fa2d user: greg date: 2012-07-14 01:09:51 summary: Make sure a shed related tool config is defined in universe_wsgi.ini before allowing automatic tool installs from a tool shed. affected #: 1 file diff -r 35ff11e3863804767d602d2fb8bff08f2c67e35f -r 02ce2ca3fa2dac4c4155b7f07f0699d519b4d853 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -945,7 +945,7 @@ @web.expose @web.require_admin def prepare_for_install( self, trans, **kwd ): - if not trans.app.toolbox.shed_tool_confs: + if not have_shed_tool_conf_for_install( trans ): message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one shed tool configuration file name with a ' message += '<b><toolbox></b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation ' message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose ' @@ -1566,3 +1566,13 @@ def get_tool_dependency( trans, id ): """Get a tool_dependency from the database via id""" return trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) ) +def have_shed_tool_conf_for_install( trans ): + if not trans.app.toolbox.shed_tool_confs: + return False + migrated_tools_conf_path, migrated_tools_conf_name = os.path.split( trans.app.config.migrated_tools_config ) + for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs: + shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] + shed_tool_conf_path, shed_tool_conf_name = os.path.split( shed_tool_conf ) + if shed_tool_conf_name != migrated_tools_conf_name: + return True + return False 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: jgoecks: Tracks: make composite tracks compatible with recent Backbone enhancements and (b) whitespace cleanup.
by Bitbucket 13 Jul '12

13 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/35ff11e38638/ changeset: 35ff11e38638 user: jgoecks date: 2012-07-13 23:55:29 summary: Tracks: make composite tracks compatible with recent Backbone enhancements and (b) whitespace cleanup. affected #: 1 file diff -r bdad5064ebc9de3cfcaeb89993eb5e326d82815c -r 35ff11e3863804767d602d2fb8bff08f2c67e35f static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -1413,10 +1413,10 @@ } view.change_chrom(chrom, new_low, new_high); }, - move_fraction : function( fraction ) { + move_fraction: function(fraction) { var view = this; var span = view.high - view.low; - this.move_delta( fraction * span ); + this.move_delta(fraction * span); }, move_delta: function(delta_chrom) { // Update low, high. @@ -3598,7 +3598,7 @@ var can_draw_now = true; // Get the track data, maybe a deferred - var tile_data = track.data_manager.get_data( region, track.mode, resolution, track.data_url_extra_params ); + var tile_data = track.data_manager.get_data(region, track.mode, resolution, track.data_url_extra_params); if ( is_deferred( tile_data ) ) { can_draw_now = false; } @@ -3657,6 +3657,7 @@ // Returned Deferred is resolved when tile can be drawn. return can_draw; }, + /** * Returns canvas height needed to display data; return value is an integer that denotes the * number of pixels required. @@ -3664,6 +3665,7 @@ get_canvas_height: function(result, mode, w_scale, canvas_width) { return this.visible_height_px; }, + /** * Draw a track tile. * @param result result from server @@ -3677,6 +3679,7 @@ draw_tile: function(result, ctx, mode, resolution, region, w_scale, ref_seq) { console.log("Warning: TiledTrack.draw_tile() not implemented."); }, + /** * Show track tile and perform associated actions. Showing tile may actually move * an existing tile rather than reshowing it. @@ -3711,11 +3714,24 @@ track.after_show_tile(tile); }, - + /** * Actions to be taken after showing tile. */ - after_show_tile: function(tile) {}, + after_show_tile: function(tile) { + // Update max height based on current tile. + this.max_height_px = Math.max(this.max_height_px, tile.html_elt.height()); + + // Update height for all tiles based on max height. + tile.html_elt.parent().children().css("height", this.max_height_px + "px"); + + // Update track height based on max height and visible height. + var track_height = this.max_height_px; + if (this.visible_height_px !== 0) { + track_height = Math.min(this.max_height_px, this.visible_height_px); + } + this.tiles_div.css("height", track_height + "px"); + }, /** * Returns a genome region that corresponds to a tile at a particular resolution @@ -3928,9 +3944,7 @@ // FIXME: this function is similar to TiledTrack.draw_helper -- can the two be merged/refactored? var track = this, key = this._gen_tile_cache_key(width, w_scale, tile_index), - tile_bounds = this._get_tile_bounds(tile_index, resolution), - tile_low = tile_bounds.get('start'), - tile_high = tile_bounds.get('end'); + region = this._get_tile_bounds(tile_index, resolution); // Init kwargs if necessary to avoid having to check if kwargs defined. if (!kwargs) { kwargs = {}; } @@ -3952,7 +3966,7 @@ for (var i = 0; i < this.drawables.length; i++) { track = this.drawables[i]; // Get the track data, maybe a deferred. - tile_data = track.data_manager.get_data( tile_low, tile_high, track.mode, resolution, track.data_url_extra_params ); + tile_data = track.data_manager.get_data(region, track.mode, resolution, track.data_url_extra_params); if ( is_deferred( tile_data ) ) { can_draw_now = false; } @@ -3961,7 +3975,7 @@ // Get seq data if needed, maybe a deferred. seq_data = null; if ( view.reference_track && w_scale > view.canvas_manager.char_width_px ) { - seq_data = view.reference_track.data_manager.get_data(tile_low, tile_high, track.mode, resolution, view.reference_track.data_url_extra_params); + seq_data = view.reference_track.data_manager.get_data(region, track.mode, resolution, view.reference_track.data_url_extra_params); if ( is_deferred( seq_data ) ) { can_draw_now = false; } @@ -3979,8 +3993,8 @@ var canvas = track.view.canvas_manager.new_canvas(), tile_bounds = track._get_tile_bounds(tile_index, resolution), - tile_low = tile_bounds.get('start'), - tile_high = tile_bounds.get('end'), + tile_low = region.get('start'), + tile_high = region.get('end'), all_data_index = 0, width = Math.ceil( (tile_high - tile_low) * w_scale ) + this.left_offset, height = 0, @@ -4020,7 +4034,7 @@ track = this.drawables[i]; tile_data = all_data[ all_data_index ]; seq_data = all_data[ all_data_index + 1 ]; - tile = track.draw_tile(tile_data, ctx, track_modes[i], resolution, tile_bounds, w_scale, seq_data); + tile = track.draw_tile(tile_data, ctx, track_modes[i], resolution, region, w_scale, seq_data); } // Don't cache, show if no tile. @@ -4045,8 +4059,7 @@ */ show_group: function() { // Create group with individual tracks. - var - group = new DrawableGroup(this.view, this.container, { + var group = new DrawableGroup(this.view, this.container, { name: this.name }), track; @@ -4390,23 +4403,6 @@ // Clear because this is set when drawing. this.max_height_px = 0; }, - /** - * Actions to be taken after showing tile. - */ - after_show_tile: function(tile) { - // Update max height based on current tile. - this.max_height_px = Math.max(this.max_height_px, tile.html_elt.height()); - - // Update height for all tiles based on max height. - tile.html_elt.parent().children().css("height", this.max_height_px + "px"); - - // Update track height based on max height and visible height. - var track_height = this.max_height_px; - if (this.visible_height_px !== 0) { - track_height = Math.min(this.max_height_px, this.visible_height_px); - } - this.tiles_div.css("height", track_height + "px"); - }, /** * Actions to be taken after draw has been completed. Draw is completed when all tiles have been 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: inithello: Show an error message during tool installation if tool_dependency_dir is unset.
by Bitbucket 13 Jul '12

13 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bdad5064ebc9/ changeset: bdad5064ebc9 user: inithello date: 2012-07-13 20:18:15 summary: Show an error message during tool installation if tool_dependency_dir is unset. affected #: 3 files diff -r 01c78c55b229e5e872ffb2320a51468a5c7ba7ee -r bdad5064ebc9de3cfcaeb89993eb5e326d82815c lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -1128,7 +1128,11 @@ break else: readme_text = '' - install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=True ) + if trans.app.config.tool_dependency_dir is None: + checked = False + else: + checked = True + install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=checked ) return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, diff -r 01c78c55b229e5e872ffb2320a51468a5c7ba7ee -r bdad5064ebc9de3cfcaeb89993eb5e326d82815c templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -85,9 +85,14 @@ </div><div class="form-row"><label>Install tool dependencies?</label> - ${install_tool_dependencies_check_box.get_html()} + <% disabled = trans.app.config.tool_dependency_dir is None %> + ${install_tool_dependencies_check_box.get_html( disabled=disabled )} <div class="toolParamHelp" style="clear: both;"> - Un-check to skip automatic installation of these tool dependencies. + %if disabled: + Set the tool_dependency_dir configuration value in your universe_wsgi.ini to automatically install tool dependencies. + %else: + Un-check to skip automatic installation of these tool dependencies. + %endif </div></div><div style="clear: both"></div> diff -r 01c78c55b229e5e872ffb2320a51468a5c7ba7ee -r bdad5064ebc9de3cfcaeb89993eb5e326d82815c templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -23,7 +23,7 @@ <br/><div class="toolForm"> - %if includes_tool_dependencies: + %if includes_tool_dependencies and trans.app.config.use_tool_dependencies: <div class="toolFormTitle">Confirm tool dependency installation</div> %else: <div class="toolFormTitle">Choose the tool panel section to contain the installed tools (optional)</div> @@ -31,7 +31,7 @@ <div class="toolFormBody"><form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies )}" method="post" ><div style="clear: both"></div> - %if includes_tool_dependencies: + %if includes_tool_dependencies and trans.app.config.use_tool_dependencies: ${render_tool_dependency_section( install_tool_dependencies_check_box, repo_info_dicts )} <div style="clear: both"></div><div class="form-row"> 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: inithello: Set tool dependency status to installed if the dependency is already installed.
by Bitbucket 13 Jul '12

13 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/01c78c55b229/ changeset: 01c78c55b229 user: inithello date: 2012-07-13 19:31:12 summary: Set tool dependency status to installed if the dependency is already installed. affected #: 1 file diff -r 2822e4550fc218bd1adc6d219bbcbbf11350afc9 -r 01c78c55b229e5e872ffb2320a51468a5c7ba7ee lib/galaxy/tool_shed/tool_dependencies/install_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py @@ -83,6 +83,10 @@ # print 'Installing tool dependencies via fabric script ', proprietary_fabfile_path else: print '\nSkipping installation of tool dependency', package_name, 'version', package_version, 'since it is installed in', install_dir, '\n' + tool_dependency = get_tool_dependency_by_name_version_type_repository( app, tool_shed_repository, package_name, package_version, 'package' ) + tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED + sa_session.add( tool_dependency ) + sa_session.flush() return tool_dependency def install_via_fabric( app, tool_dependency, actions_elem, install_dir, package_name=None, proprietary_fabfile_path=None, **kwd ): """Parse a tool_dependency.xml file's <actions> tag set to gather information for the installation via fabric.""" 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: greg: Another change to installed changed revision for the freebayes tool migration process.
by Bitbucket 13 Jul '12

13 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2822e4550fc2/ changeset: 2822e4550fc2 user: greg date: 2012-07-13 18:53:42 summary: Another change to installed changed revision for the freebayes tool migration process. affected #: 1 file diff -r 00af371b11a5ed5d0560865096d21baf99a28509 -r 2822e4550fc218bd1adc6d219bbcbbf11350afc9 scripts/migrate_tools/0003_tools.xml --- a/scripts/migrate_tools/0003_tools.xml +++ b/scripts/migrate_tools/0003_tools.xml @@ -1,6 +1,6 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"> - <repository name="freebayes" description="Galaxy Freebayes Bayesian genetic variant detector tool" changeset_revision="838dd557c84c"> + <repository name="freebayes" description="Galaxy Freebayes Bayesian genetic variant detector tool" changeset_revision="213a3d6b579a"><tool id="freebayes" version="0.0.2 " file="freebayes.xml" /></repository></toolshed> 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: greg: Change ethe installed changed revision for the freebayes tool migration process.
by Bitbucket 13 Jul '12

13 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/00af371b11a5/ changeset: 00af371b11a5 user: greg date: 2012-07-13 18:50:29 summary: Change ethe installed changed revision for the freebayes tool migration process. affected #: 1 file diff -r 1eba0880e52d5b9955eea4df6fefdb1575fee09c -r 00af371b11a5ed5d0560865096d21baf99a28509 scripts/migrate_tools/0003_tools.xml --- a/scripts/migrate_tools/0003_tools.xml +++ b/scripts/migrate_tools/0003_tools.xml @@ -1,6 +1,6 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"> - <repository name="freebayes" description="Galaxy Freebayes Bayesian genetic variant detector tool" changeset_revision="046c7983e2ff"> + <repository name="freebayes" description="Galaxy Freebayes Bayesian genetic variant detector tool" changeset_revision="838dd557c84c"><tool id="freebayes" version="0.0.2 " file="freebayes.xml" /></repository></toolshed> 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: greg: Revert my last change set.
by Bitbucket 13 Jul '12

13 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1eba0880e52d/ changeset: 1eba0880e52d user: greg date: 2012-07-13 18:37:45 summary: Revert my last change set. affected #: 1 file diff -r 1da8fb882393c68f83d08f6c85023a0c3225513b -r 1eba0880e52d5b9955eea4df6fefdb1575fee09c lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -279,10 +279,6 @@ # Handle case where all metadata is the same. if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal': return 'equal' - """ - # TODO: revisit after GCC - we temporarily prioritize contents as: 1) tools 2) datatypes 3) workflows - # by only inspecting tools if they exist. If tools don't exist, next inspect only datatypes and, finally, workflows. - # Here is the original code, with the code following the commented code replacing it. if workflow_comparison == 'subset' and datatype_comparison == 'subset': is_subset = True for guid in ancestor_guids: @@ -291,24 +287,6 @@ break if is_subset: return 'subset' - """ - if ancestor_guids and current_guids: - is_subset = True - for guid in ancestor_guids: - if guid not in current_guids: - is_subset = False - break - if is_subset: - return 'subset' - else: - return 'not equal and not subset' - elif ancestor_guids and not current_guids: - # There were tools in the ancestor changeset revision, but no tools in the current changeset revision, so no new metadata should be generated. - return 'subset' - elif datatype_comparison == 'subset': - return 'subset' - elif workflow_comparison == 'subset': - return 'subset' return 'not equal and not subset' def compare_datatypes( ancestor_datatypes, current_datatypes ): # Determine if ancestor_datatypes is the same as current_datatypes 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: greg: Pritorize tools first, followed by proprietary datatypes and then workflows when setting metadata on tool shed repositories.
by Bitbucket 13 Jul '12

13 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1da8fb882393/ changeset: 1da8fb882393 user: greg date: 2012-07-13 18:12:08 summary: Pritorize tools first, followed by proprietary datatypes and then workflows when setting metadata on tool shed repositories. affected #: 1 file diff -r 28b3364341b66ae9e3628d965db31c8dc3c57bfd -r 1da8fb882393c68f83d08f6c85023a0c3225513b lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -279,6 +279,10 @@ # Handle case where all metadata is the same. if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal': return 'equal' + """ + # TODO: revisit after GCC - we temporarily prioritize contents as: 1) tools 2) datatypes 3) workflows + # by only inspecting tools if they exist. If tools don't exist, next inspect only datatypes and, finally, workflows. + # Here is the original code, with the code following the commented code replacing it. if workflow_comparison == 'subset' and datatype_comparison == 'subset': is_subset = True for guid in ancestor_guids: @@ -287,6 +291,24 @@ break if is_subset: return 'subset' + """ + if ancestor_guids and current_guids: + is_subset = True + for guid in ancestor_guids: + if guid not in current_guids: + is_subset = False + break + if is_subset: + return 'subset' + else: + return 'not equal and not subset' + elif ancestor_guids and not current_guids: + # There were tools in the ancestor changeset revision, but no tools in the current changeset revision, so no new metadata should be generated. + return 'subset' + elif datatype_comparison == 'subset': + return 'subset' + elif workflow_comparison == 'subset': + return 'subset' return 'not equal and not subset' def compare_datatypes( ancestor_datatypes, current_datatypes ): # Determine if ancestor_datatypes is the same as current_datatypes 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: greg: Fix for transferring datasets in sample tracking.
by Bitbucket 13 Jul '12

13 Jul '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/28b3364341b6/ changeset: 28b3364341b6 user: greg date: 2012-07-13 16:15:49 summary: Fix for transferring datasets in sample tracking. affected #: 1 file diff -r 67927f25d781f7cd1fc431f992b3bd02829c3854 -r 28b3364341b66ae9e3628d965db31c8dc3c57bfd lib/galaxy/web/controllers/requests_common.py --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -104,13 +104,15 @@ if ids is not None and states is not None: ids = map( int, ids.split( "," ) ) states = states.split( "," ) - for id, state in zip( ids, states ): - sample = trans.sa_session.query( self.app.model.Sample ).get( id ) - if sample.state.name != state: - rval[ id ] = { "state": sample.state.name, - "html_state": unicode( trans.fill_template( "requests/common/sample_state.mako", - sample=sample), - 'utf-8' ) } + for tup in zip( ids, states ): + id, state = tup + if id and state: + sample = trans.sa_session.query( self.app.model.Sample ).get( id ) + if sample.state.name != state: + rval[ id ] = { "state": sample.state.name, + "html_state": unicode( trans.fill_template( "requests/common/sample_state.mako", + sample=sample), + 'utf-8' ) } return rval @web.json def sample_datasets_updates( self, trans, ids=None, datasets=None ): @@ -121,14 +123,16 @@ rval = {} if ids is not None and datasets is not None: ids = map( int, ids.split( "," ) ) - number_of_datasets_list = map(int, datasets.split( "," ) ) - for id, number_of_datasets in zip( ids, number_of_datasets_list ): - sample = trans.sa_session.query( self.app.model.Sample ).get( id ) - if len(sample.datasets) != number_of_datasets: - rval[ id ] = { "datasets": len( sample.datasets ), - "html_datasets": unicode( trans.fill_template( "requests/common/sample_datasets.mako", - sample=sample), - 'utf-8' ) } + number_of_datasets_list = map( int, datasets.split( "," ) ) + for tup in zip( ids, number_of_datasets_list ): + id, number_of_datasets = tup + if id and number_of_datasets: + sample = trans.sa_session.query( self.app.model.Sample ).get( id ) + if len( sample.datasets ) != number_of_datasets: + rval[ id ] = { "datasets": len( sample.datasets ), + "html_datasets": unicode( trans.fill_template( "requests/common/sample_datasets.mako", + sample=sample), + 'utf-8' ) } return rval @web.json def dataset_transfer_status_updates( self, trans, ids=None, transfer_status_list=None ): @@ -140,13 +144,15 @@ if ids is not None and transfer_status_list is not None: ids = ids.split( "," ) transfer_status_list = transfer_status_list.split( "," ) - for id, transfer_status in zip( ids, transfer_status_list ): - sample_dataset = trans.sa_session.query( self.app.model.SampleDataset ).get( trans.security.decode_id( id ) ) - if sample_dataset.status != transfer_status: - rval[ id ] = { "status": sample_dataset.status, - "html_status": unicode( trans.fill_template( "requests/common/sample_dataset_transfer_status.mako", - sample_dataset=sample_dataset), - 'utf-8' ) } + for tup in zip( ids, transfer_status_list ): + id, transfer_status = tup + if id and transfer_status: + sample_dataset = trans.sa_session.query( self.app.model.SampleDataset ).get( trans.security.decode_id( id ) ) + if sample_dataset.status != transfer_status: + rval[ id ] = { "status": sample_dataset.status, + "html_status": unicode( trans.fill_template( "requests/common/sample_dataset_transfer_status.mako", + sample_dataset=sample_dataset), + 'utf-8' ) } return rval @web.expose @web.require_login( "create sequencing requests" ) 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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