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

commit/galaxy-central: jgoecks: Trackster: bug fixes for 36d36384704b
by Bitbucket 07 Feb '12

07 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/63319bc07b56/ changeset: 63319bc07b56 user: jgoecks date: 2012-02-07 23:07:35 summary: Trackster: bug fixes for 36d36384704b affected #: 1 file diff -r 23b173247757c383e9f1c4fb736008a6623e7327 -r 63319bc07b56127bcd3c44ec6e950541c2c4aa0c static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1738,7 +1738,7 @@ // Calculate resolution in both pixels/base and bases/pixel; round bases/pixels for tile calculations. // TODO: require minimum difference in new resolution to update? - this.resolution_b_px = Math.round( (this.high - this.low) / this.viewport_container.width() ); + this.resolution_b_px = (this.high - this.low) / this.viewport_container.width(); this.resolution_px_b = this.viewport_container.width() / (this.high - this.low); // Overview @@ -3590,8 +3590,8 @@ * with values tile_low and tile_high. */ _get_tile_bounds: function(tile_index, resolution) { - var tile_low = tile_index * TILE_SIZE * resolution, - tile_length = TILE_SIZE * resolution, + var tile_low = Math.floor( tile_index * TILE_SIZE * resolution ), + tile_length = Math.ceil( TILE_SIZE * resolution ), // Tile high cannot be larger than view.max_high, which the chromosome length. tile_high = (tile_low + tile_length <= this.view.max_high ? tile_low + tile_length : this.view.max_high); return [tile_low, tile_high]; 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.

1 0

commit/galaxy-central: greg: Fix for loading tools from an installed tool shed repository into the tool panel outside of any sections.
by Bitbucket 07 Feb '12

07 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/23b173247757/ changeset: 23b173247757 user: greg date: 2012-02-07 22:20:48 summary: Fix for loading tools from an installed tool shed repository into the tool panel outside of any sections. affected #: 4 files diff -r 60231c4aab751817fc3937c1974e3fc11632df2e -r 23b173247757c383e9f1c4fb736008a6623e7327 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -317,10 +317,10 @@ id_elem.text = tool.id version_elem = SubElement( tool_elem, 'version' ) version_elem.text = tool.version + if not tool_section: + elem_list.append( tool_elem ) if tool_section: elem_list.append( root_elem ) - elif tool_elem: - elem_list.append( tool_elem ) return elem_list def generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ): """ diff -r 60231c4aab751817fc3937c1974e3fc11632df2e -r 23b173247757c383e9f1c4fb736008a6623e7327 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -435,9 +435,14 @@ original_section_name = tool_panel_section[ 'name' ] tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) no_changes_check_box = CheckboxField( 'no_changes', checked=True ) - message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " % ( repository.name, original_section_name ) - message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a " - message += "different section in the tool panel." + if original_section_name: + message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ + % ( repository.name, original_section_name ) + message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a " + message += "different section in the tool panel." + else: + message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % repository.name + message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section." status = 'done' return trans.fill_template( '/admin/tool_shed_repository/reselect_tool_panel_section.mako', repository=repository, diff -r 60231c4aab751817fc3937c1974e3fc11632df2e -r 23b173247757c383e9f1c4fb736008a6623e7327 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako @@ -20,7 +20,7 @@ <label>Add new tool panel section:</label><input name="new_tool_panel_section" type="textfield" value="" size="40"/><div class="toolParamHelp" style="clear: both;"> - Add a new tool panel section contain the installed tools (optional). + Add a new tool panel section to contain the installed tools (optional). </div></div><div class="form-row"> diff -r 60231c4aab751817fc3937c1974e3fc11632df2e -r 23b173247757c383e9f1c4fb736008a6623e7327 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 @@ -43,7 +43,7 @@ <label>Add new tool panel section:</label><input name="new_tool_panel_section" type="textfield" value="${new_tool_panel_section}" size="40"/><div class="toolParamHelp" style="clear: both;"> - Add a new tool panel section contain the installed tools (optional). + Add a new tool panel section to contain the installed tools (optional). </div></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.

1 0

commit/galaxy-central: greg: When an installed tool shed repository that includes tools is being reinstalled, allow the admin to select a different section in the tool panel (than was originally selected when the repository was last installed) to contain the included tools.
by Bitbucket 07 Feb '12

07 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/60231c4aab75/ changeset: 60231c4aab75 user: greg date: 2012-02-07 21:10:03 summary: When an installed tool shed repository that includes tools is being reinstalled, allow the admin to select a different section in the tool panel (than was originally selected when the repository was last installed) to contain the included tools. affected #: 3 files diff -r 31c0b88bb4eba817cebf3987565d471c64146b48 -r 60231c4aab751817fc3937c1974e3fc11632df2e lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -95,6 +95,10 @@ if operation == "get updates": return self.check_for_updates( trans, **kwd ) if operation == "activate or reinstall": + repository = get_repository( trans, kwd[ 'id' ] ) + if repository.uninstalled and repository.includes_tools: + # Only allow selecting a different section in the tool panel if the repository was uninstalled. + return self.reselect_tool_panel_section( trans, **kwd ) return self.activate_or_reinstall_repository( trans, **kwd ) if operation == "deactivate or uninstall": return self.deactivate_or_uninstall_repository( trans, **kwd ) @@ -423,8 +427,31 @@ del trans.app.toolbox.tool_panel[ item_id ] @web.expose @web.require_admin + def reselect_tool_panel_section( self, trans, **kwd ): + repository = get_repository( trans, kwd[ 'id' ] ) + # Get the location in the tool panel in which the tool was originally loaded. + metadata = repository.metadata + tool_panel_section = metadata[ 'tool_panel_section' ] + original_section_name = tool_panel_section[ 'name' ] + tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) + no_changes_check_box = CheckboxField( 'no_changes', checked=True ) + message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " % ( repository.name, original_section_name ) + message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a " + message += "different section in the tool panel." + status = 'done' + return trans.fill_template( '/admin/tool_shed_repository/reselect_tool_panel_section.mako', + repository=repository, + no_changes_check_box=no_changes_check_box, + original_section_name=original_section_name, + tool_panel_section_select_field=tool_panel_section_select_field, + message=message, + status=status ) + @web.expose + @web.require_admin def activate_or_reinstall_repository( self, trans, **kwd ): repository = get_repository( trans, kwd[ 'id' ] ) + no_changes = kwd.get( 'no_changes', '' ) + no_changes_checked = CheckboxField.is_checked( no_changes ) shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository ) uninstalled = repository.uninstalled if uninstalled: @@ -457,20 +484,46 @@ tool_panel_section = metadata[ 'tool_panel_section' ] original_section_id = tool_panel_section[ 'id' ] original_section_name = tool_panel_section[ 'name' ] - if original_section_id in [ '' ]: - tool_section = None + if no_changes_checked: + if original_section_id in [ '' ]: + tool_section = None + else: + section_key = 'section_%s' % str( original_section_id ) + if section_key in trans.app.toolbox.tool_panel: + tool_section = trans.app.toolbox.tool_panel[ section_key ] + else: + # The section in which the tool was originally loaded used to be in the tool panel, but no longer is. + elem = Element( 'section' ) + elem.attrib[ 'name' ] = original_section_name + elem.attrib[ 'id' ] = original_section_id + elem.attrib[ 'version' ] = '' + tool_section = tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ section_key ] = tool_section else: - section_key = 'section_%s' % str( original_section_id ) - if section_key in trans.app.toolbox.tool_panel: + # The user elected to change the tool panel section to contain the tools. + new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) + tool_panel_section = kwd.get( 'tool_panel_section', '' ) + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + new_section_key = 'section_%s' % str( section_id ) + if new_section_key in trans.app.toolbox.tool_panel: + # Appending a tool to an existing section in trans.app.toolbox.tool_panel + log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) + tool_section = trans.app.toolbox.tool_panel[ new_section_key ] + else: + # Appending a new section to trans.app.toolbox.tool_panel + log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) + elem = Element( 'section' ) + elem.attrib[ 'name' ] = new_tool_panel_section + elem.attrib[ 'id' ] = section_id + elem.attrib[ 'version' ] = '' + tool_section = tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ new_section_key ] = tool_section + elif tool_panel_section: + section_key = 'section_%s' % tool_panel_section tool_section = trans.app.toolbox.tool_panel[ section_key ] else: - # The section in which the tool was originally loaded used to be in the tool panel, but no longer is. - elem = Element( 'section' ) - elem.attrib[ 'name' ] = original_section_name - elem.attrib[ 'id' ] = original_section_id - elem.attrib[ 'version' ] = '' - tool_section = tools.ToolSection( elem ) - trans.app.toolbox.tool_panel[ section_key ] = tool_section + tool_section = None tool_shed_repository, metadata_dict = load_repository_contents( app=trans.app, repository_name=repository.name, description=repository.description, diff -r 31c0b88bb4eba817cebf3987565d471c64146b48 -r 60231c4aab751817fc3937c1974e3fc11632df2e templates/admin/tool_shed_repository/reselect_tool_panel_section.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako @@ -0,0 +1,38 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Choose the tool panel section to contain the installed tools (optional)</div> + <div class="toolFormBody"> + <form name="reselect_tool_panel_section" id="reselect_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='activate_or_reinstall_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + ${no_changes_check_box.get_html()} + <label style="display: inline;">No changes</label> + <div class="toolParamHelp" style="clear: both;"> + Uncheck and select a different tool panel section to load the tools into a different section in the tool panel. + </div> + </div> + <div class="form-row"> + <label>Add new tool panel section:</label> + <input name="new_tool_panel_section" type="textfield" value="" size="40"/> + <div class="toolParamHelp" style="clear: both;"> + Add a new tool panel section contain the installed tools (optional). + </div> + </div> + <div class="form-row"> + <label>Select existing tool panel section:</label> + ${tool_panel_section_select_field.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Choose an existing section in your tool panel to contain the installed tools (optional). + </div> + </div> + <div class="form-row"> + <input type="submit" name="select_tool_panel_section_button" value="Install"/> + </div> + </form> + </div> +</div> diff -r 31c0b88bb4eba817cebf3987565d471c64146b48 -r 60231c4aab751817fc3937c1974e3fc11632df2e templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -23,7 +23,7 @@ <br/><div class="toolForm"> - <div class="toolFormTitle">Choose tool panel section to contain installed tools (optional)</div> + <div class="toolFormTitle">Choose the tool panel section to contain the installed tools (optional)</div><div class="toolFormBody"><form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='install_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict, includes_tools=includes_tools )}" method="post" > %if shed_tool_conf_select_field: 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.

1 0

commit/galaxy-central: greg: Tool version grid cleanup.
by Bitbucket 07 Feb '12

07 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/31c0b88bb4eb/ changeset: 31c0b88bb4eb user: greg date: 2012-02-07 19:04:52 summary: Tool version grid cleanup. affected #: 1 file diff -r 9ba4435bfd4ee6111c511c003f1ba6a54b6cb91d -r 31c0b88bb4eba817cebf3987565d471c64146b48 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -402,11 +402,6 @@ else: tool_ids_str += '%s<br/>' % tool_id return tool_ids_str - class ToolShedRepositoryColumn( grids.TextColumn ): - def get_value( self, trans, grid, tool_version ): - if tool_version.tool_shed_repository: - return tool_version.tool_shed_repository.name - return '' # Grid definition title = "Tool versions" model_class = model.ToolVersion @@ -416,10 +411,9 @@ ToolIdColumn( "Tool id", key='tool_id', attach_popup=False ), - ToolVersionsColumn( "Version lineage by tool id (parent/child ordered)" ), - ToolShedRepositoryColumn( "Tool shed repository" ), + ToolVersionsColumn( "Version lineage by tool id (parent/child ordered)" ) ] - columns.append( grids.MulticolFilterColumn( "Search repository name", + columns.append( grids.MulticolFilterColumn( "Search tool id", cols_to_filter=[ columns[0] ], key="free-text-search", visible=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.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 07 Feb '12

07 Feb '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5c57dfac1e31/ changeset: 5c57dfac1e31 user: jgoecks date: 2012-02-07 17:30:45 summary: Trackster: small variable reference fix. affected #: 1 file diff -r b4ba8b20d78d5ae92ebab85afeb6662ca602d427 -r 5c57dfac1e3143e3931bb5d5cc774248f8060113 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -833,10 +833,11 @@ this.changed(); this.container.remove_drawable(this); + var view = this.view; this.container_div.hide(0, function() { $(this).remove(); // HACK: is there a better way to update the view? - drawable.view.update_intro_div(); + view.update_intro_div(); }); }, /** https://bitbucket.org/galaxy/galaxy-central/changeset/9ba4435bfd4e/ changeset: 9ba4435bfd4e user: jgoecks date: 2012-02-07 17:35:48 summary: Fix bug in GFFDataProvider iterator. affected #: 1 file diff -r 5c57dfac1e3143e3931bb5d5cc774248f8060113 -r 9ba4435bfd4ee6111c511c003f1ba6a54b6cb91d lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -936,7 +936,7 @@ for feature in GFFReaderWrapper( source, fix_strand=True ): # Only provide features that are in region. feature_start, feature_end = convert_gff_coords_to_bed( [ feature.start, feature.end ] ) - if feature.chrom != chrom or feature_start < start or feature_end > end: + if feature.chrom != chrom or feature_end < start or feature_start > end: continue yield feature return features_in_region_iter() 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.

1 0

commit/galaxy-central: greg: Fix for loading proprietary datatype sniffers that are included in installed tool shed repositories.
by Bitbucket 07 Feb '12

07 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b4ba8b20d78d/ changeset: b4ba8b20d78d user: greg date: 2012-02-07 17:15:20 summary: Fix for loading proprietary datatype sniffers that are included in installed tool shed repositories. affected #: 1 file diff -r 271ccd09bc2367c7e20d59afb0a7307d4016a1f5 -r b4ba8b20d78d5ae92ebab85afeb6662ca602d427 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -187,11 +187,21 @@ try: fields = dtype.split( ":" ) datatype_module = fields[0] - datatype_class = fields[1] - module = __import__( datatype_module ) - for comp in datatype_module.split( '.' )[ 1: ]: - module = getattr( module, comp ) - aclass = getattr( module, datatype_class )() + datatype_class_name = fields[1] + module = None + if imported_modules: + # See if one of the imported modules contains the datatype class name. + for imported_module in imported_modules: + if hasattr( imported_module, datatype_class_name ): + module = imported_module + break + if module is None: + # The datatype class name must be contained in one of the datatype + # modules in the Galaxy distribution. + module = __import__( datatype_module ) + for comp in datatype_module.split( '.' )[ 1: ]: + module = getattr( module, comp ) + aclass = getattr( module, datatype_class_name )() if deactivate: self.sniff_order.remove( aclass ) self.log.debug( 'Deactivated sniffer for datatype: %s' % dtype ) 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.

1 0

commit/galaxy-central: greg: Fix for 39e03997f78f - change buffer to string so older postgres versions work.
by Bitbucket 07 Feb '12

07 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/271ccd09bc23/ changeset: 271ccd09bc23 user: greg date: 2012-02-07 17:06:17 summary: Fix for 39e03997f78f - change buffer to string so older postgres versions work. affected #: 1 file diff -r 39e03997f78f7dcea23915cffe5f924e7b6bd957 -r 271ccd09bc2367c7e20d59afb0a7307d4016a1f5 lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py --- a/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py +++ b/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py @@ -76,7 +76,7 @@ for row in result: if row[1]: tool_shed_repository_id = row[0] - repository_metadata = from_json_string( _sniffnfix_pg9_hex( row[1] ) ) + repository_metadata = from_json_string( _sniffnfix_pg9_hex( str( row[1] ) ) ) # Create a new row in the tool table for each tool included in repository. We will NOT # handle tool_version_associaions because we do not have the information we need to do so. tools = repository_metadata.get( 'tools', [] ) 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.

1 0

commit/galaxy-central: natefoo: Use PG9 hex bytea fix to decode tool shed repository metadata in migration script 91.
by Bitbucket 07 Feb '12

07 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/39e03997f78f/ changeset: 39e03997f78f user: natefoo date: 2012-02-07 16:41:22 summary: Use PG9 hex bytea fix to decode tool shed repository metadata in migration script 91. affected #: 1 file diff -r f2ed09e52dfd51fb1e95dec0ec1379edefe6d56a -r 39e03997f78f7dcea23915cffe5f924e7b6bd957 lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py --- a/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py +++ b/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py @@ -11,6 +11,7 @@ now = datetime.datetime.utcnow # Need our custom types, but don't import anything else from model from galaxy.model.custom_types import * +from galaxy.model.custom_types import _sniffnfix_pg9_hex from galaxy.util.json import from_json_string, to_json_string import sys, logging @@ -75,7 +76,7 @@ for row in result: if row[1]: tool_shed_repository_id = row[0] - repository_metadata = from_json_string( str( row[1] ) ) + repository_metadata = from_json_string( _sniffnfix_pg9_hex( row[1] ) ) # Create a new row in the tool table for each tool included in repository. We will NOT # handle tool_version_associaions because we do not have the information we need to do so. tools = repository_metadata.get( 'tools', [] ) 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.

1 0

commit/galaxy-central: jgoecks: Trackster: renable data subsetting for all non-LineTracks.
by Bitbucket 07 Feb '12

07 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f2ed09e52dfd/ changeset: f2ed09e52dfd user: jgoecks date: 2012-02-07 16:17:44 summary: Trackster: renable data subsetting for all non-LineTracks. affected #: 1 file diff -r 5e1534bae3f22cb00382d4b5fe8143a2a3a70be7 -r f2ed09e52dfd51fb1e95dec0ec1379edefe6d56a static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -524,8 +524,7 @@ // only data points in request are returned. // - /* Disabling for now, more detailed data is never loaded for line tracks - TODO: can using resolution in the key solve this problem? + // TODO: can using resolution in the key enable LineTrack data to be subsetted appropriately? if (this.subset) { var key, split_key, entry_low, entry_high, mode, entry; for (var i = 0; i < this.key_ary.length; i++) { @@ -535,20 +534,20 @@ entry_high = split_key[1]; if (low >= entry_low && high <= entry_high) { - // This track has the range of data needed; check other attributes. + // This entry has requested data; return if compatible. entry = this.obj_cache[key]; - if (entry.dataset_type !== "summary_tree" && entry.extra_info !== "no_detail") { - // Data is usable. + if ( is_deferred(entry) || this.track.data_and_mode_compatible(entry, mode) ) { + // TODO: for fast lookup and processing, create new entry with only data subset? + // Entry is usable. this.move_key_to_end(key, i); return entry; } } } } - */ // Load data from server. The deferred is immediately saved until the - // data is ready, it then replaces itself with the actual data + // data is ready, it then replaces itself with the actual data. entry = this.load_data(low, high, mode, resolution, extra_params); this.set_data(low, high, entry); return entry; @@ -4042,6 +4041,10 @@ this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; this.mode = "Histogram"; TiledTrack.call(this, name, view, container, prefs, filters, tool, data_manager); + + // Cannot subset LineTrack data right now; see note in DataManager about using resolution in key + // to address this issue. + this.data_manager.subset = false; this.min_height_px = 16; this.max_height_px = 400; 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.

1 0

commit/galaxy-central: dannon: Multiple-run workflows: When run into separate new histories, naming is now based on the varied input dataset instead of the execution number, so "<workflowname> on <varied_input>".
by Bitbucket 07 Feb '12

07 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5e1534bae3f2/ changeset: 5e1534bae3f2 user: dannon date: 2012-02-07 15:45:19 summary: Multiple-run workflows: When run into separate new histories, naming is now based on the varied input dataset instead of the execution number, so "<workflowname> on <varied_input>". affected #: 1 file diff -r b45af710a58bbe64a2d98faee53e8baf6d6314a8 -r 5e1534bae3f22cb00382d4b5fe8143a2a3a70be7 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1489,7 +1489,8 @@ else: nh_name = "History from %s workflow" % workflow.name if multiple_input_key: - nh_name = '%s %d' % (nh_name, input_number + 1) + mx_ds_name = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get( single_input ).name + nh_name = '%s on %s' % (nh_name, mx_ds_name) new_history = trans.app.model.History( user=trans.user, name=nh_name ) trans.sa_session.add( new_history ) # Run each step, connecting outputs to inputs 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.

1 0