galaxy-commits May 2013

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commit/galaxy-central: Dave Bouvier: Update functional tests to reflect recent interface upgrades and enhancements.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/036f57f93b23/ Changeset: 036f57f93b23 User: Dave Bouvier Date: 2013-05-15 19:44:53 Summary: Update functional tests to reflect recent interface upgrades and enhancements. Affected #: 4 files diff -r 93013dcdc4a558791743839d90262e713aba66fd -r 036f57f93b23a62205b8541b6fd773561879827e test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -1,6 +1,7 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util - +import logging +log = logging.getLogger(__name__) repository_name = 'filtering_0000' repository_description = "Galaxy's filtering tool for test 0000" repository_long_description = "Long description of Galaxy's filtering tool for test 0000" @@ -342,8 +343,16 @@ repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) changeset_revision = self.get_repository_tip( repository ) repository_id = self.security.encode_id( repository.id ) + changelog_tuples = self.get_repository_changelog_tuples( repository ) + revision_number = -1 + revision_hash = '000000000000' + for numeric_changeset, changeset_hash in changelog_tuples: + if str( changeset_hash ) == str( changeset_revision ): + revision_number = numeric_changeset + revision_hash = changeset_hash + break # Check for the changeset revision, repository name, owner username, 'repos' in the clone url, and the captured # unicode decoding error message. - strings_displayed = [ 'Changeset %s' % changeset_revision, 'filtering_0000', 'user1', 'repos', 'added:', + strings_displayed = [ 'Changeset %d:%s' % ( revision_number, revision_hash ), 'filtering_0000', 'user1', 'repos', 'added:', 'Error decoding string:', "codec can't decode byte" ] self.load_changeset_in_tool_shed( repository_id, changeset_revision, strings_displayed=strings_displayed ) \ No newline at end of file diff -r 93013dcdc4a558791743839d90262e713aba66fd -r 036f57f93b23a62205b8541b6fd773561879827e test/tool_shed/functional/test_0420_citable_urls_for_repositories.py --- a/test/tool_shed/functional/test_0420_citable_urls_for_repositories.py +++ b/test/tool_shed/functional/test_0420_citable_urls_for_repositories.py @@ -148,9 +148,6 @@ test_user_1 = test_db_util.get_user( common.test_user_1_email ) encoded_user_id = self.security.encode_id( test_user_1.id ) encoded_repository_id = self.security.encode_id( repository.id ) - # We are checking the changeset revision pointed to by first_changeset_hash, stored in a global variable at the end of - # test_0005. The tip changeset hash should not be displayed here, but first_changeset_hash should. - tip_changeset_hash = self.get_repository_tip( repository ) # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly, # then directly load the url that the iframe should be loading and check for the expected strings. # The iframe should point to /repository/view_repository?id=<encoded repository ID> @@ -158,7 +155,7 @@ strings_displayed_in_iframe = [ 'user1', 'filtering_0420', 'Galaxy filtering tool for test 0420', first_changeset_hash ] strings_displayed_in_iframe.append( 'Sharable link to this repository revision:' ) strings_displayed_in_iframe.append( '%s/view/user1/filtering_0420/%s' % ( self.url, first_changeset_hash ) ) - strings_not_displayed_in_iframe = [ tip_changeset_hash ] + strings_not_displayed_in_iframe = [] self.load_citable_url( username='user1', repository_name='filtering_0420', changeset_revision=first_changeset_hash, @@ -173,20 +170,20 @@ test_user_1 = test_db_util.get_user( common.test_user_1_email ) encoded_user_id = self.security.encode_id( test_user_1.id ) encoded_repository_id = self.security.encode_id( repository.id ) - changeset_hash = '!!invalid!!' + invalid_changeset_hash = 'invalid' tip_revision = self.get_repository_tip( repository ) # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly, # then directly load the url that the iframe should be loading and check for the expected strings. # The iframe should point to /repository/view_repository?id=<encoded repository ID>&status=error strings_displayed = [ '/repository', 'view_repository', 'id=' + encoded_repository_id ] - strings_displayed.extend( [ 'The+change+log', 'does+not+include+revision', '%21%21invalid%21%21', 'status=error' ] ) + strings_displayed.extend( [ 'The+change+log', 'does+not+include+revision', invalid_changeset_hash, 'status=error' ] ) strings_displayed_in_iframe = [ 'user1', 'filtering_0420', 'Galaxy filtering tool for test 0420' ] strings_displayed_in_iframe.append( 'Sharable link to this repository revision:' ) - strings_displayed_in_iframe.append( '%s/view/user1/filtering_0420/%s' % ( self.url, changeset_hash ) ) - strings_not_displayed_in_iframe = [ tip_revision ] + strings_displayed_in_iframe.append( '%s/view/user1/filtering_0420/%s' % ( self.url, invalid_changeset_hash ) ) + strings_not_displayed_in_iframe = [] self.load_citable_url( username='user1', repository_name='filtering_0420', - changeset_revision=changeset_hash, + changeset_revision=invalid_changeset_hash, encoded_user_id=encoded_user_id, encoded_repository_id=encoded_repository_id, strings_displayed=strings_displayed, diff -r 93013dcdc4a558791743839d90262e713aba66fd -r 036f57f93b23a62205b8541b6fd773561879827e test/tool_shed/functional/test_1090_install_tool_from_tool_search.py --- a/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py +++ b/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py @@ -296,7 +296,7 @@ exact_matches=False, from_galaxy=True, strings_displayed=[ 'bwa_color_0090', 'bwa_base_0090', bwa_base_revision, bwa_color_revision ] ) strings_displayed=[ 'freebayes_0090', 'emboss_0090', 'filtering_0090' ] - strings_displayed.extend( [ 'bwa_color_0090', 'bwa_base_0090', 'emboss_datatypes_0090' ] ) + strings_displayed.extend( [ 'bwa_color_0090', 'bwa_base_0090' ] ) strings_displayed.extend( [ 'bwa', 'Handle', 'tool dependencies' ] ) repositories_to_install = [ bwa_color_repository, bwa_base_repository ] # BWA is a good candidate for testing the installation of tool dependencies, but it is a core requirement of functional diff -r 93013dcdc4a558791743839d90262e713aba66fd -r 036f57f93b23a62205b8541b6fd773561879827e test/tool_shed/functional/test_1300_reset_all_metadata.py --- a/test/tool_shed/functional/test_1300_reset_all_metadata.py +++ b/test/tool_shed/functional/test_1300_reset_all_metadata.py @@ -400,5 +400,14 @@ for repository in repositories: test_db_util.ga_refresh( repository ) old_metadata = repository_metadata[ self.security.encode_id( repository.id ) ] - assert repository.metadata == old_metadata, 'Metadata for installed repository %s changed after reset.' % repository.name + # When a repository with tools to be displayed in a tool panel section is deactivated and reinstalled, + # the tool panel section remains in the repository metadata. However, when the repository's metadata + # is subsequently reset, the tool panel section is removed from the repository metadata. While this + # is normal and expected behavior, the functional tests assume that repository metadata will not change + # in any way after a reset. A workaround is to remove the tool panel section from the stored repository + # metadata dict, in order to eliminate the misleading detection of changed metadata. + if 'tool_panel_section' in old_metadata and 'tool_panel_section' not in repository.metadata: + del old_metadata[ 'tool_panel_section' ] + assert repository.metadata == old_metadata, 'Metadata for %s repository %s changed after reset. \nOld: %s\nNew: %s' % \ + ( repository.status, repository.name, old_metadata, repository.metadata ) \ No newline at end of file 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: Dave Bouvier: Fix for displaying a tool in the tool shed.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/93013dcdc4a5/ Changeset: 93013dcdc4a5 User: Dave Bouvier Date: 2013-05-15 19:26:12 Summary: Fix for displaying a tool in the tool shed. Affected #: 1 file diff -r 413211aaecc51eb38fae668326d4defefda2b8f7 -r 93013dcdc4a558791743839d90262e713aba66fd templates/webapps/tool_shed/repository/tool_form.mako --- a/templates/webapps/tool_shed/repository/tool_form.mako +++ b/templates/webapps/tool_shed/repository/tool_form.mako @@ -107,7 +107,7 @@ %if trans.webapp.name == 'galaxy': ${render_galaxy_repository_actions( repository=repository )} %else: - ${render_tool_shed_repository_actions( repository, repo=None, metadata=None, changeset_revision=None )} + ${render_tool_shed_repository_actions( repository, metadata=None, changeset_revision=None )} %endif %if message: 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: Undo 69240f7da05e
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/413211aaecc5/ Changeset: 413211aaecc5 User: dan Date: 2013-05-15 19:23:45 Summary: Undo 69240f7da05e Affected #: 1 file diff -r ca0daccbb90f2a2eabfb5f64156a7c270cbd3eca -r 413211aaecc51eb38fae668326d4defefda2b8f7 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -422,10 +422,7 @@ Returns a unicode string or None """ if isinstance( value, unicode ): - try: - return value.encode( encoding, error ) - except: - return value + return value try: return unicode( value, encoding, error ) except: 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: Enhance util.unicodify to attempt to force encoding when already an unicode object.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ca0daccbb90f/ Changeset: ca0daccbb90f User: dan Date: 2013-05-15 19:07:07 Summary: Enhance util.unicodify to attempt to force encoding when already an unicode object. Affected #: 1 file diff -r 69240f7da05e4ae42803b67a507103d201186306 -r ca0daccbb90f2a2eabfb5f64156a7c270cbd3eca lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -422,7 +422,10 @@ Returns a unicode string or None """ if isinstance( value, unicode ): - return value + try: + return value.encode( encoding, error ) + except: + return value try: return unicode( value, encoding, error ) except: 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 commits-noreply＠bitbucket.org 15 May '13

15 May '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8701e8440e57/ Changeset: 8701e8440e57 User: dan Date: 2013-05-15 17:09:32 Summary: Unicode fixes for workflow names in Tool Menu. Affected #: 1 file diff -r 866ed8fd31e146792980c61489d57cc18a5036b5 -r 8701e8440e57bc8bc0b173297e60d33d4eab3734 templates/webapps/galaxy/root/tool_menu.mako --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -10,7 +10,7 @@ <div class="toolTitleNoSection"> %endif <% encoded_id = key.lstrip( 'workflow_' ) %> - <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id )}" target="_parent">${_(workflow.name)}</a> + <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id )}" target="_parent">${_( util.unicodify( workflow.name ) ) }</a></div></%def> @@ -122,7 +122,7 @@ %if t.user.stored_workflow_menu_entries: %for m in t.user.stored_workflow_menu_entries: <div class="toolTitle"> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${m.stored_workflow.name}</a> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${ util.unicodify( m.stored_workflow.name ) }</a></div> %endfor %endif https://bitbucket.org/galaxy/galaxy-central/commits/69240f7da05e/ Changeset: 69240f7da05e User: dan Date: 2013-05-15 17:13:59 Summary: Merge Affected #: 1 file diff -r 2e387c1384f1f7429a86e77e9a23b5329ca97b94 -r 69240f7da05e4ae42803b67a507103d201186306 templates/webapps/galaxy/root/tool_menu.mako --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -10,7 +10,7 @@ <div class="toolTitleNoSection"> %endif <% encoded_id = key.lstrip( 'workflow_' ) %> - <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id )}" target="_parent">${_(workflow.name)}</a> + <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id )}" target="_parent">${_( util.unicodify( workflow.name ) ) }</a></div></%def> @@ -122,7 +122,7 @@ %if t.user.stored_workflow_menu_entries: %for m in t.user.stored_workflow_menu_entries: <div class="toolTitle"> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${m.stored_workflow.name}</a> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${ util.unicodify( m.stored_workflow.name ) }</a></div> %endfor %endif https://bitbucket.org/galaxy/galaxy-central/commits/0f51ae4f1c84/ Changeset: 0f51ae4f1c84 Branch: stable User: dan Date: 2013-05-15 17:09:32 Summary: Unicode fixes for workflow names in Tool Menu. Affected #: 1 file diff -r 6861705712161c545398e6db1a7cdadda931fc7a -r 0f51ae4f1c84c5bab6cd1c93ae837696be9565e1 templates/webapps/galaxy/root/tool_menu.mako --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -10,7 +10,7 @@ <div class="toolTitleNoSection"> %endif <% encoded_id = key.lstrip( 'workflow_' ) %> - <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id )}" target="_parent">${_(workflow.name)}</a> + <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id )}" target="_parent">${_( util.unicodify( workflow.name ) ) }</a></div></%def> @@ -122,7 +122,7 @@ %if t.user.stored_workflow_menu_entries: %for m in t.user.stored_workflow_menu_entries: <div class="toolTitle"> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${m.stored_workflow.name}</a> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${ util.unicodify( m.stored_workflow.name ) }</a></div> %endfor %endif 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: Dave Bouvier: Add support for specifying the target filename in the download_file action. Set a tool dependency to the error state if the actions list specifies an unsupported action.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2e387c1384f1/ Changeset: 2e387c1384f1 User: Dave Bouvier Date: 2013-05-15 17:07:49 Summary: Add support for specifying the target filename in the download_file action. Set a tool dependency to the error state if the actions list specifies an unsupported action. Affected #: 2 files diff -r 866ed8fd31e146792980c61489d57cc18a5036b5 -r 2e387c1384f1f7429a86e77e9a23b5329ca97b94 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -92,7 +92,10 @@ # Download a single file to the working directory. filtered_actions = actions[ 1: ] url = action_dict[ 'url' ] - filename = url.split( '/' )[ -1 ] + if action_dict[ 'target_filename' ]: + filename = action_dict[ 'target_filename' ] + else: + filename = url.split( '/' )[ -1 ] common_util.url_download( work_dir, filename, url ) dir = os.path.curdir else: @@ -150,7 +153,10 @@ elif action_type == 'download_file': # Download a single file to the current directory. url = action_dict[ 'url' ] - filename = url.split( '/' )[ -1 ] + if action_dict[ 'target_filename' ]: + filename = action_dict[ 'target_filename' ] + else: + filename = url.split( '/' )[ -1 ] common_util.url_download( current_dir, filename, url ) def log_results( command, fabric_AttributeString, file_path ): diff -r 866ed8fd31e146792980c61489d57cc18a5036b5 -r 2e387c1384f1f7429a86e77e9a23b5329ca97b94 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -345,6 +345,7 @@ # <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action> if action_elem.text: action_dict[ 'url' ] = action_elem.text + action_dict[ 'target_filename' ] = action_elem.attrib.get( 'target_filename', None ) else: continue elif action_type == 'make_directory': @@ -402,8 +403,8 @@ else: continue else: - log.debug( "Skipping unsupported action type '%s'." % str( action_type ) ) - continue + log.debug( "Unsupported action type '%s'. Not proceeding." % str( action_type ) ) + raise Exception( "Unsupported action type '%s' in tool dependency definition." % str( action_type ) ) actions.append( ( action_type, action_dict ) ) if actions: actions_dict[ 'actions' ] = actions 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: Trackster: unify draw_helper functions for performance and clarity.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/866ed8fd31e1/ Changeset: 866ed8fd31e1 User: jgoecks Date: 2013-05-15 16:09:55 Summary: Trackster: unify draw_helper functions for performance and clarity. Affected #: 1 file diff -r eb04cd61c978821c88f793ca3bc51783fd550c05 -r 866ed8fd31e146792980c61489d57cc18a5036b5 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3082,6 +3082,13 @@ }, /** + * Returns a list of drawables to draw. Defaults to current track. + */ + _get_drawables: function() { + return [ this ]; + }, + + /** * Retrieves from cache, draws, or sets up drawing for a single tile. Returns either a Tile object or a * jQuery.Deferred object that is fulfilled when tile can be drawn again. */ @@ -3090,6 +3097,7 @@ if (!kwargs) { kwargs = {}; } var track = this, + drawables = this._get_drawables(), key = this._gen_tile_cache_key(w_scale, region), is_tile = function(o) { return (o && 'track' in o); }, mode = kwargs.mode || track.mode; @@ -3104,17 +3112,19 @@ } // Function that returns data/Deferreds needed to draw tile. - var get_data = function() { - // Get the track data, maybe a deferred - var tile_data = track.data_manager.get_data(region, mode, resolution, track.data_url_extra_params); - - // Get reference data if needed, maybe a deferred - var seq_data; - if ( view.reference_track ) { - seq_data = view.reference_track.data_manager.get_data(region, mode, resolution, view.reference_track.data_url_extra_params); - } + var get_tile_data = function() { + // Map drawable object to data needed for drawing. + var tile_data = _.map(drawables, function(d) { + // Get the track data/promise. + return d.data_manager.get_data(region, mode, resolution, track.data_url_extra_params); + }); - return [tile_data, seq_data]; + // Get reference data/promise. + if (view.reference_track) { + tile_data.push(view.reference_track.data_manager.get_data(region, mode, resolution, view.reference_track.data_url_extra_params)); + } + + return tile_data; }; // @@ -3122,37 +3132,54 @@ // var tile_drawn = $.Deferred(); track.tile_cache.set_elt(key, tile_drawn); - $.when.apply($, get_data()).then( function() { - var data = get_data(), - tile_data = data[0], - seq_data = data[1]; - - // Set up and draw tile. - extend(tile_data, kwargs[ 'more_tile_data' ] ); - + $.when.apply($, get_tile_data()).then( function() { + var tile_data = get_tile_data(), + tracks_data = tile_data.slice(0, tile_data.length - 1), + seq_data = tile_data[tile_data.length - 1]; + // If sequence data is available, subset to get only data in region. - if (view.reference_track) { + if (seq_data) { seq_data = view.reference_track.data_manager.subset_entry(seq_data, region); } - // HACK: this is FeatureTrack-specific. - // If track mode is Auto, determine mode and update. - if (mode === "Auto" && track.get_mode) { - mode = track.get_mode(tile_data); - track.update_auto_mode(mode); - } - - // Draw canvas. + // Get drawing modes, heights for all tracks. + var drawing_modes = [], + drawing_heights = []; + + _.each(drawables, function(d, i) { + var mode = d.mode, + data = tracks_data[i]; + if (mode === "Auto") { + mode = d.get_mode(data); + d.update_auto_mode(mode); + } + drawing_modes.push(mode); + drawing_heights.push(d.get_canvas_height(data, mode, w_scale, width)); + }) + var canvas = track.view.canvas_manager.new_canvas(), tile_low = region.get('start'), tile_high = region.get('end'), + all_data_index = 0, width = Math.ceil( (tile_high - tile_low) * w_scale ) + track.left_offset, - height = track.get_canvas_height(tile_data, mode, w_scale, width); + height = _.max(drawing_heights), + tile; + + // + // Draw all tracks on tile. + // canvas.width = width; - canvas.height = height; + // Height is specified in kwargs or is the height found above. + canvas.height = (kwargs.height ? kwargs.height : height); var ctx = canvas.getContext('2d'); ctx.translate(track.left_offset, 0); - var tile = track.draw_tile(tile_data, ctx, mode, resolution, region, w_scale, seq_data); + if (drawables.length > 1) { + ctx.globalAlpha = 0.5; + ctx.globalCompositeOperation = "source-over"; + } + _.each(drawables, function(d, i) { + tile = d.draw_tile(tracks_data[i], ctx, drawing_modes[i], resolution, region, w_scale, seq_data); + }); // Don't cache, show if no tile. if (tile !== undefined) { @@ -3470,126 +3497,8 @@ can_draw: Drawable.prototype.can_draw, - draw_helper: function(force, region, resolution, parent_element, w_scale, kwargs) { - // FIXME: this function is similar to TiledTrack.draw_helper -- can the two be merged/refactored? - - // SHARED block with TiledTrack.draw_helper(): - - var track = this, - key = this._gen_tile_cache_key(w_scale, region), - is_tile = function(o) { return (o && 'track' in o); }; - - // Init kwargs if necessary to avoid having to check if kwargs defined. - if (!kwargs) { kwargs = {}; } - - // Check tile cache, if found show existing tile in correct position - var tile = (force ? undefined : track.tile_cache.get_elt(key)); - if (tile) { - if (is_tile(tile)) { - track.show_tile(tile, parent_element, w_scale); - } - return tile; - } - - // UNIQUE block. - - // Try to get drawables' data. - var all_data = [], - track, - // Flag to track whether we can draw everything now - can_draw_now = true, - tile_data, - seq_data; - 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(region, track.mode, resolution, track.data_url_extra_params); - if ( is_deferred( tile_data ) ) { - can_draw_now = false; - } - all_data.push(tile_data); - - // 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(region, track.mode, resolution, view.reference_track.data_url_extra_params); - if ( is_deferred( seq_data ) ) { - can_draw_now = false; - } - } - all_data.push(seq_data); - } - - // If we can draw now, do so. - if ( can_draw_now ) { - // Set up and draw tile. - extend(tile_data, kwargs[ 'more_tile_data' ] ); - - var canvas = track.view.canvas_manager.new_canvas(), - 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, - track_modes = [], - i; - - // Get max height for all tracks and record track modes. - var track_canvas_height = 0; - for (i = 0; i < this.drawables.length; i++, all_data_index += 2) { - track = this.drawables[i]; - tile_data = all_data[ all_data_index ]; - - // HACK: this is FeatureTrack-specific. - // If track mode is Auto, determine mode and update. - var mode = track.mode; - if (mode === "Auto") { - mode = track.get_mode(tile_data); - track.update_auto_mode(mode); - } - track_modes.push(mode); - - track_canvas_height = track.get_canvas_height(tile_data, mode, w_scale, width); - if (track_canvas_height > height) { height = track_canvas_height; } - } - - // - // Draw all tracks on a single tile. - // - canvas.width = width; - // Height is specified in kwargs or is the height found above. - canvas.height = (kwargs.height ? kwargs.height : height); - all_data_index = 0; - var ctx = canvas.getContext('2d'); - ctx.translate(this.left_offset, 0); - ctx.globalAlpha = 0.5; - ctx.globalCompositeOperation = "source-over"; - for (i = 0; i < this.drawables.length; i++, all_data_index += 2) { - 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, region, w_scale, seq_data); - } - - // Don't cache, show if no tile. - this.tile_cache.set_elt(key, tile); - this.show_tile(tile, parent_element, w_scale); - return tile; - } - - // SHARED (somewhat) block with TiledTrack.draw_helper() - - // Can't draw now, so put Deferred in cache and draw tile when data is available. - var tile_drawn = $.Deferred(); - track = this; - track.tile_cache.set_elt(key, tile_drawn); - $.when.apply($, all_data).then(function() { - // Draw tile--force to clear Deferred from cache--and resolve. - tile = track.draw_helper(true, region, resolution, parent_element, w_scale, kwargs); - tile_drawn.resolve(tile); - }); - - return tile_drawn; + _get_drawables: function() { + return this.drawables; }, /** 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: Trackster bug fix: use computed mode rather than track mode.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb04cd61c978/ Changeset: eb04cd61c978 User: jgoecks Date: 2013-05-15 15:17:41 Summary: Trackster bug fix: use computed mode rather than track mode. Affected #: 1 file diff -r d6125e3f660caa376323218546b72e4f953dc669 -r eb04cd61c978821c88f793ca3bc51783fd550c05 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3106,12 +3106,12 @@ // Function that returns data/Deferreds needed to draw tile. var get_data = function() { // 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, mode, resolution, track.data_url_extra_params); // Get reference data if needed, maybe a deferred var seq_data; if ( view.reference_track ) { - seq_data = view.reference_track.data_manager.get_data(region, track.mode, resolution, view.reference_track.data_url_extra_params); + seq_data = view.reference_track.data_manager.get_data(region, mode, resolution, view.reference_track.data_url_extra_params); } return [tile_data, seq_data]; 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: Kyle Ellrott: Starting work on 'read-only': object stores that can be added to the distributed object store system and provide remote access to additional data sources
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/73858b780fdc/ Changeset: 73858b780fdc Branch: federate User: Kyle Ellrott Date: 2013-05-15 01:53:32 Summary: Starting work on 'read-only': object stores that can be added to the distributed object store system and provide remote access to additional data sources Affected #: 4 files diff -r 6d72b2db32c0d84032ee40f2cd86b7b09485c441 -r 73858b780fdcede620cb0e42409a856367e330b4 distributed_object_store_conf.xml --- /dev/null +++ b/distributed_object_store_conf.xml @@ -0,0 +1,16 @@ +<?xml version="1.0"?> +<backends> + <backend id="files1" type="disk" weight="1"> + <files_dir path="database/files1"/> + <extra_dir type="temp" path="database/tmp1"/> + <extra_dir type="job_work" path="database/job_working_directory1"/> + </backend> + <backend id="files2" type="disk" weight="1"> + <files_dir path="database/files2"/> + <extra_dir type="temp" path="database/tmp2"/> + <extra_dir type="job_work" path="database/job_working_directory2"/> + </backend> + <backend id="galaxy_main" type="galaxy.objectstore.remote:RemoteGalaxyStore"> + <url>https://main.g2.bx.psu.edu/</url> + </backend> +</backends> diff -r 6d72b2db32c0d84032ee40f2cd86b7b09485c441 -r 73858b780fdcede620cb0e42409a856367e330b4 distributed_object_store_conf.xml.sample --- a/distributed_object_store_conf.xml.sample +++ b/distributed_object_store_conf.xml.sample @@ -10,4 +10,7 @@ <extra_dir type="temp" path="database/tmp2"/><extra_dir type="job_work" path="database/job_working_directory2"/></backend> + </backends> diff -r 6d72b2db32c0d84032ee40f2cd86b7b09485c441 -r 73858b780fdcede620cb0e42409a856367e330b4 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -36,6 +36,7 @@ """ ObjectStore abstract interface """ + is_readonly = False def __init__(self): self.running = True self.extra_dirs = {} @@ -895,7 +896,8 @@ id = elem.get('id') weight = int(elem.get('weight', 1)) maxpctfull = float(elem.get('maxpctfull', 0)) - if elem.get('type', 'disk'): + ostype = elem.get('type', 'disk') + if ostype == 'disk': path = None extra_dirs = {} for sub in elem: @@ -911,6 +913,20 @@ log.debug(" Extra directories:") for type, dir in extra_dirs.items(): log.debug(" %s: %s" % (type, dir)) + else: + fields = ostype.split( ':' ) + ostype_module = fields[0] + ostype_class_name = fields[1] + mfields = ostype_module.split( '.' ) + module = __import__( ostype_module ) + for mod in mfields[1:]: + module = getattr( module, mod ) + ostype_class = getattr( module, ostype_class_name ) + obj = ostype_class({}) + self.backends[id] = obj + if obj.is_readonly: + weight = 0 + for i in range(0, weight): # The simplest way to do weighting: add backend ids to a # sequence the number of times equalling weight, then randomly diff -r 6d72b2db32c0d84032ee40f2cd86b7b09485c441 -r 73858b780fdcede620cb0e42409a856367e330b4 lib/galaxy/objectstore/remote.py --- /dev/null +++ b/lib/galaxy/objectstore/remote.py @@ -0,0 +1,8 @@ + +from galaxy.objectstore import ObjectStore + +class RemoteGalaxyStore(ObjectStore): + is_readonly = True + def __init__(self, params): + print "Remote Galaxy Store Loaded!!!!!" + \ No newline at end of file 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: 2 new changesets
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e99b00df40b2/ Changeset: e99b00df40b2 User: Dave Bouvier Date: 2013-05-14 22:54:12 Summary: Fix for reinstalling an uninstalled repository when leaving the no changes checkbox checked and entering text into the new tool panel section field. Affected #: 2 files diff -r 6d72b2db32c0d84032ee40f2cd86b7b09485c441 -r e99b00df40b2895ee1a36d356dc5c0b968f80f8c lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -445,7 +445,8 @@ try: tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] except KeyError: - log.debug( 'Invalid tool_panel_section_key "%s" specified. Tools will be loaded outside of sections in the tool panel.' ) + log.debug( 'Invalid tool_panel_section_key "%s" specified. Tools will be loaded outside of sections in the tool panel.', + str( tool_panel_section_key ) ) tool_section = None else: tool_section = None diff -r 6d72b2db32c0d84032ee40f2cd86b7b09485c441 -r e99b00df40b2895ee1a36d356dc5c0b968f80f8c lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -617,6 +617,9 @@ if 'tools' in metadata: # This forces everything to be loaded into the same section (or no section) in the tool panel. if no_changes_checked: + # Make sure the no_changes checkbox overrides the new_tool_panel_section if the user checked the checkbox and + # entered something into the field. + new_tool_panel_section = None if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] if not tool_panel_dict: https://bitbucket.org/galaxy/galaxy-central/commits/d6125e3f660c/ Changeset: d6125e3f660c User: Dave Bouvier Date: 2013-05-14 22:55:16 Summary: Merge. Affected #: 1 file diff -r e99b00df40b2895ee1a36d356dc5c0b968f80f8c -r d6125e3f660caa376323218546b72e4f953dc669 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -362,7 +362,7 @@ data_tables.append( data_table_name ) if bad_data_table: continue - data_manager_metadata_tool_file = os.path.join( relative_data_manager_dir, tool_file ) + data_manager_metadata_tool_file = os.path.normpath( os.path.join( relative_data_manager_dir, tool_file ) ) tool_metadata_tool_file = os.path.join( repo_files_directory, data_manager_metadata_tool_file ) tool = tools.get( tool_metadata_tool_file, None ) if tool is None: 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 May 2013