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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. 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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 14 May '13

14 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 14 May '13

14 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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commit/galaxy-central: dan: Fix for determining Data Manager Tool Filename.
by commits-noreply＠bitbucket.org 14 May '13

14 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8483f0ef8288/ Changeset: 8483f0ef8288 User: dan Date: 2013-05-14 22:52:58 Summary: Fix for determining Data Manager Tool Filename. Affected #: 1 file diff -r 6d72b2db32c0d84032ee40f2cd86b7b09485c441 -r 8483f0ef8288b6eecf65a556c75b65e944a00bb0 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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commit/galaxy-central: greg: Ehancements for the tool shed repository View changeset page: display the commit message, display both the ctx rev and the changeset hash in the title bar, and add Previous changeset and Next changeset buttons to allow for easier scrolling through the repository changelog.
by commits-noreply＠bitbucket.org 14 May '13

14 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6d72b2db32c0/ Changeset: 6d72b2db32c0 User: greg Date: 2013-05-14 21:58:09 Summary: Ehancements for the tool shed repository View changeset page: display the commit message, display both the ctx rev and the changeset hash in the title bar, and add Previous changeset and Next changeset buttons to allow for easier scrolling through the repository changelog. Affected #: 2 files diff -r c1f961549cca546214ff4430dd6a01c42cfeaa63 -r 6d72b2db32c0d84032ee40f2cd86b7b09485c441 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2681,17 +2681,39 @@ id=id, message=message, status=status ) ) - ctx_parent = ctx.parents()[0] + ctx_parent = ctx.parents()[ 0 ] + if ctx.children(): + ctx_child = ctx.children()[ 0 ] + else: + ctx_child = None modified, added, removed, deleted, unknown, ignored, clean = repo.status( node1=ctx_parent.node(), node2=ctx.node() ) anchors = modified + added + removed + deleted + unknown + ignored + clean diffs = [] for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ): diffs.append( suc.to_safe_string( diff, to_html=True ) ) metadata = self.get_metadata( trans, id, ctx_str ) + # For rendering the prev button. + if ctx_parent: + ctx_parent_rev = ctx_parent.rev() + if ctx_parent_rev < 0: + prev = None + else: + prev = "%s:%s" % ( ctx_parent_rev, ctx_parent ) + else: + prev = None + if ctx_child: + ctx_child_rev = ctx_child.rev() + next = "%s:%s" % ( ctx_child_rev, ctx_child ) + else: + next = None return trans.fill_template( '/webapps/tool_shed/repository/view_changeset.mako', repository=repository, metadata=metadata, + prev=prev, + next=next, ctx=ctx, + ctx_parent=ctx_parent, + ctx_child=ctx_child, anchors=anchors, modified=modified, added=added, diff -r c1f961549cca546214ff4430dd6a01c42cfeaa63 -r 6d72b2db32c0d84032ee40f2cd86b7b09485c441 templates/webapps/tool_shed/repository/view_changeset.mako --- a/templates/webapps/tool_shed/repository/view_changeset.mako +++ b/templates/webapps/tool_shed/repository/view_changeset.mako @@ -50,13 +50,33 @@ <div class="toolForm"><% if can_download: - title_str = 'Changeset %s' % ctx + title_str = 'Changeset %s:%s' % ( ctx.rev(), ctx ) else: - title_str = '%s changeset %s' % ( repository.name, ctx ) + title_str = '%s changeset %s:%s' % ( repository.name, ctx.rev(), ctx ) %> - <div class="toolFormTitle">${title_str | h}</div> + <div class="toolFormTitle"> + ${title_str | h} + </div><div class="toolFormBody"><table class="grid"> + %if prev or next: + <tr> + <td> + %if prev: + <a class="action-button" href="${h.url_for( controller='repository', action='view_changeset', id=trans.security.encode_id( repository.id ), ctx_str=ctx_parent )}">Previous changeset ${prev | h}</a> + %endif + %if next: + <a class="action-button" href="${h.url_for( controller='repository', action='view_changeset', id=trans.security.encode_id( repository.id ), ctx_str=ctx_child )}">Next changeset ${next | h}</a> + %endif + </td> + </tr> + %endif + <tr> + <td> + <b>Commit message:</b> + <br/>${ctx.description() | h}<br/> + </td> + </tr> %if modified: <tr><td> 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 detecting job error in data manager tools; needed as a result of recent job flow changes.
by commits-noreply＠bitbucket.org 14 May '13

14 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c1f961549cca/ Changeset: c1f961549cca User: dan Date: 2013-05-14 21:54:33 Summary: Fix for detecting job error in data manager tools; needed as a result of recent job flow changes. Affected #: 1 file diff -r 4573880b2d9b7a76abcbe2ccac824ab9338df802 -r c1f961549cca546214ff4430dd6a01c42cfeaa63 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -3157,6 +3157,10 @@ #process results of tool if job and job.state == job.states.ERROR: return + #Job state may now be 'running' instead of previous 'error', but datasets are still set to e.g. error + for dataset in out_data.itervalues(): + if dataset.state != dataset.states.OK: + return data_manager_id = job.data_manager_association.data_manager_id data_manager = self.app.data_managers.get_manager( data_manager_id, None ) assert data_manager is not None, "Invalid data manager (%s) requested. It may have been removed before the job completed." % ( data_manager_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: 4 new changesets
by commits-noreply＠bitbucket.org 14 May '13

14 May '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2c0c1070891c/ Changeset: 2c0c1070891c User: jgoecks Date: 2013-05-14 19:15:02 Summary: Trackster: LinePainter improvements to use block_color when drawing coverage plots and refactor min/max finding to us underscore functions. Affected #: 1 file diff -r 8882e45504a37ab9f87f2872df2a6749673bd741 -r 2c0c1070891cdef382f32c0c3780a06d9169a10d static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -135,20 +135,11 @@ var LinePainter = function(data, view_start, view_end, prefs, mode) { Painter.call( this, data, view_start, view_end, prefs, mode ); - var i, len; if ( this.prefs.min_value === undefined ) { - var min_value = Infinity; - for (i = 0, len = this.data.length; i < len; i++) { - min_value = Math.min( min_value, this.data[i][1] ); - } - this.prefs.min_value = min_value; + this.prefs.min_value = _.min( _.map(this.data, function(d) { return d[1]; }) ) || 0; } if ( this.prefs.max_value === undefined ) { - var max_value = -Infinity; - for (i = 0, len = this.data.length; i < len; i++) { - max_value = Math.max( max_value, this.data[i][1] ); - } - this.prefs.max_value = max_value; + this.prefs.max_value = _.max( _.map(this.data, function(d) { return d[1]; }) ) || 0; } }; @@ -184,15 +175,17 @@ delta_x_px = 10; } - // Extract RGB from preference color. - var pref_color = parseInt( this.prefs.color.slice(1), 16 ), + // Painter color can be in either block_color (FeatureTrack) or color pref (LineTrack). + var painter_color = this.prefs.block_color || this.prefs.color, + // Extract RGB from preference color. + pref_color = parseInt( painter_color.slice(1), 16 ), pref_r = (pref_color & 0xff0000) >> 16, pref_g = (pref_color & 0x00ff00) >> 8, pref_b = pref_color & 0x0000ff; // Paint track. for (var i = 0, len = data.length; i < len; i++) { - ctx.fillStyle = ctx.strokeStyle = this.prefs.color; + ctx.fillStyle = ctx.strokeStyle = painter_color; // -0.5 to offset drawing between bases. x_scaled = Math.round((data[i][0] - view_start - 0.5) * w_scale); y = data[i][1]; @@ -261,7 +254,7 @@ ctx.fillRect(x_scaled, height_px - 3, overflow_x, 3); } } - ctx.fillStyle = this.prefs.color; + ctx.fillStyle = painter_color; } if (mode === "Filled") { if (in_path) { https://bitbucket.org/galaxy/galaxy-central/commits/f4f596595970/ Changeset: f4f596595970 User: jgoecks Date: 2013-05-14 20:56:09 Summary: Add interval-to-bigwig converter, which creates a bigwig of coverage data for an interval dataset. Affected #: 2 files diff -r 2c0c1070891cdef382f32c0c3780a06d9169a10d -r f4f59659597023ad3b68b631da3b085dc98b15ed datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -17,7 +17,6 @@ </datatype><datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"><converter file="bed_to_gff_converter.xml" target_datatype="gff"/> - <converter file="interval_to_coverage.xml" target_datatype="coverage"/><converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> diff -r 2c0c1070891cdef382f32c0c3780a06d9169a10d -r f4f59659597023ad3b68b631da3b085dc98b15ed lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml @@ -0,0 +1,33 @@ +<tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage"> +  +  + <command> + + ## Remove comments and sort by chromosome. + grep -v '^#' $input1 | sort -k${input1.metadata.chromCol},${input1.metadata.chromCol} | + + ## Create simple BED by cutting chrom, start, and end columns. + awk -v OFS=' ' '{print $${input1.metadata.chromCol},$${input1.metadata.startCol},$${input1.metadata.endCol} }' | + + ## Generate coverage bedgraph. + bedtools genomecov -bg -split -i stdin -g $chromInfo + + ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this + ## should only be used on systems with large RAM. + ## | wigToBigWig stdin $chromInfo $output + + ## This can be used anywhere. + > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output + + </command> + <inputs> + <page> + <param format="interval" name="input1" type="data" label="Choose intervals"/> + </page> + </inputs> + <outputs> + <data format="bigwig" name="output"/> + </outputs> + <help> + </help> +</tool> https://bitbucket.org/galaxy/galaxy-central/commits/15224c9c15d9/ Changeset: 15224c9c15d9 User: jgoecks Date: 2013-05-14 21:46:27 Summary: Trackster: use deferred rather than flags to manage tile drawing. Affected #: 1 file diff -r f4f59659597023ad3b68b631da3b085dc98b15ed -r 15224c9c15d9de6323892207fff44520a23e3084 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3102,34 +3102,39 @@ } return tile; } - - // Flag to track whether we can draw everything now - var can_draw_now = true; - - // Get the track data, maybe a deferred - var tile_data = track.data_manager.get_data(region, mode, resolution, track.data_url_extra_params); - if ( is_deferred( tile_data ) ) { - can_draw_now = false; - } - - // 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); - if ( is_deferred( seq_data ) ) { - can_draw_now = false; + + // 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); + + // 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); + } + + return [tile_data, seq_data]; + }; + + // + // When data is available, draw tile. + // + 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' ] ); + + // If sequence data is available, subset to get only data in region. + if (view.reference_track) { + seq_data = view.reference_track.data_manager.subset_entry(seq_data, region); } - else { - // Sequence data is available, subset to get only data in region. - seq_data = view.reference_track.data_manager.subset_entry(seq_data, region); - } - } - - // If we can draw now, do so. - if ( can_draw_now ) { - // Set up and draw tile. - extend(tile_data, kwargs[ 'more_tile_data' ] ); - + // HACK: this is FeatureTrack-specific. // If track mode is Auto, determine mode and update. if (mode === "Auto" && track.get_mode) { @@ -3138,8 +3143,7 @@ } // Draw canvas. - var - canvas = track.view.canvas_manager.new_canvas(), + var canvas = track.view.canvas_manager.new_canvas(), tile_low = region.get('start'), tile_high = region.get('end'), width = Math.ceil( (tile_high - tile_low) * w_scale ) + track.left_offset, @@ -3147,26 +3151,18 @@ canvas.width = width; canvas.height = height; var ctx = canvas.getContext('2d'); - ctx.translate(this.left_offset, 0); + ctx.translate(track.left_offset, 0); var tile = track.draw_tile(tile_data, ctx, mode, resolution, region, w_scale, seq_data); - + // Don't cache, show if no tile. if (tile !== undefined) { track.tile_cache.set_elt(key, tile); track.show_tile(tile, parent_element, w_scale); } - return tile; - } - - // Can't draw now, so put Deferred in cache and draw tile when data is available. - var tile_drawn = $.Deferred(); - track.tile_cache.set_elt(key, tile_drawn); - $.when( tile_data, seq_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; }, https://bitbucket.org/galaxy/galaxy-central/commits/4573880b2d9b/ Changeset: 4573880b2d9b User: jgoecks Date: 2013-05-14 21:47:42 Summary: Automated merge. Affected #: 4 files diff -r 1a4b56a78124b26103c61f8e6e736b088e65aa6d -r 4573880b2d9b7a76abcbe2ccac824ab9338df802 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -17,7 +17,6 @@ </datatype><datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"><converter file="bed_to_gff_converter.xml" target_datatype="gff"/> - <converter file="interval_to_coverage.xml" target_datatype="coverage"/><converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> diff -r 1a4b56a78124b26103c61f8e6e736b088e65aa6d -r 4573880b2d9b7a76abcbe2ccac824ab9338df802 lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml @@ -0,0 +1,33 @@ +<tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage"> +  +  + <command> + + ## Remove comments and sort by chromosome. + grep -v '^#' $input1 | sort -k${input1.metadata.chromCol},${input1.metadata.chromCol} | + + ## Create simple BED by cutting chrom, start, and end columns. + awk -v OFS=' ' '{print $${input1.metadata.chromCol},$${input1.metadata.startCol},$${input1.metadata.endCol} }' | + + ## Generate coverage bedgraph. + bedtools genomecov -bg -split -i stdin -g $chromInfo + + ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this + ## should only be used on systems with large RAM. + ## | wigToBigWig stdin $chromInfo $output + + ## This can be used anywhere. + > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output + + </command> + <inputs> + <page> + <param format="interval" name="input1" type="data" label="Choose intervals"/> + </page> + </inputs> + <outputs> + <data format="bigwig" name="output"/> + </outputs> + <help> + </help> +</tool> diff -r 1a4b56a78124b26103c61f8e6e736b088e65aa6d -r 4573880b2d9b7a76abcbe2ccac824ab9338df802 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -135,20 +135,11 @@ var LinePainter = function(data, view_start, view_end, prefs, mode) { Painter.call( this, data, view_start, view_end, prefs, mode ); - var i, len; if ( this.prefs.min_value === undefined ) { - var min_value = Infinity; - for (i = 0, len = this.data.length; i < len; i++) { - min_value = Math.min( min_value, this.data[i][1] ); - } - this.prefs.min_value = min_value; + this.prefs.min_value = _.min( _.map(this.data, function(d) { return d[1]; }) ) || 0; } if ( this.prefs.max_value === undefined ) { - var max_value = -Infinity; - for (i = 0, len = this.data.length; i < len; i++) { - max_value = Math.max( max_value, this.data[i][1] ); - } - this.prefs.max_value = max_value; + this.prefs.max_value = _.max( _.map(this.data, function(d) { return d[1]; }) ) || 0; } }; @@ -184,15 +175,17 @@ delta_x_px = 10; } - // Extract RGB from preference color. - var pref_color = parseInt( this.prefs.color.slice(1), 16 ), + // Painter color can be in either block_color (FeatureTrack) or color pref (LineTrack). + var painter_color = this.prefs.block_color || this.prefs.color, + // Extract RGB from preference color. + pref_color = parseInt( painter_color.slice(1), 16 ), pref_r = (pref_color & 0xff0000) >> 16, pref_g = (pref_color & 0x00ff00) >> 8, pref_b = pref_color & 0x0000ff; // Paint track. for (var i = 0, len = data.length; i < len; i++) { - ctx.fillStyle = ctx.strokeStyle = this.prefs.color; + ctx.fillStyle = ctx.strokeStyle = painter_color; // -0.5 to offset drawing between bases. x_scaled = Math.round((data[i][0] - view_start - 0.5) * w_scale); y = data[i][1]; @@ -261,7 +254,7 @@ ctx.fillRect(x_scaled, height_px - 3, overflow_x, 3); } } - ctx.fillStyle = this.prefs.color; + ctx.fillStyle = painter_color; } if (mode === "Filled") { if (in_path) { diff -r 1a4b56a78124b26103c61f8e6e736b088e65aa6d -r 4573880b2d9b7a76abcbe2ccac824ab9338df802 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3102,34 +3102,39 @@ } return tile; } - - // Flag to track whether we can draw everything now - var can_draw_now = true; - - // Get the track data, maybe a deferred - var tile_data = track.data_manager.get_data(region, mode, resolution, track.data_url_extra_params); - if ( is_deferred( tile_data ) ) { - can_draw_now = false; - } - - // 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); - if ( is_deferred( seq_data ) ) { - can_draw_now = false; + + // 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); + + // 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); + } + + return [tile_data, seq_data]; + }; + + // + // When data is available, draw tile. + // + 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' ] ); + + // If sequence data is available, subset to get only data in region. + if (view.reference_track) { + seq_data = view.reference_track.data_manager.subset_entry(seq_data, region); } - else { - // Sequence data is available, subset to get only data in region. - seq_data = view.reference_track.data_manager.subset_entry(seq_data, region); - } - } - - // If we can draw now, do so. - if ( can_draw_now ) { - // Set up and draw tile. - extend(tile_data, kwargs[ 'more_tile_data' ] ); - + // HACK: this is FeatureTrack-specific. // If track mode is Auto, determine mode and update. if (mode === "Auto" && track.get_mode) { @@ -3138,8 +3143,7 @@ } // Draw canvas. - var - canvas = track.view.canvas_manager.new_canvas(), + var canvas = track.view.canvas_manager.new_canvas(), tile_low = region.get('start'), tile_high = region.get('end'), width = Math.ceil( (tile_high - tile_low) * w_scale ) + track.left_offset, @@ -3147,26 +3151,18 @@ canvas.width = width; canvas.height = height; var ctx = canvas.getContext('2d'); - ctx.translate(this.left_offset, 0); + ctx.translate(track.left_offset, 0); var tile = track.draw_tile(tile_data, ctx, mode, resolution, region, w_scale, seq_data); - + // Don't cache, show if no tile. if (tile !== undefined) { track.tile_cache.set_elt(key, tile); track.show_tile(tile, parent_element, w_scale); } - return tile; - } - - // Can't draw now, so put Deferred in cache and draw tile when data is available. - var tile_drawn = $.Deferred(); - track.tile_cache.set_elt(key, tile_drawn); - $.when( tile_data, seq_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; }, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Display the Reset all metadata on repository option in the Resporitory Actions popup menu in more pages in the tool shed than the Manage repsitory page.
by commits-noreply＠bitbucket.org 14 May '13

14 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1a4b56a78124/ Changeset: 1a4b56a78124 User: greg Date: 2013-05-14 20:30:08 Summary: Display the Reset all metadata on repository option in the Resporitory Actions popup menu in more pages in the tool shed than the Manage repsitory page. Affected #: 2 files diff -r 1cabd9fd107c14caa379e591ff3fea66c3cc5ce4 -r 1a4b56a78124b26103c61f8e6e736b088e65aa6d templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/> -<%def name="render_tool_shed_repository_actions( repository, repo=None, metadata=None, changeset_revision=None )"> +<%def name="render_tool_shed_repository_actions( repository, metadata=None, changeset_revision=None )"><% from tool_shed.util.review_util import can_browse_repository_reviews, changeset_revision_reviewed_by_user, get_review_by_repository_id_changeset_revision_user_id from tool_shed.util.shed_util_common import changeset_is_malicious @@ -54,11 +54,8 @@ else: can_download = False - if not is_deprecated: - if repo and len( repo ) > 0: - can_reset_all_metadata = True - else: - can_reset_all_metadata = False + if ( is_admin or ( trans.user and trans.user == repository.user ) ) and not repository.deleted and not repository.deprecated and not is_new: + can_reset_all_metadata = True else: can_reset_all_metadata = False diff -r 1cabd9fd107c14caa379e591ff3fea66c3cc5ce4 -r 1a4b56a78124b26103c61f8e6e736b088e65aa6d templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -88,7 +88,7 @@ ${container_javascripts()} </%def> -${render_tool_shed_repository_actions( repository, repo=repo, metadata=metadata, changeset_revision=changeset_revision )} +${render_tool_shed_repository_actions( repository, metadata=metadata, changeset_revision=changeset_revision )} %if message: ${render_msg( message, status )} 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 14 May '13

14 May '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/88c1da16340b/ Changeset: 88c1da16340b User: Dave Bouvier Date: 2013-05-14 19:44:24 Summary: Expand the installation errors dict. Affected #: 1 file diff -r d3be8f8f8096ad723644019bd742904046df54ba -r 88c1da16340bf08dca453316fbcc7ff0868de57d test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -625,6 +625,17 @@ # repository, with tool and repository dependencies also selected for installation. result, _ = run_tests( test_config ) success = result.wasSuccessful() + repository_status = get_tool_test_results_from_api( galaxy_tool_shed_url, metadata_revision_id ) + if 'test_environment' not in repository_status: + repository_status[ 'test_environment' ] = {} + test_environment = get_test_environment( repository_status[ 'test_environment' ] ) + test_environment[ 'galaxy_database_version' ] = get_database_version( app ) + test_environment[ 'galaxy_revision'] = get_repository_current_revision( os.getcwd() ) + repository_status[ 'test_environment' ] = test_environment + repository_status[ 'passed_tests' ] = [] + repository_status[ 'failed_tests' ] = [] + repository_status[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) # If the installation succeeds, configure and run functional tests for this repository. This is equivalent to # sh run_functional_tests.sh -installed if success: @@ -684,18 +695,8 @@ # }, # ] # } - repository_status = get_tool_test_results_from_api( galaxy_tool_shed_url, metadata_revision_id ) - if 'test_environment' not in repository_status: - repository_status[ 'test_environment' ] = {} - test_environment = get_test_environment( repository_status[ 'test_environment' ] ) - test_environment[ 'galaxy_database_version' ] = get_database_version( app ) - test_environment[ 'galaxy_revision'] = get_repository_current_revision( os.getcwd() ) - repository_status[ 'test_environment' ] = test_environment - repository_status[ 'passed_tests' ] = [] - repository_status[ 'failed_tests' ] = [] - repository_status[ 'installation_errors' ] = [] - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - missing_tool_dependencies = repository.includes_tool_dependencies and repository.missing_tool_dependencies + failed_tool_dependencies = repository.includes_tool_dependencies and repository.tool_dependencies_with_installation_errors + failed_repository_dependencies = repository.repository_dependencies_with_installation_errors if 'missing_test_components' not in repository_status: repository_status[ 'missing_test_components' ] = [] if not has_test_data: @@ -708,9 +709,10 @@ tool_version = tool[ 'version' ] tool_guid = tool[ 'guid' ] # In keeping with the standard display layout, add the error message to the dict for each tool individually. - failed_tests = dict( tool_id=tool_id, tool_version=tool_version, tool_guid=tool_guid, - missing_components="Repository %s is missing a test-data directory." % name ) - repository_status[ 'missing_test_components' ].append( failed_tests ) + missing_components = dict( tool_id=tool_id, tool_version=tool_version, tool_guid=tool_guid, + missing_components="Repository %s is missing a test-data directory." % name ) + if missing_components not in repository_status[ 'missing_test_components' ]: + repository_status[ 'missing_test_components' ].append( missing_components ) # Record the status of this repository in the tool shed. register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=False ) # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the @@ -719,17 +721,26 @@ # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox repositories_failed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - elif missing_tool_dependencies: + elif failed_tool_dependencies or failed_repository_dependencies: # If a tool dependency fails to install correctly, this should be considered an installation error, # and functional tests should be skipped, since the tool dependency needs to be correctly installed # for the test to be considered reliable. log.error( 'One or more tool dependencies of this repository are marked as missing.' ) log.error( 'Updating repository and skipping functional tests.' ) # In keeping with the standard display layout, add the error message to the dict for each tool individually. - for dependency in repository.missing_tool_dependencies: - test_result = dict( name=name, owner=owner, changeset_revision=changeset_revision, + for dependency in repository.tool_dependencies_with_installation_errors: + test_result = dict( type=dependency.type, + name=dependency.name, + version=dependency.version, error_message=dependency.error_message ) - repository_status[ 'installation_errors' ].append( test_result ) + repository_status[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) + for dependency in repository.repository_dependencies_with_installation_errors: + test_result = dict( tool_shed=dependency.tool_shed, + name=dependency.name, + owner=dependency.owner, + changeset_revision=dependency.changeset_revision, + error_message=dependency.error_message ) + repository_status[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) # Record the status of this repository in the tool shed. register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=False ) # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the @@ -838,6 +849,14 @@ else: # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. log.debug( 'Uninstalling repository %s', repository_info_dict[ 'name' ] ) + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + test_result = dict( tool_shed=repository.tool_shed, + name=repository.name, + owner=repository.owner, + changeset_revision=repository.changeset_revision, + error_message=repository.error_message ) + repository_status[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) + register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=False ) success = execute_uninstall_method( app ) if not success: log.error( 'Repository %s failed to uninstall.', repository_info_dict[ 'name' ] ) https://bitbucket.org/galaxy/galaxy-central/commits/344658666b2e/ Changeset: 344658666b2e User: Dave Bouvier Date: 2013-05-14 19:45:17 Summary: Display the information in the installation errors dict on repository manage page under the tool test results folder. Affected #: 2 files diff -r 88c1da16340bf08dca453316fbcc7ff0868de57d -r 344658666b2ea9e0607b9532d8c9c0d1874f2c39 lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -26,6 +26,10 @@ self.invalid_repository_dependencies = [] self.invalid_tool_dependencies = [] self.invalid_tools = [] + self.installation_errors = [] + self.current_repository_installation_errors = [] + self.repository_installation_errors = [] + self.tool_dependency_installation_errors = [] self.valid_tools = [] self.valid_data_managers = [] self.invalid_data_managers = [] @@ -195,6 +199,18 @@ return [ self.toolshed, self.repository_name, self.repository_owner, self.changeset_revision, asbool( str( self.prior_installation_required ) ) ] +class RepositoryInstallationError( object ): + """Repository installation error object""" + + def __init__( self, id=None, tool_shed=None, name=None, owner=None, changeset_revision=None, error_message=None ): + self.id = id + self.tool_shed = tool_shed + self.name = name + self.owner = owner + self.changeset_revision = changeset_revision + self.error_message = error_message + + class TestEnvironment( object ): """Tool test environment object""" @@ -250,6 +266,17 @@ return [ self.name, self.version, self.type ] +class ToolDependencyInstallationError( object ): + """Tool dependency installation error object""" + + def __init__( self, id=None, type=None, name=None, version=None, error_message=None ): + self.id = id + self.type = type + self.name = name + self.version = version + self.error_message = error_message + + class Workflow( object ): """Workflow object.""" @@ -1059,6 +1086,68 @@ tool_id=missing_test_components_dict.get( 'tool_id', '' ), tool_version=missing_test_components_dict.get( 'tool_version', '' ) ) folder.missing_test_components.append( missing_test_component ) + installation_error_dicts = tool_test_results_dict.get( 'installation_errors', {} ) + if installation_error_dicts: + current_repository_errors = installation_error_dicts.get( 'current_repository', [] ) + repository_dependency_errors = installation_error_dicts.get( 'repository_dependencies', [] ) + tool_dependency_errors = installation_error_dicts.get( 'tool_dependencies', [] ) + if current_repository_errors or repository_dependency_errors or tool_dependency_errors: + folder_id += 1 + installation_error_base_folder = Folder( id=folder_id, + key='installation_errors', + label='Installation errors', + parent=test_results_folder ) + if current_repository_errors: + folder_id += 1 + subfolder = Folder( id=folder_id, + key='current_repository_errors', + label='This repository', + parent=installation_error_base_folder ) + repository_error_id = 0 + for repository_error_dict in current_repository_errors: + repository_error_id += 1 + repository_installation_error = RepositoryInstallationError( id=repository_error_id, + tool_shed=repository_error_dict.get( 'tool_shed', '' ), + name=repository_error_dict.get( 'name', '' ), + owner=repository_error_dict.get( 'owner', '' ), + changeset_revision=repository_error_dict.get( 'changeset_revision', '' ), + error_message=repository_error_dict.get( 'error_message', '' ) ) + subfolder.current_repository_installation_errors.append( repository_installation_error ) + installation_error_base_folder.folders.append( subfolder ) + if repository_dependency_errors: + folder_id += 1 + subfolder = Folder( id=folder_id, + key='repository_dependency_errors', + label='Repository dependencies', + parent=installation_error_base_folder ) + repository_error_id = 0 + for repository_error_dict in repository_dependency_errors: + repository_error_id += 1 + repository_installation_error = RepositoryInstallationError( id=repository_error_id, + tool_shed=repository_error_dict.get( 'tool_shed', '' ), + name=repository_error_dict.get( 'name', '' ), + owner=repository_error_dict.get( 'owner', '' ), + changeset_revision=repository_error_dict.get( 'changeset_revision', '' ), + error_message=repository_error_dict.get( 'error_message', '' ) ) + subfolder.repository_installation_errors.append( repository_installation_error ) + installation_error_base_folder.folders.append( subfolder ) + if tool_dependency_errors: + folder_id += 1 + subfolder = Folder( id=folder_id, + key='tool_dependency_errors', + label='Tool dependencies', + parent=installation_error_base_folder ) + tool_dependency_error_id = 0 + for tool_dependency_error_dict in tool_dependency_errors: + tool_dependency_error_id += 1 + tool_dependency_installation_error = ToolDependencyInstallationError( id=tool_dependency_error_id, + type=tool_dependency_error_dict.get( 'type', '' ), + name=tool_dependency_error_dict.get( 'name', '' ), + version=tool_dependency_error_dict.get( 'version', '' ), + error_message=tool_dependency_error_dict.get( 'error_message', '' ) ) + subfolder.tool_dependency_installation_errors.append( tool_dependency_installation_error ) + installation_error_base_folder.folders.append( subfolder ) + test_results_folder.installation_errors.append( installation_error_base_folder ) else: tool_test_results_root_folder = None return folder_id, tool_test_results_root_folder diff -r 88c1da16340bf08dca453316fbcc7ff0868de57d -r 344658666b2ea9e0607b9532d8c9c0d1874f2c39 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -220,10 +220,12 @@ elif folder.label in [ 'Installed repository dependencies', 'Repository dependencies', 'Missing repository dependencies' ]: if folder.description: folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description ) - elif folder.label not in [ 'Installed repository dependencies' ]: + elif folder.label not in [ 'Installed repository dependencies' ] and folder.parent.label not in [ 'Installation errors' ]: folder_label = "%s<i> - installation of these additional repositories is required</i>" % folder_label if trans.webapp.name == 'galaxy': col_span_str = 'colspan="4"' + elif folder.label == 'Installation errors': + folder_label = "%s<i> - no functional tests were run for any tools in this changeset revision</i>" % folder_label elif folder.label == 'Invalid repository dependencies': folder_label = "%s<i> - click the repository dependency to see why it is invalid</i>" % folder_label elif folder.label == 'Invalid tool dependencies': @@ -345,6 +347,26 @@ ${render_missing_test_component( missing_test_component, pad, my_row, row_counter )} %endfor %endif + %if folder.installation_errors: + %for installation_error in folder.installation_errors: + ${render_folder( installation_error, pad, my_row, row_counter )} + %endfor + %endif + %if folder.tool_dependency_installation_errors: + %for tool_dependency_installation_error in folder.tool_dependency_installation_errors: + ${render_tool_dependency_installation_error( tool_dependency_installation_error, pad, my_row, row_counter )} + %endfor + %endif + %if folder.repository_installation_errors: + %for repository_installation_error in folder.repository_installation_errors: + ${render_repository_installation_error( repository_installation_error, pad, my_row, row_counter, is_current_repository=False )} + %endfor + %endif + %if folder.current_repository_installation_errors: + %for repository_installation_error in folder.current_repository_installation_errors: + ${render_repository_installation_error( repository_installation_error, pad, my_row, row_counter, is_current_repository=True )} + %endfor + %endif </%def><%def name="render_datatype( datatype, pad, parent, row_counter, row_is_header=False )"> @@ -608,6 +630,65 @@ %></%def> +<%def name="render_tool_dependency_installation_error( installation_error, pad, parent, row_counter, row_is_header=False )"> + <% encoded_id = trans.security.encode_id( installation_error.id ) %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + <td style="padding-left: ${pad+20}px;"> + <table class="grid" id="td_installation_errors"> + <tr bgcolor="#FFFFCC"> + <th>Type</th><th>Name</th><th>Version</th> + </tr> + <tr> + <td>${installation_error.name | h}</td> + <td>${installation_error.type | h}</td> + <td>${installation_error.version | h}</td> + </tr> + <tr><th>Error</th></tr> + <tr><td colspan="3">${installation_error.error_message | h}</td></tr> + </table> + </td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + +<%def name="render_repository_installation_error( installation_error, pad, parent, row_counter, row_is_header=False, is_current_repository=False )"> + <% encoded_id = trans.security.encode_id( installation_error.id ) %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + <td style="padding-left: ${pad+20}px;"> + <table class="grid" id="repository_installation_errors"> + %if not is_current_repository: + <tr bgcolor="#FFFFCC"> + <th>Tool shed</th><th>Name</th><th>Owner</th><th>Changeset revision</th> + </tr> + <tr> + <td>${installation_error.tool_shed | h}</td> + <td>${installation_error.name | h}</td> + <td>${installation_error.owner | h}</td> + <td>${installation_error.changeset_revision | h}</td> + </tr> + %endif + <tr><th>Error</th></tr> + <tr><td colspan="4">${installation_error.error_message | h}</td></tr> + </table> + </td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + <%def name="render_passed_test( passed_test, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( passed_test.id ) %><tr class="datasetRow" https://bitbucket.org/galaxy/galaxy-central/commits/1cabd9fd107c/ Changeset: 1cabd9fd107c User: Dave Bouvier Date: 2013-05-14 19:48:05 Summary: Merged. Affected #: 1 file diff -r 344658666b2ea9e0607b9532d8c9c0d1874f2c39 -r 1cabd9fd107c14caa379e591ff3fea66c3cc5ce4 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -9,6 +9,7 @@ from galaxy.tools.data_manager.manager import DataManager from galaxy.util import inflector from galaxy.util import json +from galaxy.web import url_for from galaxy.webapps.tool_shed.util import container_util import tool_shed.util.shed_util_common as suc from tool_shed.util import common_util @@ -1050,6 +1051,9 @@ is_valid = True error_message = '' toolshed = repository_elem.get( 'toolshed' ) + if not toolshed: + # Default to the current tool shed. + toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) name = repository_elem.get( 'name' ) owner = repository_elem.get( 'owner' ) changeset_revision = repository_elem.get( 'changeset_revision' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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