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

commit/galaxy-central: jgoecks: Trackster: simple framework for notifying view of changes; use framework to indicate changes when (a) config values are changed and (b) items are reordered or grouped.
by Bitbucket 07 Feb '12

07 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b45af710a58b/ changeset: b45af710a58b user: jgoecks date: 2012-02-07 15:41:59 summary: Trackster: simple framework for notifying view of changes; use framework to indicate changes when (a) config values are changed and (b) items are reordered or grouped. affected #: 1 file diff -r 97950a7e567d10884d0220f34b7612b88569fa80 -r b45af710a58bbe64a2d98faee53e8baf6d6314a8 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -790,6 +790,9 @@ extend(Drawable.prototype, { init: function() {}, + changed: function() { + this.view.changed(); + }, can_draw: function() { if (this.enabled && this.content_visible) { return true; @@ -828,13 +831,13 @@ * Remove drawable (a) from its container and (b) from the HTML. */ remove: function() { + this.changed(); + this.container.remove_drawable(this); - this.container_div.hide(0, function() { $(this).remove(); // HACK: is there a better way to update the view? - view.update_intro_div(); - view.has_changes = true; + drawable.view.update_intro_div(); }); }, /** @@ -952,11 +955,13 @@ add_drawable: function(drawable) { this.drawables.push(drawable); drawable.container = this; + this.changed(); }, /** * Add a drawable before another drawable. */ add_drawable_before: function(drawable, other) { + this.changed(); var index = this.drawables.indexOf(other); if (index !== -1) { this.drawables.splice(index, 0, drawable); @@ -974,6 +979,7 @@ if (update_html) { old_drawable.container_div.replaceWith(new_drawable.container_div); } + this.changed(); } return index; }, @@ -986,6 +992,7 @@ // Found drawable to remove. this.drawables.splice(index, 1); drawable.container = null; + this.changed(); return true; } return false; @@ -1000,6 +1007,7 @@ this.drawables.splice(index, 1); // insert into new position: this.drawables.splice(new_position, 0, drawable); + this.changed(); return true; } return false; @@ -1465,6 +1473,9 @@ this.reset(); $(window).trigger("resize"); }, + changed: function() { + this.has_changes = true; + }, /** Add or remove intro div depending on view state. */ update_intro_div: function() { if (this.drawables.length === 0) { @@ -1636,7 +1647,7 @@ add_drawable: function(drawable) { DrawableCollection.prototype.add_drawable.call(this, drawable); drawable.init(); - this.has_changes = true; + this.changed(); this.update_intro_div(); }, add_label_track: function (label_track) { @@ -1655,7 +1666,6 @@ $(this).remove(); view.update_intro_div(); }); - this.has_changes = true; } }, reset: function() { @@ -1773,6 +1783,7 @@ } this.low = Math.round(cur_center - new_half); this.high = Math.round(cur_center + new_half); + this.changed(); this.request_redraw(); }, zoom_out: function () { @@ -1784,6 +1795,7 @@ new_half = (span * this.zoom_factor) / 2; this.low = Math.round(cur_center - new_half); this.high = Math.round(cur_center + new_half); + this.changed(); this.request_redraw(); }, resize_window: function() { @@ -1815,7 +1827,7 @@ view.resize_window(); }; view.overview_drawable.request_draw(); - view.has_changes = true; + this.changed(); }, /** Close and reset overview. */ reset_overview: function() { @@ -2717,6 +2729,7 @@ }); if ( changed ) { this.onchange(); + this.track.changed(); } } }); 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: Add a new grid to view the tool version lineage by tool id (parent/child ordered) for any tool that was ever used in the local Galaxy instance. Tool ids in this grid that are associated with tools currently loaded in the tool panel are highlighted in green and are click-able, displaying the tool. Eliminate the mappers for determining lineage, and use methods instead as the mappers were problematic.
by Bitbucket 06 Feb '12

06 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/97950a7e567d/ changeset: 97950a7e567d user: greg date: 2012-02-06 21:22:56 summary: Add a new grid to view the tool version lineage by tool id (parent/child ordered) for any tool that was ever used in the local Galaxy instance. Tool ids in this grid that are associated with tools currently loaded in the tool panel are highlighted in green and are click-able, displaying the tool. Eliminate the mappers for determining lineage, and use methods instead as the mappers were problematic. affected #: 6 files diff -r 36d36384704b7eb79f37e2b5209d73fd1a3356a0 -r 97950a7e567d10884d0220f34b7612b88569fa80 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2693,31 +2693,49 @@ self.create_time = create_time self.tool_id = tool_id self.tool_shed_repository = tool_shed_repository + def get_previous_version( self, app ): + sa_session = app.model.context.current + tva = sa_session.query( app.model.ToolVersionAssociation ) \ + .filter( app.model.ToolVersionAssociation.table.c.tool_id == self.id ) \ + .first() + if tva: + return sa_session.query( app.model.ToolVersion ) \ + .filter( app.model.ToolVersion.table.c.id == tva.parent_id ) \ + .first() + return None + def get_next_version( self, app ): + sa_session = app.model.context.current + tva = sa_session.query( app.model.ToolVersionAssociation ) \ + .filter( app.model.ToolVersionAssociation.table.c.parent_id == self.id ) \ + .first() + if tva: + return sa_session.query( app.model.ToolVersion ) \ + .filter( app.model.ToolVersion.table.c.id == tva.tool_id ) \ + .first() + return None def get_versions( self, app ): sa_session = app.model.context.current tool_versions = [] # Prepend ancestors. - def __ancestors( tool_version ): + def __ancestors( app, tool_version ): # Should we handle multiple parents at each level? - previous_tva = tool_version.previous_version - if previous_tva: - parent_version = previous_tva[0].parent_version - if parent_version not in tool_versions: - tool_versions.insert( 0, parent_version ) - __ancestors( parent_version ) + previous_version = tool_version.get_previous_version( app ) + if previous_version: + if previous_version not in tool_versions: + tool_versions.insert( 0, previous_version ) + __ancestors( app, previous_version ) # Append descendants. - def __descendants( tool_version ): + def __descendants( app, tool_version ): # Should we handle multiple child siblings at each level? - next_tva = sa_session.query( app.model.ToolVersionAssociation ) \ - .filter( app.model.ToolVersionAssociation.table.c.parent_id == tool_version.id ) \ - .first() - if next_tva: - current_version = next_tva.tool_version - if current_version not in tool_versions: - tool_versions.append( current_version ) - __descendants( current_version ) - __ancestors( self ) - __descendants( self ) + next_version = tool_version.get_next_version( app ) + if next_version: + if next_version not in tool_versions: + tool_versions.append( next_version ) + __descendants( app, next_version ) + __ancestors( app, self ) + if self not in tool_versions: + tool_versions.append( self ) + __descendants( app, self ) return tool_versions def get_version_ids( self, app ): return [ tool_version.tool_id for tool_version in self.get_versions( app ) ] diff -r 36d36384704b7eb79f37e2b5209d73fd1a3356a0 -r 97950a7e567d10884d0220f34b7612b88569fa80 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1627,13 +1627,7 @@ assign_mapper( context, ToolVersion, ToolVersion.table ) -assign_mapper( context, ToolVersionAssociation, ToolVersionAssociation.table, - properties=dict( tool_version=relation( ToolVersion, - primaryjoin=( ToolVersionAssociation.table.c.tool_id == ToolVersion.table.c.id ), - backref='current_version' ), - parent_version=relation( ToolVersion, - primaryjoin=( ToolVersionAssociation.table.c.parent_id == ToolVersion.table.c.id ), - backref='previous_version' ) ) ) +assign_mapper( context, ToolVersionAssociation, ToolVersionAssociation.table ) # Set up proxy so that # Page.users_shared_with diff -r 36d36384704b7eb79f37e2b5209d73fd1a3356a0 -r 97950a7e567d10884d0220f34b7612b88569fa80 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1311,6 +1311,7 @@ group_list_grid = None quota_list_grid = None repository_list_grid = None + tool_version_list_grid = None delete_operation = None undelete_operation = None purge_operation = None @@ -1362,6 +1363,12 @@ toolbox=toolbox, message=message, status=status ) + @web.expose + @web.require_admin + def tool_versions( self, trans, **kwd ): + if 'message' not in kwd or not kwd[ 'message' ]: + kwd[ 'message' ] = 'Tool ids for tools that are currently loaded into the tool panel are highlighted in green (click to display).' + return self.tool_version_list_grid( trans, **kwd ) # Galaxy Role Stuff @web.expose @web.require_admin diff -r 36d36384704b7eb79f37e2b5209d73fd1a3356a0 -r 97950a7e567d10884d0220f34b7612b88569fa80 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -383,12 +383,64 @@ preserve_state = False use_paging = True +class ToolVersionListGrid( grids.Grid ): + class ToolIdColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool_version ): + if tool_version.tool_id in trans.app.toolbox.tools_by_id: + link = url_for( controller='tool_runner', tool_id=tool_version.tool_id ) + link_str = '<a href="%s">' % link + return '<div class="count-box state-color-ok">%s%s</a></div>' % ( link_str, tool_version.tool_id ) + return tool_version.tool_id + class ToolVersionsColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool_version ): + tool_ids_str = '' + for tool_id in tool_version.get_version_ids( trans.app ): + if tool_id in trans.app.toolbox.tools_by_id: + link = url_for( controller='tool_runner', tool_id=tool_version.tool_id ) + link_str = '<a href="%s">' % link + tool_ids_str += '<div class="count-box state-color-ok">%s%s</a></div><br/>' % ( link_str, tool_id ) + else: + tool_ids_str += '%s<br/>' % tool_id + return tool_ids_str + class ToolShedRepositoryColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool_version ): + if tool_version.tool_shed_repository: + return tool_version.tool_shed_repository.name + return '' + # Grid definition + title = "Tool versions" + model_class = model.ToolVersion + template='/admin/tool_version/grid.mako' + default_sort_key = "tool_id" + columns = [ + ToolIdColumn( "Tool id", + key='tool_id', + attach_popup=False ), + ToolVersionsColumn( "Version lineage by tool id (parent/child ordered)" ), + ToolShedRepositoryColumn( "Tool shed repository" ), + ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[0] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + global_actions = [] + operations = [] + standard_filters = [] + default_filter = {} + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( self.model_class ) + class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamParser ): user_list_grid = UserListGrid() role_list_grid = RoleListGrid() group_list_grid = GroupListGrid() quota_list_grid = QuotaListGrid() + tool_version_list_grid = ToolVersionListGrid() delete_operation = grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) undelete_operation = grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) purge_operation = grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) diff -r 36d36384704b7eb79f37e2b5209d73fd1a3356a0 -r 97950a7e567d10884d0220f34b7612b88569fa80 templates/admin/tool_version/grid.mako --- /dev/null +++ b/templates/admin/tool_version/grid.mako @@ -0,0 +1,1 @@ +<%inherit file="/grid_base.mako"/> diff -r 36d36384704b7eb79f37e2b5209d73fd1a3356a0 -r 97950a7e567d10884d0220f34b7612b88569fa80 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -63,6 +63,7 @@ <div class="toolSectionTitle">Server</div><div class="toolSectionBody"><div class="toolSectionBg"> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='tool_versions' )}" target="galaxy_main">Tool versions</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='reload_tool' )}" target="galaxy_main">Reload a tool's configuration</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='memdump' )}" target="galaxy_main">Profile memory usage</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='jobs' )}" target="galaxy_main">Manage jobs</a></div> 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: compute resolution in continous rather than discrete units; this enables precise control over tile size and number.
by Bitbucket 06 Feb '12

06 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/36d36384704b/ changeset: 36d36384704b user: jgoecks date: 2012-02-06 20:58:54 summary: Trackster: compute resolution in continous rather than discrete units; this enables precise control over tile size and number. affected #: 1 file diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 36d36384704b7eb79f37e2b5209d73fd1a3356a0 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -379,9 +379,9 @@ MIN_SQUISH_VIEW_WIDTH = 12000, // Other constants. - DENSITY = 200, - RESOLUTION = 5, - FEATURE_LEVELS = 10, + + // Number of pixels per tile, not including left offset. + TILE_SIZE = 400, DEFAULT_DATA_QUERY_WAIT = 5000, // Maximum number of chromosomes that are selectable at any one time. MAX_CHROMS_SELECTABLE = 100, @@ -1726,10 +1726,11 @@ this.low = Math.floor(low); this.high = Math.ceil(high); - // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width - this.resolution = Math.pow( RESOLUTION, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.log(RESOLUTION) ) ); - this.zoom_res = Math.pow( FEATURE_LEVELS, Math.max(0,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) ))); - + // Calculate resolution in both pixels/base and bases/pixel; round bases/pixels for tile calculations. + // TODO: require minimum difference in new resolution to update? + this.resolution_b_px = Math.round( (this.high - this.low) / this.viewport_container.width() ); + this.resolution_px_b = this.viewport_container.width() / (this.high - this.low); + // Overview var left_px = ( this.low / (this.max_high - this.max_low) * this.overview_viewport.width() ) || 0; var width_px = ( (this.high - this.low)/(this.max_high - this.max_low) * this.overview_viewport.width() ) || 0; @@ -2726,8 +2727,9 @@ var Tile = function(track, index, resolution, canvas, data) { this.track = track; this.index = index; - this.low = index * DENSITY * resolution; - this.high = (index + 1) * DENSITY * resolution; + // FIXME: find better way to calculate low, high. + this.low = index * TILE_SIZE * resolution + this.high = (index + 1) * TILE_SIZE * resolution; this.resolution = resolution; // Wrap element in div for background. this.html_elt = $("<div class='track-tile'/>").append(canvas); @@ -3348,17 +3350,14 @@ high = this.view.high, range = high - low, width = this.view.container.width(), - // w_scale units are pixels per base. - w_scale = width / range, - resolution = this.view.resolution, - // FIXME: parent element is not currently needed, but it may be useful for multitrack drawing. - parent_element = this.content_div; + w_scale = this.view.resolution_px_b, + resolution = this.view.resolution_b_px; // For overview, adjust high, low, resolution, and w_scale. if (this.is_overview) { low = this.view.max_low; high = this.view.max_high; - resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / DENSITY ) / Math.log(RESOLUTION) )); + resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / TILE_SIZE ) / Math.log(RESOLUTION) )); w_scale = width / (view.max_high - view.max_low); } @@ -3375,23 +3374,22 @@ this.content_div.children().addClass("remove"); this.max_height = 0; - // Index of first tile that overlaps visible region - var tile_index = Math.floor( low / resolution / DENSITY ); - // If any tile could not be drawn yet, this will be set to false - var all_tiles_drawn = true; - var drawn_tiles = []; - var tile_count = 0; - var is_tile = function(o) { return (o && 'track' in o) }; - // Draw or fetch and show tiles. - while ( ( tile_index * DENSITY * resolution ) < high ) { - var draw_result = this.draw_helper( force, width, tile_index, resolution, parent_element, w_scale ); + var + // Index of first tile that overlaps visible region. + tile_index = Math.floor( low / (resolution * TILE_SIZE) ), + // If any tile could not be drawn yet, this will be set to false. + all_tiles_drawn = true, + drawn_tiles = [], + is_tile = function(o) { return (o && 'track' in o) }; + // Draw tiles. + while ( ( tile_index * TILE_SIZE * resolution ) < high ) { + var draw_result = this.draw_helper( force, width, tile_index, resolution, this.content_div, w_scale ); if ( is_tile(draw_result) ) { drawn_tiles.push( draw_result ); } else { all_tiles_drawn = false; } tile_index += 1; - tile_count++; } // Step (c) for (re)moving tiles when clear_after is false. @@ -3402,7 +3400,7 @@ if (all_tiles_drawn) { // Step (c) for (re)moving tiles when clear_after is true: this.content_div.children(".remove").remove(); - track.postdraw_actions(drawn_tiles, width, w_scale, clear_after); + track.postdraw_actions(drawn_tiles, width, w_scale, clear_after); } }, /** @@ -3439,8 +3437,9 @@ draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, kwargs) { var track = this, key = this._gen_tile_cache_key(width, w_scale, tile_index), - tile_low = tile_index * DENSITY * resolution, - tile_high = tile_low + DENSITY * resolution; + tile_bounds = this._get_tile_bounds(tile_index, resolution), + tile_low = tile_bounds[0], + tile_high = tile_bounds[1]; // Init kwargs if necessary to avoid having to check if kwargs defined. if (!kwargs) { kwargs = {}; } @@ -3578,8 +3577,8 @@ * with values tile_low and tile_high. */ _get_tile_bounds: function(tile_index, resolution) { - var tile_low = tile_index * DENSITY * resolution, - tile_length = DENSITY * resolution, + var tile_low = tile_index * TILE_SIZE * resolution, + tile_length = TILE_SIZE * resolution, // Tile high cannot be larger than view.max_high, which the chromosome length. tile_high = (tile_low + tile_length <= this.view.max_high ? tile_low + tile_length : this.view.max_high); return [tile_low, tile_high]; @@ -3790,8 +3789,8 @@ // FIXME: this function is similar to TiledTrack.draw_helper -- can the two be merged/refactored? var track = this, key = this._gen_tile_cache_key(width, w_scale, tile_index), - tile_low = tile_index * DENSITY * resolution, - tile_high = tile_low + DENSITY * resolution; + tile_low = tile_index * TILE_SIZE * resolution, + tile_high = tile_low + TILE_SIZE * resolution; // Init kwargs if necessary to avoid having to check if kwargs defined. if (!kwargs) { kwargs = {}; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Bugfix for the DRMAA job name commit, ensure all characters in the job name string conform to the DRMAA spec.
by Bitbucket 06 Feb '12

06 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/74b6319b38b4/ changeset: 74b6319b38b4 user: natefoo date: 2012-02-06 19:16:23 summary: Bugfix for the DRMAA job name commit, ensure all characters in the job name string conform to the DRMAA spec. affected #: 1 file diff -r e4d1dd3bdd0dfbe8562ac352d08b1f9b497d7063 -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -1,4 +1,4 @@ -import os, sys, logging, threading, time +import os, sys, logging, threading, time, string import pprint, pwd from pwd import getpwnam import subprocess @@ -168,9 +168,12 @@ # define job attributes ofile = "%s.drmout" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) efile = "%s.drmerr" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) + job_name = "g%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) + job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) + jt = self.ds.createJobTemplate() jt.remoteCommand = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) - jt.jobName = "g%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user.replace( '@', '__at__' ) ) + jt.jobName = job_name jt.outputPath = ":%s" % ofile jt.errorPath = ":%s" % efile native_spec = self.get_native_spec( runner_url ) 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: natefoo: Set a descriptive job name when using the DRMAA runner
by Bitbucket 06 Feb '12

06 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e4d1dd3bdd0d/ changeset: e4d1dd3bdd0d user: natefoo date: 2012-02-06 19:03:24 summary: Set a descriptive job name when using the DRMAA runner affected #: 1 file diff -r 73e2dd2c815bf289751951d6127be2a14d7163e6 -r e4d1dd3bdd0dfbe8562ac352d08b1f9b497d7063 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -170,6 +170,7 @@ efile = "%s.drmerr" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) jt = self.ds.createJobTemplate() jt.remoteCommand = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) + jt.jobName = "g%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user.replace( '@', '__at__' ) ) jt.outputPath = ":%s" % ofile jt.errorPath = ":%s" % efile native_spec = self.get_native_spec( runner_url ) 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: natefoo: A couple of job running path resolution changes, fixes #713 (thanks Peter)
by Bitbucket 06 Feb '12

06 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/73e2dd2c815b/ changeset: 73e2dd2c815b user: natefoo date: 2012-02-06 18:39:19 summary: A couple of job running path resolution changes, fixes #713 (thanks Peter) affected #: 2 files diff -r e38a9eb21336ce56ba6c5ec53e7492853c2c4088 -r 73e2dd2c815bf289751951d6127be2a14d7163e6 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -577,8 +577,8 @@ job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None ) def in_directory( file, directory ): # Make both absolute. - directory = os.path.realpath( directory ) - file = os.path.realpath( file ) + directory = os.path.abspath( directory ) + file = os.path.abspath( file ) #Return true, if the common prefix of both is equal to directory #e.g. /a/b/c/d.rst and directory is /a/b, the common prefix is /a/b diff -r e38a9eb21336ce56ba6c5ec53e7492853c2c4088 -r 73e2dd2c815bf289751951d6127be2a14d7163e6 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -166,8 +166,8 @@ job_wrapper.change_state( model.Job.states.QUEUED ) # define job attributes - ofile = "%s.drmout" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) - efile = "%s.drmerr" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) + ofile = "%s.drmout" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) + efile = "%s.drmerr" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) jt = self.ds.createJobTemplate() jt.remoteCommand = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) jt.outputPath = ":%s" % ofile 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: Load empty tool sections into the in-memory tool_panel dictionary, just don't display them in the tool panel. Also include a fix for reactivating or unintallting a tool shed repository that includes tools - ToolVersion ovjects cannot be marked deleted.
by Bitbucket 06 Feb '12

06 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e38a9eb21336/ changeset: e38a9eb21336 user: greg date: 2012-02-06 16:19:43 summary: Load empty tool sections into the in-memory tool_panel dictionary, just don't display them in the tool panel. Also include a fix for reactivating or unintallting a tool shed repository that includes tools - ToolVersion ovjects cannot be marked deleted. affected #: 3 files diff -r 281bd9a8feddf90af8edf13acfa752809f7824d5 -r e38a9eb21336ce56ba6c5ec53e7492853c2c4088 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -295,7 +295,7 @@ self.load_workflow_tag_set( sub_elem, elems ) elif sub_elem.tag == 'label': self.load_label_tag_set( sub_elem, elems ) - if key not in panel_dict and section.elems: + if key not in panel_dict: panel_dict[ key ] = section def load_tool( self, config_file, guid=None ): """ diff -r 281bd9a8feddf90af8edf13acfa752809f7824d5 -r e38a9eb21336ce56ba6c5ec53e7492853c2c4088 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -499,18 +499,9 @@ metadata = repository.metadata repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) guids_to_activate = [ repository_tool_tup[1] for repository_tool_tup in repository_tools_tups ] - # Undelete the tool_version for each guid. + # Make sure we have a tool_version for each guid. for guid_to_activate in guids_to_activate: - tool_version = get_tool_version( trans.app, guid_to_activate ) - if tool_version: - if tool_version.deleted: - # This should not happen as we are currently not marking tool versions as deleted - # upon deactivation. We may decide to eliminate the tool_version.deleted column - # at some point, but we'll keep it for now in case we decide its useful. - tool_version.deleted = False - trans.sa_session.add( tool_version ) - trans.sa_session.flush() - else: + if not get_tool_version( trans.app, guid_to_activate ): # We're somehow missing a tool_version, so create a new one. tool_version = trans.model.ToolVersion( tool_id=guid_to_activate, tool_shed_repository=repository ) trans.sa_session.add( tool_version ) diff -r 281bd9a8feddf90af8edf13acfa752809f7824d5 -r e38a9eb21336ce56ba6c5ec53e7492853c2c4088 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -365,22 +365,25 @@ ${render_workflow( key, val, False )} %elif key.startswith( 'section' ): <% section = val %> - <div class="toolSectionTitle" id="title_${section.id}"> - <span>${section.name}</span> - </div> - <div id="${section.id}" class="toolSectionBody"> - <div class="toolSectionBg"> - %for section_key, section_val in section.elems.items(): - %if section_key.startswith( 'tool' ): - ${render_tool( section_val, True )} - %elif section_key.startswith( 'workflow' ): - ${render_workflow( section_key, section_val, True )} - %elif section_key.startswith( 'label' ): - ${render_label( section_val )} - %endif - %endfor + ## Render the section only if it is not empty. + %if section.elems: + <div class="toolSectionTitle" id="title_${section.id}"> + <span>${section.name}</span></div> - </div> + <div id="${section.id}" class="toolSectionBody"> + <div class="toolSectionBg"> + %for section_key, section_val in section.elems.items(): + %if section_key.startswith( 'tool' ): + ${render_tool( section_val, True )} + %elif section_key.startswith( 'workflow' ): + ${render_workflow( section_key, section_val, True )} + %elif section_key.startswith( 'label' ): + ${render_label( section_val )} + %endif + %endfor + </div> + </div> + %endif %elif key.startswith( 'label' ): ${render_label( val )} %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: jgoecks: Update default values for Cufflinks' parameters.
by Bitbucket 06 Feb '12

06 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/281bd9a8fedd/ changeset: 281bd9a8fedd user: jgoecks date: 2012-02-06 15:29:48 summary: Update default values for Cufflinks' parameters. affected #: 1 file diff -r 0b186ed35995002dc50d48a3ee38fd96d13f76bc -r 281bd9a8feddf90af8edf13acfa752809f7824d5 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -52,8 +52,8 @@ <inputs><param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/><param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help=""/> - <param name="min_isoform_fraction" type="float" value="0.05" min="0" max="1" label="Min Isoform Fraction" help=""/> - <param name="pre_mrna_fraction" type="float" value="0.05" min="0" max="1" label="Pre MRNA Fraction" help=""/> + <param name="min_isoform_fraction" type="float" value="0.10" min="0" max="1" label="Min Isoform Fraction" help=""/> + <param name="pre_mrna_fraction" type="float" value="0.15" min="0" max="1" label="Pre MRNA Fraction" help=""/><param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts."><option value="No">No</option><option value="Yes">Yes</option> 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: better attribute display for tracks created when rerunning tools.
by Bitbucket 05 Feb '12

05 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0b186ed35995/ changeset: 0b186ed35995 user: jgoecks date: 2012-02-05 20:50:23 summary: Trackster: better attribute display for tracks created when rerunning tools. affected #: 2 files diff -r 32d1ab3262ea4d45e1cae1f43f44e43d3c8899d8 -r 0b186ed35995002dc50d48a3ee38fd96d13f76bc lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -945,6 +945,8 @@ """ Process data from an iterator to a format that can be provided to client. """ + filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) + no_detail = ( "no_detail" in kwargs ) results = [] message = None offset = 0 @@ -956,7 +958,7 @@ message = ERROR_MAX_VALS % ( max_vals, "reads" ) break - payload = package_gff_feature( feature ) + payload = package_gff_feature( feature, no_detail=no_detail, filter_cols=filter_cols ) payload.insert( 0, offset ) results.append( payload ) offset += feature.raw_size diff -r 32d1ab3262ea4d45e1cae1f43f44e43d3c8899d8 -r 0b186ed35995002dc50d48a3ee38fd96d13f76bc static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2001,6 +2001,8 @@ var new_track = new current_track.constructor(track_name, view, container, "hda"); new_track.init_for_tool_data(); new_track.change_mode(current_track.mode); + new_track.set_filters_manager(current_track.filters_manager.copy(new_track)); + new_track.update_icons(); container.add_drawable(new_track); new_track.content_div.text("Starting job."); @@ -2259,6 +2261,12 @@ }; extend(NumberFilter.prototype, { /** + * Return a copy of filter. + */ + copy: function() { + return new NumberFilter(this.name, this.index, this.tool_id, this.tool_exp_name); + }, + /** * Get step for slider. */ // FIXME: make this a "static" function. @@ -2414,6 +2422,16 @@ extend(FiltersManager.prototype, { /** + * Return a copy of the manager. + */ + copy: function(new_track) { + var copy = new FiltersManager(new_track); + for (var i = 0; i < this.filters.length; i++) { + copy.add_filter(this.filters[i].copy()); + } + return copy; + }, + /** * Add a filter to the manager. */ add_filter: function(filter) { @@ -3194,12 +3212,9 @@ if (this.header_div) { // - // Create filters div. + // Setup filters. // - if (this.filters_manager) { - this.filters_div = this.filters_manager.parent_div - this.header_div.after(this.filters_div); - } + this.set_filters_manager(this.filters_manager); // // Create dynamic tool div. @@ -3223,6 +3238,14 @@ new_track.enabled = this.enabled; return new_track; }, + /** + * Set filters manager + HTML elements. + */ + set_filters_manager: function(filters_manager) { + this.filters_manager = filters_manager; + this.filters_div = this.filters_manager.parent_div; + this.header_div.after(this.filters_div); + }, /** * Returns representation of object in a dictionary for easy saving. * Use from_dict to recreate object. 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: Handle instance where BAMDataProvider iterator is None; this can occur when trying to fetch additional data.
by Bitbucket 05 Feb '12

05 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/32d1ab3262ea/ changeset: 32d1ab3262ea user: jgoecks date: 2012-02-05 18:53:23 summary: Handle instance where BAMDataProvider iterator is None; this can occur when trying to fetch additional data. affected #: 1 file diff -r 84baec18959cb7f48f450f9aa676aaa1882044c1 -r 32d1ab3262ea4d45e1cae1f43f44e43d3c8899d8 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -646,6 +646,10 @@ max_high - highest coordinate for the returned reads message - error/informative message """ + # No iterator indicates no reads. + if iterator is None: + return { 'data': [], 'message': None } + # Decode strand from read flag. def decode_strand( read_flag, mask ): strand_flag = ( read_flag & mask == 0 ) 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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