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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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commit/galaxy-central: greg: Correctly handle ToolPanelSection objects when presenting the tool panel sectin redio buttons for selecting a section to contain tools installed with a tool shed repostory into a local Galaxy instance.
by Bitbucket 03 Feb '12

03 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/84baec18959c/ changeset: 84baec18959c user: greg date: 2012-02-03 22:30:30 summary: Correctly handle ToolPanelSection objects when presenting the tool panel sectin redio buttons for selecting a section to contain tools installed with a tool shed repostory into a local Galaxy instance. affected #: 1 file diff -r 86d9c5ddbafc3f54acd8398cf3f3d9c10a5ca54c -r 84baec18959cb7f48f450f9aa676aaa1882044c1 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -797,8 +797,9 @@ def build_tool_panel_section_select_field( trans ): """Build a SelectField whose options are the sections of the current in-memory toolbox.""" options = [] - for k, tool_section in trans.app.toolbox.tool_panel.items(): - options.append( ( tool_section.name, tool_section.id ) ) + for k, v in trans.app.toolbox.tool_panel.items(): + if isinstance( v, tools.ToolSection ): + options.append( ( v.name, v.id ) ) select_field = SelectField( name='tool_panel_section', display='radio' ) for option_tup in options: select_field.add_option( option_tup[0], option_tup[1] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Make sure a tool shed repository has metadata before setting versions for contained tools.
by Bitbucket 03 Feb '12

03 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/86d9c5ddbafc/ changeset: 86d9c5ddbafc user: greg date: 2012-02-03 21:29:02 summary: Make sure a tool shed repository has metadata before setting versions for contained tools. affected #: 2 files diff -r e6464387ed3fce7f235cf5c9af1281da14a32811 -r 86d9c5ddbafc3f54acd8398cf3f3d9c10a5ca54c lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -559,23 +559,25 @@ for index, changeset_revision in enumerate( changeset_revisions ): tool_versions_dict = {} repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) - metadata = repository_metadata.metadata - tool_dicts = metadata.get( 'tools', [] ) - if index == 0: - # The first changset_revision is a special case because it will have no ancestor - # changeset_revisions in which to match tools. The parent tool id for tools in - # the first changeset_revision will be the "old_id" in the tool config. - for tool_dict in tool_dicts: - tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] - else: - for tool_dict in tool_dicts: - # We have at least 2 changeset revisions to compare tool guids and tool ids. - parent_id = get_parent_id( trans, id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], changeset_revisions[ 0:index ] ) - tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id - if tool_versions_dict: - repository_metadata.tool_versions = tool_versions_dict - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + tool_dicts = metadata.get( 'tools', [] ) + if index == 0: + # The first changset_revision is a special case because it will have no ancestor + # changeset_revisions in which to match tools. The parent tool id for tools in + # the first changeset_revision will be the "old_id" in the tool config. + for tool_dict in tool_dicts: + tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] + else: + for tool_dict in tool_dicts: + # We have at least 2 changeset revisions to compare tool guids and tool ids. + parent_id = get_parent_id( trans, id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], changeset_revisions[ 0:index ] ) + tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id + if tool_versions_dict: + repository_metadata.tool_versions = tool_versions_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ): parent_id = None # Compare from most recent to oldest. diff -r e6464387ed3fce7f235cf5c9af1281da14a32811 -r 86d9c5ddbafc3f54acd8398cf3f3d9c10a5ca54c lib/galaxy/webapps/community/model/migrate/versions/0011_add_tool_versions_column.py --- a/lib/galaxy/webapps/community/model/migrate/versions/0011_add_tool_versions_column.py +++ b/lib/galaxy/webapps/community/model/migrate/versions/0011_add_tool_versions_column.py @@ -1,5 +1,5 @@ """ -Migration script to add the new_repo_alert column to the galaxy_user table. +Migration script to add the tool_versions column to the repository_metadata table. """ from sqlalchemy import * 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 the ability to chain Galaxy tools into a lineage of tool versions. This enables workflows and the rerun button on history items to work when a new version of a tool is loaded into the Galaxy tool panel. Version information for tools included in tool shed repositories is maintained for each changeset revision in the tool shed, and this information can be retrieved from the Administrative "Manage installed tool shed repositories" menu item for installed tool s
by Bitbucket 03 Feb '12

03 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e6464387ed3f/ changeset: e6464387ed3f user: greg date: 2012-02-03 21:13:28 summary: Add the ability to chain Galaxy tools into a lineage of tool versions. This enables workflows and the rerun button on history items to work when a new version of a tool is loaded into the Galaxy tool panel. Version information for tools included in tool shed repositories is maintained for each changeset revision in the tool shed, and this information can be retrieved from the Administrative "Manage installed tool shed repositories" menu item for installed tool shed repositories that contain tools. This new functionality eliminates the need for the tool_id_guid_map table and associated features, so they have all been removed. affected #: 17 files diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2687,16 +2687,46 @@ def includes_workflows( self ): return 'workflows' in self.metadata -class ToolIdGuidMap( object ): - def __init__( self, id=None, create_time=None, tool_id=None, tool_version=None, tool_shed=None, repository_owner=None, repository_name=None, guid=None ): +class ToolVersion( object ): + def __init__( self, id=None, create_time=None, tool_id=None, tool_shed_repository=None ): self.id = id self.create_time = create_time self.tool_id = tool_id - self.tool_version = tool_version - self.tool_shed = tool_shed - self.repository_owner = repository_owner - self.repository_name = repository_name - self.guid = guid + self.tool_shed_repository = tool_shed_repository + def get_versions( self, app ): + sa_session = app.model.context.current + tool_versions = [] + # Prepend ancestors. + def __ancestors( 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 ) + # Append descendants. + def __descendants( 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 ) + return tool_versions + def get_version_ids( self, app ): + return [ tool_version.tool_id for tool_version in self.get_versions( app ) ] + +class ToolVersionAssociation( object ): + def __init__( self, id=None, tool_id=None, parent_id=None ): + self.id = id + self.tool_id = tool_id + self.parent_id = parent_id ## ---- Utility methods ------------------------------------------------------- diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -382,16 +382,17 @@ Column( "uninstalled", Boolean, default=False ), Column( "dist_to_shed", Boolean, default=False ) ) -ToolIdGuidMap.table = Table( "tool_id_guid_map", metadata, +ToolVersion.table = Table( "tool_version", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "tool_id", String( 255 ) ), - Column( "tool_version", TEXT ), - Column( "tool_shed", TrimmedString( 255 ) ), - Column( "repository_owner", TrimmedString( 255 ) ), - Column( "repository_name", TrimmedString( 255 ) ), - Column( "guid", TEXT, index=True, unique=True ) ) + Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True, nullable=True ) ) + +ToolVersionAssociation.table = Table( "tool_version_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "tool_id", Integer, ForeignKey( "tool_version.id" ), index=True, nullable=False ), + Column( "parent_id", Integer, ForeignKey( "tool_version.id" ), index=True, nullable=False ) ) Job.table = Table( "job", metadata, Column( "id", Integer, primary_key=True ), @@ -1619,9 +1620,20 @@ ratings=relation( PageRatingAssociation, order_by=PageRatingAssociation.table.c.id, backref="pages" ) ) ) -assign_mapper( context, ToolShedRepository, ToolShedRepository.table ) +assign_mapper( context, ToolShedRepository, ToolShedRepository.table, + properties=dict( tool_versions=relation( ToolVersion, + primaryjoin=( ToolShedRepository.table.c.id == ToolVersion.table.c.tool_shed_repository_id ), + backref='tool_shed_repository' ) ) ) -assign_mapper( context, ToolIdGuidMap, ToolIdGuidMap.table ) +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' ) ) ) # Set up proxy so that # Page.users_shared_with diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py @@ -0,0 +1,119 @@ +""" +Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * +from galaxy.util.json import from_json_string, to_json_string + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def nextval( table, col='id' ): + if migrate_engine.name == 'postgres': + return "nextval('%s_%s_seq')" % ( table, col ) + elif migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + return "null" + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + +def localtimestamp(): + if migrate_engine.name == 'postgres' or migrate_engine.name == 'mysql': + return "LOCALTIMESTAMP" + elif migrate_engine.name == 'sqlite': + return "current_date || ' ' || current_time" + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % db ) + +ToolVersion_table = Table( "tool_version", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_id", String( 255 ) ), + Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True, nullable=True ) ) + +ToolVersionAssociation_table = Table( "tool_version_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "tool_id", Integer, ForeignKey( "tool_version.id" ), index=True, nullable=False ), + Column( "parent_id", Integer, ForeignKey( "tool_version.id" ), index=True, nullable=False ) ) + +def upgrade(): + print __doc__ + + ToolIdGuidMap_table = Table( "tool_id_guid_map", metadata, autoload=True ) + + metadata.reflect() + # Create the tables. + try: + ToolVersion_table.create() + except Exception, e: + log.debug( "Creating tool_version table failed: %s" % str( e ) ) + try: + ToolVersionAssociation_table.create() + except Exception, e: + log.debug( "Creating tool_version_association table failed: %s" % str( e ) ) + # Populate the tool table with tools included in installed tool shed repositories. + cmd = "SELECT id, metadata FROM tool_shed_repository" + result = db_session.execute( cmd ) + count = 0 + for row in result: + if row[1]: + tool_shed_repository_id = row[0] + repository_metadata = from_json_string( str( row[1] ) ) + # Create a new row in the tool table for each tool included in repository. We will NOT + # handle tool_version_associaions because we do not have the information we need to do so. + tools = repository_metadata.get( 'tools', [] ) + for tool_dict in tools: + cmd = "INSERT INTO tool_version VALUES (%s, %s, %s, '%s', %s)" % \ + ( nextval( 'tool_version' ), localtimestamp(), localtimestamp(), tool_dict[ 'guid' ], tool_shed_repository_id ) + db_session.execute( cmd ) + count += 1 + print "Added %d rows to the new tool_version table." % count + # Drop the tool_id_guid_map table since the 2 new tables render it unnecessary. + try: + ToolIdGuidMap_table.drop() + except Exception, e: + log.debug( "Dropping tool_id_guid_map table failed: %s" % str( e ) ) + +def downgrade(): + + ToolIdGuidMap_table = Table( "tool_id_guid_map", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_id", String( 255 ) ), + Column( "tool_version", TEXT ), + Column( "tool_shed", TrimmedString( 255 ) ), + Column( "repository_owner", TrimmedString( 255 ) ), + Column( "repository_name", TrimmedString( 255 ) ), + Column( "guid", TEXT, index=True, unique=True ) ) + + metadata.reflect() + try: + ToolVersionAssociation_table.drop() + except Exception, e: + log.debug( "Dropping tool_version_association table failed: %s" % str( e ) ) + try: + ToolVersion_table.drop() + except Exception, e: + log.debug( "Dropping tool_version table failed: %s" % str( e ) ) + try: + ToolIdGuidMap_table.create() + except Exception, e: + log.debug( "Creating tool_id_guid_map table failed: %s" % str( e ) ) diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -4,7 +4,9 @@ shed. Tools included in tool_shed_install.xml that have already been installed will not be re-installed. """ +import urllib2 from galaxy.tools import ToolSection +from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * log = logging.getLogger( __name__ ) @@ -53,7 +55,7 @@ changeset_revision = elem.get( 'changeset_revision' ) # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision> clone_dir = os.path.join( self.tool_path, self.tool_shed, 'repos', self.repository_owner, name, changeset_revision ) - if self.__isinstalled( elem, clone_dir ): + if self.__isinstalled( clone_dir ): log.debug( "Skipping automatic install of repository '%s' because it has already been installed in location '%s'" % ( name, clone_dir ) ) else: if section_name and section_id: @@ -81,47 +83,59 @@ if returncode == 0: returncode, tmp_name = update_repository( current_working_dir, relative_install_dir, changeset_revision ) if returncode == 0: - metadata_dict = load_repository_contents( app=self.app, - repository_name=name, - description=description, - owner=self.repository_owner, - changeset_revision=changeset_revision, - tool_path=self.tool_path, - repository_clone_url=repository_clone_url, - relative_install_dir=relative_install_dir, - current_working_dir=current_working_dir, - tmp_name=tmp_name, - tool_shed=self.tool_shed, - tool_section=tool_section, - shed_tool_conf=self.install_tool_config, - new_install=True, - dist_to_shed=True ) - # Add a new record to the tool_id_guid_map table for each tool in the repository if one doesn't already exist. + tool_shed_repository, metadata_dict = load_repository_contents( app=self.app, + repository_name=name, + description=description, + owner=self.repository_owner, + changeset_revision=changeset_revision, + tool_path=self.tool_path, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + current_working_dir=current_working_dir, + tmp_name=tmp_name, + tool_shed=self.tool_shed, + tool_section=tool_section, + shed_tool_conf=self.install_tool_config, + new_install=True, + dist_to_shed=True ) if 'tools' in metadata_dict: - tools_mapped = 0 - for tool_dict in metadata_dict[ 'tools' ]: - flush_needed = False - tool_id = tool_dict[ 'id' ] - tool_version = tool_dict[ 'version' ] - guid = tool_dict[ 'guid' ] - tool_id_guid_map = get_tool_id_guid_map( self.app, tool_id, tool_version, self.tool_shed, self.repository_owner, name ) - if tool_id_guid_map: - if tool_id_guid_map.guid != guid: - tool_id_guid_map.guid = guid - flush_needed = True - else: - tool_id_guid_map = self.app.model.ToolIdGuidMap( tool_id=tool_id, - tool_version=tool_version, - tool_shed=self.tool_shed, - repository_owner=self.repository_owner, - repository_name=name, - guid=guid ) - flush_needed = True - if flush_needed: - self.sa_session.add( tool_id_guid_map ) - self.sa_session.flush() - tools_mapped += 1 - log.debug( "Mapped tool ids to guids for %d tools included in repository '%s'." % ( tools_mapped, name ) ) + # Get the tool_versions from the tool shed for each tool in the installed change set. + url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( tool_shed_url, name, self.repository_owner, changeset_revision ) + response = urllib2.urlopen( url ) + text = response.read() + response.close() + if text: + tool_versions_dict = from_json_string( text ) + handle_tool_versions( self.app, tool_versions_dict, tool_shed_repository ) + else: + # Set the tool versions since they seem to be missing for this repository in the tool shed. + for tool_dict in metadata_dict[ 'tools' ]: + flush_needed = False + tool_id = tool_dict[ 'guid' ] + old_tool_id = tool_dict[ 'id' ] + tool_version = tool_dict[ 'version' ] + tool_version_using_old_id = get_tool_version( self.app, old_tool_id ) + tool_version_using_guid = get_tool_version( self.app, tool_id ) + if not tool_version_using_old_id: + tool_version_using_old_id = self.app.model.ToolVersion( tool_id=old_tool_id, + tool_shed_repository=tool_shed_repository ) + self.sa_session.add( tool_version_using_old_id ) + self.sa_session.flush() + if not tool_version_using_guid: + tool_version_using_guid = self.app.model.ToolVersion( tool_id=tool_id, + tool_shed_repository=tool_shed_repository ) + self.sa_session.add( tool_version_using_guid ) + self.sa_session.flush() + # Associate the two versions as parent / child. + tool_version_association = get_tool_version_association( self.app, + tool_version_using_old_id, + tool_version_using_guid ) + if not tool_version_association: + tool_version_association = self.app.model.ToolVersionAssociation( tool_id=tool_version_using_guid.id, + parent_id=tool_version_using_old_id.id ) + self.sa_session.add( tool_version_association ) + self.sa_session.flush() else: tmp_stderr = open( tmp_name, 'rb' ) log.debug( "Error updating repository '%s': %s" % ( name, tmp_stderr.read() ) ) @@ -154,26 +168,11 @@ # The tool shed from which the repository was originally # installed must no longer be configured in tool_sheds_conf.xml. return None - def __isinstalled( self, repository_elem, clone_dir ): - name = repository_elem.get( 'name' ) - installed = False - for tool_elem in repository_elem: - tool_config = tool_elem.get( 'file' ) - tool_id = tool_elem.get( 'id' ) - tool_version = tool_elem.get( 'version' ) - tigm = get_tool_id_guid_map( self.app, tool_id, tool_version, self.tool_shed, self.repository_owner, name ) - if tigm: - # A record exists in the tool_id_guid_map table, so see if the repository is installed. - if os.path.exists( clone_dir ): - installed = True - break - if not installed: - full_path = os.path.abspath( clone_dir ) - # We may have a repository that contains no tools. - if os.path.exists( full_path ): - for root, dirs, files in os.walk( full_path ): - if '.hg' in dirs: - # Assume that the repository has been installed if we find a .hg directory. - installed = True - break - return installed + def __isinstalled( self, clone_dir ): + full_path = os.path.abspath( clone_dir ) + if os.path.exists( full_path ): + for root, dirs, files in os.walk( full_path ): + if '.hg' in dirs: + # Assume that the repository has been installed if we find a .hg directory. + return True + return False diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -120,36 +120,32 @@ return tool else: return tool - # Handle the case where the tool was used when the tool was included in the Galaxy distribution, - # but now the tool is contained in an installed tool shed repository. In this case, the original - # tool id can be mapped to the new tool id, which is the tool's guid in the tool shed repository. - # This scenarios can occur in workflows and in a history item when the rerun icon is clicked. - # The weakness here is that workflows currently handle only tool ids and not versions. - tool_id_guid_map = self.__get_tool_id_guid_map( tool_id, tool_version=tool_version ) - if tool_id_guid_map: - guid = tool_id_guid_map.guid - if guid in self.tools_by_id: - return self.tools_by_id[ guid ] - # Handle the case where a proprietary tool was initially developed and hosted in a local Galaxy - # instance, but the developer later uploaded the tool to a Galaxy tool shed, removed the original - # tool from the local Galaxy instance and installed the tool's repository from the tool shed. - for k, tool in self.tools_by_id.items(): - if tool_id == tool.old_id: - if tool_version and tool.version == tool_version: - return tool - else: - return tool + # Handle the case where the received tool_id has a tool_version. In this case, one of the following + # conditions is true. + # 1. The tool was used when it was included in the Galaxy distribution, but now the tool is contained + # in an installed tool shed repository. In this case, the original tool id can be mapped to the new + # tool id, which is the tool's guid in the tool shed repository. This scenarios can occur in + # workflows and in a history item when the rerun icon is clicked. The weakness here is that workflows + # currently handle only tool ids and not versions. + # 2. A proprietary tool was initially developed and hosted in a local Galaxy instance, but the developer + # later uploaded the tool to a Galaxy tool shed, removed the original tool from the local Galaxy + # instance and installed the tool's repository from the tool shed. + tv = self.__get_tool_version( tool_id ) + if tv: + tool_version_ids = tv.get_version_ids( self.app ) + for tool_version_id in tool_version_ids: + if tool_version_id in self.tools_by_id: + tool = self.tools_by_id[ tool_version_id ] + if tool_version and tool.version == tool_version: + return tool + else: + return tool return None - def __get_tool_id_guid_map( self, tool_id, tool_version=None ): - if tool_version: - return self.sa_session.query( self.app.model.ToolIdGuidMap ) \ - .filter( and_( self.app.model.ToolIdGuidMap.table.c.tool_id == tool_id, - self.app.model.ToolIdGuidMap.table.c.tool_version == tool_version ) ) \ - .first() - else: - return self.sa_session.query( self.app.model.ToolIdGuidMap ) \ - .filter( self.app.model.ToolIdGuidMap.table.c.tool_id == tool_id ) \ - .first() + def __get_tool_version( self, tool_id ): + """Return a ToolVersion if one exists for our tool_id""" + return self.sa_session.query( self.app.model.ToolVersion ) \ + .filter( self.app.model.ToolVersion.table.c.tool_id == tool_id ) \ + .first() def __get_tool_shed_repository( self, tool_shed, name, owner, installed_changeset_revision ): return self.sa_session.query( self.app.model.ToolShedRepository ) \ .filter( and_( self.app.model.ToolShedRepository.table.c.tool_shed == tool_shed, @@ -160,7 +156,10 @@ def load_tool_tag_set( self, elem, panel_dict, tool_path, guid=None, section=None ): try: path = elem.get( "file" ) - if guid is not None: + if guid is None: + tool_shed_repository = None + can_load = True + else: # The tool is contained in an installed tool shed repository, so load # the tool only if the repository has not been marked deleted. tool_shed = elem.find( "tool_shed" ).text @@ -218,8 +217,6 @@ # If there is not yet a tool_shed_repository record, we're in the process of installing # a new repository, so any included tools can be loaded into the tool panel. can_load = True - else: - can_load = True if can_load: tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) if guid is not None: @@ -230,6 +227,11 @@ tool.guid = guid tool.old_id = elem.find( "id" ).text tool.version = elem.find( "version" ).text + # Make sure the tool has a tool_version. + if not self.__get_tool_version( tool.id ): + tool_version = self.app.model.ToolVersion( tool_id=tool.id, tool_shed_repository=tool_shed_repository ) + self.sa_session.add( tool_version ) + self.sa_session.flush() if self.app.config.get_bool( 'enable_tool_tags', False ): tag_names = elem.get( "tags", "" ).split( "," ) for tag_name in tag_names: @@ -542,13 +544,30 @@ # Parse XML element containing configuration self.parse( root, guid=guid ) self.external_runJob_script = app.config.drmaa_external_runjob_script - @property def sa_session( self ): - """ - Returns a SQLAlchemy session - """ + """Returns a SQLAlchemy session""" return self.app.model.context + @property + def tool_version( self ): + """Return a ToolVersion if one exists for our id""" + return self.sa_session.query( self.app.model.ToolVersion ) \ + .filter( self.app.model.ToolVersion.table.c.tool_id == self.id ) \ + .first() + @property + def tool_versions( self ): + # If we have versions, return them. + tool_version = self.tool_version + if tool_version: + return tool_version.get_versions( self.app ) + return [] + @property + def tool_version_ids( self ): + # If we have versions, return a list of their tool_ids. + tool_version = self.tool_version + if tool_version: + return tool_version.get_version_ids( self.app ) + return [] def parse( self, root, guid=None ): """ Read tool configuration from the element `root` and fill in `self`. diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -110,6 +110,7 @@ dist_to_shed=dist_to_shed ) sa_session.add( tool_shed_repository ) sa_session.flush() + return tool_shed_repository def generate_datatypes_metadata( datatypes_config, metadata_dict ): """ Update the received metadata_dict with changes that have been applied @@ -358,15 +359,18 @@ tool = app.toolbox.load_tool( os.path.abspath( relative_path ), guid=guid ) repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups -def get_tool_id_guid_map( app, tool_id, version, tool_shed, repository_owner, repository_name ): +def get_tool_version( app, tool_id ): # This method is used by the InstallManager, which does not have access to trans. sa_session = app.model.context.current - return sa_session.query( app.model.ToolIdGuidMap ) \ - .filter( and_( app.model.ToolIdGuidMap.table.c.tool_id == tool_id, - app.model.ToolIdGuidMap.table.c.tool_version == version, - app.model.ToolIdGuidMap.table.c.tool_shed == tool_shed, - app.model.ToolIdGuidMap.table.c.repository_owner == repository_owner, - app.model.ToolIdGuidMap.table.c.repository_name == repository_name ) ) \ + return sa_session.query( app.model.ToolVersion ) \ + .filter( app.model.ToolVersion.table.c.tool_id == tool_id ) \ + .first() +def get_tool_version_association( app, parent_tool_version, tool_version ): + """Return a ToolVersionAssociation if one exists that associates the two received tool_versions""" + sa_session = app.model.context.current + return sa_session.query( app.model.ToolVersionAssociation ) \ + .filter( and_( app.model.ToolVersionAssociation.table.c.parent_id == parent_tool_version.id, + app.model.ToolVersionAssociation.table.c.tool_id == tool_version.id ) ) \ .first() def get_url_from_repository_tool_shed( app, repository ): """ @@ -472,6 +476,33 @@ error = tmp_stderr.read() tmp_stderr.close() log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) ) +def handle_tool_versions( app, tool_versions, tool_shed_repository ): + """ + This method is used by the InstallManager, which does not have access to trans. Using + the tool_versions dictionary retrieved from the tool shed, create the parent / child pairs + of tool versions. The tool_versions dictionary contains { tool id : parent tool id } pairs. + """ + sa_session = app.model.context.current + for tool_guid, parent_id in tool_versions.items(): + tool_version_using_tool_guid = get_tool_version( app, tool_guid ) + tool_version_using_parent_id = get_tool_version( app, parent_id ) + if not tool_version_using_tool_guid: + tool_version_using_tool_guid = app.model.ToolVersion( tool_id=tool_guid, tool_shed_repository=tool_shed_repository ) + sa_session.add( tool_version_using_tool_guid ) + sa_session.flush() + if not tool_version_using_parent_id: + tool_version_using_parent_id = app.model.ToolVersion( tool_id=parent_id, tool_shed_repository=tool_shed_repository ) + sa_session.add( tool_version_using_parent_id ) + sa_session.flush() + # Associate the two versions as parent / child. + tool_version_association = get_tool_version_association( app, + tool_version_using_parent_id, + tool_version_using_tool_guid ) + if not tool_version_association: + tool_version_association = app.model.ToolVersionAssociation( tool_id=tool_version_using_tool_guid.id, + parent_id=tool_version_using_parent_id.id ) + sa_session.add( tool_version_association ) + sa_session.flush() def load_datatype_items( app, repository, relative_install_dir, deactivate=False ): # Load proprietary datatypes. metadata = repository.metadata @@ -638,13 +669,13 @@ # deleted, undelete it. It is imperative that this happens before the call to alter_tool_panel() below because # tools will not be properly loaded if the repository is marked deleted. log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % repository_name ) - create_or_update_tool_shed_repository( app, - repository_name, - description, - changeset_revision, - repository_clone_url, - metadata_dict, - dist_to_shed=dist_to_shed ) + tool_shed_repository = create_or_update_tool_shed_repository( app, + repository_name, + description, + changeset_revision, + repository_clone_url, + metadata_dict, + dist_to_shed=dist_to_shed ) if 'tools' in metadata_dict: repository_tools_tups = get_repository_tools_tups( app, metadata_dict ) if repository_tools_tups: @@ -696,7 +727,7 @@ if display_path: # Load proprietary datatype display applications app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict ) - return metadata_dict + return tool_shed_repository, metadata_dict def alter_tool_panel( app, repository_name, repository_clone_url, changeset_revision, repository_tools_tups, tool_section, shed_tool_conf, tool_path, owner, new_install=True, deactivate=False, uninstall=False ): """ diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -1,58 +1,11 @@ +import urllib2 from galaxy.web.controllers.admin import * +from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * from galaxy import tools log = logging.getLogger( __name__ ) -class ToolIdGuidMapGrid( grids.Grid ): - class ToolIdColumn( grids.TextColumn ): - def get_value( self, trans, grid, tool_id_guid_map ): - return tool_id_guid_map.tool_id - class ToolVersionColumn( grids.TextColumn ): - def get_value( self, trans, grid, tool_id_guid_map ): - return tool_id_guid_map.tool_version - class ToolGuidColumn( grids.TextColumn ): - def get_value( self, trans, grid, tool_id_guid_map ): - return tool_id_guid_map.guid - class ToolShedColumn( grids.TextColumn ): - def get_value( self, trans, grid, tool_id_guid_map ): - return tool_id_guid_map.tool_shed - class RepositoryNameColumn( grids.TextColumn ): - def get_value( self, trans, grid, tool_id_guid_map ): - return tool_id_guid_map.repository_name - class RepositoryOwnerColumn( grids.TextColumn ): - def get_value( self, trans, grid, tool_id_guid_map ): - return tool_id_guid_map.repository_owner - # Grid definition - title = "Map tool id to guid" - model_class = model.ToolIdGuidMap - template='/admin/tool_shed_repository/grid.mako' - default_sort_key = "tool_id" - columns = [ - ToolIdColumn( "Tool id" ), - ToolVersionColumn( "Version" ), - ToolGuidColumn( "Guid" ), - ToolShedColumn( "Tool shed" ), - RepositoryNameColumn( "Repository name" ), - RepositoryOwnerColumn( "Repository owner" ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[0], columns[2], columns[4], columns[5] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - global_actions = [ - grids.GridAction( "Manage installed tool shed repositories", dict( controller='admin_toolshed', action='browse_repositories' ) ) - ] - 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 RepositoryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool_shed_repository ): @@ -96,9 +49,7 @@ key="free-text-search", visible=False, filterable="standard" ) ) - global_actions = [ - grids.GridAction( "View tool id guid map", dict( controller='admin_toolshed', action='browse_tool_id_guid_map' ) ) - ] + global_actions = [] operations = [ grids.GridOperation( "Get updates", allow_multiple=False, condition=( lambda item: not item.deleted ), @@ -122,14 +73,9 @@ class AdminToolshed( AdminGalaxy ): repository_list_grid = RepositoryListGrid() - tool_id_guid_map_grid = ToolIdGuidMapGrid() @web.expose @web.require_admin - def browse_tool_id_guid_map( self, trans, **kwd ): - return self.tool_id_guid_map_grid( trans, **kwd ) - @web.expose - @web.require_admin def browse_repository( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -267,21 +213,38 @@ if returncode == 0: owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) ) tool_shed = clean_tool_shed_url( tool_shed_url ) - metadata_dict = load_repository_contents( app=trans.app, - repository_name=name, - description=description, - owner=owner, - changeset_revision=changeset_revision, - tool_path=tool_path, - repository_clone_url=repository_clone_url, - relative_install_dir=relative_install_dir, - current_working_dir=current_working_dir, - tmp_name=tmp_name, - tool_shed=tool_shed, - tool_section=tool_section, - shed_tool_conf=shed_tool_conf, - new_install=True, - dist_to_shed=False ) + tool_shed_repository, metadata_dict = load_repository_contents( app=trans.app, + repository_name=name, + description=description, + owner=owner, + changeset_revision=changeset_revision, + tool_path=tool_path, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + current_working_dir=current_working_dir, + tmp_name=tmp_name, + tool_shed=tool_shed, + tool_section=tool_section, + shed_tool_conf=shed_tool_conf, + new_install=True, + dist_to_shed=False ) + + + if 'tools' in metadata_dict: + # Get the tool_versions from the tool shed for each tool in the installed change set. + url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( tool_shed_url, name, owner, changeset_revision ) + response = urllib2.urlopen( url ) + text = response.read() + response.close() + if text: + tool_versions_dict = from_json_string( text ) + handle_tool_versions( trans.app, tool_versions_dict, tool_shed_repository ) + else: + message += "Version information for the tools included in the <b>%s</b> repository is missing. " % name + message += "Reset all of this repository's metadata in the tool shed, then set the installed tool versions " + message += "from the installed repository's <b>Repository Actions</b> menu. " + status = 'error' installed_repository_names.append( name ) else: tmp_stderr = open( tmp_name, 'rb' ) @@ -293,7 +256,7 @@ message += '%s<br/>' % tmp_stderr.read() tmp_stderr.close() status = 'error' - if installed_repository_names: + if installed_repository_names: installed_repository_names.sort() num_repositories_installed = len( installed_repository_names ) if tool_section: @@ -332,6 +295,35 @@ status=status ) @web.expose @web.require_admin + def set_tool_versions( self, trans, **kwd ): + # Get the tool_versions from the tool shed for each tool in the installed change set. + repository = get_repository( trans, kwd[ 'id' ] ) + tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) + url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( tool_shed_url, repository.name, repository.owner, repository.changeset_revision ) + response = urllib2.urlopen( url ) + text = response.read() + response.close() + if text: + tool_versions_dict = from_json_string( text ) + handle_tool_versions( trans.app, tool_versions_dict, repository ) + message = "Tool versions have been set for all included tools." + status = 'done' + else: + message = "Version information for the tools included in the <b>%s</b> repository is missing. " % repository.name + message += "Reset all of this reppository's metadata in the tool shed, then set the installed tool versions " + message ++ "from the installed repository's <b>Repository Actions</b> menu. " + status = 'error' + shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository ) + repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) + return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', + repository=repository, + description=repository.description, + repo_files_dir=repo_files_dir, + message=message, + status=status ) + @web.expose + @web.require_admin def deactivate_or_uninstall_repository( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -392,17 +384,6 @@ log.debug( "Removed repository installation directory: %s" % str( relative_install_dir ) ) except Exception, e: log.debug( "Error removing repository installation directory %s: %s" % ( str( relative_install_dir ), str( e ) ) ) - # If the repository was installed by the InstallManager, remove - # all appropriate rows from the tool_id_guid_map database table. - if repository.dist_to_shed: - count = 0 - for tool_id_guid_map in trans.sa_session.query( trans.model.ToolIdGuidMap ) \ - .filter( and_( trans.model.ToolIdGuidMap.table.c.tool_shed==repository.tool_shed, - trans.model.ToolIdGuidMap.table.c.repository_owner==repository.owner, - trans.model.ToolIdGuidMap.table.c.repository_name==repository.name ) ): - trans.sa_session.delete( tool_id_guid_map ) - count += 1 - log.debug( "Removed %d rows from the tool_id_guid_map database table." % count ) repository.uninstalled = True repository.deleted = True trans.sa_session.add( repository ) @@ -490,21 +471,21 @@ elem.attrib[ 'version' ] = '' tool_section = tools.ToolSection( elem ) trans.app.toolbox.tool_panel[ section_key ] = tool_section - metadata_dict = load_repository_contents( app=trans.app, - repository_name=repository.name, - description=repository.description, - owner=repository.owner, - changeset_revision=repository.installed_changeset_revision, - tool_path=tool_path, - repository_clone_url=repository_clone_url, - relative_install_dir=relative_install_dir, - current_working_dir=current_working_dir, - tmp_name=tmp_name, - tool_shed=repository.tool_shed, - tool_section=tool_section, - shed_tool_conf=shed_tool_conf, - new_install=True, - dist_to_shed=False ) + tool_shed_repository, metadata_dict = load_repository_contents( app=trans.app, + repository_name=repository.name, + description=repository.description, + owner=repository.owner, + changeset_revision=repository.installed_changeset_revision, + tool_path=tool_path, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + current_working_dir=current_working_dir, + tmp_name=tmp_name, + tool_shed=repository.tool_shed, + tool_section=tool_section, + shed_tool_conf=shed_tool_conf, + new_install=True, + dist_to_shed=False ) repository.uninstalled = False repository.deleted = False trans.sa_session.add( repository ) @@ -518,6 +499,22 @@ 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. + 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: + # 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 ) + trans.sa_session.flush() tool_panel_section = metadata[ 'tool_panel_section' ] original_section_id = tool_panel_section[ 'id' ] if original_section_id in [ '' ]: @@ -653,8 +650,8 @@ # Send a request to the relevant tool shed to see if there are any updates. repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - url = '%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( tool_shed_url, url_for( '', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) + url = '%/srepository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( tool_shed_url, url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -684,20 +681,20 @@ # Update the repository metadata. repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) tool_shed = clean_tool_shed_url( tool_shed_url ) - metadata_dict = load_repository_contents( app=trans.app, - name=name, - description=repository.description, - owner=owner, - changeset_revision=changeset_revision, - tool_path=tool_path, - repository_clone_url=repository_clone_url, - relative_install_dir=relative_install_dir, - current_working_dir=current_working_dir, - tmp_name=tmp_name, - tool_shed=tool_shed, - tool_section=None, - shed_tool_conf=None, - new_install=False ) + tool_shed_repository, metadata_dict = load_repository_contents( app=trans.app, + name=name, + description=repository.description, + owner=owner, + changeset_revision=changeset_revision, + tool_path=tool_path, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + current_working_dir=current_working_dir, + tmp_name=tmp_name, + tool_shed=tool_shed, + tool_section=None, + shed_tool_conf=None, + new_install=False ) # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision repository.update_available = False diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1220,7 +1220,7 @@ for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items(): if shed_url.endswith( '/' ): shed_url = shed_url.rstrip( '/' ) - url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, url_for( '', qualified=True ), webapp ) + url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, url_for( '/', qualified=True ), webapp ) if missing_tool_tups: url += '&tool_id=' for missing_tool_tup in missing_tool_tups: diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -488,6 +488,7 @@ repo = hg.repository( get_configured_ui(), repo_dir ) if len( repo ) == 1: message, status = set_repository_metadata( trans, id, repository.tip, **kwd ) + add_repository_metadata_tool_versions( trans, id, [ repository.tip ] ) else: # The list of changeset_revisions refers to repository_metadata records that have been # created or updated. When the following loop completes, we'll delete all repository_metadata @@ -543,6 +544,7 @@ ancestor_changeset_revision = None ancestor_metadata_dict = None clean_repository_metadata( trans, id, changeset_revisions ) + add_repository_metadata_tool_versions( trans, id, changeset_revisions ) def clean_repository_metadata( trans, id, changeset_revisions ): # Delete all repository_metadata reecords associated with the repository # that have a changeset_revision that is not in changeset_revisions. @@ -551,6 +553,47 @@ if repository_metadata.changeset_revision not in changeset_revisions: trans.sa_session.delete( repository_metadata ) trans.sa_session.flush() +def add_repository_metadata_tool_versions( trans, id, changeset_revisions ): + # If a repository includes tools, build a dictionary of { 'tool id' : 'parent tool id' } + # pairs for each tool in each changeset revision. + for index, changeset_revision in enumerate( changeset_revisions ): + tool_versions_dict = {} + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + metadata = repository_metadata.metadata + tool_dicts = metadata.get( 'tools', [] ) + if index == 0: + # The first changset_revision is a special case because it will have no ancestor + # changeset_revisions in which to match tools. The parent tool id for tools in + # the first changeset_revision will be the "old_id" in the tool config. + for tool_dict in tool_dicts: + tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] + else: + for tool_dict in tool_dicts: + # We have at least 2 changeset revisions to compare tool guids and tool ids. + parent_id = get_parent_id( trans, id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], changeset_revisions[ 0:index ] ) + tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id + if tool_versions_dict: + repository_metadata.tool_versions = tool_versions_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() +def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ): + parent_id = None + # Compare from most recent to oldest. + changeset_revisions.reverse() + for changeset_revision in changeset_revisions: + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + metadata = repository_metadata.metadata + tools_dicts = metadata.get( 'tools', [] ) + for tool_dict in tools_dicts: + if tool_dict[ 'guid' ] == guid: + # The tool has not changed between the compared changeset revisions. + continue + if tool_dict[ 'id' ] == old_id and tool_dict[ 'version' ] != version: + # The tool version is different, so we've found the parent. + return tool_dict[ 'guid' ] + if parent_id is None: + # The tool did not change through all of the changeset revisions. + return old_id def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ): repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -438,7 +438,7 @@ galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) encoded_repo_info_dict, includes_tools = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) url = '%sadmin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s&includes_tools=%s' % \ - ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) ) + ( galaxy_url, url_for( '/', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) ) return trans.response.send_redirect( url ) else: # This can only occur when there is a multi-select grid with check boxes and an operation, @@ -514,7 +514,7 @@ galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) encoded_repo_info_dict, includes_tools = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) url = '%sadmin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s&includes_tools=%s' % \ - ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) ) + ( galaxy_url, url_for( '/', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) ) return trans.response.send_redirect( url ) else: # This can only occur when there is a multi-select grid with check boxes and an operation, @@ -770,9 +770,19 @@ encoded_repo_info_dict = encode( repo_info_dict ) # Redirect back to local Galaxy to perform install. url = '%sadmin_toolshed/install_repository?tool_shed_url=%s&repo_info_dict=%s&includes_tools=%s' % \ - ( galaxy_url, url_for( '', qualified=True ), encoded_repo_info_dict, str( includes_tools ) ) + ( galaxy_url, url_for( '/', qualified=True ), encoded_repo_info_dict, str( includes_tools ) ) return trans.response.send_redirect( url ) @web.expose + def get_tool_versions( self, trans, **kwd ): + name = kwd[ 'name' ] + owner = kwd[ 'owner' ] + changeset_revision = kwd[ 'changeset_revision' ] + repository = get_repository_by_name_and_owner( trans, name, owner ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) + if repository_metadata.tool_versions: + return to_json_string( repository_metadata.tool_versions ) + return '' + @web.expose def check_for_updates( self, trans, **kwd ): # Handle a request from a local Galaxy instance. If the request originated with the # Galaxy instances' UpdateManager, the value of 'webapp' will be 'update_manager'. @@ -792,7 +802,7 @@ no_update = 'false' else: # Start building up the url to redirect back to the calling Galaxy instance. - url = '%sadmin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '', qualified=True ) ) + url = '%sadmin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '/', qualified=True ) ) url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( repository.name, repository.user.username, changeset_revision ) if changeset_revision == repository.tip: diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -402,8 +402,8 @@ to_file.write( to_json_string( workflow_data ) ) return open( tmp_fname ) galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - url = '%s/workflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \ - ( galaxy_url, url_for( '', qualified=True ), repository_metadata_id, encode( workflow_name ), webapp ) + url = '%sworkflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \ + ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, encode( workflow_name ), webapp ) return trans.response.send_redirect( url ) return trans.response.send_redirect( web.url_for( controller='workflow', action='view_workflow', diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -162,10 +162,11 @@ fp.close() class RepositoryMetadata( object ): - def __init__( self, repository_id=None, changeset_revision=None, metadata=None, malicious=False ): + def __init__( self, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False ): self.repository_id = repository_id self.changeset_revision = changeset_revision self.metadata = metadata or dict() + self.tool_versions = tool_versions or dict() self.malicious = malicious class ItemRatingAssociation( object ): diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -119,6 +119,7 @@ Column( "repository_id", Integer, ForeignKey( "repository.id" ), index=True ), Column( "changeset_revision", TrimmedString( 255 ), index=True ), Column( "metadata", JSONType, nullable=True ), + Column( "tool_versions", JSONType, nullable=True ), Column( "malicious", Boolean, default=False ) ) RepositoryRatingAssociation.table = Table( "repository_rating_association", metadata, diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/webapps/community/model/migrate/versions/0011_add_tool_versions_column.py --- /dev/null +++ b/lib/galaxy/webapps/community/model/migrate/versions/0011_add_tool_versions_column.py @@ -0,0 +1,46 @@ +""" +Migration script to add the new_repo_alert column to the galaxy_user table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + RepositoryMetadata_table = Table( "repository_metadata", metadata, autoload=True ) + c = Column( "tool_versions", JSONType, nullable=True ) + try: + # Create + c.create( RepositoryMetadata_table ) + assert c is RepositoryMetadata_table.c.tool_versions + except Exception, e: + print "Adding tool_versions column to the repository_metadata table failed: %s" % str( e ) + +def downgrade(): + metadata.reflect() + # Drop new_repo_alert column from galaxy_user table. + RepositoryMetadata_table = Table( "repository_metadata", metadata, autoload=True ) + try: + RepositoryMetadata_table.c.tool_versions.drop() + except Exception, e: + print "Dropping column tool_versions from the repository_metadata table failed: %s" % str( e ) diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -194,17 +194,19 @@ @classmethod def from_workflow_step( Class, trans, step ): tool_id = step.tool_id - install_tool_id = None if trans.app.toolbox and tool_id not in trans.app.toolbox.tools_by_id: - # Handle the case where the tool was used when the tool was included in the Galaxy distribution, - # but now the tool is contained in an installed tool shed repository. In this case, the original - # tool id can be mapped to the new tool id, which is the tool's guid in the tool shed repository. - tool_id_guid_map = trans.sa_session.query( trans.model.ToolIdGuidMap ) \ - .filter( trans.model.ToolIdGuidMap.table.c.tool_id == tool_id ) \ - .first() - if tool_id_guid_map: - install_tool_id = tool_id_guid_map.guid - if ( trans.app.toolbox and tool_id in trans.app.toolbox.tools_by_id ) or install_tool_id: + # See if we have access to a different version of the tool. + # TODO: If workflows are ever enhanced to use tool version + # in addition to tool id, enhance the selection process here + # to retrieve the correct version of the tool. + tool_version = self.__get_tool_version( trans, tool_id ) + if tool_version: + tool_version_ids = tool_version.get_version_ids( trans.app ) + for tool_version_id in tool_version_ids: + if tool_version_id in trans.app.toolbox.tools_by_id: + tool_id = tool_version_id + break + if ( trans.app.toolbox and tool_id in trans.app.toolbox.tools_by_id ): module = Class( trans, tool_id ) module.state = DefaultToolState() module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) @@ -217,6 +219,11 @@ module.post_job_actions = pjadict return module return None + def __get_tool_version( self, trans, tool_id ): + # Return a ToolVersion if one exists for tool_id. + return trans.sa_session.query( trans.app.model.ToolVersion ) \ + .filter( trans.app.model.ToolVersion.table.c.tool_id == tool_id ) \ + .first() def save_to_step( self, step ): step.type = self.type step.tool_id = self.tool_id diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako --- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako +++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako @@ -84,11 +84,6 @@ <div class="toolParamHelp" style="clear: both;"> * The repository record's uninstalled column in the tool_shed_repository database table will be set to True. </div> - %if repository.dist_to_shed: - <div class="toolParamHelp" style="clear: both;"> - * All records associated with this repository will be eliminated from the tool_id_guid_map database table. - </div> - %endif <div style="clear: both"></div></div><div class="form-row"> diff -r f87dff286e86368fb33032ac567a5c9368dc990b -r e6464387ed3fce7f235cf5c9af1281da14a32811 templates/admin/tool_shed_repository/manage_repository.mako --- a/templates/admin/tool_shed_repository/manage_repository.mako +++ b/templates/admin/tool_shed_repository/manage_repository.mako @@ -8,6 +8,9 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + %if repository.includes_tools: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='set_tool_versions', id=trans.security.encode_id( repository.id ) )}">Set tool versions</a> + %endif <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or Uninstall</a></div></ul> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Use cluster_files_directory for drmaa job template.
by Bitbucket 03 Feb '12

03 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f87dff286e86/ changeset: f87dff286e86 user: natefoo date: 2012-02-03 18:22:16 summary: Use cluster_files_directory for drmaa job template. affected #: 1 file diff -r 0b7ae34da7fbc3a66f21eac243af22965c73e7cc -r f87dff286e86368fb33032ac567a5c9368dc990b lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -169,7 +169,7 @@ 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()) jt = self.ds.createJobTemplate() - jt.remoteCommand = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job_wrapper.get_id_tag()) + jt.remoteCommand = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) 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: dan: close branch
by Bitbucket 03 Feb '12

03 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1327f2219423/ changeset: 1327f2219423 branch: meme_requirement_on_fimo user: dan date: 2012-02-03 17:15:29 summary: close branch affected #: 0 files 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: jmchilton: Specify meme requirement for fimo tool.
by Bitbucket 03 Feb '12

03 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8ba74c17e809/ changeset: 8ba74c17e809 branch: meme_requirement_on_fimo user: jmchilton date: 2012-02-03 04:29:30 summary: Specify meme requirement for fimo tool. affected #: 1 file diff -r 87d5491cc3fef55931c09eb6bd688d1b10e946f5 -r 8ba74c17e8091e448ea448c563d883bb35102283 tools/meme/fimo.xml --- a/tools/meme/fimo.xml +++ b/tools/meme/fimo.xml @@ -1,4 +1,5 @@ <tool id="meme_fimo" name="FIMO" version="0.0.1"> + <requirements><requirement type="package">meme</requirement></requirements><description>- Find Individual Motif Occurrences</description><command interpreter="python">fimo_wrapper.py 'fimo --o "${$html_outfile.files_path}" --verbosity "1" 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: dannon: Slight cleanup of the previous workflow share removal commit.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/87d5491cc3fe/ changeset: 87d5491cc3fe user: dannon date: 2012-02-02 21:16:29 summary: Slight cleanup of the previous workflow share removal commit. affected #: 1 file diff -r 0a001dea361385d107989740582f855aa2b71dc4 -r 87d5491cc3fef55931c09eb6bd688d1b10e946f5 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -290,9 +290,7 @@ @web.require_login( "use Galaxy workflows" ) def sharing( self, trans, id, **kwargs ): """ Handle workflow sharing. """ - session = trans.sa_session - if 'unshare_me' in kwargs: # Remove self from shared associations with workflow. stored = self.get_stored_workflow(trans, id, False, True) @@ -332,9 +330,8 @@ if stored.importable and not stored.slug: self._make_item_accessible( trans.sa_session, stored ) - session.flush() - - return trans.fill_template( "/workflow/sharing.mako", use_panels=True, item=stored ) + session.flush() + return trans.fill_template( "/workflow/sharing.mako", use_panels=True, item=stored ) @web.expose @web.require_login( "to import a workflow", use_panels=True ) 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 Bitbucket 02 Feb '12

02 Feb '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3b2acb89495b/ changeset: 3b2acb89495b user: dannon date: 2012-02-02 20:53:34 summary: Workflows: Add the ability to remove workflows that have been shared with you. affected #: 2 files diff -r 50bf77aa34c3689a122187d7ba9b55deb348df92 -r 3b2acb89495bee2355f20fc3954baa174d486a3c lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -22,11 +22,11 @@ from galaxy.web.framework.helpers import to_unicode from galaxy.jobs.actions.post import ActionBox -class StoredWorkflowListGrid( grids.Grid ): +class StoredWorkflowListGrid( grids.Grid ): class StepsColumn( grids.GridColumn ): def get_value(self, trans, grid, workflow): return len( workflow.latest_workflow.steps ) - + # Grid definition use_panels = True title = "Saved Workflows" @@ -40,10 +40,10 @@ grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] - columns.append( - grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1] ], + columns.append( + grids.MulticolFilterColumn( + "Search", + cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, filterable="standard" ) ) operations = [ @@ -67,14 +67,14 @@ grids.PublicURLColumn( "Name", key="name", filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ), - grids.CommunityRatingColumn( "Community Rating", key="rating" ), + grids.CommunityRatingColumn( "Community Rating", key="rating" ), grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) ] - columns.append( - grids.MulticolFilterColumn( - "Search name, annotation, owner, and tags", - cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], + columns.append( + grids.MulticolFilterColumn( + "Search name, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], key="free-text-search", visible=False, filterable="standard" ) ) operations = [] @@ -84,20 +84,20 @@ def apply_query_filter( self, trans, query, **kwargs ): # A public workflow is published, has a slug, and is not deleted. return query.filter( self.model_class.published==True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False ) - + # Simple SGML parser to get all content in a single tag. class SingleTagContentsParser( sgmllib.SGMLParser ): - + def __init__( self, target_tag ): sgmllib.SGMLParser.__init__( self ) self.target_tag = target_tag self.cur_tag = None self.tag_content = "" - + def unknown_starttag( self, tag, attrs ): """ Called for each start tag. """ self.cur_tag = tag - + def handle_data( self, text ): """ Called for each block of plain text. """ if self.cur_tag == self.target_tag: @@ -106,13 +106,13 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAnnotations, UsesItemRatings ): stored_list_grid = StoredWorkflowListGrid() published_list_grid = StoredWorkflowAllPublishedGrid() - + __myexp_url = "www.myexperiment.org:80" - + @web.expose def index( self, trans ): return self.list( trans ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def list_grid( self, trans, **kwargs ): @@ -145,7 +145,7 @@ .filter( model.StoredWorkflow.deleted == False ) \ .order_by( desc( model.StoredWorkflow.update_time ) ) \ .all() - + # Legacy issue: all shared workflows must have slugs. slug_set = False for workflow_assoc in shared_by_others: @@ -157,7 +157,7 @@ return trans.fill_template( "workflow/list.mako", workflows = workflows, shared_by_others = shared_by_others ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def list_for_run( self, trans ): @@ -179,7 +179,7 @@ return trans.fill_template( "workflow/list_for_run.mako", workflows = workflows, shared_by_others = shared_by_others ) - + @web.expose def list_published( self, trans, **kwargs ): grid = self.published_list_grid( trans, **kwargs ) @@ -235,11 +235,11 @@ @web.expose def get_item_content_async( self, trans, id ): """ Returns item content in HTML format. """ - + stored = self.get_stored_workflow( trans, id, False, True ) if stored is None: raise web.httpexceptions.HTTPNotFound() - + # Get data for workflow's steps. self.get_stored_workflow_steps( trans, stored ) # Get annotations. @@ -247,7 +247,7 @@ for step in stored.latest_workflow.steps: step.annotation = self.get_item_annotation_str( trans.sa_session, stored.user, step ) return trans.stream_template_mako( "/workflow/item_content.mako", item = stored, item_data = stored.latest_workflow.steps ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def share( self, trans, id, email="", use_panels=False ): @@ -285,45 +285,55 @@ item=stored, email=email, use_panels=use_panels ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def sharing( self, trans, id, **kwargs ): """ Handle workflow sharing. """ - - # Get session and workflow. + session = trans.sa_session - stored = self.get_stored_workflow( trans, id ) - session.add( stored ) - - # Do operation on workflow. - if 'make_accessible_via_link' in kwargs: - self._make_item_accessible( trans.sa_session, stored ) - elif 'make_accessible_and_publish' in kwargs: - self._make_item_accessible( trans.sa_session, stored ) - stored.published = True - elif 'publish' in kwargs: - stored.published = True - elif 'disable_link_access' in kwargs: - stored.importable = False - elif 'unpublish' in kwargs: - stored.published = False - elif 'disable_link_access_and_unpublish' in kwargs: - stored.importable = stored.published = False - elif 'unshare_user' in kwargs: - user = session.query( model.User ).get( trans.security.decode_id( kwargs['unshare_user' ] ) ) - if not user: - error( "User not found for provided id" ) + + if 'unshare_me' in kwargs: + # Remove self from shared associations with workflow. + stored = self.get_stored_workflow(trans, id, False, True) association = session.query( model.StoredWorkflowUserShareAssociation ) \ - .filter_by( user=user, stored_workflow=stored ).one() + .filter_by( user=trans.user, stored_workflow=stored ).one() session.delete( association ) - - # Legacy issue: workflows made accessible before recent updates may not have a slug. Create slug for any workflows that need them. - if stored.importable and not stored.slug: - self._make_item_accessible( trans.sa_session, stored ) - + session.flush() + return self.list( trans ) + else: + # Get session and workflow. + stored = self.get_stored_workflow( trans, id ) + session.add( stored ) + + # Do operation on workflow. + if 'make_accessible_via_link' in kwargs: + self._make_item_accessible( trans.sa_session, stored ) + elif 'make_accessible_and_publish' in kwargs: + self._make_item_accessible( trans.sa_session, stored ) + stored.published = True + elif 'publish' in kwargs: + stored.published = True + elif 'disable_link_access' in kwargs: + stored.importable = False + elif 'unpublish' in kwargs: + stored.published = False + elif 'disable_link_access_and_unpublish' in kwargs: + stored.importable = stored.published = False + elif 'unshare_user' in kwargs: + user = session.query( model.User ).get( trans.security.decode_id( kwargs['unshare_user' ] ) ) + if not user: + error( "User not found for provided id" ) + association = session.query( model.StoredWorkflowUserShareAssociation ) \ + .filter_by( user=user, stored_workflow=stored ).one() + session.delete( association ) + + # Legacy issue: workflows made accessible before recent updates may not have a slug. Create slug for any workflows that need them. + if stored.importable and not stored.slug: + self._make_item_accessible( trans.sa_session, stored ) + session.flush() - + return trans.fill_template( "/workflow/sharing.mako", use_panels=True, item=stored ) @web.expose @@ -335,7 +345,7 @@ referer_message = "<a href='%s'>return to the previous page</a>" % referer else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) - + # Do import. session = trans.sa_session stored = self.get_stored_workflow( trans, id, check_ownership=False ) @@ -353,19 +363,19 @@ session = trans.sa_session session.add( imported_stored ) session.flush() - + # Copy annotations. self.copy_item_annotation( session, stored.user, stored, imported_stored.user, imported_stored ) for order_index, step in enumerate( stored.latest_workflow.steps ): self.copy_item_annotation( session, stored.user, step, \ imported_stored.user, imported_stored.latest_workflow.steps[order_index] ) session.flush() - + # Redirect to load galaxy frames. return trans.show_ok_message( - message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s.""" + message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s.""" % ( stored.name, web.url_for( controller='workflow' ), referer_message ), use_panels=True ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def edit_attributes( self, trans, id, **kwargs ): @@ -382,11 +392,11 @@ annotation = sanitize_html( kwargs[ 'annotation' ], 'utf-8', 'text/html' ) self.add_item_annotation( trans.sa_session, trans.get_user(), stored, annotation ) trans.sa_session.flush() - return trans.fill_template( 'workflow/edit_attributes.mako', - stored=stored, - annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) + return trans.fill_template( 'workflow/edit_attributes.mako', + stored=stored, + annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def rename( self, trans, id, new_name=None, **kwargs ): @@ -403,10 +413,10 @@ #message = "Workflow renamed to '%s'." % new_name #return self.list_grid( trans, message=message, status='done' ) else: - return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), + return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), "Rename workflow", submit_text="Rename", use_panels=True ) \ .add_text( "new_name", "Workflow Name", value=to_unicode( stored.name ) ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def rename_async( self, trans, id, new_name=None, **kwargs ): @@ -417,7 +427,7 @@ stored.latest_workflow.name = san_new_name trans.sa_session.flush() return stored.name - + @web.expose @web.require_login( "use Galaxy workflows" ) def annotate_async( self, trans, id, new_annotation=None, **kwargs ): @@ -428,7 +438,7 @@ self.add_item_annotation( trans.sa_session, trans.get_user(), stored, new_annotation ) trans.sa_session.flush() return new_annotation - + @web.expose @web.require_login( "rate items" ) @web.json @@ -443,7 +453,7 @@ stored_rating = self.rate_item( trans.sa_session, trans.get_user(), stored, rating ) return self.get_ave_item_rating_data( trans.sa_session, stored ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def set_accessible_async( self, trans, id=None, accessible=False ): @@ -459,7 +469,7 @@ stored.importable = importable trans.sa_session.flush() return - + @web.expose @web.require_login( "modify Galaxy items" ) def set_slug_async( self, trans, id, new_slug ): @@ -468,7 +478,7 @@ stored.slug = new_slug trans.sa_session.flush() return stored.slug - + @web.expose def get_embed_html_async( self, trans, id ): """ Returns HTML for embedding a workflow in a page. """ @@ -477,7 +487,7 @@ stored = self.get_stored_workflow( trans, id ) if stored: return "Embedded Workflow '%s'" % stored.name - + @web.expose @web.json @web.require_login( "use Galaxy workflows" ) @@ -489,33 +499,33 @@ trans.sa_session.flush() return_dict = { "name" : stored.name, "link" : url_for( action="display_by_username_and_slug", username=stored.user.username, slug=stored.slug ) } return return_dict - + @web.expose @web.require_login( "use Galaxy workflows" ) def gen_image( self, trans, id ): stored = self.get_stored_workflow( trans, id, check_ownership=True ) session = trans.sa_session - + workflow = stored.latest_workflow data = [] - + canvas = svgfig.canvas(style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left") text = svgfig.SVG("g") connectors = svgfig.SVG("g") boxes = svgfig.SVG("g") svgfig.Text.defaults["font-size"] = "10px" - + in_pos = {} out_pos = {} margin = 5 line_px = 16 # how much spacing between input/outputs widths = {} # store px width for boxes of each step max_width, max_x, max_y = 0, 0, 0 - + for step in workflow.steps: # Load from database representation module = module_factory.from_workflow_step( trans, step ) - + # Pack attributes into plain dictionary step_dict = { 'id': step.order_index, @@ -523,21 +533,21 @@ 'data_outputs': module.get_data_outputs(), 'position': step.position } - + input_conn_dict = {} for conn in step.input_connections: input_conn_dict[ conn.input_name ] = \ dict( id=conn.output_step.order_index, output_name=conn.output_name ) step_dict['input_connections'] = input_conn_dict - + data.append(step_dict) - + x, y = step.position['left'], step.position['top'] count = 0 - + max_len = len(module.get_name()) * 1.5 text.append( svgfig.Text(x, y + 20, module.get_name(), **{"font-size": "14px"} ).SVG() ) - + y += 45 for di in module.get_data_inputs(): cur_y = y+count*line_px @@ -547,11 +557,11 @@ text.append( svgfig.Text(x, cur_y, di['label']).SVG() ) count += 1 max_len = max(max_len, len(di['label'])) - - + + if len(module.get_data_inputs()) > 0: y += 15 - + for do in module.get_data_outputs(): cur_y = y+count*line_px if step.order_index not in out_pos: @@ -560,12 +570,12 @@ text.append( svgfig.Text(x, cur_y, do['name']).SVG() ) count += 1 max_len = max(max_len, len(do['name'])) - + widths[step.order_index] = max_len*5.5 max_x = max(max_x, step.position['left']) max_y = max(max_y, step.position['top']) max_width = max(max_width, widths[step.order_index]) - + for step_dict in data: width = widths[step_dict['id']] x, y = step_dict['position']['left'], step_dict['position']['top'] @@ -576,18 +586,18 @@ if len(step_dict['data_inputs']) > 0: box_height += 15 sep_y = y + len(step_dict['data_inputs']) * line_px + 40 - text.append( svgfig.Line(x-margin, sep_y, x+width-margin, sep_y).SVG() ) # - + text.append( svgfig.Line(x-margin, sep_y, x+width-margin, sep_y).SVG() ) # + # input/output box boxes.append( svgfig.Rect(x-margin, y+30, x+width-margin, y+30+box_height, fill="#ffffff").SVG() ) - + for conn, output_dict in step_dict['input_connections'].iteritems(): in_coords = in_pos[step_dict['id']][conn] out_conn_pos = out_pos[output_dict['id']][output_dict['output_name']] adjusted = (out_conn_pos[0] + widths[output_dict['id']], out_conn_pos[1]) text.append( svgfig.SVG("circle", cx=out_conn_pos[0]+widths[output_dict['id']]-margin, cy=out_conn_pos[1]-margin, r=5, fill="#ffffff" ) ) connectors.append( svgfig.Line(adjusted[0], adjusted[1]-margin, in_coords[0]-10, in_coords[1], arrow_end="true" ).SVG() ) - + canvas.append(connectors) canvas.append(boxes) canvas.append(text) @@ -597,8 +607,8 @@ canvas['viewBox'] = "0 0 %s %s" % (width, height) trans.response.set_content_type("image/svg+xml") return canvas.standalone_xml() - - + + @web.expose @web.require_login( "use Galaxy workflows" ) def clone( self, trans, id ): @@ -612,7 +622,7 @@ .filter_by( user=user, stored_workflow=stored ).count() == 0: error( "Workflow is not owned by or shared with current user" ) owner = False - + # Clone. new_stored = model.StoredWorkflow() new_stored.name = "Clone of '%s'" % stored.name @@ -629,7 +639,7 @@ new_swta.user_tname = swta.user_tname new_swta.user_value = swta.user_value new_swta.value = swta.value - new_stored.tags.append( new_swta ) + new_stored.tags.append( new_swta ) if not owner: new_stored.name += " shared by '%s'" % stored.user.email new_stored.user = user @@ -640,7 +650,7 @@ # Display the management page trans.set_message( 'Clone created with name "%s"' % new_stored.name ) return self.list( trans ) - + @web.expose @web.require_login( "create workflows" ) def create( self, trans, workflow_name=None, workflow_annotation="" ): @@ -672,12 +682,12 @@ return form( url_for(), "Create New Workflow", submit_text="Create", use_panels=True ) \ .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \ .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." ) - + @web.expose def delete( self, trans, id=None ): """ Mark a workflow as deleted - """ + """ # Load workflow from database stored = self.get_stored_workflow( trans, id ) # Marke as deleted and save @@ -687,7 +697,7 @@ # Display the management page trans.set_message( "Workflow '%s' deleted" % stored.name ) return self.list( trans ) - + @web.expose @web.require_login( "edit workflows" ) def editor( self, trans, id=None ): @@ -700,7 +710,7 @@ error( "Invalid workflow id" ) stored = self.get_stored_workflow( trans, id ) return trans.fill_template( "workflow/editor.mako", stored=stored, annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) ) - + @web.json def editor_form_post( self, trans, type='tool', tool_id=None, annotation=None, **incoming ): """ @@ -709,7 +719,7 @@ This is used for the form shown in the right pane when a node is selected. """ - + trans.workflow_building_mode = True module = module_factory.from_dict( trans, { 'type': type, @@ -717,7 +727,7 @@ 'tool_state': incoming.pop("tool_state") } ) module.update_state( incoming ) - + if type=='tool': return { 'tool_state': module.get_state(), @@ -737,7 +747,7 @@ 'form_html': module.get_config_form(), 'annotation': annotation } - + @web.json def get_new_module_info( self, trans, type, **kwargs ): """ @@ -855,7 +865,7 @@ # post_job_actions pja_dict = {} for pja in step.post_job_actions: - pja_dict[pja.action_type+pja.output_name] = dict(action_type = pja.action_type, + pja_dict[pja.action_type+pja.output_name] = dict(action_type = pja.action_type, output_name = pja.output_name, action_arguments = pja.action_arguments) step_dict['post_job_actions'] = pja_dict @@ -961,7 +971,7 @@ rval = dict( message="Workflow saved" ) rval['name'] = workflow.name return rval - + @web.expose @web.require_login( "use workflows" ) def export( self, trans, id=None, **kwd ): @@ -1014,27 +1024,27 @@ """ Exports a workflow to myExperiment website. """ - - # Load encoded workflow from database + + # Load encoded workflow from database user = trans.get_user() id = trans.security.decode_id( id ) trans.workflow_building_mode = True stored = trans.sa_session.query( model.StoredWorkflow ).get( id ) self.security_check( trans, stored, False, True ) - + # Convert workflow to dict. workflow_dict = self._workflow_to_dict( trans, stored ) - + # # Create and submit workflow myExperiment request. # - + # Create workflow content XML. workflow_dict_packed = simplejson.dumps( workflow_dict, indent=4, sort_keys=True ) workflow_content = trans.fill_template( "workflow/myexp_export_content.mako", \ workflow_dict_packed=workflow_dict_packed, \ workflow_steps=workflow_dict['steps'] ) - + # Create myExperiment request. request_raw = trans.fill_template( "workflow/myexp_export.mako", \ workflow_name=workflow_dict['name'], \ @@ -1043,7 +1053,7 @@ ) # strip() b/c myExperiment XML parser doesn't allow white space before XML; utf-8 handles unicode characters. request = unicode( request_raw.strip(), 'utf-8' ) - + # Do request and get result. auth_header = base64.b64encode( '%s:%s' % ( myexp_username, myexp_password )) headers = { "Content-type": "text/xml", "Accept": "text/xml", "Authorization" : "Basic %s" % auth_header } @@ -1053,7 +1063,7 @@ response = conn.getresponse() response_data = response.read() conn.close() - + # Do simple parse of response to see if export successful and provide user feedback. parser = SingleTagContentsParser( 'id' ) parser.feed( response_data ) @@ -1062,13 +1072,13 @@ if myexp_workflow_id: return trans.show_message( \ "Workflow '%s' successfully exported to myExperiment. %s" % \ - ( stored.name, workflow_list_str ), + ( stored.name, workflow_list_str ), use_panels=True ) else: return trans.show_error_message( \ "Workflow '%s' could not be exported to myExperiment. Error: %s. %s" % \ ( stored.name, response_data, workflow_list_str ), use_panels=True ) - + @web.json_pretty def for_direct_import( self, trans, id ): """ @@ -1087,15 +1097,15 @@ """ Get the latest Workflow for the StoredWorkflow identified by `id` and encode it as a json string that can be imported back into Galaxy - + This has slightly different information than the above. In particular, it does not attempt to decode forms and build UIs, it just stores the raw state. """ - + # Get workflow. stored = self.get_stored_workflow( trans, id, check_ownership=False, check_accessible=True ) - + # Stream workflow to file. stored_dict = self._workflow_to_dict( trans, stored ) valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' @@ -1146,7 +1156,7 @@ workflow_data = None if url: # Load workflow from external URL - # NOTE: blocks the web thread. + # NOTE: blocks the web thread. try: workflow_data = urllib2.urlopen( url ).read() except Exception, e: @@ -1204,9 +1214,9 @@ # A required tool is not available in the local Galaxy instance. # TODO: It would sure be nice to be able to redirect to a mako template here that displays a nice # page including the links to the configured tool sheds instead of this message, but trying - # to get the panels back is a nightmare since workflow eliminates the Galaxy panels. Someone + # to get the panels back is a nightmare since workflow eliminates the Galaxy panels. Someone # involved in workflow development needs to figure out what it will take to be able to switch - # back and forth between Galaxy (with panels ) and the workflow view (without panels ), having + # back and forth between Galaxy (with panels ) and the workflow view (without panels ), having # the Galaxy panels displayed whenever in Galaxy. message += "The workflow requires the following tools that are not available in this Galaxy instance." message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>" @@ -1222,7 +1232,7 @@ message += '<a href="%s">%s</a><br/>' % ( url, shed_name ) status = 'error' if installed_repository_file or tool_shed_url: - # Another Galaxy panels Hack: The request did not originate from the Galaxy + # Another Galaxy panels Hack: The request did not originate from the Galaxy # workflow view, so we don't need to render the Galaxy panels. action = 'center' else: @@ -1275,13 +1285,13 @@ if issubclass( base, Data ): types.add( base.__module__ + "." + base.__name__ ) visit_bases( types, base ) - for c in classes: + for c in classes: n = c.__module__ + "." + c.__name__ types = set( [ n ] ) visit_bases( types, c ) class_to_classes[ n ] = dict( ( t, True ) for t in types ) return dict( ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes ) - + @web.expose def build_from_current_history( self, trans, job_ids=None, dataset_ids=None, workflow_name=None ): user = trans.get_user() @@ -1292,7 +1302,7 @@ jobs, warnings = get_job_dict( trans ) # Render return trans.fill_template( - "workflow/build_from_current_history.mako", + "workflow/build_from_current_history.mako", jobs=jobs, warnings=warnings, history=history ) @@ -1310,7 +1320,7 @@ job_ids = [ int( id ) for id in job_ids ] dataset_ids = [ int( id ) for id in dataset_ids ] # Find each job, for security we (implicately) check that they are - # associated witha job in the current history. + # associated witha job in the current history. jobs, warnings = get_job_dict( trans ) jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() ) steps = [] @@ -1351,7 +1361,7 @@ conn.output_step = other_step conn.output_name = other_name steps.append( step ) - steps_by_job_id[ job_id ] = step + steps_by_job_id[ job_id ] = step # Store created dataset hids for assoc in job.output_datasets: hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name ) @@ -1380,8 +1390,8 @@ # Index page with message return trans.show_message( "Workflow '%s' created from current history." % workflow_name ) ## return trans.show_ok_message( "<p>Workflow '%s' created.</p><p><a target='_top' href='%s'>Click to load in workflow editor</a></p>" - ## % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) ) - + ## % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) ) + @web.expose def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ): stored = self.get_stored_workflow( trans, id, check_ownership=False ) @@ -1589,8 +1599,8 @@ trans.set_history(saved_history) def get_item( self, trans, id ): - return self.get_stored_workflow( trans, id ) - + return self.get_stored_workflow( trans, id ) + @web.expose def tag_outputs( self, trans, id, **kwargs ): stored = self.get_stored_workflow( trans, id, check_ownership=False ) @@ -1644,7 +1654,7 @@ has_upgrade_messages = True # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) - step.module.add_dummy_datasets( connections=step.input_connections ) + step.module.add_dummy_datasets( connections=step.input_connections ) # Store state with the step step.state = step.module.state # Error dict @@ -1665,7 +1675,7 @@ has_upgrade_messages=has_upgrade_messages, errors=errors, incoming=kwargs ) - + @web.expose def configure_menu( self, trans, workflow_ids=None ): user = trans.get_user() @@ -1693,7 +1703,7 @@ user.stored_workflow_menu_entries.append( m ) sess.flush() return trans.show_message( "Menu updated", refresh_frames=['tools'] ) - else: + else: user = trans.get_user() ids_in_menu = set( [ x.stored_workflow_id for x in user.stored_workflow_menu_entries ] ) workflows = trans.sa_session.query( model.StoredWorkflow ) \ @@ -1709,7 +1719,7 @@ workflows=workflows, shared_by_others=shared_by_others, ids_in_menu=ids_in_menu ) - + def _workflow_to_dict( self, trans, stored ): """ Converts a workflow to a dict of attributes suitable for exporting. @@ -1734,7 +1744,7 @@ step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) annotation_str = "" if step_annotation: - annotation_str = step_annotation.annotation + annotation_str = step_annotation.annotation # Step info step_dict = { 'id': step.order_index, @@ -1752,7 +1762,7 @@ if module.type == 'tool': pja_dict = {} for pja in step.post_job_actions: - pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, + pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, output_name = pja.output_name, action_arguments = pja.action_arguments ) step_dict[ 'post_job_actions' ] = pja_dict @@ -1868,8 +1878,8 @@ # Unpack and add post-job actions. post_job_actions = step_dict.get( 'post_job_actions', {} ) for name, pja_dict in post_job_actions.items(): - pja = PostJobAction( pja_dict[ 'action_type' ], - step, pja_dict[ 'output_name' ], + pja = PostJobAction( pja_dict[ 'action_type' ], + step, pja_dict[ 'output_name' ], pja_dict[ 'action_arguments' ] ) # Second pass to deal with connections between steps for step in steps: @@ -1894,7 +1904,7 @@ trans.sa_session.add( stored ) trans.sa_session.flush() return stored, missing_tool_tups - + ## ---- Utility methods ------------------------------------------------------- def attach_ordered_steps( workflow, steps ): @@ -1937,13 +1947,13 @@ return [ steps[i] for i in node_order ] except CycleError: return None - + def order_workflow_steps_with_levels( steps ): try: return topsort_levels( edgelist_for_workflow_steps( steps ) ) except CycleError: return None - + class FakeJob( object ): """ Fake job object for datasets that have no creating_job_associations, @@ -1952,7 +1962,7 @@ def __init__( self, dataset ): self.is_fake = True self.id = "fake_%s" % dataset.id - + def get_job_dict( trans ): """ Return a dictionary of Job -> [ Dataset ] mappings, for all finished @@ -1967,22 +1977,22 @@ if dataset.state in ( 'new', 'running', 'queued' ): warnings.add( "Some datasets still queued or running were ignored" ) continue - + #if this hda was copied from another, we need to find the job that created the origial hda job_hda = dataset while job_hda.copied_from_history_dataset_association: job_hda = job_hda.copied_from_history_dataset_association - + if not job_hda.creating_job_associations: jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] - + for assoc in job_hda.creating_job_associations: job = assoc.job if job in jobs: jobs[ job ].append( ( assoc.name, dataset ) ) else: jobs[ job ] = [ ( assoc.name, dataset ) ] - return jobs, warnings + return jobs, warnings def cleanup_param_values( inputs, values ): """ @@ -2015,7 +2025,7 @@ key = prefix + key + "_" for k in root_values.keys(): if k.startswith( key ): - del root_values[k] + del root_values[k] elif isinstance( input, Repeat ): group_values = values[key] for i, rep_values in enumerate( group_values ): @@ -2029,4 +2039,4 @@ cleanup( prefix, input.cases[current_case].inputs, group_values ) cleanup( "", inputs, values ) return associations - + diff -r 50bf77aa34c3689a122187d7ba9b55deb348df92 -r 3b2acb89495bee2355f20fc3954baa174d486a3c templates/workflow/list.mako --- a/templates/workflow/list.mako +++ b/templates/workflow/list.mako @@ -103,6 +103,7 @@ <a class="action-button" href="${h.url_for( controller='workflow', action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug )}" target="_top">View</a><a class="action-button" href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">Run</a><a class="action-button" href="${h.url_for( controller='workflow', action='clone', id=trans.security.encode_id( workflow.id ) )}">Clone</a> + <a class="action-button" confirm="Are you sure you want to remove the shared workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( controller='workflow', action='sharing', unshare_me=True, id=trans.security.encode_id( workflow.id ))}">Remove</a></div></td></tr> https://bitbucket.org/galaxy/galaxy-central/changeset/0a001dea3613/ changeset: 0a001dea3613 user: dannon date: 2012-02-02 20:55:19 summary: Merge. affected #: 7 files diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -96,7 +96,7 @@ self.retry_job_output_collection = int( kwargs.get( 'retry_job_output_collection', 0 ) ) self.job_walltime = kwargs.get( 'job_walltime', None ) self.admin_users = kwargs.get( "admin_users", "" ) - self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join(a)bx.psu.edu") + self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.smtp_username = kwargs.get( 'smtp_username', None ) diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -196,7 +196,6 @@ if job_wrapper.get_state() == model.Job.states.DELETED: log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() ) if self.app.config.cleanup_job in ( "always", "onsuccess" ): - self.cleanup( ( ofile, efile, jt.remoteCommand ) ) job_wrapper.cleanup() return @@ -334,25 +333,12 @@ except: log.exception("Job wrapper finish method failed") - # clean up the drm files - if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" ): - self.cleanup( ( ofile, efile, job_file ) ) - def fail_job( self, drm_job_state ): """ Seperated out so we can use the worker threads for it. """ self.stop_job( self.sa_session.query( self.app.model.Job ).get( drm_job_state.job_wrapper.job_id ) ) drm_job_state.job_wrapper.fail( drm_job_state.fail_message ) - if self.app.config.cleanup_job == "always": - self.cleanup( ( drm_job_state.ofile, drm_job_state.efile, drm_job_state.job_file ) ) - - def cleanup( self, files ): - for file in files: - try: - os.unlink( file ) - except Exception, e: - log.warning( "Unable to cleanup: %s" % str( e ) ) def put( self, job_wrapper ): """Add a job to the queue (by job identifier)""" @@ -440,6 +426,6 @@ # The expected output is a single line containing a single numeric value: # the DRMAA job-ID. If not the case, will throw an error. jobId = stdoutdata - return jobId; + return jobId diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -68,7 +68,7 @@ self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/community" ), self.root ) self.admin_users = kwargs.get( "admin_users", "" ) self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") - self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join(a)bx.psu.edu") + self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.smtp_username = kwargs.get( 'smtp_username', None ) diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 lib/galaxy/webapps/demo_sequencer/config.py --- a/lib/galaxy/webapps/demo_sequencer/config.py +++ b/lib/galaxy/webapps/demo_sequencer/config.py @@ -45,7 +45,7 @@ self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/demo_sequencer" ), self.root ) self.admin_users = kwargs.get( "admin_users", "" ) self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") - self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join(a)bx.psu.edu") + self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -72,6 +72,8 @@ <% subscribe_check_box.checked = True %> %endif ${subscribe_check_box.get_html()} + <p>See <a href="http://galaxyproject.org/wiki/Mailing%20Lists" target="_blank"> + all Galaxy project mailing lists</a>.</p></div> %endif %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1: diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 tools/variant_detection/freebayes.xml --- a/tools/variant_detection/freebayes.xml +++ b/tools/variant_detection/freebayes.xml @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="freebayes" name="FreeBayes" version="0.0.1"> +<tool id="freebayes" name="FreeBayes" version="0.0.2"><requirements><requirement type="package" version="0.9.4">freebayes</requirement><requirement type="package">samtools</requirement> @@ -29,11 +29,17 @@ ##outputs --vcf "${output_vcf}" - --trace "${output_trace}" - --failed-alleles "${output_failed_alleles_bed}" ##advanced options #if str( $options_type.options_type_selector ) == "advanced": + ##additional outputs + #if $options_type.output_trace_option: + --trace "${output_trace}" + #end if + #if $options_type.output_failed_alleles_option: + --failed-alleles "${output_failed_alleles_bed}" + #end if + ##additional inputs #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file": --targets "${options_type.target_limit_type.input_target_bed}" @@ -186,8 +192,13 @@ </when><when value="advanced"> - -  + +  + <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" /> + <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" /> + + + <conditional name="target_limit_type"><param name="target_limit_type_selector" type="select" label="Limit analysis to listed targets"><option value="do_not_limit" selected="True">Do not limit</option> @@ -398,8 +409,12 @@ </inputs><outputs><data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" /> - <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)" /> - <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)" /> + <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)"> + <filter>options_type['options_type_selector'] == "advanced" and options_type['output_failed_alleles_option'] is True</filter> + </data> + <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)"> + <filter>options_type['options_type_selector'] == "advanced" and options_type['output_trace_option'] is True</filter> + </data></outputs><tests><test> @@ -408,8 +423,8 @@ <param name="input_bam" ftype="bam" value="gatk/fake_phiX_reads_1.bam"/><param name="options_type_selector" value="basic"/><output name="output_vcf" file="variant_detection/freebayes/freebayes_out_1.vcf.contains" compare="contains"/> - <output name="output_trace" file="variant_detection/freebayes/freebayes_out_1.output_trace" /> - <output name="output_failed_alleles_bed" file="empty_file.dat" /> + </test></tests><help> diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -205,7 +205,7 @@ # On the user registration form, users may choose to join the mailing list. # This is the address of the list they'll be subscribed to. -#mailing_join_addr = galaxy-user-join(a)bx.psu.edu +#mailing_join_addr = galaxy-announce-join(a)bx.psu.edu # Datasets in an error state include a link to report the error. Those reports # will be sent to this address. Error reports are disabled if no address is set. 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: clements: Changed the default new user mailing list from galaxy-user to galaxy-announce, which is a much lower volume. Also added text to link to wiki page with all mailing lists.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/eadc91223171/ changeset: eadc91223171 user: clements date: 2012-02-02 06:25:41 summary: Changed the default new user mailing list from galaxy-user to galaxy-announce, which is a much lower volume. Also added text to link to wiki page with all mailing lists. affected #: 5 files diff -r 238207122b68e961dac14238fe1af0a585a9e903 -r eadc91223171926a699f5f34ce088be2a9e17783 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -96,7 +96,7 @@ self.retry_job_output_collection = int( kwargs.get( 'retry_job_output_collection', 0 ) ) self.job_walltime = kwargs.get( 'job_walltime', None ) self.admin_users = kwargs.get( "admin_users", "" ) - self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join(a)bx.psu.edu") + self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.smtp_username = kwargs.get( 'smtp_username', None ) diff -r 238207122b68e961dac14238fe1af0a585a9e903 -r eadc91223171926a699f5f34ce088be2a9e17783 lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -68,7 +68,7 @@ self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/community" ), self.root ) self.admin_users = kwargs.get( "admin_users", "" ) self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") - self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join(a)bx.psu.edu") + self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.smtp_username = kwargs.get( 'smtp_username', None ) diff -r 238207122b68e961dac14238fe1af0a585a9e903 -r eadc91223171926a699f5f34ce088be2a9e17783 lib/galaxy/webapps/demo_sequencer/config.py --- a/lib/galaxy/webapps/demo_sequencer/config.py +++ b/lib/galaxy/webapps/demo_sequencer/config.py @@ -45,7 +45,7 @@ self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/demo_sequencer" ), self.root ) self.admin_users = kwargs.get( "admin_users", "" ) self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") - self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join(a)bx.psu.edu") + self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) diff -r 238207122b68e961dac14238fe1af0a585a9e903 -r eadc91223171926a699f5f34ce088be2a9e17783 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -72,6 +72,8 @@ <% subscribe_check_box.checked = True %> %endif ${subscribe_check_box.get_html()} + <p>See <a href="http://galaxyproject.org/wiki/Mailing%20Lists" target="_blank"> + all Galaxy project mailing lists</a>.</p></div> %endif %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1: diff -r 238207122b68e961dac14238fe1af0a585a9e903 -r eadc91223171926a699f5f34ce088be2a9e17783 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -205,7 +205,7 @@ # On the user registration form, users may choose to join the mailing list. # This is the address of the list they'll be subscribed to. -#mailing_join_addr = galaxy-user-join(a)bx.psu.edu +#mailing_join_addr = galaxy-announce-join(a)bx.psu.edu # Datasets in an error state include a link to report the error. Those reports # will be sent to this address. Error reports are disabled if no address is set. 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: DRMAA runner no longer needs to clean up its stdout/stderr since they live in the working directory which is cleaned up by the job wrapper.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/238207122b68/ changeset: 238207122b68 user: natefoo date: 2012-02-02 19:25:59 summary: DRMAA runner no longer needs to clean up its stdout/stderr since they live in the working directory which is cleaned up by the job wrapper. affected #: 1 file diff -r 37e787787128662a1aba3c6c831f9dabc9de3289 -r 238207122b68e961dac14238fe1af0a585a9e903 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -196,7 +196,6 @@ if job_wrapper.get_state() == model.Job.states.DELETED: log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() ) if self.app.config.cleanup_job in ( "always", "onsuccess" ): - self.cleanup( ( ofile, efile, jt.remoteCommand ) ) job_wrapper.cleanup() return @@ -334,25 +333,12 @@ except: log.exception("Job wrapper finish method failed") - # clean up the drm files - if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" ): - self.cleanup( ( ofile, efile, job_file ) ) - def fail_job( self, drm_job_state ): """ Seperated out so we can use the worker threads for it. """ self.stop_job( self.sa_session.query( self.app.model.Job ).get( drm_job_state.job_wrapper.job_id ) ) drm_job_state.job_wrapper.fail( drm_job_state.fail_message ) - if self.app.config.cleanup_job == "always": - self.cleanup( ( drm_job_state.ofile, drm_job_state.efile, drm_job_state.job_file ) ) - - def cleanup( self, files ): - for file in files: - try: - os.unlink( file ) - except Exception, e: - log.warning( "Unable to cleanup: %s" % str( e ) ) def put( self, job_wrapper ): """Add a job to the queue (by job identifier)""" @@ -440,6 +426,6 @@ # The expected output is a single line containing a single numeric value: # the DRMAA job-ID. If not the case, will throw an error. jobId = stdoutdata - return jobId; + return jobId 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: FreeBayes: make trace and failed alleles outputs optional.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/19c4b36d6981/ changeset: 19c4b36d6981 user: dan date: 2012-02-02 17:05:05 summary: FreeBayes: make trace and failed alleles outputs optional. affected #: 1 file diff -r 50bf77aa34c3689a122187d7ba9b55deb348df92 -r 19c4b36d6981ab6d938167a7a6237f41425d6cb5 tools/variant_detection/freebayes.xml --- a/tools/variant_detection/freebayes.xml +++ b/tools/variant_detection/freebayes.xml @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="freebayes" name="FreeBayes" version="0.0.1"> +<tool id="freebayes" name="FreeBayes" version="0.0.2"><requirements><requirement type="package" version="0.9.4">freebayes</requirement><requirement type="package">samtools</requirement> @@ -29,11 +29,17 @@ ##outputs --vcf "${output_vcf}" - --trace "${output_trace}" - --failed-alleles "${output_failed_alleles_bed}" ##advanced options #if str( $options_type.options_type_selector ) == "advanced": + #additional outputs + #if $options_type.output_trace_option: + --trace "${output_trace}" + #end if + #if $options_type.output_failed_alleles_option: + --failed-alleles "${output_failed_alleles_bed}" + #end if + ##additional inputs #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file": --targets "${options_type.target_limit_type.input_target_bed}" @@ -186,8 +192,13 @@ </when><when value="advanced"> - -  + +  + <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" /> + <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" /> + + + <conditional name="target_limit_type"><param name="target_limit_type_selector" type="select" label="Limit analysis to listed targets"><option value="do_not_limit" selected="True">Do not limit</option> @@ -398,8 +409,12 @@ </inputs><outputs><data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" /> - <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)" /> - <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)" /> + <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)"> + <filter>options_type['options_type_selector'] == "advanced" and options_type['output_failed_alleles_option'] is True</filter> + </data> + <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)"> + <filter>options_type['options_type_selector'] == "advanced" and options_type['output_trace_option'] is True</filter> + </data></outputs><tests><test> @@ -408,8 +423,8 @@ <param name="input_bam" ftype="bam" value="gatk/fake_phiX_reads_1.bam"/><param name="options_type_selector" value="basic"/><output name="output_vcf" file="variant_detection/freebayes/freebayes_out_1.vcf.contains" compare="contains"/> - <output name="output_trace" file="variant_detection/freebayes/freebayes_out_1.output_trace" /> - <output name="output_failed_alleles_bed" file="empty_file.dat" /> + </test></tests><help> 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: dannon: History export - now works for a guest user.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/50bf77aa34c3/ changeset: 50bf77aa34c3 user: dannon date: 2012-02-02 16:51:13 summary: History export - now works for a guest user. affected #: 1 file diff -r 62c2a2f9142c11d1ae279ce3af395bd4fb0d4c52 -r 50bf77aa34c3689a122187d7ba9b55deb348df92 lib/galaxy/tools/actions/history_imp_exp.py --- a/lib/galaxy/tools/actions/history_imp_exp.py +++ b/lib/galaxy/tools/actions/history_imp_exp.py @@ -9,7 +9,7 @@ class ImportHistoryToolAction( ToolAction ): """Tool action used for importing a history to an archive. """ - def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None ): + def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None ): # # Create job. # @@ -20,43 +20,43 @@ job.user_id = trans.user.id start_job_state = job.state #should be job.states.NEW job.state = job.states.WAITING #we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters - trans.sa_session.add( job ) + trans.sa_session.add( job ) trans.sa_session.flush() #ensure job.id are available - + # # Setup job and job wrapper. # - + # Add association for keeping track of job, history relationship. - - # Use abspath because mkdtemp() does not, contrary to the documentation, + + # Use abspath because mkdtemp() does not, contrary to the documentation, # always return an absolute path. archive_dir = os.path.abspath( tempfile.mkdtemp() ) jiha = trans.app.model.JobImportHistoryArchive( job=job, archive_dir=archive_dir ) trans.sa_session.add( jiha ) job_wrapper = JobImportHistoryArchiveWrapper( job ) - + # # Add parameters to job_parameter table. # - + # Set additional parameters. incoming[ '__DEST_DIR__' ] = jiha.archive_dir for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): job.add_parameter( name, value ) - + job.state = start_job_state #job inputs have been configured, restore initial job state trans.sa_session.flush() # Queue the job for execution trans.app.job_queue.put( job.id, tool ) trans.log_event( "Added import history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) - + return job, odict() class ExportHistoryToolAction( ToolAction ): """Tool action used for exporting a history to an archive. """ - + def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None ): # # Get history to export. @@ -68,10 +68,10 @@ history = value del incoming[ history_param_name ] break - + if not history: raise Exception( 'There is no history to export.' ) - + # # Create the job and output dataset objects # @@ -79,22 +79,24 @@ job.session_id = trans.get_galaxy_session().id job.history_id = trans.history.id job.tool_id = tool.id - job.user_id = trans.user.id + if trans.user: + # If this is an actual user, run the job as that individual. Otherwise we're running as guest. + job.user_id = trans.user.id start_job_state = job.state #should be job.states.NEW job.state = job.states.WAITING #we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters trans.sa_session.add( job ) - + # Create dataset that will serve as archive. archive_dataset = trans.app.model.Dataset() trans.sa_session.add( archive_dataset ) - + trans.sa_session.flush() #ensure job.id and archive_dataset.id are available trans.app.object_store.create( archive_dataset ) # set the object store id, create dataset (if applicable) - + # # Setup job and job wrapper. # - + # Add association for keeping track of job, history, archive relationship. jeha = trans.app.model.JobExportHistoryArchive( job=job, history=history, \ dataset=archive_dataset, \ @@ -104,23 +106,23 @@ job_wrapper = JobExportHistoryArchiveWrapper( job ) cmd_line = job_wrapper.setup_job( trans, jeha, include_hidden=incoming[ 'include_hidden' ], \ include_deleted=incoming[ 'include_deleted' ] ) - + # # Add parameters to job_parameter table. # - + # Set additional parameters. incoming[ '__HISTORY_TO_EXPORT__' ] = history.id incoming[ '__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__' ] = cmd_line for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): job.add_parameter( name, value ) - + job.state = start_job_state #job inputs have been configured, restore initial job state trans.sa_session.flush() - - + + # Queue the job for execution trans.app.job_queue.put( job.id, tool ) trans.log_event( "Added export history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) - + return job, odict() 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: dannon: History Size wasn't filtering out 'purged' datasets in the summary size, should now reflect accurate total on disk.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/62c2a2f9142c/ changeset: 62c2a2f9142c user: dannon date: 2012-02-02 16:17:25 summary: History Size wasn't filtering out 'purged' datasets in the summary size, should now reflect accurate total on disk. affected #: 1 file diff -r 3fdaa5c7d5270564ea55b4c5997dde8c1c00a6e8 -r 62c2a2f9142c11d1ae279ce3af395bd4fb0d4c52 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -475,6 +475,7 @@ db_session = object_session( self ) rval = db_session.query( func.sum( db_session.query( HistoryDatasetAssociation.dataset_id, Dataset.total_size ).join( Dataset ) .filter( HistoryDatasetAssociation.table.c.history_id == self.id ) + .filter( Dataset.purged != True ) .distinct().subquery().c.total_size ) ).first()[0] if rval is None: rval = 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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commit/galaxy-central: jgoecks: Update version support information in Cuff* wrappers.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3fdaa5c7d527/ changeset: 3fdaa5c7d527 user: jgoecks date: 2012-02-02 16:03:02 summary: Update version support information in Cuff* wrappers. affected #: 4 files diff -r 93520b875b56905f50dd7de2b09bab189f2429ad -r 3fdaa5c7d5270564ea55b4c5997dde8c1c00a6e8 tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cuffcompare" name="Cuffcompare" version="0.0.5"> -  + <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description><requirements><requirement type="package">cufflinks</requirement> diff -r 93520b875b56905f50dd7de2b09bab189f2429ad -r 3fdaa5c7d5270564ea55b4c5997dde8c1c00a6e8 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cuffdiff" name="Cuffdiff" version="0.0.5"> -  + <description>find significant changes in transcript expression, splicing, and promoter use</description><requirements><requirement type="package">cufflinks</requirement> diff -r 93520b875b56905f50dd7de2b09bab189f2429ad -r 3fdaa5c7d5270564ea55b4c5997dde8c1c00a6e8 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cufflinks" name="Cufflinks" version="0.0.5"> -  + <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description><requirements><requirement type="package">cufflinks</requirement> diff -r 93520b875b56905f50dd7de2b09bab189f2429ad -r 3fdaa5c7d5270564ea55b4c5997dde8c1c00a6e8 tools/ngs_rna/cuffmerge_wrapper.xml --- a/tools/ngs_rna/cuffmerge_wrapper.xml +++ b/tools/ngs_rna/cuffmerge_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cuffmerge" name="Cuffmerge" version="0.0.5"> -  + <description>merge together several Cufflinks assemblies</description><requirements><requirement type="package">cufflinks</requirement> 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: Add num_threads parameter to cuffmerge wrapper script.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/93520b875b56/ changeset: 93520b875b56 user: jgoecks date: 2012-02-02 15:26:01 summary: Add num_threads parameter to cuffmerge wrapper script. affected #: 1 file diff -r 63bc8824dae5d8ab8cf45d86226fcd7f0508f46b -r 93520b875b56905f50dd7de2b09bab189f2429ad tools/ngs_rna/cuffmerge_wrapper.py --- a/tools/ngs_rna/cuffmerge_wrapper.py +++ b/tools/ngs_rna/cuffmerge_wrapper.py @@ -25,6 +25,8 @@ parser = optparse.OptionParser() parser.add_option( '-g', dest='ref_annotation', help='An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.' ) parser.add_option( '-s', dest='use_seq_data', action="store_true", help='Causes cuffmerge to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.') + parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' ) + # Wrapper / Galaxy options. parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) @@ -74,6 +76,8 @@ cmd = "cuffmerge -o cm_output " # Add options. + if options.num_threads: + cmd += ( " -p %i" % int ( options.num_threads ) ) if options.ref_annotation: cmd += " -g %s " % options.ref_annotation if options.use_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: jgoecks: Add num-threads param to cuffdiff.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/63bc8824dae5/ changeset: 63bc8824dae5 user: jgoecks date: 2012-02-02 15:15:19 summary: Add num-threads param to cuffdiff. affected #: 1 file diff -r 724bbcc69c921ebe53b780d04f2699178201941e -r 63bc8824dae5d8ab8cf45d86226fcd7f0508f46b tools/ngs_rna/cuffmerge_wrapper.xml --- a/tools/ngs_rna/cuffmerge_wrapper.xml +++ b/tools/ngs_rna/cuffmerge_wrapper.xml @@ -5,7 +5,9 @@ <requirement type="package">cufflinks</requirement></requirements><command interpreter="python"> - cuffmerge_wrapper.py + cuffmerge_wrapper.py + + --num-threads="4" ## Use annotation reference? #if $annotation.use_ref_annotation == "Yes": 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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