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September 2012

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commit/galaxy-central: carlfeberhard: historyPanel: temp fix for 2 line tooltips when placement = 'above'
by Bitbucket 11 Sep '12

11 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/63cd6402bada/ changeset: 63cd6402bada user: carlfeberhard date: 2012-09-11 17:46:15 summary: historyPanel: temp fix for 2 line tooltips when placement = 'above' affected #: 1 file diff -r 6568368038dc220ce1f66d5566570f32633055d9 -r 63cd6402badaf98f26080e71b1f0ed49db30e3ab templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -45,7 +45,7 @@ error: function() { alert( "Tagging failed" ) }, success: function(tag_elt_html) { tag_elt.html(tag_elt_html); - tag_elt.find(".tooltip").tooltip(); + tag_elt.find(".tooltip").tooltip({ placement : 'bottom' }); tag_area.slideDown("fast"); } }); @@ -86,7 +86,7 @@ annotation = "<em>Describe or add notes to dataset</em>"; } annotation_elt.html(annotation); - annotation_area.find(".tooltip").tooltip(); + annotation_area.find(".tooltip").tooltip({ placement : 'bottom' }); async_save_text( annotation_elt.attr("id"), annotation_elt.attr("id"), "${h.url_for( controller='/dataset', action='annotate_async')}?" + href_parms, @@ -229,6 +229,25 @@ tag_handling(this); annotation_handling(this); + + //TODO: hack (github has an issue on this - see how it's resolved) + // fix for two line bootstrap tooltips when placement: above + $( this ).find( '.tooltip' ).each( function(){ + console.debug( 'tooltip:', this ); + var $this = $( this ); + + // documented method - that doesn't seem to work + //$( this ).tooltip( 'destroy' ); + + $this.data( 'tooltip', false ); + var title = $this.attr( 'data-original-title' ); + $this.attr( 'data-original-title', null ); + $this.attr( 'title', title ); + + // place them on the bottom for now + $this.tooltip({ placement : 'bottom' }); + }); + }); // Trackster links Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 10 Sep '12

10 Sep '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ef7f11e99547/ changeset: ef7f11e99547 user: james_taylor date: 2012-09-10 23:09:09 summary: circster: Allow data_standalone types to work; phyloviz: add tree datatypes to sample conf affected #: 2 files diff -r 6e79399b38d22512d8438522d26945c53f95b11a -r ef7f11e995473293a2e45f5517a627ad7177a3b1 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -198,6 +198,10 @@ <display file="igv/vcf.xml" /><converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/></datatype> +  + <datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true" /> + <datatype extension="nhx" type="galaxy.datatypes.data:Newick" display_in_upload="true" /> + <datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true" /><datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/> diff -r 6e79399b38d22512d8438522d26945c53f95b11a -r ef7f11e995473293a2e45f5517a627ad7177a3b1 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -553,11 +553,14 @@ # Get dataset and indexed datatype. dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) data_sources = self._get_datasources( trans, dataset ) - indexed_type = data_sources['index']['name'] - - # Get converted dataset and append track's genome data. - converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) - data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) + if 'data_standalone' in data_sources: + indexed_type = data_sources['data_standalone']['name'] + data_provider = get_data_provider( indexed_type )( dataset ) + else: + indexed_type = data_sources['index']['name'] + # Get converted dataset and append track's genome data. + converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) + data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) # HACK: pass in additional params, which are only used for summary tree data, not BBI data. track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=3, detail_cutoff=0, draw_cutoff=0 ) } https://bitbucket.org/galaxy/galaxy-central/changeset/c71026b3d7ac/ changeset: c71026b3d7ac user: james_taylor date: 2012-09-10 23:40:56 summary: circster: render in entire window, ensure initially entire plot fits in view and is centered affected #: 2 files diff -r ef7f11e995473293a2e45f5517a627ad7177a3b1 -r c71026b3d7ac3c01ed6ee5350962de96b6ca47dd static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -823,26 +823,27 @@ className: 'circster', initialize: function(options) { - this.width = options.width; - this.height = options.height; this.total_gap = options.total_gap; this.genome = options.genome; this.dataset_arc_height = options.dataset_arc_height; this.track_gap = 5; - - // Compute radius start based on model. - this.radius_start = this.width/2 - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap); }, render: function() { var self = this, - dataset_arc_height = this.dataset_arc_height; + dataset_arc_height = this.dataset_arc_height, + width = self.$el.width(), + height = self.$el.height(), + // Compute radius start based on model, will be centered + // and fit entirely inside element by default + init_radius_start = ( Math.min(width,height)/2 + - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) ); // Set up SVG element. var svg = d3.select(self.$el[0]) .append("svg") - .attr("width", self.width) - .attr("height", self.height) + .attr("width", width) + .attr("height", height) .attr("pointer-events", "all") // Set up zooming, dragging. .append('svg:g') @@ -851,14 +852,14 @@ "translate(" + d3.event.translate + ")" + " scale(" + d3.event.scale + ")"); })) - .attr("transform", "translate(" + self.width / 2 + "," + self.height / 2 + ")") + .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") .append('svg:g') // -- Render each dataset in the visualization. -- this.model.get('tracks').each(function(track, index) { var dataset = track.get('genome_wide_data'), - radius_start = self.radius_start + index * (dataset_arc_height + self.track_gap), + radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap), // Layout chromosome arcs. layout_class = (dataset instanceof GenomeWideBigWigData ? CircsterBigWigLayout : CircsterSummaryTreeLayout ), arcs_layout = new layout_class({ diff -r ef7f11e995473293a2e45f5517a627ad7177a3b1 -r c71026b3d7ac3c01ed6ee5350962de96b6ca47dd templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -69,8 +69,7 @@ var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }')) visualization = new GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')), viz_view = new CircsterView({ - width: 700, - height: 700, + el: $('#vis'), // Gap is difficult to set because it very dependent on chromosome size and organization. total_gap: 2 * Math.PI * 0.1, genome: genome, @@ -81,7 +80,7 @@ // -- Render viz. -- viz_view.render(); - $('#vis').append(viz_view.$el); + }); </script></%def> https://bitbucket.org/galaxy/galaxy-central/changeset/6568368038dc/ changeset: 6568368038dc user: james_taylor date: 2012-09-10 23:41:20 summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central affected #: 4 files diff -r 04cd4894e8406028c6acfd521cbcef7a396748b2 -r 6568368038dc220ce1f66d5566570f32633055d9 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -198,6 +198,10 @@ <display file="igv/vcf.xml" /><converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/></datatype> +  + <datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true" /> + <datatype extension="nhx" type="galaxy.datatypes.data:Newick" display_in_upload="true" /> + <datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true" /><datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/> diff -r 04cd4894e8406028c6acfd521cbcef7a396748b2 -r 6568368038dc220ce1f66d5566570f32633055d9 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -553,11 +553,14 @@ # Get dataset and indexed datatype. dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) data_sources = self._get_datasources( trans, dataset ) - indexed_type = data_sources['index']['name'] - - # Get converted dataset and append track's genome data. - converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) - data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) + if 'data_standalone' in data_sources: + indexed_type = data_sources['data_standalone']['name'] + data_provider = get_data_provider( indexed_type )( dataset ) + else: + indexed_type = data_sources['index']['name'] + # Get converted dataset and append track's genome data. + converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) + data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) # HACK: pass in additional params, which are only used for summary tree data, not BBI data. track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) } diff -r 04cd4894e8406028c6acfd521cbcef7a396748b2 -r 6568368038dc220ce1f66d5566570f32633055d9 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -823,26 +823,27 @@ className: 'circster', initialize: function(options) { - this.width = options.width; - this.height = options.height; this.total_gap = options.total_gap; this.genome = options.genome; this.dataset_arc_height = options.dataset_arc_height; this.track_gap = 5; - - // Compute radius start based on model. - this.radius_start = this.width/2 - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap); }, render: function() { var self = this, - dataset_arc_height = this.dataset_arc_height; + dataset_arc_height = this.dataset_arc_height, + width = self.$el.width(), + height = self.$el.height(), + // Compute radius start based on model, will be centered + // and fit entirely inside element by default + init_radius_start = ( Math.min(width,height)/2 + - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) ); // Set up SVG element. var svg = d3.select(self.$el[0]) .append("svg") - .attr("width", self.width) - .attr("height", self.height) + .attr("width", width) + .attr("height", height) .attr("pointer-events", "all") // Set up zooming, dragging. .append('svg:g') @@ -851,14 +852,14 @@ "translate(" + d3.event.translate + ")" + " scale(" + d3.event.scale + ")"); })) - .attr("transform", "translate(" + self.width / 2 + "," + self.height / 2 + ")") + .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") .append('svg:g') // -- Render each dataset in the visualization. -- this.model.get('tracks').each(function(track, index) { var dataset = track.get('genome_wide_data'), - radius_start = self.radius_start + index * (dataset_arc_height + self.track_gap), + radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap), // Layout chromosome arcs. layout_class = (dataset instanceof GenomeWideBigWigData ? CircsterBigWigLayout : CircsterSummaryTreeLayout ), arcs_layout = new layout_class({ diff -r 04cd4894e8406028c6acfd521cbcef7a396748b2 -r 6568368038dc220ce1f66d5566570f32633055d9 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -69,8 +69,7 @@ var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }')) visualization = new GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')), viz_view = new CircsterView({ - width: 700, - height: 700, + el: $('#vis'), // Gap is difficult to set because it very dependent on chromosome size and organization. total_gap: 2 * Math.PI * 0.1, genome: genome, @@ -81,7 +80,7 @@ // -- Render viz. -- viz_view.render(); - $('#vis').append(viz_view.$el); + }); </script></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Bug fixes for pgcleanup.py
by Bitbucket 10 Sep '12

10 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/04cd4894e840/ changeset: 04cd4894e840 user: natefoo date: 2012-09-10 22:59:33 summary: Bug fixes for pgcleanup.py affected #: 1 file diff -r 4e69bc5d9e1e02074de22cc6e809c33f3462f587 -r 04cd4894e8406028c6acfd521cbcef7a396748b2 scripts/cleanup_datasets/pgcleanup.py --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -25,6 +25,7 @@ import galaxy.config +from galaxy.exceptions import ObjectNotFound from galaxy.objectstore import build_object_store_from_config from galaxy.util.bunch import Bunch @@ -60,6 +61,7 @@ parser.add_option('-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default=default_config) parser.add_option('-d', '--debug', action='store_true', dest='debug', help='Enable debug logging', default=False) parser.add_option('--dry-run', action='store_true', dest='dry_run', help="Dry run (rollback all transactions)", default=False) + parser.add_option('--force-retry', action='store_true', dest='force_retry', help="Retry file removals (on applicable actions)", default=False) parser.add_option('-o', '--older-than', type='int', dest='days', help='Only perform action(s) on objects that have not been updated since the specified number of days', default=14) parser.add_option('-U', '--no-update-time', action='store_false', dest='update_time', help="Don't set update_time on updated objects", default=True) parser.add_option('-s', '--sequence', dest='sequence', help='Comma-separated sequence of actions, chosen from: %s' % self.action_names, default='') @@ -68,18 +70,11 @@ self.options.sequence = [ x.strip() for x in self.options.sequence.split(',') ] def __setup_logging(self): + format = "%(funcName)s %(levelname)s %(asctime)s %(message)s" if self.options.debug: - log.setLevel('DEBUG') + logging.basicConfig(level=logging.DEBUG, format=format) else: - log.setLevel('INFO') - - format = "%(funcName)s %(levelname)s %(asctime)s %(message)s" - formatter = logging.Formatter(format) - - handler = logging.StreamHandler(sys.stdout) - handler.setFormatter(formatter) - - log.addHandler(handler) + logging.basicConfig(level=logging.INFO, format=format) def __load_config(self): log.info('Reading config from %s' % self.options.config) @@ -203,11 +198,15 @@ self.conn.commit() log.info("All changes committed") - def _remove_metadata_file(self, id, action_name): - metadata_file = Bunch(id=id) - filename = self.object_store.get_filename(metadata_file, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % id) + def _remove_metadata_file(self, id, object_store_id, action_name): + metadata_file = Bunch(id=id, object_store_id=object_store_id) - self._log('Removing from disk: %s' % filename, action_name) + try: + filename = self.object_store.get_filename(metadata_file, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % id) + self._log('Removing from disk: %s' % filename, action_name) + except ObjectNotFound: + return + if not self.options.dry_run: try: os.unlink(filename) @@ -329,7 +328,7 @@ update_time_sql = '' if self.options.update_time: update_time_sql = """, - update_time = NOW()'""" + update_time = NOW()""" sql = sql % (update_time_sql, '%s', '%s') args = (self.options.days, event_id) @@ -356,8 +355,7 @@ WITH purged_hda_ids AS ( UPDATE history_dataset_association SET purged = true%s - WHERE deleted - AND NOT purged + WHERE deleted%s AND update_time < (NOW() - interval '%s days') RETURNING id, history_id), @@ -367,7 +365,8 @@ FROM purged_hda_ids WHERE purged_hda_ids.id = metadata_file.hda_id RETURNING metadata_file.hda_id AS hda_id, - metadata_file.id AS id), + metadata_file.id AS id, + metadata_file.object_store_id AS object_store_id), deleted_icda_ids AS ( UPDATE implicitly_converted_dataset_association SET deleted = true%s @@ -403,6 +402,7 @@ SELECT purged_hda_ids.id, history.user_id, deleted_metadata_file_ids.id, + deleted_metadata_file_ids.object_store_id, deleted_icda_ids.id, deleted_icda_ids.hda_id FROM purged_hda_ids @@ -414,12 +414,19 @@ ON purged_hda_ids.history_id = history.id; """ + force_retry_sql = """ + AND NOT purged""" update_time_sql = "" - if self.options.update_time: - update_time_sql += """, + + if self.options.force_retry: + force_retry_sql = "" + else: + # only update time if not doing force retry (otherwise a lot of things would have their update times reset that were actually purged a long time ago) + if self.options.update_time: + update_time_sql = """, update_time = NOW()""" - sql = sql % (update_time_sql, '%s', update_time_sql, update_time_sql, update_time_sql, '%s', '%s', '%s', '%s') + sql = sql % (update_time_sql, force_retry_sql, '%s', update_time_sql, update_time_sql, update_time_sql, '%s', '%s', '%s', '%s') args = (self.options.days, event_id, event_id, event_id, event_id) cur = self._update(sql, args) self._flush() @@ -430,10 +437,10 @@ if tup[1] is not None and tup[1] not in self.disk_accounting_user_ids: self.disk_accounting_user_ids.append(int(tup[1])) if tup[2] is not None: - self._log('Purge of HDA %s caused deletion of MetadataFile: %s' % (tup[0], tup[2])) - self._remove_metadata_file(tup[2], 'purge_deleted_hdas') - if tup[3] is not None: - self._log('Purge of HDA %s caused deletion of ImplicitlyConvertedDatasetAssociation: %s and converted HistoryDatasetAssociation: %s' % (tup[0], tup[3], tup[4])) + self._log('Purge of HDA %s caused deletion of MetadataFile: %s in Object Store: %s' % (tup[0], tup[2], tup[3])) + self._remove_metadata_file(tup[2], tup[3], 'purge_deleted_hdas') + if tup[4] is not None: + self._log('Purge of HDA %s caused deletion of ImplicitlyConvertedDatasetAssociation: %s and converted HistoryDatasetAssociation: %s' % (tup[0], tup[4], tup[5])) self._close_logfile() def purge_deleted_histories(self): @@ -449,8 +456,7 @@ WITH purged_history_ids AS ( UPDATE history SET purged = true%s - WHERE deleted - AND NOT purged + WHERE deleted%s AND update_time < (NOW() - interval '%s days') RETURNING id, user_id), @@ -468,7 +474,8 @@ FROM purged_hda_ids WHERE purged_hda_ids.id = metadata_file.hda_id RETURNING metadata_file.hda_id AS hda_id, - metadata_file.id AS id), + metadata_file.id AS id, + metadata_file.object_store_id AS object_store_id), deleted_icda_ids AS ( UPDATE implicitly_converted_dataset_association SET deleted = true%s @@ -510,6 +517,7 @@ purged_history_ids.user_id, purged_hda_ids.id, deleted_metadata_file_ids.id, + deleted_metadata_file_ids.object_store_id, deleted_icda_ids.id, deleted_icda_ids.hda_id FROM purged_history_ids @@ -521,12 +529,18 @@ ON deleted_icda_ids.hda_parent_id = purged_hda_ids.id; """ + force_retry_sql = """ + AND NOT purged""" update_time_sql = "" - if self.options.update_time: - update_time_sql += """, + + if self.options.force_retry: + force_retry_sql = "" + else: + if self.options.update_time: + update_time_sql += """, update_time = NOW()""" - sql = sql % (update_time_sql, '%s', update_time_sql, update_time_sql, update_time_sql, update_time_sql, '%s', '%s', '%s', '%s', '%s') + sql = sql % (update_time_sql, force_retry_sql, '%s', update_time_sql, update_time_sql, update_time_sql, update_time_sql, '%s', '%s', '%s', '%s', '%s') args = (self.options.days, event_id, event_id, event_id, event_id, event_id) cur = self._update(sql, args) self._flush() @@ -539,10 +553,10 @@ if tup[2] is not None: self._log('Purge of History %s caused deletion of HistoryDatasetAssociation: %s' % (tup[0], tup[2])) if tup[3] is not None: - self._log('Purge of HDA %s caused deletion of MetadataFile: %s' % (tup[1], tup[3])) - self._remove_metadata_file(tup[3], 'purge_deleted_histories') - if tup[4] is not None: - self._log('Purge of HDA %s caused deletion of ImplicitlyConvertedDatasetAssociation: %s and converted HistoryDatasetAssociation: %s' % (tup[1], tup[4], tup[5])) + self._log('Purge of HDA %s caused deletion of MetadataFile: %s in Object Store: %s' % (tup[1], tup[3], tup[4])) + self._remove_metadata_file(tup[3], tup[4], 'purge_deleted_histories') + if tup[5] is not None: + self._log('Purge of HDA %s caused deletion of ImplicitlyConvertedDatasetAssociation: %s and converted HistoryDatasetAssociation: %s' % (tup[1], tup[5], tup[6])) self._close_logfile() def delete_exported_histories(self): @@ -559,6 +573,7 @@ SET deleted = true%s FROM job_export_history_archive WHERE job_export_history_archive.dataset_id = dataset.id + AND NOT deleted AND dataset.update_time <= (NOW() - interval '%s days') RETURNING dataset.id), dataset_events @@ -649,38 +664,52 @@ WITH purged_dataset_ids AS ( UPDATE dataset SET purged = true%s - WHERE deleted = true - AND purged = false + WHERE deleted%s AND update_time < (NOW() - interval '%s days') - RETURNING id), + RETURNING id, + object_store_id), dataset_events AS (INSERT INTO cleanup_event_dataset_association (create_time, cleanup_event_id, dataset_id) SELECT NOW(), %s, id FROM purged_dataset_ids) - SELECT id + SELECT id, + object_store_id FROM purged_dataset_ids ORDER BY id; """ + force_retry_sql = """ + AND NOT purged""" update_time_sql = "" - if self.options.update_time: - update_time_sql += """, + + if self.options.force_retry: + force_retry_sql = "" + else: + if self.options.update_time: + update_time_sql = """, update_time = NOW()""" - sql = sql % (update_time_sql, '%s', '%s') + sql = sql % (update_time_sql, force_retry_sql, '%s', '%s') args = (self.options.days, event_id) cur = self._update(sql, args) self._flush() self._open_logfile() for tup in cur: - self._log('Marked Dataset purged: %s' % tup[0]) + self._log('Marked Dataset purged: %s in Object Store: %s' % (tup[0], tup[1])) # always try to remove the "object store path" - if it's at an external_filename, that file will be untouched anyway (which is what we want) - dataset = Bunch(id=tup[0]) - filename = self.object_store.get_filename(dataset) - extra_files_dir = self.object_store.get_filename(dataset, dir_only=True, extra_dir="dataset_%d_files" % tup[0]) + dataset = Bunch(id=tup[0], object_store_id=tup[1]) + try: + filename = self.object_store.get_filename(dataset) + except ObjectNotFound, AttributeError: + continue + + try: + extra_files_dir = self.object_store.get_filename(dataset, dir_only=True, extra_dir="dataset_%d_files" % tup[0]) + except ObjectNotFound, AttributeError: + extra_files_dir = None # don't check for existence of the dataset, it should exist self._log('Removing from disk: %s' % filename) @@ -691,7 +720,7 @@ self._log('Removal of %s failed with error: %s' % (filename, e)) # extra_files_dir is optional so it's checked first - if os.path.exists(extra_files_dir): + if extra_files_dir is not None and os.path.exists(extra_files_dir): self._log('Removing from disk: %s' % extra_files_dir) if not self.options.dry_run: try: @@ -703,6 +732,10 @@ if __name__ == '__main__': cleanup = Cleanup() - cleanup._run() - cleanup._update_user_disk_usage() + try: + cleanup._run() + if cleanup.disk_accounting_user_ids: + cleanup._update_user_disk_usage() + except: + log.exception('Caught exception in run sequence:') cleanup._shutdown() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 10 Sep '12

10 Sep '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5118cb9c05f7/ changeset: 5118cb9c05f7 user: jgoecks date: 2012-09-10 20:12:52 summary: Small fixes to make summary tree compatible with Circster. affected #: 2 files diff -r 6d3023815cd77ec3045bf81ff15af884b828c38d -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 lib/galaxy/visualization/tracks/summary.py --- a/lib/galaxy/visualization/tracks/summary.py +++ b/lib/galaxy/visualization/tracks/summary.py @@ -93,8 +93,10 @@ starting_block = self.find_block( start, level ) ending_block = self.find_block( end, level ) for block in range( starting_block, ending_block + 1 ): + val = 0 if block in blocks[ level ]: - results.append( ( block * multiplier, blocks[ level ][ block ] ) ) + val = blocks[ level ][ block ] + results.append( ( block * multiplier, val ) ) return results return None diff -r 6d3023815cd77ec3045bf81ff15af884b828c38d -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -559,7 +559,7 @@ converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) # HACK: pass in additional params, which are only used for summary tree data, not BBI data. - track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=3, detail_cutoff=0, draw_cutoff=0 ) } + track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) } return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome ) https://bitbucket.org/galaxy/galaxy-central/changeset/4e69bc5d9e1e/ changeset: 4e69bc5d9e1e user: jgoecks date: 2012-09-10 20:13:09 summary: Merge affected #: 3 files diff -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 -r 4e69bc5d9e1e02074de22cc6e809c33f3462f587 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -186,6 +186,8 @@ self.os_conn_path = kwargs.get( 'os_conn_path', '/' ) self.object_store_cache_size = float(kwargs.get( 'object_store_cache_size', -1 )) self.distributed_object_store_config_file = kwargs.get( 'distributed_object_store_config_file', None ) + if self.distributed_object_store_config_file is not None: + self.distributed_object_store_config_file = resolve_path( self.distributed_object_store_config_file, self.root ) # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() diff -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 -r 4e69bc5d9e1e02074de22cc6e809c33f3462f587 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -19,6 +19,7 @@ from galaxy.security.validate_user_input import validate_publicname from paste.httpexceptions import * from galaxy.exceptions import * +from galaxy.model import NoConverterException, ConverterDependencyException from Cheetah.Template import Template diff -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 -r 4e69bc5d9e1e02074de22cc6e809c33f3462f587 scripts/cleanup_datasets/pgcleanup.py --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -90,6 +90,7 @@ config_dict = {} for key, value in config_parser.items('app:main'): config_dict[key] = value + config_dict['root_dir'] = galaxy_root self.config = galaxy.config.Configuration(**config_dict) 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: Bugfix for pgcleanup.py
by Bitbucket 10 Sep '12

10 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6b35719fdcc8/ changeset: 6b35719fdcc8 user: natefoo date: 2012-09-10 20:07:05 summary: Bugfix for pgcleanup.py affected #: 2 files diff -r 6e79399b38d22512d8438522d26945c53f95b11a -r 6b35719fdcc8356267ebe786ecd738d0c14fb52b lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -186,6 +186,8 @@ self.os_conn_path = kwargs.get( 'os_conn_path', '/' ) self.object_store_cache_size = float(kwargs.get( 'object_store_cache_size', -1 )) self.distributed_object_store_config_file = kwargs.get( 'distributed_object_store_config_file', None ) + if self.distributed_object_store_config_file is not None: + self.distributed_object_store_config_file = resolve_path( self.distributed_object_store_config_file, self.root ) # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() diff -r 6e79399b38d22512d8438522d26945c53f95b11a -r 6b35719fdcc8356267ebe786ecd738d0c14fb52b scripts/cleanup_datasets/pgcleanup.py --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -90,6 +90,7 @@ config_dict = {} for key, value in config_parser.items('app:main'): config_dict[key] = value + config_dict['root_dir'] = galaxy_root self.config = galaxy.config.Configuration(**config_dict) 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: james_taylor: Datatype conversion exceptions no imported but used in base controller.
by Bitbucket 10 Sep '12

10 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6e79399b38d2/ changeset: 6e79399b38d2 user: james_taylor date: 2012-09-10 20:05:56 summary: Datatype conversion exceptions no imported but used in base controller. affected #: 1 file diff -r 6d3023815cd77ec3045bf81ff15af884b828c38d -r 6e79399b38d22512d8438522d26945c53f95b11a lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -19,6 +19,7 @@ from galaxy.security.validate_user_input import validate_publicname from paste.httpexceptions import * from galaxy.exceptions import * +from galaxy.model import NoConverterException, ConverterDependencyException from Cheetah.Template import Template Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 10 Sep '12

10 Sep '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b64b57240149/ changeset: b64b57240149 user: nuwan_ag date: 2012-08-23 06:22:13 summary: Modified REST API to support multipart/form-data requests, to enable large file upload. affected #: 2 files diff -r dd8a939cf0a26ea9e3cb969297bbfe7d749e88f7 -r b64b572401493be2b424e7166c67473cf1f298dd lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -28,7 +28,7 @@ local_filename = local_filename ) elif type( f ) == dict and 'filename' and 'local_filename' not in f: raise Exception( 'Uploaded file was encoded in a way not understood by Galaxy.' ) - if upload_dataset['url_paste'].strip() != '': + if upload_dataset['url_paste'] and upload_dataset['url_paste'].strip() != '': upload_dataset['url_paste'], is_multi_byte = datatypes.sniff.stream_to_file( StringIO.StringIO( upload_dataset['url_paste'] ), prefix="strio_url_paste_" ) else: upload_dataset['url_paste'] = None diff -r dd8a939cf0a26ea9e3cb969297bbfe7d749e88f7 -r b64b572401493be2b424e7166c67473cf1f298dd lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -5,6 +5,7 @@ import pkg_resources import os, sys, time, socket, random, string +import inspect pkg_resources.require( "Cheetah" ) from Cheetah.Template import Template import base @@ -125,9 +126,25 @@ return error trans.set_user( provided_key.user ) if trans.request.body: - try: - payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) ) - kwargs['payload'] = payload + def extract_payload_from_request(trans, func, kwargs): + content_type = trans.request.headers['content-type'] + if content_type.startswith('multipart/form-data'): + # If the content type is a standard type such as multipart/form-data, the wsgi framework parses the request body + # and loads all field values into kwargs. However, kwargs also contains formal method parameters etc. which + # are not a part of the request body. This is a problem because it's not possible to differentiate between values + # which are a part of the request body, and therefore should be a part of the payload, and values which should not be + # in the payload. Therefore, the decorated method's formal arguments are discovered through reflection and removed from + # the payload dictionary. This helps to prevent duplicate argument conflicts in downstream methods. + payload = kwargs.copy() + named_args, _, _, _ = inspect.getargspec(func) + for arg in named_args: + payload.pop(arg, None) + else: + # When it's a non standard request body (e.g. json), the wsgi framework does not parse the request body. So do so manually. + payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) ) + return payload + try: + kwargs['payload'] = extract_payload_from_request(trans, func, kwargs) except ValueError: error_status = '400 Bad Request' error_message = 'Your request did not appear to be valid JSON, please consult the API documentation' https://bitbucket.org/galaxy/galaxy-central/changeset/5747b665127a/ changeset: 5747b665127a user: nuwan_ag date: 2012-08-23 07:09:20 summary: Also added support for x-www-form-urlencoded REST API requests, for consistencies sake. This way, API clients can post as either JSON, multi-part form data, or standard url form encoding. affected #: 1 file diff -r b64b572401493be2b424e7166c67473cf1f298dd -r 5747b665127a5e4f82e102783048358fca68083b lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -128,7 +128,7 @@ if trans.request.body: def extract_payload_from_request(trans, func, kwargs): content_type = trans.request.headers['content-type'] - if content_type.startswith('multipart/form-data'): + if content_type.startswith('application/x-www-form-urlencoded') or content_type.startswith('multipart/form-data'): # If the content type is a standard type such as multipart/form-data, the wsgi framework parses the request body # and loads all field values into kwargs. However, kwargs also contains formal method parameters etc. which # are not a part of the request body. This is a problem because it's not possible to differentiate between values @@ -140,7 +140,9 @@ for arg in named_args: payload.pop(arg, None) else: - # When it's a non standard request body (e.g. json), the wsgi framework does not parse the request body. So do so manually. + # Assume application/json content type and parse request body manually, since wsgi won't do it. However, the order of this check + # should ideally be in reverse, with the if clause being a check for application/json and the else clause assuming a standard encoding + # such as multipart/form-data. Leaving it as is for backward compatibility, just in case. payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) ) return payload try: https://bitbucket.org/galaxy/galaxy-central/changeset/6d3023815cd7/ changeset: 6d3023815cd7 user: dannon date: 2012-09-10 18:33:01 summary: Merged in nuwan_ag/galaxy-central (pull request #63) affected #: 2 files diff -r e0975c9b9bd25d44cfcacc202470bb8037da6d6f -r 6d3023815cd77ec3045bf81ff15af884b828c38d lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -28,7 +28,7 @@ local_filename = local_filename ) elif type( f ) == dict and 'filename' and 'local_filename' not in f: raise Exception( 'Uploaded file was encoded in a way not understood by Galaxy.' ) - if upload_dataset['url_paste'].strip() != '': + if upload_dataset['url_paste'] and upload_dataset['url_paste'].strip() != '': upload_dataset['url_paste'], is_multi_byte = datatypes.sniff.stream_to_file( StringIO.StringIO( upload_dataset['url_paste'] ), prefix="strio_url_paste_" ) else: upload_dataset['url_paste'] = None diff -r e0975c9b9bd25d44cfcacc202470bb8037da6d6f -r 6d3023815cd77ec3045bf81ff15af884b828c38d lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -5,6 +5,7 @@ import pkg_resources import os, sys, time, socket, random, string +import inspect pkg_resources.require( "Cheetah" ) from Cheetah.Template import Template import base @@ -125,9 +126,27 @@ return error trans.set_user( provided_key.user ) if trans.request.body: - try: - payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) ) - kwargs['payload'] = payload + def extract_payload_from_request(trans, func, kwargs): + content_type = trans.request.headers['content-type'] + if content_type.startswith('application/x-www-form-urlencoded') or content_type.startswith('multipart/form-data'): + # If the content type is a standard type such as multipart/form-data, the wsgi framework parses the request body + # and loads all field values into kwargs. However, kwargs also contains formal method parameters etc. which + # are not a part of the request body. This is a problem because it's not possible to differentiate between values + # which are a part of the request body, and therefore should be a part of the payload, and values which should not be + # in the payload. Therefore, the decorated method's formal arguments are discovered through reflection and removed from + # the payload dictionary. This helps to prevent duplicate argument conflicts in downstream methods. + payload = kwargs.copy() + named_args, _, _, _ = inspect.getargspec(func) + for arg in named_args: + payload.pop(arg, None) + else: + # Assume application/json content type and parse request body manually, since wsgi won't do it. However, the order of this check + # should ideally be in reverse, with the if clause being a check for application/json and the else clause assuming a standard encoding + # such as multipart/form-data. Leaving it as is for backward compatibility, just in case. + payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) ) + return payload + try: + kwargs['payload'] = extract_payload_from_request(trans, func, kwargs) except ValueError: error_status = '400 Bad Request' error_message = 'Your request did not appear to be valid JSON, please consult the API documentation' 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: Add a dataset cleanup script that's optimized for (and compatible only with) PostgreSQL 9.1+. Also add a bunch of tables for logging all cleanup events, which makes reversing such events trivial.
by Bitbucket 10 Sep '12

10 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e0975c9b9bd2/ changeset: e0975c9b9bd2 user: natefoo date: 2012-09-10 18:03:23 summary: Add a dataset cleanup script that's optimized for (and compatible only with) PostgreSQL 9.1+. Also add a bunch of tables for logging all cleanup events, which makes reversing such events trivial. affected #: 2 files diff -r 9207ba35fa0caad1f8eac717afceb50f5c2a61c0 -r e0975c9b9bd25d44cfcacc202470bb8037da6d6f lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py @@ -0,0 +1,83 @@ +""" +Migration script to add the cleanup_event* tables. +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +import sys, logging +from galaxy.model.custom_types import * +from sqlalchemy.exc import * +import datetime +now = datetime.datetime.utcnow + +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 ) + +# New table to log cleanup events +CleanupEvent_table = Table( "cleanup_event", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "message", TrimmedString( 1024 ) ) ) + +CleanupEventDatasetAssociation_table = Table( "cleanup_event_dataset_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "cleanup_event_id", Integer, ForeignKey( "cleanup_event.id" ), index=True, nullable=True ), + Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ) ) + +CleanupEventMetadataFileAssociation_table = Table( "cleanup_event_metadata_file_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "cleanup_event_id", Integer, ForeignKey( "cleanup_event.id" ), index=True, nullable=True ), + Column( "metadata_file_id", Integer, ForeignKey( "metadata_file.id" ), index=True ) ) + +CleanupEventHistoryAssociation_table = Table( "cleanup_event_history_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "cleanup_event_id", Integer, ForeignKey( "cleanup_event.id" ), index=True, nullable=True ), + Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ) ) + +CleanupEventHistoryDatasetAssociationAssociation_table = Table( "cleanup_event_hda_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "cleanup_event_id", Integer, ForeignKey( "cleanup_event.id" ), index=True, nullable=True ), + Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ) ) + +CleanupEventImplicitlyConvertedDatasetAssociationAssociation_table = Table( "cleanup_event_icda_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "cleanup_event_id", Integer, ForeignKey( "cleanup_event.id" ), index=True, nullable=True ), + Column( "icda_id", Integer, ForeignKey( "implicitly_converted_dataset_association.id" ), index=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + try: + CleanupEvent_table.create() + CleanupEventDatasetAssociation_table.create() + CleanupEventMetadataFileAssociation_table.create() + CleanupEventHistoryAssociation_table.create() + CleanupEventHistoryDatasetAssociationAssociation_table.create() + CleanupEventImplicitlyConvertedDatasetAssociationAssociation_table.create() + except Exception, e: + log.debug( "Creating table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + try: + CleanupEventImplicitlyConvertedDatasetAssociationAssociation_table.drop() + CleanupEventHistoryDatasetAssociationAssociation_table.drop() + CleanupEventHistoryAssociation_table.drop() + CleanupEventMetadataFileAssociation_table.drop() + CleanupEventDatasetAssociation_table.drop() + CleanupEvent_table.drop() + except Exception, e: + log.debug( "Dropping table failed: %s" % str( e ) ) diff -r 9207ba35fa0caad1f8eac717afceb50f5c2a61c0 -r e0975c9b9bd25d44cfcacc202470bb8037da6d6f scripts/cleanup_datasets/pgcleanup.py --- /dev/null +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -0,0 +1,707 @@ +#!/usr/bin/env python +""" +pgcleanup.py - A script for cleaning up datasets in Galaxy efficiently, by + bypassing the Galaxy model and operating directly on the database. + PostgreSQL 9.1 or greater is required. +""" + +import os +import sys +import shutil +import logging +import inspect +import datetime +from ConfigParser import ConfigParser +from optparse import OptionParser + +galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..')) +sys.path.insert(0, os.path.join(galaxy_root, 'lib')) + +from galaxy import eggs +eggs.require('psycopg2') +eggs.require('SQLAlchemy') +import psycopg2 +from sqlalchemy.engine.url import make_url + +import galaxy.config + +from galaxy.objectstore import build_object_store_from_config +from galaxy.util.bunch import Bunch + +log = logging.getLogger() + +class Cleanup(object): + def __init__(self): + self.options = None + self.args = None + self.config = None + self.conn = None + self.action_names = [] + self.logs = {} + self.disk_accounting_user_ids = [] + self.object_store = None + + self.__cache_action_names() + self.__parse_args() + self.__setup_logging() + self.__load_config() + self.__connect_db() + self.__load_object_store() + + def __cache_action_names(self): + for name, value in inspect.getmembers(self): + if not name.startswith('_') and inspect.ismethod(value): + self.action_names.append(name) + + def __parse_args(self): + default_config = os.path.abspath(os.path.join(galaxy_root, 'universe_wsgi.ini')) + + parser = OptionParser() + parser.add_option('-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default=default_config) + parser.add_option('-d', '--debug', action='store_true', dest='debug', help='Enable debug logging', default=False) + parser.add_option('--dry-run', action='store_true', dest='dry_run', help="Dry run (rollback all transactions)", default=False) + parser.add_option('-o', '--older-than', type='int', dest='days', help='Only perform action(s) on objects that have not been updated since the specified number of days', default=14) + parser.add_option('-U', '--no-update-time', action='store_false', dest='update_time', help="Don't set update_time on updated objects", default=True) + parser.add_option('-s', '--sequence', dest='sequence', help='Comma-separated sequence of actions, chosen from: %s' % self.action_names, default='') + ( self.options, self.args ) = parser.parse_args() + + self.options.sequence = [ x.strip() for x in self.options.sequence.split(',') ] + + def __setup_logging(self): + if self.options.debug: + log.setLevel('DEBUG') + else: + log.setLevel('INFO') + + format = "%(funcName)s %(levelname)s %(asctime)s %(message)s" + formatter = logging.Formatter(format) + + handler = logging.StreamHandler(sys.stdout) + handler.setFormatter(formatter) + + log.addHandler(handler) + + def __load_config(self): + log.info('Reading config from %s' % self.options.config) + config_parser = ConfigParser(dict(here = os.getcwd(), + database_connection = 'sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE')) + config_parser.read(self.options.config) + + config_dict = {} + for key, value in config_parser.items('app:main'): + config_dict[key] = value + + self.config = galaxy.config.Configuration(**config_dict) + + def __connect_db(self): + url = make_url(self.config.database_connection) + + log.info('Connecting to database with URL: %s' % url) + args = url.translate_connect_args() + args.update(url.query) + + assert url.get_dialect().name == 'postgres', 'This script can only be used with PostgreSQL.' + + self.conn = psycopg2.connect(**args) + + def __load_object_store(self): + self.object_store = build_object_store_from_config(self.config) + + def _open_logfile(self): + action_name = inspect.stack()[1][3] + logname = os.path.join(galaxy_root, 'scripts', 'cleanup_datasets', action_name + '.log') + + if self.options.dry_run: + log.debug('--dry-run specified, logging changes to stdout instead of log file: %s' % logname) + self.logs[action_name] = sys.stdout + else: + log.debug('Opening log file: %s' % logname) + self.logs[action_name] = open(logname, 'a') + + message = '==== Log opened: %s ' % datetime.datetime.now().isoformat() + self.logs[action_name].write(message.ljust(72, '=')) + self.logs[action_name].write('\n') + + def _log(self, message, action_name=None): + if action_name is None: + action_name = inspect.stack()[1][3] + if not message.endswith('\n'): + message += '\n' + self.logs[action_name].write(message) + + def _close_logfile(self): + action_name = inspect.stack()[1][3] + + message = '==== Log closed: %s ' % datetime.datetime.now().isoformat() + self.logs[action_name].write(message.ljust(72, '=')) + self.logs[action_name].write('\n') + + if self.options.dry_run: + log.debug('--dry-run specified, changes were logged to stdout insted of log file') + else: + log.debug('Closing log file: %s' % self.logs[action_name].name) + self.logs[action_name].close() + + del self.logs[action_name] + + def _run(self): + ok = True + for name in self.options.sequence: + if name not in self.action_names: + log.error('Unknown action in sequence: %s' % name) + ok = False + if not ok: + log.critical('Exiting due to previous error(s)') + sys.exit(1) + for name in self.options.sequence: + log.info('Calling %s' % name) + self.__getattribute__(name)() + log.info('Finished %s' % name) + + def _create_event(self, message): + """ + Create a new event in the cleanup_event table. + """ + + sql = """ + INSERT INTO cleanup_event + (create_time, message) + VALUES (NOW(), %s) + RETURNING id; + """ + + log.debug("SQL is: %s" % sql % ("'" + message + "'")) + + args = (message,) + + cur = self.conn.cursor() + log.info("Executing SQL") + cur.execute(sql, args) + log.info('Database status: %s' % cur.statusmessage) + + return cur.fetchone()[0] + + def _update(self, sql, args): + if args is not None: + log.debug('SQL is: %s' % sql % args) + else: + log.debug('SQL is: %s' % sql) + + cur = self.conn.cursor() + log.info('Executing SQL') + cur.execute(sql, args) + log.info('Database status: %s' % cur.statusmessage) + + return cur + + def _flush(self): + if self.options.dry_run: + self.conn.rollback() + log.info("--dry-run specified, all changes rolled back") + else: + self.conn.commit() + log.info("All changes committed") + + def _remove_metadata_file(self, id, action_name): + metadata_file = Bunch(id=id) + filename = self.object_store.get_filename(metadata_file, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % id) + + self._log('Removing from disk: %s' % filename, action_name) + if not self.options.dry_run: + try: + os.unlink(filename) + except Exception, e: + self._log('Removal of %s failed with error: %s' % (filename, e), action_name) + + def _update_user_disk_usage(self): + """ + Any operation that purges a HistoryDatasetAssociation may require + updating a user's disk usage. Rather than attempt to resolve dataset + copies at purge-time, simply maintain a list of users that have had + HDAs purged, and update their usages once all updates are complete. + + This could probably be done more efficiently. + """ + log.info('Recalculating disk usage for users whose HistoryDatasetAssociations were purged') + + for user_id in self.disk_accounting_user_ids: + + # TODO: h.purged = false should be unnecessary once all hdas in purged histories are purged. + sql = """ + UPDATE galaxy_user + SET disk_usage = (SELECT SUM(total_size) + FROM ( SELECT d.total_size + FROM history_dataset_association hda + JOIN history h ON h.id = hda.history_id + JOIN dataset d ON hda.dataset_id = d.id + WHERE h.user_id = %s + AND h.purged = false + AND hda.purged = false + AND d.purged = false + AND d.id NOT IN (SELECT dataset_id + FROM library_dataset_dataset_association) + GROUP BY d.id) sizes) + WHERE id = %s + RETURNING disk_usage; + """ + + args = (user_id, user_id) + cur = self._update(sql, args) + self._flush() + + for tup in cur: + # disk_usage might be None (e.g. user has purged all data) + log.debug('Updated disk usage for user id %i to %s bytes' % (user_id, tup[0])) + + def _shutdown(self): + self.object_store.shutdown() + self.conn.close() + for handle in self.logs.values(): + message = '==== Log closed at shutdown: %s ' % datetime.datetime.now().isoformat() + handle.write(message.ljust(72, '=')) + handle.write('\n') + handle.close() + + def update_hda_purged_flag(self): + """ + The old cleanup script does not mark HistoryDatasetAssociations as purged when deleted Histories are purged. This method can be used to rectify that situation. + """ + log.info('Marking purged all HistoryDatasetAssociations associated with purged Datasets') + + event_id = self._create_event(inspect.stack()[0][3]) + + # update_time is intentionally left unmodified. + sql = """ + WITH purged_hda_ids + AS ( UPDATE history_dataset_association + SET purged = true + FROM dataset + WHERE history_dataset_association.dataset_id = dataset.id + AND dataset.purged + AND NOT history_dataset_association.purged + RETURNING history_dataset_association.id), + hda_events + AS (INSERT INTO cleanup_event_hda_association + (create_time, cleanup_event_id, hda_id) + SELECT NOW(), %s, id + FROM purged_hda_ids) + SELECT id + FROM purged_hda_ids + ORDER BY id; + """ + + args = (event_id,) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked HistoryDatasetAssociation purged: %s' % tup[0]) + self._close_logfile() + + def delete_userless_histories(self): + """ + Mark deleted all "anonymous" Histories (not owned by a registered user) that are older than the specified number of days. + """ + log.info('Marking deleted all userless Histories older than %i days' % self.options.days) + + event_id = self._create_event(inspect.stack()[0][3]) + + sql = """ + WITH deleted_history_ids + AS ( UPDATE history + SET deleted = true%s + WHERE user_id is null + AND NOT deleted + AND update_time < (NOW() - interval '%s days') + RETURNING id), + history_events + AS (INSERT INTO cleanup_event_history_association + (create_time, cleanup_event_id, history_id) + SELECT NOW(), %s, id + FROM deleted_history_ids) + SELECT id + FROM deleted_history_ids + ORDER BY id; + """ + + update_time_sql = '' + if self.options.update_time: + update_time_sql = """, + update_time = NOW()'""" + + sql = sql % (update_time_sql, '%s', '%s') + args = (self.options.days, event_id) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked userless History deleted: %s' % tup[0]) + self._close_logfile() + + def purge_deleted_hdas(self): + """ + Mark purged all HistoryDatasetAssociations currently marked deleted that are older than the specified number of days. + Mark deleted all MetadataFiles whose hda_id is purged in this step. + Mark deleted all ImplicitlyConvertedDatasetAssociations whose hda_parent_id is purged in this step. + Mark purged all HistoryDatasetAssociations for which an ImplicitlyConvertedDatasetAssociation with matching hda_id is deleted in this step. + """ + log.info('Marking purged all deleted HistoryDatasetAssociations older than %i days' % self.options.days) + + event_id = self._create_event(inspect.stack()[0][3]) + + sql = """ + WITH purged_hda_ids + AS ( UPDATE history_dataset_association + SET purged = true%s + WHERE deleted + AND NOT purged + AND update_time < (NOW() - interval '%s days') + RETURNING id, + history_id), + deleted_metadata_file_ids + AS ( UPDATE metadata_file + SET deleted = true%s + FROM purged_hda_ids + WHERE purged_hda_ids.id = metadata_file.hda_id + RETURNING metadata_file.hda_id AS hda_id, + metadata_file.id AS id), + deleted_icda_ids + AS ( UPDATE implicitly_converted_dataset_association + SET deleted = true%s + FROM purged_hda_ids + WHERE purged_hda_ids.id = implicitly_converted_dataset_association.hda_parent_id + RETURNING implicitly_converted_dataset_association.hda_id AS hda_id, + implicitly_converted_dataset_association.hda_parent_id AS hda_parent_id, + implicitly_converted_dataset_association.id AS id), + deleted_icda_purged_child_hda_ids + AS ( UPDATE history_dataset_association + SET purged = true%s + FROM deleted_icda_ids where deleted_icda_ids.hda_id = history_dataset_association.id), + hda_events + AS (INSERT INTO cleanup_event_hda_association + (create_time, cleanup_event_id, hda_id) + SELECT NOW(), %s, id + FROM purged_hda_ids), + metadata_file_events + AS (INSERT INTO cleanup_event_metadata_file_association + (create_time, cleanup_event_id, metadata_file_id) + SELECT NOW(), %s, id + FROM deleted_metadata_file_ids), + icda_events + AS (INSERT INTO cleanup_event_icda_association + (create_time, cleanup_event_id, icda_id) + SELECT NOW(), %s, id + FROM deleted_icda_ids), + icda_hda_events + AS (INSERT INTO cleanup_event_hda_association + (create_time, cleanup_event_id, hda_id) + SELECT NOW(), %s, hda_id + FROM deleted_icda_ids) + SELECT purged_hda_ids.id, + history.user_id, + deleted_metadata_file_ids.id, + deleted_icda_ids.id, + deleted_icda_ids.hda_id + FROM purged_hda_ids + LEFT OUTER JOIN deleted_metadata_file_ids + ON deleted_metadata_file_ids.hda_id = purged_hda_ids.id + LEFT OUTER JOIN deleted_icda_ids + ON deleted_icda_ids.hda_parent_id = purged_hda_ids.id + LEFT OUTER JOIN history + ON purged_hda_ids.history_id = history.id; + """ + + update_time_sql = "" + if self.options.update_time: + update_time_sql += """, + update_time = NOW()""" + + sql = sql % (update_time_sql, '%s', update_time_sql, update_time_sql, update_time_sql, '%s', '%s', '%s', '%s') + args = (self.options.days, event_id, event_id, event_id, event_id) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked HistoryDatasetAssociations purged: %s' % tup[0]) + if tup[1] is not None and tup[1] not in self.disk_accounting_user_ids: + self.disk_accounting_user_ids.append(int(tup[1])) + if tup[2] is not None: + self._log('Purge of HDA %s caused deletion of MetadataFile: %s' % (tup[0], tup[2])) + self._remove_metadata_file(tup[2], 'purge_deleted_hdas') + if tup[3] is not None: + self._log('Purge of HDA %s caused deletion of ImplicitlyConvertedDatasetAssociation: %s and converted HistoryDatasetAssociation: %s' % (tup[0], tup[3], tup[4])) + self._close_logfile() + + def purge_deleted_histories(self): + """ + Mark purged all Histories marked deleted that are older than the specified number of days. + Mark purged all HistoryDatasetAssociations in Histories marked purged in this step (if not already purged). + """ + log.info('Marking purged all deleted histories that are older than the specified number of days.') + + event_id = self._create_event(inspect.stack()[0][3]) + + sql = """ + WITH purged_history_ids + AS ( UPDATE history + SET purged = true%s + WHERE deleted + AND NOT purged + AND update_time < (NOW() - interval '%s days') + RETURNING id, + user_id), + purged_hda_ids + AS ( UPDATE history_dataset_association + SET purged = true%s + FROM purged_history_ids + WHERE purged_history_ids.id = history_dataset_association.history_id + AND NOT history_dataset_association.purged + RETURNING history_dataset_association.history_id AS history_id, + history_dataset_association.id AS id), + deleted_metadata_file_ids + AS ( UPDATE metadata_file + SET deleted = true%s + FROM purged_hda_ids + WHERE purged_hda_ids.id = metadata_file.hda_id + RETURNING metadata_file.hda_id AS hda_id, + metadata_file.id AS id), + deleted_icda_ids + AS ( UPDATE implicitly_converted_dataset_association + SET deleted = true%s + FROM purged_hda_ids + WHERE purged_hda_ids.id = implicitly_converted_dataset_association.hda_parent_id + RETURNING implicitly_converted_dataset_association.hda_id AS hda_id, + implicitly_converted_dataset_association.hda_parent_id AS hda_parent_id, + implicitly_converted_dataset_association.id AS id), + deleted_icda_purged_child_hda_ids + AS ( UPDATE history_dataset_association + SET purged = true%s + FROM deleted_icda_ids where deleted_icda_ids.hda_id = history_dataset_association.id), + history_events + AS (INSERT INTO cleanup_event_history_association + (create_time, cleanup_event_id, history_id) + SELECT NOW(), %s, id + FROM purged_history_ids), + hda_events + AS (INSERT INTO cleanup_event_hda_association + (create_time, cleanup_event_id, hda_id) + SELECT NOW(), %s, id + FROM purged_hda_ids), + metadata_file_events + AS (INSERT INTO cleanup_event_metadata_file_association + (create_time, cleanup_event_id, metadata_file_id) + SELECT NOW(), %s, id + FROM deleted_metadata_file_ids), + icda_events + AS (INSERT INTO cleanup_event_icda_association + (create_time, cleanup_event_id, icda_id) + SELECT NOW(), %s, id + FROM deleted_icda_ids), + icda_hda_events + AS (INSERT INTO cleanup_event_hda_association + (create_time, cleanup_event_id, hda_id) + SELECT NOW(), %s, hda_id + FROM deleted_icda_ids) + SELECT purged_history_ids.id, + purged_history_ids.user_id, + purged_hda_ids.id, + deleted_metadata_file_ids.id, + deleted_icda_ids.id, + deleted_icda_ids.hda_id + FROM purged_history_ids + LEFT OUTER JOIN purged_hda_ids + ON purged_history_ids.id = purged_hda_ids.history_id + LEFT OUTER JOIN deleted_metadata_file_ids + ON deleted_metadata_file_ids.hda_id = purged_hda_ids.id + LEFT OUTER JOIN deleted_icda_ids + ON deleted_icda_ids.hda_parent_id = purged_hda_ids.id; + """ + + update_time_sql = "" + if self.options.update_time: + update_time_sql += """, + update_time = NOW()""" + + sql = sql % (update_time_sql, '%s', update_time_sql, update_time_sql, update_time_sql, update_time_sql, '%s', '%s', '%s', '%s', '%s') + args = (self.options.days, event_id, event_id, event_id, event_id, event_id) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked History purged: %s' % tup[0]) + if tup[1] is not None and tup[1] not in self.disk_accounting_user_ids: + self.disk_accounting_user_ids.append(int(tup[1])) + if tup[2] is not None: + self._log('Purge of History %s caused deletion of HistoryDatasetAssociation: %s' % (tup[0], tup[2])) + if tup[3] is not None: + self._log('Purge of HDA %s caused deletion of MetadataFile: %s' % (tup[1], tup[3])) + self._remove_metadata_file(tup[3], 'purge_deleted_histories') + if tup[4] is not None: + self._log('Purge of HDA %s caused deletion of ImplicitlyConvertedDatasetAssociation: %s and converted HistoryDatasetAssociation: %s' % (tup[1], tup[4], tup[5])) + self._close_logfile() + + def delete_exported_histories(self): + """ + Mark deleted all Datasets that are derivative of JobExportHistoryArchives that are older than the specified number of days. + """ + log.info('Marking deleted all Datasets that are derivative of JobExportHistoryArchives that are older than the specified number of days.') + + event_id = self._create_event(inspect.stack()[0][3]) + + sql = """ + WITH deleted_dataset_ids + AS ( UPDATE dataset + SET deleted = true%s + FROM job_export_history_archive + WHERE job_export_history_archive.dataset_id = dataset.id + AND dataset.update_time <= (NOW() - interval '%s days') + RETURNING dataset.id), + dataset_events + AS (INSERT INTO cleanup_event_dataset_association + (create_time, cleanup_event_id, dataset_id) + SELECT NOW(), %s, id + FROM deleted_dataset_ids) + SELECT id + FROM deleted_dataset_ids + ORDER BY id; + """ + + update_time_sql = "" + if self.options.update_time: + update_time_sql += """, + update_time = NOW()""" + + sql = sql % (update_time_sql, '%s', '%s') + args = (self.options.days, event_id) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked Dataset deleted: %s' % tup[0]) + self._close_logfile() + + def delete_datasets(self): + """ + Mark deleted all Datasets whose associations are all marked as deleted (LDDA) or purged (HDA) that are older than the specified number of days. + """ + log.info('Marking deleted all Datasets whose associations are all marked as deleted/purged that are older than the specified number of days.') + + event_id = self._create_event(inspect.stack()[0][3]) + + sql = """ + WITH deleted_dataset_ids + AS ( UPDATE dataset + SET deleted = true%s + WHERE NOT deleted + AND NOT EXISTS (SELECT true + FROM library_dataset_dataset_association + WHERE (NOT deleted + OR update_time >= (NOW() - interval '%s days')) + AND dataset.id = dataset_id) + AND NOT EXISTS (SELECT true + FROM history_dataset_association + WHERE (NOT purged + OR update_time >= (NOW() - interval '%s days')) + AND dataset.id = dataset_id) + RETURNING id), + dataset_events + AS (INSERT INTO cleanup_event_dataset_association + (create_time, cleanup_event_id, dataset_id) + SELECT NOW(), %s, id + FROM deleted_dataset_ids) + SELECT id + FROM deleted_dataset_ids + ORDER BY id; + """ + + update_time_sql = "" + if self.options.update_time: + update_time_sql += """, + update_time = NOW()""" + + sql = sql % (update_time_sql, '%s', '%s', '%s') + args = (self.options.days, self.options.days, event_id) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked Dataset deleted: %s' % tup[0]) + self._close_logfile() + + def purge_datasets(self): + """ + Mark purged all Datasets marked deleted that are older than the specified number of days. + """ + log.info('Marking purged all Datasets marked deleted that are older than the specified number of days.') + + # TODO: force retry option + + event_id = self._create_event(inspect.stack()[0][3]) + + sql = """ + WITH purged_dataset_ids + AS ( UPDATE dataset + SET purged = true%s + WHERE deleted = true + AND purged = false + AND update_time < (NOW() - interval '%s days') + RETURNING id), + dataset_events + AS (INSERT INTO cleanup_event_dataset_association + (create_time, cleanup_event_id, dataset_id) + SELECT NOW(), %s, id + FROM purged_dataset_ids) + SELECT id + FROM purged_dataset_ids + ORDER BY id; + """ + + update_time_sql = "" + if self.options.update_time: + update_time_sql += """, + update_time = NOW()""" + + sql = sql % (update_time_sql, '%s', '%s') + args = (self.options.days, event_id) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked Dataset purged: %s' % tup[0]) + + # always try to remove the "object store path" - if it's at an external_filename, that file will be untouched anyway (which is what we want) + dataset = Bunch(id=tup[0]) + filename = self.object_store.get_filename(dataset) + extra_files_dir = self.object_store.get_filename(dataset, dir_only=True, extra_dir="dataset_%d_files" % tup[0]) + + # don't check for existence of the dataset, it should exist + self._log('Removing from disk: %s' % filename) + if not self.options.dry_run: + try: + os.unlink(filename) + except Exception, e: + self._log('Removal of %s failed with error: %s' % (filename, e)) + + # extra_files_dir is optional so it's checked first + if os.path.exists(extra_files_dir): + self._log('Removing from disk: %s' % extra_files_dir) + if not self.options.dry_run: + try: + shutil.rmtree(extra_files_dir) + except Exception, e: + self._log('Removal of %s failed with error: %s' % (extra_files_dir, e)) + + self._close_logfile() + +if __name__ == '__main__': + cleanup = Cleanup() + cleanup._run() + cleanup._update_user_disk_usage() + cleanup._shutdown() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: rmarenco: Added the base.css generated from base.less
by Bitbucket 09 Sep '12

09 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9207ba35fa0c/ changeset: 9207ba35fa0c user: rmarenco date: 2012-09-10 00:24:51 summary: Added the base.css generated from base.less affected #: 1 file diff -r 110a69b0d387228ec7bed84814192b9c99082d7c -r 9207ba35fa0caad1f8eac717afceb50f5c2a61c0 static/june_2007_style/blue/base.css --- /dev/null +++ b/static/june_2007_style/blue/base.css @@ -0,0 +1,914 @@ +article,aside,details,figcaption,figure,footer,header,hgroup,nav,section{display:block;} +audio,canvas,video{display:inline-block;*display:inline;*zoom:1;} +audio:not([controls]){display:none;} +html{font-size:100%;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%;} +a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} +a:hover,a:active{outline:0;} +sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline;} +sup{top:-0.5em;} +sub{bottom:-0.25em;} +img{max-width:100%;vertical-align:middle;border:0;-ms-interpolation-mode:bicubic;} +#map_canvas img{max-width:none;} +button,input,select,textarea{margin:0;font-size:100%;vertical-align:middle;} +button,input{*overflow:visible;line-height:normal;} +button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0;} +button,input[type="button"],input[type="reset"],input[type="submit"]{cursor:pointer;-webkit-appearance:button;} +input[type="search"]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield;} +input[type="search"]::-webkit-search-decoration,input[type="search"]::-webkit-search-cancel-button{-webkit-appearance:none;} +textarea{overflow:auto;vertical-align:top;} +.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";} +.clearfix:after{clear:both;} +.hide-text{font:0/0 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rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#149bdf;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);-webkit-background-size:40px 40px;-moz-background-size:40px 40px;-o-background-size:40px 40px;background-size:40px 40px;-webkit-background-size:40px 40px;-moz-background-size:40px 40px;-o-background-size:40px 40px;background-size:40px 40px;} +.progress.active .bar{-webkit-animation:progress-bar-stripes 2s linear infinite;-moz-animation:progress-bar-stripes 2s linear infinite;-ms-animation:progress-bar-stripes 2s linear infinite;-o-animation:progress-bar-stripes 2s linear infinite;animation:progress-bar-stripes 2s linear infinite;} +.progress-danger .bar{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-ms-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(top, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#c43c35', GradientType=0);background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-ms-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(top, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#c43c35', GradientType=0);} +.progress-danger.progress-striped .bar{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-success .bar{background-color:#5eb95e;background-image:-moz-linear-gradient(top, #62c462, #57a957);background-image:-ms-linear-gradient(top, #62c462, #57a957);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957));background-image:-webkit-linear-gradient(top, #62c462, #57a957);background-image:-o-linear-gradient(top, #62c462, #57a957);background-image:linear-gradient(top, #62c462, #57a957);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#62c462', endColorstr='#57a957', GradientType=0);background-color:#5eb95e;background-image:-moz-linear-gradient(top, #62c462, #57a957);background-image:-ms-linear-gradient(top, #62c462, #57a957);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957));background-image:-webkit-linear-gradient(top, #62c462, #57a957);background-image:-o-linear-gradient(top, #62c462, #57a957);background-image:linear-gradient(top, #62c462, #57a957);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#62c462', endColorstr='#57a957', GradientType=0);} +.progress-success.progress-striped .bar{background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-info .bar{background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-ms-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(top, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#5bc0de', endColorstr='#339bb9', GradientType=0);background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-ms-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(top, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#5bc0de', endColorstr='#339bb9', GradientType=0);} +.progress-info.progress-striped .bar{background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-warning .bar{background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-ms-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(top, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fbb450', endColorstr='#f89406', GradientType=0);background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-ms-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(top, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fbb450', endColorstr='#f89406', GradientType=0);} +.progress-warning.progress-striped .bar{background-color:#fbb450;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#fbb450;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.accordion{margin-bottom:16px;} +.accordion-group{margin-bottom:2px;border:1px solid #e5e5e5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.accordion-heading{border-bottom:0;} +.accordion-heading .accordion-toggle{display:block;padding:8px 15px;} +.accordion-toggle{cursor:pointer;} +.accordion-inner{padding:9px 15px;border-top:1px solid #e5e5e5;} +.carousel{position:relative;margin-bottom:16px;line-height:1;} +.carousel-inner{overflow:hidden;width:100%;position:relative;} +.carousel .item{display:none;position:relative;-webkit-transition:0.6s ease-in-out left;-moz-transition:0.6s ease-in-out left;-ms-transition:0.6s ease-in-out left;-o-transition:0.6s ease-in-out left;transition:0.6s ease-in-out left;-webkit-transition:0.6s ease-in-out left;-moz-transition:0.6s ease-in-out left;-ms-transition:0.6s ease-in-out left;-o-transition:0.6s ease-in-out left;transition:0.6s ease-in-out left;} +.carousel .item>img{display:block;line-height:1;} +.carousel .active,.carousel .next,.carousel .prev{display:block;} +.carousel .active{left:0;} +.carousel .next,.carousel .prev{position:absolute;top:0;width:100%;} +.carousel .next{left:100%;} +.carousel .prev{left:-100%;} +.carousel .next.left,.carousel .prev.right{left:0;} +.carousel .active.left{left:-100%;} +.carousel .active.right{left:100%;} +.carousel-control{position:absolute;top:40%;left:15px;width:40px;height:40px;margin-top:-20px;font-size:60px;font-weight:100;line-height:30px;color:#ffffff;text-align:center;background:#222222;border:3px solid #ffffff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:0.5;filter:alpha(opacity=50);opacity:0.5;filter:alpha(opacity=50);}.carousel-control.right{left:auto;right:15px;} +.carousel-control:hover{color:#ffffff;text-decoration:none;opacity:0.9;filter:alpha(opacity=90);opacity:0.9;filter:alpha(opacity=90);} +.carousel-caption{position:absolute;left:0;right:0;bottom:0;padding:10px 15px 5px;background:#333333;background:rgba(0, 0, 0, 0.75);} +.carousel-caption h4,.carousel-caption p{color:#ffffff;} +.hero-unit{padding:60px;margin-bottom:30px;background-color:#eeeeee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;color:inherit;letter-spacing:-1px;} +.hero-unit p{font-size:18px;font-weight:200;line-height:24px;color:inherit;} 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8px;margin-left:-20px;font-size:20px;font-weight:200;line-height:1;color:#999999;} +#masthead .navbar-text{margin-bottom:0;line-height:32px;} +#masthead .navbar-link{color:#999999;}#masthead .navbar-link:hover{color:#ffffff;} +#masthead .btn,#masthead .btn-group{margin-top:1px;margin-top:1px;} +#masthead .btn-group .btn{margin:0;} +#masthead .nav{z-index:10000;background-color:#2c3143;} +#masthead .nav>li>a{padding:6px 10px 8px;cursor:pointer;}#masthead .nav>li>a:hover{color:gold;} +#masthead .dropdown-menu a,#masthead .dropdown-menu a:hover{text-decoration:none;} +#masthead .title{position:absolute;left:0;top:0;font-family:verdana;font-weight:bold;font-size:20px;line-height:1;color:white;padding:5px 20px 12px;margin-left:-15px;z-index:2000;}#masthead .title img{display:inline;width:26px;vertical-align:top;} +#masthead .title a{color:white;text-decoration:none;} +#masthead 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+.quota-meter-container{position:absolute;top:0;right:0;height:32px;} +.quota-meter{position:absolute;top:8px;right:8px;height:16px;width:100px;background-color:#c1c9e5;} +.quota-meter-bar{position:absolute;top:0;left:0;height:16px;background-color:#969db3;} +.quota-meter-bar-warn{background-color:#ffb400;} +.quota-meter-bar-error{background-color:#ff4343;} +.quota-meter-text{position:absolute;top:50%;left:0;width:100px;height:16px;margin-top:-6px;text-align:center;z-index:9001;color:#000000;white-space:nowrap;} +div.metadataForm{border:solid #aaaaaa 1px;} +div.metadataFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#cccccc;background-repeat:repeat-x;background-position:top;border-bottom:solid #aaaaaa 1px;} +div.metadataFormBody{background:#FFFFFF;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} +div.metadataFormBody div.metadataFormTitle{background:transparent;border:none;font-weight:bold;border-bottom:solid #dcb790 1px;margin-bottom:5px;} +div.metadataFormDisabled div.metadataFormTitle{background:#eee;border-color:#999;} +div.metadataFormDisabled{border-color:#999;} +div.metadataHelpBody{width:100%;overflow:auto;} +div.titleRow{font-weight:bold;border-bottom:dotted gray 1px;margin-bottom:0.5em;padding-bottom:0.25em;} +div.toolFormBody{background:#ffffff;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} +div.toolFormBody div.toolFormTitle{background:transparent;border:none;font-weight:bold;border-bottom:solid #d8b365 1px;margin-bottom:5px;} +div.toolFormDisabled div.toolFormTitle{background:#eeeeee;border-color:#999999;} +div.toolFormDisabled{border-color:#999999;} +div.toolHelp{margin-top:15px;padding:5px;} +div.toolHelpBody{width:100%;} +.toolForm.toolFormInCanvas{border:solid #d8b365 1px;}.toolForm.toolFormInCanvas 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+div.permissionContainer{padding-left:20px;} +.text-content hr{display:block;background:black;color:black;width:100%;height:1px;border:none;background:#aaa;color:#aaa;} +.text-content table{border-collapse:collapse;border-top:1px solid #ccc;border-left:1px solid #ccc;} +.text-content blockquote{color:#666;} +.text-content fieldset{border-color:#ccc;border:1px solid #ccc;} +.text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc;} +.text-content th,.text-content td{padding:.8em;} +.icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;background-repeat:no-repeat;background-position:0px 0px;padding:0;} +.tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} +.tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} +.tipsy-north{background-position:top center;} 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commit/galaxy-central: rmarenco: Added links to BioStar in the Help Menu and in tool forms + When asking to create a new post from galaxy tool form, tag is automatically fulfilled with the name of the tool + Added the url as global variable in universe
by Bitbucket 09 Sep '12

09 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/110a69b0d387/ changeset: 110a69b0d387 user: rmarenco date: 2012-09-09 23:13:00 summary: Added links to BioStar in the Help Menu and in tool forms + When asking to create a new post from galaxy tool form, tag is automatically fulfilled with the name of the tool + Added the url as global variable in universe affected #: 8 files diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1783,3 +1783,17 @@ .opacity(80); } } + +.icon-button.general-question{ + background: url(question-octagon-frame.png) no-repeat; + float: right; + margin-top: 3px; + margin-right: 4px; +} + +.icon-button.tag-question{ + background: url(question-balloon.png) no-repeat; + float: right; + margin-top: 3px; + margin-right: 4px; +} diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 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1px;padding-right:6px;} -.menubutton.popup,.menubutton.popup.split{padding-right:18px;}.menubutton.popup:after,.menubutton.popup.split:after{margin-top:6px;position:absolute;top:2px;right:6px;display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";opacity:0.3;filter:alpha(opacity=30);opacity:0.3;filter:alpha(opacity=30);} -div.popmenu-wrapper{position:absolute;top:100%;z-index:20000;}div.popmenu-wrapper ul.dropdown-menu{display:block;position:relative;float:none;} -ul.dropdown-menu a{text-decoration:none;} -ul.dropdown-menu li.head>a{text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);font-size:11px;font-weight:bold;line-height:16px;color:#999999;text-transform:uppercase;} -ul.dropdown-menu li.head>a:hover{background:inherit;border-color:transparent;} -.popup-arrow{cursor:pointer;text-decoration:none;color:#555;} -.popup-arrow:hover{color:black;} 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-div.toolTitle{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:square outside;} -div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} -div.toolTitleNoSection{padding-bottom:5px;font-weight:bold;} -#tool-search{padding-top:5px;padding-bottom:10px;position:relative;} -#loading_indicator{position:fixed;right:10px;top:10px;height:32px;width:32px;display:none;background:url(largespinner.gif);} -#content_table td{text-align:right;white-space:nowrap;padding:2px 10px;} -#content_table td.stringalign{text-align:left;} -.toolMenuAndView .toolForm{float:left;background-color:white;margin:10px;} -.icon-button.display{background:url(history-buttons.png) no-repeat 0px 0px;} -.icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} -.icon-button.display_disabled{background:url(history-buttons.png) no-repeat 0px -52px;} -.icon-button.delete{background:url(history-buttons.png) no-repeat 0px -78px;} -.icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -104px;} -.icon-button.delete_disabled{background:url(history-buttons.png) no-repeat 0px -130px;} -.icon-button.edit{background:url(history-buttons.png) no-repeat 0px -156px;} -.icon-button.edit:hover{background:url(history-buttons.png) no-repeat 0px -182px;} -.icon-button.edit_disabled{background:url(history-buttons.png) no-repeat 0px -208px;} -.icon-button.tag{background:url(fugue.png) no-repeat 0px 0px;} -.icon-button.tags{background:url(fugue.png) no-repeat 0px -26px;} -.icon-button.tag--plus{background:url(fugue.png) no-repeat 0px -52px;} -.icon-button.toggle-expand{background:url(fugue.png) no-repeat 0px -78px;} -.icon-button.toggle{background:url(fugue.png) no-repeat 0px -104px;} -.icon-button.toggle:hover{background:url(fugue.png) no-repeat 0px -130px;} -.icon-button.arrow-circle{background:url(fugue.png) no-repeat 0px -156px;} -.icon-button.chevron{background:url(fugue.png) no-repeat 0px -182px;} -.icon-button.bug{background:url(fugue.png) no-repeat 0px -208px;} -.icon-button.disk{background:url(fugue.png) no-repeat 0px -234px;} -.icon-button.information{background:url(fugue.png) no-repeat 0px -260px;} -.icon-button.annotate{background:url(fugue.png) no-repeat 0px -286px;} -.icon-button.go-to-full-screen{background:url(fugue.png) no-repeat 0px -312px;} -.icon-button.import{background:url(fugue.png) no-repeat 0px -338px;} -.icon-button.plus-button{background:url(fugue.png) no-repeat 0px -364px;} -.icon-button.plus-button:hover{background:url(fugue.png) no-repeat 0px -390px;} -.icon-button.gear{background:url(fugue.png) no-repeat 0px -416px;} -.icon-button.chart_curve{background:url(fugue.png) no-repeat 0px -442px;} -.icon-button.disk--arrow{background:url(fugue.png) no-repeat 0px -468px;} -.icon-button.disk--arrow:hover{background:url(fugue.png) no-repeat 0px -494px;} -.icon-button.cross-circle{background:url(fugue.png) no-repeat 0px -520px;} -.icon-button.cross-circle:hover{background:url(fugue.png) no-repeat 0px -546px;} -.icon-button.arrow-split{background:url(fugue.png) no-repeat 0px -572px;} -.icon-button.arrow-split:hover{background:url(fugue.png) no-repeat 0px -598px;} -.icon-button.chevron-expand:hover{background:url(fugue.png) no-repeat 0px -624px;} -.icon-button.chevron-expand{background:url(fugue.png) no-repeat 0px -650px;} -.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -676px;} -div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px 0px;} -div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} -div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} -.text-and-autocomplete-select{background:none;position:relative;padding-right:18px;}.text-and-autocomplete-select:after{margin-top:6px;position:absolute;top:2px;right:6px;width:10px;height:10px;display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";opacity:0.3;filter:alpha(opacity=30);opacity:0.3;filter:alpha(opacity=30);opacity:0.8;filter:alpha(opacity=80);opacity:0.8;filter:alpha(opacity=80);} diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c static/june_2007_style/blue/question-balloon.png Binary file static/june_2007_style/blue/question-balloon.png has changed diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c static/june_2007_style/blue/question-octagon-frame.png Binary file static/june_2007_style/blue/question-octagon-frame.png has changed diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -12,7 +12,7 @@ </%def><%def name="javascripts()"> - ${h.js( "libs/jquery/jquery", "galaxy.panels", "galaxy.base", "libs/jquery/jquery.autocomplete", "libs/jquery/jstorage" )} + ${h.js( "libs/jquery/jquery", "galaxy.panels", "galaxy.base", "libs/jquery/jquery.autocomplete", "libs/jquery/jstorage", "libs/bootstrap" )} <script type="text/javascript"> $(function() { $(window).bind("refresh_on_change", function() { @@ -282,6 +282,11 @@ tool_url = tool.action[0] + h.url_for(tool.action[1]) %> +<% + # Name of the tool in lower case + low_tool_name = tool.name.lower() +%> + %if tool_id_version_message: ${render_msg( tool_id_version_message, 'warning' )} %endif @@ -289,12 +294,17 @@ <div class="toolForm" id="${tool.id}"><form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> %if tool.has_multiple_pages: - <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div> + <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages}) %elif not tool_version_select_field: - <div class="toolFormTitle">${tool.name} (version ${tool.version})</div> + <div class="toolFormTitle">${tool.name} (version ${tool.version}) %else: - <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()}</div> + <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()} %endif +  + <a href="http://slyfox.bx.psu.edu:8080/new/post/tagged/${low_tool_name}" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> + <a href="http://slyfox.bx.psu.edu:8080/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a> +  + </div><div class="toolFormBody"><input type="hidden" name="refresh" value="refresh"><input type="hidden" name="tool_id" value="${tool.id}"> diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -71,7 +71,8 @@ ## Help tab. <% - menu_options = [ + menu_options = [ + [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8080/" ), "_blank" ] [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], [_('Tool shed wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" ), "_blank" ], [_('Galaxy wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -120,6 +120,7 @@ ## Help tab. <% menu_options = [ + [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8080/" ), "galaxy_main" ], [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -263,6 +263,9 @@ # as on the user registration and login forms. #terms_url = None +# The URL linked by the "Galaxy Q&A" link in the "Help" menu +qa_url = http://slyfox.bx.psu.edu:8080/ + # Serve static content, which must be enabled if you're not serving it via a # proxy server. These options should be self explanatory and so are not # documented individually. You can use these paths (or ones in the proxy 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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