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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 15 Jul '14

15 Jul '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/518d296e4ed8/ Changeset: 518d296e4ed8 User: jgoecks Date: 2014-07-15 17:07:41 Summary: Trackster: readd long lost code to detect unsaved changes and prompt to save on exit. Affected #: 1 file diff -r 7c5d92187dfd5b92fd05e0fcab163a8a0ef89ffa -r 518d296e4ed8646b9e738e5293dab9f77834bf17 static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -35,9 +35,62 @@ }, /** + * Save visualization, returning a Deferred object for the remote call to save. + */ + save_viz: function() { + // show dialog + Galaxy.modal.show({title: "Saving...", body: "progress" }); + + // Save bookmarks. + var bookmarks = []; + $(".bookmark").each(function() { + bookmarks.push({ + position: $(this).children(".position").text(), + annotation: $(this).children(".annotation").text() + }); + }); + + // FIXME: give unique IDs to Drawables and save overview as ID. + var overview_track_name = (view.overview_drawable ? view.overview_drawable.config.get_value('name') : null), + viz_config = { + 'view': view.to_dict(), + 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, + 'bookmarks': bookmarks + }; + + // Make call to save visualization. + return $.ajax({ + url: galaxy_config.root + "visualization/save", + type: "POST", + dataType: "json", + data: { + 'id' : view.vis_id, + 'title' : view.config.get_value('name'), + 'dbkey' : view.dbkey, + 'type' : 'trackster', + 'vis_json' : JSON.stringify(viz_config) + } + }).success(function(vis_info) { + Galaxy.modal.hide(); + view.vis_id = vis_info.vis_id; + view.has_changes = false; + + // Needed to set URL when first saving a visualization. + window.history.pushState({}, "", vis_info.url + window.location.hash); + }).error(function() { + // show dialog + Galaxy.modal.show({ + title : "Could Not Save", + body : "Could not save visualization. Please try again later.", + buttons : { "Cancel": function() { Galaxy.modal.hide(); } } + }); + }); + }, + + /** * Create button menu */ - createButtonMenu: function() { + createButtonMenu: function() { var self = this, menu = create_icon_buttons_menu([ { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { @@ -62,58 +115,13 @@ } }, { icon_class: 'disk--arrow', title: 'Save', on_click: function() { - // show dialog - Galaxy.modal.show({title: "Saving...", body: "progress" }); - - // Save bookmarks. - var bookmarks = []; - $(".bookmark").each(function() { - bookmarks.push({ - position: $(this).children(".position").text(), - annotation: $(this).children(".annotation").text() - }); - }); - - // FIXME: give unique IDs to Drawables and save overview as ID. - var overview_track_name = (view.overview_drawable ? view.overview_drawable.config.get_value('name') : null), - viz_config = { - 'view': view.to_dict(), - 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, - 'bookmarks': bookmarks - }; - - $.ajax({ - url: galaxy_config.root + "visualization/save", - type: "POST", - dataType: "json", - data: { - 'id' : view.vis_id, - 'title' : view.config.get_value('name'), - 'dbkey' : view.dbkey, - 'type' : 'trackster', - 'vis_json' : JSON.stringify(viz_config) - } - }).success(function(vis_info) { - Galaxy.modal.hide(); - view.vis_id = vis_info.vis_id; - view.has_changes = false; - - // Needed to set URL when first saving a visualization. - window.history.pushState({}, "", vis_info.url + window.location.hash); - }).error(function() { - // show dialog - Galaxy.modal.show({ - title : "Could Not Save", - body : "Could not save visualization. Please try again later.", - buttons : { "Cancel": function() { Galaxy.modal.hide() } } - }); - }); + self.save_viz(); } }, { icon_class: 'cross-circle', title: 'Close', on_click: function() { - window.location = galaxy_config.root + 'visualization'; + self.handle_unsaved_changes(view); } } ], @@ -302,7 +310,7 @@ /** * Set up keyboard navigation for a visualization. */ - init_keyboard_nav: function(view) { + init_keyboard_nav: function(view) { // Keyboard navigation. Scroll ~7% of height when scrolling up/down. $(document).keyup(function(e) { // Do not navigate if arrow keys used in input element. @@ -328,6 +336,35 @@ break; } }); + }, + + /** + * Handle unsaved changes in visualization. + */ + handle_unsaved_changes: function(view) { + if (view.has_changes) { + var self = this; + Galaxy.modal.show({ + title: "Close visualization", + body: "There are unsaved changes to your visualization which will be lost if you do not save them.", + buttons: { + "Cancel": function() { Galaxy.modal.hide(); }, + "Leave without Saving" : function() { + window.onbeforeunload = undefined; + window.location = galaxy_config.root + 'visualization'; + }, + "Save" : function() { + $.when(self.save_viz()).then(function() { + window.location = galaxy_config.root + 'visualization'; + }); + } + } + }); + + } + else { + window.location = galaxy_config.root + 'visualization'; + } } }); https://bitbucket.org/galaxy/galaxy-central/commits/08a1e9d70ebc/ Changeset: 08a1e9d70ebc User: jgoecks Date: 2014-07-15 18:19:47 Summary: Trackster: add dialog to indicate changes will be lost if navigating away from the viz. Affected #: 1 file diff -r 518d296e4ed8646b9e738e5293dab9f77834bf17 -r 08a1e9d70ebcf08bd8ec850e678a6a5a79cf9f5f static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -211,6 +211,10 @@ // initialize keyboard ui.init_keyboard_nav(view); + + $(window).on('beforeunload', function() { + return "There are unsaved changes to your visualization that will be lost if you leave this page."; + }); } }); https://bitbucket.org/galaxy/galaxy-central/commits/a34d766b17c7/ Changeset: a34d766b17c7 User: jgoecks Date: 2014-07-15 18:33:54 Summary: Trackster: bug fixes for managing state. Affected #: 2 files diff -r 08a1e9d70ebcf08bd8ec850e678a6a5a79cf9f5f -r a34d766b17c7f3a7e6683e6b2d7aa6cb2a3b7215 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -213,7 +213,9 @@ ui.init_keyboard_nav(view); $(window).on('beforeunload', function() { - return "There are unsaved changes to your visualization that will be lost if you leave this page."; + if (view.has_changes) { + return "There are unsaved changes to your visualization that will be lost if you leave this page."; + } }); } }); diff -r 08a1e9d70ebcf08bd8ec850e678a6a5a79cf9f5f -r a34d766b17c7f3a7e6683e6b2d7aa6cb2a3b7215 static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -267,9 +267,6 @@ } } - // Need to update intro div after drawables have been added. - view.update_intro_div(); - // Set overview. var overview_drawable; for (var i = 0; i < view.drawables.length; i++) { https://bitbucket.org/galaxy/galaxy-central/commits/893a727a7b7c/ Changeset: 893a727a7b7c User: jgoecks Date: 2014-07-15 18:41:06 Summary: Trackster: mark visualization changed when tracks change. Affected #: 1 file diff -r a34d766b17c7f3a7e6683e6b2d7aa6cb2a3b7215 -r 893a727a7b7cc83355bc977d034622da50af16e5 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1380,6 +1380,14 @@ drawable.init(); this.changed(); this.update_intro_div(); + + // When drawable config changes, mark view as changed. This + // captures most (all?) state change that needs to be saved. + var self = this; + drawable.config.on('change', function() { + console.log(drawable.config.get_value('name') + " changed"); + self.changed(); + }); }, add_label_track: function (label_track) { 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: Merged in dannon/galaxy-central-prmaker/stable (pull request #439)
by commits-noreply＠bitbucket.org 15 Jul '14

15 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d3b1f484c4b6/ Changeset: d3b1f484c4b6 Branch: stable User: natefoo Date: 2014-07-15 17:33:46 Summary: Merged in dannon/galaxy-central-prmaker/stable (pull request #439) #STABLE migrate104 fix w/ threadlocal. "103 is not 105" Affected #: 1 file diff -r deba1986ea22e42fb1f290f50a62b51d4cfad762 -r d3b1f484c4b6bbb3daa50fa167eef97a384890b3 lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py --- a/lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py +++ b/lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py @@ -23,6 +23,8 @@ handler.setFormatter( formatter ) log.addHandler( handler ) +metadata = MetaData() +context = scoped_session( sessionmaker( autoflush=False, autocommit=True ) ) class DeferredJob( object ): states = Bunch( NEW = 'new', @@ -37,12 +39,8 @@ self.params = params def upgrade(migrate_engine): - metadata = MetaData() metadata.bind = migrate_engine - Session = sessionmaker( bind=migrate_engine) - context = Session() - DeferredJob.table = Table( "deferred_job", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), @@ -70,12 +68,8 @@ context.flush() def downgrade(migrate_engine): - metadata = MetaData() metadata.bind = migrate_engine - Session = sessionmaker( bind=migrate_engine) - context = Session() - jobs = context.query( DeferredJob ).filter_by( plugin='GenomeTransferPlugin' ).all() for job in jobs: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Jul '14

15 Jul '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0af879ff3097/ Changeset: 0af879ff3097 Branch: stable User: dannon Date: 2014-07-11 17:54:27 Summary: Migration 104 was using a Session() object that conflicts with the threadlocal strategy, which has been causing the '103 is not 105' migration errors we've seen. scoped_session works, but the threadlocal should probably be completely deprecated moving forward (removed from universe_wsgi.ini.sample by nate just now). See http://docs.sqlalchemy.org/en/rel_0_9/core/connections.html#threadlocal-str… Affected #: 1 file diff -r b1441a96b8401fd14ab3364c5d6dfa0733df263e -r 0af879ff30978e2c3b2c6d5df2de93ae40a39a16 lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py --- a/lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py +++ b/lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py @@ -23,6 +23,8 @@ handler.setFormatter( formatter ) log.addHandler( handler ) +metadata = MetaData() +context = scoped_session( sessionmaker( autoflush=False, autocommit=True ) ) class DeferredJob( object ): states = Bunch( NEW = 'new', @@ -37,12 +39,8 @@ self.params = params def upgrade(migrate_engine): - metadata = MetaData() metadata.bind = migrate_engine - Session = sessionmaker( bind=migrate_engine) - context = Session() - DeferredJob.table = Table( "deferred_job", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), @@ -70,12 +68,8 @@ context.flush() def downgrade(migrate_engine): - metadata = MetaData() metadata.bind = migrate_engine - Session = sessionmaker( bind=migrate_engine) - context = Session() - jobs = context.query( DeferredJob ).filter_by( plugin='GenomeTransferPlugin' ).all() for job in jobs: https://bitbucket.org/galaxy/galaxy-central/commits/d3b1f484c4b6/ Changeset: d3b1f484c4b6 Branch: stable User: natefoo Date: 2014-07-15 17:33:46 Summary: Merged in dannon/galaxy-central-prmaker/stable (pull request #439) #STABLE migrate104 fix w/ threadlocal. "103 is not 105" Affected #: 1 file diff -r deba1986ea22e42fb1f290f50a62b51d4cfad762 -r d3b1f484c4b6bbb3daa50fa167eef97a384890b3 lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py --- a/lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py +++ b/lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py @@ -23,6 +23,8 @@ handler.setFormatter( formatter ) log.addHandler( handler ) +metadata = MetaData() +context = scoped_session( sessionmaker( autoflush=False, autocommit=True ) ) class DeferredJob( object ): states = Bunch( NEW = 'new', @@ -37,12 +39,8 @@ self.params = params def upgrade(migrate_engine): - metadata = MetaData() metadata.bind = migrate_engine - Session = sessionmaker( bind=migrate_engine) - context = Session() - DeferredJob.table = Table( "deferred_job", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), @@ -70,12 +68,8 @@ context.flush() def downgrade(migrate_engine): - metadata = MetaData() metadata.bind = migrate_engine - Session = sessionmaker( bind=migrate_engine) - context = Session() - jobs = context.query( DeferredJob ).filter_by( plugin='GenomeTransferPlugin' ).all() for job in jobs: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Visualization bug fixes.
by commits-noreply＠bitbucket.org 14 Jul '14

14 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7c5d92187dfd/ Changeset: 7c5d92187dfd User: jgoecks Date: 2014-07-14 20:07:04 Summary: Visualization bug fixes. Affected #: 2 files diff -r d09b3a2bd7b2f0fe07f9894923b9a73d02176a82 -r 7c5d92187dfd5b92fd05e0fcab163a8a0ef89ffa lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -194,7 +194,7 @@ max_vals = data_provider.get_default_max_vals() # Get reference sequence and mean depth for region; these is used by providers for aligned reads. - ref_seq = None + region = None mean_depth = None if isinstance( data_provider, (SamDataProvider, BamDataProvider ) ): # Get reference sequence. diff -r d09b3a2bd7b2f0fe07f9894923b9a73d02176a82 -r 7c5d92187dfd5b92fd05e0fcab163a8a0ef89ffa static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -1462,6 +1462,7 @@ if (num_samples === 1) { row_height = feature_height = (w_scale < ctx.canvas.manager.char_width_px ? this.prefs.summary_height : row_height); + paint_utils.row_height = row_height; // No summary when there's a single sample. draw_summary = false; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 14 Jul '14

14 Jul '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/46df437c4059/ Changeset: 46df437c4059 User: jgoecks Date: 2014-07-14 16:13:44 Summary: Clean up for fetching genome reference data for visualization. Affected #: 3 files diff -r 018d08d81c1e58e9aa42e8c5b179c413f6fb509b -r 46df437c405989b2d93fcccc0937aa804f0d9555 lib/galaxy/visualization/genomes.py --- a/lib/galaxy/visualization/genomes.py +++ b/lib/galaxy/visualization/genomes.py @@ -31,10 +31,11 @@ A genomic region on an individual chromosome. """ - def __init__( self, chrom = None, start = 0, end = 0 ): + def __init__( self, chrom = None, start = 0, end = 0, sequence=None ): self.chrom = chrom self.start = int( start ) self.end = int( end ) + self.sequence = sequence def __str__( self ): return self.chrom + ":" + str( self.start ) + "-" + str( self.end ) @@ -356,6 +357,6 @@ twobit = TwoBitFile( open( twobit_file_name ) ) if chrom in twobit: seq_data = twobit[chrom].get( int(low), int(high) ) - return { 'dataset_type': 'refseq', 'data': seq_data } + return GenomeRegion( chrom=chrom, start=low, end=high, sequence=seq_data ) except IOError: return None diff -r 018d08d81c1e58e9aa42e8c5b179c413f6fb509b -r 46df437c405989b2d93fcccc0937aa804f0d9555 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -199,9 +199,9 @@ if isinstance( data_provider, (SamDataProvider, BamDataProvider ) ): # Get reference sequence. if dataset.dbkey: - data_dict = self.app.genomes.reference( trans, dbkey=dataset.dbkey, chrom=chrom, low=low, high=high ) - if data_dict: - ref_seq = data_dict[ 'data' ] + region = self.app.genomes.reference( trans, dbkey=dataset.dbkey, chrom=chrom, low=low, high=high ) + if region: + ref_seq = region.sequence # Get mean depth. if not indexer: diff -r 018d08d81c1e58e9aa42e8c5b179c413f6fb509b -r 46df437c405989b2d93fcccc0937aa804f0d9555 lib/galaxy/webapps/galaxy/api/genomes.py --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/lib/galaxy/webapps/galaxy/api/genomes.py @@ -36,7 +36,8 @@ # Return info. rval = None if reference: - rval = self.app.genomes.reference( trans, dbkey=id, chrom=chrom, low=low, high=high ) + region = self.app.genomes.reference( trans, dbkey=id, chrom=chrom, low=low, high=high ) + rval = { 'dataset_type': 'refseq', 'data': region.sequence } else: rval = self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low ) return rval https://bitbucket.org/galaxy/galaxy-central/commits/d09b3a2bd7b2/ Changeset: d09b3a2bd7b2 User: jgoecks Date: 2014-07-14 17:35:14 Summary: Aligned read visualization data providers: do reference-based compression for complete read rather than read in requested region so that read representation is uniform. Affected #: 3 files diff -r 46df437c405989b2d93fcccc0937aa804f0d9555 -r d09b3a2bd7b2f0fe07f9894923b9a73d02176a82 lib/galaxy/visualization/data_providers/cigar.py --- a/lib/galaxy/visualization/data_providers/cigar.py +++ b/lib/galaxy/visualization/data_providers/cigar.py @@ -18,7 +18,7 @@ return read_seq, cigar # Set up position for reference, read. - ref_seq_pos = read_start - ref_seq_start + ref_seq_pos = read_start read_pos = 0 # Create new read sequence, cigar. @@ -27,42 +27,30 @@ cigar_ops = 'MIDNSHP=X' for op_tuple in cigar: op, op_len = op_tuple - + # Op is index into string 'MIDNSHP=X' if op == 0: # Match - # If region falls outside ref_seq data, leave as M. - if ref_seq_start - read_start > op_len: - # Region falls completely outside of reference. - new_cigar += '%iM' % ( op_len ) - else: - # Some of region overlap reference. - total_count = 0 - if read_start < ref_seq_start: - new_cigar += '%iM' % ( ref_seq_start - read_start ) - read_pos = ref_seq_start - read_start - ref_seq_pos = 0 - total_count = read_pos + # Transform Ms to =s and Xs using reference. + new_op = '' + total_count = 0 + while total_count < op_len and ref_seq_pos < len( ref_seq ): + match, count = _match_mismatch_counter( read_seq, read_pos, ref_seq, ref_seq_pos ) + # Use min because count cannot exceed remainder of operation. + count = min( count, op_len - total_count ) + if match: + new_op = '=' + else: + new_op = 'X' + # Include mismatched bases in new read sequence. + new_read_seq += read_seq[ read_pos:read_pos + count ] + new_cigar += '%i%s' % ( count, new_op ) + total_count += count + read_pos += count + ref_seq_pos += count - # Transform Ms to =s and Xs using reference. - new_op = '' - while total_count < op_len and ref_seq_pos < len( ref_seq ): - match, count = _match_mismatch_counter( read_seq, read_pos, ref_seq, ref_seq_pos ) - # Use min because count cannot exceed remainder of operation. - count = min( count, op_len - total_count ) - if match: - new_op = '=' - else: - new_op = 'X' - # Include mismatched bases in new read sequence. - new_read_seq += read_seq[ read_pos:read_pos + count ] - new_cigar += '%i%s' % ( count, new_op ) - total_count += count - read_pos += count - ref_seq_pos += count - - # If end of read falls outside of ref_seq data, leave as M. - if total_count < op_len: - new_cigar += '%iM' % ( op_len - total_count ) + # If end of read falls outside of ref_seq data, leave as M. + if total_count < op_len: + new_cigar += '%iM' % ( op_len - total_count ) elif op == 1: # Insertion new_cigar += '%i%s' % ( op_len, cigar_ops[ op ] ) # Include insertion bases in new read sequence. diff -r 46df437c405989b2d93fcccc0937aa804f0d9555 -r d09b3a2bd7b2f0fe07f9894923b9a73d02176a82 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -1068,8 +1068,8 @@ ''' read_seq, read_cigar = get_ref_based_read_seq_and_cigar( read[ seq_field ].upper(), read[ start_field ], - ref_seq, - start, + ref_seq.sequence, + ref_seq.start, read[ cigar_field ] ) read[ seq_field ] = read_seq read[ cigar_field ] = read_cigar @@ -1088,7 +1088,7 @@ # if possible. Otherwise, convert cigar. if ref_seq: # Uppercase for easy comparison. - ref_seq = ref_seq.upper() + ref_seq.sequence = ref_seq.sequence.upper() process_read = compress_seq_and_cigar else: process_read = convert_cigar diff -r 46df437c405989b2d93fcccc0937aa804f0d9555 -r d09b3a2bd7b2f0fe07f9894923b9a73d02176a82 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -199,9 +199,11 @@ if isinstance( data_provider, (SamDataProvider, BamDataProvider ) ): # Get reference sequence. if dataset.dbkey: - region = self.app.genomes.reference( trans, dbkey=dataset.dbkey, chrom=chrom, low=low, high=high ) - if region: - ref_seq = region.sequence + # FIXME: increase region 500bp each way to provide sequence for overlapping reads. As reads + # get longer, this will need to be increased and/or a handle to the genomic data may be need + # to be given to the data provider. + region = self.app.genomes.reference( trans, dbkey=dataset.dbkey, chrom=chrom, + low=( int( low ) - 500 ), high=( int( high ) + 500 ) ) # Get mean depth. if not indexer: @@ -212,7 +214,7 @@ # Get and return data from data_provider. result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ), - ref_seq=ref_seq, mean_depth=mean_depth, **kwargs ) + ref_seq=region, mean_depth=mean_depth, **kwargs ) result.update( { 'dataset_type': data_provider.dataset_type, 'extra_info': extra_info } ) return result 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: davebgx: Merge fix from stable.
by commits-noreply＠bitbucket.org 14 Jul '14

14 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/018d08d81c1e/ Changeset: 018d08d81c1e User: davebgx Date: 2014-07-14 15:19:10 Summary: Merge fix from stable. Affected #: 1 file diff -r 5b7e495d6f2fefe2b51da8bc438e4053b2a7a6af -r 018d08d81c1e58e9aa42e8c5b179c413f6fb509b lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -703,7 +703,9 @@ filename = action_dict[ 'target_filename' ] else: filename = url.split( '/' )[ -1 ] - self.url_download( work_dir, filename, url ) + if current_dir is not None: + work_dir = current_dir + self.url_download( work_dir, filename, url, extract=action_dict[ 'extract' ] ) if initial_download: dir = os.path.curdir return tool_dependency, filtered_actions, dir 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: davebgx: When executing a download_file action, take into account that the current working directory may have been modified by previous steps.
by commits-noreply＠bitbucket.org 14 Jul '14

14 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/deba1986ea22/ Changeset: deba1986ea22 Branch: stable User: davebgx Date: 2014-07-09 16:39:01 Summary: When executing a download_file action, take into account that the current working directory may have been modified by previous steps. Affected #: 1 file diff -r b1441a96b8401fd14ab3364c5d6dfa0733df263e -r deba1986ea22e42fb1f290f50a62b51d4cfad762 lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -447,7 +447,9 @@ filename = action_dict[ 'target_filename' ] else: filename = url.split( '/' )[ -1 ] - td_common_util.url_download( work_dir, filename, url ) + if current_dir is not None: + work_dir = current_dir + td_common_util.url_download( work_dir, filename, url, extract=action_dict[ 'extract' ] ) if initial_download: dir = os.path.curdir return tool_dependency, filtered_actions, dir Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug in visualization data provider: correctly hash identifier.
by commits-noreply＠bitbucket.org 12 Jul '14

12 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5b7e495d6f2f/ Changeset: 5b7e495d6f2f User: jgoecks Date: 2014-07-13 01:41:55 Summary: Fix bug in visualization data provider: correctly hash identifier. Affected #: 1 file diff -r 20094b0c186b6231251838d96662ad202622ef22 -r 5b7e495d6f2fefe2b51da8bc438e4053b2a7a6af lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -1057,7 +1057,7 @@ r1 = [ read['start'], read['end'], read['cigar'], read['strand'], read['seq'] ] r2 = [ read['mate_start'], read['mate_start'] ] - results.append( [ "%i_%s" % ( read_start, qname ), read_start, read_end, qname, r1, r2, [read[ 'mapq' ], 125] ] ) + results.append( [ hash( "%i_%s" % ( read_start, qname ) ), read_start, read_end, qname, r1, r2, [read[ 'mapq' ], 125] ] ) # Clean up. TODO: is this needed? If so, we'll need a cleanup function after processing the data. # bamfile.close() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Visualization genome data providers: readd require numpy because it is a dependency of bx-python.
by commits-noreply＠bitbucket.org 11 Jul '14

11 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/20094b0c186b/ Changeset: 20094b0c186b User: jgoecks Date: 2014-07-11 19:53:04 Summary: Visualization genome data providers: readd require numpy because it is a dependency of bx-python. Affected #: 1 file diff -r b74c56d994efbb0e8330d9dd75c682358c963497 -r 20094b0c186b6231251838d96662ad202622ef22 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -8,6 +8,7 @@ import random import math +pkg_resources.require( "numpy" ) pkg_resources.require( "bx-python" ) pkg_resources.require( "pysam" ) from bx.interval_index_file import Indexes Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Visualization genome data providers: remove dependency on numpy.
by commits-noreply＠bitbucket.org 11 Jul '14

11 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b74c56d994ef/ Changeset: b74c56d994ef User: jgoecks Date: 2014-07-11 18:20:40 Summary: Visualization genome data providers: remove dependency on numpy. Affected #: 1 file diff -r 154429911adcedfefb26776670805f4591baf502 -r b74c56d994efbb0e8330d9dd75c682358c963497 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -6,11 +6,10 @@ import pkg_resources import itertools import random +import math pkg_resources.require( "bx-python" ) pkg_resources.require( "pysam" ) -pkg_resources.require( "numpy" ) -import numpy from bx.interval_index_file import Indexes from bx.bbi.bigwig_file import BigWigFile from bx.bbi.bigbed_file import BigBedFile @@ -1179,7 +1178,7 @@ var = summary.sum_squares[0] - mean if valid_count > 1: var /= valid_count - 1 - sd = numpy.sqrt( var ) + sd = math.sqrt( var ) min_val = summary.min_val[0] max_val = summary.max_val[0] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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