August 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 3 new changesets
by Bitbucket 15 Aug '11

15 Aug '11

3 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/83c4366e0641/ changeset: 83c4366e0641 branch: xml_filetype user: peterjc date: 2011-06-06 12:48:17 summary: Implement GenericXml filetype ('xml'). Closes issue #568 affected #: 2 files (1.3 KB) --- a/lib/galaxy/datatypes/registry.py Fri Jun 03 17:00:20 2011 -0400 +++ b/lib/galaxy/datatypes/registry.py Mon Jun 06 11:48:17 2011 +0100 @@ -180,7 +180,8 @@ 'tabular' : tabular.Tabular(), 'taxonomy' : tabular.Taxonomy(), 'txt' : data.Text(), - 'wig' : interval.Wiggle() + 'wig' : interval.Wiggle(), + 'xml' : xml.GenericXml(), } self.mimetypes_by_extension = { 'ab1' : 'application/octet-stream', @@ -211,7 +212,8 @@ 'tabular' : 'text/plain', 'taxonomy' : 'text/plain', 'txt' : 'text/plain', - 'wig' : 'text/plain' + 'wig' : 'text/plain', + 'xml' : 'application/xml', } # super supertype fix for input steps in workflows. if 'data' not in self.datatypes_by_extension: @@ -224,6 +226,7 @@ binary.Bam(), binary.Sff(), xml.BlastXml(), + xml.GenericXml(), sequence.Maf(), sequence.Lav(), sequence.csFasta(), --- a/lib/galaxy/datatypes/xml.py Fri Jun 03 17:00:20 2011 -0400 +++ b/lib/galaxy/datatypes/xml.py Mon Jun 06 11:48:17 2011 +0100 @@ -7,7 +7,43 @@ log = logging.getLogger(__name__) -class BlastXml( data.Text ): +class GenericXml( data.Text ): + """Base format class for any XML file.""" + file_ext = "xml" + + def set_peek( self, dataset, is_multi_byte=False ): + """Set the peek and blurb text""" + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = 'XML data' + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def sniff( self, filename ): + """ + Determines whether the file is XML or not + + >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' ) + >>> GenericXml().sniff( fname ) + True + >>> fname = get_test_fname( 'tblastn_four_human_vs_rhodopsin.xml' ) + >>> BlastXml().sniff( fname ) + True + >>> fname = get_test_fname( 'interval.interval' ) + >>> GenericXml().sniff( fname ) + False + """ + #TODO - Use a context manager on Python 2.5+ to close handle + handle = open(filename) + line = handle.readline() + handle.close() + + #TODO - Is there a more robust way to do this? + return line.startswith('<?xml ') + + +class BlastXml( GenericXml ): """NCBI Blast XML Output data""" file_ext = "blastxml" @@ -52,7 +88,7 @@ return True -class MEMEXml( data.Text ): +class MEMEXml( GenericXml ): """MEME XML Output data""" file_ext = "memexml" http://bitbucket.org/galaxy/galaxy-central/changeset/b005f35a1104/ changeset: b005f35a1104 branch: xml_filetype user: natefoo date: 2011-08-15 19:27:43 summary: Close the xml_filetype branch. affected #: 0 files (0 bytes) http://bitbucket.org/galaxy/galaxy-central/changeset/6165799c4e49/ changeset: 6165799c4e49 user: natefoo date: 2011-08-15 19:28:40 summary: Merged the xml_filetype branch from Peter Cock, which adds a generic XML datatype. affected #: 2 files (1.3 KB) --- a/lib/galaxy/datatypes/registry.py Mon Aug 15 09:18:52 2011 -0400 +++ b/lib/galaxy/datatypes/registry.py Mon Aug 15 13:28:40 2011 -0400 @@ -170,7 +170,8 @@ 'tabular' : tabular.Tabular(), 'taxonomy' : tabular.Taxonomy(), 'txt' : data.Text(), - 'wig' : interval.Wiggle() + 'wig' : interval.Wiggle(), + 'xml' : xml.GenericXml(), } self.mimetypes_by_extension = { 'ab1' : 'application/octet-stream', @@ -201,7 +202,8 @@ 'tabular' : 'text/plain', 'taxonomy' : 'text/plain', 'txt' : 'text/plain', - 'wig' : 'text/plain' + 'wig' : 'text/plain', + 'xml' : 'application/xml', } # super supertype fix for input steps in workflows. if 'data' not in self.datatypes_by_extension: @@ -214,6 +216,7 @@ binary.Bam(), binary.Sff(), xml.BlastXml(), + xml.GenericXml(), sequence.Maf(), sequence.Lav(), sequence.csFasta(), --- a/lib/galaxy/datatypes/xml.py Mon Aug 15 09:18:52 2011 -0400 +++ b/lib/galaxy/datatypes/xml.py Mon Aug 15 13:28:40 2011 -0400 @@ -7,7 +7,43 @@ log = logging.getLogger(__name__) -class BlastXml( data.Text ): +class GenericXml( data.Text ): + """Base format class for any XML file.""" + file_ext = "xml" + + def set_peek( self, dataset, is_multi_byte=False ): + """Set the peek and blurb text""" + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = 'XML data' + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def sniff( self, filename ): + """ + Determines whether the file is XML or not + + >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' ) + >>> GenericXml().sniff( fname ) + True + >>> fname = get_test_fname( 'tblastn_four_human_vs_rhodopsin.xml' ) + >>> BlastXml().sniff( fname ) + True + >>> fname = get_test_fname( 'interval.interval' ) + >>> GenericXml().sniff( fname ) + False + """ + #TODO - Use a context manager on Python 2.5+ to close handle + handle = open(filename) + line = handle.readline() + handle.close() + + #TODO - Is there a more robust way to do this? + return line.startswith('<?xml ') + + +class BlastXml( GenericXml ): """NCBI Blast XML Output data""" file_ext = "blastxml" @@ -52,7 +88,7 @@ return True -class MEMEXml( data.Text ): +class MEMEXml( GenericXml ): """MEME XML Output data""" file_ext = "memexml" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Change the bugs_email config setting to be the url to our new support wiki.
by Bitbucket 15 Aug '11

15 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b87e47a7c193/ changeset: b87e47a7c193 user: greg date: 2011-08-15 15:18:52 summary: Change the bugs_email config setting to be the url to our new support wiki. affected #: 8 files (2.6 KB) --- a/community_wsgi.ini.sample Sun Aug 14 19:49:26 2011 -0400 +++ b/community_wsgi.ini.sample Mon Aug 15 09:18:52 2011 -0400 @@ -55,6 +55,9 @@ # path to sendmail sendmail_path = /usr/sbin/sendmail +# The URL linked by the "Support" link in the "Help" menu. +#support_url = http://wiki.g2.bx.psu.edu/Support + # Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) ## use_heartbeat = True --- a/lib/galaxy/config.py Sun Aug 14 19:49:26 2011 -0400 +++ b/lib/galaxy/config.py Mon Aug 15 09:18:52 2011 -0400 @@ -106,7 +106,6 @@ self.brand = kwargs.get( 'brand', None ) self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' ) self.wiki_url = kwargs.get( 'wiki_url', 'http://g2.trac.bx.psu.edu/' ) - self.bugs_email = kwargs.get( 'bugs_email', None ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.library_import_dir = kwargs.get( 'library_import_dir', None ) --- a/lib/galaxy/web/controllers/root.py Sun Aug 14 19:49:26 2011 -0400 +++ b/lib/galaxy/web/controllers/root.py Mon Aug 15 09:18:52 2011 -0400 @@ -484,49 +484,6 @@ except: return trans.show_error_message( "<p>Failed to make secondary dataset primary.</p>" ) - # @web.expose - # def masthead( self, trans, active_view=None ): - # brand = trans.app.config.get( "brand", "" ) - # if brand: - # brand ="<span class='brand'>/%s</span>" % brand - # wiki_url = trans.app.config.get( "wiki_url", "http://g2.trac.bx.psu.edu/" ) - # bugs_email = trans.app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" ) - # blog_url = trans.app.config.get( "blog_url", "http://g2.trac.bx.psu.edu/blog" ) - # screencasts_url = trans.app.config.get( "screencasts_url", "http://g2.trac.bx.psu.edu/wiki/ScreenCasts" ) - # admin_user = "false" - # admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) - # user = trans.get_user() - # if user: - # user_email = trans.get_user().email - # if user_email in admin_users: - # admin_user = "true" - # return trans.fill_template( "/root/masthead.mako", brand=brand, wiki_url=wiki_url, - # blog_url=blog_url,bugs_email=bugs_email, screencasts_url=screencasts_url, admin_user=admin_user, active_view=active_view ) - - # @web.expose - # def dataset_errors( self, trans, id=None, **kwd ): - # """View/fix errors associated with dataset""" - # data = trans.app.model.HistoryDatasetAssociation.get( id ) - # p = kwd - # if p.get("fix_errors", None): - # # launch tool to create new, (hopefully) error free dataset - # tool_params = {} - # tool_params["tool_id"] = 'fix_errors' - # tool_params["runtool_btn"] = 'T' - # tool_params["input"] = id - # tool_params["ext"] = data.ext - # # send methods selected - # repair_methods = data.datatype.repair_methods( data ) - # methods = [] - # for method, description in repair_methods: - # if method in p: methods.append(method) - # tool_params["methods"] = ",".join(methods) - # url = "/tool_runner/index?" + urllib.urlencode(tool_params) - # trans.response.send_redirect(url) - # else: - # history = trans.app.model.History.get( data.history_id ) - # return trans.fill_template('dataset/validation.tmpl', data=data, history=history) - # ---- Debug methods ---------------------------------------------------- @web.expose --- a/lib/galaxy/web/controllers/user.py Sun Aug 14 19:49:26 2011 -0400 +++ b/lib/galaxy/web/controllers/user.py Mon Aug 15 09:18:52 2011 -0400 @@ -109,10 +109,10 @@ action = 'login' if auto_associate: action = 'openid_manage' - if trans.app.config.bugs_email is not None: - contact = '<a href="mailto:%s">contact support</a>' % trans.app.config.bugs_email + if trans.app.config.support_url is not None: + contact = '<a href="%s">support</a>' % trans.app.config.support_url else: - contact = 'contact support' + contact = 'support' message = 'Verification failed for an unknown reason. Please contact support for assistance.' status = 'error' consumer = trans.app.openid_manager.get_consumer( trans ) --- a/lib/galaxy/webapps/community/config.py Sun Aug 14 19:49:26 2011 -0400 +++ b/lib/galaxy/webapps/community/config.py Mon Aug 15 09:18:52 2011 -0400 @@ -66,7 +66,6 @@ self.brand = kwargs.get( 'brand', None ) self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' ) self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) - self.bugs_email = kwargs.get( 'bugs_email', None ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False --- a/lib/galaxy/webapps/demo_sequencer/config.py Sun Aug 14 19:49:26 2011 -0400 +++ b/lib/galaxy/webapps/demo_sequencer/config.py Mon Aug 15 09:18:52 2011 -0400 @@ -50,7 +50,6 @@ self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.brand = kwargs.get( 'brand', None ) self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) - self.bugs_email = kwargs.get( 'bugs_email', None ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False --- a/lib/galaxy/webapps/reports/config.py Sun Aug 14 19:49:26 2011 -0400 +++ b/lib/galaxy/webapps/reports/config.py Mon Aug 15 09:18:52 2011 -0400 @@ -34,7 +34,6 @@ self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.brand = kwargs.get( 'brand', None ) self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) - self.bugs_email = kwargs.get( 'bugs_email', None ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False --- a/universe_wsgi.ini.sample Sun Aug 14 19:49:26 2011 -0400 +++ b/universe_wsgi.ini.sample Mon Aug 15 09:18:52 2011 -0400 @@ -210,8 +210,8 @@ # The URL linked by the "Galaxy Wiki" link in the "Help" menu. #wiki_url = http://wiki.g2.bx.psu.edu/ -# The URL linked by the "Email comments..." link in the "Help" menu. -#bugs_email = mailto:galaxy-bugs@bx.psu.edu +# The URL linked by the "Support" link in the "Help" menu. +#support_url = http://wiki.g2.bx.psu.edu/Support # The URL linked by the "How to Cite..." link in the "Help" menu. #citation_url = http://wiki.g2.bx.psu.edu/Citing%20Galaxy Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: (1) GFF parsing improvements; and (2) output improvements for extract genomic dna tool.
by Bitbucket 14 Aug '11

14 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3c7416baa157/ changeset: 3c7416baa157 user: jgoecks date: 2011-08-15 01:49:26 summary: (1) GFF parsing improvements; and (2) output improvements for extract genomic dna tool. affected #: 2 files (1.3 KB) --- a/lib/galaxy/datatypes/util/gff_util.py Fri Aug 12 10:33:26 2011 +0100 +++ b/lib/galaxy/datatypes/util/gff_util.py Sun Aug 14 19:49:26 2011 -0400 @@ -87,6 +87,13 @@ intervals_copy.append( interval.copy() ) return GFFFeature(self.reader, self.chrom_col, self.feature_col, self.start_col, self.end_col, self.strand_col, self.score_col, self.strand, intervals=intervals_copy ) + + def lines( self ): + lines = [] + for interval in self.intervals: + lines.append( '\t'.join( interval.fields ) ) + return lines + class GFFIntervalToBEDReaderWrapper( NiceReaderWrapper ): """ @@ -209,6 +216,10 @@ #finally: #raw_size += len( self.current_line ) + # Ignore comments. + if isinstance( interval, Comment ): + continue + # If interval not associated with feature, break. group = interval.attributes.get( 'group', None ) # GFF test: --- a/tools/extract/extract_genomic_dna.py Fri Aug 12 10:33:26 2011 +0100 +++ b/tools/extract/extract_genomic_dna.py Sun Aug 14 19:49:26 2011 -0400 @@ -14,6 +14,7 @@ pkg_resources.require( "bx-python" ) import sys, string, os, re, tempfile, subprocess from bx.cookbook import doc_optparse +from bx.intervals.io import Header, Comment import bx.seq.nib import bx.seq.twobit from galaxy.tools.util.galaxyops import * @@ -111,9 +112,17 @@ # # Fetch sequences. # + + # Get feature's line(s). + def get_lines( feature ): + if isinstance( feature, gff_util.GFFFeature ): + return feature.lines() + else: + return [ feature.rstrip( '\r\n' ) ] + skipped_lines = 0 first_invalid_line = 0 - invalid_line = '' + invalid_lines = [] fout = open( output_filename, "w" ) warnings = [] warning = '' @@ -121,7 +130,13 @@ file_iterator = open( input_filename ) if gff_format and interpret_features: file_iterator = gff_util.GFFReaderWrapper( file_iterator, fix_strand=False ) - for i, feature in enumerate( file_iterator ): + line_count = 1 + for feature in file_iterator: + # Ignore comments, headers. + if isinstance( feature, ( Header, Comment ) ): + line_count += 1 + continue + if gff_format and interpret_features: # Processing features. gff_util.convert_gff_coords_to_bed( feature ) @@ -145,18 +160,18 @@ except: warning = "Invalid chrom, start or end column values. " warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line + if not invalid_lines: + invalid_lines = get_lines( feature ) + first_invalid_line = line_count + skipped_lines += len( invalid_lines ) continue if start > end: warning = "Invalid interval, start '%d' > end '%d'. " % ( start, end ) warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line + if not invalid_lines: + invalid_lines = get_lines( feature ) + first_invalid_line = line_count + skipped_lines += len( invalid_lines ) continue if strand not in ['+', '-']: @@ -174,13 +189,13 @@ nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) ) try: sequence = nib.get( start, end-start ) - except: + except Exception, e: warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey ) warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line + if not invalid_lines: + invalid_lines = get_lines( feature ) + first_invalid_line = line_count + skipped_lines += len( invalid_lines ) continue elif seq_path and os.path.isfile( seq_path ): if not(twobitfile): @@ -194,29 +209,29 @@ else: sequence = twobitfile[chrom][start:end] except: - warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey ) + warning = "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. " %( start, end-start, chrom ) warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line + if not invalid_lines: + invalid_lines = get_lines( feature ) + first_invalid_line = line_count + skipped_lines += len( invalid_lines ) continue else: warning = "Chromosome by name '%s' was not found for build '%s'. " % ( chrom, dbkey ) warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line + if not invalid_lines: + invalid_lines = get_lines( feature ) + first_invalid_line = line_count + skipped_lines += len( invalid_lines ) continue if sequence == '': warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " \ % ( chrom, start, end, dbkey ) warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line + if not invalid_lines: + invalid_lines = get_lines( feature ) + first_invalid_line = line_count + skipped_lines += len( invalid_lines ) continue if includes_strand_col and strand == "-": sequence = reverse_complement( sequence ) @@ -248,6 +263,12 @@ else: format_str = "%s\t%s\n" fout.write( format_str % ( meta_data, str( sequence ) ) ) + + # Update line count. + if isinstance( feature, gff_util.GFFFeature ): + line_count += len( feature.intervals ) + else: + line_count += 1 fout.close() @@ -256,6 +277,7 @@ warn_msg += warnings[0] print warn_msg if skipped_lines: - print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, invalid_line ) + # Error message includes up to the first 10 skipped lines. + print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, '\n'.join( invalid_lines[:10] ) ) if __name__ == "__main__": __main__() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: peterjc: Add missing requirement and fix incorrect help text in extract sequence tool
by Bitbucket 12 Aug '11

12 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/896846341a36/ changeset: 896846341a36 user: peterjc date: 2011-08-12 11:33:26 summary: Add missing requirement and fix incorrect help text in extract sequence tool affected #: 1 file (125 bytes) --- a/tools/extract/extract_genomic_dna.xml Thu Aug 11 18:37:14 2011 -0400 +++ b/tools/extract/extract_genomic_dna.xml Fri Aug 12 10:33:26 2011 +0100 @@ -1,4 +1,4 @@ -<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.1"> +<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.2"><description>using coordinates from assembled/unassembled genomes</description><command interpreter="python"> extract_genomic_dna.py $input $out_file1 -o $out_format -d $dbkey @@ -51,6 +51,9 @@ </change_format></data></outputs> + <requirements> + <requirement type="binary">faToTwoBit</requirement> + </requirements><tests><test><param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> @@ -110,7 +113,7 @@ .. class:: warningmark -This tool requires tabular formatted data. If your data is not TAB delimited, use *Text Manipulation->Convert*. +This tool requires interval or gff (special tabular formatted data). If your data is not TAB delimited, first use *Text Manipulation->Convert*. .. class:: warningmark Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 11 Aug '11

11 Aug '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c5acbf5f1c38/ changeset: c5acbf5f1c38 user: james_taylor date: 2011-08-12 00:36:51 summary: remove delayed draw and replace with synchronized drawing through requestAnimationFrame (or a fallback) affected #: 1 file (214 bytes) --- a/static/scripts/trackster.js Thu Aug 11 10:14:53 2011 -0400 +++ b/static/scripts/trackster.js Thu Aug 11 18:36:51 2011 -0400 @@ -23,6 +23,20 @@ // end class_module encapsulation }; +/** + * Find browser's reeuestAnimationFrame method or fallback on a setTimeout + */ +var requestAnimationFrame = (function(){ + return window.requestAnimationFrame || + window.webkitRequestAnimationFrame || + window.mozRequestAnimationFrame || + window.oRequestAnimationFrame || + window.msRequestAnimationFrame || + function( callback, element ) { + window.setTimeout(callback, 1000 / 60); + }; + })(); + /** * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig. @@ -529,8 +543,8 @@ if (this.vis_id !== undefined) { this.hidden_input = $("<input/>").attr("type", "hidden").val(this.vis_id).appendTo(this.nav_controls); } - this.zo_link = $("<a id='zoom-out' />").click(function() { view.zoom_out(); view.redraw(); }).appendTo(this.nav_controls); - this.zi_link = $("<a id='zoom-in' />").click(function() { view.zoom_in(); view.redraw(); }).appendTo(this.nav_controls); + this.zo_link = $("<a id='zoom-out' />").click(function() { view.zoom_out(); view.request_redraw(); }).appendTo(this.nav_controls); + this.zi_link = $("<a id='zoom-in' />").click(function() { view.zoom_in(); view.request_redraw(); }).appendTo(this.nav_controls); // Get initial set of chroms. this.load_chroms({low: 0}, callback); @@ -634,7 +648,7 @@ view.low = Math.round(min / width * span) + old_low; view.high = Math.round(max / width * span) + old_low; $(d.proxy).remove(); - view.redraw(); + view.request_redraw(); }); this.add_label_track( new LabelTrack( this, this.top_labeltrack ) ); @@ -742,7 +756,7 @@ view.chrom_select.val(view.chrom); view.max_high = found.len-1; // -1 because we're using 0-based indexing. view.reset(); - view.redraw(true); + view.request_redraw(true); for (var track_id = 0, len = view.tracks.length; track_id < len; track_id++) { var track = view.tracks[track_id]; @@ -756,7 +770,7 @@ view.high = Math.min(high, view.max_high); } view.reset_overview(); - view.redraw(); + view.request_redraw(); } }, go_to: function(str) { @@ -797,7 +811,7 @@ view.high -= delta_chrom; view.low -= delta_chrom; } - view.redraw(); + view.request_redraw(); }, /** * Add a track to the view. @@ -834,10 +848,14 @@ this.low = this.max_low; this.high = this.max_high; this.viewport_container.find(".yaxislabel").remove(); - }, + }, + request_redraw: function( nodraw ) { + var view = this; + requestAnimationFrame( function() { view.redraw( nodraw ) } ); + }, redraw: function(nodraw) { - var span = this.high - this.low, - low = this.low, + + var low = this.low, high = this.high; if (low < this.max_low) { @@ -846,6 +864,7 @@ if (high > this.max_high) { high = this.max_high; } + var span = this.high - this.low; if (this.high !== 0 && span < this.min_separation) { high = low + this.min_separation; } @@ -893,7 +912,7 @@ } this.low = Math.round(cur_center - new_half); this.high = Math.round(cur_center + new_half); - this.redraw(); + this.request_redraw(); }, zoom_out: function () { if (this.max_high === 0) { @@ -904,12 +923,12 @@ new_half = (span * this.zoom_factor) / 2; this.low = Math.round(cur_center - new_half); this.high = Math.round(cur_center + new_half); - this.redraw(); + this.request_redraw(); }, resize_window: function() { this.viewport_container.height( this.container.height() - this.top_container.height() - this.bottom_container.height() ); this.nav_container.width( this.container.width() ); - this.redraw(); + this.request_redraw(); }, /** Show a track in the overview. */ set_overview: function(track) { @@ -2084,41 +2103,28 @@ this.max_height = 0; // Index of first tile that overlaps visible region var tile_index = Math.floor( low / resolution / DENSITY ); - // A list of tiles drawn/retrieved. + // If any tile could not be drawn yet, this will be set to false + var all_tiles_drawn = true; var drawn_tiles = []; var tile_count = 0; // Draw or fetch and show tiles. while ( ( tile_index * DENSITY * resolution ) < high ) { - // Check in cache - var key = this._gen_tile_cache_key(width, w_scale, tile_index); - var cached = this.tile_cache.get(key); - var tile_low = tile_index * DENSITY * this.view.resolution; - var tile_high = tile_low + DENSITY * this.view.resolution; - if (!force && cached) { - drawn_tiles.push(cached); - this.show_tile(cached, parent_element, w_scale); + tile = this.draw_helper( force, width, tile_index, resolution, parent_element, w_scale ) + if ( tile ) { + drawn_tiles.push( tile ); } else { - this.delayed_draw(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles); + all_tiles_drawn = false; } tile_index += 1; tile_count++; } - // // Use interval to check if tiles have been drawn. When all tiles are drawn, call post-draw actions. - // var track = this; - var intervalId = setInterval(function() { - if (drawn_tiles.length === tile_count) { - // All tiles have been drawn. - clearInterval(intervalId); - track.postdraw_actions(drawn_tiles, width, w_scale, clear_after); - } - }, 50); - - // + if ( all_tiles_drawn ) { + track.postdraw_actions(drawn_tiles, width, w_scale, clear_after); + } // Draw child tracks. - // for (var i = 0; i < this.child_tracks.length; i++) { this.child_tracks[i].draw(force, clear_after); } @@ -2152,55 +2158,65 @@ } }, /** - * Do actual tile drawing. + * Handle a single tile, either from cache or by setting up a deferred + * operation and then requesting another redraw */ - delayed_draw: function(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) { + draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) { + var track = this, + key = this._gen_tile_cache_key(width, w_scale, tile_index), tile_low = tile_index * DENSITY * resolution, tile_high = tile_low + DENSITY * resolution; + + // Check tile cache, if found show existing tile in correct position + var tile = (force ? undefined : track.tile_cache.get(key)); + if (tile) { + track.show_tile(tile, parent_element, w_scale); + return tile; + } + + // Helper to determine if object is jQuery deferred + var is_deferred = function ( d ) { + return ( 'isResolved' in d ); + } - // Helper method. - var draw_and_show_tile = function(id, result, resolution, tile_index, parent_element, w_scale, seq_data) { - // DEBUG: this is still called too many times when moving slowly, - // console.log( "draw_and_show_tile", resolution, tile_index, w_scale ); - var tile = track.draw_tile(result, resolution, tile_index, w_scale, seq_data); + // Flag to track whether we can draw everything now + var can_draw_now = true + + // Get the track data, maybe a deferred + var tile_data = track.data_manager.get_data( tile_low, tile_high, track.mode, resolution, track.data_url_extra_params ); + if ( is_deferred( tile_data ) ) { + can_draw_now = false; + } + + // Get seq data if needed, maybe a deferred + var seq_data; + if ( view.reference_track && w_scale > view.canvas_manager.char_width_px ) { + seq_data = view.reference_track.data_manager.get_data(tile_low, tile_high, track.mode, resolution, view.reference_track.data_url_extra_params) + if ( is_deferred( seq_data ) ) { + can_draw_now = false; + } + } + + // If we can draw now, do so + if ( can_draw_now ) { + extend( tile_data, more_tile_data ); + var tile = track.draw_tile(tile_data, resolution, tile_index, w_scale, seq_data); track.tile_cache.set(key, tile); // Don't show if no tile - if (tile === undefined) { - return; + if (tile !== undefined) { + track.show_tile(tile, parent_element, w_scale); } - track.show_tile(tile, parent_element, w_scale); - drawn_tiles.push(tile); - }; - // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data - var id = setTimeout(function() { - if (tile_low <= track.view.high && tile_high >= track.view.low) { - // Show/draw tile: check cache for tile; if tile not in cache, draw it. - var tile = (force ? undefined : track.tile_cache.get(key)); - if (tile) { - track.show_tile(tile, parent_element, w_scale); - drawn_tiles.push(tile); - } - else { - // - // Really draw tile: get data, seq data if available, and draw tile. - // - $.when(track.data_manager.get_data(tile_low, tile_high, track.mode, resolution, track.data_url_extra_params)).then(function(tile_data) { - extend(tile_data, more_tile_data); - // If sequence data needed, get that and draw. Otherwise draw. - if (view.reference_track && w_scale > view.canvas_manager.char_width_px) { - $.when(view.reference_track.data_manager.get_data(tile_low, tile_high, track.mode, resolution, - view.reference_track.data_url_extra_params)).then(function(seq_data) { - draw_and_show_tile(id, tile_data, resolution, tile_index, parent_element, w_scale, seq_data); - }); - } - else { - draw_and_show_tile(id, tile_data, resolution, tile_index, parent_element, w_scale); - } - }); - } - } - }, 50); + return tile + } + + // Can't draw now, so trigger another redraw when the data is ready + $.when( tile_data, seq_data ).then( function() { + view.request_redraw(); + }); + + // Indicate to caller that this tile could not be drawn + return null; }, /** * Show track tile and perform associated actions. @@ -2585,9 +2601,7 @@ } } - // // If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max. - // if (track.mode == "Histogram") { // Get global max. var global_max = -1; @@ -2599,11 +2613,10 @@ } for (var i = 0; i < tiles.length; i++) { - if (tiles[i].max_val !== global_max) { - var tile = tiles[i]; + var tile = tiles[i]; + if (tile.max_val !== global_max) { tile.canvas.remove(); - track.delayed_draw(true, track._gen_tile_cache_key(width, w_scale, tile.index), tile.index, - tile.resolution, tile.canvas.parent(), w_scale, [], { max: global_max }); + track.draw_helper(true, width, tile.index, tile.resolution, tile.canvas.parent(), w_scale, [], { max: global_max }); } } } http://bitbucket.org/galaxy/galaxy-central/changeset/06f0bca6de24/ changeset: 06f0bca6de24 user: james_taylor date: 2011-08-12 00:37:14 summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central affected #: 1 file (214 bytes) --- a/static/scripts/trackster.js Thu Aug 11 14:33:15 2011 -0400 +++ b/static/scripts/trackster.js Thu Aug 11 18:37:14 2011 -0400 @@ -23,6 +23,20 @@ // end class_module encapsulation }; +/** + * Find browser's reeuestAnimationFrame method or fallback on a setTimeout + */ +var requestAnimationFrame = (function(){ + return window.requestAnimationFrame || + window.webkitRequestAnimationFrame || + window.mozRequestAnimationFrame || + window.oRequestAnimationFrame || + window.msRequestAnimationFrame || + function( callback, element ) { + window.setTimeout(callback, 1000 / 60); + }; + })(); + /** * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig. @@ -529,8 +543,8 @@ if (this.vis_id !== undefined) { this.hidden_input = $("<input/>").attr("type", "hidden").val(this.vis_id).appendTo(this.nav_controls); } - this.zo_link = $("<a id='zoom-out' />").click(function() { view.zoom_out(); view.redraw(); }).appendTo(this.nav_controls); - this.zi_link = $("<a id='zoom-in' />").click(function() { view.zoom_in(); view.redraw(); }).appendTo(this.nav_controls); + this.zo_link = $("<a id='zoom-out' />").click(function() { view.zoom_out(); view.request_redraw(); }).appendTo(this.nav_controls); + this.zi_link = $("<a id='zoom-in' />").click(function() { view.zoom_in(); view.request_redraw(); }).appendTo(this.nav_controls); // Get initial set of chroms. this.load_chroms({low: 0}, callback); @@ -634,7 +648,7 @@ view.low = Math.round(min / width * span) + old_low; view.high = Math.round(max / width * span) + old_low; $(d.proxy).remove(); - view.redraw(); + view.request_redraw(); }); this.add_label_track( new LabelTrack( this, this.top_labeltrack ) ); @@ -742,7 +756,7 @@ view.chrom_select.val(view.chrom); view.max_high = found.len-1; // -1 because we're using 0-based indexing. view.reset(); - view.redraw(true); + view.request_redraw(true); for (var track_id = 0, len = view.tracks.length; track_id < len; track_id++) { var track = view.tracks[track_id]; @@ -756,7 +770,7 @@ view.high = Math.min(high, view.max_high); } view.reset_overview(); - view.redraw(); + view.request_redraw(); } }, go_to: function(str) { @@ -797,7 +811,7 @@ view.high -= delta_chrom; view.low -= delta_chrom; } - view.redraw(); + view.request_redraw(); }, /** * Add a track to the view. @@ -834,10 +848,14 @@ this.low = this.max_low; this.high = this.max_high; this.viewport_container.find(".yaxislabel").remove(); - }, + }, + request_redraw: function( nodraw ) { + var view = this; + requestAnimationFrame( function() { view.redraw( nodraw ) } ); + }, redraw: function(nodraw) { - var span = this.high - this.low, - low = this.low, + + var low = this.low, high = this.high; if (low < this.max_low) { @@ -846,6 +864,7 @@ if (high > this.max_high) { high = this.max_high; } + var span = this.high - this.low; if (this.high !== 0 && span < this.min_separation) { high = low + this.min_separation; } @@ -893,7 +912,7 @@ } this.low = Math.round(cur_center - new_half); this.high = Math.round(cur_center + new_half); - this.redraw(); + this.request_redraw(); }, zoom_out: function () { if (this.max_high === 0) { @@ -904,12 +923,12 @@ new_half = (span * this.zoom_factor) / 2; this.low = Math.round(cur_center - new_half); this.high = Math.round(cur_center + new_half); - this.redraw(); + this.request_redraw(); }, resize_window: function() { this.viewport_container.height( this.container.height() - this.top_container.height() - this.bottom_container.height() ); this.nav_container.width( this.container.width() ); - this.redraw(); + this.request_redraw(); }, /** Show a track in the overview. */ set_overview: function(track) { @@ -2084,41 +2103,28 @@ this.max_height = 0; // Index of first tile that overlaps visible region var tile_index = Math.floor( low / resolution / DENSITY ); - // A list of tiles drawn/retrieved. + // If any tile could not be drawn yet, this will be set to false + var all_tiles_drawn = true; var drawn_tiles = []; var tile_count = 0; // Draw or fetch and show tiles. while ( ( tile_index * DENSITY * resolution ) < high ) { - // Check in cache - var key = this._gen_tile_cache_key(width, w_scale, tile_index); - var cached = this.tile_cache.get(key); - var tile_low = tile_index * DENSITY * this.view.resolution; - var tile_high = tile_low + DENSITY * this.view.resolution; - if (!force && cached) { - drawn_tiles.push(cached); - this.show_tile(cached, parent_element, w_scale); + tile = this.draw_helper( force, width, tile_index, resolution, parent_element, w_scale ) + if ( tile ) { + drawn_tiles.push( tile ); } else { - this.delayed_draw(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles); + all_tiles_drawn = false; } tile_index += 1; tile_count++; } - // // Use interval to check if tiles have been drawn. When all tiles are drawn, call post-draw actions. - // var track = this; - var intervalId = setInterval(function() { - if (drawn_tiles.length === tile_count) { - // All tiles have been drawn. - clearInterval(intervalId); - track.postdraw_actions(drawn_tiles, width, w_scale, clear_after); - } - }, 50); - - // + if ( all_tiles_drawn ) { + track.postdraw_actions(drawn_tiles, width, w_scale, clear_after); + } // Draw child tracks. - // for (var i = 0; i < this.child_tracks.length; i++) { this.child_tracks[i].draw(force, clear_after); } @@ -2152,55 +2158,65 @@ } }, /** - * Do actual tile drawing. + * Handle a single tile, either from cache or by setting up a deferred + * operation and then requesting another redraw */ - delayed_draw: function(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) { + draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) { + var track = this, + key = this._gen_tile_cache_key(width, w_scale, tile_index), tile_low = tile_index * DENSITY * resolution, tile_high = tile_low + DENSITY * resolution; + + // Check tile cache, if found show existing tile in correct position + var tile = (force ? undefined : track.tile_cache.get(key)); + if (tile) { + track.show_tile(tile, parent_element, w_scale); + return tile; + } + + // Helper to determine if object is jQuery deferred + var is_deferred = function ( d ) { + return ( 'isResolved' in d ); + } - // Helper method. - var draw_and_show_tile = function(id, result, resolution, tile_index, parent_element, w_scale, seq_data) { - // DEBUG: this is still called too many times when moving slowly, - // console.log( "draw_and_show_tile", resolution, tile_index, w_scale ); - var tile = track.draw_tile(result, resolution, tile_index, w_scale, seq_data); + // Flag to track whether we can draw everything now + var can_draw_now = true + + // Get the track data, maybe a deferred + var tile_data = track.data_manager.get_data( tile_low, tile_high, track.mode, resolution, track.data_url_extra_params ); + if ( is_deferred( tile_data ) ) { + can_draw_now = false; + } + + // Get seq data if needed, maybe a deferred + var seq_data; + if ( view.reference_track && w_scale > view.canvas_manager.char_width_px ) { + seq_data = view.reference_track.data_manager.get_data(tile_low, tile_high, track.mode, resolution, view.reference_track.data_url_extra_params) + if ( is_deferred( seq_data ) ) { + can_draw_now = false; + } + } + + // If we can draw now, do so + if ( can_draw_now ) { + extend( tile_data, more_tile_data ); + var tile = track.draw_tile(tile_data, resolution, tile_index, w_scale, seq_data); track.tile_cache.set(key, tile); // Don't show if no tile - if (tile === undefined) { - return; + if (tile !== undefined) { + track.show_tile(tile, parent_element, w_scale); } - track.show_tile(tile, parent_element, w_scale); - drawn_tiles.push(tile); - }; - // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data - var id = setTimeout(function() { - if (tile_low <= track.view.high && tile_high >= track.view.low) { - // Show/draw tile: check cache for tile; if tile not in cache, draw it. - var tile = (force ? undefined : track.tile_cache.get(key)); - if (tile) { - track.show_tile(tile, parent_element, w_scale); - drawn_tiles.push(tile); - } - else { - // - // Really draw tile: get data, seq data if available, and draw tile. - // - $.when(track.data_manager.get_data(tile_low, tile_high, track.mode, resolution, track.data_url_extra_params)).then(function(tile_data) { - extend(tile_data, more_tile_data); - // If sequence data needed, get that and draw. Otherwise draw. - if (view.reference_track && w_scale > view.canvas_manager.char_width_px) { - $.when(view.reference_track.data_manager.get_data(tile_low, tile_high, track.mode, resolution, - view.reference_track.data_url_extra_params)).then(function(seq_data) { - draw_and_show_tile(id, tile_data, resolution, tile_index, parent_element, w_scale, seq_data); - }); - } - else { - draw_and_show_tile(id, tile_data, resolution, tile_index, parent_element, w_scale); - } - }); - } - } - }, 50); + return tile + } + + // Can't draw now, so trigger another redraw when the data is ready + $.when( tile_data, seq_data ).then( function() { + view.request_redraw(); + }); + + // Indicate to caller that this tile could not be drawn + return null; }, /** * Show track tile and perform associated actions. @@ -2585,9 +2601,7 @@ } } - // // If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max. - // if (track.mode == "Histogram") { // Get global max. var global_max = -1; @@ -2599,11 +2613,10 @@ } for (var i = 0; i < tiles.length; i++) { - if (tiles[i].max_val !== global_max) { - var tile = tiles[i]; + var tile = tiles[i]; + if (tile.max_val !== global_max) { tile.canvas.remove(); - track.delayed_draw(true, track._gen_tile_cache_key(width, w_scale, tile.index), tile.index, - tile.resolution, tile.canvas.parent(), w_scale, [], { max: global_max }); + track.draw_helper(true, width, tile.index, tile.resolution, tile.canvas.parent(), w_scale, [], { max: global_max }); } } } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Documentation and white space fixes for Trackster.
by Bitbucket 11 Aug '11

11 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4b345ffa951c/ changeset: 4b345ffa951c user: jgoecks date: 2011-08-11 20:33:15 summary: Documentation and white space fixes for Trackster. affected #: 1 file (38 bytes) --- a/static/scripts/trackster.js Thu Aug 11 12:49:36 2011 -0400 +++ b/static/scripts/trackster.js Thu Aug 11 14:33:15 2011 -0400 @@ -3393,15 +3393,15 @@ /** * Abstract object for painting feature tracks. Subclasses must implement draw_element() for painting to work. */ -var FeaturePainter = function( data, view_start, view_end, prefs, mode ) { - Painter.call( this, data, view_start, view_end, prefs, mode ); +var FeaturePainter = function(data, view_start, view_end, prefs, mode) { + Painter.call(this, data, view_start, view_end, prefs, mode); } FeaturePainter.prototype.default_prefs = { block_color: "#FFF", connector_color: "#FFF" }; -extend( FeaturePainter.prototype, { +extend(FeaturePainter.prototype, { - get_required_height: function( rows_required ) { + get_required_height: function(rows_required) { // y_scale is the height per row var required_height = y_scale = this.get_row_height(), mode = this.mode; // If using a packing mode, need to multiply by the number of slots used @@ -3412,7 +3412,10 @@ return required_height + Math.max( Math.round( y_scale / 2 ), 5 ); }, - draw: function( ctx, width, height, slots ) { + /** + * Draw data on ctx using slots and within the rectangle defined by width and height. + */ + draw: function(ctx, width, height, slots) { var data = this.data, view_start = this.view_start, view_end = this.view_end; ctx.save(); @@ -3434,9 +3437,8 @@ slot = (slots && slots[feature_uid] !== undefined ? slots[feature_uid] : null); // Draw feature if there's overlap and mode is dense or feature is slotted (as it must be for all non-dense modes). - if ( ( feature_start < view_end && feature_end > view_start ) && (this.mode == "Dense" || slot !== null)) { - this.draw_element(ctx, this.mode, feature, slot, view_start, view_end, w_scale, y_scale, - width ); + if ( ( feature_start < view_end && feature_end > view_start ) && (this.mode == "Dense" || slot !== null) ) { + this.draw_element(ctx, this.mode, feature, slot, view_start, view_end, w_scale, y_scale, width); } } @@ -3444,9 +3446,11 @@ }, /** - * Abstract function for drawing an individual feature. NOTE: this method must be implemented by subclasses for drawing to work. + * Abstract function for drawing an individual feature. */ - draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) {} + draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) { + console.log("WARNING: Unimplemented function."); + } }); // Constants specific to feature tracks moved here (HACKING, these should @@ -3462,11 +3466,11 @@ LABEL_SPACING = 2, CONNECTOR_COLOR = "#ccc"; -var LinkedFeaturePainter = function( data, view_start, view_end, prefs, mode ) { - FeaturePainter.call( this, data, view_start, view_end, prefs, mode ); +var LinkedFeaturePainter = function(data, view_start, view_end, prefs, mode) { + FeaturePainter.call(this, data, view_start, view_end, prefs, mode); } -extend( LinkedFeaturePainter.prototype, FeaturePainter.prototype, { +extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, { /** * Height of a single row, depends on mode @@ -3488,7 +3492,10 @@ return y_scale; }, - draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) { + /** + * Draw a feature. + */ + draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) { var feature_uid = feature[0], feature_start = feature[1], @@ -3621,8 +3628,7 @@ block_thick_start += 2; block_thick_end -= 2; } - ctx.fillRect( block_thick_start, y_center + 1, - block_thick_end - block_thick_start, thick_height ); + ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height); } } } @@ -3646,11 +3652,11 @@ }); -var VariantPainter = function( data, view_start, view_end, prefs, mode ) { - FeaturePainter.call( this, data, view_start, view_end, prefs, mode ); +var VariantPainter = function(data, view_start, view_end, prefs, mode) { + FeaturePainter.call(this, data, view_start, view_end, prefs, mode); } -extend( VariantPainter.prototype, FeaturePainter.prototype, { +extend(VariantPainter.prototype, FeaturePainter.prototype, { draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) { var feature = data[i], feature_uid = feature[0], @@ -3701,14 +3707,14 @@ } }); -var ReadPainter = function( data, view_start, view_end, prefs, mode, ref_seq ) { - FeaturePainter.call( this, data, view_start, view_end, prefs, mode ); +var ReadPainter = function(data, view_start, view_end, prefs, mode, ref_seq) { + FeaturePainter.call(this, data, view_start, view_end, prefs, mode); this.ref_seq = ref_seq; }; -ReadPainter.prototype.default_prefs = extend( {}, FeaturePainter.prototype.default_prefs, { show_insertions: false } ); +ReadPainter.prototype.default_prefs = extend({}, FeaturePainter.prototype.default_prefs, { show_insertions: false }); -extend( ReadPainter.prototype, FeaturePainter.prototype, { +extend(ReadPainter.prototype, FeaturePainter.prototype, { /** * Returns y_scale based on mode. */ @@ -3728,6 +3734,7 @@ } return y_scale; }, + /** * Draw a single read. */ @@ -3920,6 +3927,7 @@ } } }, + /** * Draw a complete read pair */ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Very basic "high water mark" per-user job limits.
by Bitbucket 11 Aug '11

11 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ed6608267375/ changeset: ed6608267375 user: natefoo date: 2011-08-11 18:49:36 summary: Very basic "high water mark" per-user job limits. affected #: 2 files (1.5 KB) --- a/lib/galaxy/config.py Thu Aug 11 10:14:53 2011 -0400 +++ b/lib/galaxy/config.py Thu Aug 11 12:49:36 2011 -0400 @@ -86,9 +86,11 @@ self.external_service_type_path = resolve_path( kwargs.get( 'external_service_type_path', 'external_service_types' ), self.root ) # Tasked job runner. self.use_tasked_jobs = string_as_bool( kwargs.get( 'use_tasked_jobs', False ) ) + self.local_task_queue_workers = int(kwargs.get("local_task_queue_workers", 2)) # The transfer manager and deferred job queue self.enable_beta_job_managers = string_as_bool( kwargs.get( 'enable_beta_job_managers', 'False' ) ) - self.local_task_queue_workers = int(kwargs.get("local_task_queue_workers", 2)) + # Per-user Job concurrency limitations + self.user_job_limit = int( kwargs.get( 'user_job_limit', 0 ) ) self.default_cluster_job_runner = kwargs.get( 'default_cluster_job_runner', 'local:///' ) self.pbs_application_server = kwargs.get('pbs_application_server', "" ) self.pbs_dataset_server = kwargs.get('pbs_dataset_server', "" ) --- a/lib/galaxy/jobs/__init__.py Thu Aug 11 10:14:53 2011 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Aug 11 12:49:36 2011 -0400 @@ -11,6 +11,8 @@ from galaxy.util.expressions import ExpressionContext from galaxy.jobs.actions.post import ActionBox +from sqlalchemy.sql.expression import and_, or_ + import pkg_resources pkg_resources.require( "PasteDeploy" ) @@ -163,6 +165,10 @@ .options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ) \ .filter( model.Job.state == model.Job.states.NEW ).all() else: + # Get job objects and append to watch queue for any which were + # previously waiting + for job_id in self.waiting_jobs: + jobs_to_check.append( self.sa_session.query( model.Job ).get( job_id ) ) try: while 1: message = self.queue.get_nowait() @@ -174,10 +180,6 @@ jobs_to_check.append( self.sa_session.query( model.Job ).get( job_id ) ) except Empty: pass - # Get job objects and append to watch queue for any which were - # previously waiting - for job_id in self.waiting_jobs: - jobs_to_check.append( self.sa_session.query( model.Job ).get( job_id ) ) # Iterate over new and waiting jobs and look for any that are # ready to run new_waiting_jobs = [] @@ -256,6 +258,28 @@ elif idata.state != idata.states.OK and not ( idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id ): # need to requeue return JOB_WAIT + return self.__check_user_jobs( job ) + + def __check_user_jobs( self, job ): + if not self.app.config.user_job_limit: + return JOB_READY + if job.user: + user_jobs = self.sa_session.query( model.Job ) \ + .options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ) \ + .filter( and_( model.Job.user_id == job.user.id, + or_( model.Job.state == model.Job.states.RUNNING, + model.Job.state == model.Job.states.QUEUED ) ) ).all() + elif job.galaxy_session: + user_jobs = self.sa_session.query( model.Job ) \ + .options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ) \ + .filter( and_( model.Job.session_id == job.galaxy_session.id, + or_( model.Job.state == model.Job.states.RUNNING, + model.Job.state == model.Job.states.QUEUED ) ) ).all() + else: + log.warning( 'Job %s is not associated with a user or session so job concurrency limit cannot be checked.' % job.id ) + return JOB_READY + if len( user_jobs ) >= self.app.config.user_job_limit: + return JOB_WAIT return JOB_READY def put( self, job_id, tool ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Add GTF-guide option to Cufflinks wrapper. Patch from Ilya Chorny.
by Bitbucket 11 Aug '11

11 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0ef81af1de09/ changeset: 0ef81af1de09 user: jgoecks date: 2011-08-11 16:14:53 summary: Add GTF-guide option to Cufflinks wrapper. Patch from Ilya Chorny. affected #: 2 files (843 bytes) --- a/tools/ngs_rna/cufflinks_wrapper.py Thu Aug 11 09:53:14 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.py Thu Aug 11 10:14:53 2011 -0400 @@ -33,6 +33,7 @@ For, example, for paired end runs with fragments selected at 300bp, \ where each end is 50bp, you should set -r to be 200. The default is 45bp.') parser.add_option( '-G', '--GTF', dest='GTF', help='Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.' ) + parser.add_option( '-g', '--GTF-guide', dest='GTFguide', help='use reference transcript annotation to guide assembly' ) # Normalization options. parser.add_option( "-N", "--quartile-normalization", dest="do_normalization", action="store_true" ) @@ -104,6 +105,8 @@ cmd += ( " -m %i" % int ( options.inner_mean_dist ) ) if options.GTF: cmd += ( " -G %s" % options.GTF ) + if options.GTFguide: + cmd += ( " -g %s" % options.GTFguide ) if options.num_importance_samples: cmd += ( " --num-importance-samples %i" % int ( options.num_importance_samples ) ) if options.max_mle_iterations: --- a/tools/ngs_rna/cufflinks_wrapper.xml Thu Aug 11 09:53:14 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Thu Aug 11 10:14:53 2011 -0400 @@ -14,9 +14,12 @@ -j $pre_mrna_fraction ## Include reference annotation? - #if $reference_annotation.use_ref == "Yes": + #if $reference_annotation.use_ref == "use reference annotation": -G $reference_annotation.reference_annotation_file #end if + #if $reference_annotation.use_ref == "use reference annotation guide": + -g $reference_annotation_guide.reference_annotation_guide_file + #end if ## Set paired-end parameters? #if $singlePaired.sPaired == "Yes": @@ -53,17 +56,21 @@ <conditional name="reference_annotation"><param name="use_ref" type="select" label="Use Reference Annotation"><option value="No">No</option> - <option value="Yes">Yes</option> + <option value="Use reference annotation">Use reference annotation</option> + <option value="Use reference annotation guide">Use reference annotation as guide</option></param><when value="No"></when> - <when value="Yes"> - <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> - </when> + <when value="Use reference annotation"> + <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Aonnotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + </when> + <when value="Use reference annotation guide"> + <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Aonnotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + </when></conditional><conditional name="bias_correction"><param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."> - <option value="Yes">Yes</option><option value="No">No</option> + <option value="Yes">Yes</option></param><when value="Yes"><conditional name="seq_source"> 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: Remove unspecified build validator from extract_genomic_dna tool because it can work with a custom fasta.
by Bitbucket 11 Aug '11

11 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/07de40a5a0b9/ changeset: 07de40a5a0b9 user: jgoecks date: 2011-08-11 15:53:14 summary: Remove unspecified build validator from extract_genomic_dna tool because it can work with a custom fasta. affected #: 1 file (63 bytes) --- a/tools/extract/extract_genomic_dna.xml Wed Aug 10 16:50:04 2011 -0400 +++ b/tools/extract/extract_genomic_dna.xml Thu Aug 11 09:53:14 2011 -0400 @@ -23,9 +23,7 @@ #end if </command><inputs> - <param format="interval,gff" name="input" type="data" label="Fetch sequences for intervals in"> - <validator type="unspecified_build" /> - </param> + <param format="interval,gff" name="input" type="data" label="Fetch sequences for intervals in"/><param name="interpret_features" type="select" label="Interpret features when possible" help="Only meaningful for GFF, GTF datasets."><option value="yes">Yes</option><option value="no">No</option> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Set Trackster overview height correctly.
by Bitbucket 10 Aug '11

10 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/431c06394bb1/ changeset: 431c06394bb1 user: jgoecks date: 2011-08-10 22:50:04 summary: Set Trackster overview height correctly. affected #: 1 file (5 bytes) --- a/static/scripts/trackster.js Wed Aug 10 16:42:01 2011 -0400 +++ b/static/scripts/trackster.js Wed Aug 10 16:50:04 2011 -0400 @@ -920,7 +920,7 @@ view.overview_close.show(); view.overview_viewport.append(tile.canvas); view.overview_highlight.show().height(tile.canvas.height()); - view.overview_viewport.height(tile.canvas.height() + view.overview_box.height()); + view.overview_viewport.height(tile.canvas.height() + view.overview_box.outerHeight()); view.resize_window(); // Update view, track states. 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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