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

commit/galaxy-central: jgoecks: Fix bug in setting shared visualization's viewport.
by Bitbucket 04 Oct '11

04 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/04d8beeae538/ changeset: 04d8beeae538 user: jgoecks date: 2011-10-04 16:14:25 summary: Fix bug in setting shared visualization's viewport. affected #: 1 file (-1 bytes) --- a/templates/visualization/display.mako Tue Oct 04 09:38:33 2011 +1100 +++ b/templates/visualization/display.mako Tue Oct 04 10:14:25 2011 -0400 @@ -92,7 +92,8 @@ var callback = function() { view.change_chrom( '${config['viewport']['chrom']}', ${config['viewport']['start']}, ${config['viewport']['end']} ); } %endif view = create_visualization( container_element, "${config.get('title') | h}", - "${config.get('vis_id')}", "${config.get('dbkey')}", callback, + "${config.get('vis_id')}", "${config.get('dbkey')}", + JSON.parse('${ h.to_json_string( config.get( 'viewport', dict() ) ) }'), JSON.parse('${ h.to_json_string( config.get('tracks') ) }'), JSON.parse('${ h.to_json_string( config.get('bookmarks') ) }') ); 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: fubar: Increase size limit for display of html files to 10000000 bytes - mirdeep2 creates very large html objects.
by Bitbucket 03 Oct '11

03 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3c87628a9907/ changeset: 3c87628a9907 user: fubar date: 2011-10-04 00:38:33 summary: Increase size limit for display of html files to 10000000 bytes - mirdeep2 creates very large html objects. Size limit for display should probably be configurable. affected #: 1 file (-1 bytes) --- a/lib/galaxy/web/controllers/dataset.py Mon Oct 03 17:12:41 2011 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Tue Oct 04 09:38:33 2011 +1100 @@ -376,6 +376,8 @@ raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name ) max_peek_size = 1000000 # 1 MB + if isinstance(data.datatype, datatypes.images.Html): + max_peek_size = 10000000 # 10 MB for html if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size: return open( data.file_name ) else: 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 typos.
by Bitbucket 03 Oct '11

03 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/aebbf6bdf5a6/ changeset: aebbf6bdf5a6 user: jgoecks date: 2011-10-03 23:12:41 summary: Fix typos. affected #: 1 file (-1 bytes) --- a/tools/ngs_rna/cufflinks_wrapper.xml Mon Oct 03 15:10:21 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon Oct 03 17:12:41 2011 -0400 @@ -61,10 +61,10 @@ </param><when value="No"></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."/> + <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 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."/> + <param format="gff3,gtf" name="reference_annotation_guide_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></conditional><conditional name="bias_correction"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for 538c42806e79.
by Bitbucket 03 Oct '11

03 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/772d868754da/ changeset: 772d868754da user: dan date: 2011-10-03 21:10:21 summary: Fix for 538c42806e79. affected #: 1 file (-1 bytes) --- a/lib/galaxy/datatypes/genetics.py Mon Oct 03 15:08:21 2011 -0400 +++ b/lib/galaxy/datatypes/genetics.py Mon Oct 03 15:10:21 2011 -0400 @@ -288,7 +288,7 @@ rval.append( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) ) else: rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) ) - rval.append( '</ul></div></html>' ) + rval.append( '</ul></div></html>' ) return "\n".join( rval ) def regenerate_primary_file(self,dataset): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix Tabs to 4 spaces in lib/galaxy/datatypes/genetics.py.
by Bitbucket 03 Oct '11

03 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/538c42806e79/ changeset: 538c42806e79 user: dan date: 2011-10-03 21:08:21 summary: Fix Tabs to 4 spaces in lib/galaxy/datatypes/genetics.py. affected #: 1 file (-1 bytes) --- a/lib/galaxy/datatypes/genetics.py Mon Oct 03 13:34:32 2011 -0400 +++ b/lib/galaxy/datatypes/genetics.py Mon Oct 03 15:08:21 2011 -0400 @@ -53,9 +53,9 @@ header = file(dataset.file_name,'r').readlines()[0].strip().split('\t') dataset.metadata.columns = len(header) t = ['numeric' for x in header] - t[0] = 'string' + t[0] = 'string' dataset.metadata.column_types = t - return True + return True def as_ucsc_display_file( self, dataset, **kwd ): """ @@ -113,8 +113,8 @@ f = open(dataset.file_name,'r') d = f.readlines()[:5] if len(d) == 0: - out = "Cannot find anything to parse in %s" % dataset.name - return out + out = "Cannot find anything to parse in %s" % dataset.name + return out hasheader = 0 try: test = ['%f' % x for x in d[0][1:]] # first is name - see if starts all numerics @@ -123,7 +123,7 @@ try: # Generate column header out.append( '<tr>' ) - if hasheader: + if hasheader: for i, name in enumerate(d[0].split() ): out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) d.pop(0) @@ -285,10 +285,10 @@ if composite_file.optional: opt_text = ' (optional)' if composite_file.get('description'): - rval.append( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) ) + rval.append( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) ) else: - rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) ) - rval.append( '</ul></div></html>' ) + rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) ) + rval.append( '</ul></div></html>' ) return "\n".join( rval ) def regenerate_primary_file(self,dataset): @@ -641,9 +641,9 @@ if not dataset.dataset.purged: pp = os.path.join(dataset.extra_files_path,'%s.pheno' % dataset.metadata.base_name) try: - p = file(pp,'r').readlines() + p = file(pp,'r').readlines() except: - p = ['##failed to find %s' % pp,] + p = ['##failed to find %s' % pp,] dataset.peek = ''.join(p[:5]) dataset.blurb = 'Galaxy Rexpression composite file' else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: fix display of reference data.
by Bitbucket 03 Oct '11

03 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0238b2b4b84e/ changeset: 0238b2b4b84e user: jgoecks date: 2011-10-03 19:34:32 summary: Trackster: fix display of reference data. affected #: 1 file (-1 bytes) --- a/static/scripts/trackster.js Mon Oct 03 11:11:16 2011 -0400 +++ b/static/scripts/trackster.js Mon Oct 03 13:34:32 2011 -0400 @@ -1157,12 +1157,13 @@ */ add_drawable: function(drawable) { DrawableCollection.prototype.add_drawable.call(this, drawable); - if (drawable.init) { drawable.init(); } + drawable.init(); this.has_changes = true; this.update_intro_div(); }, add_label_track: function (label_track) { label_track.view = this; + label_track.init(); this.label_tracks.push(label_track); }, /** @@ -2196,6 +2197,7 @@ // // Tracks with no dataset id are handled differently. + // FIXME: is this really necessary? // if (!track.dataset_id) { return; @@ -2728,6 +2730,10 @@ this.container_div.addClass( "label-track" ); }; extend(LabelTrack.prototype, Track.prototype, { + init: function() { + // Enable by default because there should always be data when drawing track. + this.enabled = true; + }, _draw: function() { var view = this.view, range = view.high - view.low, @@ -2767,6 +2773,10 @@ this.tile_cache = new Cache(CACHED_TILES_LINE); }; extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + init: function() { + // Enable by default because there should always be data when drawing track. + this.enabled = true; + }, /** * Draw ReferenceTrack tile. */ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Tweak validator for input bed file in SICER tool to work around workflow editor issue.
by Bitbucket 03 Oct '11

03 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/61c45145fce6/ changeset: 61c45145fce6 user: dan date: 2011-10-03 17:11:16 summary: Tweak validator for input bed file in SICER tool to work around workflow editor issue. affected #: 1 file (-1 bytes) --- a/tools/peak_calling/sicer_wrapper.xml Mon Oct 03 10:52:19 2011 -0400 +++ b/tools/peak_calling/sicer_wrapper.xml Mon Oct 03 11:11:16 2011 -0400 @@ -31,7 +31,7 @@ </requirements><inputs><param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" > - <validator type="expression" message="SICER is not available for the genome.">value.dbkey in [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]</validator> + <validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]</validator></param><param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="True"><options> 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 for getting reference data for a built-in genome build.
by Bitbucket 03 Oct '11

03 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/070c57978648/ changeset: 070c57978648 user: jgoecks date: 2011-10-03 16:52:19 summary: Fix for getting reference data for a built-in genome build. affected #: 1 file (-1 bytes) --- a/lib/galaxy/web/controllers/tracks.py Mon Oct 03 10:40:36 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Mon Oct 03 10:52:19 2011 -0400 @@ -420,7 +420,7 @@ twobit_file_name = None if dbkey in self.available_genomes: # Built-in twobit. - twobit_file_name = TwoBitFile( open( self.available_genomes[dbkey] ) ) + twobit_file_name = self.available_genomes[dbkey] else: # From custom build. # TODO: how to make this work for shared visualizations? 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: Fix for Python 2.4.
by Bitbucket 03 Oct '11

03 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ef6295bd2712/ changeset: ef6295bd2712 user: natefoo date: 2011-10-03 16:40:36 summary: Fix for Python 2.4. affected #: 1 file (-1 bytes) --- a/lib/galaxy/web/controllers/admin.py Fri Sep 30 18:38:30 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon Oct 03 10:40:36 2011 -0400 @@ -311,7 +311,7 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="Manage users and groups", id=item.id, webapp="galaxy" ) if not item.default else dict( operation="Change amount", id=item.id, webapp="galaxy" ) ), + link=( lambda item: dict( operation="Change amount", id=item.id, webapp="galaxy" ) ), model_class=model.Quota, attach_popup=True, filterable="advanced" ), 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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