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commit/galaxy-central: kanwei: set_peek should check for None, not false
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3070455afbdd/ changeset: r5236:3070455afbdd user: kanwei date: 2011-03-18 19:12:10 summary: set_peek should check for None, not false affected #: 3 files (36 bytes) --- a/lib/galaxy/datatypes/data.py Fri Mar 18 13:51:51 2011 -0400 +++ b/lib/galaxy/datatypes/data.py Fri Mar 18 14:12:10 2011 -0400 @@ -422,7 +422,7 @@ dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if line_count is None: # See if line_count is stored in the metadata - if dataset.metadata.data_lines: + if dataset.metadata.data_lines is not None: dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, "line") ) else: # Number of lines is not known ( this should not happen ), and auto-detect is --- a/lib/galaxy/datatypes/interval.py Fri Mar 18 13:51:51 2011 -0400 +++ b/lib/galaxy/datatypes/interval.py Fri Mar 18 14:12:10 2011 -0400 @@ -66,7 +66,7 @@ dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if line_count is None: # See if line_count is stored in the metadata - if dataset.metadata.data_lines: + if dataset.metadata.data_lines is not None: dataset.blurb = "%s regions" % util.commaify( str( dataset.metadata.data_lines ) ) else: # Number of lines is not known ( this should not happen ), and auto-detect is --- a/lib/galaxy/datatypes/tabular.py Fri Mar 18 13:51:51 2011 -0400 +++ b/lib/galaxy/datatypes/tabular.py Fri Mar 18 14:12:10 2011 -0400 @@ -398,7 +398,7 @@ dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if line_count is None: # See if line_count is stored in the metadata - if dataset.metadata.data_lines: + if dataset.metadata.data_lines is not None: dataset.blurb = "%s genomic coordinates" % util.commaify( str( dataset.metadata.data_lines ) ) else: # Number of lines is not known ( this should not happen ), and auto-detect is 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 issues with navigation input: (a) arrow keys no longer perform navigation and (b) invalid chromosome names are handled well.
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dc9b64810fde/ changeset: r5235:dc9b64810fde user: jgoecks date: 2011-03-18 18:51:51 summary: Trackster: fix issues with navigation input: (a) arrow keys no longer perform navigation and (b) invalid chromosome names are handled well. affected #: 2 files (530 bytes) --- a/static/scripts/trackster.js Fri Mar 18 13:40:58 2011 -0400 +++ b/static/scripts/trackster.js Fri Mar 18 13:51:51 2011 -0400 @@ -367,9 +367,9 @@ view.go_to( $(this).val() ); } $(this).hide(); + $(this).val(''); view.location_span.show(); view.chrom_select.show(); - return false; } }; this.nav_input = $("<input/>").addClass("nav-input").hide().bind("keyup focusout", submit_nav).appendTo(this.nav_controls); @@ -377,6 +377,7 @@ this.location_span.bind("click", function() { view.location_span.hide(); view.chrom_select.hide(); + view.nav_input.val(view.chrom + ":" + view.low + "-" + view.high); view.nav_input.css("display", "inline-block"); view.nav_input.select(); view.nav_input.focus(); @@ -520,7 +521,14 @@ url: chrom_url, data: url_parms, dataType: "json", - success: function ( result ) { + success: function (result) { + // Show error if could not load chroms. + if (result.chrom_info.length === 0) { + alert("Invalid chromosome: " + url_parms.chrom); + return; + } + + // Load chroms. if (result.reference) { view.add_label_track( new ReferenceTrack(view) ); } @@ -543,13 +551,12 @@ view.chrom_start_index = result.start_index; }, error: function() { - alert( "Could not load chroms for this dbkey:", view.dbkey ); + alert("Could not load chroms for this dbkey:", view.dbkey); } }); }, change_chrom: function(chrom, low, high) { - // Don't do anything if chrom is "None" (hackish but some browsers already have this set), or null/blank if (!chrom || chrom === "None") { return; --- a/templates/tracks/browser.mako Fri Mar 18 13:40:58 2011 -0400 +++ b/templates/tracks/browser.mako Fri Mar 18 13:51:51 2011 -0400 @@ -256,6 +256,11 @@ // Keyboard navigation. Scroll ~7% of height when scrolling up/down. // $(document).keydown(function(e) { + // Do not navigate if arrow keys used in input element. + if ($(e.srcElement).is(':input')) { + return; + } + // Key codes: left == 37, up == 38, right == 39, down == 40 switch(e.which) { case 37: 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 minor typo in 5233:b5f4df8c3956
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ad11762fe328/ changeset: r5234:ad11762fe328 user: dan date: 2011-03-18 18:40:58 summary: Fix minor typo in 5233:b5f4df8c3956 affected #: 1 file (3 bytes) --- a/scripts/tools/maf/check_loc_file.py Fri Mar 18 13:39:19 2011 -0400 +++ b/scripts/tools/maf/check_loc_file.py Fri Mar 18 13:40:58 2011 -0400 @@ -45,7 +45,7 @@ #existing species for spec in species_exist: if spec not in species_found_in_maf: - print "Line %i, %s claims to be have blocks for %s, but was not found in MAF files." % ( i, uid, spec ) + print "Line %i, %s claims to have blocks for %s, but was not found in MAF files." % ( i, uid, spec ) for spec in species_found_in_maf: if spec not in species_exist: print "Line %i, %s contains %s, but is not listed in loc file." % ( i, uid, spec ) 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: Add a script that will check a maf_index.loc file for inconsistencies between listed information and content of MAF indexes and files.
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b5f4df8c3956/ changeset: r5233:b5f4df8c3956 user: dan date: 2011-03-18 18:39:19 summary: Add a script that will check a maf_index.loc file for inconsistencies between listed information and content of MAF indexes and files. affected #: 1 file (0 bytes) 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 typo in 5093:1dfad17e81a8 that broke page editor.
by Bitbucket 17 Mar '11

17 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/642f1f9e5e3a/ changeset: r5231:642f1f9e5e3a user: jgoecks date: 2011-03-17 22:39:16 summary: Fix typo in 5093:1dfad17e81a8 that broke page editor. affected #: 1 file (1 byte) --- a/templates/page/editor.mako Thu Mar 17 15:44:05 2011 -0400 +++ b/templates/page/editor.mako Thu Mar 17 17:39:16 2011 -0400 @@ -21,7 +21,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "jquery.event.drag", "jquery.event.drop", "jquery.event.hover", "jquery.form", "json2", "jstorage" + ${h.js( "jquery.event.drag", "jquery.event.drop", "jquery.event.hover", "jquery.form", "json2", "jstorage", "galaxy.base", "jquery.wymeditor", "jquery.autocomplete", "autocomplete_tagging")} <script type="text/javascript"> 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: And 1em margin to the top and bottom of tables in Pages.
by Bitbucket 17 Mar '11

17 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4f14387d3178/ changeset: r5230:4f14387d3178 user: dan date: 2011-03-17 20:44:05 summary: And 1em margin to the top and bottom of tables in Pages. affected #: 1 file (61 bytes) --- a/templates/page/display.mako Thu Mar 17 09:57:25 2011 -0400 +++ b/templates/page/display.mako Thu Mar 17 15:44:05 2011 -0400 @@ -98,6 +98,8 @@ padding: 8px 5px 5px; min-width: 500px; border: none; + margin-top: 1em; + margin-bottom: 1em; } .page-body caption { text-align: left; 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 check for displaying old-style display applications when line count approximation is used. Additional cleaner link display for display applications which was started in 4886:f820c9d2c285.
by Bitbucket 17 Mar '11

17 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0861dc121b0f/ changeset: r5229:0861dc121b0f user: dan date: 2011-03-17 14:57:25 summary: Fix check for displaying old-style display applications when line count approximation is used. Additional cleaner link display for display applications which was started in 4886:f820c9d2c285. affected #: 3 files (37 bytes) --- a/lib/galaxy/datatypes/interval.py Wed Mar 16 22:27:15 2011 -0400 +++ b/lib/galaxy/datatypes/interval.py Thu Mar 17 09:57:25 2011 -0400 @@ -144,7 +144,7 @@ return dataset.has_data() \ and dataset.state == dataset.states.OK \ and dataset.metadata.columns > 0 \ - and dataset.metadata.data_lines > 0 \ + and dataset.metadata.data_lines != 0 \ and dataset.metadata.chromCol \ and dataset.metadata.startCol \ and dataset.metadata.endCol --- a/lib/galaxy/datatypes/tabular.py Wed Mar 16 22:27:15 2011 -0400 +++ b/lib/galaxy/datatypes/tabular.py Thu Mar 17 09:57:25 2011 -0400 @@ -235,7 +235,7 @@ return dataset.has_data() \ and dataset.state == dataset.states.OK \ and dataset.metadata.columns > 0 \ - and dataset.metadata.data_lines > 0 + and dataset.metadata.data_lines != 0 except: return False def as_gbrowse_display_file( self, dataset, **kwd ): --- a/templates/root/history_common.mako Wed Mar 16 22:27:15 2011 -0400 +++ b/templates/root/history_common.mako Thu Mar 17 09:57:25 2011 -0400 @@ -179,6 +179,7 @@ %for display_name, display_link in display_links: <a target="${target_frame}" href="${display_link}">${_(display_name)}</a> %endfor + <br /> %endif %endfor %for display_app in data.get_display_applications( trans ).itervalues(): 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: When using re_match comparison method in functional tests and line counts do not match, print out first 40 lines of the history file.
by Bitbucket 17 Mar '11

17 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b32617347a63/ changeset: r5228:b32617347a63 user: dan date: 2011-03-17 03:27:15 summary: When using re_match comparison method in functional tests and line counts do not match, print out first 40 lines of the history file. affected #: 1 file (66 bytes) --- a/test/base/twilltestcase.py Wed Mar 16 18:36:27 2011 -0400 +++ b/test/base/twilltestcase.py Wed Mar 16 22:27:15 2011 -0400 @@ -109,7 +109,7 @@ """Checks the contents of 2 files for differences using re.match""" local_file = open( file1, 'U' ).readlines() #regex file history_data = open( file2, 'U' ).readlines() - assert len( local_file ) == len( history_data ), 'Data File and Regular Expression File contain a different number of lines (%s != %s)' % ( len( local_file ), len( history_data ) ) + assert len( local_file ) == len( history_data ), 'Data File and Regular Expression File contain a different number of lines (%s != %s)\nHistory Data (first 40 lines):\n%s' % ( len( local_file ), len( history_data ), ''.join( history_data[:40] ) ) if attributes is None: attributes = {} if attributes.get( 'sort', 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: kanwei: Description text for viz metadata column
by Bitbucket 16 Mar '11

16 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f889ddcd4a8a/ changeset: r5227:f889ddcd4a8a user: kanwei date: 2011-03-16 23:36:27 summary: Description text for viz metadata column affected #: 2 files (78 bytes) --- a/lib/galaxy/datatypes/interval.py Wed Mar 16 10:41:38 2011 -0400 +++ b/lib/galaxy/datatypes/interval.py Wed Mar 16 18:36:27 2011 -0400 @@ -400,7 +400,7 @@ MetadataElement( name="endCol", default=3, desc="End column", param=metadata.ColumnParameter ) MetadataElement( name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 ) MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False ) - MetadataElement( name="viz_filter_cols", default=[4], param=metadata.ColumnParameter, multiple=True ) + MetadataElement( name="viz_filter_cols", desc="Score column for visualization", default=[4], param=metadata.ColumnParameter, multiple=True ) ###do we need to repeat these? they are the same as should be inherited from interval type def set_meta( self, dataset, overwrite = True, **kwd ): --- a/lib/galaxy/datatypes/tabular.py Wed Mar 16 10:41:38 2011 -0400 +++ b/lib/galaxy/datatypes/tabular.py Wed Mar 16 18:36:27 2011 -0400 @@ -493,7 +493,7 @@ MetadataElement( name="columns", default=10, desc="Number of columns", readonly=True, visible=False ) MetadataElement( name="column_types", default=['str','int','str','str','str','int','str','list','str','str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) - MetadataElement( name="viz_filter_cols", default=[5], param=metadata.ColumnParameter, multiple=True ) + MetadataElement( name="viz_filter_cols", desc="Score column for visualization", default=[5], param=metadata.ColumnParameter, multiple=True ) def sniff( self, filename ): try: 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: Update CCAT to version 3.0.
by Bitbucket 16 Mar '11

16 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3b8dec50ea26/ changeset: r5226:3b8dec50ea26 user: dan date: 2011-03-16 15:41:38 summary: Update CCAT to version 3.0. affected #: 14 files (177 bytes) Diff too large to display. 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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