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

commit/galaxy-central: 2 new changesets
by Bitbucket 21 Mar '11

21 Mar '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ca9a43ca12f5/ changeset: r5241:ca9a43ca12f5 user: jgoecks date: 2011-03-21 18:01:24 summary: Add count GFF features tool and tests. Tool counts the number of features in a GFF file; this is different than the number of lines b/c GFF features are often multiline. affected #: 5 files (1.5 KB) --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count_gff_features_out1.txt Mon Mar 21 13:01:24 2011 -0400 @@ -0,0 +1,1 @@ +3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count_gff_features_out2.txt Mon Mar 21 13:01:24 2011 -0400 @@ -0,0 +1,1 @@ +14 --- a/tool_conf.xml.sample Mon Mar 21 11:08:32 2011 -0400 +++ b/tool_conf.xml.sample Mon Mar 21 13:01:24 2011 -0400 @@ -142,6 +142,8 @@ <tool file="stats/plot_from_lda.xml" /><tool file="regVariation/t_test_two_samples.xml" /><tool file="regVariation/compute_q_values.xml" /> + <label text="GFF" id="gff" /> + <tool file="stats/count_gff_features.xml" /></section><section name="Wavelet Analysis" id="dwt"><tool file="discreteWavelet/execute_dwt_IvC_all.xml" /> --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/stats/count_gff_features.py Mon Mar 21 13:01:24 2011 -0400 @@ -0,0 +1,18 @@ +#!/usr/bin/env python +# This tool takes a gff file as input and counts the number of features in it. + +import sys, fileinput +from galaxy import eggs +from galaxy.datatypes.util.gff_util import GFFReaderWrapper +from bx.intervals.io import GenomicInterval + +# Get args. +input_file = sys.argv[1:] + +# Count features. +count = 0 +for feature in GFFReaderWrapper( fileinput.FileInput( input_file ), fix_strand=True ): + if isinstance( feature, GenomicInterval ): + count += 1 + +print count \ No newline at end of file --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/stats/count_gff_features.xml Mon Mar 21 13:01:24 2011 -0400 @@ -0,0 +1,26 @@ +<tool id="count_gff_features" name="Count GFF Features" version="0.1"> + <description></description> + <command interpreter="python"> + count_gff_features.py $input > $output + </command> + <inputs> + <param format="gff" name="input" type="data" label="GFF Dataset to Filter"/> + </inputs> + <outputs> + <data format="txt" name="output"/> + </outputs> + <tests> + <test> + <param name="input" value="gff2bed_in2.gff"/> + <output name="output" file="count_gff_features_out1.txt"/> + </test> + <test> + <param name="input" value="gff_filter_by_feature_count_out1.gff"/> + <output name="output" file="count_gff_features_out2.txt"/> + </test> + </tests> + <help> + Counts the number of features in a GFF dataset. GFF features are often spread across multiple lines; this tool counts the number of + features in dataset rather than the number of lines. + </help> +</tool> http://bitbucket.org/galaxy/galaxy-central/changeset/8d476956222e/ changeset: r5242:8d476956222e user: jgoecks date: 2011-03-21 20:24:05 summary: Merge. affected #: 0 files (0 bytes) --- a/tools/filters/trimmer.xml Mon Mar 21 13:01:24 2011 -0400 +++ b/tools/filters/trimmer.xml Mon Mar 21 15:24:05 2011 -0400 @@ -1,11 +1,11 @@ -<tool id="trimmer" name="Trim" version="0.0.1"> - <description>leading or trailing characters</description> +<tool id="trimmer" name="Trim" version="0.0.1"> + <description>leading or trailing characters</description><command interpreter="python"> - trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 - </command> - <inputs> + trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 + </command> + <inputs><param format="tabular,txt" name="input1" type="data" label="this dataset"/> - <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> + <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /><param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/><param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/><param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)"> @@ -30,9 +30,9 @@ <option value="94">^</option><option value="35">#</option></param> - </inputs> - <outputs> - <data name="out_file1" format="input" metadata_source="input1"/> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/></outputs><tests><test> @@ -55,42 +55,42 @@ </test></tests> - - <help> - - -**What it does** - -Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). - ------ - -**Example 1** - -Trimming this dataset:: + + <help> + + +**What it does** + +Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). + +----- + +**Example 1** + +Trimming this dataset:: 1234567890 - abcdefghijk - + abcdefghijk + by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce:: 23456 - bcdef + bcdef ----- -**Eaxmple 2** +**Example 2** Trimming column 2 of this dataset:: - bcde 12345 fghij 67890 - fghij 67890 abcde 12345 + abcde 12345 fghij 67890 + fghij 67890 abcde 12345 -by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: +by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: - abcde 234 fghij 67890 - fghij 789 abcde 12345 - + abcde 234 fghij 67890 + fghij 789 abcde 12345 + ----- **Trimming FASTQ datasets** @@ -111,10 +111,10 @@ **Note** that headers are skipped. -.. class:: warningmark - -**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. +.. class:: warningmark - - </help> -</tool> +**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. + + + </help> +</tool> --- a/tools/new_operations/join.xml Mon Mar 21 13:01:24 2011 -0400 +++ b/tools/new_operations/join.xml Mon Mar 21 15:24:05 2011 -0400 @@ -11,12 +11,12 @@ <param name="min" size="4" type="integer" value="1" help="(bp)"><label>with min overlap</label></param> - <param name="fill" type="select" label="Return"> - <option value="none">Only records that are joined (INNER JOIN)</option> - <option value="right">All records of first dataset (fill null with ".")</option> - <option value="left">All records of second dataset (fill null with ".")</option> - <option value="both">All records of both datasets (fill nulls with ".")</option> - </param> + <param name="fill" type="select" label="Return"> + <option value="none">Only records that are joined (INNER JOIN)</option> + <option value="right">All records of first dataset (fill null with ".")</option> + <option value="left">All records of second dataset (fill null with ".")</option> + <option value="both">All records of both datasets (fill nulls with ".")</option> + </param></inputs><outputs><data format="interval" name="output" metadata_source="input1" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Typos in tool confs
by Bitbucket 21 Mar '11

21 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5541018c4738/ changeset: r5240:5541018c4738 user: kanwei date: 2011-03-21 18:48:28 summary: Typos in tool confs affected #: 2 files (38 bytes) --- a/tools/filters/trimmer.xml Mon Mar 21 11:08:32 2011 -0400 +++ b/tools/filters/trimmer.xml Mon Mar 21 13:48:28 2011 -0400 @@ -1,11 +1,11 @@ -<tool id="trimmer" name="Trim" version="0.0.1"> - <description>leading or trailing characters</description> +<tool id="trimmer" name="Trim" version="0.0.1"> + <description>leading or trailing characters</description><command interpreter="python"> - trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 - </command> - <inputs> + trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 + </command> + <inputs><param format="tabular,txt" name="input1" type="data" label="this dataset"/> - <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> + <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /><param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/><param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/><param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)"> @@ -30,9 +30,9 @@ <option value="94">^</option><option value="35">#</option></param> - </inputs> - <outputs> - <data name="out_file1" format="input" metadata_source="input1"/> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/></outputs><tests><test> @@ -55,42 +55,42 @@ </test></tests> - - <help> - - -**What it does** - -Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). - ------ - -**Example 1** - -Trimming this dataset:: + + <help> + + +**What it does** + +Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). + +----- + +**Example 1** + +Trimming this dataset:: 1234567890 - abcdefghijk - + abcdefghijk + by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce:: 23456 - bcdef + bcdef ----- -**Eaxmple 2** +**Example 2** Trimming column 2 of this dataset:: - bcde 12345 fghij 67890 - fghij 67890 abcde 12345 + abcde 12345 fghij 67890 + fghij 67890 abcde 12345 -by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: +by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: - abcde 234 fghij 67890 - fghij 789 abcde 12345 - + abcde 234 fghij 67890 + fghij 789 abcde 12345 + ----- **Trimming FASTQ datasets** @@ -111,10 +111,10 @@ **Note** that headers are skipped. -.. class:: warningmark - -**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. +.. class:: warningmark - - </help> -</tool> +**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. + + + </help> +</tool> --- a/tools/new_operations/join.xml Mon Mar 21 11:08:32 2011 -0400 +++ b/tools/new_operations/join.xml Mon Mar 21 13:48:28 2011 -0400 @@ -11,12 +11,12 @@ <param name="min" size="4" type="integer" value="1" help="(bp)"><label>with min overlap</label></param> - <param name="fill" type="select" label="Return"> - <option value="none">Only records that are joined (INNER JOIN)</option> - <option value="right">All records of first dataset (fill null with ".")</option> - <option value="left">All records of second dataset (fill null with ".")</option> - <option value="both">All records of both datasets (fill nulls with ".")</option> - </param> + <param name="fill" type="select" label="Return"> + <option value="none">Only records that are joined (INNER JOIN)</option> + <option value="right">All records of first dataset (fill null with ".")</option> + <option value="left">All records of second dataset (fill null with ".")</option> + <option value="both">All records of both datasets (fill nulls with ".")</option> + </param></inputs><outputs><data format="interval" name="output" metadata_source="input1" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Added row id print and pre/post value prints to the migration script addressing form value errors.
by Bitbucket 21 Mar '11

21 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6ffd5bca9d84/ changeset: r5239:6ffd5bca9d84 user: dannon date: 2011-03-21 16:08:32 summary: Added row id print and pre/post value prints to the migration script addressing form value errors. affected #: 1 file (348 bytes) --- a/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Fri Mar 18 15:23:27 2011 -0400 +++ b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Mon Mar 21 11:08:32 2011 -0400 @@ -20,7 +20,6 @@ def _sniffnfix_pg9_hex(value): """ Sniff for and fix postgres 9 hex decoding issue - """ try: if value[0] == 'x': @@ -33,7 +32,6 @@ def upgrade(): print __doc__ metadata.reflect() - cmd = "SELECT form_values.id as id, form_values.content as field_values, form_definition.fields as fields " \ + " FROM form_definition, form_values " \ + " WHERE form_values.form_definition_id=form_definition.id " \ @@ -50,6 +48,12 @@ # content field is corrupted fields_list = from_json_string( _sniffnfix_pg9_hex( str( row['fields'] ) ) ) field_values_str = _sniffnfix_pg9_hex( str( row['field_values'] ) ) + try: + #Encoding errors? Just to be safe. + print "Attempting to fix row %s" % row['id'] + print "Prior to replacement: %s" % field_values_str + except: + pass field_values_dict = {} # look for each field name in the values and extract its value (string) for index in range( len(fields_list) ): @@ -84,10 +88,15 @@ json_values = to_json_string(field_values_dict) cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( json_values, int( row['id'] ) ) db_session.execute( cmd ) + try: + print "Post replacement: %s" % json_values + except: + pass if corrupted_rows: print 'Fixed %i corrupted rows.' % corrupted_rows else: print 'No corrupted rows found.' def downgrade(): - pass \ No newline at end of file + pass + 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 recently used tool submenu that was caused by changeset 4967:d6559b2d69fc
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4c5bf02bb0e8/ changeset: r5238:4c5bf02bb0e8 user: jgoecks date: 2011-03-18 20:23:27 summary: Fix bug in recently used tool submenu that was caused by changeset 4967:d6559b2d69fc affected #: 1 file (48 bytes) --- a/templates/root/tool_menu.mako Fri Mar 18 14:42:08 2011 -0400 +++ b/templates/root/tool_menu.mako Fri Mar 18 15:23:27 2011 -0400 @@ -199,10 +199,10 @@ var found_in_list = false; // Look for new tool in current list. If found, rearrange list to move tool to top. + var new_tool_info_id = new_tool_info.id.toLowerCase().replace(/[^a-z0-9_]/, "_") recently_used_elts.each( function(index) { var anchor = $(this).find("a"); - var tool_id = anchor.attr("id").split("-")[1]; - if (tool_id === new_tool_info.id) { + if (anchor.hasClass("link-" + new_tool_info_id)) { found_in_list = true; // If tool is first, do nothing. @@ -219,7 +219,7 @@ // If tool not in list, create new element, remove last element, and put new element first in list. if (!found_in_list) { new_tool_elt = $("<div class='toolTitle'> \ - <a id='link-" + new_tool_info.id + "' href='" + new_tool_info.link + "' target='" + + <a class='link-" + new_tool_info.id + "' href='" + new_tool_info.link + "' target='" + new_tool_info.target + "' minsizehint='" + new_tool_info.minsizehint + "'>" + new_tool_info.name + "</a> " + new_tool_info.description + " \ </div>"); 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 feature track bugs so that intervals are correctly drawn as half-open.
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/622acea0a86b/ changeset: r5237:622acea0a86b user: jgoecks date: 2011-03-18 19:42:08 summary: Trackster: fix feature track bugs so that intervals are correctly drawn as half-open. affected #: 1 file (30 bytes) --- a/static/scripts/trackster.js Fri Mar 18 14:12:10 2011 -0400 +++ b/static/scripts/trackster.js Fri Mar 18 14:42:08 2011 -0400 @@ -2348,7 +2348,8 @@ var feature_uid = feature[0], feature_start = feature[1], - feature_end = feature[2], + // -1 b/c intervals are half-open. + feature_end = feature[2] - 1, feature_name = feature[3], f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), @@ -2440,8 +2441,9 @@ for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) { var block = feature_blocks[k], block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), - block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) ); - + // -1 b/c intervals are half-open. + block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) ); + // Skip drawing if block not on tile. if (block_start > block_end) { continue; } @@ -2453,8 +2455,7 @@ // If block intersects with thick region, draw block as thick. if (thick_start !== undefined && !(block_start > thick_end || block_end < thick_start) ) { var block_thick_start = Math.max(block_start, thick_start), - // -1 b/c intervals are half-open. - block_thick_end = Math.min(block_end, thick_end-1); + block_thick_end = Math.min(block_end, thick_end); ctx.fillRect(block_thick_start + left_offset, y_center + 1, block_thick_end - block_thick_start, thick_height); } 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: 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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