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

commit/galaxy-central: natefoo: When comparing bam files in the test framework, convert them to sam for comparison.
by Bitbucket 23 Feb '11

23 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/93783833e6b1/ changeset: r5116:93783833e6b1 user: natefoo date: 2011-02-23 20:53:54 summary: When comparing bam files in the test framework, convert them to sam for comparison. affected #: 2 files (949 bytes) --- a/test/base/twilltestcase.py Wed Feb 23 14:01:58 2011 -0500 +++ b/test/base/twilltestcase.py Wed Feb 23 14:53:54 2011 -0500 @@ -1,7 +1,7 @@ import pkg_resources pkg_resources.require( "twill==0.9" ) -import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, tarfile, zipfile, tempfile, re, shutil +import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, tarfile, zipfile, tempfile, re, shutil, subprocess from itertools import * import twill @@ -633,6 +633,9 @@ try: if attributes is None: attributes = {} + if attributes.get( 'ftype', None ) == 'bam': + local_fh, temp_name = self._bam_to_sam( local_name, temp_name ) + local_name = local_fh.name compare = attributes.get( 'compare', 'diff' ) extra_files = attributes.get( 'extra_files', None ) if compare == 'diff': @@ -658,6 +661,17 @@ finally: os.remove( temp_name ) + def _bam_to_sam( self, local_name, temp_name ): + temp_local = tempfile.NamedTemporaryFile( suffix='.sam', prefix='local_bam_converted_to_sam_' ) + fd, temp_temp = tempfile.mkstemp( suffix='.sam', prefix='history_bam_converted_to_sam_' ) + os.close( fd ) + p = subprocess.Popen( args="samtools view %s -o %s" % ( local_name, temp_local.name ), shell=True ) + assert not p.wait(), 'Converting local (test-data) bam to sam failed' + p = subprocess.Popen( args="samtools view %s -o %s" % ( temp_name, temp_temp ), shell=True ) + assert not p.wait(), 'Converting history bam to sam failed' + os.remove( temp_name ) + return temp_local, temp_temp + def verify_extra_files_content( self, extra_files, hda_id ): files_list = [] for extra_type, extra_value, extra_name, extra_attributes in extra_files: --- a/test/functional/test_get_data.py Wed Feb 23 14:01:58 2011 -0500 +++ b/test/functional/test_get_data.py Wed Feb 23 14:53:54 2011 -0500 @@ -389,7 +389,7 @@ self.upload_file( '1.bam' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" - self.verify_dataset_correctness( '1.bam', hid=str( hda.hid ) ) + self.verify_dataset_correctness( '1.bam', hid=str( hda.hid ), attributes={ 'ftype' : 'bam' } ) self.check_history_for_string( '<span class="bam">bam</span>' ) # Make sure the Bam index was created assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 1.bam" 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: dannon: Initial commit of Mosaik and Freebayes.
by Bitbucket 23 Feb '11

23 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7b2bc40bad02/ changeset: r5115:7b2bc40bad02 user: dannon date: 2011-02-23 20:01:58 summary: Initial commit of Mosaik and Freebayes. affected #: 5 files (302 bytes) --- a/tool_conf.xml.sample Wed Feb 23 13:54:06 2011 -0500 +++ b/tool_conf.xml.sample Wed Feb 23 14:01:58 2011 -0500 @@ -291,6 +291,7 @@ <tool file="metag_tools/megablast_xml_parser.xml" /><tool file="sr_mapping/PerM.xml" /><tool file="sr_mapping/srma_wrapper.xml" /> + <tool file="sr_mapping/mosaik.xml"/></section><section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" /> @@ -369,6 +370,7 @@ <tool file="human_genome_variation/beam.xml" /><tool file="human_genome_variation/lps.xml" /><tool file="human_genome_variation/hilbertvis.xml" /> + <tool file="human_genome_variation/freebayes.xml" /></section><section name="VCF Tools" id="vcf_tools"><tool file="vcf_tools/intersect.xml" /> --- a/tool_data_table_conf.xml.sample Wed Feb 23 13:54:06 2011 -0500 +++ b/tool_data_table_conf.xml.sample Wed Feb 23 14:01:58 2011 -0500 @@ -80,4 +80,9 @@ <columns>value, name, path</columns><file path="tool-data/ccat_configurations.loc" /></table> +  + <table name="mosaik_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/mosaik_index.loc" /> + </table></tables> 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: Update bwa_wrapper to use the test data repository. bwa_color_wrapper will need to be done once the test data repository is updated to contain the data it uses.
by Bitbucket 23 Feb '11

23 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a6141e135830/ changeset: r5114:a6141e135830 user: natefoo date: 2011-02-23 19:54:06 summary: Update bwa_wrapper to use the test data repository. bwa_color_wrapper will need to be done once the test data repository is updated to contain the data it uses. affected #: 1 file (258 bytes) --- a/tools/sr_mapping/bwa_wrapper.xml Wed Feb 23 11:56:16 2011 -0500 +++ b/tools/sr_mapping/bwa_wrapper.xml Wed Feb 23 13:54:06 2011 -0500 @@ -139,8 +139,7 @@ python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out1.u.sam bwa_wrapper_out1.sam --><param name="refGenomeSource" value="indexed" /> -  - <param name="indices" value="/galaxy/data/phiX/bwa_index/phiX.fa" /> + <param name="indices" value="phiX" /><param name="sPaired" value="single" /><param name="input1" value="bwa_wrapper_in1.fastqsanger" ftype="fastqsanger" /><param name="source_select" value="pre_set" /> @@ -195,8 +194,7 @@ python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out3.u.sam bwa_wrapper_out3.sam --><param name="refGenomeSource" value="indexed" /> -  - <param name="indices" value="/galaxy/data/phiX/bwa_index/phiX.fa" /> + <param name="indices" value="phiX" /><param name="sPaired" value="paired" /><param name="input1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" /><param name="input2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" /> 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: rc: Bug fix: checkbox values were not getting saved for samples in the sample grid. Issue #476
by Bitbucket 23 Feb '11

23 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b54ef1e11b77/ changeset: r5113:b54ef1e11b77 user: rc date: 2011-02-23 17:56:16 summary: Bug fix: checkbox values were not getting saved for samples in the sample grid. Issue #476 affected #: 2 files (890 bytes) --- a/lib/galaxy/web/controllers/requests_common.py Wed Feb 23 10:40:30 2011 -0500 +++ b/lib/galaxy/web/controllers/requests_common.py Wed Feb 23 11:56:16 2011 -0500 @@ -1432,7 +1432,11 @@ field_values = {} for field_index, field in enumerate( request.type.sample_form.fields ): field_name = field['name'] - field_value = util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), sample.values.content[ field_name ] ) ) + input_value = params.get( 'sample_%i_field_%i' % ( index, field_index ), sample.values.content[ field_name ] ) + if field['type'] == CheckboxField.__name__: + field_value = CheckboxField.is_checked( input_value ) + else: + field_value = util.restore_text( input_value ) field_values[ field_name ] = field_value library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans=trans, user=request.user, @@ -1504,8 +1508,13 @@ workflow_dict['mappings'][int(k[len(kwd_tag):])] = {'ds_tag':v} field_values = {} for field_index, field in enumerate( request.type.sample_form.fields ): - field_name = field['name'] - field_values[ field_name ] = util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) + field_name = field['name'] + input_value = params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) + if field['type'] == CheckboxField.__name__: + field_value = CheckboxField.is_checked( input_value ) + else: + field_value = util.restore_text( input_value ) + field_values[ field_name ] = field_value library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans=trans, user=request.user, sample_index=index, --- a/templates/requests/common/common.mako Wed Feb 23 10:40:30 2011 -0500 +++ b/templates/requests/common/common.mako Wed Feb 23 11:56:16 2011 -0500 @@ -591,7 +591,11 @@ %endfor </select> %elif field_type == 'CheckboxField': - <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/> + %if field_value is True: + <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes" checked="checked"/><input type="hidden" name="sample_${index}_field_${field_index}" value="Yes"/> + %else: + <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/><input type="hidden" name="sample_${index}_field_${field_index}" value="Yes"/> + %endif %endif <div class="toolParamHelp" style="clear: both;"><i>${'('+field['required']+')' }</i> 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: Enhance GFF reader to handle headers and comments.
by Bitbucket 23 Feb '11

23 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4426265b87be/ changeset: r5112:4426265b87be user: jgoecks date: 2011-02-23 16:40:30 summary: Enhance GFF reader to handle headers and comments. affected #: 1 file (308 bytes) --- a/lib/galaxy/datatypes/util/gff_util.py Tue Feb 22 18:49:57 2011 -0500 +++ b/lib/galaxy/datatypes/util/gff_util.py Wed Feb 23 10:40:30 2011 -0500 @@ -3,6 +3,7 @@ """ import pkg_resources; pkg_resources.require( "bx-python" ) from bx.intervals.io import * +from bx.tabular.io import Header, Comment class GFFInterval( GenomicInterval ): """ @@ -148,6 +149,12 @@ self.seed_interval = GenomicIntervalReader.next( self ) except ParseError, e: handle_parse_error( e ) + + # If header or comment, clear seed interval and return it. + if isinstance( self.seed_interval, ( Header, Comment ) ): + return_val = self.seed_interval + self.seed_interval = None + return return_val # Initialize feature name from seed. feature_group = self.seed_interval.attributes.get( 'group', None ) # For GFF 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: Refactor javascript in tool_form.mako; fix indentation for repeat groups
by Bitbucket 22 Feb '11

22 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9171601965fc/ changeset: r5111:9171601965fc user: kanwei date: 2011-02-23 00:49:57 summary: Refactor javascript in tool_form.mako; fix indentation for repeat groups affected #: 1 file (235 bytes) --- a/templates/tool_form.mako Tue Feb 22 18:41:15 2011 -0500 +++ b/templates/tool_form.mako Tue Feb 22 18:49:57 2011 -0500 @@ -29,6 +29,42 @@ } }); }); + + // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements + $( 'li ul.toolParameterExpandableCollapsable' ).each( function() { + var el = $(this), + parent_li = el.parent('li'), + sub_ul = el.remove(); + + parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() { + sub_ul.toggle(); + (this).html( sub_ul.is(":hidden") ? '[+]' : '[-]' ); + }); + parent_li.append( sub_ul ); + }); + + $( 'ul ul.toolParameterExpandableCollapsable' ).each( function(i) { + var el = $(this); + if (el.attr("default_state") === "collapsed") { + el.hide(); + } + }); + + function checkUncheckAll( name, check ) { + $("input[name=" + name + "][type='checkbox']").attr('checked', !!check); + } + + // Inserts the Select All / Unselect All buttons for checkboxes + $("div.checkUncheckAllPlaceholder").each( function() { + var check_name = $(this).attr("checkbox_name"); + select_link = $("<a class='action-button'></a>").text("Select All").click(function() { + checkUncheckAll(check_name, true); + }); + unselect_link = $("<a class='action-button'></a>").text("Unselect All").click(function() { + checkUncheckAll(check_name, false); + }); + $(this).append(select_link).append(" ").append(unselect_link); + }); }); %if not add_frame.debug: @@ -36,13 +72,6 @@ location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); } %endif -function checkUncheckAll( name, check ) { - if (!check) { - $("input[name=" + name + "][type='checkbox']").attr('checked', false); - } else { - $("input[name=" + name + "][type='checkbox']").attr('checked', true ); - } -} </script></head> @@ -59,16 +88,16 @@ <% repeat_state = tool_state[input.name] %> %for i in range( len( repeat_state ) ): <div class="repeat-group-item"> - <% - if input.name in errors: - rep_errors = errors[input.name][i] - else: - rep_errors = dict() - index = repeat_state[i]['__index__'] - %> - <div class="form-title-row"><b>${input.title} ${i + 1}</b></div> - ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + <% + if input.name in errors: + rep_errors = errors[input.name][i] + else: + rep_errors = dict() + index = repeat_state[i]['__index__'] + %> + <div class="form-title-row"><b>${input.title} ${i + 1}</b></div> + ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} + <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div></div> %if rep_errors.has_key( '__index__' ): <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> @@ -231,37 +260,4 @@ </div> %endif </body> - -<script type="text/javascript"> -##For Drilldown Parameters adds expand/collapse buttons and collapses collapsed elements - $( function() { - $( 'li > ul' ).each( function( i ) { - if ( $( this )[0].className == 'toolParameterExpandableCollapsable' ) - { - var parent_li = $( this ).parent( 'li' ); - var sub_ul = $( this ).remove(); - parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() { - sub_ul.toggle(); - $( this )[0].innerHTML = ( sub_ul[0].style.display=='none' ) ? '[+]' : '[-]'; - }); - parent_li.append( sub_ul ); - } - }); - $( 'ul ul' ).each( function(i) { - if ( $( this )[0].className == 'toolParameterExpandableCollapsable' && this.attributes.getNamedItem( 'default_state' ).value == 'collapsed' ) - { - $( this ).hide(); - } - }); - }); - -##inserts the Select All / Unselect All buttons for checkboxes -$( function() { - $("div.checkUncheckAllPlaceholder").each( function( i ) { - $( this )[0].innerHTML = '<a class="action-button" onclick="checkUncheckAll( \'' + this.attributes.getNamedItem( 'checkbox_name' ).value + '\', true );"><span>Select All</span></a><a class="action-button" onclick="checkUncheckAll( \'' + this.attributes.getNamedItem( 'checkbox_name' ).value + '\', false );"><span>Unselect All</span></a>'; - }); -}); - -</script> - </html> 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 output dataset type for 'Extract GFF features' tool to be input dataset type.
by Bitbucket 22 Feb '11

22 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6506489984e1/ changeset: r5110:6506489984e1 user: jgoecks date: 2011-02-23 00:41:15 summary: Set output dataset type for 'Extract GFF features' tool to be input dataset type. affected #: 1 file (26 bytes) --- a/tools/filters/gff/extract_GFF_Features.xml Tue Feb 22 18:10:52 2011 -0500 +++ b/tools/filters/gff/extract_GFF_Features.xml Tue Feb 22 18:41:15 2011 -0500 @@ -59,7 +59,7 @@ </conditional></inputs><outputs> - <data format="gff" name="out_file1" /> + <data format="input" name="out_file1" metadata_source="input1"/></outputs><tests><test> 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: Remove overflow from help text in tool forms, for IE
by Bitbucket 22 Feb '11

22 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a2f92ea84931/ changeset: r5109:a2f92ea84931 user: kanwei date: 2011-02-23 00:10:52 summary: Remove overflow from help text in tool forms, for IE affected #: 3 files (3 bytes) --- a/static/june_2007_style/base.css.tmpl Tue Feb 22 17:24:10 2011 -0500 +++ b/static/june_2007_style/base.css.tmpl Tue Feb 22 18:10:52 2011 -0500 @@ -107,12 +107,12 @@ border-color: ${layout_border}; } -div.toolHelp { +div.toolHelp { + margin-top: 10px; } -div.toolHelpBody { +div.toolHelpBody { width: 100%; - overflow: auto; } div.metadataForm { --- a/static/june_2007_style/blue/base.css Tue Feb 22 17:24:10 2011 -0500 +++ b/static/june_2007_style/blue/base.css Tue Feb 22 18:10:52 2011 -0500 @@ -21,8 +21,8 @@ div.toolFormBody div.toolFormTitle{background:transparent;border:none;font-weight:bold;border-bottom:solid #d8b365 1px;margin-bottom:5px;} div.toolFormDisabled div.toolFormTitle{background:#eee;border-color:#999;} div.toolFormDisabled{border-color:#999;} -div.toolHelp{} -div.toolHelpBody{width:100%;overflow:auto;} +div.toolHelp{margin-top:10px;} +div.toolHelpBody{width:100%;} div.metadataForm{border:solid #aaaaaa 1px;} div.metadataFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#cccccc;background-repeat:repeat-x;background-position:top;border-bottom:solid #aaaaaa 1px;} div.metadataFormBody{background:#FFFFFF;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} --- a/static/june_2007_style/blue/trackster.css Tue Feb 22 17:24:10 2011 -0500 +++ b/static/june_2007_style/blue/trackster.css Tue Feb 22 18:10:52 2011 -0500 @@ -25,7 +25,7 @@ .track-content{overflow:hidden;text-align:center;border-bottom:1px solid #bbb;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;} .label-track .track-content{background:white;} .track-tile{background:white;} -.track-tile canvas{position:relative;z-index:100;border:solid white;border-width: 2px 0px 0px 0px;} +.track-tile canvas{position:relative;z-index:100;border:solid white;border-width:2px 0px 0px 0px;} .track.error .track-content{background-color:#ECB4AF;background-image:none;padding:2px 0;} .track.nodata .track-content{background-color:#eee;background-image:none;padding:2px 0;} .loading{min-height:100px;} 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: Fix IE error when clicking on links in tool pane. Small refactoring as well
by Bitbucket 22 Feb '11

22 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5edac6f53bc2/ changeset: r5108:5edac6f53bc2 user: kanwei date: 2011-02-22 23:24:10 summary: Fix IE error when clicking on links in tool pane. Small refactoring as well affected #: 1 file (185 bytes) --- a/templates/root/tool_menu.mako Tue Feb 22 17:14:16 2011 -0500 +++ b/templates/root/tool_menu.mako Tue Feb 22 17:24:10 2011 -0500 @@ -70,28 +70,26 @@ $( "div.toolSectionTitle > span" ).wrap( "<a href='#'></a>" ) var last_expanded = null; $( "div.toolSectionTitle" ).each( function() { - var body = $(this).next( "div.toolSectionBody" ); - $(this).click( function() { - if ( body.is( ":hidden" ) ) { + var body = $(this).next( "div.toolSectionBody" ); + $(this).click( function() { + if ( body.is( ":hidden" ) ) { if ( last_expanded ) { last_expanded.slideUp( "fast" ); } last_expanded = body; body.slideDown( "fast" ); - } - else { - body.slideUp( "fast" ); - last_expanded = null; - } - return false; - }); + } else { + body.slideUp( "fast" ); + last_expanded = null; + } + return false; + }); }); // Log clicks on tools. - $("div.toolTitle > a").click( function() - { + $("div.toolTitle > a").click( function() { var tool_title = $(this).attr('id').split("-")[1]; - var section_title = $(this).parents("div.toolSectionWrapper").find("div.toolSectionTitle").text().trim(); + var section_title = $.trim( $(this).parents("div.toolSectionWrapper").find("div.toolSectionTitle").text() ); var search_active = $(this).parents("div.toolTitle").hasClass("search_match"); // Log action. @@ -106,18 +104,17 @@ }); // Init searching. - $("#tool-search-query").click( function (){ + $("#tool-search-query").click( function () { $(this).focus(); $(this).select(); - }) - .keyup( function () { + }).keyup( function () { // Remove italics. $(this).css("font-style", "normal"); // Don't update if same value as last time if ( this.value.length < 3 ) { reset_tool_search(false); - } else if ( this.value != this.lastValue ) { + } else if ( this.value !== this.lastValue ) { // Add class to denote that searching is active. $(this).addClass("search_active"); // input.addClass(config.loadingClass); @@ -138,7 +135,7 @@ $(".toolSectionWrapper").hide(); // This hides all tools but not workflows link (which is in a .toolTitle div). $(".toolSectionWrapper").find(".toolTitle").hide(); - if ( data.length != 0 ) { + if ( data.length !== 0 ) { // Map tool ids to element ids and join them. var s = $.map( data, function( n, i ) { return ".link-" + n.toLowerCase().replace(/[^a-z0-9_]/g,'_'); } ).join( ", " ); @@ -146,14 +143,13 @@ $(s).each( function() { // Add class to denote match. $(this).parent().addClass("search_match"); - if ($(this).parents("#recently_used_wrapper").length == 0) + if ($(this).parents("#recently_used_wrapper").length === 0) { // Default behavior. $(this).parent().show().parent().parent().show().parent().show(); - else if ($(this).parents(".user_pref_visible").length != 0) + } else if ($(this).parents(".user_pref_visible").length !== 0) { // RU menu is visible, so filter it as normal. $(this).parent().show().parent().parent().show().parent().show(); - else - { + } else { // RU menu is not visible, so set up classes and visibility so that if menu shown matching is // aleady in place. $(this).parent().show(); @@ -162,22 +158,21 @@ // Hide labels that have no visible children. $(".toolPanelLabel").each( function() { - var this_label = $(this); - var next = this_label.next(); - var no_visible_tools = true; - // Look through tools following label and, if none are visible, hide label. - while (next.length != 0 && next.hasClass("toolTitle")) - { - if (next.is(":visible")) - { - no_visible_tools = false; - break; - } - else - next = next.next(); + var this_label = $(this); + var next = this_label.next(); + var no_visible_tools = true; + // Look through tools following label and, if none are visible, hide label. + while (next.length !== 0 && next.hasClass("toolTitle")) { + if (next.is(":visible")) { + no_visible_tools = false; + break; + } else { + next = next.next(); + } } - if (no_visible_tools) + if (no_visible_tools) { this_label.hide(); + } }); } else { $("#search-no-results").show(); @@ -191,8 +186,7 @@ }); // Update recently used tools menu. Function inserts a new item and removes the last item. - function update_recently_used() - { + function update_recently_used() { $.ajax({ url: "${h.url_for( controller='/user', action='get_most_recently_used_tool_async' )}", dataType: 'json', @@ -208,15 +202,13 @@ 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 (tool_id === new_tool_info.id) { found_in_list = true; // If tool is first, do nothing. - if (index == 0) + if (index === 0) { return; - else - { + } else { // Tool not first; reorder. $(this).remove(); first_elt.before($(this)); @@ -225,8 +217,7 @@ }); // If tool not in list, create new element, remove last element, and put new element first in list. - if (!found_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='" + new_tool_info.target + "' minsizehint='" + new_tool_info.minsizehint + "'>" + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Copy datasets feature:
by Bitbucket 22 Feb '11

22 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/174ad45c7323/ changeset: r5107:174ad45c7323 user: kanwei date: 2011-02-22 23:14:16 summary: Copy datasets feature: - Fix functional tests - Populate previously selected target history if attempt fails affected #: 4 files (671 bytes) --- a/lib/galaxy/web/controllers/dataset.py Tue Feb 22 16:56:11 2011 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Tue Feb 22 17:14:16 2011 -0500 @@ -753,7 +753,7 @@ return trans.fill_template( "show_params.mako", history=trans.get_history(), hda=hda, tool=tool, params_objects=params_objects ) @web.expose - def copy_datasets( self, trans, source_history=None, source_dataset_ids="", target_history_ids="", new_history_name="", do_copy=False, **kwd ): + def copy_datasets( self, trans, source_history=None, source_dataset_ids="", target_history_id=None, target_history_ids="", new_history_name="", do_copy=False, **kwd ): params = util.Params( kwd ) user = trans.get_user() if source_history is not None: @@ -763,14 +763,16 @@ refresh_frames = [] if source_dataset_ids: if not isinstance( source_dataset_ids, list ): - source_dataset_ids = source_dataset_ids.split( "," ) - source_dataset_ids = map( trans.security.decode_id, source_dataset_ids ) + source_dataset_ids = source_dataset_ids.split(",") + source_dataset_ids = set(map( trans.security.decode_id, source_dataset_ids )) else: source_dataset_ids = [] - if target_history_ids: + if target_history_id: + target_history_ids = [ trans.security.decode_id(target_history_id) ] + elif target_history_ids: if not isinstance( target_history_ids, list ): - target_history_ids = target_history_ids.split( "," ) - target_history_ids = [ trans.security.decode_id(h) for h in target_history_ids if h ] + target_history_ids = target_history_ids.split(",") + target_history_ids = set([ trans.security.decode_id(h) for h in target_history_ids if h ]) else: target_history_ids = [] done_msg = error_msg = "" @@ -818,6 +820,7 @@ source_history = history, current_history = trans.get_history(), source_dataset_ids = source_dataset_ids, + target_history_id = target_history_id, target_history_ids = target_history_ids, source_datasets = source_datasets, target_histories = target_histories, --- a/templates/dataset/copy_view.mako Tue Feb 22 16:56:11 2011 -0500 +++ b/templates/dataset/copy_view.mako Tue Feb 22 17:14:16 2011 -0500 @@ -79,16 +79,19 @@ <div class="toolFormTitle">Destination History:</div><div class="toolFormBody"><div class="form-row" id="single-destination"> - <select id="single-dest-select" name="target_history_ids"> + <select id="single-dest-select" name="target_history_id"><option value=""></option> %for i, hist in enumerate(target_histories): <% encoded_id = trans.security.encode_id(hist.id) source_history_text = "" + selected = "" if hist == source_history: source_history_text = " (source history)" + if encoded_id == target_history_id: + selected = " selected='selected'" %> - <option value="${encoded_id}">${i + 1}: ${h.truncate(hist.name, 30)}${source_history_text}</option> + <option value="${encoded_id}"${selected}>${i + 1}: ${h.truncate(hist.name, 30)}${source_history_text}</option> %endfor </select><br /><br /><a style="margin-left: 10px;" href="javascript:void(0);" id="select-multiple">Choose multiple histories</a> --- a/test/base/twilltestcase.py Tue Feb 22 16:56:11 2011 -0500 +++ b/test/base/twilltestcase.py Tue Feb 22 17:14:16 2011 -0500 @@ -543,12 +543,15 @@ tc.submit( 'change' ) self.check_page_for_string( 'Changed the type of dataset' ) self.home() - def copy_history_item( self, source_dataset_ids='', target_history_ids=[], all_target_history_ids=[], + def copy_history_item( self, source_dataset_id=None, target_history_id=None, all_target_history_ids=[], deleted_history_ids=[] ): - """Copy 1 or more history_dataset_associations to 1 or more histories""" + """ + Copy 1 history_dataset_association to 1 history (Limited by twill since it doesn't support multiple + field names, such as checkboxes + """ self.home() - self.visit_url( "%s/dataset/copy_datasets?source_dataset_ids=%s" % ( self.url, source_dataset_ids ) ) - self.check_page_for_string( 'Source History Items' ) + self.visit_url( "%s/dataset/copy_datasets?source_dataset_ids=%s" % ( self.url, source_dataset_id ) ) + self.check_page_for_string( 'Source History:' ) # Make sure all of users active histories are displayed for id in all_target_history_ids: self.check_page_for_string( id ) @@ -559,12 +562,10 @@ raise AssertionError, "deleted history id %d displayed in list of target histories" % id except: pass - # Check each history to which we want to copy the item - for id in target_history_ids: - tc.fv( '1', 'target_history_ids', id ) + + tc.fv( '1', 'target_history_id', target_history_id ) tc.submit( 'do_copy' ) - no_source_ids = len( source_dataset_ids.split( ',' ) ) - check_str = '%d datasets copied to %d histories.' % ( no_source_ids, len( target_history_ids ) ) + check_str = '1 dataset copied to 1 history' self.check_page_for_string( check_str ) self.home() def get_hids_in_history( self ): --- a/test/functional/test_history_functions.py Tue Feb 22 16:56:11 2011 -0500 +++ b/test/functional/test_history_functions.py Tue Feb 22 17:14:16 2011 -0500 @@ -726,16 +726,16 @@ .first() assert hda1 is not None, "Problem retrieving hda1 from database" # We'll just test copying 1 hda - source_dataset_ids=str( hda1.id ) + source_dataset_ids=self.security.encode_id( hda1.id ) # The valid list of target histories is only the user's active histories - all_target_history_ids = [ str( hda.id ) for hda in admin_user.active_histories ] + all_target_history_ids = [ self.security.encode_id( hda.id ) for hda in admin_user.active_histories ] # Since history1 and history2 have been deleted, they should not be displayed in the list of target histories # on the copy_view.mako form - deleted_history_ids = [ str( history1.id ), str( history2.id ) ] + deleted_history_ids = [ self.security.encode_id( history1.id ), self.security.encode_id( history2.id ) ] # Test copying to the current history - target_history_ids=[ str( history6.id ) ] - self.copy_history_item( source_dataset_ids=source_dataset_ids, - target_history_ids=target_history_ids, + target_history_id = self.security.encode_id( history6.id ) + self.copy_history_item( source_dataset_id=source_dataset_ids, + target_history_id=target_history_id, all_target_history_ids=all_target_history_ids, deleted_history_ids=deleted_history_ids ) sa_session.refresh( history6 ) @@ -751,12 +751,12 @@ assert history7 is not None, "Problem retrieving history7 from database" # Switch back to our history from which we want to copy self.switch_history( id=self.security.encode_id( history6.id ), name=history6.name ) - target_history_ids=[ str( history7.id ) ] - all_target_history_ids = [ str( hda.id ) for hda in admin_user.active_histories ] + target_history_id = self.security.encode_id( history7.id ) + all_target_history_ids = [ self.security.encode_id( hda.id ) for hda in admin_user.active_histories ] # Test copying to the a history that is not the current history - target_history_ids=[ str( history7.id ) ] - self.copy_history_item( source_dataset_ids=source_dataset_ids, - target_history_ids=target_history_ids, + target_history_ids=[ self.security.encode_id( history7.id ) ] + self.copy_history_item( source_dataset_id=source_dataset_ids, + target_history_id=target_history_id, all_target_history_ids=all_target_history_ids, deleted_history_ids=deleted_history_ids ) # Switch to the history to which we copied Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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